Citrus Sinensis ID: 047219

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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-------540-------550-------560-------
Protein Sequence
MASLRRLAKTASVWRVLTASRASPRGQPRRLPHRSLEQQIRFSASEIQRPKLLDDTPGPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDLC
Secondary Structure (PSIPRED)
ccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccccccHHHHHHHcccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHcccccccccccEEEEEcccEEEEEEcccccccHHHHHHHHHHcccccccccccccEEEEEcccccccEEEEcccccccccccccccccccccccccEEEEEEEEccccccccHHHHccccccccccccccEEEEccccccccccccccccccccccccccccHHHHHHHHHHHHHHHccccHHHHHHHcccccccccccccEEEEEccccccHHHHHHHHHHHHcccccccccEEEEccHHHHHHHccccHHHHHHHHHHHHccccccEEEEEccccccccccccccHHHHHHHHHHHHHHccccccccEEEEEcccccccccccccccccEEEEEccccHHHHHHHHHHHHccccHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccHEccccccccccccccHHHHHHHHHHcccHHHHHHHHHHHHHcccccEEccccccccccHHHHHHHHHHHHHHHHHHcccccccccccEEEEEcccccccccccccccEEEEcccHHHHccccccccccccEEEEEEEccccccHEEccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccHHHHcccEEEcccHHHHHEcccccccEEEcccccEEEEEcccccHHccccHHHHHHHHHHHHccccccHHHHHHHccHHHHHcccccccEEEEEcccccHHHHHHHHHHHHcccccccEccEEEEccHHHHHHHHcccHHHHHHHHHHHHHHcccEEEEEEcHHHHccccccccccHHHHHHHHHHHHHccccccccEEEEEEccccccccHHHcccccEEEEEccccHHHHHHHHHHHHcccccccHHHHHHHcccccHHHHHHHHHHHHHHHHHHHcccccHHHHHHHccccHHHHHHHHHHccccHHHHHHHHHHHHHHHcccccccccc
Coil and Loop (DISEMBL)
MASLRRLAKTASVWRVLTasrasprgqprrlphrslEQQIRFSaseiqrpkllddtpgpssihpaILAGLFGVGALNIayadgdqgagtakpslpsessssyENLEEIAKKERQRIEELLKRkgmhygscptftvavkgqkvtikfqvppaceipQLIANLVSHLglkveehgggsdmglRAWDSAVAWQLtlkppekqnesggdraqsgdmnaregDLCILIFRSlitsdkpeiefikkgsltSEELDALVSVLQLAGrriygldepqlntskseisweniagydqqkREIEDTILLslqspevyddiargtrckfesnrpravlfegppgtgktSCARVIANqagampwqgvplmyVPLEVVMSKYYGESERLLGKVFSLAnelpngaiifldevdsfavardSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATnrkqdldpalISRFDsmitfglpdheNRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRgqitkdgeqaclpplqEYIESATNRRRSLLDAAEQSHQNinnhrtkkqpldlc
Flexible Loop (DISEMBL)
maslrrlaktasvwrvltasrasprgqprrlphrsleqqirfsaseiqrpklLDDTPGPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKpslpsessssyENLEEIAKKERQRIEELLkrkgmhygscPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLkppekqnesggdraqsgdmnaREGDLCILIFRslitsdkpEIEFIkkgsltseeLDALVSVLQLAGRRiygldepqlntskseiswENIAGYDQQKREIEDTILLSLQSPEVYDDIARGtrckfesnrpravlfegppgtgkTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAtnrkqdldpalISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATateemsgrDIRDVCQQAERSWASkiirgqitkdgeqacLPPLQEYIESATNRRRSLLDAAEqshqninnhrtkkqpldlc
Low Complexity Region (SEG)
MASLRRLAKTASVWRVLTASRASPRGQPRRLPHRSLEQQIRFSASEIQRPKLLDDTPGPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKpslpsessssyenleeIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHltkaelaelatateeMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDLC
Disordered region (IsUnstruct)
************VWRV*********************************************IHPAILAGLFGVGALNIAYAD************************************LLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTL***********************GDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLN***SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAEL***********IRDVCQQAERSWASKIIRGQITKDGEQACLP****************************************
Disordered Region (DISOPRED)
*********T********************************************DTPGPSSIHPAILAGLFGVGALNIA****************************************LKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLK***************GDMNAREGDLCI*********************LTSEELDALVSVLQLAG****************EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF****************SVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRG**********LPPLQEYIES*TN**********************K******
Disordered Region (DISEMBL)
MASLRRLAKTASVWRVLTAS***********PHRSLEQQIRFSASEIQRPKLLDDTPGPSSIHPAILAGLFGVGALNIAYADGD**********************EIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPP**************DMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNH**********
Disordered Region (DISPRO)
*AS*RRLAKTASVWR*****************************SEIQRPKLLDDTPGPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVAR***MHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQP***C
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASLRRLAKTASVWRVLTASRASPRGQPRRLPHRSLEQQIRFSASEIQRPKLLDDTPGPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSSxxxxxxxxxxxxxxxxxxxxxKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDLC
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	567	2.2.26 [Sep-21-2011]
O28972	733	Cell division cycle prote	yes	no	0.384	0.297	0.377	1e-33
Q58556	903	Cell division cycle prote	yes	no	0.382	0.240	0.376	1e-32
Q8TX03	436	Proteasome-activating nuc	yes	no	0.372	0.483	0.375	7e-32
P25694	835	Cell division control pro	yes	no	0.379	0.257	0.4	2e-31
Q60QD1	591	Fidgetin-like protein 1 O	N/A	no	0.435	0.417	0.322	2e-31
O28303	398	Proteasome-activating nuc	no	no	0.395	0.562	0.370	7e-31
O26824	410	Proteasome-activating nuc	yes	no	0.380	0.526	0.368	8e-31
O05209	745	VCP-like ATPase OS=Thermo	yes	no	0.393	0.299	0.353	9e-31
Q5AWS6	823	Cell division control pro	yes	no	0.379	0.261	0.374	1e-30
Q9P3A7	815	Cell division cycle prote	yes	no	0.384	0.267	0.378	1e-30

>sp|O28972|Y1297_ARCFU Cell division cycle protein 48 homolog AF_1297 OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=AF_1297 PE=3 SV=1

 Score =  145 bits (365), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 92/244 (37%), Positives = 137/244 (56%), Gaps = 26/244 (10%)

Query: 269 QLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFE 328
           ++  +  ++++E+I G  ++ R + + I L L+ PE++       R   E   P+ VL  
Sbjct: 171 EVKRAVPDVTYEDIGGLKRELRLVREMIELPLKHPELFQ------RLGIEP--PKGVLLY 222

Query: 329 GPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE--VVMSKYYGESERLLGKVFSLANEL 386
           GPPGTGKT  A+ +AN+  A         ++P+    +MSKYYGESE+ L ++F  A E 
Sbjct: 223 GPPGTGKTLIAKAVANEVDAH--------FIPISGPEIMSKYYGESEQRLREIFEEAKE- 273

Query: 387 PNG-AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLD 445
            N  +IIF+DE+DS A  R+    E  RR+++ LL  +DG E    V+VIAATNR   +D
Sbjct: 274 -NAPSIIFIDEIDSIAPKREEVTGEVERRVVAQLLALMDGLEARGDVIVIAATNRPDAID 332

Query: 446 PAL--ISRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDV 500
           PAL    RFD  I  G+PD E R+EI   + + +  AE   L ELA  T    G D+  +
Sbjct: 333 PALRRPGRFDREIEIGVPDKEGRKEILEIHTRKMPLAEDVDLEELAELTNGFVGADLEAL 392

Query: 501 CQQA 504
           C++A
Sbjct: 393 CKEA 396

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (taxid: 224325)

>sp|Q58556|Y1156_METJA Cell division cycle protein 48 homolog MJ1156 OS=Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) GN=MJ1156 PE=3 SV=1

 Score =  141 bits (356), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 90/239 (37%), Positives = 136/239 (56%), Gaps = 22/239 (9%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           T   ++++E+I G  ++ +++ + I L ++ PE+++        K     P+ VL  GPP
Sbjct: 171 TKVPDVTYEDIGGLKEEVKKVREMIELPMRHPELFE--------KLGIEPPKGVLLVGPP 222

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG-A 390
           GTGKT  A+ +AN+AGA  +    ++  P   +MSKY GE+E  L K+F  A E  N  +
Sbjct: 223 GTGKTLLAKAVANEAGANFY----VINGP--EIMSKYVGETEENLRKIFEEAEE--NAPS 274

Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL-- 448
           IIF+DE+D+ A  RD    E  RR+++ LL  +DG +   +VVVI ATNR   LDPAL  
Sbjct: 275 IIFIDEIDAIAPKRDEATGEVERRLVAQLLTLMDGLKGRGQVVVIGATNRPNALDPALRR 334

Query: 449 ISRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
             RFD  I  G+PD E R+EI   + +++  AE   L  LA  T    G D+  +C++A
Sbjct: 335 PGRFDREIVIGVPDREGRKEILQIHTRNMPLAEDVDLDYLADVTHGFVGADLAALCKEA 393

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (taxid: 243232)

>sp|Q8TX03|PAN_METKA Proteasome-activating nucleotidase OS=Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) GN=pan PE=3 SV=1

 Score =  139 bits (350), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 90/240 (37%), Positives = 133/240 (55%), Gaps = 29/240 (12%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           ++S+++I G D+Q REI + +   L+ PE+++ +            P+ VL  GPPGTGK
Sbjct: 175 DVSYDDIGGLDEQIREIREVVEKPLKEPELFEKVG--------VEPPKGVLLYGPPGTGK 226

Query: 336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
           T  A+ +AN A A        + +    ++ K+ GE  RL+ ++F LA E    +IIF+D
Sbjct: 227 TLLAKAVANHADAT------FIRLAAPELVQKFIGEGARLVRELFELARE-KAPSIIFID 279

Query: 396 EVDSFAVARDSEMHEAT------RRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
           E+D+    R   M +AT      +R L+ LL ++DGF+    + VIAATNRK  LDPAL+
Sbjct: 280 EIDAIGARR---MRDATSGDREVQRTLTQLLAEMDGFDPLDDIKVIAATNRKDILDPALL 336

Query: 450 --SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
              RFD  I   LPD E R EI   + + +  AE   L +LA  TE  SG DI+ +C +A
Sbjct: 337 RPGRFDRHIKIPLPDEEGRYEIFKIHTRDMNLAEDVDLQKLAKITEGASGADIKAICTEA 396

ATPase which is responsible for recognizing, binding, unfolding and translocation of substrate proteins into the archaeal 20S proteasome core particle. Is essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Unfolding activity requires energy from ATP hydrolysis, whereas ATP binding alone promotes ATPase-20S proteasome association which triggers gate opening, and supports translocation of unfolded substrates.

Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938) (taxid: 190192)

>sp|P25694|CDC48_YEAST Cell division control protein 48 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=CDC48 PE=1 SV=3

 Score =  137 bits (346), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 94/235 (40%), Positives = 128/235 (54%), Gaps = 20/235 (8%)

Query: 275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTG 334
           +E+ +++I G  +Q  +I + + L L+ P+++  I  G +       PR VL  GPPGTG
Sbjct: 209 NEVGYDDIGGCRKQMAQIREMVELPLRHPQLFKAI--GIKP------PRGVLMYGPPGTG 260

Query: 335 KTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFL 394
           KT  AR +AN+ GA  +    L+  P   VMSK  GESE  L K F  A E    AIIF+
Sbjct: 261 KTLMARAVANETGAFFF----LINGP--EVMSKMAGESESNLRKAFEEA-EKNAPAIIFI 313

Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL--ISRF 452
           DE+DS A  RD    E  RR++S LL  +DG +    VVVIAATNR   +DPAL    RF
Sbjct: 314 DEIDSIAPKRDKTNGEVERRVVSQLLTLMDGMKARSNVVVIAATNRPNSIDPALRRFGRF 373

Query: 453 DSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQA 504
           D  +  G+PD   R E+   + K++  A   +L  LA  T    G DI  +C +A
Sbjct: 374 DREVDIGIPDATGRLEVLRIHTKNMKLADDVDLEALAAETHGYVGADIASLCSEA 428

Involved in spindle disassembly, degradation of ubiquitinated proteins and protein export from the endoplasmic reticulum to the cytoplasm. Acts as a chaperone that collects ubiquitinated substrates. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q60QD1|FIGL1_CAEBR Fidgetin-like protein 1 OS=Caenorhabditis briggsae GN=figl-1 PE=3 SV=1

 Score =  137 bits (346), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 88/273 (32%), Positives = 145/273 (53%), Gaps = 26/273 (9%)

Query: 241 GSLTSEELDALVS--VLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILL 298
           G    E +D L S   L+     I  L E ++ +  ++I W ++AG +  K+ +++ ++L
Sbjct: 275 GGGKDERMDGLRSEPTLKHFDENIISLIESEIMSVNNQIGWADVAGLEGAKKALKEIVVL 334

Query: 299 SLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY 358
             Q P+++     G R       P+ VL  GPPGTGKT   R +A+QA A          
Sbjct: 335 PFQRPDIFT----GLRAP-----PKGVLLFGPPGTGKTMIGRCVASQAQAT------FFN 379

Query: 359 VPLEVVMSKYYGESERLLGKVFSLAN-ELPNGAIIFLDEVDSFAVARDSEMHEATRRILS 417
           +    + SK+ GE E+L+  +FS+A  +LP  ++IF+DE+DS   AR    HE++RRI +
Sbjct: 380 ISASSLTSKWVGEGEKLVRALFSVARLKLP--SVIFIDEIDSLLSARSESEHESSRRIKT 437

Query: 418 VLLRQIDGFEQ--DKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK 475
             L Q+DG     D++++V+ ATNR Q+LD A   RF   +   LP+ ++R +I     +
Sbjct: 438 EFLVQLDGVNTAPDERLLVLGATNRPQELDEAARRRFQKRLYIALPEPDSRTQIVENLLR 497

Query: 476 ----HLTKAELAELATATEEMSGRDIRDVCQQA 504
                +T   L ++   T+  SG D+R +C +A
Sbjct: 498 GTRHEITDHNLEKIRRLTDGYSGADMRQLCTEA 530

Has a role in spindle assembly which acts in the progression through mitosis during embryogenesis. Required for fertility.

Caenorhabditis briggsae (taxid: 6238)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: -

>sp|O28303|PAN_ARCFU Proteasome-activating nucleotidase OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) GN=pan PE=1 SV=1

 Score =  135 bits (341), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 93/251 (37%), Positives = 132/251 (52%), Gaps = 27/251 (10%)

Query: 262 IYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNR 321
           +YG +  +    K E+S+E+I G D Q  EI + + L L  PE++ ++            
Sbjct: 127 VYGFEVEE----KPEVSYEDIGGLDVQIEEIREAVELPLLKPELFAEVG--------IEP 174

Query: 322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFS 381
           P+ VL  GPPGTGKT  A+ +ANQ  A   + V   +V       KY GE  RL+ +VF 
Sbjct: 175 PKGVLLYGPPGTGKTLLAKAVANQTRATFIRVVGSEFV------QKYIGEGARLVREVFQ 228

Query: 382 LANELPNGAIIFLDEVDSFAVAR---DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT 438
           LA E    +IIF+DE+D+ A  R   D+      +R +  LL ++DGF+    V VI AT
Sbjct: 229 LAKE-KAPSIIFIDELDAIAARRTNSDTSGDREVQRTMMQLLAELDGFDPRGDVKVIGAT 287

Query: 439 NRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMS 493
           NR   LDPA++   RFD +I   LP  E R +I   + + +  AE     ELA  TE  S
Sbjct: 288 NRIDILDPAILRPGRFDRIIEVPLPTFEGRIQIFKIHTRKMKLAEDVDFKELARITEGAS 347

Query: 494 GRDIRDVCQQA 504
           G DI+ +C +A
Sbjct: 348 GADIKAICTEA 358

ATPase which is responsible for recognizing, binding, unfolding and translocation of substrate proteins into the archaeal 20S proteasome core particle. Is essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Unfolding activity requires energy from ATP hydrolysis, whereas ATP binding alone promotes ATPase-20S proteasome association which triggers gate opening, and supports translocation of unfolded substrates.

Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126) (taxid: 224325)

>sp|O26824|PAN_METTH Proteasome-activating nucleotidase OS=Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) GN=pan PE=3 SV=1

 Score =  135 bits (340), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 88/239 (36%), Positives = 130/239 (54%), Gaps = 23/239 (9%)

Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
           K ++S+E I G ++Q RE+++T+ L L+ PE+++ I            P+ VL  GPPGT
Sbjct: 145 KPDVSYEQIGGLEEQVREVKETVELPLKKPELFEKIG--------IEPPKGVLLYGPPGT 196

Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIF 393
           GKT  A+ +A++  A   + V   +V       KY GE  RL+  VF LA E  + +IIF
Sbjct: 197 GKTLLAKAVAHETNATFIKIVASEFV------RKYIGEGARLVRGVFELAKE-KSPSIIF 249

Query: 394 LDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI- 449
           +DE+D+ A  R        R   R L  LL ++DGFE    V ++AATNR   LDPAL+ 
Sbjct: 250 IDEIDAVAAKRLKSSTSGDREVQRTLMQLLAELDGFESRGNVGIVAATNRPDILDPALLR 309

Query: 450 -SRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAE---LATATEEMSGRDIRDVCQQA 504
             RFD  I   LP+ + R+EI   +   +  AE  +   LA  T+  SG D++ +C +A
Sbjct: 310 PGRFDRFIEVPLPNEDGRREILKIHTSGMALAEEVDIELLARITDGASGADLKAICTEA 368

ATPase which is responsible for recognizing, binding, unfolding and translocation of substrate proteins into the archaeal 20S proteasome core particle. Is essential for opening the gate of the 20S proteasome via an interaction with its C-terminus, thereby allowing substrate entry and access to the site of proteolysis. Thus, the C-termini of the proteasomal ATPase function like a 'key in a lock' to induce gate opening and therefore regulate proteolysis. Unfolding activity requires energy from ATP hydrolysis, whereas ATP binding alone promotes ATPase-20S proteasome association which triggers gate opening, and supports translocation of unfolded substrates.

Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H) (taxid: 187420)

>sp|O05209|VAT_THEAC VCP-like ATPase OS=Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) GN=vat PE=1 SV=1

 Score =  135 bits (340), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 89/252 (35%), Positives = 134/252 (53%), Gaps = 29/252 (11%)

Query: 275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTG 334
           S IS+E+I G  +Q  +I + I L L+ PE+++        +     P+ V+  GPPGTG
Sbjct: 185 SRISYEDIGGLSEQLGKIREMIELPLKHPELFE--------RLGITPPKGVILYGPPGTG 236

Query: 335 KTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFL 394
           KT  AR +AN++GA        + +    +MSKYYG+SE+ L ++FS A E    +IIF+
Sbjct: 237 KTLIARAVANESGAN------FLSINGPEIMSKYYGQSEQKLREIFSKAEETAP-SIIFI 289

Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL--ISRF 452
           DE+DS A  R+    E  RR+++ LL  +DG ++   V+VI ATNR   +DPAL    RF
Sbjct: 290 DEIDSIAPKREEVQGEVERRVVAQLLTLMDGMKERGHVIVIGATNRIDAIDPALRRPGRF 349

Query: 453 DSMITFGLPDHENRQEIAAQYAKHL--------TKAELAELATATEEMSGRD----IRDV 500
           D  I  G+PD   R+EI   + +++            L E+A  T    G D    +R+ 
Sbjct: 350 DREIEIGVPDRNGRKEILMIHTRNMPLGMSEEEKNKFLEEMADYTYGFVGADLAALVRES 409

Query: 501 CQQAERSWASKI 512
              A R +  +I
Sbjct: 410 AMNALRRYLPEI 421

Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165) (taxid: 273075)

>sp|Q5AWS6|CDC48_EMENI Cell division control protein 48 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=cdc48 PE=1 SV=2

 Score =  135 bits (339), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 88/235 (37%), Positives = 127/235 (54%), Gaps = 20/235 (8%)

Query: 275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTG 334
           +E+ +++I G  +Q  +I + + L L+ P+++  I            PR +L  GPPGTG
Sbjct: 220 NEVGYDDIGGCRKQMAQIRELVELPLRHPQLFKSIG--------IKPPRGILMYGPPGTG 271

Query: 335 KTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFL 394
           KT  AR +AN+ GA  +    L+  P   +MSK  GESE  L K F  A E  + AIIF+
Sbjct: 272 KTLMARAVANETGAFFF----LINGP--EIMSKMAGESESNLRKAFEEA-EKNSPAIIFI 324

Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL--ISRF 452
           DE+DS A  R+    E  RR++S LL  +DG +    VVV+AATNR   +DPAL    RF
Sbjct: 325 DEIDSIAPKREKTNGEVERRVVSQLLTLMDGMKARSNVVVMAATNRPNSIDPALRRFGRF 384

Query: 453 DSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
           D  +  G+PD   R EI + + K++   E   L  +A  T    G D+  +C +A
Sbjct: 385 DREVDIGIPDPTGRLEILSIHTKNMKLGEDVDLETIAAETHGYVGSDLASLCSEA 439

Involved in spindle disassembly, degradation of ubiquitinated proteins and protein export from the endoplasmic reticulum to the cytoplasm (By similarity). Involved in osmoadaptation.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

>sp|Q9P3A7|CDC48_SCHPO Cell division cycle protein 48 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=cdc48 PE=1 SV=2

 Score =  134 bits (338), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 90/238 (37%), Positives = 132/238 (55%), Gaps = 20/238 (8%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           +S +E+ +++I G  +Q  +I + + L L+ P+++  I  G +       PR +L  GPP
Sbjct: 216 SSLAEVGYDDIGGCRRQMAQIRELVELPLRHPQLFKSI--GIKP------PRGILMYGPP 267

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI 391
           GTGKT  AR +AN+ GA  +    L+  P   +MSK  GESE  L K F  A E  + AI
Sbjct: 268 GTGKTLMARAVANETGAFFF----LINGP--EIMSKMAGESESNLRKAFEEA-EKNSPAI 320

Query: 392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL--I 449
           IF+DE+DS A  R+    E  RR++S LL  +DG +    VVV+AATNR   +DPAL   
Sbjct: 321 IFIDEIDSIAPKREKTNGEVERRVVSQLLTLMDGMKARSNVVVMAATNRPNSIDPALRRF 380

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQA 504
            RFD  +  G+PD   R EI   + K++  A   +L ++A  T    G D+  +C +A
Sbjct: 381 GRFDREVDVGIPDPTGRLEILRIHTKNMKLADDVDLEQIAAETHGYVGSDLASLCSEA 438

Involved in spindle disassembly, degradation of ubiquitinated proteins and protein export from the endoplasmic reticulum to the cytoplasm.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

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	567
224118112	562	predicted protein [Populus trichocarpa]	0.925	0.934	0.711	0.0
255554761	587	26S protease regulatory subunit, putativ	0.971	0.938	0.673	0.0
449433992	585	PREDICTED: ATPase family AAA domain-cont	0.947	0.917	0.612	0.0
359494833	596	PREDICTED: AAA ATPase forming ring-shape	0.970	0.922	0.617	0.0
449518017	521	PREDICTED: ATPase family AAA domain-cont	0.851	0.927	0.663	0.0
356557945	573	PREDICTED: katanin p60 ATPase-containing	0.818	0.809	0.675	0.0
42566294	609	AAA-type ATPase family protein [Arabidop	0.973	0.906	0.570	0.0
297809595	602	AAA-type ATPase family protein [Arabidop	0.968	0.911	0.569	1e-177
3377851	536	contains similarity to ATPases associate	0.858	0.908	0.598	1e-175
357143971	592	PREDICTED: uncharacterized protein LOC10	0.797	0.763	0.588	1e-162

>gi|224118112|ref|XP_002331561.1| predicted protein [Populus trichocarpa] gi|222873785|gb|EEF10916.1| predicted protein [Populus trichocarpa]

 Score =  781 bits (2018), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 402/565 (71%), Positives = 443/565 (78%), Gaps = 40/565 (7%)

Query: 35  SLEQQIRFSASEIQRPKLLDDTPG-PSSIHPAILAGLFGVGALNIAYADGDQGAGTAKPS 93
           S   QI  S+SEI RP+   +    P+S+ PA+LA   GVG L +A+AD D+ A      
Sbjct: 6   SFNHQIHSSSSEILRPRWASNANELPNSLFPALLASFIGVGMLQVAHADSDENASKPPLP 65

Query: 94  LPSESSSSYENLEEIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACE 153
               S SSY +LEEIAKKERQRIEELLK KG+ YGS P FT+AVKGQKVTIKFQ+PPAC+
Sbjct: 66  S-ESSPSSYGDLEEIAKKERQRIEELLKSKGIKYGSFPRFTIAVKGQKVTIKFQIPPACD 124

Query: 154 IPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMN 213
            PQLIANLVS+LG+KV+E G GSDM LRAWDSAVAWQLTL  PEKQ E  G+R  SGDM 
Sbjct: 125 TPQLIANLVSNLGVKVDERGAGSDMSLRAWDSAVAWQLTLNYPEKQKEISGERGHSGDMK 184

Query: 214 AREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGR------------- 260
             EGDLCIL+FRSLI+SDKPE+EFIK GSL++ ELDA VSVLQLAG              
Sbjct: 185 VPEGDLCILLFRSLISSDKPEVEFIKSGSLSTTELDAFVSVLQLAGSKLRPLDRKPAEGS 244

Query: 261 ------------------RIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQS 302
                             RIYGLDEP +N+S ++ISWENIAGYDQQKREIEDTILL+LQS
Sbjct: 245 ARVPSADKSVASLESMGVRIYGLDEPLVNSSSNDISWENIAGYDQQKREIEDTILLALQS 304

Query: 303 PEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE 362
           PEVYDDIARGTR KFESNRPRAVLFEGPPGTGKTSCARVIA QAG      VPL+Y+PLE
Sbjct: 305 PEVYDDIARGTRRKFESNRPRAVLFEGPPGTGKTSCARVIATQAG------VPLLYLPLE 358

Query: 363 VVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQ 422
           VVMSKYYGESERLLGKVF+LANE+PNGAIIFLDEVDSFA ARDSEMHEATRRILSVLLRQ
Sbjct: 359 VVMSKYYGESERLLGKVFTLANEIPNGAIIFLDEVDSFAAARDSEMHEATRRILSVLLRQ 418

Query: 423 IDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAEL 482
           IDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPD +NRQEIAAQYAKHLT++EL
Sbjct: 419 IDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDRQNRQEIAAQYAKHLTESEL 478

Query: 483 AELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRS 542
            E A  TE+MSGRDIRDVCQQAERSWASKIIRGQ +KDG Q  LPPL EY ESA NRR++
Sbjct: 479 EEFARVTEDMSGRDIRDVCQQAERSWASKIIRGQASKDGGQGNLPPLAEYTESAMNRRKA 538

Query: 543 LLDAAEQSHQNINNHRTKKQPLDLC 567
           L   AEQ  Q  +  R +K  LD C
Sbjct: 539 LASIAEQKSQG-SIMRPQKPQLDTC 562

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255554761|ref|XP_002518418.1| 26S protease regulatory subunit, putative [Ricinus communis] gi|223542263|gb|EEF43805.1| 26S protease regulatory subunit, putative [Ricinus communis]

 Score =  746 bits (1926), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/603 (67%), Positives = 452/603 (74%), Gaps = 52/603 (8%)

Query: 1   MASLRRLAKTASVWRVLTASRA---SPRGQPRRLPHRSLEQQIRFSASEIQRPKLLDDTP 57
           MASL RL +    W   +  +    SP    R L H      I   ASEIQ    L    
Sbjct: 1   MASLGRLLRRRPSWSRFSCPKTLKPSPNHFLRPLHH----LHICSPASEIQ----LSTID 52

Query: 58  GPS-SIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQRI 116
           GP  SI PA+ AG  G+G   +AYAD DQ A  AKPSLPSES SSY++LEEIA KERQRI
Sbjct: 53  GPYYSILPAVFAGFLGLGMFQVAYADSDQAA--AKPSLPSESPSSYKDLEEIATKERQRI 110

Query: 117 EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGS 176
           E LLK +G+  GS P F VAVKGQKVTIKFQ+PPAC+   LIANLVS+LGLKV+E  GGS
Sbjct: 111 EGLLKLRGIKNGSYPRFMVAVKGQKVTIKFQIPPACDALHLIANLVSNLGLKVDERAGGS 170

Query: 177 DMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIE 236
           DM LRAWDSAVAWQLTL  PEK  E+G D+ Q  DMN  EGDLCI +FRSLI++DK EIE
Sbjct: 171 DMLLRAWDSAVAWQLTLSSPEKHKEAGVDKGQFVDMNTAEGDLCIFLFRSLISTDKAEIE 230

Query: 237 FIKKGSLTSEELDALVSVLQLAGRR-------------------------------IYGL 265
           FIK GSL++ ELDALVSVLQLAG R                               IYGL
Sbjct: 231 FIKGGSLSTTELDALVSVLQLAGDRLKSLQRIPGEGAARMPSADKSVATLESMGVRIYGL 290

Query: 266 DEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAV 325
           +EP +N+SK EISW NIAGYDQQK+EIEDTILL+L SPEVYD+IARGTR KFESNRPRAV
Sbjct: 291 NEPHINSSKGEISWNNIAGYDQQKQEIEDTILLALHSPEVYDNIARGTRRKFESNRPRAV 350

Query: 326 LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE 385
           LFEGPPGTGKTSCARVIA QAG      VPL+YVPLEVVMSKYYGESE+LLGKVF+LANE
Sbjct: 351 LFEGPPGTGKTSCARVIATQAG------VPLLYVPLEVVMSKYYGESEKLLGKVFALANE 404

Query: 386 LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLD 445
           LPNGAIIFLDEVDSFAVARD+EMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLD
Sbjct: 405 LPNGAIIFLDEVDSFAVARDNEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLD 464

Query: 446 PALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAE 505
           PALISRFDSMITFGLPD +NRQEI AQYAKHL ++++ ELA  T++MSGRDI+DVCQQAE
Sbjct: 465 PALISRFDSMITFGLPDEQNRQEIVAQYAKHLKRSDIEELAKVTDQMSGRDIKDVCQQAE 524

Query: 506 RSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKK-QPL 564
           RSWASKIIRG+  +DGEQ  LP L EYIESA  RR++LL  A+Q     N  R++    L
Sbjct: 525 RSWASKIIRGKADRDGEQGNLPTLSEYIESALIRRQALLSIADQRSGGFNPSRSRSGSRL 584

Query: 565 DLC 567
           DLC
Sbjct: 585 DLC 587

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449433992|ref|XP_004134780.1| PREDICTED: ATPase family AAA domain-containing protein 1-B-like [Cucumis sativus]

 Score =  718 bits (1853), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/611 (61%), Positives = 446/611 (72%), Gaps = 74/611 (12%)

Query: 1   MASLRRLAKTASVWRVLTA------SRASPRGQPRRLPHRSLEQQIRFSASEIQRPKLLD 54
           M+ L R+++TA  WR+L +      S AS     R   H+           E  +P  L 
Sbjct: 1   MSVLNRISRTARAWRILASFKLKESSSASQSFYLRHFGHQP----------EHFKPGSLS 50

Query: 55  DTPGPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQ 114
           +   P  ++PAI+AG+ GVGA+ IAYA+ ++   T  P       S++ ++E+IAKKER 
Sbjct: 51  NGREPCFLYPAIVAGMVGVGAMEIAYAEAEESTSTPPPP---RDLSTHADMEDIAKKERL 107

Query: 115 RIEELLKR-KGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHG 173
           RI E LKR KG  YG+CP FTV VKGQKV+IKFQVPP+CE+  LIANLVS+LGLKVEE  
Sbjct: 108 RITEQLKRNKGTKYGACPRFTVGVKGQKVSIKFQVPPSCEVSHLIANLVSNLGLKVEETA 167

Query: 174 GGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKP 233
           GGSDM LRAWDS VAWQLTL  P+ Q E+G ++  S +M+A +GDL +LIF SLITSDK 
Sbjct: 168 GGSDMLLRAWDSPVAWQLTLSRPKSQKEAGENKGNSIEMDADDGDLTVLIFHSLITSDKT 227

Query: 234 EIEFIKKGSLTSEELDALVSVLQLAGRR-------------------------------- 261
           EIEFIK+GSL+++ELD+LVSVLQLAG R                                
Sbjct: 228 EIEFIKQGSLSTKELDSLVSVLQLAGGRLGESRSFERKSKEESTQMPSSEKSISSLEAMG 287

Query: 262 --IYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFES 319
             +YGLD P LN++K+EISW+NIAGYDQQKREIED+IL++L +PE++DDIA GTR KFES
Sbjct: 288 VKVYGLDGPHLNSTKNEISWDNIAGYDQQKREIEDSILMTLHNPELFDDIAHGTRRKFES 347

Query: 320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKV 379
           N+PRAVLFEGPPGTGKTS ARVIANQAG      VPL+YVPLEV+MSKYYGESERLLGKV
Sbjct: 348 NKPRAVLFEGPPGTGKTSSARVIANQAG------VPLVYVPLEVIMSKYYGESERLLGKV 401

Query: 380 FSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATN 439
           FSLAN+L  GAIIFLDEVDSFA++RDSE+HEATRR+LSVLLRQIDGFEQD+KV+VIAATN
Sbjct: 402 FSLANDLSTGAIIFLDEVDSFAISRDSEIHEATRRVLSVLLRQIDGFEQDRKVIVIAATN 461

Query: 440 RKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRD 499
           RKQDLDPALISRFD MITFGLPD  NR+EIAAQYAK LT+ EL E A  TE MSGRDIRD
Sbjct: 462 RKQDLDPALISRFDMMITFGLPDERNREEIAAQYAKQLTQPELKEFARNTEGMSGRDIRD 521

Query: 500 VCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNH-- 557
           +CQQAERSWASKIIRG+++K GE   LPPL+EYIE A NRR++L        Q I++H  
Sbjct: 522 ICQQAERSWASKIIRGKVSKTGEHGILPPLEEYIECAMNRRKAL--------QTIDDHEI 573

Query: 558 ----RTKKQPL 564
               RTKK  L
Sbjct: 574 KDPNRTKKTQL 584

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359494833|ref|XP_002267342.2| PREDICTED: AAA ATPase forming ring-shaped complexes-like [Vitis vinifera] gi|297741773|emb|CBI33002.3| unnamed protein product [Vitis vinifera]

 Score =  712 bits (1838), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 373/604 (61%), Positives = 434/604 (71%), Gaps = 54/604 (8%)

Query: 1   MASLRRLAKTASVWRVLTASRASPRGQPRRLP---HRSLEQQIRFSASEIQRPKLLDDTP 57
           MAS+ RL K A  WR + + +       R  P   HR  EQQI    SE Q P      P
Sbjct: 1   MASVWRLLKAAQSWRPIVSPKTLTPPPLRFPPRFCHRPFEQQINPRISEAQLP------P 54

Query: 58  GPSSIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSS-----YENLEEIAKKE 112
              SI P++L GLFG G L IA+A+ D GA        S  S S     Y NLEE A+K 
Sbjct: 55  VSVSIVPSVLVGLFGFGLLEIAHAESDPGADKTPLPSQSSPSPSESPPSYTNLEENARKL 114

Query: 113 RQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEH 172
           R R+EEL++ KGM YGS P FTVA+KGQKVTIKFQ+PP CE+P LIA LV+ LG+KVEE 
Sbjct: 115 RDRLEELIRTKGMKYGSYPRFTVALKGQKVTIKFQIPPTCEVPCLIAKLVAQLGMKVEER 174

Query: 173 GGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDK 232
            GGSDM +RAWDS +AWQL L    KQN++G ++  S   NA EGDLCILIF+SLI++DK
Sbjct: 175 SGGSDMIMRAWDSGIAWQLMLSRLGKQNKTGAEQVHSQYTNANEGDLCILIFQSLISADK 234

Query: 233 PEIEFIKKGSLTSEELDALVSVLQLA---------------------------------- 258
            EIEFIK+GS +SEELDALVSVLQ A                                  
Sbjct: 235 AEIEFIKQGSFSSEELDALVSVLQFAGGRVEQNKTLERRPRGDAPQMHSAQKSIASLEAM 294

Query: 259 GRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFE 318
           G R++G DEPQ   SK+E+ W+NIAGYDQQKR+IED I+ +L SP+VYDD+ARGTR KFE
Sbjct: 295 GVRVFGADEPQGGLSKNEVLWDNIAGYDQQKRQIEDEIVFALHSPDVYDDVARGTRQKFE 354

Query: 319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGK 378
           SNRPRAVLFEGPPGTGKTSCARVIANQA      GVPL+Y+PLE +MSKYYGESERLLGK
Sbjct: 355 SNRPRAVLFEGPPGTGKTSCARVIANQA------GVPLVYLPLESIMSKYYGESERLLGK 408

Query: 379 VFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT 438
           VF  ANE P GAI+FLDEVDSFAV+R  EMHEATRRILSV+LRQIDGFEQDKKVVVIAAT
Sbjct: 409 VFVHANEFPEGAIVFLDEVDSFAVSRSREMHEATRRILSVILRQIDGFEQDKKVVVIAAT 468

Query: 439 NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIR 498
           NRKQDLDPAL+SRFDSMITFGLPD+ +RQ+IAAQ+AKHLT++EL E ATATE MSGRDIR
Sbjct: 469 NRKQDLDPALMSRFDSMITFGLPDNHDRQKIAAQFAKHLTESELVEFATATEGMSGRDIR 528

Query: 499 DVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHR 558
           D+CQQAER WASK+IRGQ  KDG+Q  LPP+Q YIESA  R  +LL  A+Q  +  N ++
Sbjct: 529 DICQQAERHWASKVIRGQAPKDGDQVILPPIQVYIESAKTRANTLLSIADQKTEKSNRNQ 588

Query: 559 TKKQ 562
           T+ Q
Sbjct: 589 TQPQ 592

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449518017|ref|XP_004166040.1| PREDICTED: ATPase family AAA domain-containing protein 1-B-like [Cucumis sativus]

 Score =  694 bits (1791), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 353/532 (66%), Positives = 412/532 (77%), Gaps = 49/532 (9%)

Query: 70  LFGVGALNIAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQRIEELLKR-KGMHYG 128
           + GVGA+ IAYA+ ++   T  P       S++ ++E+IAKKER RI E LKR KG  YG
Sbjct: 1   MVGVGAMEIAYAEAEESTSTPPPP---RDLSTHADMEDIAKKERLRITEQLKRNKGTKYG 57

Query: 129 SCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVA 188
           +CP FTV VKGQKV+IKFQVPP+CE+  LIANLVS+LGLKVEE  GGSDM LRAWDS VA
Sbjct: 58  ACPRFTVGVKGQKVSIKFQVPPSCEVSHLIANLVSNLGLKVEETAGGSDMLLRAWDSPVA 117

Query: 189 WQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEEL 248
           WQLTL  P+ Q E+G ++  S +M+A +GDL +LIF SLITSDK EIEFIK+GSL+++EL
Sbjct: 118 WQLTLSRPKSQKEAGENKGNSIEMDADDGDLTVLIFHSLITSDKTEIEFIKQGSLSTKEL 177

Query: 249 DALVSVLQLAGRR----------------------------------IYGLDEPQLNTSK 274
           D+LVSVLQLAG R                                  +YGLD P LN++K
Sbjct: 178 DSLVSVLQLAGGRLGESRSFERKSKEESTQMPSSEKSISSLEAMGVKVYGLDGPHLNSTK 237

Query: 275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTG 334
           +EISW+NIAGYDQQKREIED+IL++L +PE++DDIA GTR KFESN+PRAVLFEGPPGTG
Sbjct: 238 NEISWDNIAGYDQQKREIEDSILMTLHNPELFDDIAHGTRRKFESNKPRAVLFEGPPGTG 297

Query: 335 KTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFL 394
           KTS ARVIANQAG      VPL+YVPLEV+MSKYYGESERLLGKVFSLAN+L  GAIIFL
Sbjct: 298 KTSSARVIANQAG------VPLVYVPLEVIMSKYYGESERLLGKVFSLANDLSTGAIIFL 351

Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDS 454
           DEVDSFA++RDSE+HEATRR+LSVLLRQIDGFEQD+KV+VIAATNRKQDLDPALISRFD 
Sbjct: 352 DEVDSFAISRDSEIHEATRRVLSVLLRQIDGFEQDRKVIVIAATNRKQDLDPALISRFDM 411

Query: 455 MITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIR 514
           MITFGLPD  NR+EIAAQYAK LT+ EL E A  TE MSGRDIRD+CQQAERSWASKIIR
Sbjct: 412 MITFGLPDERNREEIAAQYAKQLTQPELKEFARNTEGMSGRDIRDICQQAERSWASKIIR 471

Query: 515 GQITKDGEQACLPPLQEYIESATNRRRSL--LDAAEQSHQNINNHRTKKQPL 564
           G+++K GE   LPPL+EYIE A NRR++L  +D  E    NI   RTKK  L
Sbjct: 472 GKVSKTGEHGILPPLEEYIECAMNRRKALQTIDDHEIKDPNI---RTKKTQL 520

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557945|ref|XP_003547270.1| PREDICTED: katanin p60 ATPase-containing subunit A1-like [Glycine max]

 Score =  689 bits (1777), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 352/521 (67%), Positives = 398/521 (76%), Gaps = 57/521 (10%)

Query: 61  SIHPAILAGLFGVGALNIAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQRIEELL 120
           S+ P +LAG+FG G +  AYAD   GA                +++E AKKER+RIEELL
Sbjct: 58  SLLPVVLAGIFGTGFVEAAYAD--NGA---------------VDVQESAKKERERIEELL 100

Query: 121 KRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGL 180
           + +G+ YGS P FTV+VKGQKV+IKFQ+PP CE+ QLIANL +HLG K E HGGGSDM L
Sbjct: 101 RSRGIRYGSYPRFTVSVKGQKVSIKFQIPPNCEVSQLIANLTAHLGTKAEGHGGGSDMLL 160

Query: 181 RAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKK 240
           RAWDS VAWQLTL  P K     G+   S D+ A + DLCILIF SLI SDK EIEFIK+
Sbjct: 161 RAWDSTVAWQLTLTHPSKLKHIQGNNLSSTDIIADDRDLCILIFHSLIGSDKAEIEFIKQ 220

Query: 241 GSLTSEELDALVSVLQLAGR----------------------------------RIYGLD 266
           G L+ EELDA VSVLQLAG                                   RIYGLD
Sbjct: 221 GDLSPEELDAFVSVLQLAGNKLGQRNTLERKPREETEKVPSVDKSISDLEGMGVRIYGLD 280

Query: 267 EPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVL 326
           EP   ++  EISW+NIAGY+ QKR +EDTILL+L SPEVYDDIARGTR KFESNRPRAVL
Sbjct: 281 EPVGISNDGEISWDNIAGYEHQKRVVEDTILLALHSPEVYDDIARGTRHKFESNRPRAVL 340

Query: 327 FEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL 386
           FEGPPGTGKTSCARVIANQAG      VPL+YVPLE +MS++YG+SERLLGKVFSLAN L
Sbjct: 341 FEGPPGTGKTSCARVIANQAG------VPLLYVPLEAIMSEFYGKSERLLGKVFSLANTL 394

Query: 387 PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDP 446
           PNGAIIFLDE+DSFA ARD+EMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK+DLDP
Sbjct: 395 PNGAIIFLDEIDSFAAARDNEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKEDLDP 454

Query: 447 ALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAER 506
           ALISRFDSMI FGLPDH+NRQEIA++YAKHL+K EL ELA  TE+MSGRDIRDVCQQAER
Sbjct: 455 ALISRFDSMIAFGLPDHQNRQEIASKYAKHLSKPELDELARVTEDMSGRDIRDVCQQAER 514

Query: 507 SWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAA 547
           SWASKIIRGQ+ K+GE+A LPPLQEYIE AT+R+ +L  AA
Sbjct: 515 SWASKIIRGQVPKEGEKAQLPPLQEYIECATSRQEALHSAA 555

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|42566294|ref|NP_192327.3| AAA-type ATPase family protein [Arabidopsis thaliana] gi|332656970|gb|AEE82370.1| AAA-type ATPase family protein [Arabidopsis thaliana]

 Score =  647 bits (1668), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 355/622 (57%), Positives = 430/622 (69%), Gaps = 70/622 (11%)

Query: 1   MASLRRLAKTASVWR-VLTASRA-----SPRGQP-RRLPHRSLEQQIRFSASEIQRP-KL 52
           MA L +L + +  WR  L+ S++     SPR +  RR  H    +Q     +++ R    
Sbjct: 1   MAILDKLFRASRAWRGSLSHSKSMVPSQSPRARELRRCFHHGNFEQSNSKVNQVLRSCST 60

Query: 53  LDDTPGPSSIHPAILAGLFGVGALNIAYADGDQGAG--TAKPSLPSESSSSYE-----NL 105
           L+D+P   S+ PA+L  LF VG + +AYA+ D+     ++ P  P++ +SS       N 
Sbjct: 61  LNDSPY-FSMAPAVLGALFSVGVIGVAYAESDEANNDKSSAPIDPNDETSSAPIDPPPNY 119

Query: 106 EEIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHL 165
            +IAKKER R+EEL++ KG  YGS P F VAV+GQK+T+KFQVP  CE+ QLI+N+ S L
Sbjct: 120 VDIAKKERARVEELIQSKGTQYGSYPRFNVAVRGQKITLKFQVPSTCEVAQLISNIGSQL 179

Query: 166 GLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFR 225
           G+KV +  GGSDM LRAWD+ VAWQ+TL+  E + + G     S D       LCILIF 
Sbjct: 180 GVKVSDRTGGSDMLLRAWDNPVAWQITLRSVENKKKLGESEDDSDDD------LCILIFG 233

Query: 226 SLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGR------------------------- 260
           SL+TSDK E+EFIKKGSLT+EEL+A VS L +AG                          
Sbjct: 234 SLLTSDKVEVEFIKKGSLTTEELEAFVSALGVAGTKAGQNKGSGSRGSTRDSSTDKSISQ 293

Query: 261 ------RIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTR 314
                 RIYG+++P  + S  EISW+NIAGYDQQKREIEDTIL++L SPEVYDDI RGTR
Sbjct: 294 LESMGVRIYGVNKPLGDDSMDEISWDNIAGYDQQKREIEDTILMALHSPEVYDDIVRGTR 353

Query: 315 CKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER 374
            KFESNRPRAVLFEGPPGTGKTSCARVIANQAG      +PL+YVPLE VMSKYYGESER
Sbjct: 354 SKFESNRPRAVLFEGPPGTGKTSCARVIANQAG------IPLLYVPLEAVMSKYYGESER 407

Query: 375 LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVV 434
           LLG VFS ANELP+GAIIFLDE+D+FA++RDSEMHEATRR+LSVLLRQIDGFEQ+KKVVV
Sbjct: 408 LLGAVFSQANELPDGAIIFLDEIDAFAISRDSEMHEATRRVLSVLLRQIDGFEQEKKVVV 467

Query: 435 IAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSG 494
           IAATNRKQDLDPALISRFDSMI F LPD + RQEI AQYAK L+K EL +LA ATE MSG
Sbjct: 468 IAATNRKQDLDPALISRFDSMIMFDLPDLQTRQEIIAQYAKQLSKPELVQLAQATEAMSG 527

Query: 495 RDIRDVCQQAERSWASKIIR----GQITK------DGEQACLPPLQEYIESATNRRRSLL 544
           RDIRDVCQ AER+WASKII     GQ+ +      + ++  LPP+QEY+ESA  RR+SL 
Sbjct: 528 RDIRDVCQGAERTWASKIINLYIVGQLIRRAKAGGEEQKITLPPIQEYLESAEARRKSLR 587

Query: 545 DAAEQSHQNINNHRTKKQPLDL 566
              EQ  Q     R+KK  LD 
Sbjct: 588 SVTEQKEQKF-AARSKKPLLDF 608

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297809595|ref|XP_002872681.1| AAA-type ATPase family protein [Arabidopsis lyrata subsp. lyrata] gi|297318518|gb|EFH48940.1| AAA-type ATPase family protein [Arabidopsis lyrata subsp. lyrata]

 Score =  629 bits (1621), Expect = e-177,   Method: Compositional matrix adjust.
 Identities = 352/618 (56%), Positives = 422/618 (68%), Gaps = 69/618 (11%)

Query: 1   MASLRRLAKTASVWR-VLTASRASPRGQPR-RLPHRSLEQ----QIRFSASEIQRP-KLL 53
           MA L +L + +  WR  L+ S++    QPR R  HR        Q     +++ R    +
Sbjct: 1   MAVLDKLFRASRAWRGSLSHSKSVAPSQPRARELHRCFYSGTFDQSNSKVNQVLRSCSTI 60

Query: 54  DDTPGPSSIHPAILAGLFGVGALNIAYADGDQ-------------GAGTAKPSLPSESSS 100
           +++P   SI PA+L  LF VGA+ +AYA+ D+              A   K S P +   
Sbjct: 61  NESPY-FSIAPAVLGALFSVGAIGVAYAESDEVFFTDSSLKLTFLKATNDKSSAPIDPPP 119

Query: 101 SYENLEEIAKKERQRIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIAN 160
           +Y +   IAKKER RIEEL+  KG  YGS P F VAV+GQK+T+KFQVP  CE+ QLI+N
Sbjct: 120 NYVD---IAKKERARIEELISSKGTQYGSYPRFNVAVRGQKITLKFQVPSTCEVAQLISN 176

Query: 161 LVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLC 220
           + S LG+KV +  GGSDM LRAWD+ VAWQ+TL+  E + + G     S D       LC
Sbjct: 177 IGSQLGVKVSDRTGGSDMLLRAWDNPVAWQITLRSVENKKKLGESEDDSDDD------LC 230

Query: 221 ILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGR-------------------- 260
           ILIF SL+TSDK E+EFIKKGSLT+EEL+A VS L++AG                     
Sbjct: 231 ILIFGSLLTSDKVEVEFIKKGSLTTEELEAFVSALRVAGTKAGQNKGGGVRGSARESSTD 290

Query: 261 -----------RIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDI 309
                      RIYG+++P  + S  +ISW+NIAGYDQQKREIEDTIL++L SPEVYDDI
Sbjct: 291 KSISQLESMGVRIYGVNKPLGDDSIDDISWDNIAGYDQQKREIEDTILMALHSPEVYDDI 350

Query: 310 ARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY 369
            RGTR KFESNRPRAVLFEGPPGTGKTSCARVIANQAG      +PL+YVPLE VMSKYY
Sbjct: 351 VRGTRSKFESNRPRAVLFEGPPGTGKTSCARVIANQAG------IPLLYVPLEAVMSKYY 404

Query: 370 GESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD 429
           GESERLLG VFS ANELP+GAIIFLDE+D+FA++RDSEMHEATRR+LSVLLRQIDGFEQD
Sbjct: 405 GESERLLGDVFSQANELPDGAIIFLDEIDAFAISRDSEMHEATRRVLSVLLRQIDGFEQD 464

Query: 430 KKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATAT 489
           KKVVVIAATNRKQDLDPALISRFDSMI F LPD + RQEI  QYAK L+K EL +LA AT
Sbjct: 465 KKVVVIAATNRKQDLDPALISRFDSMIMFDLPDLQTRQEIITQYAKQLSKPELVQLAQAT 524

Query: 490 EEMSGRDIRDVCQQAERSWASKII-RGQITKDGEQACLPPLQEYIESATNRRRSLLDAAE 548
           E MSGRDIRDVCQ AER+WASK+I R +   +  +  LPP+QEY+ESA  RR++LL   E
Sbjct: 525 EAMSGRDIRDVCQGAERTWASKLIRRAKAGGEERKITLPPIQEYLESAEARRKALLSVTE 584

Query: 549 QSHQNINNHRTKKQPLDL 566
           Q        R+KK  LD 
Sbjct: 585 QKEPKF-AARSKKPLLDF 601

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|3377851|gb|AAC28233.1| contains similarity to ATPases associated with various cellular activities (Pfam: AAA.hmm, score: 155.05) [Arabidopsis thaliana] gi|7267174|emb|CAB77886.1| putative vesicle transfer ATPase [Arabidopsis thaliana]

 Score =  622 bits (1605), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 331/553 (59%), Positives = 392/553 (70%), Gaps = 66/553 (11%)

Query: 62  IHPAILAGLFGVGALNIAYADGDQGAG--TAKPSLPSESSSSYE-----NLEEIAKKERQ 114
           + PA+L  LF VG + +AYA+ D+     ++ P  P++ +SS       N  +IAKKER 
Sbjct: 1   MAPAVLGALFSVGVIGVAYAESDEANNDKSSAPIDPNDETSSAPIDPPPNYVDIAKKERA 60

Query: 115 RIEELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGG 174
           R+EEL++ KG  YGS P F VA+     T+KFQVP  CE+ QLI+N+ S LG+KV +  G
Sbjct: 61  RVEELIQSKGTQYGSYPRFNVAI-----TLKFQVPSTCEVAQLISNIGSQLGVKVSDRTG 115

Query: 175 GSDMGLRAWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPE 234
           GSDM LRAWD+ VAWQ+TL+  E + + G     S D       LCILIF SL+TSDK E
Sbjct: 116 GSDMLLRAWDNPVAWQITLRSVENKKKLGESEDDSDDD------LCILIFGSLLTSDKVE 169

Query: 235 IEFIKKGSLTSEELDALVSVLQLAGR-------------------------------RIY 263
           +EFIKKGSLT+EEL+A VS L +AG                                RIY
Sbjct: 170 VEFIKKGSLTTEELEAFVSALGVAGTKAGQNKGSGSRGSTRDSSTDKSISQLESMGVRIY 229

Query: 264 GLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPR 323
           G+++P  + S  EISW+NIAGYDQQKREIEDTIL++L SPEVYDDI RGTR KFESNRPR
Sbjct: 230 GVNKPLGDDSMDEISWDNIAGYDQQKREIEDTILMALHSPEVYDDIVRGTRSKFESNRPR 289

Query: 324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA 383
           AVLFEGPPGTGKTSCARVIANQAG      +PL+YVPLE VMSKYYGESERLLG VFS A
Sbjct: 290 AVLFEGPPGTGKTSCARVIANQAG------IPLLYVPLEAVMSKYYGESERLLGAVFSQA 343

Query: 384 NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD 443
           NELP+GAIIFLDE+D+FA++RDSEMHEATRR+LSVLLRQIDGFEQ+KKVVVIAATNRKQD
Sbjct: 344 NELPDGAIIFLDEIDAFAISRDSEMHEATRRVLSVLLRQIDGFEQEKKVVVIAATNRKQD 403

Query: 444 LDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQ 503
           LDPALISRFDSMI F LPD + RQEI AQYAK L+K EL +LA ATE MSGRDIRDVCQ 
Sbjct: 404 LDPALISRFDSMIMFDLPDLQTRQEIIAQYAKQLSKPELVQLAQATEAMSGRDIRDVCQG 463

Query: 504 AERSWASKIIR----GQITK------DGEQACLPPLQEYIESATNRRRSLLDAAEQSHQN 553
           AER+WASKII     GQ+ +      + ++  LPP+QEY+ESA  RR+SL    EQ  Q 
Sbjct: 464 AERTWASKIINLYIVGQLIRRAKAGGEEQKITLPPIQEYLESAEARRKSLRSVTEQKEQK 523

Query: 554 INNHRTKKQPLDL 566
               R+KK  LD 
Sbjct: 524 F-AARSKKPLLDF 535

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357143971|ref|XP_003573120.1| PREDICTED: uncharacterized protein LOC100829112 [Brachypodium distachyon]

 Score =  579 bits (1492), Expect = e-162,   Method: Compositional matrix adjust.
 Identities = 300/510 (58%), Positives = 359/510 (70%), Gaps = 58/510 (11%)

Query: 78  IAYADGDQGAGTAKPSLPSESSSSYENLEEIAKKERQRIEELLKRKGMHYGSCPTFTVAV 137
           +AYAD +   G    +     S+     E++A+KE++RI EL++ +GM  GS P F VA+
Sbjct: 85  VAYADANNEKGVVDTAEWVPVSADAAVGEDLARKEKKRIMELIESRGMPLGSYPQFDVAM 144

Query: 138 KGQKVTIKFQVPPACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAWDSAVAWQLTLKPPE 197
           KGQKV +KF VP  C I  LI +LV HLGL+ E+ GGGS+M LRAWDSA A Q+TL PP+
Sbjct: 145 KGQKVVVKFNVPSTCNISCLIVDLVKHLGLEAEQFGGGSEMLLRAWDSAAARQITLNPPK 204

Query: 198 KQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKP----EIEFIKKGSLTSEELDALVS 253
                       GD N  E  LC+LIF  L+ S+      EIEFIK  S + +EL+AL+S
Sbjct: 205 MTG--------IGDNN--EDHLCVLIFEPLVGSEYSVSPMEIEFIKPSSFSLKELEALIS 254

Query: 254 VLQLAGRR-------------------------------------IYGLDEPQLNTSKSE 276
            L+LAG++                                     +YG DE         
Sbjct: 255 ALKLAGQKDIKASSGKASSKGKDQRSKHLPSIDKTVSDLEAMGVKVYGFDEASSVPMDGT 314

Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           + WENIAGY+ QKREIEDT+LL+LQ+PEVYDDIARGTRCKFE+NRPRAVLFEGPPGTGKT
Sbjct: 315 LMWENIAGYEPQKREIEDTVLLALQNPEVYDDIARGTRCKFETNRPRAVLFEGPPGTGKT 374

Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDE 396
           S ARVIA QAG      VPL+YVPLE++MSKYYGESERLLG VFSLAN+LP G IIFLDE
Sbjct: 375 SSARVIAKQAG------VPLLYVPLEIIMSKYYGESERLLGSVFSLANKLPEGGIIFLDE 428

Query: 397 VDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMI 456
           VDSFA+ARDSEMHEATRRILSV+LRQIDGFEQD++VVVIAATNRK+DLDPALISRFDS+I
Sbjct: 429 VDSFAIARDSEMHEATRRILSVILRQIDGFEQDRRVVVIAATNRKEDLDPALISRFDSII 488

Query: 457 TFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQ 516
            FGLPD ++R EIAAQYAKHL+K ELA  +  TEEM+GRDIRD+C QAER WASK+IRGQ
Sbjct: 489 CFGLPDQQSRAEIAAQYAKHLSKPELARFSIVTEEMAGRDIRDICMQAERRWASKLIRGQ 548

Query: 517 ITKDGE-QACLPPLQEYIESATNRRRSLLD 545
           I KDG+ +  LPP+ EY+  A  RR+SL D
Sbjct: 549 IPKDGKGEPALPPIDEYVACAEQRRKSLPD 578

Source: Brachypodium distachyon

Species: Brachypodium distachyon

Genus: Brachypodium

Family: Poaceae

Order: Poales

Class: Liliopsida

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	567
TAIR|locus:2137261	609	AT4G04180 [Arabidopsis thalian	0.562	0.523	0.675	1.5e-162
WB|WBGene00004503	414	rpt-3 [Caenorhabditis elegans	0.476	0.652	0.343	1.7e-27
CGD|CAL0005827	428	RPT4 [Candida albicans (taxid:	0.444	0.588	0.341	2.6e-27
WB|WBGene00017981	594	figl-1 [Caenorhabditis elegans	0.398	0.380	0.32	3.6e-27
UNIPROTKB|O16299	594	figl-1 "Fidgetin-like protein	0.398	0.380	0.32	3.6e-27
TAIR|locus:2028200	399	AT1G45000 [Arabidopsis thalian	0.442	0.629	0.342	3.6e-27
FB|FBgn0028868	384	CG4701 [Drosophila melanogaste	0.410	0.606	0.324	6e-27
TAIR|locus:2161258	408	RPT3 "regulatory particle trip	0.382	0.531	0.376	6e-27
ZFIN|ZDB-GENE-030616-44	362	atad1b "ATPase family, AAA dom	0.437	0.685	0.311	7.7e-27
TAIR|locus:2159996	399	RPT4A "regulatory particle tri	0.442	0.629	0.339	1e-26

TAIR|locus:2137261 AT4G04180 [Arabidopsis thaliana (taxid:3702)]

 Score = 1081 (385.6 bits), Expect = 1.5e-162, Sum P(2) = 1.5e-162
 Identities = 227/336 (67%), Positives = 255/336 (75%)

Query:   240 KGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLS 299
             +GS      D  +S L+  G RIYG+++P  + S  EISW+NIAGYDQQKREIEDTIL++
Sbjct:   279 RGSTRDSSTDKSISQLESMGVRIYGVNKPLGDDSMDEISWDNIAGYDQQKREIEDTILMA 338

Query:   300 LQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV 359
             L SPEVYDDI RGTR KFESNRPRAVLFEGPPGTGKTSCARVIANQAG      +PL+YV
Sbjct:   339 LHSPEVYDDIVRGTRSKFESNRPRAVLFEGPPGTGKTSCARVIANQAG------IPLLYV 392

Query:   360 PLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL 419
             PLE VMSKYYGESERLLG VFS ANELP+GAIIFLDE+D+FA++RDSEMHEATRR+LSVL
Sbjct:   393 PLEAVMSKYYGESERLLGAVFSQANELPDGAIIFLDEIDAFAISRDSEMHEATRRVLSVL 452

Query:   420 LRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHXXX 479
             LRQIDGFEQ+KKVVVIAATNRKQDLDPALISRFDSMI F LPD + RQEI AQYAK    
Sbjct:   453 LRQIDGFEQEKKVVVIAATNRKQDLDPALISRFDSMIMFDLPDLQTRQEIIAQYAKQLSK 512

Query:   480 XXXXXXXXXXXXMSGRDIRDVCQQAERSWASKIIR----GQITK----DGEQA--CLPPL 529
                         MSGRDIRDVCQ AER+WASKII     GQ+ +     GE+    LPP+
Sbjct:   513 PELVQLAQATEAMSGRDIRDVCQGAERTWASKIINLYIVGQLIRRAKAGGEEQKITLPPI 572

Query:   530 QEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLD 565
             QEY+ESA  RR+SL    EQ  Q     R+KK  LD
Sbjct:   573 QEYLESAEARRKSLRSVTEQKEQKFAA-RSKKPLLD 607

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

WB|WBGene00004503 rpt-3 [Caenorhabditis elegans (taxid:6239)]

 Score = 313 (115.2 bits), Expect = 1.7e-27, P = 1.7e-27
 Identities = 103/300 (34%), Positives = 142/300 (47%)

Query:   236 EFIKKG-SLTSEEL-DALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIE 293
             E +K G S+   +  +ALV VL         +  P     K +IS+ +I G D QK+E+ 
Sbjct:   118 ELLKPGCSVALHKYSNALVDVLPPEADSSIQMLRPD---EKPDISYGDIGGLDMQKQEVR 174

Query:   294 DTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIA-NQAGAMPWQ 352
             + + L L   E+Y  I          + PR VL  GPPG GKT  A+ +A N A +    
Sbjct:   175 EAVELPLTHGELYQQIG--------IDPPRGVLMYGPPGCGKTMLAKAVAANTAASF--- 223

Query:   353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEAT 412
                +  V  E V  KY GE  R++  VF LA E  + +IIF+DE+D+ A  R      A 
Sbjct:   224 ---IRVVGSEFVQ-KYLGEGPRMVRDVFRLAKE-NSPSIIFIDEIDAIATKRFDAQTGAD 278

Query:   413 R---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQ 467
             R   RIL  LL Q+DGF+Q   V VI ATNR+  LDPAL+   R D  I F LPD   ++
Sbjct:   279 REVQRILLELLNQMDGFDQSTNVKVIMATNRQDTLDPALLRPGRLDRKIEFPLPDRRQKR 338

Query:   468 EIAAQYAKHXXXXXXXXXXXXXXX---MSGRDIRDVCQQAERSWASKIIRGQITKDGEQA 524
              + +                       +SG DI  +CQ+A      +     +TKD E+A
Sbjct:   339 LVFSTVCSRMNLSDDVDLEDWVARPDKISGADINSICQEAGMQAVRENRYVVLTKDLEKA 398

GO:0000166 "nucleotide binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

GO:0000003 "reproduction" evidence=IMP

GO:0002119 "nematode larval development" evidence=IMP

GO:0008340 "determination of adult lifespan" evidence=IMP

CGD|CAL0005827 RPT4 [Candida albicans (taxid:5476)]

 Score = 314 (115.6 bits), Expect = 2.6e-27, P = 2.6e-27
 Identities = 95/278 (34%), Positives = 137/278 (49%)

Query:   236 EFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDT 295
             E +K G   S ++  L +++++  R +  L          EIS+  I G  +Q RE+ + 
Sbjct:   129 ENLKNGVRVSLDMTTL-TIMRILPREVDPLVYNMTTFEPGEISFNGIGGLTEQIRELREV 187

Query:   296 ILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP 355
             I L L++PE++      TR   +   P+ VL  GPPGTGKT  A+ +A   GA       
Sbjct:   188 IELPLKNPELF------TRVGIKP--PKGVLLYGPPGTGKTLLAKAVAATIGAN------ 233

Query:   356 LMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRI 415
              ++ P   ++ KY GES RL+ ++F+ A E     IIF+DEVD+    R SE   A R I
Sbjct:   234 FIFSPASAIVDKYIGESARLIREMFAYAKE-HEPCIIFMDEVDAIGGRRFSEGTSADREI 292

Query:   416 ---LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEI- 469
                L  LL Q+DGF+   +  +I ATNR   LDPAL+   R D  I  GLP+   R EI 
Sbjct:   293 QRTLMELLNQMDGFDTLGQTKIIMATNRPDTLDPALLRAGRLDRKIEIGLPNEAGRLEIF 352

Query:   470 ---AAQYAKHXXXXXXXXXXXXXXXMSGRDIRDVCQQA 504
                 ++ AK                 +G DIR+V  +A
Sbjct:   353 KIHTSKVAKQGEFDFEAAVKMSDG-FNGADIRNVVTEA 389

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0070682 "proteasome regulatory particle assembly" evidence=IEA

GO:0032968 "positive regulation of transcription elongation from RNA polymerase II promoter" evidence=IEA

GO:0045899 "positive regulation of RNA polymerase II transcriptional preinitiation complex assembly" evidence=IEA

GO:0030433 "ER-associated protein catabolic process" evidence=IEA

GO:0006289 "nucleotide-excision repair" evidence=IEA

WB|WBGene00017981 figl-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 312 (114.9 bits), Expect = 3.6e-27, Sum P(4) = 3.6e-27
 Identities = 80/250 (32%), Positives = 129/250 (51%)

Query:   262 IYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNR 321
             I  L E ++ +  +EI W ++AG +  K+ + + ++L  + P+V+     G R       
Sbjct:   298 IISLIESEIMSVNNEIGWADVAGLEGAKKALREIVVLPFKRPDVFT----GIRAP----- 348

Query:   322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFS 381
             P+ VL  GPPGTGKT   R +A+Q  A          +    + SK+ GE E+L+  +FS
Sbjct:   349 PKGVLLFGPPGTGKTMIGRCVASQCKAT------FFNISASSLTSKWVGEGEKLVRALFS 402

Query:   382 LAN-ELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ--DKKVVVIAAT 438
             +A  +LP+  +IF+DE+DS   +R    HE++RRI +  L Q+DG     D++++V+ AT
Sbjct:   403 VARLKLPS--VIFIDEIDSLLSSRSESEHESSRRIKTEFLVQLDGVNTAPDERLLVLGAT 460

Query:   439 NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQY---AKHXXXXXXXXXXXXXXX-MSG 494
             NR Q+LD A   RF   +   LP+ E+R +I        +H                 SG
Sbjct:   461 NRPQELDEAARRRFQKRLYIALPEPESRTQIVQNLLVGTRHDITNHNLERIRELTDGYSG 520

Query:   495 RDIRDVCQQA 504
              D+R +C +A
Sbjct:   521 ADMRQLCTEA 530

GO:0000166 "nucleotide binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0006310 "DNA recombination" evidence=IEA

GO:0009378 "four-way junction helicase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0045931 "positive regulation of mitotic cell cycle" evidence=IMP

UNIPROTKB|O16299 figl-1 "Fidgetin-like protein 1" [Caenorhabditis elegans (taxid:6239)]

 Score = 312 (114.9 bits), Expect = 3.6e-27, Sum P(4) = 3.6e-27
 Identities = 80/250 (32%), Positives = 129/250 (51%)

Query:   262 IYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNR 321
             I  L E ++ +  +EI W ++AG +  K+ + + ++L  + P+V+     G R       
Sbjct:   298 IISLIESEIMSVNNEIGWADVAGLEGAKKALREIVVLPFKRPDVFT----GIRAP----- 348

Query:   322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFS 381
             P+ VL  GPPGTGKT   R +A+Q  A          +    + SK+ GE E+L+  +FS
Sbjct:   349 PKGVLLFGPPGTGKTMIGRCVASQCKAT------FFNISASSLTSKWVGEGEKLVRALFS 402

Query:   382 LAN-ELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ--DKKVVVIAAT 438
             +A  +LP+  +IF+DE+DS   +R    HE++RRI +  L Q+DG     D++++V+ AT
Sbjct:   403 VARLKLPS--VIFIDEIDSLLSSRSESEHESSRRIKTEFLVQLDGVNTAPDERLLVLGAT 460

Query:   439 NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQY---AKHXXXXXXXXXXXXXXX-MSG 494
             NR Q+LD A   RF   +   LP+ E+R +I        +H                 SG
Sbjct:   461 NRPQELDEAARRRFQKRLYIALPEPESRTQIVQNLLVGTRHDITNHNLERIRELTDGYSG 520

Query:   495 RDIRDVCQQA 504
              D+R +C +A
Sbjct:   521 ADMRQLCTEA 530

GO:0005515 "protein binding" evidence=IPI

GO:0046034 "ATP metabolic process" evidence=IDA

GO:0016787 "hydrolase activity" evidence=IDA

GO:0000287 "magnesium ion binding" evidence=IDA

TAIR|locus:2028200 AT1G45000 [Arabidopsis thaliana (taxid:3702)]

 Score = 310 (114.2 bits), Expect = 3.6e-27, P = 3.6e-27
 Identities = 96/280 (34%), Positives = 140/280 (50%)

Query:   238 IKKGSLTSEE---LD-ALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIE 293
             + K  LTS     LD   +++++   R +  +    L+     IS+  + G   Q RE+ 
Sbjct:    93 VDKEKLTSGTRVVLDMTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLGDQIRELR 152

Query:   294 DTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG 353
             ++I L L +PE++  +  G +       P+ VL  GPPGTGKT  AR IA+   A     
Sbjct:   153 ESIELPLMNPELF--LRVGIK------PPKGVLLYGPPGTGKTLLARAIASNIDAN---- 200

Query:   354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATR 413
                + V    ++ KY GES RL+ ++F+ A E     IIF+DE+D+    R SE   A R
Sbjct:   201 --FLKVVSSAIIDKYIGESARLIREMFNYARE-HQPCIIFMDEIDAIGGRRFSEGTSADR 257

Query:   414 RI---LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQE 468
              I   L  LL Q+DGF+Q  KV +I ATNR   LDPAL+   R D  I   LP+ ++R E
Sbjct:   258 EIQRTLMELLNQLDGFDQLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRME 317

Query:   469 I----AAQYAKHXXXXXXXXXXXXXXXMSGRDIRDVCQQA 504
             I    A+  AKH                +G D+R++C +A
Sbjct:   318 ILKIHASGIAKHGEIDYEAIVKLGEG-FNGADLRNICTEA 356

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0005730 "nucleolus" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=RCA

GO:0009506 "plasmodesma" evidence=IDA

GO:0030244 "cellulose biosynthetic process" evidence=RCA

GO:0048193 "Golgi vesicle transport" evidence=RCA

FB|FBgn0028868 CG4701 [Drosophila melanogaster (taxid:7227)]

 Score = 308 (113.5 bits), Expect = 6.0e-27, P = 6.0e-27
 Identities = 82/253 (32%), Positives = 133/253 (52%)

Query:   276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
             +ISW +IAG D   +E+ +T++L ++  +++      +R K     P+ VL  GPPG GK
Sbjct:    91 DISWSDIAGLDGTIQELRETVVLPVRHRKLF------SRSKLW-RAPKGVLLHGPPGCGK 143

Query:   336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
             T  A+ IA  AG      +  + + + V+  K+YGES++L   VF+LA +L    IIF+D
Sbjct:   144 TLIAKAIAKDAG------MRFINLDVGVLTDKWYGESQKLATAVFTLAKKL-QPCIIFID 196

Query:   396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK--VVVIAATNRKQDLDPALISRFD 453
             E++SF   R S  HEAT  I +  + Q DG   +    V+V+ ATNR QDLD A++ R  
Sbjct:   197 EIESFLRMRGSNDHEATAMIKTQFMLQWDGLMSNTNICVLVLGATNRPQDLDKAILRRMP 256

Query:   454 SMITFGLP-DHENRQ--EIAAQYAKHXXXXXXXXXXXXXXXMSGRDIRDVCQQAERSWAS 510
             +    G+P D + R+  ++  Q  +                 SG D+R++C+ A      
Sbjct:   257 AQFHIGVPRDCQRREILQLILQTEQLSPSVNLKELARLTIGFSGSDLRELCRHASMYRMR 316

Query:   511 KIIRGQITKDGEQ 523
             + +R ++   GE+
Sbjct:   317 QFMREKLNT-GEE 328

GO:0005524 "ATP binding" evidence=ISS

GO:0005741 "mitochondrial outer membrane" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

TAIR|locus:2161258 RPT3 "regulatory particle triple-A ATPase 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 308 (113.5 bits), Expect = 6.0e-27, P = 6.0e-27
 Identities = 91/242 (37%), Positives = 119/242 (49%)

Query:   272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
             + K ++S+ +I G D QK+EI + + L L   E+Y  I          + PR VL  GPP
Sbjct:   147 SEKPDVSYNDIGGCDIQKQEIREAVELPLTHHELYKQIG--------IDPPRGVLLYGPP 198

Query:   332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG-A 390
             GTGKT  A+ +AN   A       +  V  E V  KY GE  R++  VF LA E  N  A
Sbjct:   199 GTGKTMLAKAVANHTTA-----AFIRVVGSEFVQ-KYLGEGPRMVRDVFRLAKE--NAPA 250

Query:   391 IIFLDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPA 447
             IIF+DEVD+ A AR      A R   RIL  LL Q+DGF+Q   V VI ATNR   LDPA
Sbjct:   251 IIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIMATNRADTLDPA 310

Query:   448 LI--SRFDSMITFGLPDHENRQ---EIAAQYAKHXXXXXXXXXXXXXXXMSGRDIRDVCQ 502
             L+   R D  I F LPD   ++   ++                      +S  +I  +CQ
Sbjct:   311 LLRPGRLDRKIEFPLPDRRQKRLVFQVCTSKMNLSDEVDLEDYVSRPDKISAAEIAAICQ 370

Query:   503 QA 504
             +A
Sbjct:   371 EA 372

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IGI;ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=RCA;TAS

GO:0005634 "nucleus" evidence=TAS

GO:0005618 "cell wall" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006094 "gluconeogenesis" evidence=RCA

GO:0006635 "fatty acid beta-oxidation" evidence=RCA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=RCA

GO:0007010 "cytoskeleton organization" evidence=RCA

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0009735 "response to cytokinin stimulus" evidence=RCA

GO:0009853 "photorespiration" evidence=RCA

GO:0010498 "proteasomal protein catabolic process" evidence=RCA

GO:0043090 "amino acid import" evidence=RCA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0043248 "proteasome assembly" evidence=RCA

GO:0048767 "root hair elongation" evidence=RCA

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0080129 "proteasome core complex assembly" evidence=RCA

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=IDA

ZFIN|ZDB-GENE-030616-44 atad1b "ATPase family, AAA domain containing 1b" [Danio rerio (taxid:7955)]

 Score = 307 (113.1 bits), Expect = 7.7e-27, P = 7.7e-27
 Identities = 85/273 (31%), Positives = 143/273 (52%)

Query:   276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
             +I+W +IAG D+   E++DT++L +Q   +++    G+R       P+ VL  GPPG GK
Sbjct:    91 QITWHDIAGLDEVITELKDTVILPIQKRHLFE----GSRLL---QPPKGVLLYGPPGCGK 143

Query:   336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
             T  A+  A +AG   ++ + L   P   +  K+YGES++L   VFSLA +L   +IIF+D
Sbjct:   144 TLIAKATAKEAG---FRFINLQ--P-STLTDKWYGESQKLAAAVFSLAIKL-QPSIIFID 196

Query:   396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK--KVVVIAATNRKQDLDPALISRFD 453
             E+DSF   R S  HEAT  + +  +   DG + D   +V+++ ATNR QDLD A++ R  
Sbjct:   197 EIDSFLRNRSSSDHEATAMMKAQFMSLWDGLDTDYNCQVIIMGATNRPQDLDSAILRRMP 256

Query:   454 SMITFGLPDHENRQEIAAQYAKHXXXXXX---XXXXXXXXXMSGRDIRDVCQQAERSWAS 510
             +      P+   R++I     ++                   SG D+R++C+ A    A 
Sbjct:   257 TRFHINQPNVRQRKDILKLILENENVESAVELSEIAKQTDGFSGSDLREMCRDA----AL 312

Query:   511 KIIRGQITKDG-EQACLPPL-QEYIESATNRRR 541
               +R  + ++  E+  + P+ QE ++ A  + +
Sbjct:   313 LCVRDFVHQESPEEDFIRPIRQEDLQRAIEKMK 345

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0045202 "synapse" evidence=IEA

GO:0005777 "peroxisome" evidence=IEA

GO:0030054 "cell junction" evidence=IEA

GO:0045211 "postsynaptic membrane" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

TAIR|locus:2159996 RPT4A "regulatory particle triple-A ATPase 4A" [Arabidopsis thaliana (taxid:3702)]

 Score = 306 (112.8 bits), Expect = 1.0e-26, P = 1.0e-26
 Identities = 95/280 (33%), Positives = 139/280 (49%)

Query:   238 IKKGSLTSEE---LD-ALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIE 293
             + K  LTS     LD   +++++   R +  +    L+     IS+  + G   Q RE+ 
Sbjct:    93 VDKEKLTSGTRVVLDMTTLTIMRALPREVDPVVYNMLHEDPGNISYSAVGGLGDQIRELR 152

Query:   294 DTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG 353
             ++I L L +PE++  +  G +       P+ VL  GPPGTGKT  AR IA+   A     
Sbjct:   153 ESIELPLMNPELF--LRVGIK------PPKGVLLYGPPGTGKTLLARAIASNIDAN---- 200

Query:   354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATR 413
                + V    ++ KY GES RL+ ++F+ A E     IIF+DE+D+    R SE   A R
Sbjct:   201 --FLKVVSSAIIDKYIGESARLIREMFNYARE-HQPCIIFMDEIDAIGGRRFSEGTSADR 257

Query:   414 RI---LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQE 468
              I   L  LL Q+DGF+   KV +I ATNR   LDPAL+   R D  I   LP+ ++R +
Sbjct:   258 EIQRTLMELLNQLDGFDNLGKVKMIMATNRPDVLDPALLRPGRLDRKIEIPLPNEQSRMD 317

Query:   469 I----AAQYAKHXXXXXXXXXXXXXXXMSGRDIRDVCQQA 504
             I    AA  AKH                +G D+R++C +A
Sbjct:   318 ILKIHAAGIAKHGEIDYEAIVKLAEG-FNGADLRNICTEA 356

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISM;TAS

GO:0005737 "cytoplasm" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=IGI;ISS

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0030163 "protein catabolic process" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=TAS

GO:0005618 "cell wall" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=RCA

GO:0043248 "proteasome assembly" evidence=RCA

GO:0051788 "response to misfolded protein" evidence=RCA

GO:0008540 "proteasome regulatory particle, base subcomplex" evidence=IDA

---

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

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: gw1.166.117.1 hypothetical protein (478 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

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	567
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	1e-46
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	3e-45
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	5e-40
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	1e-38
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	2e-38
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	6e-37
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-36
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	9e-36
COG1223	368	COG1223, COG1223, Predicted ATPase (AAA+ superfami	3e-35
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	7e-34
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	2e-26
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	1e-24
TIGR03689	512	TIGR03689, pup_AAA, proteasome ATPase	7e-24
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	3e-23
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	1e-21
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	3e-20
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	9e-20
smart00382	148	smart00382, AAA, ATPases associated with a variety	7e-14
CHL00195	489	CHL00195, ycf46, Ycf46; Provisional	1e-09
pfam07728	135	pfam07728, AAA_5, AAA domain (dynein-related subfa	4e-08
PHA02544	316	PHA02544, 44, clamp loader, small subunit; Provisi	3e-07
TIGR03922	557	TIGR03922, T7SS_EccA, type VII secretion AAA-ATPas	2e-06
TIGR02881	261	TIGR02881, spore_V_K, stage V sporulation protein	8e-06
PRK13342	413	PRK13342, PRK13342, recombination factor protein R	1e-05
COG0714	329	COG0714, COG0714, MoxR-like ATPases [General funct	2e-05
TIGR02928	365	TIGR02928, TIGR02928, orc1/cdc6 family replication	9e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	0.001
COG2256	436	COG2256, MGS1, ATPase related to the helicase subu	0.002
COG2255	332	COG2255, RuvB, Holliday junction resolvasome, heli	0.002
pfam05496	231	pfam05496, RuvB_N, Holliday junction DNA helicase	0.003
PRK00080	328	PRK00080, ruvB, Holliday junction DNA helicase Ruv	0.004
PRK00440	319	PRK00440, rfc, replication factor C small subunit;	0.004
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	0.004

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score =  170 bits (432), Expect = 1e-46
 Identities = 86/252 (34%), Positives = 137/252 (54%), Gaps = 22/252 (8%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           +++ ++I G ++ K E+++ I   L+ PE++  +            P+ VL  GPPGTGK
Sbjct: 238 DVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLR--------PPKGVLLYGPPGTGK 289

Query: 336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
           T  A+ +A ++ +        + V    ++SK+ GESE+ + ++F  A +L   +IIF+D
Sbjct: 290 TLLAKAVALESRS------RFISVKGSELLSKWVGESEKNIRELFEKARKL-APSIIFID 342

Query: 396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFD 453
           E+DS A  R      + RR++  LL ++DG E+ + V+VIAATNR  DLDPAL+   RFD
Sbjct: 343 EIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGVLVIAATNRPDDLDPALLRPGRFD 402

Query: 454 SMITFGLPDHENRQEIAAQYAKH-----LTKAELAELATATEEMSGRDIRDVCQQAERSW 508
            +I   LPD E R EI   + +          +L ELA  TE  SG DI  + ++A    
Sbjct: 403 RLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEA 462

Query: 509 ASKIIRGQITKD 520
             +  R ++T D
Sbjct: 463 LREARRREVTLD 474

Length = 494

>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

 Score =  164 bits (417), Expect = 3e-45
 Identities = 98/271 (36%), Positives = 143/271 (52%), Gaps = 47/271 (17%)

Query: 247 ELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVY 306
           E+D  VSV+++        +E      K ++++E+I G D+Q +EI + + L L++PE++
Sbjct: 132 EVDPRVSVMEV--------EE------KPDVTYEDIGGLDEQIQEIREVVELPLKNPELF 177

Query: 307 DDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS 366
           +++          + P+ VL  GPPGTGKT  A+ +ANQ  A            + VV S
Sbjct: 178 EELG--------IDPPKGVLLYGPPGTGKTLLAKAVANQTDA----------TFIRVVGS 219

Query: 367 ----KYYGESERLLGKVFSLANE-LPNGAIIFLDEVDSFAVARDSEMHEATR---RILSV 418
               KY GE  RL+ ++F LA E  P  +IIF+DE+D+    R        R   R +  
Sbjct: 220 ELVQKYIGEGARLVRELFELAREKAP--SIIFIDEIDAIGAKRFDSGTSGDREVQRTMLE 277

Query: 419 LLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKH 476
           LL Q+DGF+    V VI ATNR   LDPAL+   RFD  I F LPD E R EI   + + 
Sbjct: 278 LLNQLDGFDPRGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRK 337

Query: 477 LTKAE---LAELATATEEMSGRDIRDVCQQA 504
           +  A+   L  LA  TE  SG D++ +C +A
Sbjct: 338 MNLADDVDLELLARLTEGFSGADLKAICTEA 368

Length = 406

>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular activities (AAA)

 Score =  141 bits (358), Expect = 5e-40
 Identities = 60/138 (43%), Positives = 87/138 (63%), Gaps = 9/138 (6%)

Query: 325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN 384
           +L  GPPGTGKT+ A+ +A + GA      P + +    ++SKY GESE+ L ++F  A 
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGA------PFIEISGSELVSKYVGESEKRLRELFEAAK 54

Query: 385 ELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK-KVVVIAATNRKQD 443
           +L    +IF+DE+D+ A +R S     +RR+++ LL ++DGF     KV+VIAATNR   
Sbjct: 55  KL-APCVIFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPDK 113

Query: 444 LDPALI-SRFDSMITFGL 460
           LDPAL+  RFD +I F L
Sbjct: 114 LDPALLRGRFDRIIEFPL 131

AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131

>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like protein; Provisional

 Score =  145 bits (368), Expect = 1e-38
 Identities = 93/242 (38%), Positives = 127/242 (52%), Gaps = 25/242 (10%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           + K ++++ +I G D QK+EI + + L L  PE+Y+ I          + PR VL  GPP
Sbjct: 137 SEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG--------IDPPRGVLLYGPP 188

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG-A 390
           GTGKT  A+ +A+   A   + V   +V       KY GE  R++  VF LA E  N  +
Sbjct: 189 GTGKTMLAKAVAHHTTATFIRVVGSEFV------QKYLGEGPRMVRDVFRLARE--NAPS 240

Query: 391 IIFLDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPA 447
           IIF+DEVDS A  R      A R   RIL  LL Q+DGF+Q   V VI ATNR   LDPA
Sbjct: 241 IIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQTTNVKVIMATNRADTLDPA 300

Query: 448 LI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQ 502
           L+   R D  I F LPD   ++ I       +  +E   L +  +  E++S  DI  +CQ
Sbjct: 301 LLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQ 360

Query: 503 QA 504
           +A
Sbjct: 361 EA 362

Length = 398

>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase; Provisional

 Score =  145 bits (368), Expect = 2e-38
 Identities = 86/246 (34%), Positives = 131/246 (53%), Gaps = 37/246 (15%)

Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
              +++E+I G ++Q RE+ + + L L+ PE+++++            P+ VL  GPPGT
Sbjct: 125 SPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVG--------IEPPKGVLLYGPPGT 176

Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS----KYYGESERLLGKVFSLANELPNG 389
           GKT  A+ +A++  A            + VV S    K+ GE  RL+ ++F LA E    
Sbjct: 177 GKTLLAKAVAHETNA----------TFIRVVGSELVQKFIGEGARLVRELFELARE-KAP 225

Query: 390 AIIFLDEVDSFAVARDSEMHEAT------RRILSVLLRQIDGFEQDKKVVVIAATNRKQD 443
           +IIF+DE+D+ A  R       T      +R L  LL ++DGF+    V +IAATNR   
Sbjct: 226 SIIFIDEIDAIAAKR---TDSGTSGDREVQRTLMQLLAEMDGFDPRGNVKIIAATNRIDI 282

Query: 444 LDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIR 498
           LDPA++   RFD +I   LPD E R EI   + + +  A+   L ELA  TE  SG D++
Sbjct: 283 LDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLK 342

Query: 499 DVCQQA 504
            +C +A
Sbjct: 343 AICTEA 348

Length = 389

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score =  145 bits (368), Expect = 6e-37
 Identities = 89/235 (37%), Positives = 135/235 (57%), Gaps = 21/235 (8%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
            + W +I G ++ K+E+ + +   L+ PE+++ +  G R       P+ VL  GPPGTGK
Sbjct: 449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKM--GIR------PPKGVLLFGPPGTGK 500

Query: 336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
           T  A+ +A ++GA        + V    ++SK+ GESE+ + ++F  A +    AIIF D
Sbjct: 501 TLLAKAVATESGA------NFIAVRGPEILSKWVGESEKAIREIFRKARQ-AAPAIIFFD 553

Query: 396 EVDSFAVARDSEMHEA-TRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRF 452
           E+D+ A AR +    + T RI++ LL ++DG ++   VVVIAATNR   LDPAL+   RF
Sbjct: 554 EIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPDILDPALLRPGRF 613

Query: 453 DSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
           D +I    PD E R+EI   + + +  AE   L ELA  TE  +G DI  VC++A
Sbjct: 614 DRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREA 668

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733

>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily

 Score =  144 bits (365), Expect = 2e-36
 Identities = 88/255 (34%), Positives = 140/255 (54%), Gaps = 23/255 (9%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           ++++E+I G  + K +I + + L ++ PE+++              P+ VL  GPPGTGK
Sbjct: 174 KVTYEDIGGLKEAKEKIREMVELPMKHPELFE--------HLGIEPPKGVLLYGPPGTGK 225

Query: 336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG-AIIFL 394
           T  A+ +AN+AGA        + +    +MSKYYGESE  L ++F  A E  N  +IIF+
Sbjct: 226 TLLAKAVANEAGAY------FISINGPEIMSKYYGESEERLREIFKEAEE--NAPSIIFI 277

Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL--ISRF 452
           DE+D+ A  R+    E  +R+++ LL  +DG +   +V+VI ATNR   LDPAL    RF
Sbjct: 278 DEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRF 337

Query: 453 DSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQAERSWA 509
           D  I   +PD   R+EI   + +++  AE   L +LA  T    G D+  + ++A  +  
Sbjct: 338 DREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAAL 397

Query: 510 SKIIR-GQITKDGEQ 523
            + IR G+I  + E+
Sbjct: 398 RRFIREGKINFEAEE 412

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. Length = 733

>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family

 Score =  137 bits (346), Expect = 9e-36
 Identities = 90/239 (37%), Positives = 131/239 (54%), Gaps = 23/239 (9%)

Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
           +  +S+E+I G ++Q REI + + L L+ PE+++++            P+ VL  GPPGT
Sbjct: 116 RPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVG--------IEPPKGVLLYGPPGT 167

Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIF 393
           GKT  A+ +A++  A       +  V  E+V  KY GE  RL+ ++F LA E    +IIF
Sbjct: 168 GKTLLAKAVAHETNA-----TFIRVVGSELV-RKYIGEGARLVREIFELAKE-KAPSIIF 220

Query: 394 LDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI- 449
           +DE+D+ A  R        R   R L  LL ++DGF+    V VIAATNR   LDPAL+ 
Sbjct: 221 IDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPRGNVKVIAATNRPDILDPALLR 280

Query: 450 -SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
             RFD +I   LPD E R EI   + + +  AE   L  +A  TE  SG D++ +C +A
Sbjct: 281 PGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEA 339

Many proteins may score above the trusted cutoff because an internal. Length = 364

>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General function prediction only]

 Score =  135 bits (342), Expect = 3e-35
 Identities = 84/234 (35%), Positives = 133/234 (56%), Gaps = 23/234 (9%)

Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
                S+I+ +++ G ++ KR+    I+  L++PE + D A           P+ VLF G
Sbjct: 111 DREIISDITLDDVIGQEEAKRKCR-LIMEYLENPERFGDWA-----------PKNVLFYG 158

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG 389
           PPGTGKT  A+ +AN+A       VPL+ V    ++ ++ G+  R + +++  A +    
Sbjct: 159 PPGTGKTMMAKALANEAK------VPLLLVKATELIGEHVGDGARRIHELYERARKAAP- 211

Query: 390 AIIFLDEVDSFAVARD-SEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
            I+F+DE+D+ A+ R   E+      I++ LL ++DG ++++ VV IAATNR + LDPA+
Sbjct: 212 CIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENEGVVTIAATNRPELLDPAI 271

Query: 449 ISRFDSMITFGLPDHENRQEIAAQYAKHL---TKAELAELATATEEMSGRDIRD 499
            SRF+  I F LP+ E R EI   YAK       A+L  LA  T+ MSGRDI++
Sbjct: 272 RSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKE 325

Length = 368

>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like protein; Provisional

 Score =  133 bits (336), Expect = 7e-34
 Identities = 97/273 (35%), Positives = 144/273 (52%), Gaps = 47/273 (17%)

Query: 245 SEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPE 304
            +E+D LVSV+++        D+  L       S+ +I G +QQ +EI++ + L L  PE
Sbjct: 162 LDEVDPLVSVMKV--------DKAPLE------SYADIGGLEQQIQEIKEAVELPLTHPE 207

Query: 305 VYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV 364
           +YDDI  G +       P+ V+  GPPGTGKT  A+ +AN+  A            L VV
Sbjct: 208 LYDDI--GIK------PPKGVILYGPPGTGKTLLAKAVANETSA----------TFLRVV 249

Query: 365 MS----KYYGESERLLGKVFSLANE-LPNGAIIFLDEVDSFAVAR---DSEMHEATRRIL 416
            S    KY G+  +L+ ++F +A E  P  +I+F+DE+D+    R    S   +  +R +
Sbjct: 250 GSELIQKYLGDGPKLVRELFRVAEENAP--SIVFIDEIDAIGTKRYDATSGGEKEIQRTM 307

Query: 417 SVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYA 474
             LL Q+DGF+    V VI ATNR + LDPALI   R D  I F  PD + ++ I   + 
Sbjct: 308 LELLNQLDGFDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHT 367

Query: 475 KHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
             +T AE   L E   A +E+SG DI+ +C +A
Sbjct: 368 SKMTLAEDVDLEEFIMAKDELSGADIKAICTEA 400

Length = 438

>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH

 Score =  112 bits (283), Expect = 2e-26
 Identities = 81/256 (31%), Positives = 129/256 (50%), Gaps = 48/256 (18%)

Query: 269 QLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFE 328
            LN  K +++++++AG D+ K E+ + I+  L++P  +  +  G +       P+ VL  
Sbjct: 44  LLNEEKPKVTFKDVAGIDEAKEELME-IVDFLKNPSKFTKL--GAKI------PKGVLLV 94

Query: 329 GPPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESERLLGK 378
           GPPGTGKT  A+ +A +AG      VP           M+V +        G S     +
Sbjct: 95  GPPGTGKTLLAKAVAGEAG------VPFFSISGSDFVEMFVGV--------GAS-----R 135

Query: 379 VFSLANELPNGA--IIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVV 433
           V  L  +    A  IIF+DE+D+    R + +   ++   + L+ LL ++DGF  +  V+
Sbjct: 136 VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVI 195

Query: 434 VIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATA 488
           VIAATNR   LDPAL+   RFD  +   LPD + R+EI   +AK+   A    L  +A  
Sbjct: 196 VIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARR 255

Query: 489 TEEMSGRDIRDVCQQA 504
           T   SG D+ ++  +A
Sbjct: 256 TPGFSGADLANLLNEA 271

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 495

>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated

 Score =  107 bits (270), Expect = 1e-24
 Identities = 77/242 (31%), Positives = 122/242 (50%), Gaps = 30/242 (12%)

Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
            + I++ +IAG ++ K E E  ++  L+ PE +  +         +  P+ VL  GPPGT
Sbjct: 177 DTGITFRDIAGIEEAKEEFE-EVVSFLKKPERFTAVG--------AKIPKGVLLVGPPGT 227

Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGAII 392
           GKT  A+ IA +A       VP   +     +  + G     +  +F  A E  P   I+
Sbjct: 228 GKTLLAKAIAGEA------EVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSP--CIV 279

Query: 393 FLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
           F+DE+D+    R + +   ++   + L+ LL ++DGF+ +K V+VIAATNR   LD AL+
Sbjct: 280 FIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAALL 339

Query: 450 --SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE-----LAELATATEEMSGRDIRDVCQ 502
              RFD  IT  LPD E R +I   +A++  K       L  +A  T   SG D+ ++  
Sbjct: 340 RPGRFDRQITVSLPDREGRLDILKVHARN--KKLSPDVSLELIARRTPGFSGADLANLLN 397

Query: 503 QA 504
           +A
Sbjct: 398 EA 399

Length = 638

>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase

 Score =  104 bits (262), Expect = 7e-24
 Identities = 70/216 (32%), Positives = 105/216 (48%), Gaps = 27/216 (12%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           ++++ +I G   Q  +I D + L    PE+Y     G +       P+ VL  GPPG GK
Sbjct: 178 DVTYADIGGLGSQIEQIRDAVELPFLHPELYR--EYGLK------PPKGVLLYGPPGCGK 229

Query: 336 TSCARVIANQAGAMPWQGVPLMYVPLEV----VMSKYYGESERLLGKVFSLANELP---N 388
           T  A+ +AN   A            L +    +++KY GE+ER +  +F  A E      
Sbjct: 230 TLIAKAVANSLAARIGAEGGGKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASEGR 289

Query: 389 GAIIFLDEVDSFAVAR----DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDL 444
             I+F DE+DS    R     S++ E T  ++  LL +IDG E    V+VI A+NR+  +
Sbjct: 290 PVIVFFDEMDSLFRTRGSGVSSDV-ETT--VVPQLLAEIDGVESLDNVIVIGASNREDMI 346

Query: 445 DPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLT 478
           DPA++   R D  I    PD E   +I   +AK+LT
Sbjct: 347 DPAILRPGRLDVKIRIERPDAEAAADI---FAKYLT 379

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 [Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 512

>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

 Score =  102 bits (257), Expect = 3e-23
 Identities = 77/221 (34%), Positives = 110/221 (49%), Gaps = 22/221 (9%)

Query: 298 LSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM 357
           L L+ PE++         K     P+ VL  GPPGTGKT  AR +AN+       G   +
Sbjct: 2   LPLKEPELFK--------KLGIEPPKGVLLHGPPGTGKTLLARALANE-------GAEFL 46

Query: 358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILS 417
            +    ++SKY GESE  L ++F  A +L   +IIF+DE+D+ A  R S+  E  RR+++
Sbjct: 47  SINGPEILSKYVGESELRLRELFEEAEKL-APSIIFIDEIDALAPKRSSDQGEVERRVVA 105

Query: 418 VLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAK 475
            LL  +DG +   +V+VI ATNR   LDPA     RFD  I   LPD   R EI   + +
Sbjct: 106 QLLALMDGLK-RGQVIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEILQIHTR 164

Query: 476 HLTKAE---LAELATATEEMSGRDIRDVCQQAERSWASKII 513
            +          LA  T   SG D+  + ++A      + I
Sbjct: 165 LMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAI 205

Length = 494

>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed

 Score = 98.6 bits (245), Expect = 1e-21
 Identities = 74/248 (29%), Positives = 123/248 (49%), Gaps = 29/248 (11%)

Query: 265 LDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRA 324
           L E Q+ T+     + ++AG D+ K E+ + ++  L+ P  +         K     P+ 
Sbjct: 142 LTEDQIKTT-----FADVAGCDEAKEEVAE-LVEYLREPSRFQ--------KLGGKIPKG 187

Query: 325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN 384
           VL  GPPGTGKT  A+ IA +A       VP   +     +  + G     +  +F  A 
Sbjct: 188 VLMVGPPGTGKTLLAKAIAGEAK------VPFFTISGSDFVEMFVGVGASRVRDMFEQAK 241

Query: 385 ELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRK 441
           +     IIF+DE+D+    R + +   H+   + L+ +L ++DGFE ++ ++VIAATNR 
Sbjct: 242 KAAP-CIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRP 300

Query: 442 QDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHL---TKAELAELATATEEMSGRD 496
             LDPAL+   RFD  +  GLPD   R++I   + + +      + A +A  T   SG D
Sbjct: 301 DVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGAD 360

Query: 497 IRDVCQQA 504
           + ++  +A
Sbjct: 361 LANLVNEA 368

Length = 644

>gnl|CDD|99707 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

 Score = 87.2 bits (216), Expect = 3e-20
 Identities = 48/147 (32%), Positives = 63/147 (42%), Gaps = 14/147 (9%)

Query: 318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLG 377
           E   P+ +L  GPPGTGKT+ AR IAN+       G P +Y+    ++            
Sbjct: 15  ELPPPKNLLLYGPPGTGKTTLARAIANELFRP---GAPFLYLNASDLLEGLVVAELFGHF 71

Query: 378 KVFSL--ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVI 435
            V  L    E     ++F+DE+DS +         A   +L VL    D     + V VI
Sbjct: 72  LVRLLFELAEKAKPGVLFIDEIDSLSR-------GAQNALLRVLETLNDLRIDRENVRVI 124

Query: 436 AATNRK--QDLDPALISRFDSMITFGL 460
            ATNR    DLD AL  R D  I   L
Sbjct: 125 GATNRPLLGDLDRALYDRLDIRIVIPL 151

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. Length = 151

>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

 Score = 92.8 bits (231), Expect = 9e-20
 Identities = 81/256 (31%), Positives = 130/256 (50%), Gaps = 48/256 (18%)

Query: 269 QLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFE 328
                + ++++ ++AG D+ K E+ + ++  L++P+ Y  +      K     P+ VL  
Sbjct: 139 LYLEDQVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGA----KI----PKGVLLV 189

Query: 329 GPPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESE-RLLG 377
           GPPGTGKT  A+ +A +AG      VP           M+V +        G S  R L 
Sbjct: 190 GPPGTGKTLLAKAVAGEAG------VPFFSISGSDFVEMFVGV--------GASRVRDL- 234

Query: 378 KVFSLANE-LPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVV 433
             F  A +  P   IIF+DE+D+    R + +   ++   + L+ LL ++DGF  ++ V+
Sbjct: 235 --FEQAKKNAP--CIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGNEGVI 290

Query: 434 VIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATA 488
           VIAATNR   LDPAL+   RFD  I   LPD + R++I   +AK+   AE   L ++A  
Sbjct: 291 VIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARG 350

Query: 489 TEEMSGRDIRDVCQQA 504
           T   SG D+ ++  +A
Sbjct: 351 TPGFSGADLANLLNEA 366

Length = 596

>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular activities

 Score = 68.9 bits (168), Expect = 7e-14
 Identities = 44/154 (28%), Positives = 66/154 (42%), Gaps = 18/154 (11%)

Query: 321 RPRAVLFEGPPGTGKTSCARVIANQ-----------AGAMPWQGVPLMYVPLEVVMSKYY 369
               +L  GPPG+GKT+ AR +A +            G    + V    + + V   K  
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 370 GESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD 429
           G  E  L    +LA +L    ++ LDE+ S   A    +      +L   LR +   + +
Sbjct: 61  GSGELRLRLALALARKLKPD-VLILDEITSLLDAEQEAL-----LLLLEELRLLLLLKSE 114

Query: 430 KKVVVIAATNRKQDLDPALI-SRFDSMITFGLPD 462
           K + VI  TN ++DL PAL+  RFD  I   L  
Sbjct: 115 KNLTVILTTNDEKDLGPALLRRRFDRRIVLLLIL 148

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. Length = 148

>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional

 Score = 60.4 bits (147), Expect = 1e-09
 Identities = 51/188 (27%), Positives = 90/188 (47%), Gaps = 23/188 (12%)

Query: 322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFS 381
           PR +L  G  GTGK+  A+ IAN      WQ +PL+ + +  +     GESE  + ++  
Sbjct: 259 PRGLLLVGIQGTGKSLTAKAIAND-----WQ-LPLLRLDVGKLFGGIVGESESRMRQMIR 312

Query: 382 LANELPNGAIIFLDEVD-SFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR 440
           +A  L +  I+++DE+D +F+ +        T R+L+  +  +   E+   V V+A  N 
Sbjct: 313 IAEAL-SPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLS--EKKSPVFVVATANN 369

Query: 441 KQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKA--------ELAELATATE 490
              L   ++   RFD +    LP  E R++I   +  HL K         ++ +L+  + 
Sbjct: 370 IDLLPLEILRKGRFDEIFFLDLPSLEEREKI---FKIHLQKFRPKSWKKYDIKKLSKLSN 426

Query: 491 EMSGRDIR 498
           + SG +I 
Sbjct: 427 KFSGAEIE 434

Length = 489

>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily)

 Score = 51.9 bits (125), Expect = 4e-08
 Identities = 40/154 (25%), Positives = 56/154 (36%), Gaps = 46/154 (29%)

Query: 325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE-------RLLG 377
           VL  GPPGTGK+  A  +   A A+     P+ YV     +++   E +          G
Sbjct: 2   VLLVGPPGTGKSELAERL---AAAL--SNRPVFYVQ----LTRDTTEEDLKGRRNIDPGG 52

Query: 378 KVF---SLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL--------LRQIDGF 426
             +    L      G I  LDE++            A   +L+ L        L   +G 
Sbjct: 53  ASWVDGPLVRAAREGEIAVLDEIN-----------RANPDVLNSLLSLLDERRLLLPEGG 101

Query: 427 EQDKK----VVVIAATNR----KQDLDPALISRF 452
           E  K       +IA  N       +L PAL SRF
Sbjct: 102 ELVKAAPDGFRLIATMNPLDRGLNELSPALRSRF 135

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 135

>gnl|CDD|222866 PHA02544, 44, clamp loader, small subunit; Provisional

 Score = 51.9 bits (125), Expect = 3e-07
 Identities = 41/168 (24%), Positives = 61/168 (36%), Gaps = 47/168 (27%)

Query: 318 ESNR-PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLL 376
           +  R P  +L    PGTGKT+ A+ + N+ GA        ++V          G      
Sbjct: 38  KKGRIPNMLLHSPSPGTGKTTVAKALCNEVGAEV------LFVN---------GSD---- 78

Query: 377 GKVFSLANELPN----------GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF 426
            ++  + N L            G +I +DE D         + +A R      LR    F
Sbjct: 79  CRIDFVRNRLTRFASTVSLTGGGKVIIIDEFD------RLGLADAQR-----HLR---SF 124

Query: 427 --EQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQ 472
                K    I   N K  +   L SR   +I FG+P  E + E+  Q
Sbjct: 125 MEAYSKNCSFIITANNKNGIIEPLRSRCR-VIDFGVPTKEEQIEMMKQ 171

Length = 316

>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA

 Score = 50.2 bits (120), Expect = 2e-06
 Identities = 43/147 (29%), Positives = 68/147 (46%), Gaps = 18/147 (12%)

Query: 321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVF 380
               +LF GPPGTGKT+ ARV+A     +     PL+    EV  +   G+     G+  
Sbjct: 311 TSNHMLFAGPPGTGKTTIARVVAKIYCGLGVLRKPLV---REVSRADLIGQYI---GESE 364

Query: 381 SLANELPNGA---IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK-KVVVIA 436
           +  NE+ + A   ++FLDE  +       +        +  LL ++   E D+ ++VVI 
Sbjct: 365 AKTNEIIDSALGGVLFLDEAYTLVETGYGQKDPFGLEAIDTLLARM---ENDRDRLVVIG 421

Query: 437 ATNRKQ-----DLDPALISRFDSMITF 458
           A  RK      +++  L SRF  +I F
Sbjct: 422 AGYRKDLDKFLEVNEGLRSRFTRVIEF 448

This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc [Protein fate, Protein and peptide secretion and trafficking]. Length = 557

>gnl|CDD|163057 TIGR02881, spore_V_K, stage V sporulation protein K

 Score = 47.4 bits (113), Expect = 8e-06
 Identities = 50/224 (22%), Positives = 104/224 (46%), Gaps = 49/224 (21%)

Query: 326 LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER--LLG------ 377
           +F+G PGTGKT+ AR++              ++  + V+   +  E ER  L+G      
Sbjct: 46  IFKGNPGTGKTTVARILGK------------LFKEMNVLSKGHLIEVERADLVGEYIGHT 93

Query: 378 --KVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVI 435
             K   +  +   G ++F+DE  ++++AR  E  +  +  +  L++ ++   +++ V+++
Sbjct: 94  AQKTREVIKK-ALGGVLFIDE--AYSLARGGE-KDFGKEAIDTLVKGMED-NRNEFVLIL 148

Query: 436 AATNRKQD----LDPALISRFDSMITFGLPDH-------------ENRQEIAAQYAKHLT 478
           A  + + D    L+P L SRF   I F  PD+             + R+    + AK   
Sbjct: 149 AGYSDEMDYFLSLNPGLRSRFPISIDF--PDYTVEELMEIAERMVKEREYKLTEEAKWKL 206

Query: 479 KAELAELATATE-EMS-GRDIRDVCQQAERSWASKII-RGQITK 519
           +  L ++   +  E S  R +R++ ++A R  A +++ +   +K
Sbjct: 207 REHLYKVDQLSSREFSNARYVRNIIEKAIRRQAVRLLDKSDYSK 250

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group [Cellular processes, Sporulation and germination]. Length = 261

>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed

 Score = 47.4 bits (114), Expect = 1e-05
 Identities = 15/32 (46%), Positives = 21/32 (65%)

Query: 317 FESNRPRAVLFEGPPGTGKTSCARVIANQAGA 348
            E+ R  +++  GPPGTGKT+ AR+IA    A
Sbjct: 31  IEAGRLSSMILWGPPGTGKTTLARIIAGATDA 62

Length = 413

>gnl|CDD|223786 COG0714, COG0714, MoxR-like ATPases [General function prediction only]

 Score = 46.3 bits (110), Expect = 2e-05
 Identities = 48/194 (24%), Positives = 66/194 (34%), Gaps = 41/194 (21%)

Query: 323 RAVLFEGPPGTGKTSCARVIANQAGA--MPWQGVPLM------YVPLEVVMSKYYGESER 374
             VL EGPPG GKT  AR +A   G   +  Q  P +             +    GE   
Sbjct: 44  GHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRF 103

Query: 375 LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL-----RQI-----D 424
           + G +F  A       I+ LDE++            A   + + LL     RQ+      
Sbjct: 104 VPGPLF--AAV---RVILLLDEIN-----------RAPPEVQNALLEALEERQVTVPGLT 147

Query: 425 GFEQDKKVVVIAATN-----RKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTK 479
                   +VIA  N         L  AL+ RF   I    PD E  +E     A+    
Sbjct: 148 TIRLPPPFIVIATQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSE--EEERIILARVGGV 205

Query: 480 AELAELATATEEMS 493
            EL   +     +S
Sbjct: 206 DELDLESLVKPVLS 219

Length = 329

>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation protein

 Score = 41.5 bits (98), Expect = 9e-04
 Identities = 35/160 (21%), Positives = 63/160 (39%), Gaps = 35/160 (21%)

Query: 320 NRPRAVLFEGPPGTGKTSCARVIANQA-GAMPWQGVPLMYVPLE--------VVMSKYYG 370
           +RP  V   G  GTGKT+  + +  +   A   + V ++ V +          V+ +   
Sbjct: 38  SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDTLYQVLVELAN 97

Query: 371 E--------------SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRIL 416
           +              +  +  +++   NE  +  II LDE+D      D         +L
Sbjct: 98  QLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDDD--------LL 149

Query: 417 SVLLR-QIDGFEQDKKVVVIAATNR---KQDLDPALISRF 452
             L R + +G   + KV VI  +N    +++LDP + S  
Sbjct: 150 YQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSL 189

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 [DNA metabolism, DNA replication, recombination, and repair]. Length = 365

>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit; Provisional

 Score = 41.1 bits (97), Expect = 0.001
 Identities = 27/92 (29%), Positives = 34/92 (36%), Gaps = 37/92 (40%)

Query: 322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV------------VMSKYY 369
            +A+L  GPPG GKTS A  +AN  G              EV            V+ +  
Sbjct: 39  KKALLLYGPPGVGKTSLAHALANDYG-------------WEVIELNASDQRTADVIERVA 85

Query: 370 GESER---LLGKVFSLANELPNGAIIFLDEVD 398
           GE+     L G             +I LDEVD
Sbjct: 86  GEAATSGSLFGA---------RRKLILLDEVD 108

Length = 482

>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

 Score = 40.7 bits (96), Expect = 0.002
 Identities = 40/140 (28%), Positives = 65/140 (46%), Gaps = 35/140 (25%)

Query: 318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLG 377
           E+    +++  GPPGTGKT+ AR+IA    A         +  L  V S   G  +  L 
Sbjct: 44  EAGHLHSMILWGPPGTGKTTLARLIAGTTNA--------AFEALSAVTS---GVKD--LR 90

Query: 378 KVFSLANE---LPNGAIIFLDEVDSFAVAR-DSEMHEATRRILSVLLRQIDGFEQDKKVV 433
           ++   A +   L    I+FLDE+  F  A+ D+        +L  +        ++  ++
Sbjct: 91  EIIEEARKNRLLGRRTILFLDEIHRFNKAQQDA--------LLPHV--------ENGTII 134

Query: 434 VIAAT--NRKQDLDPALISR 451
           +I AT  N   +L+PAL+SR
Sbjct: 135 LIGATTENPSFELNPALLSR 154

Length = 436

>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

 Score = 40.2 bits (95), Expect = 0.002
 Identities = 14/24 (58%), Positives = 17/24 (70%)

Query: 325 VLFEGPPGTGKTSCARVIANQAGA 348
           VL  GPPG GKT+ A +IAN+ G 
Sbjct: 55  VLLFGPPGLGKTTLAHIIANELGV 78

Length = 332

>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB N-terminus

 Score = 39.0 bits (92), Expect = 0.003
 Identities = 14/24 (58%), Positives = 17/24 (70%)

Query: 325 VLFEGPPGTGKTSCARVIANQAGA 348
           VL  GPPG GKT+ A +IAN+ G 
Sbjct: 53  VLLYGPPGLGKTTLANIIANEMGV 76

The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. Length = 231

>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed

 Score = 39.3 bits (93), Expect = 0.004
 Identities = 14/24 (58%), Positives = 17/24 (70%)

Query: 325 VLFEGPPGTGKTSCARVIANQAGA 348
           VL  GPPG GKT+ A +IAN+ G 
Sbjct: 54  VLLYGPPGLGKTTLANIIANEMGV 77

Length = 328

>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 38/107 (35%), Positives = 49/107 (45%), Gaps = 25/107 (23%)

Query: 326 LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER----LLGKVFS 381
           LF GPPGTGKT+ A  +A +     W+        LE+  S      ER    +  K+  
Sbjct: 42  LFAGPPGTGKTTAALALARELYGEDWR----ENF-LELNAS-----DERGIDVIRNKIKE 91

Query: 382 LANELPNGA----IIFLDEVDSF------AVARDSEMH-EATRRILS 417
            A   P G     IIFLDE D+       A+ R  EM+ + TR ILS
Sbjct: 92  FARTAPVGGAPFKIIFLDEADNLTSDAQQALRRTMEMYSQNTRFILS 138

Length = 319

>gnl|CDD|233847 TIGR02397, dnaX_nterm, DNA polymerase III, subunit gamma and tau

 Score = 39.1 bits (92), Expect = 0.004
 Identities = 15/27 (55%), Positives = 18/27 (66%), Gaps = 1/27 (3%)

Query: 318 ESNR-PRAVLFEGPPGTGKTSCARVIA 343
           ++ R   A LF GP GTGKTS AR+ A
Sbjct: 31  KNGRIAHAYLFSGPRGTGKTSIARIFA 57

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis [DNA metabolism, DNA replication, recombination, and repair]. Length = 355

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	567
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	100.0
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.98
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.97
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.97
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.97
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.97
CHL00195	489	ycf46 Ycf46; Provisional	99.97
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.96
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.96
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.96
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.96
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.96
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.96
CHL00176	638	ftsH cell division protein; Validated	99.96
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.95
COG2204	464	AtoC Response regulator containing CheY-like recei	99.94
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.94
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.93
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.93
CHL00206	2281	ycf2 Ycf2; Provisional	99.93
CHL00181	287	cbbX CbbX; Provisional	99.88
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.87
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.87
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.87
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.85
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.85
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.84
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.84
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.84
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.83
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.82
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.82
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.82
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.82
PF00004	132	AAA: ATPase family associated with various cellula	99.81
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.8
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.79
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	99.79
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.78
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.77
KOG2028	554	consensus ATPase related to the helicase subunit o	99.76
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.75
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.75
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.75
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.74
PRK15115	444	response regulator GlrR; Provisional	99.74
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.74
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.73
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.72
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.71
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.7
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.7
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.69
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	99.69
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.69
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	99.68
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.68
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.67
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.67
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.66
PLN03025	319	replication factor C subunit; Provisional	99.66
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK13342	413	recombination factor protein RarA; Reviewed	99.66
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.65
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.65
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.65
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.64
PHA02544	316	44 clamp loader, small subunit; Provisional	99.64
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.64
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.63
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.63
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.63
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.63
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.63
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.62
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.62
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.62
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.62
PRK10865	857	protein disaggregation chaperone; Provisional	99.61
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.61
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.61
PRK12402	337	replication factor C small subunit 2; Reviewed	99.61
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.6
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.6
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.6
PRK10865	857	protein disaggregation chaperone; Provisional	99.6
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.6
PRK13341	725	recombination factor protein RarA/unknown domain f	99.59
CHL00095	821	clpC Clp protease ATP binding subunit	99.59
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.59
PRK12422	445	chromosomal replication initiation protein; Provis	99.59
PRK04195	482	replication factor C large subunit; Provisional	99.59
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.59
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.59
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.58
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK08084	235	DNA replication initiation factor; Provisional	99.58
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.57
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.57
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.57
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.57
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.56
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.56
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.56
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.56
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.56
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.56
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.56
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.56
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.55
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.55
CHL00095	821	clpC Clp protease ATP binding subunit	99.54
PRK06893	229	DNA replication initiation factor; Validated	99.54
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.54
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.54
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.54
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.53
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.53
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.53
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.53
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.53
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.52
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.52
PRK05642	234	DNA replication initiation factor; Validated	99.52
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.51
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.51
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.5
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.5
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.5
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.5
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.5
PRK08727	233	hypothetical protein; Validated	99.5
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.5
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.48
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.48
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.48
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.48
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.46
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.45
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.45
PHA02244	383	ATPase-like protein	99.44
PRK06620	214	hypothetical protein; Validated	99.43
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.43
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.41
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.41
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.4
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.4
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.39
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.38
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	99.38
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.38
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.38
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.37
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.36
smart00350	509	MCM minichromosome maintenance proteins.	99.33
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.32
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	99.31
PRK09087	226	hypothetical protein; Validated	99.29
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.29
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	99.29
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.28
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.27
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.26
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	99.26
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.26
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.25
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.25
PRK13531	498	regulatory ATPase RavA; Provisional	99.24
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	99.23
COG0714	329	MoxR-like ATPases [General function prediction onl	99.21
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.2
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.2
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	99.19
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	99.18
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	99.17
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.16
PRK08769	319	DNA polymerase III subunit delta'; Validated	99.16
smart00382	148	AAA ATPases associated with a variety of cellular	99.14
PRK07993	334	DNA polymerase III subunit delta'; Validated	99.14
PRK06871	325	DNA polymerase III subunit delta'; Validated	99.13
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	99.12
PF07726	131	AAA_3: ATPase family associated with various cellu	99.11
PRK13765	637	ATP-dependent protease Lon; Provisional	99.07
PRK04132	846	replication factor C small subunit; Provisional	99.06
COG4650	531	RtcR Sigma54-dependent transcription regulator con	99.05
PRK06964	342	DNA polymerase III subunit delta'; Validated	99.05
COG0606	490	Predicted ATPase with chaperone activity [Posttran	99.03
PRK06090	319	DNA polymerase III subunit delta'; Validated	99.03
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.02
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	99.01
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	99.0
PRK09862	506	putative ATP-dependent protease; Provisional	98.99
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	98.96
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.96
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.96
PRK08116	268	hypothetical protein; Validated	98.94
PF02359	87	CDC48_N: Cell division protein 48 (CDC48), N-termi	98.92
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.91
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	98.91
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.89
PRK12377	248	putative replication protein; Provisional	98.89
PRK08181	269	transposase; Validated	98.84
PRK07952	244	DNA replication protein DnaC; Validated	98.83
PRK06835	329	DNA replication protein DnaC; Validated	98.83
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.8
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.79
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.75
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.75
PRK06526	254	transposase; Provisional	98.72
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.71
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	98.7
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.66
PRK08939	306	primosomal protein DnaI; Reviewed	98.65
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.64
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.64
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.64
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.63
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.63
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	98.63
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.62
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.6
PF13173	128	AAA_14: AAA domain	98.57
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.56
PRK06921	266	hypothetical protein; Provisional	98.54
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.52
PRK09183	259	transposase/IS protein; Provisional	98.52
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.51
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.49
PF05729	166	NACHT: NACHT domain	98.45
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.42
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	98.37
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	98.36
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	98.31
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	98.28
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.24
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.2
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.19
KOG0481	729	consensus DNA replication licensing factor, MCM5 c	98.14
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.1
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.09
PHA00729	226	NTP-binding motif containing protein	98.06
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.06
PF14516	331	AAA_35: AAA-like domain	98.05
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	98.03
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.03
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.99
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.96
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.95
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	97.94
PLN03210	1153	Resistant to P. syringae 6; Provisional	97.94
KOG0479	818	consensus DNA replication licensing factor, MCM3 c	97.93
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.91
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.86
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.8
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.78
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.76
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.74
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.72
cd01128	249	rho_factor Transcription termination factor rho is	97.67
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.66
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.59
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.58
COG1485	367	Predicted ATPase [General function prediction only	97.58
PRK09376	416	rho transcription termination factor Rho; Provisio	97.58
PRK14700	300	recombination factor protein RarA; Provisional	97.54
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	97.5
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.47
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	97.45
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.45
PRK15455	644	PrkA family serine protein kinase; Provisional	97.41
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.41
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.41
PRK06067	234	flagellar accessory protein FlaH; Validated	97.39
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.39
PRK11823	446	DNA repair protein RadA; Provisional	97.37
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.36
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.33
PHA02624	647	large T antigen; Provisional	97.32
PRK06762	166	hypothetical protein; Provisional	97.3
PRK10536	262	hypothetical protein; Provisional	97.3
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.29
PRK04296	190	thymidine kinase; Provisional	97.29
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.27
PRK04841	903	transcriptional regulator MalT; Provisional	97.27
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.27
PRK08118	167	topology modulation protein; Reviewed	97.25
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.24
PRK05973	237	replicative DNA helicase; Provisional	97.23
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.22
PRK07261	171	topology modulation protein; Provisional	97.22
PHA02774	613	E1; Provisional	97.18
TIGR00767	415	rho transcription termination factor Rho. Members	97.17
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.17
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.15
PRK09354	349	recA recombinase A; Provisional	97.15
PRK00131	175	aroK shikimate kinase; Reviewed	97.14
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	97.1
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.08
COG0529	197	CysC Adenylylsulfate kinase and related kinases [I	97.08
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.07
smart00487	201	DEXDc DEAD-like helicases superfamily.	97.07
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.07
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.02
PRK13949	169	shikimate kinase; Provisional	97.02
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	97.02
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	97.0
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.94
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	96.94
KOG2383	467	consensus Predicted ATPase [General function predi	96.93
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.93
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.93
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.92
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.91
PRK14974	336	cell division protein FtsY; Provisional	96.9
PRK12608	380	transcription termination factor Rho; Provisional	96.89
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	96.87
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.86
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	96.86
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.86
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.85
PRK13695	174	putative NTPase; Provisional	96.85
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	96.81
PF13479	213	AAA_24: AAA domain	96.79
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.79
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.79
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.79
PRK13947	171	shikimate kinase; Provisional	96.78
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	96.77
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.76
PRK14532	188	adenylate kinase; Provisional	96.76
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.74
PRK03839	180	putative kinase; Provisional	96.74
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.73
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.72
cd03216	163	ABC_Carb_Monos_I This family represents the domain	96.71
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	96.7
PRK08233	182	hypothetical protein; Provisional	96.69
PRK04040	188	adenylate kinase; Provisional	96.68
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	96.67
PRK00625	173	shikimate kinase; Provisional	96.66
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	96.66
PLN02200	234	adenylate kinase family protein	96.64
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	96.64
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	96.61
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.59
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	96.59
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.59
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	96.59
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	96.59
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	96.58
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	96.58
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.58
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.57
PRK04328	249	hypothetical protein; Provisional	96.56
PRK05541	176	adenylylsulfate kinase; Provisional	96.55
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.51
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.51
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	96.51
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.5
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.47
PRK13948	182	shikimate kinase; Provisional	96.46
PRK14737	186	gmk guanylate kinase; Provisional	96.45
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	96.45
PHA02530	300	pseT polynucleotide kinase; Provisional	96.44
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.42
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	96.41
PRK06217	183	hypothetical protein; Validated	96.41
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.41
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.41
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	96.4
COG4608	268	AppF ABC-type oligopeptide transport system, ATPas	96.4
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.4
PRK14527	191	adenylate kinase; Provisional	96.39
PRK00889	175	adenylylsulfate kinase; Provisional	96.38
KOG3928	461	consensus Mitochondrial ribosome small subunit com	96.38
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	96.37
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.36
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.36
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.36
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.35
PF07088	484	GvpD: GvpD gas vesicle protein; InterPro: IPR00978	96.35
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	96.35
PRK14531	183	adenylate kinase; Provisional	96.35
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.34
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	96.33
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	96.32
PRK14530	215	adenylate kinase; Provisional	96.31
cd03246	173	ABCC_Protease_Secretion This family represents the	96.31
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.3
cd03115	173	SRP The signal recognition particle (SRP) mediates	96.3
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	96.28
PRK06547	172	hypothetical protein; Provisional	96.28
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.28
PTZ00088	229	adenylate kinase 1; Provisional	96.28
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	96.27
PRK06696	223	uridine kinase; Validated	96.27
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	96.27
TIGR00152	188	dephospho-CoA kinase. This model produces scores i	96.27
PLN02674	244	adenylate kinase	96.26
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	96.26
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	96.26
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.26
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	96.24
PRK14730	195	coaE dephospho-CoA kinase; Provisional	96.23
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	96.23
PRK05537	568	bifunctional sulfate adenylyltransferase subunit 1	96.22
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.22
PTZ00202	550	tuzin; Provisional	96.21
PRK03846	198	adenylylsulfate kinase; Provisional	96.2
COG1124	252	DppF ABC-type dipeptide/oligopeptide/nickel transp	96.2
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.2
COG4178	604	ABC-type uncharacterized transport system, permeas	96.19
PF13245	76	AAA_19: Part of AAA domain	96.19
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.18
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	96.15
PRK03731	171	aroL shikimate kinase II; Reviewed	96.15
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.15
PRK10436	462	hypothetical protein; Provisional	96.15
PRK00409	782	recombination and DNA strand exchange inhibitor pr	96.14
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.14
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.14
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	96.14
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	96.13
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.13
PRK13764	602	ATPase; Provisional	96.13
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.12
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.11
PRK14528	186	adenylate kinase; Provisional	96.11
PRK08485	206	DNA polymerase III subunit delta'; Validated	96.11
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.09
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	96.08
PRK13946	184	shikimate kinase; Provisional	96.08
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.08
PRK05057	172	aroK shikimate kinase I; Reviewed	96.07
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	96.07
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	96.06
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	96.06
TIGR00455	184	apsK adenylylsulfate kinase (apsK). Important resi	96.05
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.05
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.04
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.03
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.99
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	95.99
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	95.99
PRK13808	333	adenylate kinase; Provisional	95.98
PF08303	168	tRNA_lig_kinase: tRNA ligase kinase domain; InterP	95.97
PRK02496	184	adk adenylate kinase; Provisional	95.97
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	95.97
TIGR02238	313	recomb_DMC1 meiotic recombinase Dmc1. This model d	95.96
COG2274	709	SunT ABC-type bacteriocin/lantibiotic exporters, c	95.96
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.95
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.94
TIGR01526	325	nadR_NMN_Atrans nicotinamide-nucleotide adenylyltr	95.94
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	95.88
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	95.88
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	95.88
PRK13889	988	conjugal transfer relaxase TraA; Provisional	95.85
PLN02459	261	probable adenylate kinase	95.84
PTZ00035	337	Rad51 protein; Provisional	95.83
PRK00279	215	adk adenylate kinase; Reviewed	95.82
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	95.81
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	95.81
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	95.78
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	95.77
cd01125	239	repA Hexameric Replicative Helicase RepA. RepA is	95.76
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.75
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	95.74
TIGR02239	316	recomb_RAD51 DNA repair protein RAD51. This eukary	95.74
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	95.73
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	95.71
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	95.7
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	95.68
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	95.67
PRK14526	211	adenylate kinase; Provisional	95.67
PRK11174	588	cysteine/glutathione ABC transporter membrane/ATP-	95.66
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	95.66

>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=6e-45  Score=369.20  Aligned_cols=225  Identities=39%  Similarity=0.643  Sum_probs=212.4

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|+++++++|+|.+++||++|++|+++|        ..+|++||||||||||||+||||+|++.     
T Consensus       143 ~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~G--------I~PPKGVLLYGPPGTGKTLLAkAVA~~T-----  209 (406)
T COG1222         143 EEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELG--------IDPPKGVLLYGPPGTGKTLLAKAVANQT-----  209 (406)
T ss_pred             ccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcC--------CCCCCceEeeCCCCCcHHHHHHHHHhcc-----
Confidence            467889999999999999999999999999999999997        9999999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +..|+.+.++++..+|.|+..+.++++|..|++++| |||||||||.++.+|-+.   ..+..|+++-+||.+||++..
T Consensus       210 -~AtFIrvvgSElVqKYiGEGaRlVRelF~lArekaP-sIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~  287 (406)
T COG1222         210 -DATFIRVVGSELVQKYIGEGARLVRELFELAREKAP-SIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDP  287 (406)
T ss_pred             -CceEEEeccHHHHHHHhccchHHHHHHHHHHhhcCC-eEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCC
Confidence             778999999999999999999999999999999996 999999999999988643   455678899999999999999


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      .+++-||+|||+++-|||+|+|  |||+.|+|++|+.+.|.+||+.|+++|...   +++.++..+.|+||+||+++|.+
T Consensus       288 ~~nvKVI~ATNR~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictE  367 (406)
T COG1222         288 RGNVKVIMATNRPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTE  367 (406)
T ss_pred             CCCeEEEEecCCccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHH
Confidence            9999999999999999999999  999999999999999999999999997643   79999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |-+.|.+.
T Consensus       368 AGm~AiR~  375 (406)
T COG1222         368 AGMFAIRE  375 (406)
T ss_pred             HhHHHHHh
Confidence            99988775

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.2e-43  Score=382.40  Aligned_cols=260  Identities=39%  Similarity=0.582  Sum_probs=239.8

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...++++|+||+|+++.|++|.+.|.+|++||+.|.++|        ..+|++||||||||||||++||++|+++     
T Consensus       426 ve~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~G--------i~ppkGVLlyGPPGC~KT~lAkalAne~-----  492 (693)
T KOG0730|consen  426 VEMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFG--------ISPPKGVLLYGPPGCGKTLLAKALANEA-----  492 (693)
T ss_pred             ccCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhc--------CCCCceEEEECCCCcchHHHHHHHhhhh-----
Confidence            567999999999999999999999999999999999987        8999999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                       +++|+++.+++++++|+|++|+.++++|+.|+..+| +||||||||.+...|.+..+.+..|++++||++||++....+
T Consensus       493 -~~nFlsvkgpEL~sk~vGeSEr~ir~iF~kAR~~aP-~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~~k~  570 (693)
T KOG0730|consen  493 -GMNFLSVKGPELFSKYVGESERAIREVFRKARQVAP-CIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEALKN  570 (693)
T ss_pred             -cCCeeeccCHHHHHHhcCchHHHHHHHHHHHhhcCC-eEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccccCc
Confidence             889999999999999999999999999999999986 999999999999999877778999999999999999999999


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      |+|||+||+|+.+|++|++  |||..|++++||.+.|.+||+.++++++..   ++++++..|.||||+||..+|++|..
T Consensus       571 V~ViAATNRpd~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq~A~~  650 (693)
T KOG0730|consen  571 VLVIAATNRPDMIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQEAAL  650 (693)
T ss_pred             EEEEeccCChhhcCHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHHHHHH
Confidence            9999999999999999999  999999999999999999999999997643   78999999999999999999999999


Q ss_pred             HHHHHHHhccccccCcccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhHH
Q 047219          507 SWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNIN  555 (567)
Q Consensus       507 ~a~~r~i~~~i~~~~~~~~~~~l~e~le~~e~~~~~li~~al~~~~~~~  555 (567)
                      .|+++.+.         ......+.+.++++..++++-...++.|++..
T Consensus       651 ~a~~e~i~---------a~~i~~~hf~~al~~~r~s~~~~~~~~Ye~fa  690 (693)
T KOG0730|consen  651 LALRESIE---------ATEITWQHFEEALKAVRPSLTSELLEKYEDFA  690 (693)
T ss_pred             HHHHHhcc---------cccccHHHHHHHHHhhcccCCHHHHHHHHHHh
Confidence            98887664         22344567777777777888887777776653

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=9.1e-41  Score=355.30  Aligned_cols=264  Identities=29%  Similarity=0.527  Sum_probs=230.4

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|++++..+|..+|.+|.++|++|+.+|        ...|.+||||||||||||+||+|+|++.     
T Consensus       503 ~tVPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lG--------i~~PsGvLL~GPPGCGKTLlAKAVANEa-----  569 (802)
T KOG0733|consen  503 ATVPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALG--------IDAPSGVLLCGPPGCGKTLLAKAVANEA-----  569 (802)
T ss_pred             eecCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhC--------CCCCCceEEeCCCCccHHHHHHHHhhhc-----
Confidence            356899999999999999999999999999999999997        8889999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                       +.||+.+.+++++++|+|+++..++.+|..|+..+| ||||+||||.|.+.|.........+++++||..||+++.+.+
T Consensus       570 -g~NFisVKGPELlNkYVGESErAVR~vFqRAR~saP-CVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~R~g  647 (802)
T KOG0733|consen  570 -GANFISVKGPELLNKYVGESERAVRQVFQRARASAP-CVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEERRG  647 (802)
T ss_pred             -cCceEeecCHHHHHHHhhhHHHHHHHHHHHhhcCCC-eEEEecchhhcCcccCCCCchhHHHHHHHHHHHhcccccccc
Confidence             899999999999999999999999999999999986 999999999999999998888999999999999999999999


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHh--h---CHHHHHHHHHhcc--CCCHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKH--L---TKAELAELATATE--EMSGRDIRDVCQ  502 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~--~---~~~~l~~la~~t~--g~s~~dL~~L~~  502 (567)
                      |.||+|||+|+-+||++++  |||..+++++|+.++|.+||+.++++  .   .+.+++.++..+.  ||+|+||..||+
T Consensus       648 V~viaATNRPDiIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvr  727 (802)
T KOG0733|consen  648 VYVIAATNRPDIIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVR  727 (802)
T ss_pred             eEEEeecCCCcccchhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHH
Confidence            9999999999999999999  99999999999999999999999984  2   2347899999887  999999999999


Q ss_pred             HHHHHHHHHHHhccccccCccc------CCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 047219          503 QAERSWASKIIRGQITKDGEQA------CLPPLQEYIESATNRRRSLLDAAEQSH  551 (567)
Q Consensus       503 ~a~~~a~~r~i~~~i~~~~~~~------~~~~l~e~le~~e~~~~~li~~al~~~  551 (567)
                      +|...++++.+.. .+......      +...+..+-+++...+.++-++--..|
T Consensus       728 eAsi~AL~~~~~~-~~~~~~~~~~~~~~~~~t~~hF~eA~~~i~pSv~~~dr~~Y  781 (802)
T KOG0733|consen  728 EASILALRESLFE-IDSSEDDVTVRSSTIIVTYKHFEEAFQRIRPSVSERDRKKY  781 (802)
T ss_pred             HHHHHHHHHHHhh-ccccCcccceeeeeeeecHHHHHHHHHhcCCCccHHHHHHH
Confidence            9999998887753 22211111      122344555555555555554433333

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=1.9e-40  Score=380.89  Aligned_cols=367  Identities=28%  Similarity=0.466  Sum_probs=300.1

Q ss_pred             hcchhhhH-HHHHHHhCCCCCCccceEEEEe-cceEEEEEEecCC-C----CcchHHHHHHHhhCceecccCCCceeEEE
Q 047219          109 AKKERQRI-EELLKRKGMHYGSCPTFTVAVK-GQKVTIKFQVPPA-C----EIPQLIANLVSHLGLKVEEHGGGSDMGLR  181 (567)
Q Consensus       109 ~~~~~~~~-~~~~~~~g~~~g~~~~~~v~~~-g~~~~~~~~~~~~-~----~~~~~~~~~~~~~~~~~~~~~~~~~v~v~  181 (567)
                      +|+|++|| ++.|.+||+.+||+    |+|. |++.++|++||.. +    +++++++.+|+|+|+++||     .|+|+
T Consensus        14 ~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~   84 (733)
T TIGR01243        14 VGRGIVRIDRQTAARLGVEPGDF----VEIEKGDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGD-----TVTVE   84 (733)
T ss_pred             CCCCeEeeCHHHHHhcCCCCCCE----EEEecCCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCC-----eEEEe
Confidence            49999999 69999999999999    9999 8899999999852 2    5788999999999999999     99999


Q ss_pred             eecccccceeEecCCCCccccCCCccccCcccccccchheeeeceeecCCCCceeeeccCcCCHHHHHHHHHHHhhhcc-
Q 047219          182 AWDSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGR-  260 (567)
Q Consensus       182 ~~~~~~a~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  260 (567)
                      ++++++|++|+++|... ...+...        .......+.++|+..|+.+.+.+.... .     ...+....+.+. 
T Consensus        85 ~~~~~~~~~~~~~~~~~-~~~~~~~--------~~~~~~~~~~~~~~~g~~~~~~~~~~~-~-----~~~v~~~~p~~~~  149 (733)
T TIGR01243        85 RAEVKEAKKVVLAPTQP-IRFGRDF--------VDYVKEFLLGKPISKGETVIVPVLEGA-L-----PFVVVSTQPAGFV  149 (733)
T ss_pred             ecCCCccceEeeccccc-cccccch--------HHHHHHHHcCCCCCCCCEEEecccCcc-e-----eEEEEecCCCCcE
Confidence            99999999999998633 2122111        123456667788888887655443211 1     000111111111 


Q ss_pred             ------cccccCccc---cccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCC
Q 047219          261 ------RIYGLDEPQ---LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP  331 (567)
Q Consensus       261 ------~~~~~~~~~---~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~Gpp  331 (567)
                            .+.....+.   .....+.++|++|+|++++++.+++++..++.+|++|+.++        ..+++++||||||
T Consensus       150 ~~~~~t~~~~~~~~~~~~~~~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~g--------i~~~~giLL~Gpp  221 (733)
T TIGR01243       150 YVTEATEVEIREKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLG--------IEPPKGVLLYGPP  221 (733)
T ss_pred             EECCCceEEecCCccccccccCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC--------CCCCceEEEECCC
Confidence                  011111111   11234779999999999999999999999999999999886        7889999999999


Q ss_pred             CCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHH
Q 047219          332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEA  411 (567)
Q Consensus       332 GTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~  411 (567)
                      |||||++|+++|+++      +.+++.+++.++.++++|+.+..++.+|+.+....+ ++|||||||.+.++++......
T Consensus       222 GtGKT~laraia~~~------~~~~i~i~~~~i~~~~~g~~~~~l~~lf~~a~~~~p-~il~iDEid~l~~~r~~~~~~~  294 (733)
T TIGR01243       222 GTGKTLLAKAVANEA------GAYFISINGPEIMSKYYGESEERLREIFKEAEENAP-SIIFIDEIDAIAPKREEVTGEV  294 (733)
T ss_pred             CCChHHHHHHHHHHh------CCeEEEEecHHHhcccccHHHHHHHHHHHHHHhcCC-cEEEeehhhhhcccccCCcchH
Confidence            999999999999999      677999999999999999999999999999987764 9999999999998877655566


Q ss_pred             HHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHH
Q 047219          412 TRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELA  486 (567)
Q Consensus       412 ~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la  486 (567)
                      ..+++++|+..++++.....++||++||+++.+++++++  ||+..+.++.|+.++|.+|++.+.+.+.   ...++.++
T Consensus       295 ~~~~~~~Ll~~ld~l~~~~~vivI~atn~~~~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la  374 (733)
T TIGR01243       295 EKRVVAQLLTLMDGLKGRGRVIVIGATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLA  374 (733)
T ss_pred             HHHHHHHHHHHhhccccCCCEEEEeecCChhhcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHH
Confidence            678889999999998888899999999999999999998  9999999999999999999998887654   34688999


Q ss_pred             HhccCCCHHHHHHHHHHHHHHHHHHHHh
Q 047219          487 TATEEMSGRDIRDVCQQAERSWASKIIR  514 (567)
Q Consensus       487 ~~t~g~s~~dL~~L~~~a~~~a~~r~i~  514 (567)
                      ..++||+++|+..+|+.+.+.+.++.+.
T Consensus       375 ~~t~G~~gadl~~l~~~a~~~al~r~~~  402 (733)
T TIGR01243       375 EVTHGFVGADLAALAKEAAMAALRRFIR  402 (733)
T ss_pred             HhCCCCCHHHHHHHHHHHHHHHHHHHhh
Confidence            9999999999999999999998888764

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>KOG0733 consensus Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.4e-39  Score=344.49  Aligned_cols=224  Identities=35%  Similarity=0.610  Sum_probs=212.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      ++++|++|+|++....+|.+++.. +++|+.|..+|        ..||++||||||||||||.||+|||+++      ++
T Consensus       185 snv~f~diGG~d~~~~el~~li~~-i~~Pe~~~~lG--------v~PprGvLlHGPPGCGKT~lA~AiAgel------~v  249 (802)
T KOG0733|consen  185 SNVSFSDIGGLDKTLAELCELIIH-IKHPEVFSSLG--------VRPPRGVLLHGPPGCGKTSLANAIAGEL------GV  249 (802)
T ss_pred             CCcchhhccChHHHHHHHHHHHHH-hcCchhHhhcC--------CCCCCceeeeCCCCccHHHHHHHHhhhc------CC
Confidence            468999999999999999999876 99999999987        8999999999999999999999999999      99


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC----C
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD----K  430 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~----~  430 (567)
                      ||+.|++.++.+.+.|+++++++++|+.|+..+| ||+||||||.+.++|+....+..++++.+|+..||++...    .
T Consensus       250 Pf~~isApeivSGvSGESEkkiRelF~~A~~~aP-civFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~  328 (802)
T KOG0733|consen  250 PFLSISAPEIVSGVSGESEKKIRELFDQAKSNAP-CIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGD  328 (802)
T ss_pred             ceEeecchhhhcccCcccHHHHHHHHHHHhccCC-eEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCC
Confidence            9999999999999999999999999999999986 9999999999999999999999999999999999998654    6


Q ss_pred             cEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .|+||+|||+|+.||++|++  ||++.|.+..|+...|.+||+..++++...   ++.++|..|+||.|+||.+||.+|.
T Consensus       329 ~VlVIgATnRPDslDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~~Aa  408 (802)
T KOG0733|consen  329 PVLVIGATNRPDSLDPALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCREAA  408 (802)
T ss_pred             CeEEEecCCCCcccCHHHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHHHHH
Confidence            79999999999999999999  999999999999999999999999976543   7899999999999999999999999


Q ss_pred             HHHHHHHHh
Q 047219          506 RSWASKIIR  514 (567)
Q Consensus       506 ~~a~~r~i~  514 (567)
                      .-+.+|++.
T Consensus       409 ~vAikR~ld  417 (802)
T KOG0733|consen  409 FVAIKRILD  417 (802)
T ss_pred             HHHHHHHhh
Confidence            999999876

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=6.8e-39  Score=348.31  Aligned_cols=292  Identities=28%  Similarity=0.474  Sum_probs=245.5

Q ss_pred             cCCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCC
Q 047219          242 SLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNR  321 (567)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~  321 (567)
                      .++++++.+..+.++.....      ..-.+..|+++|+||+|.+++|.+|.+.|.+||+||++|..         +.++
T Consensus       640 ~l~~edf~kals~~~~~fs~------aiGAPKIPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfss---------glrk  704 (953)
T KOG0736|consen  640 LLTEEDFDKALSRLQKEFSD------AIGAPKIPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSS---------GLRK  704 (953)
T ss_pred             eecHHHHHHHHHHHHHhhhh------hcCCCCCCccchhcccCHHHHHHHHHHHhcCcccChhhhhc---------cccc
Confidence            44566666666655543221      11234679999999999999999999999999999999964         2566


Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      ..+||||||||||||++|+|+|.++      ..+|..+.++++...|+|++|+++|++|++|+..+| ||||+||+|+++
T Consensus       705 RSGILLYGPPGTGKTLlAKAVATEc------sL~FlSVKGPELLNMYVGqSE~NVR~VFerAR~A~P-CVIFFDELDSlA  777 (953)
T KOG0736|consen  705 RSGILLYGPPGTGKTLLAKAVATEC------SLNFLSVKGPELLNMYVGQSEENVREVFERARSAAP-CVIFFDELDSLA  777 (953)
T ss_pred             cceeEEECCCCCchHHHHHHHHhhc------eeeEEeecCHHHHHHHhcchHHHHHHHHHHhhccCC-eEEEeccccccC
Confidence            7899999999999999999999999      889999999999999999999999999999998875 999999999999


Q ss_pred             hhhhh--hhHHHHHHHHHHHHHhhcCcc--cCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCC-CHHHHHHHHHHHH
Q 047219          402 VARDS--EMHEATRRILSVLLRQIDGFE--QDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLP-DHENRQEIAAQYA  474 (567)
Q Consensus       402 ~~~q~--~l~~~~~~vl~~LL~~ld~~~--~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P-~~~eR~eIL~~~~  474 (567)
                      ++|..  ..+.++.|++.+||.++|++.  ...+|.||+|||+|+.|||+|++  |||..++++++ +.+.+..+|+.++
T Consensus       778 P~RG~sGDSGGVMDRVVSQLLAELDgls~~~s~~VFViGATNRPDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlT  857 (953)
T KOG0736|consen  778 PNRGRSGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVIGATNRPDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALT  857 (953)
T ss_pred             ccCCCCCCccccHHHHHHHHHHHhhcccCCCCCceEEEecCCCccccChhhcCCCccceeEEecCCccHHHHHHHHHHHH
Confidence            99864  456789999999999999997  56789999999999999999999  99999999888 5677888999999


Q ss_pred             HhhCHH---HHHHHHHhcc-CCCHHHHHHHHHHHHHHHHHHHHhccccc----c--CcccCCCcHHHHHHHHHHHHHHHH
Q 047219          475 KHLTKA---ELAELATATE-EMSGRDIRDVCQQAERSWASKIIRGQITK----D--GEQACLPPLQEYIESATNRRRSLL  544 (567)
Q Consensus       475 ~~~~~~---~l~~la~~t~-g~s~~dL~~L~~~a~~~a~~r~i~~~i~~----~--~~~~~~~~l~e~le~~e~~~~~li  544 (567)
                      ++|..+   ++.++++.++ .|+|+|+-.+|..||.+|++|.+.+....    +  ..........++++++++.+.++.
T Consensus       858 rkFkLdedVdL~eiAk~cp~~~TGADlYsLCSdA~l~AikR~i~~ie~g~~~~~e~~~~~v~V~~eDflks~~~l~PSvS  937 (953)
T KOG0736|consen  858 RKFKLDEDVDLVEIAKKCPPNMTGADLYSLCSDAMLAAIKRTIHDIESGTISEEEQESSSVRVTMEDFLKSAKRLQPSVS  937 (953)
T ss_pred             HHccCCCCcCHHHHHhhCCcCCchhHHHHHHHHHHHHHHHHHHHHhhhccccccccCCceEEEEHHHHHHHHHhcCCccc
Confidence            987644   7888888776 59999999999999999999988753221    1  111222356788999988889999


Q ss_pred             HHHHHHHhhHH
Q 047219          545 DAAEQSHQNIN  555 (567)
Q Consensus       545 ~~al~~~~~~~  555 (567)
                      ++.+.+|..++
T Consensus       938 ~~EL~~ye~vr  948 (953)
T KOG0736|consen  938 EQELLRYEMVR  948 (953)
T ss_pred             HHHHHHHHHHH
Confidence            99888877654

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.7e-38  Score=322.46  Aligned_cols=228  Identities=36%  Similarity=0.584  Sum_probs=210.2

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|.+.|+||.|++++|+-|+|++.+|+..|++|+.+         ..|.++||++||||||||+||+|+|.++      
T Consensus       205 ~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~Gi---------rrPWkgvLm~GPPGTGKTlLAKAvATEc------  269 (491)
T KOG0738|consen  205 RNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGI---------RRPWKGVLMVGPPGTGKTLLAKAVATEC------  269 (491)
T ss_pred             cCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhc---------ccccceeeeeCCCCCcHHHHHHHHHHhh------
Confidence            4577999999999999999999999999999999987         4778999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh-hhHHHHHHHHHHHHHhhcCcccC--
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS-EMHEATRRILSVLLRQIDGFEQD--  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~-~l~~~~~~vl~~LL~~ld~~~~~--  429 (567)
                      +..|+.|+.+.+.++|.|++++.++-+|+.|+.++| ++|||||||.|...|.. ..++..+++.++||.+||+....  
T Consensus       270 ~tTFFNVSsstltSKwRGeSEKlvRlLFemARfyAP-StIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e  348 (491)
T KOG0738|consen  270 GTTFFNVSSSTLTSKWRGESEKLVRLLFEMARFYAP-STIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLE  348 (491)
T ss_pred             cCeEEEechhhhhhhhccchHHHHHHHHHHHHHhCC-ceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccc
Confidence            778999999999999999999999999999999996 99999999999998875 46778899999999999998532  


Q ss_pred             --CcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 --KKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 --~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                        ..|.|+|+||.|++||++|++||...|.|++|+.+.|..+|+..++...   ...++.+++.++||+|+||..+|++|
T Consensus       349 ~~k~VmVLAATN~PWdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCreA  428 (491)
T KOG0738|consen  349 NSKVVMVLAATNFPWDIDEALRRRLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVCREA  428 (491)
T ss_pred             cceeEEEEeccCCCcchHHHHHHHHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHHHHH
Confidence              3489999999999999999999999999999999999999999988643   34789999999999999999999999


Q ss_pred             HHHHHHHHHhcc
Q 047219          505 ERSWASKIIRGQ  516 (567)
Q Consensus       505 ~~~a~~r~i~~~  516 (567)
                      .+++.+|.+.+.
T Consensus       429 sm~~mRR~i~g~  440 (491)
T KOG0738|consen  429 SMMAMRRKIAGL  440 (491)
T ss_pred             HHHHHHHHHhcC
Confidence            999999988754

>KOG0734 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-37  Score=326.60  Aligned_cols=222  Identities=33%  Similarity=0.554  Sum_probs=208.2

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ....+++|+|+-|.+++|++|.|.+ .+|+.|+.|.++|        ...|++|||+||||||||+||||+|.+.     
T Consensus       296 ~~~~nv~F~dVkG~DEAK~ELeEiV-efLkdP~kftrLG--------GKLPKGVLLvGPPGTGKTlLARAvAGEA-----  361 (752)
T KOG0734|consen  296 EQMKNVTFEDVKGVDEAKQELEEIV-EFLKDPTKFTRLG--------GKLPKGVLLVGPPGTGKTLLARAVAGEA-----  361 (752)
T ss_pred             hhhcccccccccChHHHHHHHHHHH-HHhcCcHHhhhcc--------CcCCCceEEeCCCCCchhHHHHHhhccc-----
Confidence            3455789999999999999999976 6899999999987        8999999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                       ++||++..++++..-++|...++++.+|..|+.++| |||||||||.+..+|........+.++++||..||++..+..
T Consensus       362 -~VPFF~~sGSEFdEm~VGvGArRVRdLF~aAk~~AP-cIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~qNeG  439 (752)
T KOG0734|consen  362 -GVPFFYASGSEFDEMFVGVGARRVRDLFAAAKARAP-CIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQNEG  439 (752)
T ss_pred             -CCCeEeccccchhhhhhcccHHHHHHHHHHHHhcCC-eEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCcCCc
Confidence             999999999999999999999999999999999996 999999999999999887777889999999999999999999


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      ++||++||.++.||++|.|  |||+.+.++.||.+.|.+||+.|+.+....   +..-+++-+.||+|+||.+|++.|+-
T Consensus       440 iIvigATNfpe~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlVNqAAl  519 (752)
T KOG0734|consen  440 IIVIGATNFPEALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLVNQAAL  519 (752)
T ss_pred             eEEEeccCChhhhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHHHHHHH
Confidence            9999999999999999999  999999999999999999999999986543   78899999999999999999999885


Q ss_pred             HHH
Q 047219          507 SWA  509 (567)
Q Consensus       507 ~a~  509 (567)
                      .++
T Consensus       520 kAa  522 (752)
T KOG0734|consen  520 KAA  522 (752)
T ss_pred             HHH
Confidence            544

>KOG0727 consensus 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=5e-36  Score=290.81  Aligned_cols=225  Identities=38%  Similarity=0.641  Sum_probs=209.4

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ..+|.++|.||+|++-+|+++++.+++||.+-++|+++|        ..+|++||+|||||||||+||+++|+..     
T Consensus       147 ~ekpdvsy~diggld~qkqeireavelplt~~~ly~qig--------idpprgvllygppg~gktml~kava~~t-----  213 (408)
T KOG0727|consen  147 DEKPDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIG--------IDPPRGVLLYGPPGTGKTMLAKAVANHT-----  213 (408)
T ss_pred             CCCCCccccccccchhhHHHHHHHHhccchHHHHHHHhC--------CCCCcceEEeCCCCCcHHHHHHHHhhcc-----
Confidence            467899999999999999999999999999999999998        8999999999999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh---hhHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS---EMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~---~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       ...|+.+.++++..+|.|+....++.+|..|++++| +||||||||.++.++-+   +..+..++++-+||..||++..
T Consensus       214 -~a~firvvgsefvqkylgegprmvrdvfrlakenap-siifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq  291 (408)
T KOG0727|consen  214 -TAAFIRVVGSEFVQKYLGEGPRMVRDVFRLAKENAP-SIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQ  291 (408)
T ss_pred             -chheeeeccHHHHHHHhccCcHHHHHHHHHHhccCC-cEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCc
Confidence             667999999999999999999999999999999996 99999999999988754   3455678899999999999999


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..++-||++||+.+.+||+|++  |+|+.|+|++|+.++++-++...+.+|.   ..+++.+.......+++||..+|++
T Consensus       292 ~~nvkvimatnradtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicqe  371 (408)
T KOG0727|consen  292 TTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQE  371 (408)
T ss_pred             ccceEEEEecCcccccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHHH
Confidence            9999999999999999999999  9999999999999999999999988864   3378888888899999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |-+.+.+.
T Consensus       372 agm~avr~  379 (408)
T KOG0727|consen  372 AGMLAVRE  379 (408)
T ss_pred             HhHHHHHh
Confidence            99887764

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.6e-35  Score=293.07  Aligned_cols=225  Identities=33%  Similarity=0.534  Sum_probs=207.9

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ..+|++.|+|+.|++.+|+.|++.+.+|+++|.+|..-         ..|.+++||||||||||+.||+|+|.+.     
T Consensus       125 ~EKPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGk---------R~PwrgiLLyGPPGTGKSYLAKAVATEA-----  190 (439)
T KOG0739|consen  125 REKPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGK---------RKPWRGILLYGPPGTGKSYLAKAVATEA-----  190 (439)
T ss_pred             ccCCCCchhhhccchhHHHHHHhheeecccchhhhcCC---------CCcceeEEEeCCCCCcHHHHHHHHHhhc-----
Confidence            36789999999999999999999999999999999742         4567999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-cCC
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-QDK  430 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-~~~  430 (567)
                       +..|+.++.++++++|.|++++.+..+|+.|+++.| +||||||||.|.+.+.+...+..+++..+||-+|.+.- .+.
T Consensus       191 -nSTFFSvSSSDLvSKWmGESEkLVknLFemARe~kP-SIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d~~  268 (439)
T KOG0739|consen  191 -NSTFFSVSSSDLVSKWMGESEKLVKNLFEMARENKP-SIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGNDND  268 (439)
T ss_pred             -CCceEEeehHHHHHHHhccHHHHHHHHHHHHHhcCC-cEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccCCC
Confidence             567999999999999999999999999999999985 99999999999999999999999999999999999874 456


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      .++|+++||.|+.||.++++||+..|+|++|+...|..+++.++..    +...++..++..|+||+|+||.-+++.+.|
T Consensus       269 gvLVLgATNiPw~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalm  348 (439)
T KOG0739|consen  269 GVLVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALM  348 (439)
T ss_pred             ceEEEecCCCchhHHHHHHHHhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEehhhhh
Confidence            8999999999999999999999999999999999999999998764    567899999999999999999999999987


Q ss_pred             HHHHHH
Q 047219          507 SWASKI  512 (567)
Q Consensus       507 ~a~~r~  512 (567)
                      .-.+++
T Consensus       349 ePvRkv  354 (439)
T KOG0739|consen  349 EPVRKV  354 (439)
T ss_pred             hhHHHh
Confidence            776665

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.1e-35  Score=297.52  Aligned_cols=228  Identities=36%  Similarity=0.601  Sum_probs=209.4

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .-.++|+||+|++.+++.+.+.+.+|+++|++|...+ -      ..++++|||+||||||||.+|+++|++.      +
T Consensus        86 ~I~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~-L------l~p~kGiLL~GPpG~GKTmlAKA~Akea------g  152 (386)
T KOG0737|consen   86 EIGVSFDDIGGLEEVKDALQELVILPLRRPELFAKGK-L------LRPPKGILLYGPPGTGKTMLAKAIAKEA------G  152 (386)
T ss_pred             hceeehhhccchHHHHHHHHHHHhhcccchhhhcccc-c------ccCCccceecCCCCchHHHHHHHHHHHc------C
Confidence            3458999999999999999999999999999997322 1      4689999999999999999999999999      8


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc--
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK--  431 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~--  431 (567)
                      .+|+.+..+.++++|||+.++.++.+|..|....| +||||||+|++...|+...+++...+.++|....|++..+.+  
T Consensus       153 a~fInv~~s~lt~KWfgE~eKlv~AvFslAsKl~P-~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~~~~r  231 (386)
T KOG0737|consen  153 ANFINVSVSNLTSKWFGEAQKLVKAVFSLASKLQP-SIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSKDSER  231 (386)
T ss_pred             CCcceeeccccchhhHHHHHHHHHHHHhhhhhcCc-ceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCCCCce
Confidence            88999999999999999999999999999998875 999999999999999888999999999999999999977655  


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a  508 (567)
                      |+|++|||+|.++|++++||++..+++++|+.++|.+|++.+++.-.   .-++.+++..|.||||.||+.+|..|....
T Consensus       232 VlVlgATNRP~DlDeAiiRR~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC~~Aa~~~  311 (386)
T KOG0737|consen  232 VLVLGATNRPFDLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELCRLAALRP  311 (386)
T ss_pred             EEEEeCCCCCccHHHHHHHhCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHHHHHhHhH
Confidence            99999999999999999999999999999999999999999987643   337999999999999999999999999877


Q ss_pred             HHHHHhc
Q 047219          509 ASKIIRG  515 (567)
Q Consensus       509 ~~r~i~~  515 (567)
                      .+.++..
T Consensus       312 ire~~~~  318 (386)
T KOG0737|consen  312 IRELLVS  318 (386)
T ss_pred             HHHHHHh
Confidence            7777654

>KOG0728 consensus 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.1e-34  Score=279.24  Aligned_cols=224  Identities=34%  Similarity=0.583  Sum_probs=206.5

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|.-+|+-|+|++.+++++++.|++|.+|||+|+.+|        ...|+++|||||||||||++|+++|+..      
T Consensus       140 KvPDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLG--------IaQPKGvlLygppgtGktLlaraVahht------  205 (404)
T KOG0728|consen  140 KVPDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALG--------IAQPKGVLLYGPPGTGKTLLARAVAHHT------  205 (404)
T ss_pred             hCCccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcC--------CCCCcceEEecCCCCchhHHHHHHHhhc------
Confidence            45677899999999999999999999999999999997        8899999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      .+.|+.++++++..+|.|+....++++|--|++++| +|||+||||++...+.+.   .....++..-+||.++|+++..
T Consensus       206 ~c~firvsgselvqk~igegsrmvrelfvmarehap-siifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfeat  284 (404)
T KOG0728|consen  206 DCTFIRVSGSELVQKYIGEGSRMVRELFVMAREHAP-SIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEAT  284 (404)
T ss_pred             ceEEEEechHHHHHHHhhhhHHHHHHHHHHHHhcCC-ceEeeecccccccccccCCCCccHHHHHHHHHHHHhccccccc
Confidence            778999999999999999999999999999999996 999999999998776542   2345577788899999999999


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .++-||++||+.+-||++|++  |+|+.|+|++|+.+.|.+|++.+.+++..-   ++..+++...|-++++++.+|.+|
T Consensus       285 knikvimatnridild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vctea  364 (404)
T KOG0728|consen  285 KNIKVIMATNRIDILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVCTEA  364 (404)
T ss_pred             cceEEEEeccccccccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhhhhh
Confidence            999999999999999999999  999999999999999999999999887543   789999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      -+.+++.
T Consensus       365 gm~alre  371 (404)
T KOG0728|consen  365 GMYALRE  371 (404)
T ss_pred             hHHHHHH
Confidence            9877653

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=100.00  E-value=2.5e-34  Score=280.22  Aligned_cols=210  Identities=39%  Similarity=0.650  Sum_probs=191.0

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...++++|+|++|++++|++++- |...|.+|+.|.+|.           |++||||||||||||++|+++|++.     
T Consensus       113 e~~~~it~ddViGqEeAK~kcrl-i~~yLenPe~Fg~WA-----------PknVLFyGppGTGKTm~Akalane~-----  175 (368)
T COG1223         113 EIISDITLDDVIGQEEAKRKCRL-IMEYLENPERFGDWA-----------PKNVLFYGPPGTGKTMMAKALANEA-----  175 (368)
T ss_pred             hhhccccHhhhhchHHHHHHHHH-HHHHhhChHHhcccC-----------cceeEEECCCCccHHHHHHHHhccc-----
Confidence            35678999999999999999975 557899999998774           8999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh-hHHHHHHHHHHHHHhhcCcccCC
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE-MHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~-l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                       .++++.+.+.++.++++|+..++++++++.|.+.+| ||+||||+|.++..+.-. +..-..++++.||+.||++..+.
T Consensus       176 -kvp~l~vkat~liGehVGdgar~Ihely~rA~~~aP-civFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~ene  253 (368)
T COG1223         176 -KVPLLLVKATELIGEHVGDGARRIHELYERARKAAP-CIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKENE  253 (368)
T ss_pred             -CCceEEechHHHHHHHhhhHHHHHHHHHHHHHhcCC-eEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCcccCC
Confidence             889999999999999999999999999999999986 999999999999877533 33335678999999999999999


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L  500 (567)
                      .|+.||+||+++.||+++++||...|+|.+|+.++|.+|++.+++.|+..   .++.++..+.|+|++||..-
T Consensus       254 GVvtIaaTN~p~~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikek  326 (368)
T COG1223         254 GVVTIAATNRPELLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEK  326 (368)
T ss_pred             ceEEEeecCChhhcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHH
Confidence            99999999999999999999999999999999999999999999998643   68999999999999999653

>KOG0726 consensus 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=9e-35  Score=286.94  Aligned_cols=225  Identities=34%  Similarity=0.592  Sum_probs=205.6

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.-+|.||+|++.++++|++.+++||.|||+|+..|        ..+|++|+|||+||||||+||+|+||..     
T Consensus       177 eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemG--------ikpPKGVIlyG~PGTGKTLLAKAVANqT-----  243 (440)
T KOG0726|consen  177 EKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMG--------IKPPKGVILYGEPGTGKTLLAKAVANQT-----  243 (440)
T ss_pred             ccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcC--------CCCCCeeEEeCCCCCchhHHHHHHhccc-----
Confidence            345778999999999999999999999999999999987        8999999999999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       ...|+.+-++++..+|.|+..+.++++|.-|.+++| +|+||||||.+..++-+.   ..+..++..-+||+++|++..
T Consensus       244 -SATFlRvvGseLiQkylGdGpklvRqlF~vA~e~ap-SIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFds  321 (440)
T KOG0726|consen  244 -SATFLRVVGSELIQKYLGDGPKLVRELFRVAEEHAP-SIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDS  321 (440)
T ss_pred             -chhhhhhhhHHHHHHHhccchHHHHHHHHHHHhcCC-ceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccc
Confidence             567999999999999999999999999999999996 999999999999888654   344567777789999999999


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      +++|-||++||+.+.|||+|.+  |+|+.|+|+.||...++.|+..|+..+...   .++.+...-..+|++||+++|.+
T Consensus       322 rgDvKvimATnrie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAictE  401 (440)
T KOG0726|consen  322 RGDVKVIMATNRIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICTE  401 (440)
T ss_pred             cCCeEEEEecccccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHHH
Confidence            9999999999999999999999  999999999999999999999999887644   67778777788999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |-+.+++.
T Consensus       402 aGllAlRe  409 (440)
T KOG0726|consen  402 AGLLALRE  409 (440)
T ss_pred             HhHHHHHH
Confidence            98877664

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=8.4e-34  Score=306.17  Aligned_cols=224  Identities=32%  Similarity=0.513  Sum_probs=211.7

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      +.|+||+|+.++++.+++.+++|-++|.+|....        .+.+.++|||||||||||+||-++|..+      +.+|
T Consensus       664 i~w~digg~~~~k~~l~~~i~~P~kyp~if~~~p--------lr~~~giLLyGppGcGKT~la~a~a~~~------~~~f  729 (952)
T KOG0735|consen  664 IRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCP--------LRLRTGILLYGPPGCGKTLLASAIASNS------NLRF  729 (952)
T ss_pred             CCceecccHHHHHHHHHHHHhccccchHHHhhCC--------cccccceEEECCCCCcHHHHHHHHHhhC------CeeE
Confidence            8999999999999999999999999999999875        6788999999999999999999999999      8889


Q ss_pred             EEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEE
Q 047219          357 MYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIA  436 (567)
Q Consensus       357 ~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIa  436 (567)
                      +.+.++++.++|.|.+++.++.+|..|...+ |||||+||+|+++++|......+..|++++||..||+.+.-..|.|+|
T Consensus       730 isvKGPElL~KyIGaSEq~vR~lF~rA~~a~-PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Egl~GV~i~a  808 (952)
T KOG0735|consen  730 ISVKGPELLSKYIGASEQNVRDLFERAQSAK-PCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEGLDGVYILA  808 (952)
T ss_pred             EEecCHHHHHHHhcccHHHHHHHHHHhhccC-CeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccccceEEEEE
Confidence            9999999999999999999999999998776 599999999999999998888899999999999999999999999999


Q ss_pred             eeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          437 ATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       437 aTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      +|.+|+.+||+|+|  |+|+.+.-+.|+..+|.+|++.+...+..   .+++.++..|+||+|+||..++..|...+.++
T Consensus       809 aTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll~~A~l~avh~  888 (952)
T KOG0735|consen  809 ATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLLYNAQLAAVHE  888 (952)
T ss_pred             ecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHHHHHHHHHHHH
Confidence            99999999999999  99999999999999999999999886543   37899999999999999999999999999888


Q ss_pred             HHhc
Q 047219          512 IIRG  515 (567)
Q Consensus       512 ~i~~  515 (567)
                      ++..
T Consensus       889 ~l~~  892 (952)
T KOG0735|consen  889 ILKR  892 (952)
T ss_pred             HHHh
Confidence            8753

>KOG0731 consensus AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.6e-34  Score=314.96  Aligned_cols=224  Identities=35%  Similarity=0.595  Sum_probs=204.9

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      .....++|.|+.|.+++|++|.|.+ .+|++|+.|+++|        +..|+++||+||||||||+||+|+|.+.     
T Consensus       303 ~~~t~V~FkDVAG~deAK~El~E~V-~fLKNP~~Y~~lG--------AKiPkGvLL~GPPGTGKTLLAKAiAGEA-----  368 (774)
T KOG0731|consen  303 EGNTGVKFKDVAGVDEAKEELMEFV-KFLKNPEQYQELG--------AKIPKGVLLVGPPGTGKTLLAKAIAGEA-----  368 (774)
T ss_pred             CCCCCCccccccCcHHHHHHHHHHH-HHhcCHHHHHHcC--------CcCcCceEEECCCCCcHHHHHHHHhccc-----
Confidence            3445699999999999999999987 6899999999997        8999999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh----hhHHHHHHHHHHHHHhhcCcc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS----EMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~----~l~~~~~~vl~~LL~~ld~~~  427 (567)
                       ++||+.++++++...+.|....+++.+|..|+.++| ||+||||||.+...++.    ......+..+++||..||++.
T Consensus       369 -gVPF~svSGSEFvE~~~g~~asrvr~lf~~ar~~aP-~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~  446 (774)
T KOG0731|consen  369 -GVPFFSVSGSEFVEMFVGVGASRVRDLFPLARKNAP-SIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFE  446 (774)
T ss_pred             -CCceeeechHHHHHHhcccchHHHHHHHHHhhccCC-eEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCc
Confidence             999999999999999999989999999999999996 99999999999988852    233445678999999999999


Q ss_pred             cCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC----HHHHHHHHHhccCCCHHHHHHHH
Q 047219          428 QDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT----KAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       428 ~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~----~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ....|+|+++||+++.+|++|++  |||+.|.++.|+..+|.+|++.|+++..    ..++.+++..|+||+|+||.++|
T Consensus       447 ~~~~vi~~a~tnr~d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~  526 (774)
T KOG0731|consen  447 TSKGVIVLAATNRPDILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLC  526 (774)
T ss_pred             CCCcEEEEeccCCccccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhh
Confidence            99999999999999999999999  9999999999999999999999998743    34677799999999999999999


Q ss_pred             HHHHHHHHHH
Q 047219          502 QQAERSWASK  511 (567)
Q Consensus       502 ~~a~~~a~~r  511 (567)
                      ++|+-.++++
T Consensus       527 neaa~~a~r~  536 (774)
T KOG0731|consen  527 NEAALLAARK  536 (774)
T ss_pred             hHHHHHHHHh
Confidence            9999777664

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.2e-33  Score=275.38  Aligned_cols=227  Identities=33%  Similarity=0.548  Sum_probs=209.2

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.-+|+||+|++.++++|.+.+.+|+.|++.|+.+|        ..+|+++|+|||||||||++||+.|.+.     
T Consensus       163 DekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lg--------i~pPKGvLmYGPPGTGKTlmARAcAaqT-----  229 (424)
T KOG0652|consen  163 DEKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLG--------IRPPKGVLMYGPPGTGKTLMARACAAQT-----  229 (424)
T ss_pred             ccCCcccccccccHHHHHHHHHHHhccccccHHHHHhcC--------CCCCCceEeeCCCCCcHHHHHHHHHHhc-----
Confidence            456778999999999999999999999999999999987        8999999999999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       ...|..+.++.+...|.|+..+.++..|..|++.+| +||||||+|.+..++.+.   ..+..++..-+||..+|++..
T Consensus       230 -~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP-~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss  307 (424)
T KOG0652|consen  230 -NATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAP-TIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSS  307 (424)
T ss_pred             -cchHHHhcchHHHhhhhcchHHHHHHHHHHhhccCC-eEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCC
Confidence             566889999999999999999999999999999986 999999999999887543   345567778889999999999


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ...+-||++||+.+-|||+|++  |+|+.|+|+.|+.+.|..|++.|.+++.   +..++++++.+.+|+|+..+++|-+
T Consensus       308 ~~~vKviAATNRvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQcKAVcVE  387 (424)
T KOG0652|consen  308 DDRVKVIAATNRVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQCKAVCVE  387 (424)
T ss_pred             ccceEEEeecccccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchhheeeehh
Confidence            9999999999999999999998  9999999999999999999999999875   3478999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 047219          504 AERSWASKII  513 (567)
Q Consensus       504 a~~~a~~r~i  513 (567)
                      |-|.+++|-.
T Consensus       388 AGMiALRr~a  397 (424)
T KOG0652|consen  388 AGMIALRRGA  397 (424)
T ss_pred             hhHHHHhccc
Confidence            9998888743

>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional

Probab=100.00  E-value=1.3e-32  Score=293.64  Aligned_cols=224  Identities=39%  Similarity=0.650  Sum_probs=202.4

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|.++|+||+|++.++++|++.+.+|+.+|++|+++|        ..+|+++||+||||||||++|+++|+++      
T Consensus       138 ~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~G--------l~~pkgvLL~GppGTGKT~LAkalA~~l------  203 (398)
T PTZ00454        138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIG--------IDPPRGVLLYGPPGTGKTMLAKAVAHHT------  203 (398)
T ss_pred             CCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcC--------CCCCceEEEECCCCCCHHHHHHHHHHhc------
Confidence            46889999999999999999999999999999999887        7899999999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh---hhHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS---EMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~---~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+.++.+..++.|+.+..++.+|..|...+| +||||||||.+..++.+   ......++++.+++..++++...
T Consensus       204 ~~~fi~i~~s~l~~k~~ge~~~~lr~lf~~A~~~~P-~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~~  282 (398)
T PTZ00454        204 TATFIRVVGSEFVQKYLGEGPRMVRDVFRLARENAP-SIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQT  282 (398)
T ss_pred             CCCEEEEehHHHHHHhcchhHHHHHHHHHHHHhcCC-eEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCCC
Confidence            678999999999999999999999999999988875 99999999999876532   22345567888999999988777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||+|||+++.+|+++++  ||+..|+|+.|+.++|.+|++.++.++.   ..++..++..+.||+++||.++|++|
T Consensus       283 ~~v~VI~aTN~~d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA  362 (398)
T PTZ00454        283 TNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEA  362 (398)
T ss_pred             CCEEEEEecCCchhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            899999999999999999998  9999999999999999999999988754   33788999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      .+.+.++
T Consensus       363 ~~~A~r~  369 (398)
T PTZ00454        363 GMQAVRK  369 (398)
T ss_pred             HHHHHHc
Confidence            9887765

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=2.6e-33  Score=273.77  Aligned_cols=224  Identities=33%  Similarity=0.590  Sum_probs=204.3

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ..+|.++|.|++|..++++++++.++.|+.|||.|-.+|        ..+|++||+|||||||||++|||+|+..     
T Consensus       169 eekpdvty~dvggckeqieklrevve~pll~perfv~lg--------idppkgvllygppgtgktl~aravanrt-----  235 (435)
T KOG0729|consen  169 EEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLG--------IDPPKGVLLYGPPGTGKTLCARAVANRT-----  235 (435)
T ss_pred             ecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcC--------CCCCCceEEeCCCCCchhHHHHHHhccc-----
Confidence            567999999999999999999999999999999999887        8999999999999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.-|+.+-++++..+|+|+....++++|+.|+... -||||+||||.+.+.+-+.   .....++..-+|+.++|++..
T Consensus       236 -dacfirvigselvqkyvgegarmvrelf~martkk-aciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdp  313 (435)
T KOG0729|consen  236 -DACFIRVIGSELVQKYVGEGARMVRELFEMARTKK-ACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDP  313 (435)
T ss_pred             -CceEEeehhHHHHHHHhhhhHHHHHHHHHHhcccc-eEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCC
Confidence             66699999999999999999999999999998765 4999999999999887543   233456777788899999999


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      .+++-|+++||+|+.|||+|++  |+|+.++|.+|+++.|..|++.|++.+..+   -++-++..+..-++++|+.+|.+
T Consensus       314 rgnikvlmatnrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgaeirsvcte  393 (435)
T KOG0729|consen  314 RGNIKVLMATNRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAEIRSVCTE  393 (435)
T ss_pred             CCCeEEEeecCCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchHHHHHHHH
Confidence            9999999999999999999999  999999999999999999999999887643   56778899999999999999999


Q ss_pred             HHHHHHH
Q 047219          504 AERSWAS  510 (567)
Q Consensus       504 a~~~a~~  510 (567)
                      |-|-+.+
T Consensus       394 agmfair  400 (435)
T KOG0729|consen  394 AGMFAIR  400 (435)
T ss_pred             hhHHHHH
Confidence            9886654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=5.9e-32  Score=310.68  Aligned_cols=269  Identities=32%  Similarity=0.538  Sum_probs=226.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++.+++.|++.+.++++++++|++++        ..+++++|||||||||||++|+++|+++      
T Consensus       446 ~~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g--------~~~~~giLL~GppGtGKT~lakalA~e~------  511 (733)
T TIGR01243       446 EVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMG--------IRPPKGVLLFGPPGTGKTLLAKAVATES------  511 (733)
T ss_pred             cccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcC--------CCCCceEEEECCCCCCHHHHHHHHHHhc------
Confidence            35678999999999999999999999999999999886        7889999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh-hHHHHHHHHHHHHHhhcCcccCCc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE-MHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~-l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      +.+|+.+.++++.++|+|++++.++.+|..|+..++ +||||||||.|.+.++.. .....++++++|+..|+++....+
T Consensus       512 ~~~fi~v~~~~l~~~~vGese~~i~~~f~~A~~~~p-~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~~~~  590 (733)
T TIGR01243       512 GANFIAVRGPEILSKWVGESEKAIREIFRKARQAAP-AIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQELSN  590 (733)
T ss_pred             CCCEEEEehHHHhhcccCcHHHHHHHHHHHHHhcCC-EEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccCCCC
Confidence            788999999999999999999999999999998874 999999999999877643 234567899999999999888889


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      ++||+|||+++.+|+++++  ||+..+++++|+.++|.+|++.+.++++   ..+++.++..+.||+++||..+|++|..
T Consensus       591 v~vI~aTn~~~~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~~~A~~  670 (733)
T TIGR01243       591 VVVIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAM  670 (733)
T ss_pred             EEEEEeCCChhhCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            9999999999999999998  9999999999999999999999888754   3368999999999999999999999999


Q ss_pred             HHHHHHHhcccc----cc---CcccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhHHh
Q 047219          507 SWASKIIRGQIT----KD---GEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINN  556 (567)
Q Consensus       507 ~a~~r~i~~~i~----~~---~~~~~~~~l~e~le~~e~~~~~li~~al~~~~~~~s  556 (567)
                      .+.++.+.....    ..   ..........++.+++...+.++....+.+|.....
T Consensus       671 ~a~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~f~~al~~~~ps~~~~~~~~~~~~~~  727 (733)
T TIGR01243       671 AALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEALKKVKPSVSKEDMLRYERLAK  727 (733)
T ss_pred             HHHHHHhhhccchhhhcccccccccCcccHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence            888876542110    00   001112344566666666666665655555554433

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=7.9e-32  Score=297.04  Aligned_cols=226  Identities=37%  Similarity=0.591  Sum_probs=209.8

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++++|++.+++.+++.+..+++++++|..++        ..+++++|||||||||||++|+++|+++      
T Consensus       235 ~~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~--------~~~~~giLl~GpPGtGKT~lAkava~~~------  300 (494)
T COG0464         235 EDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLG--------LRPPKGVLLYGPPGTGKTLLAKAVALES------  300 (494)
T ss_pred             CCCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcC--------CCCCCeeEEECCCCCCHHHHHHHHHhhC------
Confidence            56789999999999999999999999999999998754        6888999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +.+|+.+..+++.++|+|+++++++.+|..|+..+| |||||||+|.+...+.........+++++++.++++.....+|
T Consensus       301 ~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~~~~p-~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~~~~v  379 (494)
T COG0464         301 RSRFISVKGSELLSKWVGESEKNIRELFEKARKLAP-SIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEKAEGV  379 (494)
T ss_pred             CCeEEEeeCHHHhccccchHHHHHHHHHHHHHcCCC-cEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCccCce
Confidence            788999999999999999999999999999998875 9999999999999988766666689999999999999999999


Q ss_pred             EEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhh-----CHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          433 VVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHL-----TKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~-----~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      +||+|||+++.+|+++++  ||+..++|++|+..+|.+|++.++...     ...++..+++.+.||+++||..+|++|.
T Consensus       380 ~vi~aTN~p~~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~  459 (494)
T COG0464         380 LVIAATNRPDDLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAA  459 (494)
T ss_pred             EEEecCCCccccCHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHH
Confidence            999999999999999999  999999999999999999999999842     2457899999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          506 RSWASKII  513 (567)
Q Consensus       506 ~~a~~r~i  513 (567)
                      +.+.+...
T Consensus       460 ~~~~~~~~  467 (494)
T COG0464         460 LEALREAR  467 (494)
T ss_pred             HHHHHHhc
Confidence            88877764

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.98  E-value=2.1e-31  Score=284.73  Aligned_cols=224  Identities=36%  Similarity=0.638  Sum_probs=200.7

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|.++|++|+|++++++++++.+..++.+|++|+.+|        ..+|+++||+||||||||++|+++|+++      
T Consensus       124 ~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g--------~~~p~gvLL~GppGtGKT~lAkaia~~~------  189 (389)
T PRK03992        124 ESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVG--------IEPPKGVLLYGPPGTGKTLLAKAVAHET------  189 (389)
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcC--------CCCCCceEEECCCCCChHHHHHHHHHHh------
Confidence            55789999999999999999999999999999999886        7899999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhh---HHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l---~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+|+.++++.+..+|.|+.+..++.+|..+....+ +||||||||.+...+.+..   ....++.+..++..++++...
T Consensus       190 ~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~p-~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~~  268 (389)
T PRK03992        190 NATFIRVVGSELVQKFIGEGARLVRELFELAREKAP-SIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDPR  268 (389)
T ss_pred             CCCEEEeehHHHhHhhccchHHHHHHHHHHHHhcCC-eEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCCC
Confidence            677999999999999999999999999999988764 9999999999987654322   234466778888888888777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||+|||+++.++++|++  ||+..|+|+.|+.++|.+|++.++..+.   ..++..++..+.||+++||+.+|++|
T Consensus       269 ~~v~VI~aTn~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA  348 (389)
T PRK03992        269 GNVKIIAATNRIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEA  348 (389)
T ss_pred             CCEEEEEecCChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            899999999999999999997  9999999999999999999999988753   24689999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      .+.+.++
T Consensus       349 ~~~a~~~  355 (389)
T PRK03992        349 GMFAIRD  355 (389)
T ss_pred             HHHHHHc
Confidence            9877664

>KOG0730 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=3.3e-31  Score=286.40  Aligned_cols=360  Identities=27%  Similarity=0.425  Sum_probs=267.5

Q ss_pred             HHHHHHhCCCCCCccceEEEEecceE---EEEEEecCCCC-cchHHHHHHHhhCceecccCCCceeEEEee-ccccccee
Q 047219          117 EELLKRKGMHYGSCPTFTVAVKGQKV---TIKFQVPPACE-IPQLIANLVSHLGLKVEEHGGGSDMGLRAW-DSAVAWQL  191 (567)
Q Consensus       117 ~~~~~~~g~~~g~~~~~~v~~~g~~~---~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~-~~~~a~~v  191 (567)
                      +..|.++|+..|      |.+.|++.   ..+++|+.+|+ .+++....|.|+-+..++     .+.+.+. .++.+.++
T Consensus        34 ~~~~~~~~l~~g------~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~r~~l~~~~~~-----~~~~~~~p~v~~~~~i  102 (693)
T KOG0730|consen   34 EGAMDKLGLLRG------VLLDGKKRREPVDAVVQDETSELIGRQTMVSRSNLRLQLGR-----LLHSSDCPSVKRPARI  102 (693)
T ss_pred             HHHHhhhcCCcc------eEEECccccCCccceeccCCccccchhhheeccchhhcccc-----eecccCCCCcccccee
Confidence            678999999999      44888762   44566655454 466667777777777666     5666652 34455567


Q ss_pred             EecCCCCccc-cCCCccccCcccccccchheeeeceeecCCCCceeeeccCcCCHHHHHHHHHHHhhhcc-cccccCccc
Q 047219          192 TLKPPEKQNE-SGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGR-RIYGLDEPQ  269 (567)
Q Consensus       192 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~  269 (567)
                      .+.|...+.. +..     ..+............+|+..++.. .... .-.+...+....- ....... .....+...
T Consensus       103 ~~l~~~~~~~~i~~-----~~~d~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~~~~~~~~~~-~v~~~t~~~~~~~~~~~  174 (693)
T KOG0730|consen  103 AVLPVDDTSEGIAG-----ELFDVLERPFLLEALRPLVKGDTF-AGLN-PAEFKVLELDPSP-QVTPDTELSYLGEPAKR  174 (693)
T ss_pred             eeeehhhccccchh-----hhhhhhhhhhhhhhhCccccccch-hhhh-hhhhhccccccch-hcCccchhhhcCCCccc
Confidence            7777544321 111     111111222233344555444443 0000 0000000000000 0000000 011111111


Q ss_pred             cccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       270 ~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      .....+.++ .+++|...++..+++++.+++.+|.+|..++        .++|+++|+|||||||||.+++++|++.   
T Consensus       175 ~~~~~~~~~-~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g--------~~~prg~Ll~gppg~Gkt~l~~aVa~e~---  242 (693)
T KOG0730|consen  175 EEEELPEVG-DDIGGLKRQLSVIRELVELPLRHPALFKSIG--------IKPPRGLLLYGPPGTGKTFLVRAVANEY---  242 (693)
T ss_pred             ccccccccc-cccchhHHHHHHHHHHHHhhhcchhhhhhcC--------CCCCCCccccCCCCCChHHHHHHHHHHh---
Confidence            111136677 8999999999999999999999999999886        8999999999999999999999999999   


Q ss_pred             CCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          350 PWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       350 ~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                         +..++.++++++++++.|++++.++..|+++.....+++|||||+|.+.+++..... +..++..+++.++++....
T Consensus       243 ---~a~~~~i~~peli~k~~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~~-~e~Rv~sqlltL~dg~~~~  318 (693)
T KOG0730|consen  243 ---GAFLFLINGPELISKFPGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGADD-VESRVVSQLLTLLDGLKPD  318 (693)
T ss_pred             ---CceeEecccHHHHHhcccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccch-HHHHHHHHHHHHHhhCcCc
Confidence               778999999999999999999999999999999885699999999999998876655 7889999999999999888


Q ss_pred             CcEEEEEeeCCCCCCChHHHh-ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS-RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s-Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .+++||++||+++.|+++++| |||+.+.+..|+..+|.+|++.+++.+.   ..++..++..++||+|+||..+|.+|.
T Consensus       319 ~~vivl~atnrp~sld~alRRgRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~ea~  398 (693)
T KOG0730|consen  319 AKVIVLAATNRPDSLDPALRRGRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCREAS  398 (693)
T ss_pred             CcEEEEEecCCccccChhhhcCCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHHHHH
Confidence            999999999999999999998 9999999999999999999999998754   458999999999999999999999999


Q ss_pred             HHHHHH
Q 047219          506 RSWASK  511 (567)
Q Consensus       506 ~~a~~r  511 (567)
                      +.+.++
T Consensus       399 ~~~~r~  404 (693)
T KOG0730|consen  399 LQATRR  404 (693)
T ss_pred             HHHhhh
Confidence            888877

>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=2.7e-31  Score=290.27  Aligned_cols=224  Identities=33%  Similarity=0.552  Sum_probs=205.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ....++|+|+.|.+++|+++.+.+ .+|++|+.|..+|        +.-|+++||+||||||||+||+++|.+.      
T Consensus       143 ~~~~v~F~DVAG~dEakeel~EiV-dfLk~p~ky~~lG--------akiPkGvlLvGpPGTGKTLLAkAvAgEA------  207 (596)
T COG0465         143 DQVKVTFADVAGVDEAKEELSELV-DFLKNPKKYQALG--------AKIPKGVLLVGPPGTGKTLLAKAVAGEA------  207 (596)
T ss_pred             cccCcChhhhcCcHHHHHHHHHHH-HHHhCchhhHhcc--------cccccceeEecCCCCCcHHHHHHHhccc------
Confidence            357799999999999999999977 6899999999987        7899999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      ++||+.++++++...++|-...++|.+|.+|++++| ||+||||||.+...+...   .++..+.+++++|..||++..+
T Consensus       208 ~VPFf~iSGS~FVemfVGvGAsRVRdLF~qAkk~aP-~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~~  286 (596)
T COG0465         208 GVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAP-CIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGGN  286 (596)
T ss_pred             CCCceeccchhhhhhhcCCCcHHHHHHHHHhhccCC-CeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCCC
Confidence            999999999999999999999999999999999996 999999999998887532   4455667999999999999988


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      ..|++|++||+++-+|++|+|  |||+.+.++.||...|.+|++.|+++..   ..++..+++.|.||+++|+.+++++|
T Consensus       287 ~gviviaaTNRpdVlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEA  366 (596)
T COG0465         287 EGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEA  366 (596)
T ss_pred             CceEEEecCCCcccchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhHHHH
Confidence            999999999999999999999  9999999999999999999999988743   23677799999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          505 ERSWASKI  512 (567)
Q Consensus       505 ~~~a~~r~  512 (567)
                      .-.++++-
T Consensus       367 al~aar~n  374 (596)
T COG0465         367 ALLAARRN  374 (596)
T ss_pred             HHHHHHhc
Confidence            97766653

>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional

Probab=99.97  E-value=8.9e-31  Score=281.45  Aligned_cols=224  Identities=36%  Similarity=0.606  Sum_probs=199.9

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|..+|+||+|++.+++++++.+..++.+|++|+.++        ..+++++||+||||||||++|+++|+++      
T Consensus       176 ~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~g--------i~~p~gVLL~GPPGTGKT~LAraIA~el------  241 (438)
T PTZ00361        176 KAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIG--------IKPPKGVILYGPPGTGKTLLAKAVANET------  241 (438)
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcC--------CCCCcEEEEECCCCCCHHHHHHHHHHhh------
Confidence            45779999999999999999999999999999999886        7899999999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      ..+|+.+.++++.++|.|+....++.+|..|.... ++||||||||.+..++...   .....++.+.+++..++++...
T Consensus       242 ~~~fi~V~~seL~~k~~Ge~~~~vr~lF~~A~~~~-P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~~  320 (438)
T PTZ00361        242 SATFLRVVGSELIQKYLGDGPKLVRELFRVAEENA-PSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDSR  320 (438)
T ss_pred             CCCEEEEecchhhhhhcchHHHHHHHHHHHHHhCC-CcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhccc
Confidence            66789999999999999999999999999998876 4999999999998766432   2234466777888889888777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .++.||+|||+++.+++++++  ||+..|+|+.|+.++|.+|++.++.++.   ..+++.++..+.||+++||+++|.+|
T Consensus       321 ~~V~VI~ATNr~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA  400 (438)
T PTZ00361        321 GDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEA  400 (438)
T ss_pred             CCeEEEEecCChHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHH
Confidence            899999999999999999987  9999999999999999999999987764   23688999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      .+.|.++
T Consensus       401 ~~~Alr~  407 (438)
T PTZ00361        401 GLLALRE  407 (438)
T ss_pred             HHHHHHh
Confidence            9887665

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.97  E-value=7.1e-30  Score=281.41  Aligned_cols=223  Identities=33%  Similarity=0.553  Sum_probs=198.7

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...+.++|+||+|++++++++++.+. ++++++.|.+++        ...|+++||+||||||||++|+++|+++     
T Consensus        47 ~~~~~~~~~di~g~~~~k~~l~~~~~-~l~~~~~~~~~g--------~~~~~giLL~GppGtGKT~la~alA~~~-----  112 (495)
T TIGR01241        47 EEKPKVTFKDVAGIDEAKEELMEIVD-FLKNPSKFTKLG--------AKIPKGVLLVGPPGTGKTLLAKAVAGEA-----  112 (495)
T ss_pred             CCCCCCCHHHhCCHHHHHHHHHHHHH-HHHCHHHHHhcC--------CCCCCcEEEECCCCCCHHHHHHHHHHHc-----
Confidence            34678999999999999999998776 489999998876        6788999999999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+++.++++++.+.+.|...+.++.+|+.+...+| +||||||||.+..+++..   ......+++++|+..++++..
T Consensus       113 -~~~~~~i~~~~~~~~~~g~~~~~l~~~f~~a~~~~p-~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~  190 (495)
T TIGR01241       113 -GVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAP-CIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGT  190 (495)
T ss_pred             -CCCeeeccHHHHHHHHhcccHHHHHHHHHHHHhcCC-CEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccC
Confidence             788999999999999999999999999999988774 999999999999877652   233456788999999999888


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+++||+|||+++.+|++|++  ||+..++++.|+.++|.+|++.++....   ..++..++..+.||+++||+.+|++
T Consensus       191 ~~~v~vI~aTn~~~~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~e  270 (495)
T TIGR01241       191 NTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNE  270 (495)
T ss_pred             CCCeEEEEecCChhhcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHH
Confidence            8899999999999999999998  9999999999999999999999987643   4478899999999999999999999


Q ss_pred             HHHHHHH
Q 047219          504 AERSWAS  510 (567)
Q Consensus       504 a~~~a~~  510 (567)
                      |...+.+
T Consensus       271 A~~~a~~  277 (495)
T TIGR01241       271 AALLAAR  277 (495)
T ss_pred             HHHHHHH
Confidence            8765543

HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.97  E-value=2.7e-29  Score=273.68  Aligned_cols=217  Identities=24%  Similarity=0.350  Sum_probs=185.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .+..+|++|+|++..|+.+.+....+   +..+...        +...|+++||+||||||||++|+++|+++      +
T Consensus       222 ~~~~~~~dvgGl~~lK~~l~~~~~~~---~~~~~~~--------gl~~pkGILL~GPpGTGKTllAkaiA~e~------~  284 (489)
T CHL00195        222 SVNEKISDIGGLDNLKDWLKKRSTSF---SKQASNY--------GLPTPRGLLLVGIQGTGKSLTAKAIANDW------Q  284 (489)
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHh---hHHHHhc--------CCCCCceEEEECCCCCcHHHHHHHHHHHh------C
Confidence            45688999999999999998765432   2222222        36889999999999999999999999999      8


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh-hhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS-EMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~-~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      .+++.+++..+.++++|+++.+++.+|..|...+| |||||||||.+...++. .......+++..|+.+++.  ...++
T Consensus       285 ~~~~~l~~~~l~~~~vGese~~l~~~f~~A~~~~P-~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~--~~~~V  361 (489)
T CHL00195        285 LPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSP-CILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSE--KKSPV  361 (489)
T ss_pred             CCEEEEEhHHhcccccChHHHHHHHHHHHHHhcCC-cEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhc--CCCce
Confidence            89999999999999999999999999999988875 99999999998765432 2344567888999998884  35679


Q ss_pred             EEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC-----HHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          433 VVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT-----KAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~-----~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      +||+|||+++.+|+++++  |||..++++.|+.++|.+|++.++.+..     ..+++.++..+.||+++||+++|.+|.
T Consensus       362 ~vIaTTN~~~~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~  441 (489)
T CHL00195        362 FVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAM  441 (489)
T ss_pred             EEEEecCChhhCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHH
Confidence            999999999999999998  9999999999999999999999998752     447899999999999999999999988


Q ss_pred             HHHHH
Q 047219          506 RSWAS  510 (567)
Q Consensus       506 ~~a~~  510 (567)
                      ..+..
T Consensus       442 ~~A~~  446 (489)
T CHL00195        442 YIAFY  446 (489)
T ss_pred             HHHHH
Confidence            66543

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.96  E-value=6.2e-29  Score=263.92  Aligned_cols=224  Identities=38%  Similarity=0.643  Sum_probs=197.4

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++++++.+..++.+|++|+.+|        ..+|+++||+||||||||++|+++|+++      
T Consensus       115 ~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g--------~~~p~gvLL~GppGtGKT~lakaia~~l------  180 (364)
T TIGR01242       115 ERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVG--------IEPPKGVLLYGPPGTGKTLLAKAVAHET------  180 (364)
T ss_pred             cCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcC--------CCCCceEEEECCCCCCHHHHHHHHHHhC------
Confidence            45789999999999999999999999999999999886        7889999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+.+..+..+++|+....++.+|..+.... ++||||||+|.+...+...   .....++.+..++..++++...
T Consensus       181 ~~~~~~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~-p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~~  259 (364)
T TIGR01242       181 NATFIRVVGSELVRKYIGEGARLVREIFELAKEKA-PSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDPR  259 (364)
T ss_pred             CCCEEecchHHHHHHhhhHHHHHHHHHHHHHHhcC-CcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCCC
Confidence            66788889999999999999999999999988776 4999999999997665432   1233456677888888887767


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .++.||+|||+++.+++++++  ||+..++|+.|+.++|.+|++.++..+..   .++..++..+.||+++||+.+|.+|
T Consensus       260 ~~v~vI~ttn~~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~~A  339 (364)
T TIGR01242       260 GNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEA  339 (364)
T ss_pred             CCEEEEEecCChhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            899999999999999999997  99999999999999999999998876532   3688999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      .+.+.++
T Consensus       340 ~~~a~~~  346 (364)
T TIGR01242       340 GMFAIRE  346 (364)
T ss_pred             HHHHHHh
Confidence            9887664

Many proteins may score above the trusted cutoff because an internal

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.96  E-value=5.6e-29  Score=271.04  Aligned_cols=227  Identities=29%  Similarity=0.466  Sum_probs=191.8

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-  350 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-  350 (567)
                      ...|.++|++|+|++.+++++++.+.+++.+|++|+.++        ..+|+++|||||||||||++|+++++++.... 
T Consensus       174 ~~~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~g--------l~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~  245 (512)
T TIGR03689       174 EEVPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYD--------LKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIG  245 (512)
T ss_pred             ecCCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhcc--------CCCCcceEEECCCCCcHHHHHHHHHHhhccccc
Confidence            456889999999999999999999999999999999886        78899999999999999999999999985431 


Q ss_pred             ---CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCC---CCcEEEEcCcchhhhhhhhh-hHHHHHHHHHHHHHhh
Q 047219          351 ---WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELP---NGAIIFLDEVDSFAVARDSE-MHEATRRILSVLLRQI  423 (567)
Q Consensus       351 ---~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a---~~~ILfIDEID~L~~~~q~~-l~~~~~~vl~~LL~~l  423 (567)
                         .....|+.+..+++.++|.|+++..++.+|+.+...+   .++||||||+|.+..++... ..+...+++++|+..+
T Consensus       246 ~~~~~~~~fl~v~~~eLl~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s~d~e~~il~~LL~~L  325 (512)
T TIGR03689       246 AETGDKSYFLNIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSEL  325 (512)
T ss_pred             cccCCceeEEeccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHh
Confidence               1123466777888999999999999999999887642   36999999999998776543 2344567889999999


Q ss_pred             cCcccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHh-hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          424 DGFEQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKH-LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       424 d~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~-~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                      +++....+++||+|||+++.||++|+|  ||+..|+|+.|+.++|.+|++.++.. ++.  ... .....|++++++..+
T Consensus       326 Dgl~~~~~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~l~l--~~~-l~~~~g~~~a~~~al  402 (512)
T TIGR03689       326 DGVESLDNVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDSLPL--DAD-LAEFDGDREATAAAL  402 (512)
T ss_pred             cccccCCceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhccCCc--hHH-HHHhcCCCHHHHHHH
Confidence            999887899999999999999999998  99999999999999999999998764 332  122 344689999999999


Q ss_pred             HHHHHHHHH
Q 047219          501 CQQAERSWA  509 (567)
Q Consensus       501 ~~~a~~~a~  509 (567)
                      |+++.....
T Consensus       403 ~~~av~~~~  411 (512)
T TIGR03689       403 IQRAVDHLY  411 (512)
T ss_pred             HHHHHHHHh
Confidence            999875443

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.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=2.3e-29  Score=285.76  Aligned_cols=232  Identities=33%  Similarity=0.538  Sum_probs=212.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ....+.|++|+|++..+..|+|++..||.+|+.|+.+.        ..+|++|||+||||||||++|+++|..+... ..
T Consensus       258 ~~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~--------itpPrgvL~~GppGTGkTl~araLa~~~s~~-~~  328 (1080)
T KOG0732|consen  258 VDSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFN--------ITPPRGVLFHGPPGTGKTLMARALAAACSRG-NR  328 (1080)
T ss_pred             hhcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcc--------cCCCcceeecCCCCCchhHHHHhhhhhhccc-cc
Confidence            45668999999999999999999999999999999876        8999999999999999999999999988543 12


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      .+.|+.-.+.+..++|+|+.+.+++.+|++|+...| .|+|+||||-|++.+..........++..||..|+++...+.|
T Consensus       329 kisffmrkgaD~lskwvgEaERqlrllFeeA~k~qP-SIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGldsRgqV  407 (1080)
T KOG0732|consen  329 KISFFMRKGADCLSKWVGEAERQLRLLFEEAQKTQP-SIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDSRGQV  407 (1080)
T ss_pred             ccchhhhcCchhhccccCcHHHHHHHHHHHHhccCc-eEEeccccccccccccchHHHhhhhHHHHHHHhccCCCCCCce
Confidence            556777788899999999999999999999999885 9999999999999998877777788999999999999999999


Q ss_pred             EEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhh----CHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          433 VVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHL----TKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~----~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +||+|||+++.++++|++  ||+++++|++|+.+.|.+|+..+.++.    ....+..+++.+.||.++||+.+|.+|..
T Consensus       408 vvigATnRpda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLCTeAal  487 (1080)
T KOG0732|consen  408 VVIGATNRPDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALCTEAAL  487 (1080)
T ss_pred             EEEcccCCccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHHHHHhh
Confidence            999999999999999998  999999999999999999999998874    45688999999999999999999999998


Q ss_pred             HHHHHHHh
Q 047219          507 SWASKIIR  514 (567)
Q Consensus       507 ~a~~r~i~  514 (567)
                      .+.++-.+
T Consensus       488 ~~~~r~~P  495 (1080)
T KOG0732|consen  488 IALRRSFP  495 (1080)
T ss_pred             hhhccccC
Confidence            87776543

>KOG0651 consensus 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=5.3e-30  Score=255.58  Aligned_cols=219  Identities=36%  Similarity=0.589  Sum_probs=199.8

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ...+++|++++|.-.++.++++.|+.++.+|++|.+++        ..+|++++||||||||||++|++++..+      
T Consensus       125 ~~~~~s~~~~ggl~~qirelre~ielpl~np~lf~rvg--------Ik~Pkg~ll~GppGtGKTlla~~Vaa~m------  190 (388)
T KOG0651|consen  125 DPRNISFENVGGLFYQIRELREVIELPLTNPELFLRVG--------IKPPKGLLLYGPPGTGKTLLARAVAATM------  190 (388)
T ss_pred             CccccCHHHhCChHHHHHHHHhheEeeccCchhccccC--------CCCCceeEEeCCCCCchhHHHHHHHHhc------
Confidence            34568999999999999999999999999999999876        8999999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +++|+.+..+.+.+++.|++.+.+++.|..|.+..+ ||||+||||.+.+.+...   ..+..++++-.|+..|+++...
T Consensus       191 g~nfl~v~ss~lv~kyiGEsaRlIRemf~yA~~~~p-ciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~l  269 (388)
T KOG0651|consen  191 GVNFLKVVSSALVDKYIGESARLIRDMFRYAREVIP-CIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDTL  269 (388)
T ss_pred             CCceEEeeHhhhhhhhcccHHHHHHHHHHHHhhhCc-eEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchhc
Confidence            899999999999999999999999999999999986 999999999998877432   3456778888999999999999


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      +.|-+|+|||+++.|+|+|++  |+++.+++++|+...|.+|++.+.+.+.   .-+.+.+.+.++||.++|+++.|.++
T Consensus       270 ~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~gad~rn~~tEa  349 (388)
T KOG0651|consen  270 HRVKTIMATNRPDTLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNGADLRNVCTEA  349 (388)
T ss_pred             ccccEEEecCCccccchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhccChHHHhhhcccc
Confidence            999999999999999999999  9999999999999999999998876533   33578888899999999999999887


Q ss_pred             HH
Q 047219          505 ER  506 (567)
Q Consensus       505 ~~  506 (567)
                      =+
T Consensus       350 g~  351 (388)
T KOG0651|consen  350 GM  351 (388)
T ss_pred             cc
Confidence            64

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.96  E-value=3.3e-29  Score=264.22  Aligned_cols=260  Identities=32%  Similarity=0.525  Sum_probs=216.7

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+++.|+++.|++.+++.+.+.+.+|+.+|++|..+         ..+++++||.||||||||+|++|||.++      
T Consensus       146 ~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~gl---------r~p~rglLLfGPpgtGKtmL~~aiAsE~------  210 (428)
T KOG0740|consen  146 TLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGL---------REPVRGLLLFGPPGTGKTMLAKAIATES------  210 (428)
T ss_pred             cCCcccccCCcchhhHHHHhhhhhhhcccchHhhhcc---------ccccchhheecCCCCchHHHHHHHHhhh------
Confidence            4567999999999999999999999999999999877         5788999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc--cCC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE--QDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~--~~~  430 (567)
                      +..|+.++++.+.++|.|+.++.++.+|.-|+...| +|+||||||.+..++.+...+...+...+++-.+++..  ...
T Consensus       211 ~atff~iSassLtsK~~Ge~eK~vralf~vAr~~qP-svifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s~~~d  289 (428)
T KOG0740|consen  211 GATFFNISASSLTSKYVGESEKLVRALFKVARSLQP-SVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNSAPDD  289 (428)
T ss_pred             cceEeeccHHHhhhhccChHHHHHHHHHHHHHhcCC-eEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccCCCCC
Confidence            778999999999999999999999999999998875 99999999999999988888888888888888877764  345


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +|+||+|||.|+.+|+++++||...++|+.|+.+.|..+++.++..    +...++..+++.+.||++.||.++|.+|.+
T Consensus       290 rvlvigaTN~P~e~Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~kea~~  369 (428)
T KOG0740|consen  290 RVLVIGATNRPWELDEAARRRFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKEAAM  369 (428)
T ss_pred             eEEEEecCCCchHHHHHHHHHhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHHhhc
Confidence            8999999999999999999999999999999999999999999875    456689999999999999999999999996


Q ss_pred             HHHHHHHhc-ccc-ccCcccCCCcHHHHHHHHHHHHHHHHHHHH
Q 047219          507 SWASKIIRG-QIT-KDGEQACLPPLQEYIESATNRRRSLLDAAE  548 (567)
Q Consensus       507 ~a~~r~i~~-~i~-~~~~~~~~~~l~e~le~~e~~~~~li~~al  548 (567)
                      .-.+..... .+. ..........+.++-.+++..+......-+
T Consensus       370 ~p~r~~~~~~~~~~~~~~~~r~i~~~df~~a~~~i~~~~s~~~l  413 (428)
T KOG0740|consen  370 GPLRELGGTTDLEFIDADKIRPITYPDFKNAFKNIKPSVSLEGL  413 (428)
T ss_pred             CchhhcccchhhhhcchhccCCCCcchHHHHHHhhccccCcccc
Confidence            443332221 111 111122223444555555554454444433

>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]

Probab=99.96  E-value=3.6e-29  Score=267.04  Aligned_cols=306  Identities=19%  Similarity=0.226  Sum_probs=242.2

Q ss_pred             eeeeceeecCCCCceeeeccCcCCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhc
Q 047219          221 ILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSL  300 (567)
Q Consensus       221 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l  300 (567)
                      +...-|+...+.+...+.  -.....++..+...+........         ....++|++|+|.+.++.++.+.+... 
T Consensus       197 i~~~~pv~~~g~l~G~v~--~~~~~~~l~~l~~~~~~~~~~~~---------~~a~y~f~~Iig~S~~m~~~~~~akr~-  264 (560)
T COG3829         197 IVNVAPVYADGQLIGVVG--ISKDVSELERLTRELEESEGLLR---------LKAKYTFDDIIGESPAMLRVLELAKRI-  264 (560)
T ss_pred             eEeeccEecCCcEEEEEE--eecchHHHHHHHHHHHHHhhhhc---------cccccchhhhccCCHHHHHHHHHHHhh-
Confidence            445556666654433332  11122445555555544322221         446689999999999999999988765 


Q ss_pred             cChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcCeEEechhhHHhhhhchhHHHHHH
Q 047219          301 QSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVPLMYVPLEVVMSKYYGESERLLGK  378 (567)
Q Consensus       301 ~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~~~~i~~~~l~s~~~G~~~~~l~~  378 (567)
                                        +..+.+|||.|++||||.++|++||+.+++.  ||+.+||..++...+.|.+||+...    
T Consensus       265 ------------------A~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaAiPe~LlESELFGye~G----  322 (560)
T COG3829         265 ------------------AKTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAAIPETLLESELFGYEKG----  322 (560)
T ss_pred             ------------------cCCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEecccCCHHHHHHHHhCcCCc----
Confidence                              7889999999999999999999999999875  8889999999999999999998665    


Q ss_pred             HHHHHhc--------CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-------CCC
Q 047219          379 VFSLANE--------LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-------KQD  443 (567)
Q Consensus       379 ~f~~A~~--------~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-------~~~  443 (567)
                      .|+.|..        .+++|+||||||..|+...|.++++++++  .++.+.......+.+|+||+|||+       .+.
T Consensus       323 AFTGA~~~GK~GlfE~A~gGTLFLDEIgempl~LQaKLLRVLQE--kei~rvG~t~~~~vDVRIIAATN~nL~~~i~~G~  400 (560)
T COG3829         323 AFTGASKGGKPGLFELANGGTLFLDEIGEMPLPLQAKLLRVLQE--KEIERVGGTKPIPVDVRIIAATNRNLEKMIAEGT  400 (560)
T ss_pred             cccccccCCCCcceeeccCCeEEehhhccCCHHHHHHHHHHHhh--ceEEecCCCCceeeEEEEEeccCcCHHHHHhcCc
Confidence            3444432        35589999999999999999999999988  777777777777889999999998       568


Q ss_pred             CChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHHH-------HHHHHHHHh--
Q 047219          444 LDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAE-------RSWASKIIR--  514 (567)
Q Consensus       444 Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a~-------~~a~~r~i~--  514 (567)
                      |+.+|++|+ +++.+.+|++++|.+++..++.+|......++.....++++..+..|.++.|       .+..+|.+.  
T Consensus       401 FReDLYYRL-NV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L~~y~WPGNVRELeNviER~v~~~  479 (560)
T COG3829         401 FREDLYYRL-NVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALLLRYDWPGNVRELENVIERAVNLV  479 (560)
T ss_pred             chhhheeee-ceeeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHhCCCCchHHHHHHHHHHHHhcc
Confidence            999999999 9999999999999999999999999888888989999999999999999999       566666653  


Q ss_pred             c---ccccc--------C------c--ccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          515 G---QITKD--------G------E--QACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       515 ~---~i~~~--------~------~--~~~~~~l~e~le~~e~~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                      +   .++..        .      .  .....++.+.++..|   +.+|..++++|++.++++++.+++|.
T Consensus       480 ~~~~~I~~~~lp~~~l~~k~~~~~~~~~~~~~~l~~~~e~~E---k~~I~~aL~~~~gn~~~aAk~LgIsr  547 (560)
T COG3829         480 ESDGLIDADDLPAFALEEKEPRPETTKQIEVGSLKEALEEYE---KHLIREALERHGGNKSKAAKELGISR  547 (560)
T ss_pred             CCcceeehhhcchhhhcccccCcCcccCcccccHHHHHHHHH---HHHHHHHHHHhCCCHHHHHHHhCCCH
Confidence            0   01100        0      0  112235777777777   99999999999999999999999985

>CHL00176 ftsH cell division protein; Validated

Probab=99.96  E-value=3.6e-28  Score=272.45  Aligned_cols=223  Identities=34%  Similarity=0.552  Sum_probs=196.0

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ....++|+||+|.+++++++.+.+ .++++++.|+.++        ...++++||+||||||||++|+++|+++      
T Consensus       176 ~~~~~~f~dv~G~~~~k~~l~eiv-~~lk~~~~~~~~g--------~~~p~gVLL~GPpGTGKT~LAralA~e~------  240 (638)
T CHL00176        176 ADTGITFRDIAGIEEAKEEFEEVV-SFLKKPERFTAVG--------AKIPKGVLLVGPPGTGKTLLAKAIAGEA------  240 (638)
T ss_pred             cCCCCCHHhccChHHHHHHHHHHH-HHHhCHHHHhhcc--------CCCCceEEEECCCCCCHHHHHHHHHHHh------
Confidence            345689999999999999999876 4589999998876        7789999999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh---hhHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS---EMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~---~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.++++++++++...+.|.....++.+|..+...+| +||||||||.+...+..   ......+.++++|+..++++..+
T Consensus       241 ~~p~i~is~s~f~~~~~g~~~~~vr~lF~~A~~~~P-~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~  319 (638)
T CHL00176        241 EVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSP-CIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGN  319 (638)
T ss_pred             CCCeeeccHHHHHHHhhhhhHHHHHHHHHHHhcCCC-cEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCC
Confidence            789999999999998989888889999999988775 99999999999866542   22344567889999999998888


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhh---CHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHL---TKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~---~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||++||+++.+|++|++  ||++.+.++.|+.++|.+|++.+++..   ...++..++..+.||+++||+.++++|
T Consensus       320 ~~ViVIaaTN~~~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneA  399 (638)
T CHL00176        320 KGVIVIAATNRVDILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEA  399 (638)
T ss_pred             CCeeEEEecCchHhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            899999999999999999998  999999999999999999999998763   344788999999999999999999998


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      ...++++
T Consensus       400 al~a~r~  406 (638)
T CHL00176        400 AILTARR  406 (638)
T ss_pred             HHHHHHh
Confidence            7665543

>PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional

Probab=99.95  E-value=1.4e-26  Score=239.10  Aligned_cols=220  Identities=17%  Similarity=0.261  Sum_probs=173.1

Q ss_pred             CCCCcccc-cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          275 SEISWENI-AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       275 ~~~~~~dI-iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ...+|+++ +|+--...-+...+...          .++.....+..+|.+++||||||||||++|++||+++      +
T Consensus       110 ~~~~f~~~~g~~~~~p~f~dk~~~hi----------~kn~l~~~~ik~PlgllL~GPPGcGKTllAraiA~el------g  173 (413)
T PLN00020        110 RTRSFDNLVGGYYIAPAFMDKVAVHI----------AKNFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKM------G  173 (413)
T ss_pred             hhcchhhhcCccccCHHHHHHHHHHH----------HhhhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHc------C
Confidence            34677888 66655555554433221          1111112347899999999999999999999999999      8


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcC----CCCcEEEEcCcchhhhhhhhhhHHHHHHHH-HHHHHhhcCc--
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANEL----PNGAIIFLDEVDSFAVARDSEMHEATRRIL-SVLLRQIDGF--  426 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~----a~~~ILfIDEID~L~~~~q~~l~~~~~~vl-~~LL~~ld~~--  426 (567)
                      ++++.+++.++.++|+|++++.++.+|..|...    ..+|||||||||.+.+.+......+..+++ .+|+..+|+.  
T Consensus       174 ~~~i~vsa~eL~sk~vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~  253 (413)
T PLN00020        174 IEPIVMSAGELESENAGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTN  253 (413)
T ss_pred             CCeEEEEHHHhhcCcCCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCcc
Confidence            889999999999999999999999999999753    246999999999999988655455544554 7899988753  


Q ss_pred             ----------ccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHh--hCHHHHHHHHHhccC-
Q 047219          427 ----------EQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKH--LTKAELAELATATEE-  491 (567)
Q Consensus       427 ----------~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~--~~~~~l~~la~~t~g-  491 (567)
                                .....|.||+|||+++.|+++|+|  ||+..+  ..|+.++|.+|++.+++.  +...++.+++..+.| 
T Consensus       254 v~l~G~w~~~~~~~~V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~~~dv~~Lv~~f~gq  331 (413)
T PLN00020        254 VSLGGDWREKEEIPRVPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVSREDVVKLVDTFPGQ  331 (413)
T ss_pred             ccccccccccccCCCceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCCHHHHHHHHHcCCCC
Confidence                      345679999999999999999999  998865  589999999999999876  456788888888877 


Q ss_pred             ---CCHHHHHHHHHHHHHHHHHHH
Q 047219          492 ---MSGRDIRDVCQQAERSWASKI  512 (567)
Q Consensus       492 ---~s~~dL~~L~~~a~~~a~~r~  512 (567)
                         |.++--..+..++.+.+..+.
T Consensus       332 ~~Df~GAlrar~yd~~v~~~i~~~  355 (413)
T PLN00020        332 PLDFFGALRARVYDDEVRKWIAEV  355 (413)
T ss_pred             CchhhhHHHHHHHHHHHHHHHHHh
Confidence               566666677777776666655

>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]

Probab=99.94  E-value=8.6e-27  Score=249.29  Aligned_cols=265  Identities=20%  Similarity=0.247  Sum_probs=216.8

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCc
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGV  354 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~  354 (567)
                      ..+.+++|.+.+++++++.+...                   +....+|||+|++||||.++||+||+.+.+.  ||+.+
T Consensus       138 ~~~~~liG~S~am~~l~~~i~kv-------------------A~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVav  198 (464)
T COG2204         138 SLGGELVGESPAMQQLRRLIAKV-------------------APSDASVLITGESGTGKELVARAIHQASPRAKGPFIAV  198 (464)
T ss_pred             cccCCceecCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceee
Confidence            46789999999999999999876                   7888999999999999999999999999864  88899


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHH---HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSL---ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~---A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ||..++.+.+.+++||+.+..+...-..   .-+.+++|+||||||..|+...|.++++++++  .++.+...+...+.+
T Consensus       199 NcaAip~~l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl~~Q~kLLRvLqe--~~~~rvG~~~~i~vd  276 (464)
T COG2204         199 NCAAIPENLLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPLELQVKLLRVLQE--REFERVGGNKPIKVD  276 (464)
T ss_pred             ecccCCHHHHHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCCHHHHHHHHHHHHc--CeeEecCCCccccee
Confidence            9999999999999999865422211100   01445689999999999999999999888876  566666666666789


Q ss_pred             EEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          432 VVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       432 viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      |+||++||.       .+.|.++|++|+ +++.+..|++++|.++|..++++|......++.....++++..+..|+.|.
T Consensus       277 vRiIaaT~~dL~~~v~~G~FReDLyyRL-nV~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y~  355 (464)
T COG2204         277 VRIIAATNRDLEEEVAAGRFREDLYYRL-NVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAYD  355 (464)
T ss_pred             eEEEeecCcCHHHHHHcCCcHHHHHhhh-ccceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhCC
Confidence            999999997       567999999999 999999999999999999999999998888888888899999999999999


Q ss_pred             H-------HHHHHHHHhccc----cccC----------------cccC-C--CcHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 047219          505 E-------RSWASKIIRGQI----TKDG----------------EQAC-L--PPLQEYIESATNRRRSLLDAAEQSHQNI  554 (567)
Q Consensus       505 ~-------~~a~~r~i~~~i----~~~~----------------~~~~-~--~~l~e~le~~e~~~~~li~~al~~~~~~  554 (567)
                      |       .++++|......    +.+.                .... .  .++.+.++.+|   +.+|..++..+++.
T Consensus       356 WPGNVREL~N~ver~~il~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~E---r~~I~~aL~~~~g~  432 (464)
T COG2204         356 WPGNVRELENVVERAVILSEGPEIEVEDLPLEILAPAAEALAGPAGEAALPGLPLGEALAEVE---RQLILQALERTGGN  432 (464)
T ss_pred             CChHHHHHHHHHHHHHhcCCccccchhhccccccccccccccccccccccccccHHHHHHHHH---HHHHHHHHHHhCCC
Confidence            9       677777654321    1100                0000 0  13566777777   99999999999999


Q ss_pred             HhhhhccCCCCC
Q 047219          555 NNHRTKKQPLDL  566 (567)
Q Consensus       555 ~s~~~~~~~l~~  566 (567)
                      ++++++.+++++
T Consensus       433 ~~~aA~~LGi~R  444 (464)
T COG2204         433 KSEAAERLGISR  444 (464)
T ss_pred             HHHHHHHHCCCH
Confidence            999999888875

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.94  E-value=8.1e-26  Score=255.55  Aligned_cols=221  Identities=32%  Similarity=0.553  Sum_probs=193.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      ...+|+++.|.+..++++.+.+.. +..++.|..++        ...++++||+||||||||++|+++++++      +.
T Consensus       147 ~~~~~~di~g~~~~~~~l~~i~~~-~~~~~~~~~~~--------~~~~~gill~G~~G~GKt~~~~~~a~~~------~~  211 (644)
T PRK10733        147 IKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLG--------GKIPKGVLMVGPPGTGKTLLAKAIAGEA------KV  211 (644)
T ss_pred             hhCcHHHHcCHHHHHHHHHHHHHH-hhCHHHHHhcC--------CCCCCcEEEECCCCCCHHHHHHHHHHHc------CC
Confidence            346799999999999999998764 67788786654        5778899999999999999999999999      78


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccCCc
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      +|+.++++++...+.|.....++.+|..+...+| +||||||||.+...+...   ......+++++++..|+++..+..
T Consensus       212 ~f~~is~~~~~~~~~g~~~~~~~~~f~~a~~~~P-~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~  290 (644)
T PRK10733        212 PFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAP-CIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEG  290 (644)
T ss_pred             CEEEEehHHhHHhhhcccHHHHHHHHHHHHhcCC-cEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCC
Confidence            8999999999999999999999999999987764 999999999998776542   223445688999999999988889


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      ++||+|||+++.+|+++++  ||++.+.|+.|+.++|.+|++.+++..+   ..++..++..+.||+++||.++|++|..
T Consensus       291 vivIaaTN~p~~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~  370 (644)
T PRK10733        291 IIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAAL  370 (644)
T ss_pred             eeEEEecCChhhcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            9999999999999999998  9999999999999999999999998753   3367789999999999999999999987


Q ss_pred             HHHHH
Q 047219          507 SWASK  511 (567)
Q Consensus       507 ~a~~r  511 (567)
                      .++++
T Consensus       371 ~a~r~  375 (644)
T PRK10733        371 FAARG  375 (644)
T ss_pred             HHHHc
Confidence            66643

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.93  E-value=6.6e-26  Score=238.74  Aligned_cols=230  Identities=30%  Similarity=0.463  Sum_probs=195.6

Q ss_pred             CCCCCccc--ccCcHHHHHHHHHHH-HHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          274 KSEISWEN--IAGYDQQKREIEDTI-LLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       274 ~~~~~~~d--IiG~~~~k~~L~e~i-~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      .|...|++  |+|++..-..+-+.. ..-.--|++.+++|        ..--+++|||||||||||++||.|.+.+++. 
T Consensus       213 ~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lG--------i~HVKGiLLyGPPGTGKTLiARqIGkMLNAr-  283 (744)
T KOG0741|consen  213 NPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLG--------IKHVKGILLYGPPGTGKTLIARQIGKMLNAR-  283 (744)
T ss_pred             CCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcC--------ccceeeEEEECCCCCChhHHHHHHHHHhcCC-
Confidence            46667776  579998877665433 22234468888876        7788999999999999999999999999754 


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC-------CCCcEEEEcCcchhhhhhhhh--hHHHHHHHHHHHHH
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-------PNGAIIFLDEVDSFAVARDSE--MHEATRRILSVLLR  421 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~-------a~~~ILfIDEID~L~~~~q~~--l~~~~~~vl~~LL~  421 (567)
                          .---++++++.++|+|+++.+++.+|..|.+.       ..-.||++||||.+...|.+.  ...+...++++||.
T Consensus       284 ----ePKIVNGPeIL~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLs  359 (744)
T KOG0741|consen  284 ----EPKIVNGPEILNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLS  359 (744)
T ss_pred             ----CCcccCcHHHHHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHH
Confidence                23457899999999999999999999988731       223699999999999988764  34577889999999


Q ss_pred             hhcCcccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC-------HHHHHHHHHhccCC
Q 047219          422 QIDGFEQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT-------KAELAELATATEEM  492 (567)
Q Consensus       422 ~ld~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~-------~~~l~~la~~t~g~  492 (567)
                      .||+.+.-.+++||+-||+.+.+|++|+|  ||...+++.+||...|.+|++.|+..|.       +.++++++..|..|
T Consensus       360 KmDGVeqLNNILVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNf  439 (744)
T KOG0741|consen  360 KMDGVEQLNNILVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNF  439 (744)
T ss_pred             hcccHHhhhcEEEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCC
Confidence            99999999999999999999999999999  9999999999999999999999998753       23789999999999


Q ss_pred             CHHHHHHHHHHHHHHHHHHHHhcc
Q 047219          493 SGRDIRDVCQQAERSWASKIIRGQ  516 (567)
Q Consensus       493 s~~dL~~L~~~a~~~a~~r~i~~~  516 (567)
                      ||++|+.+++.|...|..|.+...
T Consensus       440 SGAEleglVksA~S~A~nR~vk~~  463 (744)
T KOG0741|consen  440 SGAELEGLVKSAQSFAMNRHVKAG  463 (744)
T ss_pred             chhHHHHHHHHHHHHHHHhhhccC
Confidence            999999999999999999988643

>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]

Probab=99.93  E-value=7.4e-26  Score=238.82  Aligned_cols=266  Identities=23%  Similarity=0.292  Sum_probs=205.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQ  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~  352 (567)
                      +...+.+|||.+.++.++.+.|+..                   +....+|||.|++||||..+||+||+.+.+.  +|+
T Consensus       218 ~~~~~~~iIG~S~am~~ll~~i~~V-------------------A~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kPfV  278 (550)
T COG3604         218 VVLEVGGIIGRSPAMRQLLKEIEVV-------------------AKSDSTVLIRGETGTGKELVARAIHQLSPRRDKPFV  278 (550)
T ss_pred             hhcccccceecCHHHHHHHHHHHHH-------------------hcCCCeEEEecCCCccHHHHHHHHHhhCcccCCCce
Confidence            4678889999999999999999876                   7888999999999999999999999999865  899


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      .+||..++.+.+.|++||+....+...+..-+   +.+++|+||||||..|+...|.++++++|+  .++.+...+....
T Consensus       279 ~~NCAAlPesLlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL~lQaKLLRvLQe--gEieRvG~~r~ik  356 (550)
T COG3604         279 KLNCAALPESLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGELPLALQAKLLRVLQE--GEIERVGGDRTIK  356 (550)
T ss_pred             eeeccccchHHHHHHHhcccccccccchhccCcceeecCCCeEechhhccCCHHHHHHHHHHHhh--cceeecCCCceeE
Confidence            99999999999999999997664443332211   456789999999999999999999999888  6777777776677


Q ss_pred             CcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHH---------------HHHHHHH
Q 047219          430 KKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKA---------------ELAELAT  487 (567)
Q Consensus       430 ~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~---------------~l~~la~  487 (567)
                      .+|+||+|||+       .+.|..+|++|+ .++.+.+|++++|.+++..++.+|.++               .++.+..
T Consensus       357 VDVRiIAATNRDL~~~V~~G~FRaDLYyRL-sV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~  435 (550)
T COG3604         357 VDVRVIAATNRDLEEMVRDGEFRADLYYRL-SVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSS  435 (550)
T ss_pred             EEEEEEeccchhHHHHHHcCcchhhhhhcc-cccccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHc
Confidence            89999999998       668999999999 899999999999999999888765544               4555555


Q ss_pred             hccCCCHHHHHHHHHHHHHHHHHHHHh-ccc-c--c----------c------CcccCCC---cHHHHHHHHHHHHHHHH
Q 047219          488 ATEEMSGRDIRDVCQQAERSWASKIIR-GQI-T--K----------D------GEQACLP---PLQEYIESATNRRRSLL  544 (567)
Q Consensus       488 ~t~g~s~~dL~~L~~~a~~~a~~r~i~-~~i-~--~----------~------~~~~~~~---~l~e~le~~e~~~~~li  544 (567)
                      +.+.-+.++|++++..+...+ .+.+. +.+ .  .          .      ......+   .+.+..+.++   +..|
T Consensus       436 y~wPGNVRELen~veRavlla-~~~~~~~d~~~l~~~~~~~~~~~~~~~~p~~~~~~~~p~~~~l~~~~~~~e---R~~I  511 (550)
T COG3604         436 YEWPGNVRELENVVERAVLLA-GRLTRRGDLCTLELSLSALLWKTLPAPEPSALPEPALPGEHTLREATEEFE---RQLI  511 (550)
T ss_pred             CCCCCcHHHHHHHHHHHHHHh-cccCCCcceeehhhhhhccccccCCCCCccccCCccCCCcccchhhhHHHH---HHHH
Confidence            555556666666666655433 11111 110 0  0          0      0011112   3444455444   9999


Q ss_pred             HHHHHHHhhHHhhhhccCCCCC
Q 047219          545 DAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       545 ~~al~~~~~~~s~~~~~~~l~~  566 (567)
                      .+++++++++...+++.++++.
T Consensus       512 ~~aL~~~~~~~a~AAr~LGl~~  533 (550)
T COG3604         512 IAALEETNGNWAGAARRLGLTR  533 (550)
T ss_pred             HHHHHHhCCcHHHHHHHhCCCH
Confidence            9999999999998998877753

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.93  E-value=2e-25  Score=263.01  Aligned_cols=184  Identities=19%  Similarity=0.281  Sum_probs=152.4

Q ss_pred             ccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh--------------------------
Q 047219          315 CKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY--------------------------  368 (567)
Q Consensus       315 ~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~--------------------------  368 (567)
                      ..+|..+|+||||+||||||||+||+|+|.++      ++||+.++++++.+++                          
T Consensus      1623 lrLGl~pPKGILLiGPPGTGKTlLAKALA~es------~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~ 1696 (2281)
T CHL00206       1623 LRLALSPSRGILVIGSIGTGRSYLVKYLATNS------YVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRD 1696 (2281)
T ss_pred             HHcCCCCCCceEEECCCCCCHHHHHHHHHHhc------CCceEEEEHHHHhhcccccccccccccccccccccccccccc
Confidence            44568999999999999999999999999999      8999999999988654                          


Q ss_pred             ---------------hchhHH--HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---c
Q 047219          369 ---------------YGESER--LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---Q  428 (567)
Q Consensus       369 ---------------~G~~~~--~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---~  428 (567)
                                     .+..+.  .++.+|+.|+.++| |||||||||.+..+...      ...+++|+..|++..   .
T Consensus      1697 ~~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SP-CIIFIDEIDaL~~~ds~------~ltL~qLLneLDg~~~~~s 1769 (2281)
T CHL00206       1697 LDTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSP-CIIWIPNIHDLNVNESN------YLSLGLLVNSLSRDCERCS 1769 (2281)
T ss_pred             cchhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCC-eEEEEEchhhcCCCccc------eehHHHHHHHhccccccCC
Confidence                           112222  37889999999985 99999999999866211      123678888888753   3


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHH--Hhh--CH--HHHHHHHHhccCCCHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYA--KHL--TK--AELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~--~~~--~~--~~l~~la~~t~g~s~~dL~~L  500 (567)
                      ..+|+||||||+|+.|||||++  |||+.|.++.|+..+|.+++..+.  +++  ..  .+++.+|..|.||+|+||.++
T Consensus      1770 ~~~VIVIAATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanL 1849 (2281)
T CHL00206       1770 TRNILVIASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVAL 1849 (2281)
T ss_pred             CCCEEEEEeCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHH
Confidence            5689999999999999999999  999999999999999999988653  222  21  257899999999999999999


Q ss_pred             HHHHHHHHHHH
Q 047219          501 CQQAERSWASK  511 (567)
Q Consensus       501 ~~~a~~~a~~r  511 (567)
                      |++|...++.+
T Consensus      1850 vNEAaliAirq 1860 (2281)
T CHL00206       1850 TNEALSISITQ 1860 (2281)
T ss_pred             HHHHHHHHHHc
Confidence            99999766654

>CHL00181 cbbX CbbX; Provisional

Probab=99.88  E-value=3.9e-21  Score=197.54  Aligned_cols=223  Identities=22%  Similarity=0.305  Sum_probs=167.3

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCCcCeE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQGVPLM  357 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~~~~~  357 (567)
                      +++++|++++|++|++.+.+ +..+++++++|...     ..++.+++|+||||||||++|+++++.+.... ....+++
T Consensus        22 ~~~l~Gl~~vK~~i~e~~~~-~~~~~~~~~~g~~~-----~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~   95 (287)
T CHL00181         22 DEELVGLAPVKTRIREIAAL-LLIDRLRKNLGLTS-----SNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLL   95 (287)
T ss_pred             HHhcCCcHHHHHHHHHHHHH-HHHHHHHHHcCCCC-----CCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceE
Confidence            35799999999999998866 44566666655211     23456799999999999999999999874321 1234689


Q ss_pred             EechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEe
Q 047219          358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAA  437 (567)
Q Consensus       358 ~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaa  437 (567)
                      +++..++.+.++|++......+|+.+.    ++||||||+|.|......  .....+.+..|+..|+..  ..+++||++
T Consensus        96 ~v~~~~l~~~~~g~~~~~~~~~l~~a~----ggVLfIDE~~~l~~~~~~--~~~~~e~~~~L~~~me~~--~~~~~vI~a  167 (287)
T CHL00181         96 TVTRDDLVGQYIGHTAPKTKEVLKKAM----GGVLFIDEAYYLYKPDNE--RDYGSEAIEILLQVMENQ--RDDLVVIFA  167 (287)
T ss_pred             EecHHHHHHHHhccchHHHHHHHHHcc----CCEEEEEccchhccCCCc--cchHHHHHHHHHHHHhcC--CCCEEEEEe
Confidence            999999999999988877777877654    689999999998643221  123356677888888753  467888888


Q ss_pred             eCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh------ccCCC-HHHHHHHH
Q 047219          438 TNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATA------TEEMS-GRDIRDVC  501 (567)
Q Consensus       438 TN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~------t~g~s-~~dL~~L~  501 (567)
                      ++...     .++|+|++||+..++|+.++.+++.+|+..++..    +..+....+...      ...+. ++++++++
T Consensus       168 g~~~~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~v  247 (287)
T CHL00181        168 GYKDRMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPEAEKALLDYIKKRMEQPLFANARSVRNAL  247 (287)
T ss_pred             CCcHHHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHH
Confidence            86422     3579999999999999999999999999999875    333333333332      12334 89999999


Q ss_pred             HHHHHHHHHHHHhc
Q 047219          502 QQAERSWASKIIRG  515 (567)
Q Consensus       502 ~~a~~~a~~r~i~~  515 (567)
                      ..+....+.|+...
T Consensus       248 e~~~~~~~~r~~~~  261 (287)
T CHL00181        248 DRARMRQANRIFES  261 (287)
T ss_pred             HHHHHHHHHHHHcC
Confidence            99999999998764

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.87  E-value=6.6e-21  Score=195.75  Aligned_cols=222  Identities=20%  Similarity=0.297  Sum_probs=170.4

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-CCcCeEE
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-QGVPLMY  358 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~~~~~~~  358 (567)
                      ++++|++++|++|.+.+.+ +..++.+.+.|...     ..+..+++|+||||||||++|+++++.+....+ ...++++
T Consensus        22 ~~l~Gl~~vk~~i~e~~~~-~~~~~~r~~~g~~~-----~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~   95 (284)
T TIGR02880        22 RELIGLKPVKTRIREIAAL-LLVERLRQRLGLAS-----AAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVS   95 (284)
T ss_pred             HhccCHHHHHHHHHHHHHH-HHHHHHHHHhCCCc-----CCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEE
Confidence            3689999999999998876 66777777765321     234568999999999999999999998754321 1336899


Q ss_pred             echhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEee
Q 047219          359 VPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT  438 (567)
Q Consensus       359 i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaT  438 (567)
                      ++++++.+.++|++...+..+|+.+.    +++|||||++.|....+.  .....+.+..|+..|+.  ...+++||+++
T Consensus        96 v~~~~l~~~~~g~~~~~~~~~~~~a~----~gvL~iDEi~~L~~~~~~--~~~~~~~~~~Ll~~le~--~~~~~~vI~a~  167 (284)
T TIGR02880        96 VTRDDLVGQYIGHTAPKTKEILKRAM----GGVLFIDEAYYLYRPDNE--RDYGQEAIEILLQVMEN--QRDDLVVILAG  167 (284)
T ss_pred             ecHHHHhHhhcccchHHHHHHHHHcc----CcEEEEechhhhccCCCc--cchHHHHHHHHHHHHhc--CCCCEEEEEeC
Confidence            99999999999998888888888764    699999999998543222  12334566778888874  34678888888


Q ss_pred             CCC--C---CCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh----CHHHHHHHHHh-------ccCCCHHHHHHHHH
Q 047219          439 NRK--Q---DLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL----TKAELAELATA-------TEEMSGRDIRDVCQ  502 (567)
Q Consensus       439 N~~--~---~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~----~~~~l~~la~~-------t~g~s~~dL~~L~~  502 (567)
                      +..  +   .++|+|++||+..|+|+.++.+++.+|+..++++.    ..+....+..+       .+.-+.+++++++.
T Consensus       168 ~~~~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~~a~~~L~~~l~~~~~~~~~GN~R~lrn~ve  247 (284)
T TIGR02880       168 YKDRMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSAEAEEAFADYIALRRTQPHFANARSIRNAID  247 (284)
T ss_pred             CcHHHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHHHhccccCHHHHHHHHHHHHHhCCCCCCChHHHHHHHHH
Confidence            642  2   35899999999999999999999999999988763    34444444444       34457899999999


Q ss_pred             HHHHHHHHHHHhc
Q 047219          503 QAERSWASKIIRG  515 (567)
Q Consensus       503 ~a~~~a~~r~i~~  515 (567)
                      .+..+.+.|+...
T Consensus       248 ~~~~~~~~r~~~~  260 (284)
T TIGR02880       248 RARLRQANRLFCD  260 (284)
T ss_pred             HHHHHHHHHHhcC
Confidence            9999999988754

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.87  E-value=8.4e-22  Score=206.31  Aligned_cols=256  Identities=16%  Similarity=0.178  Sum_probs=174.8

Q ss_pred             ccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcCeEEe
Q 047219          282 IAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVPLMYV  359 (567)
Q Consensus       282 IiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~~~~i  359 (567)
                      |+|.+..++++.+.+...                   +....+|||+|++||||+++|++||..+.+.  +|+.++|..+
T Consensus         1 liG~S~~m~~~~~~~~~~-------------------a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~   61 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRL-------------------APLDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAAL   61 (329)
T ss_pred             CCcCCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCC
Confidence            579999999999988765                   5677899999999999999999999988653  3444444444


Q ss_pred             chhhHHhhhhchhHHHH-------HHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          360 PLEVVMSKYYGESERLL-------GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       360 ~~~~l~s~~~G~~~~~l-------~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +...+.+.+||.....+       ...|+    .+.+++||||||+.|+...|..+.++++.  ..+.........+.++
T Consensus        62 ~~~~l~~~lfG~~~g~~~ga~~~~~G~~~----~a~gGtL~Ldei~~L~~~~Q~~Ll~~l~~--~~~~~~g~~~~~~~~~  135 (329)
T TIGR02974        62 SENLLDSELFGHEAGAFTGAQKRHQGRFE----RADGGTLFLDELATASLLVQEKLLRVIEY--GEFERVGGSQTLQVDV  135 (329)
T ss_pred             ChHHHHHHHhccccccccCcccccCCchh----hCCCCEEEeCChHhCCHHHHHHHHHHHHc--CcEEecCCCceeccce
Confidence            44445556666532211       11233    33479999999999998776665554433  1111112222234689


Q ss_pred             EEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhc-cCCCHHHHHHHHHHH
Q 047219          433 VVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATAT-EEMSGRDIRDVCQQA  504 (567)
Q Consensus       433 iVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t-~g~s~~dL~~L~~~a  504 (567)
                      ++|++||.       .+.++++|++|| ..+.|.+|++++|.+++..++++|......++.... .++++..+..|+++.
T Consensus       136 RiI~at~~~l~~~~~~g~fr~dL~~rl-~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~y~  214 (329)
T TIGR02974       136 RLVCATNADLPALAAEGRFRADLLDRL-AFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEYH  214 (329)
T ss_pred             EEEEechhhHHHHhhcCchHHHHHHHh-cchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHhCC
Confidence            99999986       356899999999 678899999999999999998877665555554444 567888888888877


Q ss_pred             H-------HHHHHHHHhcc----ccc----------c-----C----c-----cc----------CC-CcHHHHHHHHHH
Q 047219          505 E-------RSWASKIIRGQ----ITK----------D-----G----E-----QA----------CL-PPLQEYIESATN  538 (567)
Q Consensus       505 ~-------~~a~~r~i~~~----i~~----------~-----~----~-----~~----------~~-~~l~e~le~~e~  538 (567)
                      |       .+.+++.+...    +..          .     .    .     ..          .. .++.+.++.+| 
T Consensus       215 WPGNvrEL~n~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~E-  293 (329)
T TIGR02974       215 WPGNVRELKNVVERSVYRHGLEEAPIDEIIIDPFASPWRPKQAAPAVDEVNSTPTDLPSPSSIAAAFPLDLKQAQQDYE-  293 (329)
T ss_pred             CCchHHHHHHHHHHHHHhCCCCccchhhccccccccccccccccccccccccccccccccccccccccccHHHHHHHHH-
Confidence            7       33344433210    000          0     0    0     00          00 13444555555 


Q ss_pred             HHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          539 RRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       539 ~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                        +.+|..++.+++++++++++.+++++
T Consensus       294 --~~~I~~aL~~~~gn~~~aA~~LGisr  319 (329)
T TIGR02974       294 --IELLQQALAEAQFNQRKAAELLGLTY  319 (329)
T ss_pred             --HHHHHHHHHHhCCCHHHHHHHhCCCH
Confidence              99999999999999999999999875

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.87  E-value=1.2e-20  Score=191.68  Aligned_cols=222  Identities=25%  Similarity=0.339  Sum_probs=163.3

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCCcCeE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQGVPLM  357 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~~~~~  357 (567)
                      +++++|++.+|+.|++.+.++... ......|..     ..+...+++|+||||||||++|+++|+.+.... ....+++
T Consensus         5 l~~~~Gl~~vk~~i~~~~~~~~~~-~~~~~~g~~-----~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v   78 (261)
T TIGR02881         5 LSRMVGLDEVKALIKEIYAWIQIN-EKRKEEGLK-----TSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLI   78 (261)
T ss_pred             HHHhcChHHHHHHHHHHHHHHHHH-HHHHHcCCC-----CCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceE
Confidence            578999999999999988765332 222222211     134457899999999999999999999874321 1244688


Q ss_pred             EechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEe
Q 047219          358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAA  437 (567)
Q Consensus       358 ~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaa  437 (567)
                      .++++++.++++|+....+..+|+.+.    ++||||||+|.|....+.   ....+.++.|+..++..  ..++++|++
T Consensus        79 ~~~~~~l~~~~~g~~~~~~~~~~~~a~----~~VL~IDE~~~L~~~~~~---~~~~~~i~~Ll~~~e~~--~~~~~vila  149 (261)
T TIGR02881        79 EVERADLVGEYIGHTAQKTREVIKKAL----GGVLFIDEAYSLARGGEK---DFGKEAIDTLVKGMEDN--RNEFVLILA  149 (261)
T ss_pred             EecHHHhhhhhccchHHHHHHHHHhcc----CCEEEEechhhhccCCcc---chHHHHHHHHHHHHhcc--CCCEEEEec
Confidence            999999999999999888888887764    689999999999743221   12345667788888753  456777777


Q ss_pred             eCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc---------cCCCHHHHHH
Q 047219          438 TNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT---------EEMSGRDIRD  499 (567)
Q Consensus       438 TN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t---------~g~s~~dL~~  499 (567)
                      ++..+     .++|+|++||+..++|+.++.+++.+|++.++..    +..+....+....         ..-+++.+++
T Consensus       150 ~~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n  229 (261)
T TIGR02881       150 GYSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRN  229 (261)
T ss_pred             CCcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHH
Confidence            65422     4789999999889999999999999999998874    3344444443221         1246789999


Q ss_pred             HHHHHHHHHHHHHHhc
Q 047219          500 VCQQAERSWASKIIRG  515 (567)
Q Consensus       500 L~~~a~~~a~~r~i~~  515 (567)
                      ++..|.++.+.|++..
T Consensus       230 ~~e~a~~~~~~r~~~~  245 (261)
T TIGR02881       230 IIEKAIRRQAVRLLDK  245 (261)
T ss_pred             HHHHHHHHHHHHHhcc
Confidence            9999999888887754

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=99.85  E-value=1.4e-20  Score=194.89  Aligned_cols=226  Identities=22%  Similarity=0.334  Sum_probs=165.0

Q ss_pred             CCCCCcccccCcHHHH---HHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          274 KSEISWENIAGYDQQK---REIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k---~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      ..+-++++++|++..+   .-|+++++                     .....+++|||||||||||+|+.||+..    
T Consensus        18 mRP~~lde~vGQ~HLlg~~~~lrr~v~---------------------~~~l~SmIl~GPPG~GKTTlA~liA~~~----   72 (436)
T COG2256          18 LRPKSLDEVVGQEHLLGEGKPLRRAVE---------------------AGHLHSMILWGPPGTGKTTLARLIAGTT----   72 (436)
T ss_pred             hCCCCHHHhcChHhhhCCCchHHHHHh---------------------cCCCceeEEECCCCCCHHHHHHHHHHhh----
Confidence            3457899999998875   34444443                     5677899999999999999999999999    


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~  427 (567)
                        +.+|..+++..-       ..+.++.+++.++..   ....||||||||.|...+|+.+           |..++   
T Consensus        73 --~~~f~~~sAv~~-------gvkdlr~i~e~a~~~~~~gr~tiLflDEIHRfnK~QQD~l-----------Lp~vE---  129 (436)
T COG2256          73 --NAAFEALSAVTS-------GVKDLREIIEEARKNRLLGRRTILFLDEIHRFNKAQQDAL-----------LPHVE---  129 (436)
T ss_pred             --CCceEEeccccc-------cHHHHHHHHHHHHHHHhcCCceEEEEehhhhcChhhhhhh-----------hhhhc---
Confidence              777888876432       236678888888543   2368999999999987766544           44443   


Q ss_pred             cCCcEEEEEee--CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----h-------CHHHHHHHHHhccCCCH
Q 047219          428 QDKKVVVIAAT--NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----L-------TKAELAELATATEEMSG  494 (567)
Q Consensus       428 ~~~~viVIaaT--N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~-------~~~~l~~la~~t~g~s~  494 (567)
                       ++.+++|+||  |+...++++|+||+ .++++...+.++...+++.-+..    +       .++..+.++..+.|   
T Consensus       130 -~G~iilIGATTENPsF~ln~ALlSR~-~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~G---  204 (436)
T COG2256         130 -NGTIILIGATTENPSFELNPALLSRA-RVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNG---  204 (436)
T ss_pred             -CCeEEEEeccCCCCCeeecHHHhhhh-heeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCc---
Confidence             5789999988  78889999999999 99999999999999999873321    2       24456666665554   


Q ss_pred             HHHHHHHHHHHHHHHHHHHhccccccCcccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhH-----HhhhhccCCC
Q 047219          495 RDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNI-----NNHRTKKQPL  564 (567)
Q Consensus       495 ~dL~~L~~~a~~~a~~r~i~~~i~~~~~~~~~~~l~e~le~~e~~~~~li~~al~~~~~~-----~s~~~~~~~l  564 (567)
                       |.+.+++...+.+..  ..     ..  . .-. .+.++...+++...+++-.+.||++     ||.|..+.+-
T Consensus       205 -D~R~aLN~LE~~~~~--~~-----~~--~-~~~-~~~l~~~l~~~~~~~Dk~gD~hYdliSA~hKSvRGSD~dA  267 (436)
T COG2256         205 -DARRALNLLELAALS--AE-----PD--E-VLI-LELLEEILQRRSARFDKDGDAHYDLISALHKSVRGSDPDA  267 (436)
T ss_pred             -hHHHHHHHHHHHHHh--cC-----CC--c-ccC-HHHHHHHHhhhhhccCCCcchHHHHHHHHHHhhccCCcCH
Confidence             777777766543321  10     10  0 111 3567777777777899999999996     7777776653

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.85  E-value=5.7e-21  Score=199.98  Aligned_cols=259  Identities=19%  Similarity=0.228  Sum_probs=171.9

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcCe
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVPL  356 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~~  356 (567)
                      +++++|.+..++.+.+.+...                   +..+.+|||+|++||||+++|++||..+.+.  +|+.++|
T Consensus         5 ~~~liG~S~~~~~~~~~i~~~-------------------a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c   65 (326)
T PRK11608          5 KDNLLGEANSFLEVLEQVSRL-------------------APLDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNC   65 (326)
T ss_pred             cCccEECCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeC
Confidence            578999999999999999866                   5667899999999999999999999988643  3444444


Q ss_pred             EEechhhHHhhhhchhHHHH-------HHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          357 MYVPLEVVMSKYYGESERLL-------GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       357 ~~i~~~~l~s~~~G~~~~~l-------~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      ..++...+.+.+||......       ...+    ..+.+++|||||||.|+...|..+...++.  ..+.........+
T Consensus        66 ~~~~~~~~~~~lfg~~~~~~~g~~~~~~g~l----~~a~gGtL~l~~i~~L~~~~Q~~L~~~l~~--~~~~~~g~~~~~~  139 (326)
T PRK11608         66 AALNENLLDSELFGHEAGAFTGAQKRHPGRF----ERADGGTLFLDELATAPMLVQEKLLRVIEY--GELERVGGSQPLQ  139 (326)
T ss_pred             CCCCHHHHHHHHccccccccCCcccccCCch----hccCCCeEEeCChhhCCHHHHHHHHHHHhc--CcEEeCCCCceee
Confidence            44433344555666432111       1122    233479999999999987765554443322  0111111111223


Q ss_pred             CcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHh-ccCCCHHHHHHHH
Q 047219          430 KKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATA-TEEMSGRDIRDVC  501 (567)
Q Consensus       430 ~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~-t~g~s~~dL~~L~  501 (567)
                      .++++|++|+.       .+.++++|++|| ..+.+.+|++++|.+++..+++++......++... ..++++..++.|.
T Consensus       140 ~~~RiI~~s~~~l~~l~~~g~f~~dL~~~l-~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~  218 (326)
T PRK11608        140 VNVRLVCATNADLPAMVAEGKFRADLLDRL-AFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLL  218 (326)
T ss_pred             ccEEEEEeCchhHHHHHHcCCchHHHHHhc-CCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHH
Confidence            47999999976       357999999999 67889999999999999998887755544444333 2467777777777


Q ss_pred             HHHH-------HHHHHHHHh---c-cccccC-----------c---c-c---CCC----cHHHHHHHHHHHHHHHHHHHH
Q 047219          502 QQAE-------RSWASKIIR---G-QITKDG-----------E---Q-A---CLP----PLQEYIESATNRRRSLLDAAE  548 (567)
Q Consensus       502 ~~a~-------~~a~~r~i~---~-~i~~~~-----------~---~-~---~~~----~l~e~le~~e~~~~~li~~al  548 (567)
                      ++.|       ++.+++.+.   + .+....           .   . .   ...    ++.+.++.+|   +.+|..++
T Consensus       219 ~y~WPGNvrEL~~vl~~a~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~E---r~~I~~aL  295 (326)
T PRK11608        219 NYRWPGNIRELKNVVERSVYRHGTSEYPLDNIIIDPFKRRPAEEAIAVSETTSLPTLPLDLREWQHQQE---KELLQRSL  295 (326)
T ss_pred             hCCCCcHHHHHHHHHHHHHHhcCCCCCchhhcccccccccccccccccccccccccccccHHHHHHHHH---HHHHHHHH
Confidence            7777       334444332   1 010000           0   0 0   001    2444445555   99999999


Q ss_pred             HHHhhHHhhhhccCCCCC
Q 047219          549 QSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       549 ~~~~~~~s~~~~~~~l~~  566 (567)
                      ..++++++++++.+++|+
T Consensus       296 ~~~~gn~~~aA~~LGIsR  313 (326)
T PRK11608        296 QQAKFNQKRAAELLGLTY  313 (326)
T ss_pred             HHhCCCHHHHHHHhCCCH
Confidence            999999999999999885

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.84  E-value=8.5e-21  Score=210.23  Aligned_cols=262  Identities=17%  Similarity=0.217  Sum_probs=173.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQ  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~  352 (567)
                      ...+|++++|.+..++++.+.+...                   +....+|||+|++||||+++|+++|..+.+.  +|+
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~-------------------A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv  259 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKL-------------------AMLDAPLLITGDTGTGKDLLAYACHLRSPRGKKPFL  259 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeE
Confidence            4578999999999999999888754                   5567889999999999999999999988654  444


Q ss_pred             CcCeEEechhhHHhhhhchhHHH-------HHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERL-------LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG  425 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~-------l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~  425 (567)
                      .++|..++...+.+.+||+....       ...+|+.    +.+++||||||+.|+...|..+..+.++  ..+....+.
T Consensus       260 ~inca~~~~~~~e~elFG~~~~~~~~~~~~~~g~~e~----a~~GtL~LdeI~~L~~~~Q~~Ll~~l~~--~~~~~~g~~  333 (520)
T PRK10820        260 ALNCASIPDDVVESELFGHAPGAYPNALEGKKGFFEQ----ANGGSVLLDEIGEMSPRMQAKLLRFLND--GTFRRVGED  333 (520)
T ss_pred             EeccccCCHHHHHHHhcCCCCCCcCCcccCCCChhhh----cCCCEEEEeChhhCCHHHHHHHHHHHhc--CCcccCCCC
Confidence            55555555445556667653211       1123433    3379999999999998877665554432  112222222


Q ss_pred             cccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHH
Q 047219          426 FEQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIR  498 (567)
Q Consensus       426 ~~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~  498 (567)
                      .....+++||++|+.       .+.++++|++|+ ..+.+.+|++++|.+++..+++++......++.....++++..+.
T Consensus       334 ~~~~~~vRiI~st~~~l~~l~~~g~f~~dL~~rL-~~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls~~a~~  412 (520)
T PRK10820        334 HEVHVDVRVICATQKNLVELVQKGEFREDLYYRL-NVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNT  412 (520)
T ss_pred             cceeeeeEEEEecCCCHHHHHHcCCccHHHHhhc-CeeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHH
Confidence            223467899999976       346899999999 679999999999999998887766554444443333456666666


Q ss_pred             HHHHHHH-------HHHHHHHHh---c-cccccC-------c------ccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 047219          499 DVCQQAE-------RSWASKIIR---G-QITKDG-------E------QACLPPLQEYIESATNRRRSLLDAAEQSHQNI  554 (567)
Q Consensus       499 ~L~~~a~-------~~a~~r~i~---~-~i~~~~-------~------~~~~~~l~e~le~~e~~~~~li~~al~~~~~~  554 (567)
                      .|+++.|       ++.+.+.+.   + .+....       .      .....++.+.++.+|   +.++.+++..+. .
T Consensus       413 ~L~~y~WPGNvreL~nvl~~a~~~~~~~~i~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~E---~~~i~~~l~~~~-~  488 (520)
T PRK10820        413 VLTRYGWPGNVRQLKNAIYRALTQLEGYELRPQDILLPDYDAAVAVGEDAMEGSLDEITSRFE---RSVLTRLYRNYP-S  488 (520)
T ss_pred             HHhcCCCCCHHHHHHHHHHHHHHhCCCCcccHHHcCCcccccccccccccccCCHHHHHHHHH---HHHHHHHHHHCC-C
Confidence            6666666       223333321   1 111110       0      000125666666666   888998888765 5


Q ss_pred             HhhhhccCCCCC
Q 047219          555 NNHRTKKQPLDL  566 (567)
Q Consensus       555 ~s~~~~~~~l~~  566 (567)
                      ++++++.+++|.
T Consensus       489 ~~~aA~~LGisr  500 (520)
T PRK10820        489 TRKLAKRLGVSH  500 (520)
T ss_pred             HHHHHHHhCCCH
Confidence            668888888875

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.84  E-value=5.3e-21  Score=210.91  Aligned_cols=261  Identities=16%  Similarity=0.202  Sum_probs=174.2

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQ  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~  352 (567)
                      ...+|++|+|.+..++.+++.+...                   +....+|||+|++||||+++|++||+.+.+.  +|+
T Consensus       207 ~~~~f~~iiG~S~~m~~~~~~i~~~-------------------A~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv  267 (526)
T TIGR02329       207 TRYRLDDLLGASAPMEQVRALVRLY-------------------ARSDATVLILGESGTGKELVAQAIHQLSGRRDFPFV  267 (526)
T ss_pred             cccchhheeeCCHHHHHHHHHHHHH-------------------hCCCCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEE
Confidence            3477999999999999999999765                   5677899999999999999999999988553  555


Q ss_pred             CcCeEEechhhHHhhhhchhHHHH--------HHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLL--------GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQID  424 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l--------~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld  424 (567)
                      .++|..++.+.+.+.+||+.+..+        ..+|+.    +.+++||||||+.|+...|..+.+++++  ..+.....
T Consensus       268 ~inC~~l~e~lleseLFG~~~gaftga~~~~~~Gl~e~----A~gGTLfLdeI~~Lp~~~Q~~Ll~~L~~--~~~~r~g~  341 (526)
T TIGR02329       268 AINCGAIAESLLEAELFGYEEGAFTGARRGGRTGLIEA----AHRGTLFLDEIGEMPLPLQTRLLRVLEE--REVVRVGG  341 (526)
T ss_pred             EeccccCChhHHHHHhcCCcccccccccccccccchhh----cCCceEEecChHhCCHHHHHHHHHHHhc--CcEEecCC
Confidence            555555555566777888644321        123332    3479999999999998877766655543  12222222


Q ss_pred             CcccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHH------------HH-
Q 047219          425 GFEQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAEL------------AE-  484 (567)
Q Consensus       425 ~~~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l------------~~-  484 (567)
                      ....+.++++|++||.       .+.|+++|++|+ ..+.+.+|++++|.+++..+++++.....            .. 
T Consensus       342 ~~~~~~dvRiIaat~~~l~~~v~~g~fr~dL~~rL-~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~  420 (526)
T TIGR02329       342 TEPVPVDVRVVAATHCALTTAVQQGRFRRDLFYRL-SILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVL  420 (526)
T ss_pred             CceeeecceEEeccCCCHHHHhhhcchhHHHHHhc-CCcEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHh
Confidence            2233457899999986       346889999999 78999999999999999988877544322            22 


Q ss_pred             ------HHHhccCCCHHHHHHHHHHHHHHHHHHHHhccccccCc-----------cc---CCCcHHHHHHHHHHHHHHHH
Q 047219          485 ------LATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGE-----------QA---CLPPLQEYIESATNRRRSLL  544 (567)
Q Consensus       485 ------la~~t~g~s~~dL~~L~~~a~~~a~~r~i~~~i~~~~~-----------~~---~~~~l~e~le~~e~~~~~li  544 (567)
                            +..+.|..+-++|++++.++....... -.+.++.+..           ..   ....+.    ..++.++.+|
T Consensus       421 ~~~~~~L~~y~WPGNvrEL~nvier~~i~~~~~-~~~~I~~~~l~~~~~~~~~~~~~~~~~~~~l~----~~~~~Er~~I  495 (526)
T TIGR02329       421 AGVADPLQRYPWPGNVRELRNLVERLALELSAM-PAGALTPDVLRALAPELAEASGKGKTSALSLR----ERSRVEALAV  495 (526)
T ss_pred             HHHHHHHHhCCCCchHHHHHHHHHHHHHhcccC-CCCccCHHHhhhhchhhcccccccccCccchH----HHHHHHHHHH
Confidence                  444444444555555544443221100 0001111100           00   001222    2234459999


Q ss_pred             HHHHHHHhhHHhhhhccCCCCC
Q 047219          545 DAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       545 ~~al~~~~~~~s~~~~~~~l~~  566 (567)
                      ..++.+++++++++++.+++|+
T Consensus       496 ~~aL~~~~Gn~~~aA~~LGIsR  517 (526)
T TIGR02329       496 RAALERFGGDRDAAAKALGISR  517 (526)
T ss_pred             HHHHHHcCCCHHHHHHHhCCCH
Confidence            9999999999999999999985

At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.84  E-value=8.6e-21  Score=209.96  Aligned_cols=260  Identities=20%  Similarity=0.227  Sum_probs=173.9

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVP  355 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~  355 (567)
                      .+.+++|.+..++++.+.+...                   +..+.+|||+|++||||+++|++||+.+.+.  +|+.++
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~-------------------a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~  245 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVV-------------------AASDLNVLILGETGVGKELVARAIHAASPRADKPLVYLN  245 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHH-------------------hCCCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEE
Confidence            6789999999999999999865                   6778899999999999999999999998654  333444


Q ss_pred             eEEechhhHHhhhhchhHHHHH-------HHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          356 LMYVPLEVVMSKYYGESERLLG-------KVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~-------~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      |..++.+.+.+.+||+....+.       ..|+    .+.+++|||||||.|+...|..+.++++.  ..+....+....
T Consensus       246 c~~~~~~~~e~~lfG~~~g~~~ga~~~~~g~~~----~a~gGtL~ldeI~~L~~~~Q~~Ll~~l~~--~~~~~~g~~~~~  319 (509)
T PRK05022        246 CAALPESLAESELFGHVKGAFTGAISNRSGKFE----LADGGTLFLDEIGELPLALQAKLLRVLQY--GEIQRVGSDRSL  319 (509)
T ss_pred             cccCChHHHHHHhcCccccccCCCcccCCcchh----hcCCCEEEecChhhCCHHHHHHHHHHHhc--CCEeeCCCCcce
Confidence            4444444445566775322111       1233    23479999999999997766655544332  111111111223


Q ss_pred             CCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHH
Q 047219          429 DKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       429 ~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ..++++|++||.       .+.|.++|++|+ ..+.|.+|++++|.+++..+++++......++.....+++...+..|.
T Consensus       320 ~~~~RiI~~t~~~l~~~~~~~~f~~dL~~rl-~~~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~  398 (509)
T PRK05022        320 RVDVRVIAATNRDLREEVRAGRFRADLYHRL-SVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALL  398 (509)
T ss_pred             ecceEEEEecCCCHHHHHHcCCccHHHHhcc-cccEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHH
Confidence            458999999986       356999999999 789999999999999999888776555444443333456666666666


Q ss_pred             HHHH-------HHHHHHHHh---c-------cccccC---c-----------c----cCCCcHHHHHHHHHHHHHHHHHH
Q 047219          502 QQAE-------RSWASKIIR---G-------QITKDG---E-----------Q----ACLPPLQEYIESATNRRRSLLDA  546 (567)
Q Consensus       502 ~~a~-------~~a~~r~i~---~-------~i~~~~---~-----------~----~~~~~l~e~le~~e~~~~~li~~  546 (567)
                      ++.|       ++.+++...   +       .++...   .           .    ....++.+.++.+|   +.+|.+
T Consensus       399 ~y~WPGNvrEL~~~i~ra~~~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~E---r~~I~~  475 (509)
T PRK05022        399 AYDWPGNVRELEHVISRAALLARARGAGRIVTLEAQHLDLPAEVALPPPEAAAAPAAVVSQNLREATEAFQ---RQLIRQ  475 (509)
T ss_pred             hCCCCCcHHHHHHHHHHHHHhcCCCccCccceecHHHcCcccccccCccccccccccccccCHHHHHHHHH---HHHHHH
Confidence            6665       233333221   1       010000   0           0    00113445555555   999999


Q ss_pred             HHHHHhhHHhhhhccCCCCC
Q 047219          547 AEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       547 al~~~~~~~s~~~~~~~l~~  566 (567)
                      ++.+++++++++++.++++.
T Consensus       476 aL~~~~gn~~~aA~~LGisr  495 (509)
T PRK05022        476 ALAQHQGNWAAAARALELDR  495 (509)
T ss_pred             HHHHcCCCHHHHHHHhCCCH
Confidence            99999999999999999875

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.83  E-value=1.3e-20  Score=207.70  Aligned_cols=259  Identities=19%  Similarity=0.223  Sum_probs=173.2

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHH--------hC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQ--------AG  347 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~--------l~  347 (567)
                      ..+|++|+|.+..++++++.+...                   +....+|||+|++||||+++|++||+.        +.
T Consensus       215 ~~~f~~iiG~S~~m~~~~~~i~~~-------------------A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~  275 (538)
T PRK15424        215 RYVLGDLLGQSPQMEQVRQTILLY-------------------ARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQG  275 (538)
T ss_pred             ccchhheeeCCHHHHHHHHHHHHH-------------------hCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCc
Confidence            357999999999999999998765                   567789999999999999999999998        44


Q ss_pred             CC--CCCCcCeEEechhhHHhhhhchhHHHHH--------HHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHH
Q 047219          348 AM--PWQGVPLMYVPLEVVMSKYYGESERLLG--------KVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILS  417 (567)
Q Consensus       348 ~~--~~~~~~~~~i~~~~l~s~~~G~~~~~l~--------~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~  417 (567)
                      +.  +|+.++|..++.+.+.+.+||+.+..+.        .+|+    .+.+++||||||+.|+...|..+.+++++  .
T Consensus       276 r~~~pfv~inCaal~e~lleseLFG~~~gaftga~~~~~~Gl~e----~A~gGTLfLdeI~~Lp~~~Q~kLl~~L~e--~  349 (538)
T PRK15424        276 KKSHPFVAVNCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFE----IAHGGTLFLDEIGEMPLPLQTRLLRVLEE--K  349 (538)
T ss_pred             cCCCCeEEeecccCChhhHHHHhcCCccccccCccccccCCchh----ccCCCEEEEcChHhCCHHHHHHHHhhhhc--C
Confidence            32  4555555555555667778886443211        2333    33479999999999998877766655443  1


Q ss_pred             HHHHhhcCcccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHH--------
Q 047219          418 VLLRQIDGFEQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAEL--------  482 (567)
Q Consensus       418 ~LL~~ld~~~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l--------  482 (567)
                      .+.........+.++++|++||.       .+.|+++|++|+ ..+.+.+|++++|.+++..+++++.....        
T Consensus       350 ~~~r~G~~~~~~~dvRiIaat~~~L~~~v~~g~Fr~dL~yrL-~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~  428 (538)
T PRK15424        350 EVTRVGGHQPVPVDVRVISATHCDLEEDVRQGRFRRDLFYRL-SILRLQLPPLRERVADILPLAESFLKQSLAALSAPFS  428 (538)
T ss_pred             eEEecCCCceeccceEEEEecCCCHHHHHhcccchHHHHHHh-cCCeecCCChhhchhHHHHHHHHHHHHHHHHcCCCCC
Confidence            22222222234567899999986       346889999999 88999999999999999988876544321        


Q ss_pred             -----------HHHHHhccCCCHHHHHHHHHHHHHHHHHHHHhccccccCc-------ccCCCcHHHHHHHHHHHHHHHH
Q 047219          483 -----------AELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGE-------QACLPPLQEYIESATNRRRSLL  544 (567)
Q Consensus       483 -----------~~la~~t~g~s~~dL~~L~~~a~~~a~~r~i~~~i~~~~~-------~~~~~~l~e~le~~e~~~~~li  544 (567)
                                 ..+..+.|..+.++|++++..+......... ..++....       ......+.  ...   .++..|
T Consensus       429 ~~a~~~~~~a~~~L~~y~WPGNvREL~nvier~~i~~~~~~~-~~i~~~~l~~~~~~~~~~~~~~~--~~~---~Er~~I  502 (538)
T PRK15424        429 AALRQGLQQCETLLLHYDWPGNVRELRNLMERLALFLSVEPT-PDLTPQFLQLLLPELARESAKTP--APR---LLAATL  502 (538)
T ss_pred             HHHHHhhHHHHHHHHhCCCCchHHHHHHHHHHHHHhcCCCCc-CccCHHHhhhhcccccccccccc--hhH---HHHHHH
Confidence                       3344444555556666666554432110000 01110000       00000110  111   247899


Q ss_pred             HHHHHHHhhHHhhhhccCCCCC
Q 047219          545 DAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       545 ~~al~~~~~~~s~~~~~~~l~~  566 (567)
                      .+++.+++++++++++.+++|+
T Consensus       503 ~~~L~~~~Gn~~~aA~~LGIsR  524 (538)
T PRK15424        503 QQALERFNGDKTAAANYLGISR  524 (538)
T ss_pred             HHHHHHhCCCHHHHHHHhCCCH
Confidence            9999999999999999999985

>PF05496 RuvB_N: Holliday junction DNA helicase ruvB N-terminus; InterPro: IPR008824 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=99.82  E-value=1.8e-19  Score=175.87  Aligned_cols=196  Identities=22%  Similarity=0.299  Sum_probs=124.6

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ...+.+|+|++|+++.+..+.-.+......                .....++|||||||+||||||+.||+++      
T Consensus        17 ~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r----------------~~~l~h~lf~GPPG~GKTTLA~IIA~e~------   74 (233)
T PF05496_consen   17 RLRPKSLDEFIGQEHLKGNLKILIRAAKKR----------------GEALDHMLFYGPPGLGKTTLARIIANEL------   74 (233)
T ss_dssp             HTS-SSCCCS-S-HHHHHHHHHHHHHHHCT----------------TS---EEEEESSTTSSHHHHHHHHHHHC------
T ss_pred             hcCCCCHHHccCcHHHHhhhHHHHHHHHhc----------------CCCcceEEEECCCccchhHHHHHHHhcc------
Confidence            345569999999999999987766543221                3456799999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-----
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-----  427 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-----  427 (567)
                      +.+|..++++.+...      ..+..++...   .++.||||||||.|....|+.+..++++.  . +..+-+..     
T Consensus        75 ~~~~~~~sg~~i~k~------~dl~~il~~l---~~~~ILFIDEIHRlnk~~qe~LlpamEd~--~-idiiiG~g~~ar~  142 (233)
T PF05496_consen   75 GVNFKITSGPAIEKA------GDLAAILTNL---KEGDILFIDEIHRLNKAQQEILLPAMEDG--K-IDIIIGKGPNARS  142 (233)
T ss_dssp             T--EEEEECCC--SC------HHHHHHHHT-----TT-EEEECTCCC--HHHHHHHHHHHHCS--E-EEEEBSSSSS-BE
T ss_pred             CCCeEeccchhhhhH------HHHHHHHHhc---CCCcEEEEechhhccHHHHHHHHHHhccC--e-EEEEeccccccce
Confidence            777888877543221      1222333332   24689999999999877655554444320  0 00000100     


Q ss_pred             ---cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          428 ---QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       428 ---~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                         .-.++.+|+||++.+.+...|+.||.....+..++.++...|++..+..    +..+....++..+.| +++-..++
T Consensus       143 ~~~~l~~FTligATTr~g~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rsrG-tPRiAnrl  221 (233)
T PF05496_consen  143 IRINLPPFTLIGATTRAGLLSSPLRDRFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRSRG-TPRIANRL  221 (233)
T ss_dssp             EEEE----EEEEEESSGCCTSHCCCTTSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCTTT-SHHHHHHH
T ss_pred             eeccCCCceEeeeeccccccchhHHhhcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhcCC-ChHHHHHH
Confidence               1146999999999999999999999888899999999999999876654    456788889988876 67665555


Q ss_pred             HHH
Q 047219          501 CQQ  503 (567)
Q Consensus       501 ~~~  503 (567)
                      ++.
T Consensus       222 l~r  224 (233)
T PF05496_consen  222 LRR  224 (233)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            544

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the N-terminal region of the proteins.; GO: 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1IQP_B 3PFI_B 1IXR_C 1HQC_B 1IXS_B.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.82  E-value=2.4e-20  Score=211.98  Aligned_cols=261  Identities=16%  Similarity=0.172  Sum_probs=170.2

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQG  353 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~  353 (567)
                      ..+|++++|.+..++++.+.+...                   +....+|||+|++||||+++|++||+.+.+.  +|+.
T Consensus       321 ~~~~~~l~g~s~~~~~~~~~~~~~-------------------a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~  381 (638)
T PRK11388        321 SHTFDHMPQDSPQMRRLIHFGRQA-------------------AKSSFPVLLCGEEGVGKALLAQAIHNESERAAGPYIA  381 (638)
T ss_pred             cccccceEECCHHHHHHHHHHHHH-------------------hCcCCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEE
Confidence            457999999999999999988765                   5667789999999999999999999998643  4444


Q ss_pred             cCeEEechhhHHhhhhchhHHH----HHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          354 VPLMYVPLEVVMSKYYGESERL----LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~----l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      ++|..++.+.+.+.+||+....    ....|    +.+.+++||||||+.|+...|..+.+++++  ..+.........+
T Consensus       382 vnc~~~~~~~~~~elfg~~~~~~~~~~~g~~----~~a~~GtL~ldei~~l~~~~Q~~Ll~~l~~--~~~~~~~~~~~~~  455 (638)
T PRK11388        382 VNCQLYPDEALAEEFLGSDRTDSENGRLSKF----ELAHGGTLFLEKVEYLSPELQSALLQVLKT--GVITRLDSRRLIP  455 (638)
T ss_pred             EECCCCChHHHHHHhcCCCCcCccCCCCCce----eECCCCEEEEcChhhCCHHHHHHHHHHHhc--CcEEeCCCCceEE
Confidence            4444444445566777753100    00112    234479999999999987766655444322  0111111111123


Q ss_pred             CcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          430 KKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       430 ~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .++++|+||+.       ...|+++|++|+ ..+.+.+|++++|.+++..+++++......++... .+++...+..|.+
T Consensus       456 ~~~riI~~t~~~l~~~~~~~~f~~dL~~~l-~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~-~~~s~~a~~~L~~  533 (638)
T PRK11388        456 VDVRVIATTTADLAMLVEQNRFSRQLYYAL-HAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTR-LKIDDDALARLVS  533 (638)
T ss_pred             eeEEEEEeccCCHHHHHhcCCChHHHhhhh-ceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCC-CCcCHHHHHHHHc
Confidence            47899999986       357999999999 88999999999999999988877654433333222 2456666666666


Q ss_pred             HHH-------HHHHHHHHh---c-cccccCc-----c-c-----CCCcH--HHHHHHHHHHHHHHHHHHHHHHhhHHhhh
Q 047219          503 QAE-------RSWASKIIR---G-QITKDGE-----Q-A-----CLPPL--QEYIESATNRRRSLLDAAEQSHQNINNHR  558 (567)
Q Consensus       503 ~a~-------~~a~~r~i~---~-~i~~~~~-----~-~-----~~~~l--~e~le~~e~~~~~li~~al~~~~~~~s~~  558 (567)
                      +.|       ++.+++.+.   + .++.+..     . .     ....+  ...++++|   +..|.+++.+++++++++
T Consensus       534 y~WPGNvreL~~~l~~~~~~~~~~~i~~~~lp~~~~~~~~~~~~~~~~~~~~~~l~~~E---~~~i~~al~~~~gn~~~a  610 (638)
T PRK11388        534 YRWPGNDFELRSVIENLALSSDNGRIRLSDLPEHLFTEQATDDVSATRLSTSLSLAELE---KEAIINAAQVCGGRIQEM  610 (638)
T ss_pred             CCCCChHHHHHHHHHHHHHhCCCCeecHHHCchhhhcccccccccccccccchhHHHHH---HHHHHHHHHHhCCCHHHH
Confidence            665       233333221   1 1110000     0 0     00011  12244444   999999999999999999


Q ss_pred             hccCCCCC
Q 047219          559 TKKQPLDL  566 (567)
Q Consensus       559 ~~~~~l~~  566 (567)
                      ++.+++++
T Consensus       611 A~~LGisR  618 (638)
T PRK11388        611 AALLGIGR  618 (638)
T ss_pred             HHHHCCCH
Confidence            99999885

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.82  E-value=7.2e-20  Score=184.12  Aligned_cols=195  Identities=28%  Similarity=0.411  Sum_probs=156.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC---CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA---MPW  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~---~~~  351 (567)
                      -.--|+.++--...|+++...+...+...+.-.    ++.   -....+-+||+||||||||+|++++|+.+.-   ..+
T Consensus       137 F~glWEsLiyds~lK~~ll~Ya~s~l~fsek~v----ntn---lIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y  209 (423)
T KOG0744|consen  137 FDGLWESLIYDSNLKERLLSYAASALLFSEKKV----NTN---LITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRY  209 (423)
T ss_pred             hhhhHHHHhhcccHHHHHHHHHHHHHHHHhcCC----CCc---eeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCcc
Confidence            334688899889999999887765544433211    100   1345677999999999999999999999852   244


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC--CCCc--EEEEcCcchhhhhhhhhhH----HHHHHHHHHHHHhh
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL--PNGA--IIFLDEVDSFAVARDSEMH----EATRRILSVLLRQI  423 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~--a~~~--ILfIDEID~L~~~~q~~l~----~~~~~vl~~LL~~l  423 (567)
                      ....++.+++..+.++||+++.+.+..+|++..+.  .+++  .++|||+++|+..|.....    .-.-|+++.+|+++
T Consensus       210 ~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQl  289 (423)
T KOG0744|consen  210 YKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQL  289 (423)
T ss_pred             ccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHH
Confidence            46678999999999999999999999999987643  1233  4569999999988754322    22458899999999


Q ss_pred             cCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh
Q 047219          424 DGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       424 d~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      |.++...+|++++|+|-.+.+|.++..|-|.+.++++|+...+.+|++..+..
T Consensus       290 DrlK~~~NvliL~TSNl~~siD~AfVDRADi~~yVG~Pt~~ai~~IlkscieE  342 (423)
T KOG0744|consen  290 DRLKRYPNVLILATSNLTDSIDVAFVDRADIVFYVGPPTAEAIYEILKSCIEE  342 (423)
T ss_pred             HHhccCCCEEEEeccchHHHHHHHhhhHhhheeecCCccHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999987654

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.82  E-value=2.4e-20  Score=207.79  Aligned_cols=267  Identities=19%  Similarity=0.207  Sum_probs=169.1

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ....++++|+|.+..++++.+.+...                   +....+|||+||+||||+++|++||+.+.+.   +
T Consensus       190 ~~~~~~~~liG~s~~~~~~~~~~~~~-------------------a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~---~  247 (534)
T TIGR01817       190 RRSGKEDGIIGKSPAMRQVVDQARVV-------------------ARSNSTVLLRGESGTGKELIAKAIHYLSPRA---K  247 (534)
T ss_pred             cccCccCceEECCHHHHHHHHHHHHH-------------------hCcCCCEEEECCCCccHHHHHHHHHHhCCCC---C
Confidence            34578999999999999999998765                   5667899999999999999999999998643   3


Q ss_pred             cCeEEechh-----hHHhhhhchhHHHHHHHHH---HHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC
Q 047219          354 VPLMYVPLE-----VVMSKYYGESERLLGKVFS---LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG  425 (567)
Q Consensus       354 ~~~~~i~~~-----~l~s~~~G~~~~~l~~~f~---~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~  425 (567)
                      .+|+.++|.     .+.+.+||+....+.....   .....+.+++||||||+.|+...|..+..+++.  ..+......
T Consensus       248 ~pfv~i~c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~~~Q~~Ll~~l~~--~~~~~~~~~  325 (534)
T TIGR01817       248 RPFVKVNCAALSETLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISPAFQAKLLRVLQE--GEFERVGGN  325 (534)
T ss_pred             CCeEEeecCCCCHHHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCHHHHHHHHHHHhc--CcEEECCCC
Confidence            455555554     4455566643221110000   001233479999999999987766555444322  011111111


Q ss_pred             cccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHH
Q 047219          426 FEQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIR  498 (567)
Q Consensus       426 ~~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~  498 (567)
                      ...+.++++|++|+.       ...|+++|++|+ ..+.+.+|++++|.+++..+++++......++... .+++...+.
T Consensus       326 ~~~~~~~riI~~s~~~l~~~~~~~~f~~~L~~rl-~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~-~~~s~~a~~  403 (534)
T TIGR01817       326 RTLKVDVRLVAATNRDLEEAVAKGEFRADLYYRI-NVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRP-LTITPSAIR  403 (534)
T ss_pred             ceEeecEEEEEeCCCCHHHHHHcCCCCHHHHHHh-cCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCC-CCCCHHHHH
Confidence            122347899999976       357999999999 78889999999999999888877654433333322 356666666


Q ss_pred             HHHHHHH-------HHHHHHHHh---c-cccccCcc-------------c------------------C-C---CcHHHH
Q 047219          499 DVCQQAE-------RSWASKIIR---G-QITKDGEQ-------------A------------------C-L---PPLQEY  532 (567)
Q Consensus       499 ~L~~~a~-------~~a~~r~i~---~-~i~~~~~~-------------~------------------~-~---~~l~e~  532 (567)
                      .|.++.|       ++.+++.+.   + .++.+...             .                  . .   .+....
T Consensus       404 ~L~~~~WPGNvrEL~~v~~~a~~~~~~~~I~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  483 (534)
T TIGR01817       404 VLMSCKWPGNVRELENCLERTATLSRSGTITRSDFSCQSGQCLSPMLAKTCPHGHISIDPLAGTTPPHSPASAALPGEPG  483 (534)
T ss_pred             HHHhCCCCChHHHHHHHHHHHHHhCCCCcccHHHCchhhccccccccccccccccccccccccccccccccccccccccc
Confidence            6666665       233333321   1 11100000             0                  0 0   000000


Q ss_pred             HHHHHHHHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          533 IESATNRRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       533 le~~e~~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                      +...+..++..|..++..++++++++++.+++++
T Consensus       484 ~~~~~~~Er~~i~~aL~~~~gn~~~aA~~LGisr  517 (534)
T TIGR01817       484 LSGPTLSERERLIAALEQAGWVQAKAARLLGMTP  517 (534)
T ss_pred             chhHHHHHHHHHHHHHHHhCCCHHHHHHHHCCCH
Confidence            1112223488999999999999999999999875

This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.

>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=99.81  E-value=3.3e-19  Score=160.32  Aligned_cols=130  Identities=36%  Similarity=0.624  Sum_probs=114.6

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhh
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~  404 (567)
                      |||+||||||||++|+.+++.+      +.+++.+++..+.+.+.++..+.+..+|..+.....++||||||+|.+....
T Consensus         1 ill~G~~G~GKT~l~~~la~~l------~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~   74 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL------GFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKS   74 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT------TSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHC
T ss_pred             CEEECcCCCCeeHHHHHHHhhc------ccccccccccccccccccccccccccccccccccccceeeeeccchhccccc
Confidence            6899999999999999999999      7889999999999999999999999999999877634999999999999887


Q ss_pred             hhhhHHHHHHHHHHHHHhhcCcccC-CcEEEEEeeCCCCCCChHHH-hccceEEEecC
Q 047219          405 DSEMHEATRRILSVLLRQIDGFEQD-KKVVVIAATNRKQDLDPALI-SRFDSMITFGL  460 (567)
Q Consensus       405 q~~l~~~~~~vl~~LL~~ld~~~~~-~~viVIaaTN~~~~Ld~aL~-sRf~~~I~i~~  460 (567)
                      +..........+..|+..++..... .+++||++||.++.+++.++ +||+..++++.
T Consensus        75 ~~~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~~i~~~l~~~rf~~~i~~~~  132 (132)
T PF00004_consen   75 QPSSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPDKIDPALLRSRFDRRIEFPL  132 (132)
T ss_dssp             STSSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGGGSCHHHHSTTSEEEEEE-S
T ss_pred             ccccccccccccceeeecccccccccccceeEEeeCChhhCCHhHHhCCCcEEEEcCC
Confidence            4445566677888999999887654 57999999999999999999 99999998863

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 ....

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.80  E-value=3.5e-19  Score=203.89  Aligned_cols=261  Identities=18%  Similarity=0.258  Sum_probs=172.7

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      +..|++++|.+..++.+.+.+...                   +....+|||+||+|||||++|++||+.+.+.   +.+
T Consensus       372 n~~~~~liG~S~~~~~~~~~~~~~-------------------a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~---~~~  429 (686)
T PRK15429        372 DSEFGEIIGRSEAMYSVLKQVEMV-------------------AQSDSTVLILGETGTGKELIARAIHNLSGRN---NRR  429 (686)
T ss_pred             cccccceeecCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCcCHHHHHHHHHHhcCCC---CCC
Confidence            357889999999999999988765                   5667899999999999999999999988644   345


Q ss_pred             eEEechh-----hHHhhhhchhHH--------HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHh
Q 047219          356 LMYVPLE-----VVMSKYYGESER--------LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQ  422 (567)
Q Consensus       356 ~~~i~~~-----~l~s~~~G~~~~--------~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~  422 (567)
                      |+.++|.     .+.+.+||....        ..+ .|+    .+.+++||||||+.|....|..+..+++.  ..+...
T Consensus       430 ~v~i~c~~~~~~~~~~~lfg~~~~~~~g~~~~~~g-~le----~a~~GtL~Ldei~~L~~~~Q~~L~~~l~~--~~~~~~  502 (686)
T PRK15429        430 MVKMNCAAMPAGLLESDLFGHERGAFTGASAQRIG-RFE----LADKSSLFLDEVGDMPLELQPKLLRVLQE--QEFERL  502 (686)
T ss_pred             eEEEecccCChhHhhhhhcCcccccccccccchhh-HHH----hcCCCeEEEechhhCCHHHHHHHHHHHHh--CCEEeC
Confidence            5555554     445566664221        122 233    23479999999999987766655444432  111111


Q ss_pred             hcCcccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHH
Q 047219          423 IDGFEQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGR  495 (567)
Q Consensus       423 ld~~~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~  495 (567)
                      ........++++|++|+.       ...|+.+|++|+ ..+.|.+|++++|.+++..+++++......++.....+++..
T Consensus       503 g~~~~~~~~~RiI~~t~~~l~~~~~~~~f~~~L~~~l-~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~  581 (686)
T PRK15429        503 GSNKIIQTDVRLIAATNRDLKKMVADREFRSDLYYRL-NVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAE  581 (686)
T ss_pred             CCCCcccceEEEEEeCCCCHHHHHHcCcccHHHHhcc-CeeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHH
Confidence            111123467899999986       346889999999 788999999999999999888877655555554445567777


Q ss_pred             HHHHHHHHHH-------HHHHHHHHh---c-cccccCcc-----cCCCcHHHHHHHHHHHHHHHHHHHHHHHhhHHh---
Q 047219          496 DIRDVCQQAE-------RSWASKIIR---G-QITKDGEQ-----ACLPPLQEYIESATNRRRSLLDAAEQSHQNINN---  556 (567)
Q Consensus       496 dL~~L~~~a~-------~~a~~r~i~---~-~i~~~~~~-----~~~~~l~e~le~~e~~~~~li~~al~~~~~~~s---  556 (567)
                      .++.|.++.|       ++.+++.+.   + .+..+...     .........+...++.++.+|.+++++++++++   
T Consensus       582 al~~L~~y~WPGNvrEL~~~i~~a~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~Er~~I~~aL~~~~gn~~~~~  661 (686)
T PRK15429        582 TLRTLSNMEWPGNVRELENVIERAVLLTRGNVLQLSLPDITLPEPETPPAATVVAQEGEDEYQLIVRVLKETNGVVAGPK  661 (686)
T ss_pred             HHHHHHhCCCCCcHHHHHHHHHHHHHhCCCCcccccCchhhcccccccccccccccHHHHHHHHHHHHHHHcCCCcccHH
Confidence            7777777777       333444332   1 11111000     000000000011123448999999999999875   


Q ss_pred             hhhccCCCCC
Q 047219          557 HRTKKQPLDL  566 (567)
Q Consensus       557 ~~~~~~~l~~  566 (567)
                      .+++.+++++
T Consensus       662 ~aA~~LGi~R  671 (686)
T PRK15429        662 GAAQRLGLKR  671 (686)
T ss_pred             HHHHHhCCCH
Confidence            9999888875

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.79  E-value=1.2e-17  Score=172.27  Aligned_cols=208  Identities=31%  Similarity=0.462  Sum_probs=157.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +.-.+++++-.....+.|++....- .+            ......+-++||||||||||||++|+-||..+      ++
T Consensus       350 gk~pl~~ViL~psLe~Rie~lA~aT-aN------------TK~h~apfRNilfyGPPGTGKTm~ArelAr~S------Gl  410 (630)
T KOG0742|consen  350 GKDPLEGVILHPSLEKRIEDLAIAT-AN------------TKKHQAPFRNILFYGPPGTGKTMFARELARHS------GL  410 (630)
T ss_pred             CCCCcCCeecCHHHHHHHHHHHHHh-cc------------cccccchhhheeeeCCCCCCchHHHHHHHhhc------CC
Confidence            3344777777777777776654321 11            01123455899999999999999999999999      66


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhh-hhHHHHHHHHHHHHHhhcCcccCCcEE
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDS-EMHEATRRILSVLLRQIDGFEQDKKVV  433 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~-~l~~~~~~vl~~LL~~ld~~~~~~~vi  433 (567)
                      .+..+.+.++.- +-.+.-..+..+|+-++....+-+|||||.|.+.-++.. ...+..+..++.||---.  ....+++
T Consensus       411 DYA~mTGGDVAP-lG~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLfRTG--dqSrdiv  487 (630)
T KOG0742|consen  411 DYAIMTGGDVAP-LGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLFRTG--DQSRDIV  487 (630)
T ss_pred             ceehhcCCCccc-cchHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHHHhc--ccccceE
Confidence            665555544321 222344678899999998888889999999999877764 456666777777764322  2467899


Q ss_pred             EEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhC------------------------------HHHHH
Q 047219          434 VIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLT------------------------------KAELA  483 (567)
Q Consensus       434 VIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~------------------------------~~~l~  483 (567)
                      ++.+||+|++||.++-.|+|.+++|++|..++|..++..++.++.                              ...+.
T Consensus       488 LvlAtNrpgdlDsAV~DRide~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~  567 (630)
T KOG0742|consen  488 LVLATNRPGDLDSAVNDRIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCS  567 (630)
T ss_pred             EEeccCCccchhHHHHhhhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHH
Confidence            999999999999999999999999999999999999999887421                              12467


Q ss_pred             HHHHhccCCCHHHHHHHHHHH
Q 047219          484 ELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       484 ~la~~t~g~s~~dL~~L~~~a  504 (567)
                      +.+..|.||||++|..|+.-.
T Consensus       568 EaAkkTeGfSGREiakLva~v  588 (630)
T KOG0742|consen  568 EAAKKTEGFSGREIAKLVASV  588 (630)
T ss_pred             HHHHhccCCcHHHHHHHHHHH
Confidence            889999999999999987643

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=99.79  E-value=3.7e-19  Score=180.94  Aligned_cols=258  Identities=19%  Similarity=0.242  Sum_probs=192.2

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--C
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--P  350 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~  350 (567)
                      ..+...|+.|++.+..++.+.+.....                   +-...++||.|++||||.++|++-|..+.+.  +
T Consensus       197 ~~~~~~F~~~v~~S~~mk~~v~qA~k~-------------------AmlDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~p  257 (511)
T COG3283         197 AQDVSGFEQIVAVSPKMKHVVEQAQKL-------------------AMLDAPLLITGETGTGKDLLAKACHLASPRHSKP  257 (511)
T ss_pred             cccccchHHHhhccHHHHHHHHHHHHh-------------------hccCCCeEEecCCCchHHHHHHHHhhcCcccCCC
Confidence            345568999999999999998877654                   5567789999999999999999999999876  6


Q ss_pred             CCCcCeEEechhhHHhhhhchhH--HHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESE--RLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~--~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      |..++|..++.+.-.+++||+..  +-...+|+.|.    ++++|||||..|++..|.+++++.++  ..|-+..+..+.
T Consensus       258 FlalNCA~lPe~~aEsElFG~apg~~gk~GffE~An----gGTVlLDeIgEmSp~lQaKLLRFL~D--GtFRRVGee~Ev  331 (511)
T COG3283         258 FLALNCASLPEDAAESELFGHAPGDEGKKGFFEQAN----GGTVLLDEIGEMSPRLQAKLLRFLND--GTFRRVGEDHEV  331 (511)
T ss_pred             eeEeecCCCchhHhHHHHhcCCCCCCCccchhhhcc----CCeEEeehhhhcCHHHHHHHHHHhcC--CceeecCCcceE
Confidence            77777777777888889998754  22334666554    89999999999999999888888766  566677776677


Q ss_pred             CCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHH
Q 047219          429 DKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       429 ~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ..+|+||+||..       .+.+.++|++|+ +++.+.+|++++|.+++..+++.|-.+..+++......++..-+..|.
T Consensus       332 ~vdVRVIcatq~nL~~lv~~g~fReDLfyRL-NVLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~  410 (511)
T COG3283         332 HVDVRVICATQVNLVELVQKGKFREDLFYRL-NVLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLT  410 (511)
T ss_pred             EEEEEEEecccccHHHHHhcCchHHHHHHHh-heeeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHH
Confidence            789999999975       568999999999 999999999999999999999887766666666666666666666666


Q ss_pred             HHHH-------HHHHHHHH---hc-ccc-----c---cC-----cccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhHHhh
Q 047219          502 QQAE-------RSWASKII---RG-QIT-----K---DG-----EQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNH  557 (567)
Q Consensus       502 ~~a~-------~~a~~r~i---~~-~i~-----~---~~-----~~~~~~~l~e~le~~e~~~~~li~~al~~~~~~~s~  557 (567)
                      ++.|       .++.-|..   .+ .+.     .   +.     ......++++.+..+|   ++++++.-..|-...+.
T Consensus       411 ~y~WpGNVRqL~N~iyRA~s~~Eg~~l~i~~i~Lp~~~~~~~~~~~~~~gsLdei~~~fE---~~VL~rly~~yPStRkL  487 (511)
T COG3283         411 RYAWPGNVRQLKNAIYRALTLLEGYELRIEDILLPDYDAATVVGEDALEGSLDEIVSRFE---RSVLTRLYRSYPSTRKL  487 (511)
T ss_pred             HcCCCccHHHHHHHHHHHHHHhccCccchhhcccCCcccccccchhhccCCHHHHHHHHH---HHHHHHHHHhCCcHHHH
Confidence            6666       12222211   11 111     0   00     0111236778888887   88887776666555444


Q ss_pred             hh
Q 047219          558 RT  559 (567)
Q Consensus       558 ~~  559 (567)
                      ++
T Consensus       488 Ak  489 (511)
T COG3283         488 AK  489 (511)
T ss_pred             HH
Confidence            43

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.78  E-value=9.2e-19  Score=190.59  Aligned_cols=264  Identities=19%  Similarity=0.213  Sum_probs=168.5

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVP  355 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~  355 (567)
                      .+.+++|.+..++.+.+.+...                   .....+++|+|++||||+++|+++|..+.+.  +|+.++
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~-------------------a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~  197 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKI-------------------APSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAIN  197 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEE
Confidence            4567999999999888877543                   4556789999999999999999999988643  333333


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHH---HHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFS---LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~---~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      |..++.+.+.+.+||.....+.....   ..-..+.+++||||||+.|+...|..+.++++..  .+.........+.++
T Consensus       198 c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~~q~~l~~~l~~~--~~~~~~~~~~~~~~~  275 (445)
T TIGR02915       198 CAAIPENLLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPLNLQAKLLRFLQER--VIERLGGREEIPVDV  275 (445)
T ss_pred             CCCCChHHHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCCHHHHHHHHHHHhhC--eEEeCCCCceeeece
Confidence            33333344455556643221100000   0012345799999999999877666554444320  111111111223578


Q ss_pred             EEEEeeCCC-------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          433 VVIAATNRK-------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       433 iVIaaTN~~-------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ++|++|+..       +.++++|++|+ ..+.+.+|++++|.+++..+++++.......+.....++++..++.|..+.|
T Consensus       276 rii~~~~~~l~~~~~~~~~~~~L~~~l-~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~w  354 (445)
T TIGR02915       276 RIVCATNQDLKRMIAEGTFREDLFYRI-AEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAHAW  354 (445)
T ss_pred             EEEEecCCCHHHHHHcCCccHHHHHHh-ccceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHhCCC
Confidence            999999873       67999999999 7899999999999999998887765544443333344566666666666666


Q ss_pred             -------HHHHHHHHh---c-ccccc-----Ccc-cCC---CcHHHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccCCCC
Q 047219          506 -------RSWASKIIR---G-QITKD-----GEQ-ACL---PPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLD  565 (567)
Q Consensus       506 -------~~a~~r~i~---~-~i~~~-----~~~-~~~---~~l~e~le~~e~~~~~li~~al~~~~~~~s~~~~~~~l~  565 (567)
                             ++.+++.+.   + .++..     ... ...   .++.+.++.+|   +.+|.+++.+++++++++++.+++|
T Consensus       355 pgNvreL~~~i~~a~~~~~~~~i~~~~l~~~~~~~~~~~~~~~l~~~~~~~E---~~~i~~al~~~~gn~~~aA~~Lgis  431 (445)
T TIGR02915       355 PGNVRELENKVKRAVIMAEGNQITAEDLGLDARERAETPLEVNLREVRERAE---REAVRKAIARVDGNIARAAELLGIT  431 (445)
T ss_pred             CChHHHHHHHHHHHHHhCCCCcccHHHcCCccccccccccccCHHHHHHHHH---HHHHHHHHHHhCCCHHHHHHHhCCC
Confidence                   233333321   1 11100     000 000   13444455555   8999999999999999999999998


Q ss_pred             C
Q 047219          566 L  566 (567)
Q Consensus       566 ~  566 (567)
                      +
T Consensus       432 r  432 (445)
T TIGR02915       432 R  432 (445)
T ss_pred             H
Confidence            6

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=99.77  E-value=7.6e-19  Score=192.56  Aligned_cols=261  Identities=18%  Similarity=0.219  Sum_probs=167.7

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      .+.+++|.+..++.+.+.+...                   .....++||+|++|||||++|+++|..+.+.   ..+|+
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~-------------------~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~---~~~~i  193 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRL-------------------SRSSISVLINGESGTGKELVAHALHRHSPRA---KAPFI  193 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHH-------------------hccCCeEEEEeCCCCcHHHHHHHHHhcCCCC---CCCeE
Confidence            4568999999999988877643                   4567789999999999999999999988654   34555


Q ss_pred             Eechh-----hHHhhhhchhHHHHHHHH---HHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          358 YVPLE-----VVMSKYYGESERLLGKVF---SLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       358 ~i~~~-----~l~s~~~G~~~~~l~~~f---~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      .++|.     .+.+.+||+.........   ......+.+++||||||+.|+...|..+..+++.  ..+....+.....
T Consensus       194 ~i~c~~~~~~~~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~~~q~~L~~~l~~--~~~~~~~~~~~~~  271 (469)
T PRK10923        194 ALNMAAIPKDLIESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPLDVQTRLLRVLAD--GQFYRVGGYAPVK  271 (469)
T ss_pred             eeeCCCCCHHHHHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCHHHHHHHHHHHhc--CcEEeCCCCCeEE
Confidence            55554     445555664322110000   0001233479999999999987766554443322  1111111111223


Q ss_pred             CcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          430 KKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       430 ~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .++++|+||+.       .+.+.++|++|| ..+.+.+|++++|.+++..+++++.......+.....++++..+..|++
T Consensus       272 ~~~rii~~~~~~l~~~~~~~~~~~~L~~~l-~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~  350 (469)
T PRK10923        272 VDVRIIAATHQNLEQRVQEGKFREDLFHRL-NVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTR  350 (469)
T ss_pred             eeEEEEEeCCCCHHHHHHcCCchHHHHHHh-cceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHh
Confidence            57899999976       347899999999 7899999999999999998888765554444433344566666666666


Q ss_pred             HHH-------HHHHHHHHh---c-cccccC-----ccc-----------C------------------CCcHHHHHHHHH
Q 047219          503 QAE-------RSWASKIIR---G-QITKDG-----EQA-----------C------------------LPPLQEYIESAT  537 (567)
Q Consensus       503 ~a~-------~~a~~r~i~---~-~i~~~~-----~~~-----------~------------------~~~l~e~le~~e  537 (567)
                      +.|       ++.+++.+.   + .+..+.     ...           .                  ...+.+.++.+|
T Consensus       351 ~~wpgNv~eL~~~i~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~E  430 (469)
T PRK10923        351 LAWPGNVRQLENTCRWLTVMAAGQEVLIQDLPGELFESTVPESTSQMQPDSWATLLAQWADRALRSGHQNLLSEAQPELE  430 (469)
T ss_pred             CCCCChHHHHHHHHHHHHHhCCCCcccHHHCcHhhhccccccccccccccccccccccccccccccccchhhHHHHHHHH
Confidence            666       233333221   0 010000     000           0                  001223444444


Q ss_pred             HHHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          538 NRRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       538 ~~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                         +.+|..++.+++++++++++.+++++
T Consensus       431 ---~~~i~~aL~~~~gn~~~aA~~Lgisr  456 (469)
T PRK10923        431 ---RTLLTTALRHTQGHKQEAARLLGWGR  456 (469)
T ss_pred             ---HHHHHHHHHHhCCCHHHHHHHhCCCH
Confidence               99999999999999999999999885

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=99.76  E-value=1.2e-17  Score=170.27  Aligned_cols=212  Identities=23%  Similarity=0.319  Sum_probs=143.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC----CCCcEEEE
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL----PNGAIIFL  394 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~----a~~~ILfI  394 (567)
                      .+.-.+++||||||||||+|||.|++.....   .+.|+.+++..-.       -..++.+|+.++..    ....||||
T Consensus       159 q~~ipSmIlWGppG~GKTtlArlia~tsk~~---SyrfvelSAt~a~-------t~dvR~ife~aq~~~~l~krkTilFi  228 (554)
T KOG2028|consen  159 QNRIPSMILWGPPGTGKTTLARLIASTSKKH---SYRFVELSATNAK-------TNDVRDIFEQAQNEKSLTKRKTILFI  228 (554)
T ss_pred             cCCCCceEEecCCCCchHHHHHHHHhhcCCC---ceEEEEEeccccc-------hHHHHHHHHHHHHHHhhhcceeEEEe
Confidence            4556789999999999999999999988554   3457776654322       24567777776532    34589999


Q ss_pred             cCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEee--CCCCCCChHHHhccceEEEecCCCHHHHHHHHHH
Q 047219          395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT--NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       395 DEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaT--N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~  472 (567)
                      |||+.+...+|+.           ||...    ..+.+++|++|  |+...++.+|++|| .++.++..+.++...||..
T Consensus       229 DEiHRFNksQQD~-----------fLP~V----E~G~I~lIGATTENPSFqln~aLlSRC-~VfvLekL~~n~v~~iL~r  292 (554)
T KOG2028|consen  229 DEIHRFNKSQQDT-----------FLPHV----ENGDITLIGATTENPSFQLNAALLSRC-RVFVLEKLPVNAVVTILMR  292 (554)
T ss_pred             HHhhhhhhhhhhc-----------cccee----ccCceEEEecccCCCccchhHHHHhcc-ceeEeccCCHHHHHHHHHH
Confidence            9999997665543           33333    35789999988  77889999999999 9999999999999998887


Q ss_pred             HHHh-----------------hCHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHhccccccCcccCCCcHHHHHHH
Q 047219          473 YAKH-----------------LTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIES  535 (567)
Q Consensus       473 ~~~~-----------------~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~i~~~i~~~~~~~~~~~l~e~le~  535 (567)
                      -...                 +....++.++..+.|    |-+..++...+.+..-..+..-.    ...+..+ +.+.+
T Consensus       293 aia~l~dser~~~~l~n~s~~ve~siidyla~lsdG----DaR~aLN~Lems~~m~~tr~g~~----~~~~lSi-dDvke  363 (554)
T KOG2028|consen  293 AIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDG----DARAALNALEMSLSMFCTRSGQS----SRVLLSI-DDVKE  363 (554)
T ss_pred             HHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCc----hHHHHHHHHHHHHHHHHhhcCCc----ccceecH-HHHHH
Confidence            4431                 122345666666665    44444444443322211111100    1112233 33444


Q ss_pred             HHHHHHHHHHHHHHHHhhH-----HhhhhccCCCC
Q 047219          536 ATNRRRSLLDAAEQSHQNI-----NNHRTKKQPLD  565 (567)
Q Consensus       536 ~e~~~~~li~~al~~~~~~-----~s~~~~~~~l~  565 (567)
                      ..++...+|+++++.||+.     +|+|..+.+-+
T Consensus       364 ~lq~s~~~YDr~Ge~HYntISA~HKSmRG~D~nAs  398 (554)
T KOG2028|consen  364 GLQRSHILYDRAGEEHYNTISALHKSMRGSDQNAS  398 (554)
T ss_pred             HHhhccceecccchhHHHHHHHHHHhhcCCccchH
Confidence            4556678999999999996     77887777654

>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]

Probab=99.75  E-value=3e-17  Score=163.35  Aligned_cols=194  Identities=24%  Similarity=0.309  Sum_probs=143.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      .+..|++.+|++..|+++.-++...-.+                .....|+||+||||.||||||+.||+++      ++
T Consensus        21 RP~~l~efiGQ~~vk~~L~ifI~AAk~r----------------~e~lDHvLl~GPPGlGKTTLA~IIA~Em------gv   78 (332)
T COG2255          21 RPKTLDEFIGQEKVKEQLQIFIKAAKKR----------------GEALDHVLLFGPPGLGKTTLAHIIANEL------GV   78 (332)
T ss_pred             CcccHHHhcChHHHHHHHHHHHHHHHhc----------------CCCcCeEEeeCCCCCcHHHHHHHHHHHh------cC
Confidence            4568999999999999998877654222                4667899999999999999999999999      88


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-------
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-------  427 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-------  427 (567)
                      ++...+++.+...      ..+-.++..   ..++.||||||||.|.+...+.+..+++...   +..+-+..       
T Consensus        79 n~k~tsGp~leK~------gDlaaiLt~---Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~---lDI~IG~gp~Arsv~  146 (332)
T COG2255          79 NLKITSGPALEKP------GDLAAILTN---LEEGDVLFIDEIHRLSPAVEEVLYPAMEDFR---LDIIIGKGPAARSIR  146 (332)
T ss_pred             CeEecccccccCh------hhHHHHHhc---CCcCCeEEEehhhhcChhHHHHhhhhhhhee---EEEEEccCCccceEe
Confidence            8888887766431      223334443   3357899999999998765444444433211   01111100       


Q ss_pred             -cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh----CHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          428 -QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL----TKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       428 -~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~----~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                       .-..+.+|+||.+.+.+...|+.||....+++.++.++..+|+......+    ..+....++..+.| +++--..|++
T Consensus       147 ldLppFTLIGATTr~G~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRG-TPRIAnRLLr  225 (332)
T COG2255         147 LDLPPFTLIGATTRAGMLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRSRG-TPRIANRLLR  225 (332)
T ss_pred             ccCCCeeEeeeccccccccchhHHhcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhccC-CcHHHHHHHH
Confidence             12579999999999999999999999999999999999999999887754    46678888888776 4554444444


Q ss_pred             H
Q 047219          503 Q  503 (567)
Q Consensus       503 ~  503 (567)
                      .
T Consensus       226 R  226 (332)
T COG2255         226 R  226 (332)
T ss_pred             H
Confidence            4

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.75  E-value=3.1e-18  Score=180.85  Aligned_cols=205  Identities=21%  Similarity=0.300  Sum_probs=147.0

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ......+++++|.+...+++++.+...                   .....+||+.|++||||+++|+.||..+.+.  .
T Consensus        71 ~~~~~~~~~LIG~~~~~~~~~eqik~~-------------------ap~~~~vLi~GetGtGKel~A~~iH~~s~r~--~  129 (403)
T COG1221          71 YLKSEALDDLIGESPSLQELREQIKAY-------------------APSGLPVLIIGETGTGKELFARLIHALSARR--A  129 (403)
T ss_pred             hccchhhhhhhccCHHHHHHHHHHHhh-------------------CCCCCcEEEecCCCccHHHHHHHHHHhhhcc--c
Confidence            345567899999999999999999763                   6778899999999999999999999776552  2


Q ss_pred             CcCeEEechh-----hHHhhhhchhHHHHH-------HHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHH
Q 047219          353 GVPLMYVPLE-----VVMSKYYGESERLLG-------KVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL  420 (567)
Q Consensus       353 ~~~~~~i~~~-----~l~s~~~G~~~~~l~-------~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL  420 (567)
                      ..||+.+||.     ...+++||+.+..+.       .+|    +.+.+|+||||||+.|++..|..+..++++  ..+.
T Consensus       130 ~~PFI~~NCa~~~en~~~~eLFG~~kGaftGa~~~k~Glf----e~A~GGtLfLDEI~~LP~~~Q~kLl~~le~--g~~~  203 (403)
T COG1221         130 EAPFIAFNCAAYSENLQEAELFGHEKGAFTGAQGGKAGLF----EQANGGTLFLDEIHRLPPEGQEKLLRVLEE--GEYR  203 (403)
T ss_pred             CCCEEEEEHHHhCcCHHHHHHhccccceeecccCCcCchh----eecCCCEEehhhhhhCCHhHHHHHHHHHHc--CceE
Confidence            4455555554     455567776444322       233    334589999999999998877777666655  3343


Q ss_pred             HhhcCcccCCcEEEEEeeCC--CCCCCh--HHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHH---------------
Q 047219          421 RQIDGFEQDKKVVVIAATNR--KQDLDP--ALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---------------  481 (567)
Q Consensus       421 ~~ld~~~~~~~viVIaaTN~--~~~Ld~--aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~---------------  481 (567)
                      +..+....+.+|++|+|||.  .+.+..  +|++|+ ..+.+.+|++++|.+++..++++|....               
T Consensus       204 rvG~~~~~~~dVRli~AT~~~l~~~~~~g~dl~~rl-~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~~a  282 (403)
T COG1221         204 RVGGSQPRPVDVRLICATTEDLEEAVLAGADLTRRL-NILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSPEA  282 (403)
T ss_pred             ecCCCCCcCCCceeeeccccCHHHHHHhhcchhhhh-cCceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHH
Confidence            34443345679999999974  344555  888877 6788899999999999999888765443               


Q ss_pred             HHHHHHhccCCCHHHHHHHHHHHH
Q 047219          482 LAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       482 l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ...+..+.+.-+.++|++++.++.
T Consensus       283 ~~~L~~y~~pGNirELkN~Ve~~~  306 (403)
T COG1221         283 LRALLAYDWPGNIRELKNLVERAV  306 (403)
T ss_pred             HHHHHhCCCCCcHHHHHHHHHHHH
Confidence            444444544455556666555554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.75  E-value=7.4e-17  Score=167.03  Aligned_cols=196  Identities=21%  Similarity=0.261  Sum_probs=136.0

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      +|++++|++++++.|...+......                ...+.+++|+||||||||++|+++++++      +..+.
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~----------------~~~~~~~ll~Gp~G~GKT~la~~ia~~~------~~~~~   59 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMR----------------QEALDHLLLYGPPGLGKTTLAHIIANEM------GVNLK   59 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhc----------------CCCCCeEEEECCCCCCHHHHHHHHHHHh------CCCEE
Confidence            6899999999999998887543111                2456789999999999999999999998      44455


Q ss_pred             EechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC-c------ccCC
Q 047219          358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG-F------EQDK  430 (567)
Q Consensus       358 ~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~-~------~~~~  430 (567)
                      .+.++....      ...+...+..   ...+.+|||||||.+....+..+...+.+....+  .++. .      ....
T Consensus        60 ~~~~~~~~~------~~~l~~~l~~---~~~~~vl~iDEi~~l~~~~~e~l~~~~~~~~~~~--v~~~~~~~~~~~~~~~  128 (305)
T TIGR00635        60 ITSGPALEK------PGDLAAILTN---LEEGDVLFIDEIHRLSPAVEELLYPAMEDFRLDI--VIGKGPSARSVRLDLP  128 (305)
T ss_pred             EeccchhcC------chhHHHHHHh---cccCCEEEEehHhhhCHHHHHHhhHHHhhhheee--eeccCccccceeecCC
Confidence            544332211      0112222222   2236899999999998665443333222211100  0010 0      0123


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      .+.+|++||++..++++|++||...+.++.|+.++..++++..+..    +..+.++.+++.+.|. ++.+..++..+|.
T Consensus       129 ~~~li~~t~~~~~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~-pR~~~~ll~~~~~  207 (305)
T TIGR00635       129 PFTLVGATTRAGMLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGT-PRIANRLLRRVRD  207 (305)
T ss_pred             CeEEEEecCCccccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCC-cchHHHHHHHHHH
Confidence            4889999999999999999999888999999999999999988764    5677888999988875 4666777777764


Q ss_pred             H
Q 047219          507 S  507 (567)
Q Consensus       507 ~  507 (567)
                      .
T Consensus       208 ~  208 (305)
T TIGR00635       208 F  208 (305)
T ss_pred             H
Confidence            3

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.74  E-value=1.6e-17  Score=174.85  Aligned_cols=203  Identities=25%  Similarity=0.355  Sum_probs=155.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      .+-+|+.++-..+.|+.|.+-+..+++..+.|++.|.+|        -++.|||||||||||+++.|+|+++      +.
T Consensus       196 HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkaw--------KRGYLLYGPPGTGKSS~IaAmAn~L------~y  261 (457)
T KOG0743|consen  196 HPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAW--------KRGYLLYGPPGTGKSSFIAAMANYL------NY  261 (457)
T ss_pred             CCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcch--------hccceeeCCCCCCHHHHHHHHHhhc------CC
Confidence            348999999999999999999999999999999998655        4899999999999999999999999      66


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhh---hh--hHH--HHHHHHHHHHHhhcCcc
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARD---SE--MHE--ATRRILSVLLRQIDGFE  427 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q---~~--l~~--~~~~vl~~LL~~ld~~~  427 (567)
                      .++.++..+....      ..++.++....   +.+||+|.+||+-...+.   ..  ..+  ...-++..||..+|++-
T Consensus       262 dIydLeLt~v~~n------~dLr~LL~~t~---~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlw  332 (457)
T KOG0743|consen  262 DIYDLELTEVKLD------SDLRHLLLATP---NKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLW  332 (457)
T ss_pred             ceEEeeeccccCc------HHHHHHHHhCC---CCcEEEEeecccccccccccccccccccCCcceeehHHhhhhhcccc
Confidence            6776665543321      12566655443   468999999998643221   10  000  11235678999999986


Q ss_pred             cCC--cEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhh-CHHHHHHHHHhccC--CCHHHHHHH
Q 047219          428 QDK--KVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHL-TKAELAELATATEE--MSGRDIRDV  500 (567)
Q Consensus       428 ~~~--~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~-~~~~l~~la~~t~g--~s~~dL~~L  500 (567)
                      ...  .-++|+|||..+.|||||+|  |+|..|++...+...-+.++..++..- +...+.++.+...+  .+++|+...
T Consensus       333 Sscg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~l~~~~~~tPA~V~e~  412 (457)
T KOG0743|consen  333 SSCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDEIERLIEETEVTPAQVAEE  412 (457)
T ss_pred             ccCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHHHhhcCccCHHHHHHH
Confidence            655  78999999999999999999  999999999999999999998887642 23444444444443  588887544

>PRK15115 response regulator GlrR; Provisional

Probab=99.74  E-value=6.1e-18  Score=184.10  Aligned_cols=258  Identities=16%  Similarity=0.208  Sum_probs=162.0

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .++|.+..++.+.+.+...                   .....+++|+|++|||||++|+++|+...+.   +.+|+.++
T Consensus       135 ~lig~s~~~~~~~~~~~~~-------------------a~~~~~vli~Ge~GtGk~~lA~~ih~~s~r~---~~~f~~i~  192 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMV-------------------AQSDVSVLINGQSGTGKEILAQAIHNASPRA---SKPFIAIN  192 (444)
T ss_pred             cccccCHHHHHHHHHHHhh-------------------ccCCCeEEEEcCCcchHHHHHHHHHHhcCCC---CCCeEEEe
Confidence            5788888877777666543                   3456789999999999999999999998654   44566666


Q ss_pred             hh-----hHHhhhhchhHHHHHHHH---HHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          361 LE-----VVMSKYYGESERLLGKVF---SLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       361 ~~-----~l~s~~~G~~~~~l~~~f---~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      |.     .+.+.+||..........   ......+.+++|||||||.|+...|..+..+++.  ..+...........++
T Consensus       193 c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~~~q~~L~~~l~~--~~~~~~g~~~~~~~~~  270 (444)
T PRK15115        193 CGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDEIGDMPAPLQVKLLRVLQE--RKVRPLGSNRDIDIDV  270 (444)
T ss_pred             CCCCCHHHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEccccCCHHHHHHHHHHHhh--CCEEeCCCCceeeeeE
Confidence            54     344445554321110000   0001233469999999999998766655544332  1111111111223478


Q ss_pred             EEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          433 VVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       433 iVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ++|++|+.       .+.|+++|++|+ ..+.+.+|++++|.+++..+++++.............++++..+..|..+.|
T Consensus       271 rii~~~~~~l~~~~~~~~f~~~l~~~l-~~~~i~lPpLr~R~eDi~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~W  349 (444)
T PRK15115        271 RIISATHRDLPKAMARGEFREDLYYRL-NVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTASW  349 (444)
T ss_pred             EEEEeCCCCHHHHHHcCCccHHHHHhh-ceeeecCCChHhccccHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCC
Confidence            99999986       347889999999 7899999999999999988777654443333333334556666666666665


Q ss_pred             -------HHHHHHHHh---c-cccccCc-------ccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          506 -------RSWASKIIR---G-QITKDGE-------QACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       506 -------~~a~~r~i~---~-~i~~~~~-------~~~~~~l~e~le~~e~~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                             ++.+++.+.   + .++....       ....+.+...++.+|   +.+|.+++..++++++++++.+++|+
T Consensus       350 pgNvreL~~~i~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~E---~~~i~~al~~~~gn~~~aA~~Lgisr  425 (444)
T PRK15115        350 PGNVRQLVNVIEQCVALTSSPVISDALVEQALEGENTALPTFVEARNQFE---LNYLRKLLQITKGNVTHAARMAGRNR  425 (444)
T ss_pred             CChHHHHHHHHHHHHHhCCCCccChhhhhhhhcccccccccHHHHHHHHH---HHHHHHHHHHhCCCHHHHHHHhCCCH
Confidence                   233333221   1 1111100       001123333444444   99999999999999999999999985

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.74  E-value=5.7e-18  Score=184.80  Aligned_cols=261  Identities=17%  Similarity=0.176  Sum_probs=162.0

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      .+..++|.+..+..+.+.+...                   .....++|++|++||||+++|+++|..+.+.   +.+|+
T Consensus       141 ~~~~ii~~S~~~~~~~~~~~~~-------------------a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~---~~~~~  198 (457)
T PRK11361        141 QWGHILTNSPAMMDICKDTAKI-------------------ALSQASVLISGESGTGKELIARAIHYNSRRA---KGPFI  198 (457)
T ss_pred             cccceecccHHHhHHHHHHHHH-------------------cCCCcEEEEEcCCCccHHHHHHHHHHhCCCC---CCCeE
Confidence            4567899999888888776654                   4566789999999999999999999987643   34455


Q ss_pred             Eechh-----hHHhhhhchhHHHHHHH---HHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          358 YVPLE-----VVMSKYYGESERLLGKV---FSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       358 ~i~~~-----~l~s~~~G~~~~~l~~~---f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      .++|.     .+.+.+||.........   .......+.+++|||||||.|....|..+..+++..  .+.........+
T Consensus       199 ~i~c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~~~q~~L~~~l~~~--~~~~~~~~~~~~  276 (457)
T PRK11361        199 KVNCAALPESLLESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPLVLQAKLLRILQER--EFERIGGHQTIK  276 (457)
T ss_pred             EEECCCCCHHHHHHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCCHHHHHHHHHHHhcC--cEEeCCCCceee
Confidence            55554     44555666432111000   000112344799999999999877655444333220  000011111223


Q ss_pred             CcEEEEEeeCCC-------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          430 KKVVVIAATNRK-------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       430 ~~viVIaaTN~~-------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .++++|++||..       +.++++|++|+ ..+.+..|++++|.+++..++.++.............+++...+..|..
T Consensus       277 ~~~rii~~t~~~l~~~~~~g~~~~~l~~~l-~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~  355 (457)
T PRK11361        277 VDIRIIAATNRDLQAMVKEGTFREDLFYRL-NVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTA  355 (457)
T ss_pred             eceEEEEeCCCCHHHHHHcCCchHHHHHHh-ccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHc
Confidence            578999999863       57899999999 7799999999999999988776554433322222233455555555555


Q ss_pred             HHH-------HHHHHHHHh---c-ccccc-----C----c----c-c---CCCcHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 047219          503 QAE-------RSWASKIIR---G-QITKD-----G----E----Q-A---CLPPLQEYIESATNRRRSLLDAAEQSHQNI  554 (567)
Q Consensus       503 ~a~-------~~a~~r~i~---~-~i~~~-----~----~----~-~---~~~~l~e~le~~e~~~~~li~~al~~~~~~  554 (567)
                      +.|       .+.+++.+.   + .++..     .    .    . .   ...++.+.++.+|   +.+|..++.+++++
T Consensus       356 ~~wpgNv~eL~~~~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~E---~~~i~~al~~~~gn  432 (457)
T PRK11361        356 WSWPGNIRELSNVIERAVVMNSGPIIFSEDLPPQIRQPVCNAGEVKTAPVGERNLKEEIKRVE---KRIIMEVLEQQEGN  432 (457)
T ss_pred             CCCCCcHHHHHHHHHHHHHhCCCCcccHHHChHhhhcccccccccccccccccchhhHHHHHH---HHHHHHHHHHhCCC
Confidence            444       222222211   0 01000     0    0    0 0   0013444555555   99999999999999


Q ss_pred             HhhhhccCCCCC
Q 047219          555 NNHRTKKQPLDL  566 (567)
Q Consensus       555 ~s~~~~~~~l~~  566 (567)
                      ++++++.+++|+
T Consensus       433 ~~~aA~~LGisr  444 (457)
T PRK11361        433 RTRTALMLGISR  444 (457)
T ss_pred             HHHHHHHHCCCH
Confidence            999999999885

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.73  E-value=2.1e-16  Score=165.77  Aligned_cols=198  Identities=21%  Similarity=0.256  Sum_probs=137.9

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      +.+|++++|+++.++.+...+......                ..++.++||+||||||||++|+++|+++      +..
T Consensus        21 P~~~~~~vG~~~~~~~l~~~l~~~~~~----------------~~~~~~~ll~GppG~GKT~la~~ia~~l------~~~   78 (328)
T PRK00080         21 PKSLDEFIGQEKVKENLKIFIEAAKKR----------------GEALDHVLLYGPPGLGKTTLANIIANEM------GVN   78 (328)
T ss_pred             cCCHHHhcCcHHHHHHHHHHHHHHHhc----------------CCCCCcEEEECCCCccHHHHHHHHHHHh------CCC
Confidence            458999999999999998877532111                3557799999999999999999999999      445


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-------c
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-------Q  428 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-------~  428 (567)
                      +..++++.+..      ...+..++...   ..+++|||||||.+....++.+...+++..  +.-.++.-.       .
T Consensus        79 ~~~~~~~~~~~------~~~l~~~l~~l---~~~~vl~IDEi~~l~~~~~e~l~~~~e~~~--~~~~l~~~~~~~~~~~~  147 (328)
T PRK00080         79 IRITSGPALEK------PGDLAAILTNL---EEGDVLFIDEIHRLSPVVEEILYPAMEDFR--LDIMIGKGPAARSIRLD  147 (328)
T ss_pred             eEEEecccccC------hHHHHHHHHhc---ccCCEEEEecHhhcchHHHHHHHHHHHhcc--eeeeeccCccccceeec
Confidence            65555443221      12233333332   346899999999997554332211111100  000001000       1


Q ss_pred             CCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      ..++.+|++||+...++++|++||...+.|+.|+.+++.++++..+..    +..+.+..++..+.| +++.+..+++.+
T Consensus       148 l~~~~li~at~~~~~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G-~pR~a~~~l~~~  226 (328)
T PRK00080        148 LPPFTLIGATTRAGLLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRSRG-TPRIANRLLRRV  226 (328)
T ss_pred             CCCceEEeecCCcccCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCC-CchHHHHHHHHH
Confidence            134789999999999999999999889999999999999999988764    566788899988877 457777777776


Q ss_pred             HHH
Q 047219          505 ERS  507 (567)
Q Consensus       505 ~~~  507 (567)
                      +..
T Consensus       227 ~~~  229 (328)
T PRK00080        227 RDF  229 (328)
T ss_pred             HHH
Confidence            643

>TIGR00763 lon ATP-dependent protease La

Probab=99.72  E-value=2.1e-16  Score=183.01  Aligned_cols=204  Identities=25%  Similarity=0.314  Sum_probs=145.1

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++++|++++++.+.+.+......+               ...+.+++|+||||||||++|++||+.+      +.+++.+
T Consensus       320 ~~~~G~~~~k~~i~~~~~~~~~~~---------------~~~~~~lll~GppG~GKT~lAk~iA~~l------~~~~~~i  378 (775)
T TIGR00763       320 EDHYGLKKVKERILEYLAVQKLRG---------------KMKGPILCLVGPPGVGKTSLGKSIAKAL------NRKFVRF  378 (775)
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhc---------------CCCCceEEEECCCCCCHHHHHHHHHHHh------cCCeEEE
Confidence            458899999999988765331111               2234479999999999999999999999      5567766


Q ss_pred             chhhH------H---hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC-----
Q 047219          360 PLEVV------M---SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG-----  425 (567)
Q Consensus       360 ~~~~l------~---s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~-----  425 (567)
                      ++..+      .   ..|.|.....+...|..+....  .||||||||.+....+...       .+.|+..+|.     
T Consensus       379 ~~~~~~~~~~i~g~~~~~~g~~~g~i~~~l~~~~~~~--~villDEidk~~~~~~~~~-------~~aLl~~ld~~~~~~  449 (775)
T TIGR00763       379 SLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKN--PLFLLDEIDKIGSSFRGDP-------ASALLEVLDPEQNNA  449 (775)
T ss_pred             eCCCcccHHHHcCCCCceeCCCCchHHHHHHHhCcCC--CEEEEechhhcCCccCCCH-------HHHHHHhcCHHhcCc
Confidence            54322      1   2455666666667777765443  5999999999986544322       1233333331     


Q ss_pred             c--------ccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHH--------------hhCHHHHH
Q 047219          426 F--------EQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK--------------HLTKAELA  483 (567)
Q Consensus       426 ~--------~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~--------------~~~~~~l~  483 (567)
                      +        ....++++|+|||..+.++++|++|| .+|+|+.|+.+++.+|++.++.              .+.++.+.
T Consensus       450 f~d~~~~~~~d~s~v~~I~TtN~~~~i~~~L~~R~-~vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~  528 (775)
T TIGR00763       450 FSDHYLDVPFDLSKVIFIATANSIDTIPRPLLDRM-EVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALL  528 (775)
T ss_pred             cccccCCceeccCCEEEEEecCCchhCCHHHhCCe-eEEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHH
Confidence            1        11257899999999999999999999 6899999999999999987652              13445566


Q ss_pred             HHHH-hccCCCHHHHHHHHHHHHHHHHHHHHh
Q 047219          484 ELAT-ATEEMSGRDIRDVCQQAERSWASKIIR  514 (567)
Q Consensus       484 ~la~-~t~g~s~~dL~~L~~~a~~~a~~r~i~  514 (567)
                      .+++ ++..+..++|+..+....+.++.+++.
T Consensus       529 ~i~~~~~~e~g~R~l~r~i~~~~~~~~~~~~~  560 (775)
T TIGR00763       529 LLIKYYTREAGVRNLERQIEKICRKAAVKLVE  560 (775)
T ss_pred             HHHHhcChhcCChHHHHHHHHHHHHHHHHHHh
Confidence            5554 455567788888888888777776664

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.71  E-value=2e-17  Score=180.85  Aligned_cols=260  Identities=18%  Similarity=0.226  Sum_probs=161.6

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      +..++|.+...+++.+.+...                   .....++++.|++||||+++|+++|....+.   ..+|+.
T Consensus       133 ~~~lig~s~~~~~v~~~i~~~-------------------a~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~---~~~~~~  190 (463)
T TIGR01818       133 SAELIGEAPAMQEVFRAIGRL-------------------SRSDITVLINGESGTGKELVARALHRHSPRA---NGPFIA  190 (463)
T ss_pred             ccceeecCHHHHHHHHHHHHH-------------------hCcCCeEEEECCCCCCHHHHHHHHHHhCCCC---CCCeEE
Confidence            456899999998888777543                   4556789999999999999999999988644   345555


Q ss_pred             echh-----hHHhhhhchhHHHHHHHHH---HHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          359 VPLE-----VVMSKYYGESERLLGKVFS---LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       359 i~~~-----~l~s~~~G~~~~~l~~~f~---~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      ++|.     .+.+.+||+....+.....   .....+.+++||||||+.|....|..+.++++.  ..+....+......
T Consensus       191 ~~c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~~~q~~ll~~l~~--~~~~~~~~~~~~~~  268 (463)
T TIGR01818       191 LNMAAIPKDLIESELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPLDAQTRLLRVLAD--GEFYRVGGRTPIKV  268 (463)
T ss_pred             EeCCCCCHHHHHHHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCHHHHHHHHHHHhc--CcEEECCCCceeee
Confidence            5554     4455556643211111000   001234479999999999987755444333221  00000111112234


Q ss_pred             cEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          431 KVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       431 ~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ++++|++|+.       .+.++++|++|+ ..+.+.+|++++|.+++..+++++.......+.....+++...+..|..+
T Consensus       269 ~~rii~~~~~~l~~~~~~~~f~~~L~~rl-~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  347 (463)
T TIGR01818       269 DVRIVAATHQNLEALVRQGKFREDLFHRL-NVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQL  347 (463)
T ss_pred             eeEEEEeCCCCHHHHHHcCCcHHHHHHHh-CcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhC
Confidence            7899999986       347889999999 77899999999999999988876554433333333345555555555555


Q ss_pred             HH-------HHHHHHHHh---c-cccccCc-----c---------c---------------------CCCcHHHHHHHHH
Q 047219          504 AE-------RSWASKIIR---G-QITKDGE-----Q---------A---------------------CLPPLQEYIESAT  537 (567)
Q Consensus       504 a~-------~~a~~r~i~---~-~i~~~~~-----~---------~---------------------~~~~l~e~le~~e  537 (567)
                      .|       ++.+++.+.   + .++....     .         .                     ....+.+.++.+|
T Consensus       348 ~wpgNvreL~~~~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E  427 (463)
T TIGR01818       348 RWPGNVRQLENLCRWLTVMASGDEVLVSDLPAELALTGRPASAPDSDGQDSWDEALEAWAKQALSRGEQGLLDRALPEFE  427 (463)
T ss_pred             CCCChHHHHHHHHHHHHHhCCCCcccHHhchHHHhccccccccccccccccccccccccccccccccccchHHHHHHHHH
Confidence            55       222222221   0 0100000     0         0                     0011222344444


Q ss_pred             HHHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          538 NRRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       538 ~~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                         +.+|..++..++++++++++.+++|+
T Consensus       428 ---~~~i~~al~~~~gn~~~aA~~Lgisr  453 (463)
T TIGR01818       428 ---RPLLEAALQHTRGHKQEAAALLGWGR  453 (463)
T ss_pred             ---HHHHHHHHHHcCCCHHHHHHHhCCCH
Confidence               89999999999999999999999885

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.70  E-value=5.8e-16  Score=173.18  Aligned_cols=190  Identities=18%  Similarity=0.203  Sum_probs=139.2

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      ...+|++|+|++..++.|++.+..                    .+.++.+||+||+|||||++|+++++.+++.. ...
T Consensus        11 RPqtFdEVIGQe~Vv~~L~~aL~~--------------------gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~   70 (830)
T PRK07003         11 RPKDFASLVGQEHVVRALTHALDG--------------------GRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTS   70 (830)
T ss_pred             CCCcHHHHcCcHHHHHHHHHHHhc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCC
Confidence            457899999999999999887752                    45577789999999999999999999996531 111


Q ss_pred             cC-----------------eEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 VP-----------------LMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .+                 ++.++...      ....+.++.+++.+..   .....|+||||+|.|...          
T Consensus        71 ~PCG~C~sCr~I~~G~h~DviEIDAas------~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT~~----------  134 (830)
T PRK07003         71 QPCGVCRACREIDEGRFVDYVEMDAAS------NRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLTNH----------  134 (830)
T ss_pred             CCCcccHHHHHHhcCCCceEEEecccc------cccHHHHHHHHHHHHhccccCCceEEEEeChhhCCHH----------
Confidence            12                 22222211      0112334555554432   234579999999999632          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.||+.|+.  .+.+++||++||.+..|.+.|+||| ..+.|..++.++..+.|+..+..    +..+.+..+++..
T Consensus       135 -A~NALLKtLEE--PP~~v~FILaTtd~~KIp~TIrSRC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A  210 (830)
T PRK07003        135 -AFNAMLKTLEE--PPPHVKFILATTDPQKIPVTVLSRC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQALRLLARAA  210 (830)
T ss_pred             -HHHHHHHHHHh--cCCCeEEEEEECChhhccchhhhhe-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             44677887773  4668999999999999999999999 89999999999999999887764    5577888888887


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.++..+++.+++
T Consensus       211 ~G-smRdALsLLdQAi  225 (830)
T PRK07003        211 QG-SMRDALSLTDQAI  225 (830)
T ss_pred             CC-CHHHHHHHHHHHH
Confidence            76 4556556655555

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.70  E-value=4.3e-16  Score=172.26  Aligned_cols=191  Identities=17%  Similarity=0.191  Sum_probs=139.0

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC---
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP---  350 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~---  350 (567)
                      ..+.+|++|+|++..++.|++.+..                    .+.++.+||+||+|||||++|+.+++.+.+..   
T Consensus        10 YRPqtFddVIGQe~vv~~L~~al~~--------------------gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~   69 (700)
T PRK12323         10 WRPRDFTTLVGQEHVVRALTHALEQ--------------------QRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADG   69 (700)
T ss_pred             hCCCcHHHHcCcHHHHHHHHHHHHh--------------------CCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccc
Confidence            3457899999999999999988752                    45677889999999999999999999996521   


Q ss_pred             ---CCCc-----------------CeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhh
Q 047219          351 ---WQGV-----------------PLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSE  407 (567)
Q Consensus       351 ---~~~~-----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~  407 (567)
                         ...-                 .++.++...      ...-+.++++.+.+..   .....|+||||+|.|..     
T Consensus        70 ~~g~~~~PCG~C~sC~~I~aG~hpDviEIdAas------~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls~-----  138 (700)
T PRK12323         70 EGGITAQPCGQCRACTEIDAGRFVDYIEMDAAS------NRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLTN-----  138 (700)
T ss_pred             cccCCCCCCcccHHHHHHHcCCCCcceEecccc------cCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcCH-----
Confidence               0001                 222332221      0112344555544332   23457999999999963     


Q ss_pred             hHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHH
Q 047219          408 MHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELA  483 (567)
Q Consensus       408 l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~  483 (567)
                            ...+.||+.++.  .+.+++||++||.+..|.+.++||| ..+.|..++.++..+.++..+..    +..+.+.
T Consensus       139 ------~AaNALLKTLEE--PP~~v~FILaTtep~kLlpTIrSRC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~  209 (700)
T PRK12323        139 ------HAFNAMLKTLEE--PPEHVKFILATTDPQKIPVTVLSRC-LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALR  209 (700)
T ss_pred             ------HHHHHHHHhhcc--CCCCceEEEEeCChHhhhhHHHHHH-HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHH
Confidence                  345778888873  5678999999999999999999999 89999999999998888877654    3455677


Q ss_pred             HHHHhccCCCHHHHHHHHHHHH
Q 047219          484 ELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       484 ~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .++....| +.++..+++..++
T Consensus       210 ~IA~~A~G-s~RdALsLLdQai  230 (700)
T PRK12323        210 LLAQAAQG-SMRDALSLTDQAI  230 (700)
T ss_pred             HHHHHcCC-CHHHHHHHHHHHH
Confidence            77777665 5667666666544

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.69  E-value=5.7e-16  Score=178.43  Aligned_cols=188  Identities=21%  Similarity=0.287  Sum_probs=142.2

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -.+++++|+++.+..+.+.+.                     .....+++|+||||||||++|+++|+.+...    .+.
T Consensus       179 ~~l~~~igr~~ei~~~~~~L~---------------------~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~  237 (731)
T TIGR02639       179 GKIDPLIGREDELERTIQVLC---------------------RRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLK  237 (731)
T ss_pred             CCCCcccCcHHHHHHHHHHHh---------------------cCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhc
Confidence            357889999999998876653                     3446789999999999999999999987432    233


Q ss_pred             CcCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +..++.+++..+.  .++.|+.+..++.+|+.+.... ++||||||||.|.+........  ....+.|...+.    ++
T Consensus       238 ~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~-~~ILfiDEih~l~~~g~~~~~~--~~~~~~L~~~l~----~g  310 (731)
T TIGR02639       238 NAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEP-NAILFIDEIHTIVGAGATSGGS--MDASNLLKPALS----SG  310 (731)
T ss_pred             CCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccC-CeEEEEecHHHHhccCCCCCcc--HHHHHHHHHHHh----CC
Confidence            6678899988887  4789999999999999987664 5899999999998654321111  112233444443    57


Q ss_pred             cEEEEEeeCCC-----CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhccCCC
Q 047219          431 KVVVIAATNRK-----QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATEEMS  493 (567)
Q Consensus       431 ~viVIaaTN~~-----~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~g~s  493 (567)
                      .+.+|++||..     ...|++|.+|| ..++++.|+.+++.+|++.+...        +.++.+..++..+..|-
T Consensus       311 ~i~~IgaTt~~e~~~~~~~d~al~rRf-~~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi  385 (731)
T TIGR02639       311 KLRCIGSTTYEEYKNHFEKDRALSRRF-QKIDVGEPSIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYI  385 (731)
T ss_pred             CeEEEEecCHHHHHHHhhhhHHHHHhC-ceEEeCCCCHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhccc
Confidence            89999999863     35799999999 58999999999999999976653        35566666666665543

>PF00158 Sigma54_activat: Sigma-54 interaction domain; InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor

Probab=99.69  E-value=1.1e-17  Score=158.90  Aligned_cols=148  Identities=21%  Similarity=0.317  Sum_probs=100.3

Q ss_pred             ccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          282 IAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       282 IiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      |+|.+..++++++.+...                   +..+.+|||+|++||||+++|++||+.+.+.   ..+|+.++|
T Consensus         1 liG~s~~m~~~~~~~~~~-------------------a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~---~~pfi~vnc   58 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRA-------------------ASSDLPVLITGETGTGKELLARAIHNNSPRK---NGPFISVNC   58 (168)
T ss_dssp             SS--SHHHHHHHHHHHHH-------------------TTSTS-EEEECSTTSSHHHHHHHHHHCSTTT---TS-EEEEET
T ss_pred             CEeCCHHHHHHHHHHHHH-------------------hCCCCCEEEEcCCCCcHHHHHHHHHHhhhcc---cCCeEEEeh
Confidence            689999999999999876                   6677999999999999999999999988654   456666666


Q ss_pred             h-----hHHhhhhchhHH-------HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          362 E-----VVMSKYYGESER-------LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       362 ~-----~l~s~~~G~~~~-------~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      .     .+...+||....       ....+|+.|.    +++||||||+.|++..|..+..+++.  ..+....+....+
T Consensus        59 ~~~~~~~~e~~LFG~~~~~~~~~~~~~~G~l~~A~----~GtL~Ld~I~~L~~~~Q~~Ll~~l~~--~~~~~~g~~~~~~  132 (168)
T PF00158_consen   59 AALPEELLESELFGHEKGAFTGARSDKKGLLEQAN----GGTLFLDEIEDLPPELQAKLLRVLEE--GKFTRLGSDKPVP  132 (168)
T ss_dssp             TTS-HHHHHHHHHEBCSSSSTTTSSEBEHHHHHTT----TSEEEEETGGGS-HHHHHHHHHHHHH--SEEECCTSSSEEE
T ss_pred             hhhhcchhhhhhhccccccccccccccCCceeecc----ceEEeecchhhhHHHHHHHHHHHHhh--chhcccccccccc
Confidence            4     455667775321       1124555544    79999999999998876665555433  1111112222345


Q ss_pred             CcEEEEEeeCC-------CCCCChHHHhccceEEEe
Q 047219          430 KKVVVIAATNR-------KQDLDPALISRFDSMITF  458 (567)
Q Consensus       430 ~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i  458 (567)
                      .+++||++|+.       .+.|.++|++|+ ..+.+
T Consensus       133 ~~~RiI~st~~~l~~~v~~g~fr~dLy~rL-~~~~i  167 (168)
T PF00158_consen  133 VDVRIIASTSKDLEELVEQGRFREDLYYRL-NVFTI  167 (168)
T ss_dssp             --EEEEEEESS-HHHHHHTTSS-HHHHHHH-TTEEE
T ss_pred             ccceEEeecCcCHHHHHHcCCChHHHHHHh-ceEec
Confidence            68999999986       468999999998 55544

These have a conserved domain of about 230 residues involved in the ATP-dependent [, ] interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems [] and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction []. The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1NY6_K 3M0E_G 1NY5_A 1OJL_A 3DZD_B 2C9C_A 2C98_A 2C96_A 2BJV_A 2C99_A ....

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.69  E-value=1.7e-15  Score=163.74  Aligned_cols=190  Identities=17%  Similarity=0.197  Sum_probs=135.5

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-  352 (567)
                      ..+.+|++++|++.+++.|+..+..                    ...++.+||+||||||||++|+++|+.+.+.... 
T Consensus        12 yRP~~f~dvVGQe~iv~~L~~~i~~--------------------~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~   71 (484)
T PRK14956         12 YRPQFFRDVIHQDLAIGALQNALKS--------------------GKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIG   71 (484)
T ss_pred             hCCCCHHHHhChHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccC
Confidence            3457899999999999999887752                    3456679999999999999999999998653110 


Q ss_pred             Cc-----------------CeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHH
Q 047219          353 GV-----------------PLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEAT  412 (567)
Q Consensus       353 ~~-----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~  412 (567)
                      ..                 .++.+++..      ......++.+.+.+..   .....|+||||+|.|...         
T Consensus        72 ~~pCg~C~sC~~i~~g~~~dviEIdaas------~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls~~---------  136 (484)
T PRK14956         72 NEPCNECTSCLEITKGISSDVLEIDAAS------NRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLTDQ---------  136 (484)
T ss_pred             ccccCCCcHHHHHHccCCccceeechhh------cccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcCHH---------
Confidence            11                 122332211      0112334444444332   223579999999999633         


Q ss_pred             HHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh
Q 047219          413 RRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATA  488 (567)
Q Consensus       413 ~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~  488 (567)
                        .++.||+.++.  .+.++++|++|+.+..+.+.+++|| ..+.|..++.++..+.++..+..    +..+.+..++..
T Consensus       137 --A~NALLKtLEE--Pp~~viFILaTte~~kI~~TI~SRC-q~~~f~~ls~~~i~~~L~~i~~~Egi~~e~eAL~~Ia~~  211 (484)
T PRK14956        137 --SFNALLKTLEE--PPAHIVFILATTEFHKIPETILSRC-QDFIFKKVPLSVLQDYSEKLCKIENVQYDQEGLFWIAKK  211 (484)
T ss_pred             --HHHHHHHHhhc--CCCceEEEeecCChhhccHHHHhhh-heeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence              45677887773  5678999999999999999999999 88999999998888888887764    456778888877


Q ss_pred             ccCCCHHHHHHHHHHH
Q 047219          489 TEEMSGRDIRDVCQQA  504 (567)
Q Consensus       489 t~g~s~~dL~~L~~~a  504 (567)
                      ..| +.++.-.++..+
T Consensus       212 S~G-d~RdAL~lLeq~  226 (484)
T PRK14956        212 GDG-SVRDMLSFMEQA  226 (484)
T ss_pred             cCC-hHHHHHHHHHHH
Confidence            766 344544444443

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=99.68  E-value=9e-17  Score=175.16  Aligned_cols=254  Identities=21%  Similarity=0.246  Sum_probs=184.4

Q ss_pred             cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcCeEEech
Q 047219          283 AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVPLMYVPL  361 (567)
Q Consensus       283 iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~~~~i~~  361 (567)
                      ++.+...+.+...++..                   ....-++|+.|+|||||..+||+||+.+... +|+.+||..++.
T Consensus       316 ~~~d~s~a~l~rk~~rv-------------------~~~~~pvll~GEtGtGKe~laraiH~~s~~~gpfvAvNCaAip~  376 (606)
T COG3284         316 PLLDPSRATLLRKAERV-------------------AATDLPVLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPE  376 (606)
T ss_pred             cccCHHHHHHHHHHHHH-------------------hhcCCCeEecCCcchhHHHHHHHHHhcccccCCeEEEEeccchH
Confidence            46666666666655543                   4566789999999999999999999999743 788888888988


Q ss_pred             hhHHhhhhchhHHHHHHHHHHH----hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEe
Q 047219          362 EVVMSKYYGESERLLGKVFSLA----NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAA  437 (567)
Q Consensus       362 ~~l~s~~~G~~~~~l~~~f~~A----~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaa  437 (567)
                      ..+.+++||+........+.+-    -+.+++++||+|||..|+-..|..+++++++  ..++...... .+.++.||+|
T Consensus       377 ~liesELFGy~~GafTga~~kG~~g~~~~A~gGtlFldeIgd~p~~~Qs~LLrVl~e--~~v~p~g~~~-~~vdirvi~a  453 (606)
T COG3284         377 ALIESELFGYVAGAFTGARRKGYKGKLEQADGGTLFLDEIGDMPLALQSRLLRVLQE--GVVTPLGGTR-IKVDIRVIAA  453 (606)
T ss_pred             HhhhHHHhccCccccccchhccccccceecCCCccHHHHhhhchHHHHHHHHHHHhh--CceeccCCcc-eeEEEEEEec
Confidence            9999999998766544333322    2456789999999999999988888887766  4444444444 6779999999


Q ss_pred             eCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----------hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          438 TNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----------LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       438 TN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----------~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                      |++       .+.|.++||+|+ ..+.|.+|++++|.+.+..+.+.          ++.+.+..+..+-|.-+.++|.++
T Consensus       454 th~dl~~lv~~g~fredLyyrL-~~~~i~lP~lr~R~d~~~~l~~~~~~~~~~~~~l~~~~~~~l~~~~WPGNirel~~v  532 (606)
T COG3284         454 THRDLAQLVEQGRFREDLYYRL-NAFVITLPPLRERSDRIPLLDRILKRENDWRLQLDDDALARLLAYRWPGNIRELDNV  532 (606)
T ss_pred             cCcCHHHHHHcCCchHHHHHHh-cCeeeccCchhcccccHHHHHHHHHHccCCCccCCHHHHHHHHhCCCCCcHHHHHHH
Confidence            987       568999999999 88999999999999877765442          345566777777777777777777


Q ss_pred             HHHHHHHHHHHHHhccccccCcccCCCc-H-HHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccCCCCCC
Q 047219          501 CQQAERSWASKIIRGQITKDGEQACLPP-L-QEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDLC  567 (567)
Q Consensus       501 ~~~a~~~a~~r~i~~~i~~~~~~~~~~~-l-~e~le~~e~~~~~li~~al~~~~~~~s~~~~~~~l~~~  567 (567)
                      +..+...+    -.|.+...    .+++ + .+.....++.++..+-+++..++++.+.+++.+++|++
T Consensus       533 ~~~~~~l~----~~g~~~~~----dlp~~l~~~~~~~~~~~~~~~l~~al~~~~~~is~aa~~lgi~R~  593 (606)
T COG3284         533 IERLAALS----DGGRIRVS----DLPPELLEEQATPREDIEKAALLAALQATNGNISEAARLLGISRS  593 (606)
T ss_pred             HHHHHHcC----CCCeeEcc----cCCHHHHhhhcccccchHHHHHHHHHHHcCCCHHHHHHHhCCCHH
Confidence            76654221    11111111    1111 1 11111244555888999999999999999999999863

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.68  E-value=5.8e-16  Score=171.94  Aligned_cols=211  Identities=22%  Similarity=0.331  Sum_probs=141.6

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---C
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---P  350 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~  350 (567)
                      ..+.+|++++|++..++.++..+.                     ...+.++||+||||||||++|+++|+++.+.   +
T Consensus        59 ~rp~~f~~iiGqs~~i~~l~~al~---------------------~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~  117 (531)
T TIGR02902        59 TRPKSFDEIIGQEEGIKALKAALC---------------------GPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASP  117 (531)
T ss_pred             hCcCCHHHeeCcHHHHHHHHHHHh---------------------CCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCC
Confidence            344789999999999999886542                     4556799999999999999999999876432   2


Q ss_pred             CC-CcCeEEechhh-------HHhhhhchhHHHH---HHHH---------HHHhcCCCCcEEEEcCcchhhhhhhhhhHH
Q 047219          351 WQ-GVPLMYVPLEV-------VMSKYYGESERLL---GKVF---------SLANELPNGAIIFLDEVDSFAVARDSEMHE  410 (567)
Q Consensus       351 ~~-~~~~~~i~~~~-------l~s~~~G~~~~~l---~~~f---------~~A~~~a~~~ILfIDEID~L~~~~q~~l~~  410 (567)
                      +. +.+|+.++|..       +...++|.....+   ...|         ..+...+.+++|||||||.|....|..+..
T Consensus       118 ~~~~~~fi~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~~~q~~LL~  197 (531)
T TIGR02902       118 FKEGAAFVEIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHPVQMNKLLK  197 (531)
T ss_pred             cCCCCCEEEEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCHHHHHHHHH
Confidence            22 45778887753       1222222100000   0000         001123457999999999999887776666


Q ss_pred             HHHHHHHHHH----Hhhc-----------CcccCCcEEEEEee-CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHH
Q 047219          411 ATRRILSVLL----RQID-----------GFEQDKKVVVIAAT-NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       411 ~~~~vl~~LL----~~ld-----------~~~~~~~viVIaaT-N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~  474 (567)
                      .+++-...+.    ...+           ....+.++++|++| |.++.+++++++|| ..+.|+.++.+++.++++..+
T Consensus       198 ~Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrsR~-~~I~f~pL~~eei~~Il~~~a  276 (531)
T TIGR02902       198 VLEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRSRC-VEIFFRPLLDEEIKEIAKNAA  276 (531)
T ss_pred             HHHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhhhh-heeeCCCCCHHHHHHHHHHHH
Confidence            5543111110    0000           01124567777665 56899999999999 788999999999999999988


Q ss_pred             Hh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Q 047219          475 KH----LTKAELAELATATEEMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       475 ~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a  508 (567)
                      ++    +.++.++.+..+++  +++++.++++.|...+
T Consensus       277 ~k~~i~is~~al~~I~~y~~--n~Rel~nll~~Aa~~A  312 (531)
T TIGR02902       277 EKIGINLEKHALELIVKYAS--NGREAVNIVQLAAGIA  312 (531)
T ss_pred             HHcCCCcCHHHHHHHHHhhh--hHHHHHHHHHHHHHHH
Confidence            75    45667777777665  6899999998887544

Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.67  E-value=2.2e-15  Score=169.71  Aligned_cols=234  Identities=22%  Similarity=0.274  Sum_probs=167.2

Q ss_pred             CCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHh---ccChhhHHhhhhcccccccC
Q 047219          243 LTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLS---LQSPEVYDDIARGTRCKFES  319 (567)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~---l~~pelf~~l~~~~~~~~~~  319 (567)
                      ++.+++..+++.++..++.-...++..........--+.|+|+++++..+.+.|...   |..|               .
T Consensus       454 v~~~~Ia~vv~~~TgIPv~~l~~~e~~kll~le~~L~~rViGQd~AV~avs~aIrraRaGL~dp---------------~  518 (786)
T COG0542         454 VDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERRLKKRVIGQDEAVEAVSDAIRRARAGLGDP---------------N  518 (786)
T ss_pred             cCHHHHHHHHHHHHCCChhhhchhhHHHHHHHHHHHhcceeChHHHHHHHHHHHHHHhcCCCCC---------------C
Confidence            444667888888887766533333333333344455678999999999999999764   1121               3


Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh------------hchhHHHHHHHHHHHhcCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY------------YGESERLLGKVFSLANELP  387 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~------------~G~~~~~l~~~f~~A~~~a  387 (567)
                      +|..++||.||+|+|||.||+++|..+...   ..+++.+++++++.++            +|+.+   +..++++.+..
T Consensus       519 rPigsFlF~GPTGVGKTELAkaLA~~Lfg~---e~aliR~DMSEy~EkHsVSrLIGaPPGYVGyee---GG~LTEaVRr~  592 (786)
T COG0542         519 RPIGSFLFLGPTGVGKTELAKALAEALFGD---EQALIRIDMSEYMEKHSVSRLIGAPPGYVGYEE---GGQLTEAVRRK  592 (786)
T ss_pred             CCceEEEeeCCCcccHHHHHHHHHHHhcCC---CccceeechHHHHHHHHHHHHhCCCCCCceecc---ccchhHhhhcC
Confidence            444578889999999999999999999654   4679999999988763            44433   34566666777


Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc---------CCcEEEEEeeCC------------------
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ---------DKKVVVIAATNR------------------  440 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~---------~~~viVIaaTN~------------------  440 (567)
                      |++||+||||++-.           .++++.||+.+|.-.-         -.++++|+|||-                  
T Consensus       593 PySViLlDEIEKAH-----------pdV~nilLQVlDdGrLTD~~Gr~VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~  661 (786)
T COG0542         593 PYSVILLDEIEKAH-----------PDVFNLLLQVLDDGRLTDGQGRTVDFRNTIIIMTSNAGSEEILRDADGDDFADKE  661 (786)
T ss_pred             CCeEEEechhhhcC-----------HHHHHHHHHHhcCCeeecCCCCEEecceeEEEEecccchHHHHhhccccccchhh
Confidence            89999999999854           4578888888876421         247999999985                  


Q ss_pred             ----------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-------------CHHHHHHHHHhcc--CCCHH
Q 047219          441 ----------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-------------TKAELAELATATE--EMSGR  495 (567)
Q Consensus       441 ----------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-------------~~~~l~~la~~t~--g~s~~  495 (567)
                                ...|.|+|++|+|.+|.|...+.+...+|+...+..+             .++..+.++....  .|-.+
T Consensus       662 ~~~~~v~~~l~~~F~PEFLNRid~II~F~~L~~~~l~~Iv~~~L~~l~~~L~~~~i~l~~s~~a~~~l~~~gyd~~~GAR  741 (786)
T COG0542         662 ALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAKRLAERGITLELSDEAKDFLAEKGYDPEYGAR  741 (786)
T ss_pred             hHHHHHHHHHHhhCCHHHHhhcccEEeccCCCHHHHHHHHHHHHHHHHHHHHhCCceEEECHHHHHHHHHhccCCCcCch
Confidence                      1137899999999999999999999999999877643             3334444544332  35566


Q ss_pred             HHHHHHHHHHHHH
Q 047219          496 DIRDVCQQAERSW  508 (567)
Q Consensus       496 dL~~L~~~a~~~a  508 (567)
                      -|+.+++.-....
T Consensus       742 pL~R~Iq~~i~~~  754 (786)
T COG0542         742 PLRRAIQQEIEDP  754 (786)
T ss_pred             HHHHHHHHHHHHH
Confidence            6766666555433

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.67  E-value=1.3e-16  Score=173.32  Aligned_cols=261  Identities=16%  Similarity=0.196  Sum_probs=166.1

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .++|.+..++.+.+.+...                   .....+++++|++||||+++|+++|..+.+.   ..+|+.++
T Consensus       140 ~lig~s~~~~~~~~~i~~~-------------------~~~~~~vli~ge~g~gk~~~a~~ih~~s~~~---~~~~i~~~  197 (441)
T PRK10365        140 GMVGKSPAMQHLLSEIALV-------------------APSEATVLIHGDSGTGKELVARAIHASSARS---EKPLVTLN  197 (441)
T ss_pred             ceEecCHHHHHHHHHHhhc-------------------cCCCCeEEEEecCCCCHHHHHHHHHHcCCCC---CCCeeeee
Confidence            4778888887777666433                   4556889999999999999999999988654   34555555


Q ss_pred             hh-----hHHhhhhchhHHHHHHHHH---HHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          361 LE-----VVMSKYYGESERLLGKVFS---LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       361 ~~-----~l~s~~~G~~~~~l~~~f~---~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      |.     .+.+.+||...........   .....+.+|+||||||+.|+...|..+....+.  ..+....+....+.++
T Consensus       198 c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~~~q~~l~~~l~~--~~~~~~~~~~~~~~~~  275 (441)
T PRK10365        198 CAALNESLLESELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPMMQVRLLRAIQE--REVQRVGSNQTISVDV  275 (441)
T ss_pred             CCCCCHHHHHHHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCHHHHHHHHHHHcc--CcEEeCCCCceeeece
Confidence            54     4444555542221100000   001223479999999999987766544433322  0010111111123478


Q ss_pred             EEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          433 VVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       433 iVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ++|++|+.       ...++++|++|+ ..+.+..|++++|.+++..+++++......+......++++..+..|+.+.|
T Consensus       276 rii~~t~~~~~~~~~~~~~~~~l~~~l-~~~~i~~ppLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~w  354 (441)
T PRK10365        276 RLIAATHRDLAAEVNAGRFRQDLYYRL-NVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHYDW  354 (441)
T ss_pred             EEEEeCCCCHHHHHHcCCchHHHHHHh-ccceecCCChhhcchhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhCCC
Confidence            89999876       346899999999 7899999999999999999888776555444444445688888888888888


Q ss_pred             -------HHHHHHHHhc----cccccCcc-----cCCCc-HHHHHHHHHHHHHHHHHHHHHHHhhHHhhhhccCCCCC
Q 047219          506 -------RSWASKIIRG----QITKDGEQ-----ACLPP-LQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDL  566 (567)
Q Consensus       506 -------~~a~~r~i~~----~i~~~~~~-----~~~~~-l~e~le~~e~~~~~li~~al~~~~~~~s~~~~~~~l~~  566 (567)
                             ++.+++.+..    .++.....     ..... -...+..+++.++.+|.+++.+++++++++++.+++|+
T Consensus       355 pgN~reL~~~~~~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~l~~~e~~~i~~~l~~~~gn~~~aa~~Lgisr  432 (441)
T PRK10365        355 PGNIRELENAVERAVVLLTGEYISERELPLAIASTPIPLGQSQDIQPLVEVEKEVILAALEKTGGNKTEAARQLGITR  432 (441)
T ss_pred             CCHHHHHHHHHHHHHHhCCCCccchHhCchhhcccccCcccccchhhHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCH
Confidence                   4455554321    11111000     00000 00001223344489999999999999999999999885

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.66  E-value=2.6e-15  Score=160.53  Aligned_cols=196  Identities=18%  Similarity=0.254  Sum_probs=135.6

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC--
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP--  355 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~--  355 (567)
                      .|++|+|++.+++.|++++.....++..+           +...++++||+||||+|||++|+++|+.+.+..-.+.+  
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~~~~-----------~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg   71 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADVAAA-----------GSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCG   71 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhcccccccc-----------CCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCC
Confidence            58999999999999999997543322111           13467889999999999999999999988543100111  


Q ss_pred             ---------------eEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHH
Q 047219          356 ---------------LMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILS  417 (567)
Q Consensus       356 ---------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~  417 (567)
                                     +..+..+.   ..  ..-..++.+++.+...   ++..|+||||+|.|...           ..+
T Consensus        72 ~C~~C~~~~~~~hpD~~~i~~~~---~~--i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~~-----------aan  135 (394)
T PRK07940         72 ECRACRTVLAGTHPDVRVVAPEG---LS--IGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTER-----------AAN  135 (394)
T ss_pred             CCHHHHHHhcCCCCCEEEecccc---cc--CCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCHH-----------HHH
Confidence                           11222111   11  1123466777666532   34579999999999643           336


Q ss_pred             HHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHH
Q 047219          418 VLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDI  497 (567)
Q Consensus       418 ~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL  497 (567)
                      .|++.++.  .+.++++|.+|+.++.+.+.++||| ..+.|+.|+.++..+.+.... .+..+....++..+.|..+..+
T Consensus       136 aLLk~LEe--p~~~~~fIL~a~~~~~llpTIrSRc-~~i~f~~~~~~~i~~~L~~~~-~~~~~~a~~la~~s~G~~~~A~  211 (394)
T PRK07940        136 ALLKAVEE--PPPRTVWLLCAPSPEDVLPTIRSRC-RHVALRTPSVEAVAEVLVRRD-GVDPETARRAARASQGHIGRAR  211 (394)
T ss_pred             HHHHHhhc--CCCCCeEEEEECChHHChHHHHhhC-eEEECCCCCHHHHHHHHHHhc-CCCHHHHHHHHHHcCCCHHHHH
Confidence            67777774  4456666666666899999999999 899999999998887776332 3566677788888888777776


Q ss_pred             HHHHHHH
Q 047219          498 RDVCQQA  504 (567)
Q Consensus       498 ~~L~~~a  504 (567)
                      ..+....
T Consensus       212 ~l~~~~~  218 (394)
T PRK07940        212 RLATDEE  218 (394)
T ss_pred             HHhcChH
Confidence            6554433

>PLN03025 replication factor C subunit; Provisional

Probab=99.66  E-value=5.9e-15  Score=154.25  Aligned_cols=186  Identities=15%  Similarity=0.222  Sum_probs=128.8

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++++++.|+..+.                     .....++||+||||||||++|+++|+++....+ .
T Consensus         7 yrP~~l~~~~g~~~~~~~L~~~~~---------------------~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~-~   64 (319)
T PLN03025          7 YRPTKLDDIVGNEDAVSRLQVIAR---------------------DGNMPNLILSGPPGTGKTTSILALAHELLGPNY-K   64 (319)
T ss_pred             cCCCCHHHhcCcHHHHHHHHHHHh---------------------cCCCceEEEECCCCCCHHHHHHHHHHHHhcccC-c
Confidence            345789999999999998887654                     223346999999999999999999999854322 2


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHH-Hhc-----CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSL-ANE-----LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~-A~~-----~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~  427 (567)
                      ..+..++.++..+.      ..++..... +..     .....+++|||+|.|....|           +.|+..++.  
T Consensus        65 ~~~~eln~sd~~~~------~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~~aq-----------~aL~~~lE~--  125 (319)
T PLN03025         65 EAVLELNASDDRGI------DVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTSGAQ-----------QALRRTMEI--  125 (319)
T ss_pred             cceeeecccccccH------HHHHHHHHHHHhccccCCCCCeEEEEEechhhcCHHHH-----------HHHHHHHhc--
Confidence            23555555432211      112222111 111     12357999999999975433           344455543  


Q ss_pred             cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          428 QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       428 ~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      .+..+++|.+||....+.++|++|| ..++|..|+.++....+...++.    +..+.+..++....|    |++.+++.
T Consensus       126 ~~~~t~~il~~n~~~~i~~~L~SRc-~~i~f~~l~~~~l~~~L~~i~~~egi~i~~~~l~~i~~~~~g----DlR~aln~  200 (319)
T PLN03025        126 YSNTTRFALACNTSSKIIEPIQSRC-AIVRFSRLSDQEILGRLMKVVEAEKVPYVPEGLEAIIFTADG----DMRQALNN  200 (319)
T ss_pred             ccCCceEEEEeCCccccchhHHHhh-hcccCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC----CHHHHHHH
Confidence            2345678888998889999999999 78999999999999999888764    456777777776544    66666665


Q ss_pred             HH
Q 047219          504 AE  505 (567)
Q Consensus       504 a~  505 (567)
                      ..
T Consensus       201 Lq  202 (319)
T PLN03025        201 LQ  202 (319)
T ss_pred             HH
Confidence            54

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=3.5e-15  Score=169.74  Aligned_cols=196  Identities=18%  Similarity=0.215  Sum_probs=137.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++.+++.|++++..                    .+.++.+||+||||||||++|+++|+.+.+.. ..+
T Consensus        11 RP~tFddIIGQe~Iv~~LknaI~~--------------------~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~   70 (944)
T PRK14949         11 RPATFEQMVGQSHVLHALTNALTQ--------------------QRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTA   70 (944)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHh--------------------CCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCC
Confidence            447899999999999999887752                    35567789999999999999999999997531 111


Q ss_pred             cCeEEec-hhhHHhhhh-------c---hhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHH
Q 047219          354 VPLMYVP-LEVVMSKYY-------G---ESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL  419 (567)
Q Consensus       354 ~~~~~i~-~~~l~s~~~-------G---~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~L  419 (567)
                      .+|...+ |-.+....+       +   ..-..++.+.+.+..   .++..|+||||+|.|...           .++.|
T Consensus        71 ~pCg~C~sC~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT~e-----------AqNAL  139 (944)
T PRK14949         71 TPCGVCSSCVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLSRS-----------SFNAL  139 (944)
T ss_pred             CCCCCchHHHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcCHH-----------HHHHH
Confidence            2232211 111111100       0   112234444443332   234579999999999633           55778


Q ss_pred             HHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHH
Q 047219          420 LRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGR  495 (567)
Q Consensus       420 L~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~  495 (567)
                      |+.|+.  .+.++++|++|+.+..|.+.|++|| ..++|..++.++..+.|...+..    +..+.+..++..+.| +.+
T Consensus       140 LKtLEE--PP~~vrFILaTTe~~kLl~TIlSRC-q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S~G-d~R  215 (944)
T PRK14949        140 LKTLEE--PPEHVKFLLATTDPQKLPVTVLSRC-LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAANG-SMR  215 (944)
T ss_pred             HHHHhc--cCCCeEEEEECCCchhchHHHHHhh-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHH
Confidence            888873  5678889888988899999999999 89999999999999988887753    456678888888766 556


Q ss_pred             HHHHHHHHHH
Q 047219          496 DIRDVCQQAE  505 (567)
Q Consensus       496 dL~~L~~~a~  505 (567)
                      ++..++..+.
T Consensus       216 ~ALnLLdQal  225 (944)
T PRK14949        216 DALSLTDQAI  225 (944)
T ss_pred             HHHHHHHHHH
Confidence            6666665433

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=3e-15  Score=163.58  Aligned_cols=177  Identities=20%  Similarity=0.287  Sum_probs=126.8

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-CC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-QG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~~  353 (567)
                      .+.+|++++|++.+++.|+..+..                    ...+.++||+||||||||++|+++|+.+..... ..
T Consensus         9 RP~~~~divGq~~i~~~L~~~i~~--------------------~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~   68 (472)
T PRK14962          9 RPKTFSEVVGQDHVKKLIINALKK--------------------NSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGV   68 (472)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCC
Confidence            457899999999998888876642                    355677999999999999999999999864311 01


Q ss_pred             c-----------------CeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 V-----------------PLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~-----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .                 .++.+++..      ...-..++.+.+.+..   .+...+|||||+|.|...          
T Consensus        69 ~pc~~c~~c~~i~~g~~~dv~el~aa~------~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt~~----------  132 (472)
T PRK14962         69 EPCNECRACRSIDEGTFMDVIELDAAS------NRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLTKE----------  132 (472)
T ss_pred             CCCcccHHHHHHhcCCCCccEEEeCcc------cCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhHHH----------
Confidence            1                 233333321      0112334444444332   234579999999998633          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.|+..++.  .++.+++|++|+.+..+.+++++|| ..++|..++.++...+++..+..    +..+.++.++..+
T Consensus       133 -a~~~LLk~LE~--p~~~vv~Ilattn~~kl~~~L~SR~-~vv~f~~l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s  208 (472)
T PRK14962        133 -AFNALLKTLEE--PPSHVVFVLATTNLEKVPPTIISRC-QVIEFRNISDELIIKRLQEVAEAEGIEIDREALSFIAKRA  208 (472)
T ss_pred             -HHHHHHHHHHh--CCCcEEEEEEeCChHhhhHHHhcCc-EEEEECCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence             33556666663  4567888888877789999999999 79999999999999999887753    5677888888876


Q ss_pred             cC
Q 047219          490 EE  491 (567)
Q Consensus       490 ~g  491 (567)
                      .|
T Consensus       209 ~G  210 (472)
T PRK14962        209 SG  210 (472)
T ss_pred             CC
Confidence            54

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.66  E-value=3.9e-15  Score=160.95  Aligned_cols=179  Identities=25%  Similarity=0.396  Sum_probs=125.1

Q ss_pred             CCCCcccccCcHHHHHH---HHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          275 SEISWENIAGYDQQKRE---IEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~---L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      .+.++++++|++..+..   +++++.                     .....+++|+||||||||++|+++++.+     
T Consensus         7 RP~~l~d~vGq~~~v~~~~~L~~~i~---------------------~~~~~~ilL~GppGtGKTtLA~~ia~~~-----   60 (413)
T PRK13342          7 RPKTLDEVVGQEHLLGPGKPLRRMIE---------------------AGRLSSMILWGPPGTGKTTLARIIAGAT-----   60 (413)
T ss_pred             CCCCHHHhcCcHHHhCcchHHHHHHH---------------------cCCCceEEEECCCCCCHHHHHHHHHHHh-----
Confidence            34679999999999766   766663                     3445689999999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +..++.+++....       ...++.+++.+..   ...+.+|||||+|.+....+           +.|+..++    
T Consensus        61 -~~~~~~l~a~~~~-------~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~~~q-----------~~LL~~le----  117 (413)
T PRK13342         61 -DAPFEALSAVTSG-------VKDLREVIEEARQRRSAGRRTILFIDEIHRFNKAQQ-----------DALLPHVE----  117 (413)
T ss_pred             -CCCEEEEeccccc-------HHHHHHHHHHHHHhhhcCCceEEEEechhhhCHHHH-----------HHHHHHhh----
Confidence             5567777764321       1234445544432   22468999999999864432           34445444    


Q ss_pred             CCcEEEEEee--CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh-------hCHHHHHHHHHhccCCCHHHHHH
Q 047219          429 DKKVVVIAAT--NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH-------LTKAELAELATATEEMSGRDIRD  499 (567)
Q Consensus       429 ~~~viVIaaT--N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-------~~~~~l~~la~~t~g~s~~dL~~  499 (567)
                      .+.+++|++|  |....++++|++|| ..+.|..++.++...++...+..       +..+.++.++..+.| ..+.+.+
T Consensus       118 ~~~iilI~att~n~~~~l~~aL~SR~-~~~~~~~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~G-d~R~aln  195 (413)
T PRK13342        118 DGTITLIGATTENPSFEVNPALLSRA-QVFELKPLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANG-DARRALN  195 (413)
T ss_pred             cCcEEEEEeCCCChhhhccHHHhccc-eeeEeCCCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCC-CHHHHHH
Confidence            2467777765  44567999999999 89999999999999999887643       445666777776643 3444444


Q ss_pred             HHHHH
Q 047219          500 VCQQA  504 (567)
Q Consensus       500 L~~~a  504 (567)
                      ++..+
T Consensus       196 ~Le~~  200 (413)
T PRK13342        196 LLELA  200 (413)
T ss_pred             HHHHH
Confidence            44443

>KOG0736 consensus Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones]

Probab=99.65  E-value=5.2e-15  Score=162.85  Aligned_cols=187  Identities=27%  Similarity=0.384  Sum_probs=156.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      .....+||+|+||||||++++++|.++      +.+++.++|.++.+..-+..+.++...|..|+... ++||||-++|.
T Consensus       429 ~~~~~vLLhG~~g~GK~t~V~~vas~l------g~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~-pavifl~~~dv  501 (953)
T KOG0736|consen  429 TLNPSVLLHGPPGSGKTTVVRAVASEL------GLHLLEVDCYELVAESASHTETKLQAIFSRARRCS-PAVLFLRNLDV  501 (953)
T ss_pred             ccceEEEEeCCCCCChHHHHHHHHHHh------CCceEeccHHHHhhcccchhHHHHHHHHHHHhhcC-ceEEEEeccce
Confidence            345679999999999999999999999      88999999999999999999999999999999886 59999999999


Q ss_pred             hhhhhhhhhHHHHHHHHHHHHHhhcCc-ccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhC
Q 047219          400 FAVARDSEMHEATRRILSVLLRQIDGF-EQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLT  478 (567)
Q Consensus       400 L~~~~q~~l~~~~~~vl~~LL~~ld~~-~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~  478 (567)
                      |...+++....-....+..++. .+.. .....++||++|+..+.+++.+++.|-.+|.++.|+.++|.+|++.++.+..
T Consensus       502 l~id~dgged~rl~~~i~~~ls-~e~~~~~~~~~ivv~t~~s~~~lp~~i~~~f~~ei~~~~lse~qRl~iLq~y~~~~~  580 (953)
T KOG0736|consen  502 LGIDQDGGEDARLLKVIRHLLS-NEDFKFSCPPVIVVATTSSIEDLPADIQSLFLHEIEVPALSEEQRLEILQWYLNHLP  580 (953)
T ss_pred             eeecCCCchhHHHHHHHHHHHh-cccccCCCCceEEEEeccccccCCHHHHHhhhhhccCCCCCHHHHHHHHHHHHhccc
Confidence            9866555333233334444444 2222 3567899999999999999999998888999999999999999999988753


Q ss_pred             ---HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHh
Q 047219          479 ---KAELAELATATEEMSGRDIRDVCQQAERSWASKIIR  514 (567)
Q Consensus       479 ---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~i~  514 (567)
                         +..+..++..+.||+.+|+..++.+.-.++..++..
T Consensus       581 ~n~~v~~k~~a~~t~gfs~~~L~~l~~~~s~~~~~~i~~  619 (953)
T KOG0736|consen  581 LNQDVNLKQLARKTSGFSFGDLEALVAHSSLAAKTRIKN  619 (953)
T ss_pred             cchHHHHHHHHHhcCCCCHHHHHHHhcCchHHHHHHHHh
Confidence               347789999999999999999999886555555544

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.65  E-value=2e-15  Score=175.63  Aligned_cols=187  Identities=22%  Similarity=0.310  Sum_probs=140.2

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -+++.++|+++.++++.+.+.                     .+...+++|+||||||||++|+.+|+.+...    .+.
T Consensus       184 ~~ld~~iGr~~ei~~~i~~l~---------------------r~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~  242 (852)
T TIGR03345       184 GKIDPVLGRDDEIRQMIDILL---------------------RRRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALR  242 (852)
T ss_pred             CCCCcccCCHHHHHHHHHHHh---------------------cCCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCcccc
Confidence            467899999998877776553                     3445688999999999999999999988432    234


Q ss_pred             CcCeEEechhhHHh--hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~s--~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +..++.++...+..  .+.|+.+..++.+++.+.....++||||||||.|.+......   .+...+.|+..+    .++
T Consensus       243 ~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~---~~d~~n~Lkp~l----~~G  315 (852)
T TIGR03345       243 NVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAG---QGDAANLLKPAL----ARG  315 (852)
T ss_pred             CCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCccc---cccHHHHhhHHh----hCC
Confidence            56678888777663  688999999999999987654468999999999986432211   011223333333    367


Q ss_pred             cEEEEEeeCCC-----CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhccCC
Q 047219          431 KVVVIAATNRK-----QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATEEM  492 (567)
Q Consensus       431 ~viVIaaTN~~-----~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~g~  492 (567)
                      .+.+|+||+..     ..++++|.+|| ..|.++.|+.+++.+||+.+...        +.++.+..++..+.+|
T Consensus       316 ~l~~IgaTT~~e~~~~~~~d~AL~rRf-~~i~v~eps~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ry  389 (852)
T TIGR03345       316 ELRTIAATTWAEYKKYFEKDPALTRRF-QVVKVEEPDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRY  389 (852)
T ss_pred             CeEEEEecCHHHHhhhhhccHHHHHhC-eEEEeCCCCHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccc
Confidence            89999999864     35899999999 78999999999999998766542        3466777777776655

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=4.9e-15  Score=163.39  Aligned_cols=190  Identities=19%  Similarity=0.213  Sum_probs=136.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++.+++.|+.++..                    ...++.+||+||+|||||++|+++|+.+.+.. ...
T Consensus        11 RP~~f~divGq~~v~~~L~~~~~~--------------------~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~   70 (509)
T PRK14958         11 RPRCFQEVIGQAPVVRALSNALDQ--------------------QYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSA   70 (509)
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHh--------------------CCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCc
Confidence            457899999999999999988853                    45677899999999999999999999996531 111


Q ss_pred             cC-----------------eEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 VP-----------------LMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .+                 +++++...      ...-+.++.+.+.+.   ..++..|+||||+|.|...          
T Consensus        71 ~pCg~C~~C~~i~~g~~~d~~eidaas------~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~~----------  134 (509)
T PRK14958         71 NPCNDCENCREIDEGRFPDLFEVDAAS------RTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSGH----------  134 (509)
T ss_pred             ccCCCCHHHHHHhcCCCceEEEEcccc------cCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCHH----------
Confidence            11                 33333221      011233455554433   2234579999999999743          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.|++.++.  .+..+++|.+|+.+..+.+.+++|| ..++|..++.++....+...+..    +..+.+..++...
T Consensus       135 -a~naLLk~LEe--pp~~~~fIlattd~~kl~~tI~SRc-~~~~f~~l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s  210 (509)
T PRK14958        135 -SFNALLKTLEE--PPSHVKFILATTDHHKLPVTVLSRC-LQFHLAQLPPLQIAAHCQHLLKEENVEFENAALDLLARAA  210 (509)
T ss_pred             -HHHHHHHHHhc--cCCCeEEEEEECChHhchHHHHHHh-hhhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             34677777774  4567888888888889999999999 88999999988888777777654    4566777888776


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.+++.+++..++
T Consensus       211 ~G-slR~al~lLdq~i  225 (509)
T PRK14958        211 NG-SVRDALSLLDQSI  225 (509)
T ss_pred             CC-cHHHHHHHHHHHH
Confidence            54 6667767666554

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.64  E-value=9.2e-15  Score=155.43  Aligned_cols=190  Identities=17%  Similarity=0.214  Sum_probs=134.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~  353 (567)
                      .+.+|++|+|++..++.++..+..                    .+.++.+||+||||||||++|+++++.+... ....
T Consensus        11 rP~~~~~iiGq~~~~~~l~~~~~~--------------------~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~   70 (363)
T PRK14961         11 RPQYFRDIIGQKHIVTAISNGLSL--------------------GRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITS   70 (363)
T ss_pred             CCCchhhccChHHHHHHHHHHHHc--------------------CCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            447899999999999999887752                    3566778999999999999999999998642 1111


Q ss_pred             cC-----------------eEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 VP-----------------LMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      -+                 +..++...      ...-..++.+.+.+..   .+...++||||+|.|...          
T Consensus        71 ~pc~~c~~c~~~~~~~~~d~~~~~~~~------~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~~~----------  134 (363)
T PRK14961         71 NPCRKCIICKEIEKGLCLDLIEIDAAS------RTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLSRH----------  134 (363)
T ss_pred             CCCCCCHHHHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcCHH----------
Confidence            12                 22222210      0112334555544432   223469999999998532          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.|++.++.  .+..+.+|.+|+..+.+.+.+++|| ..++|..|+.++..+.+...++.    +..+.+..++..+
T Consensus       135 -a~naLLk~lEe--~~~~~~fIl~t~~~~~l~~tI~SRc-~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s  210 (363)
T PRK14961        135 -SFNALLKTLEE--PPQHIKFILATTDVEKIPKTILSRC-LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHA  210 (363)
T ss_pred             -HHHHHHHHHhc--CCCCeEEEEEcCChHhhhHHHHhhc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             33567777764  4567788888888888999999999 89999999999999999887764    5567778888877


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.+++.+++..++
T Consensus       211 ~G-~~R~al~~l~~~~  225 (363)
T PRK14961        211 HG-SMRDALNLLEHAI  225 (363)
T ss_pred             CC-CHHHHHHHHHHHH
Confidence            65 5666666665554

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.64  E-value=1.2e-14  Score=151.22  Aligned_cols=162  Identities=22%  Similarity=0.323  Sum_probs=113.8

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ....+.++++++|+++.++.++..+..                    ...++.+||+||||+|||++|++++++.     
T Consensus        13 ~kyrP~~~~~~~~~~~~~~~l~~~~~~--------------------~~~~~~lll~G~~G~GKT~la~~l~~~~-----   67 (316)
T PHA02544         13 QKYRPSTIDECILPAADKETFKSIVKK--------------------GRIPNMLLHSPSPGTGKTTVAKALCNEV-----   67 (316)
T ss_pred             eccCCCcHHHhcCcHHHHHHHHHHHhc--------------------CCCCeEEEeeCcCCCCHHHHHHHHHHHh-----
Confidence            344557999999999999999887741                    3556777889999999999999999998     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                       +.++.+++++.  .. .......+..........+.+.+|+|||+|.+....       .+   ..|...++.  .+.+
T Consensus        68 -~~~~~~i~~~~--~~-~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~~~-------~~---~~L~~~le~--~~~~  131 (316)
T PHA02544         68 -GAEVLFVNGSD--CR-IDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLAD-------AQ---RHLRSFMEA--YSKN  131 (316)
T ss_pred             -CccceEeccCc--cc-HHHHHHHHHHHHHhhcccCCCeEEEEECcccccCHH-------HH---HHHHHHHHh--cCCC
Confidence             45577777765  11 111112222222222122346899999999883221       11   223333443  3457


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +.+|++||....+.+++++|| ..+.++.|+.+++.+++..+..
T Consensus       132 ~~~Ilt~n~~~~l~~~l~sR~-~~i~~~~p~~~~~~~il~~~~~  174 (316)
T PHA02544        132 CSFIITANNKNGIIEPLRSRC-RVIDFGVPTKEEQIEMMKQMIV  174 (316)
T ss_pred             ceEEEEcCChhhchHHHHhhc-eEEEeCCCCHHHHHHHHHHHHH
Confidence            789999999999999999999 7899999999999988776543

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.64  E-value=9.8e-15  Score=163.60  Aligned_cols=189  Identities=20%  Similarity=0.261  Sum_probs=136.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++.+++.|++.+..                    .+.++.+||+||+|||||++|+++|+.+.+.. ...
T Consensus        11 RP~~f~divGQe~vv~~L~~~l~~--------------------~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~   70 (647)
T PRK07994         11 RPQTFAEVVGQEHVLTALANALDL--------------------GRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITA   70 (647)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCC
Confidence            447899999999999999887752                    35667789999999999999999999996531 111


Q ss_pred             cCe-----------------EEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 VPL-----------------MYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~~~-----------------~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .+|                 +.++...    .  ..-+.++.+.+.+.   ..++..|+||||+|.|...          
T Consensus        71 ~pCg~C~~C~~i~~g~~~D~ieidaas----~--~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls~~----------  134 (647)
T PRK07994         71 TPCGECDNCREIEQGRFVDLIEIDAAS----R--TKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLSRH----------  134 (647)
T ss_pred             CCCCCCHHHHHHHcCCCCCceeecccc----c--CCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCCHH----------
Confidence            222                 2232221    0  11233444444433   2234579999999999633          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.||+.++  +.+..+++|++|+.+..+.+.+++|| ..++|..++.++..+.|...+..    +....+..++...
T Consensus       135 -a~NALLKtLE--EPp~~v~FIL~Tt~~~kLl~TI~SRC-~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~~aL~~Ia~~s  210 (647)
T PRK07994        135 -SFNALLKTLE--EPPEHVKFLLATTDPQKLPVTILSRC-LQFHLKALDVEQIRQQLEHILQAEQIPFEPRALQLLARAA  210 (647)
T ss_pred             -HHHHHHHHHH--cCCCCeEEEEecCCccccchHHHhhh-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             4577888887  35678889999999999999999999 99999999999999888887753    4556777787776


Q ss_pred             cCCCHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQA  504 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a  504 (567)
                      .| +.++...++..+
T Consensus       211 ~G-s~R~Al~lldqa  224 (647)
T PRK07994        211 DG-SMRDALSLTDQA  224 (647)
T ss_pred             CC-CHHHHHHHHHHH
Confidence            65 455555555443

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.63  E-value=8.4e-15  Score=159.79  Aligned_cols=190  Identities=20%  Similarity=0.253  Sum_probs=140.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC---
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW---  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~---  351 (567)
                      .+.+|+||+|++..++.|.+.+..                    .+.++++||+||+|||||++|+.+|+.+++...   
T Consensus         8 RP~~f~dliGQe~vv~~L~~a~~~--------------------~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~   67 (491)
T PRK14964          8 RPSSFKDLVGQDVLVRILRNAFTL--------------------NKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTS   67 (491)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCC
Confidence            347899999999999988877642                    466789999999999999999999998754210   


Q ss_pred             ---------------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          352 ---------------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       352 ---------------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                                     ....++.+++..-      ..-+.++.+.+.+..   .+...+++|||+|.|...          
T Consensus        68 ~pCg~C~~C~~i~~~~~~Dv~eidaas~------~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls~~----------  131 (491)
T PRK14964         68 DPCGTCHNCISIKNSNHPDVIEIDAASN------TSVDDIKVILENSCYLPISSKFKVYIIDEVHMLSNS----------  131 (491)
T ss_pred             CCccccHHHHHHhccCCCCEEEEecccC------CCHHHHHHHHHHHHhccccCCceEEEEeChHhCCHH----------
Confidence                           1233455544311      122345555555542   234579999999998632          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.|++.++.  .+..+++|.+|+....+.+.+++|| ..++|..++.++..+.+...+..    +..+.+..++..+
T Consensus       132 -A~NaLLK~LEe--Pp~~v~fIlatte~~Kl~~tI~SRc-~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s  207 (491)
T PRK14964        132 -AFNALLKTLEE--PAPHVKFILATTEVKKIPVTIISRC-QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENS  207 (491)
T ss_pred             -HHHHHHHHHhC--CCCCeEEEEEeCChHHHHHHHHHhh-eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             45677888874  5567888888888888999999999 88999999999999998887764    5677888888887


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.+++.+++..+.
T Consensus       208 ~G-slR~alslLdqli  222 (491)
T PRK14964        208 SG-SMRNALFLLEQAA  222 (491)
T ss_pred             CC-CHHHHHHHHHHHH
Confidence            55 6666666666554

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.63  E-value=1e-14  Score=166.99  Aligned_cols=200  Identities=19%  Similarity=0.253  Sum_probs=143.4

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--C--CCC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--P--WQG  353 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~--~~~  353 (567)
                      .++.++|.++.++++.+.+.                     .....++||+||||||||++|+++|+..-..  +  +.+
T Consensus       184 ~~~~liGR~~ei~~~i~iL~---------------------r~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~  242 (758)
T PRK11034        184 GIDPLIGREKELERAIQVLC---------------------RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMAD  242 (758)
T ss_pred             CCCcCcCCCHHHHHHHHHHh---------------------ccCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcC
Confidence            45679999999999988664                     2345778999999999999999999876322  1  235


Q ss_pred             cCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          354 VPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..++.++...+.  .++.|+.+.+++.+|..+.... ++||||||||.|.+.......  .....+.|...+    ..+.
T Consensus       243 ~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~-~~ILfIDEIh~L~g~g~~~~g--~~d~~nlLkp~L----~~g~  315 (758)
T PRK11034        243 CTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDT-NSILFIDEIHTIIGAGAASGG--QVDAANLIKPLL----SSGK  315 (758)
T ss_pred             CeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhcC-CCEEEeccHHHHhccCCCCCc--HHHHHHHHHHHH----hCCC
Confidence            566666666665  4678899999999999887654 589999999999765432111  111222232222    3578


Q ss_pred             EEEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhcc-----CCC
Q 047219          432 VVVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATE-----EMS  493 (567)
Q Consensus       432 viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~-----g~s  493 (567)
                      +.+|++||.++     ..|++|.+|| ..|.++.|+.+++.+||+.+...        +.++.+......+.     .+.
T Consensus       316 i~vIgATt~~E~~~~~~~D~AL~rRF-q~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~l  394 (758)
T PRK11034        316 IRVIGSTTYQEFSNIFEKDRALARRF-QKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHL  394 (758)
T ss_pred             eEEEecCChHHHHHHhhccHHHHhhC-cEEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccC
Confidence            99999999754     5799999999 68999999999999999987654        34445544444333     344


Q ss_pred             HHHHHHHHHHHHH
Q 047219          494 GRDIRDVCQQAER  506 (567)
Q Consensus       494 ~~dL~~L~~~a~~  506 (567)
                      +...-.++.+|..
T Consensus       395 PdKaidlldea~a  407 (758)
T PRK11034        395 PDKAIDVIDEAGA  407 (758)
T ss_pred             hHHHHHHHHHHHH
Confidence            5566777777663

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.63  E-value=1.1e-14  Score=161.62  Aligned_cols=190  Identities=18%  Similarity=0.214  Sum_probs=137.1

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++.+++.|..++..                    .+.++.+||+||+|||||++|+++|+.+.+.. ...
T Consensus        10 RPktFddVIGQe~vv~~L~~aI~~--------------------grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~   69 (702)
T PRK14960         10 RPRNFNELVGQNHVSRALSSALER--------------------GRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTS   69 (702)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCC
Confidence            447899999999999999888752                    45678899999999999999999999986531 111


Q ss_pred             c-----------------CeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 V-----------------PLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~-----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .                 .++.+++..-      ..-+.++.+...+..   .+++.|+||||+|.|...          
T Consensus        70 ~pCg~C~sC~~I~~g~hpDviEIDAAs~------~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~~----------  133 (702)
T PRK14960         70 TPCEVCATCKAVNEGRFIDLIEIDAASR------TKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLSTH----------  133 (702)
T ss_pred             CCCccCHHHHHHhcCCCCceEEeccccc------CCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCHH----------
Confidence            1                 2333333210      112344555544332   234579999999998643          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.|++.++.  .+..+.+|++|+.+..+.+.+++|| ..+.|..++.++....+...+..    +..+.+..++..+
T Consensus       134 -A~NALLKtLEE--PP~~v~FILaTtd~~kIp~TIlSRC-q~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S  209 (702)
T PRK14960        134 -SFNALLKTLEE--PPEHVKFLFATTDPQKLPITVISRC-LQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESA  209 (702)
T ss_pred             -HHHHHHHHHhc--CCCCcEEEEEECChHhhhHHHHHhh-heeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             34667777774  4567888888888888999999999 89999999999999988887764    5677888888887


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.+++.+++..+.
T Consensus       210 ~G-dLRdALnLLDQaI  224 (702)
T PRK14960        210 QG-SLRDALSLTDQAI  224 (702)
T ss_pred             CC-CHHHHHHHHHHHH
Confidence            65 5555555554443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.63  E-value=5e-15  Score=148.99  Aligned_cols=190  Identities=21%  Similarity=0.247  Sum_probs=133.6

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+-+|+++.|++.+++.|+..+.                     .....++|||||||||||+.|++++++++......
T Consensus        30 YrPkt~de~~gQe~vV~~L~~a~~---------------------~~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~   88 (346)
T KOG0989|consen   30 YRPKTFDELAGQEHVVQVLKNALL---------------------RRILPHYLFYGPPGTGKTSTALAFARALNCEQLFP   88 (346)
T ss_pred             hCCCcHHhhcchHHHHHHHHHHHh---------------------hcCCceEEeeCCCCCcHhHHHHHHHHHhcCccccc
Confidence            345689999999999999998875                     23456899999999999999999999996532222


Q ss_pred             cCeEEechhhHHhhhhch-hHHHHHHHHHHH-----hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc
Q 047219          354 VPLMYVPLEVVMSKYYGE-SERLLGKVFSLA-----NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~-~~~~l~~~f~~A-----~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~  427 (567)
                      ..+...+.+...+.-++. .-+.+..+....     ....+..|++|||.|.|..+           ..+.|.+.|+.  
T Consensus        89 ~rvl~lnaSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmtsd-----------aq~aLrr~mE~--  155 (346)
T KOG0989|consen   89 CRVLELNASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMTSD-----------AQAALRRTMED--  155 (346)
T ss_pred             cchhhhcccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhhHH-----------HHHHHHHHHhc--
Confidence            233334444443322211 111111111111     11234489999999999744           44566677775  


Q ss_pred             cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          428 QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       428 ~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      ....+++|..||....+...+.+|| ..+.|+....+.....|+.++..    +.++.++.++....|    ||+....
T Consensus       156 ~s~~trFiLIcnylsrii~pi~SRC-~KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~al~~I~~~S~G----dLR~Ait  229 (346)
T KOG0989|consen  156 FSRTTRFILICNYLSRIIRPLVSRC-QKFRFKKLKDEDIVDRLEKIASKEGVDIDDDALKLIAKISDG----DLRRAIT  229 (346)
T ss_pred             cccceEEEEEcCChhhCChHHHhhH-HHhcCCCcchHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC----cHHHHHH
Confidence            4568899999999999999999999 88999888888888888887764    667788888887766    5544443

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.63  E-value=4e-15  Score=170.27  Aligned_cols=241  Identities=18%  Similarity=0.274  Sum_probs=152.3

Q ss_pred             CCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCC
Q 047219          243 LTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRP  322 (567)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p  322 (567)
                      ++..++..+++.+...+......++..........--..|+|++++++.|.+.+......      +.      ....+.
T Consensus       421 v~~~~i~~v~~~~tgip~~~~~~~~~~~l~~l~~~L~~~ViGQ~~ai~~l~~~i~~~~~g------l~------~~~kp~  488 (758)
T PRK11034        421 VNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMSRAG------LG------HEHKPV  488 (758)
T ss_pred             cChhhHHHHHHHHhCCChhhhhhhHHHHHHHHHHHhcceEeCcHHHHHHHHHHHHHHhcc------cc------CCCCCc
Confidence            445566666666665544332222221111112223356899999999999988754111      00      002334


Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH-----hhhhchhHH----HHHHHHHHHhcCCCCcEEE
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM-----SKYYGESER----LLGKVFSLANELPNGAIIF  393 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~-----s~~~G~~~~----~l~~~f~~A~~~a~~~ILf  393 (567)
                      .++||+||||||||.+|+++|+.+      +.+++.++++++.     ++++|....    .....+..+....|.+|||
T Consensus       489 ~~~Lf~GP~GvGKT~lAk~LA~~l------~~~~i~id~se~~~~~~~~~LiG~~~gyvg~~~~g~L~~~v~~~p~sVll  562 (758)
T PRK11034        489 GSFLFAGPTGVGKTEVTVQLSKAL------GIELLRFDMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLL  562 (758)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh------CCCcEEeechhhcccccHHHHcCCCCCcccccccchHHHHHHhCCCcEEE
Confidence            579999999999999999999999      5567777777653     344443211    1112333333344579999


Q ss_pred             EcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---------cCCcEEEEEeeCCC-----------------------
Q 047219          394 LDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---------QDKKVVVIAATNRK-----------------------  441 (567)
Q Consensus       394 IDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---------~~~~viVIaaTN~~-----------------------  441 (567)
                      |||||++.+.           +++.|++.++.-.         .-.++++|+|||.-                       
T Consensus       563 lDEieka~~~-----------v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~  631 (758)
T PRK11034        563 LDEIEKAHPD-----------VFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEE  631 (758)
T ss_pred             eccHhhhhHH-----------HHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHH
Confidence            9999998644           4455555554321         12478899999931                       


Q ss_pred             --CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh-------------hCHHHHHHHHHh--ccCCCHHHHHHHHHHH
Q 047219          442 --QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH-------------LTKAELAELATA--TEEMSGRDIRDVCQQA  504 (567)
Q Consensus       442 --~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-------------~~~~~l~~la~~--t~g~s~~dL~~L~~~a  504 (567)
                        ..|.|+|+.|++.++.|..++.++..+|+...+..             +.+...+.++..  ...+-.+.|+.++...
T Consensus       632 ~~~~f~pefl~Rid~ii~f~~L~~~~l~~I~~~~l~~~~~~l~~~~i~l~~~~~~~~~l~~~~~~~~~GAR~l~r~i~~~  711 (758)
T PRK11034        632 IKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQDN  711 (758)
T ss_pred             HHHhcCHHHHccCCEEEEcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCceECHHHHHHHHHhCCCCCCCCchHHHHHHHH
Confidence              23789999999999999999999999999877653             234455556543  2234567777777766


Q ss_pred             HHHHHHHH
Q 047219          505 ERSWASKI  512 (567)
Q Consensus       505 ~~~a~~r~  512 (567)
                      ....+...
T Consensus       712 l~~~la~~  719 (758)
T PRK11034        712 LKKPLANE  719 (758)
T ss_pred             HHHHHHHH
Confidence            65444433

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.62  E-value=2.3e-14  Score=157.45  Aligned_cols=197  Identities=20%  Similarity=0.219  Sum_probs=139.5

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-C
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-Q  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~  352 (567)
                      ..+.+|++++|++..++.|+..+..                    .+.+.++||+||||||||++|+++|+.+.+... .
T Consensus        15 yRP~~f~dliGq~~vv~~L~~ai~~--------------------~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~   74 (507)
T PRK06645         15 YRPSNFAELQGQEVLVKVLSYTILN--------------------DRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALIT   74 (507)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCCHHHHHHHHHHHhcCccccc
Confidence            4557899999999999998886642                    456789999999999999999999999965311 0


Q ss_pred             C----cCeEEe-chhhHHhhh----------hchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          353 G----VPLMYV-PLEVVMSKY----------YGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       353 ~----~~~~~i-~~~~l~s~~----------~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      +    .+|... +|..+....          -......++.+++.+...   +...|+||||+|.|...           
T Consensus        75 ~~~~~~~C~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls~~-----------  143 (507)
T PRK06645         75 ENTTIKTCEQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLSKG-----------  143 (507)
T ss_pred             cCcCcCCCCCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcCHH-----------
Confidence            0    111111 111111100          011234566666665432   34579999999998632           


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhcc
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATE  490 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~  490 (567)
                      .++.|++.++.  .+..+++|++|+..+.+.+.+++|| ..++|..++.++....++..++.    +..+.+..++..+.
T Consensus       144 a~naLLk~LEe--pp~~~vfI~aTte~~kI~~tI~SRc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~  220 (507)
T PRK06645        144 AFNALLKTLEE--PPPHIIFIFATTEVQKIPATIISRC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSE  220 (507)
T ss_pred             HHHHHHHHHhh--cCCCEEEEEEeCChHHhhHHHHhcc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            34567777763  4667888888888889999999999 78999999999999999988864    45667888888776


Q ss_pred             CCCHHHHHHHHHHHH
Q 047219          491 EMSGRDIRDVCQQAE  505 (567)
Q Consensus       491 g~s~~dL~~L~~~a~  505 (567)
                      | +.+++.+++..+.
T Consensus       221 G-slR~al~~Ldkai  234 (507)
T PRK06645        221 G-SARDAVSILDQAA  234 (507)
T ss_pred             C-CHHHHHHHHHHHH
Confidence            5 6666666665554

>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=99.62  E-value=3.2e-14  Score=140.91  Aligned_cols=199  Identities=19%  Similarity=0.293  Sum_probs=124.6

Q ss_pred             CCCCccccc-Cc--HHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          275 SEISWENIA-GY--DQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       275 ~~~~~~dIi-G~--~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ++++|++.+ |.  ..+...+......+                   .....+++||||+|+|||+|.++++++.... .
T Consensus         3 ~~~tFdnfv~g~~N~~a~~~~~~ia~~~-------------------~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~-~   62 (219)
T PF00308_consen    3 PKYTFDNFVVGESNELAYAAAKAIAENP-------------------GERYNPLFLYGPSGLGKTHLLQAIANEAQKQ-H   62 (219)
T ss_dssp             TT-SCCCS--TTTTHHHHHHHHHHHHST-------------------TTSSSEEEEEESTTSSHHHHHHHHHHHHHHH-C
T ss_pred             CCCccccCCcCCcHHHHHHHHHHHHhcC-------------------CCCCCceEEECCCCCCHHHHHHHHHHHHHhc-c
Confidence            568999985 53  33344443333211                   2334579999999999999999999987421 1


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      .+..++++++.++...+..........-|......  ..+|+||+++.+..+         +.+...|...++.+...+.
T Consensus        63 ~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~--~DlL~iDDi~~l~~~---------~~~q~~lf~l~n~~~~~~k  131 (219)
T PF00308_consen   63 PGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRS--ADLLIIDDIQFLAGK---------QRTQEELFHLFNRLIESGK  131 (219)
T ss_dssp             TTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCT--SSEEEEETGGGGTTH---------HHHHHHHHHHHHHHHHTTS
T ss_pred             ccccceeecHHHHHHHHHHHHHcccchhhhhhhhc--CCEEEEecchhhcCc---------hHHHHHHHHHHHHHHhhCC
Confidence            15679999999888765433222111122222233  469999999999755         2233455555555555566


Q ss_pred             EEEEEeeCCCCC---CChHHHhccce--EEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          432 VVVIAATNRKQD---LDPALISRFDS--MITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       432 viVIaaTN~~~~---Ld~aL~sRf~~--~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .+||++...|..   ++++|.+||..  .+.+..|+.+.|.++++..+..    ++++.++.++.... -+.++|..+++
T Consensus       132 ~li~ts~~~P~~l~~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l~~~v~~~l~~~~~-~~~r~L~~~l~  210 (219)
T PF00308_consen  132 QLILTSDRPPSELSGLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAKERGIELPEEVIEYLARRFR-RDVRELEGALN  210 (219)
T ss_dssp             EEEEEESS-TTTTTTS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHHHTT--S-HHHHHHHHHHTT-SSHHHHHHHHH
T ss_pred             eEEEEeCCCCccccccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCCcHHHHHHHHHhhc-CCHHHHHHHHH
Confidence            666666555554   67999999954  8899999999999999998875    56667777777754 36667766666


Q ss_pred             HHH
Q 047219          503 QAE  505 (567)
Q Consensus       503 ~a~  505 (567)
                      ...
T Consensus       211 ~l~  213 (219)
T PF00308_consen  211 RLD  213 (219)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

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.

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.62  E-value=1.1e-14  Score=159.09  Aligned_cols=172  Identities=17%  Similarity=0.237  Sum_probs=118.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ..++++||||||||||+|++++++++... ..+..++++++..+...+...........|......  ..+|+|||||.+
T Consensus       147 ~~~~l~l~G~~G~GKThL~~ai~~~~~~~-~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~--~dlLiiDDi~~l  223 (450)
T PRK00149        147 AYNPLFIYGGVGLGKTHLLHAIGNYILEK-NPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRS--VDVLLIDDIQFL  223 (450)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHHh-CCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhc--CCEEEEehhhhh
Confidence            34679999999999999999999998432 114568899999887766544322111222222222  469999999998


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccc--eEEEecCCCHHHHHHHHHHHHH
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFD--SMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      .++..         ....|+..++.+...+..+||++...+..   ++++|++||.  ..++|+.|+.++|.+|++..+.
T Consensus       224 ~~~~~---------~~~~l~~~~n~l~~~~~~iiits~~~p~~l~~l~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~  294 (450)
T PRK00149        224 AGKER---------TQEEFFHTFNALHEAGKQIVLTSDRPPKELPGLEERLRSRFEWGLTVDIEPPDLETRIAILKKKAE  294 (450)
T ss_pred             cCCHH---------HHHHHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHH
Confidence            75521         11233343333333344566666655554   7799999995  4899999999999999999887


Q ss_pred             h----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          476 H----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       476 ~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .    ++++.++.++....+ +.++|..+++...
T Consensus       295 ~~~~~l~~e~l~~ia~~~~~-~~R~l~~~l~~l~  327 (450)
T PRK00149        295 EEGIDLPDEVLEFIAKNITS-NVRELEGALNRLI  327 (450)
T ss_pred             HcCCCCCHHHHHHHHcCcCC-CHHHHHHHHHHHH
Confidence            4    577788888888655 5666666666554

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.62  E-value=1.6e-14  Score=161.54  Aligned_cols=197  Identities=18%  Similarity=0.220  Sum_probs=139.3

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQ  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~  352 (567)
                      ..+.+|++|+|++.+++.|++.+..                    .+.++.+||+||+|||||++|+++++.+.+.. ..
T Consensus        10 YRP~tFddIIGQe~vv~~L~~ai~~--------------------~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~   69 (709)
T PRK08691         10 WRPKTFADLVGQEHVVKALQNALDE--------------------GRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQH   69 (709)
T ss_pred             hCCCCHHHHcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCC
Confidence            3457899999999999999988752                    45678899999999999999999999986531 11


Q ss_pred             CcCeEEec-hhhHHhh-h---------hchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHH
Q 047219          353 GVPLMYVP-LEVVMSK-Y---------YGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSV  418 (567)
Q Consensus       353 ~~~~~~i~-~~~l~s~-~---------~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~  418 (567)
                      ..+|.... |..+... +         .....+.++.+++.+..   .+...|+||||+|.|...           .++.
T Consensus        70 ~~pCg~C~sCr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls~~-----------A~NA  138 (709)
T PRK08691         70 GEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLSKS-----------AFNA  138 (709)
T ss_pred             CCCCcccHHHHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccCHH-----------HHHH
Confidence            12222111 1111110 0         01122345666554432   234579999999988532           3467


Q ss_pred             HHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCH
Q 047219          419 LLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSG  494 (567)
Q Consensus       419 LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~  494 (567)
                      |++.++.  .+..+.+|++|+.+..+.+.+++|| ..+.|..++.++....|...+..    +....+..+++...| +.
T Consensus       139 LLKtLEE--Pp~~v~fILaTtd~~kL~~TIrSRC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~G-sl  214 (709)
T PRK08691        139 MLKTLEE--PPEHVKFILATTDPHKVPVTVLSRC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAG-SM  214 (709)
T ss_pred             HHHHHHh--CCCCcEEEEEeCCccccchHHHHHH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCC-CH
Confidence            7777774  4567888889998999999999999 88999999999999999888775    456678888887654 66


Q ss_pred             HHHHHHHHHHH
Q 047219          495 RDIRDVCQQAE  505 (567)
Q Consensus       495 ~dL~~L~~~a~  505 (567)
                      +++.+++..+.
T Consensus       215 RdAlnLLDqai  225 (709)
T PRK08691        215 RDALSLLDQAI  225 (709)
T ss_pred             HHHHHHHHHHH
Confidence            67767666554

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.61  E-value=7.6e-15  Score=171.14  Aligned_cols=171  Identities=20%  Similarity=0.276  Sum_probs=130.2

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -.++.++|++..++++.+.+.                     .+...+++|+||||||||++|+++|..+...    .+.
T Consensus       175 ~~l~~vigr~~ei~~~i~iL~---------------------r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~  233 (857)
T PRK10865        175 GKLDPVIGRDEEIRRTIQVLQ---------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLK  233 (857)
T ss_pred             CCCCcCCCCHHHHHHHHHHHh---------------------cCCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhC
Confidence            357889999998888877664                     3445689999999999999999999988532    223


Q ss_pred             CcCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +.+++.++...+.  .++.|+.+..++.+|+.+.....++||||||+|.|.+........   +..+.|...+    .++
T Consensus       234 ~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~---d~~~~lkp~l----~~g  306 (857)
T PRK10865        234 GRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAM---DAGNMLKPAL----ARG  306 (857)
T ss_pred             CCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccch---hHHHHhcchh----hcC
Confidence            6778888877765  468899999999999986554446899999999998664322111   1122333322    467


Q ss_pred             cEEEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh
Q 047219          431 KVVVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       431 ~viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      .+.+|++|+..+     .+|++|.+|| ..|.+..|+.+++..|++.+...
T Consensus       307 ~l~~IgaTt~~e~r~~~~~d~al~rRf-~~i~v~eP~~~~~~~iL~~l~~~  356 (857)
T PRK10865        307 ELHCVGATTLDEYRQYIEKDAALERRF-QKVFVAEPSVEDTIAILRGLKER  356 (857)
T ss_pred             CCeEEEcCCCHHHHHHhhhcHHHHhhC-CEEEeCCCCHHHHHHHHHHHhhh
Confidence            899999999865     4899999999 47889999999999999877643

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.61  E-value=1.7e-14  Score=155.50  Aligned_cols=172  Identities=17%  Similarity=0.249  Sum_probs=116.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHH-HHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER-LLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~-~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ...+++||||+|||||+|++++++++... ..+..++++++.++...+...... ....+.+... .  ..+|+|||||.
T Consensus       135 ~~n~l~l~G~~G~GKThL~~ai~~~l~~~-~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~-~--~dlLiiDDi~~  210 (405)
T TIGR00362       135 AYNPLFIYGGVGLGKTHLLHAIGNEILEN-NPNAKVVYVSSEKFTNDFVNALRNNKMEEFKEKYR-S--VDLLLIDDIQF  210 (405)
T ss_pred             cCCeEEEECCCCCcHHHHHHHHHHHHHHh-CCCCcEEEEEHHHHHHHHHHHHHcCCHHHHHHHHH-h--CCEEEEehhhh
Confidence            45679999999999999999999988432 114678899998887665443221 1112222222 2  36999999999


Q ss_pred             hhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccce--EEEecCCCHHHHHHHHHHHH
Q 047219          400 FAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFDS--MITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       400 L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~~--~I~i~~P~~~eR~eIL~~~~  474 (567)
                      +.++..         ....|+..++.....+..+||+++..+..   +++.|++||..  .++|+.|+.++|.+|++..+
T Consensus       211 l~~~~~---------~~~~l~~~~n~~~~~~~~iiits~~~p~~l~~l~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~  281 (405)
T TIGR00362       211 LAGKER---------TQEEFFHTFNALHENGKQIVLTSDRPPKELPGLEERLRSRFEWGLVVDIEPPDLETRLAILQKKA  281 (405)
T ss_pred             hcCCHH---------HHHHHHHHHHHHHHCCCCEEEecCCCHHHHhhhhhhhhhhccCCeEEEeCCCCHHHHHHHHHHHH
Confidence            875421         11233333333323334455555555443   67899999954  79999999999999999988


Q ss_pred             Hh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          475 KH----LTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       475 ~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      ..    ++++.++.++....+ +.++|..+++....
T Consensus       282 ~~~~~~l~~e~l~~ia~~~~~-~~r~l~~~l~~l~~  316 (405)
T TIGR00362       282 EEEGLELPDEVLEFIAKNIRS-NVRELEGALNRLLA  316 (405)
T ss_pred             HHcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHH
Confidence            74    567788888887654 67777777776553

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).

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.61  E-value=1.1e-14  Score=170.35  Aligned_cols=238  Identities=22%  Similarity=0.237  Sum_probs=152.5

Q ss_pred             cCCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCC
Q 047219          242 SLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNR  321 (567)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~  321 (567)
                      .++..++..+++.+...+......++..........-...|+|++.+++.+.+.+......      +.      ....+
T Consensus       527 ~v~~~~i~~v~~~~tgip~~~~~~~e~~~l~~l~~~l~~~v~GQ~~av~~v~~~i~~~~~g------l~------~~~~p  594 (852)
T TIGR03346       527 EVTAEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAG------LS------DPNRP  594 (852)
T ss_pred             CcCHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHhcc------CC------CCCCC
Confidence            4677788888888776655433333222211222234567999999999999988754110      00      00234


Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh-----hh-------chhHHHHHHHHHHHhcCCCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK-----YY-------GESERLLGKVFSLANELPNG  389 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~-----~~-------G~~~~~l~~~f~~A~~~a~~  389 (567)
                      ...+||+||||||||++|+++|..+...   +.+++.++++++...     ++       |+.+   ...+..+....|.
T Consensus       595 ~~~~Lf~Gp~GvGKt~lA~~La~~l~~~---~~~~i~~d~s~~~~~~~~~~l~g~~~g~~g~~~---~g~l~~~v~~~p~  668 (852)
T TIGR03346       595 IGSFLFLGPTGVGKTELAKALAEFLFDD---EDAMVRIDMSEYMEKHSVARLIGAPPGYVGYEE---GGQLTEAVRRKPY  668 (852)
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHhcCC---CCcEEEEechhhcccchHHHhcCCCCCccCccc---ccHHHHHHHcCCC
Confidence            5679999999999999999999998544   456888887765432     22       2211   1123333334467


Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc---------ccCCcEEEEEeeCCC-------------------
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF---------EQDKKVVVIAATNRK-------------------  441 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~---------~~~~~viVIaaTN~~-------------------  441 (567)
                      +|||||||+.+.+..+           +.|++.++.-         ..-.+++||+|||..                   
T Consensus       669 ~vlllDeieka~~~v~-----------~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~  737 (852)
T TIGR03346       669 SVVLFDEVEKAHPDVF-----------NVLLQVLDDGRLTDGQGRTVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREA  737 (852)
T ss_pred             cEEEEeccccCCHHHH-----------HHHHHHHhcCceecCCCeEEecCCcEEEEeCCcchHhHhhhcccccHHHHHHH
Confidence            8999999999875533           3444444321         112467899999971                   


Q ss_pred             ------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-------------CHHHHHHHHHhcc--CCCHHHHHHH
Q 047219          442 ------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-------------TKAELAELATATE--EMSGRDIRDV  500 (567)
Q Consensus       442 ------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-------------~~~~l~~la~~t~--g~s~~dL~~L  500 (567)
                            +.|.|+|++|++.++.|.+++.++..+|+...+..+             ..+..+.++...+  .+..+.|+++
T Consensus       738 ~~~~~~~~F~pel~~Rid~IivF~PL~~e~l~~I~~l~L~~l~~~l~~~~~~l~i~~~a~~~L~~~~~~~~~gaR~L~~~  817 (852)
T TIGR03346       738 VMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKRLAERKITLELSDAALDFLAEAGYDPVYGARPLKRA  817 (852)
T ss_pred             HHHHHHhhcCHHHhcCcCeEEecCCcCHHHHHHHHHHHHHHHHHHHHHCCCeecCCHHHHHHHHHhCCCCCCCchhHHHH
Confidence                  137789999999999999999999999988776532             3334555555433  4556666666


Q ss_pred             HHHHHHHH
Q 047219          501 CQQAERSW  508 (567)
Q Consensus       501 ~~~a~~~a  508 (567)
                      +.......
T Consensus       818 i~~~i~~~  825 (852)
T TIGR03346       818 IQREIENP  825 (852)
T ss_pred             HHHHHHHH
Confidence            66555433

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.61  E-value=4.4e-14  Score=147.91  Aligned_cols=192  Identities=20%  Similarity=0.287  Sum_probs=129.1

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      .+.+|++++|++++++.+.+.+.                     .+...++||+||||||||++|+++++++....+ ..
T Consensus        10 ~P~~~~~~~g~~~~~~~L~~~~~---------------------~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~~-~~   67 (337)
T PRK12402         10 RPALLEDILGQDEVVERLSRAVD---------------------SPNLPHLLVQGPPGSGKTAAVRALARELYGDPW-EN   67 (337)
T ss_pred             CCCcHHHhcCCHHHHHHHHHHHh---------------------CCCCceEEEECCCCCCHHHHHHHHHHHhcCccc-cc
Confidence            45689999999999999888664                     222347999999999999999999999864321 23


Q ss_pred             CeEEechhhHHhhh-------------hch-------hHHHHHHHHHHHhc----CCCCcEEEEcCcchhhhhhhhhhHH
Q 047219          355 PLMYVPLEVVMSKY-------------YGE-------SERLLGKVFSLANE----LPNGAIIFLDEVDSFAVARDSEMHE  410 (567)
Q Consensus       355 ~~~~i~~~~l~s~~-------------~G~-------~~~~l~~~f~~A~~----~a~~~ILfIDEID~L~~~~q~~l~~  410 (567)
                      +++++++.++....             ++.       ....++.+......    ..+..+|||||+|.+....      
T Consensus        68 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~~~------  141 (337)
T PRK12402         68 NFTEFNVADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALREDA------  141 (337)
T ss_pred             ceEEechhhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCHHH------
Confidence            56777776543221             111       01222332222221    1335799999999986432      


Q ss_pred             HHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHH
Q 047219          411 ATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELA  486 (567)
Q Consensus       411 ~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la  486 (567)
                           ...|...++..  +..+.+|.+++.+..+.+.|.+|+ ..+.+..|+.++...++...+..    +..+.++.++
T Consensus       142 -----~~~L~~~le~~--~~~~~~Il~~~~~~~~~~~L~sr~-~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~al~~l~  213 (337)
T PRK12402        142 -----QQALRRIMEQY--SRTCRFIIATRQPSKLIPPIRSRC-LPLFFRAPTDDELVDVLESIAEAEGVDYDDDGLELIA  213 (337)
T ss_pred             -----HHHHHHHHHhc--cCCCeEEEEeCChhhCchhhcCCc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence                 12344444432  234566667766777888999998 78999999999999999987764    5677888888


Q ss_pred             HhccCCCHHHHHHHHHHHHH
Q 047219          487 TATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       487 ~~t~g~s~~dL~~L~~~a~~  506 (567)
                      ..+.    +|++.+.+....
T Consensus       214 ~~~~----gdlr~l~~~l~~  229 (337)
T PRK12402        214 YYAG----GDLRKAILTLQT  229 (337)
T ss_pred             HHcC----CCHHHHHHHHHH
Confidence            7763    356666655543

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.60  E-value=2.7e-14  Score=155.98  Aligned_cols=188  Identities=24%  Similarity=0.308  Sum_probs=149.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      .-.+.++||+||+|||||.|++++++++....  .+.+..++|+.+..+-+....+.+..+|..+.+++| +||+||++|
T Consensus       428 v~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~--~~hv~~v~Cs~l~~~~~e~iQk~l~~vfse~~~~~P-SiIvLDdld  504 (952)
T KOG0735|consen  428 VFRHGNILLNGPKGSGKTNLVKALFDYYSKDL--IAHVEIVSCSTLDGSSLEKIQKFLNNVFSEALWYAP-SIIVLDDLD  504 (952)
T ss_pred             ccccccEEEeCCCCCCHhHHHHHHHHHhcccc--ceEEEEEechhccchhHHHHHHHHHHHHHHHHhhCC-cEEEEcchh
Confidence            34567899999999999999999999986321  456788899988887777788889999999999996 999999999


Q ss_pred             hhhhhhh--hhhHHHHHHHHHHHH-HhhcCc-ccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHH
Q 047219          399 SFAVARD--SEMHEATRRILSVLL-RQIDGF-EQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       399 ~L~~~~q--~~l~~~~~~vl~~LL-~~ld~~-~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~  472 (567)
                      .|+....  ..........+..++ ..+..+ ..+..+.||++.+....+++-|.+  +|+.++.++.|+..+|.+||..
T Consensus       505 ~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~qtl~~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~  584 (952)
T KOG0735|consen  505 CLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQTLNPLLVSPLLFQIVIALPAPAVTRRKEILTT  584 (952)
T ss_pred             hhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhhhcChhhcCccceEEEEecCCcchhHHHHHHHH
Confidence            9987322  222223233333444 333222 344567999999999999999988  8999999999999999999999


Q ss_pred             HHHhh----CHHHHHHHHHhccCCCHHHHHHHHHHHHHHHH
Q 047219          473 YAKHL----TKAELAELATATEEMSGRDIRDVCQQAERSWA  509 (567)
Q Consensus       473 ~~~~~----~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~  509 (567)
                      .+.+-    ..++++-++..|+||...|+..++.+|...+.
T Consensus       585 ~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVeRai~~a~  625 (952)
T KOG0735|consen  585 IFSKNLSDITMDDLDFLSVKTEGYLATDLVIFVERAIHEAF  625 (952)
T ss_pred             HHHhhhhhhhhHHHHHHHHhcCCccchhHHHHHHHHHHHHH
Confidence            88763    34567779999999999999999999886555

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.60  E-value=6.5e-14  Score=154.26  Aligned_cols=177  Identities=19%  Similarity=0.251  Sum_probs=127.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CC--
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PW--  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~--  351 (567)
                      .+.+|++|+|++.+++.|...+..                    ...++.+||+||||||||++|+++++.+.+. +.  
T Consensus         9 RP~~~~dvvGq~~v~~~L~~~i~~--------------------~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~   68 (504)
T PRK14963          9 RPITFDEVVGQEHVKEVLLAALRQ--------------------GRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPK   68 (504)
T ss_pred             CCCCHHHhcChHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCC
Confidence            457899999999999999888752                    3456678999999999999999999998542 10  


Q ss_pred             --------------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          352 --------------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       352 --------------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                                    ....+..++...      ......++.+.+.+..   .....++||||+|.+..           .
T Consensus        69 ~cg~C~sc~~i~~~~h~dv~el~~~~------~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls~-----------~  131 (504)
T PRK14963         69 PCGECESCLAVRRGAHPDVLEIDAAS------NNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMSK-----------S  131 (504)
T ss_pred             CCCcChhhHHHhcCCCCceEEecccc------cCCHHHHHHHHHHHhhccccCCCeEEEEECccccCH-----------H
Confidence                          012234444321      0112334444333332   23457999999998752           2


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhcc
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATE  490 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~  490 (567)
                      .++.|++.++.  .+..+++|.+||.+..+.+.+.+|| ..++|..|+.++..+.+...++.    +..+.+..++..+.
T Consensus       132 a~naLLk~LEe--p~~~t~~Il~t~~~~kl~~~I~SRc-~~~~f~~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~  208 (504)
T PRK14963        132 AFNALLKTLEE--PPEHVIFILATTEPEKMPPTILSRT-QHFRFRRLTEEEIAGKLRRLLEAEGREAEPEALQLVARLAD  208 (504)
T ss_pred             HHHHHHHHHHh--CCCCEEEEEEcCChhhCChHHhcce-EEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            34667777764  3457788888888899999999999 78999999999999999887764    35667788887766


Q ss_pred             C
Q 047219          491 E  491 (567)
Q Consensus       491 g  491 (567)
                      |
T Consensus       209 G  209 (504)
T PRK14963        209 G  209 (504)
T ss_pred             C
Confidence            5

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.60  E-value=1.3e-14  Score=167.24  Aligned_cols=236  Identities=22%  Similarity=0.297  Sum_probs=147.8

Q ss_pred             CCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhccccccc-CCC
Q 047219          243 LTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFE-SNR  321 (567)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~-~~~  321 (567)
                      ++..++..+++.+...+......++..........-.+.|+|++++++.+.+.+....        .+  .   .. ..+
T Consensus       417 v~~~~i~~~i~~~tgiP~~~~~~~~~~~l~~l~~~l~~~v~GQ~~ai~~l~~~i~~~~--------~g--~---~~~~~p  483 (731)
T TIGR02639       417 VSVKDIENVVAKMAHIPVKTVSVDDREKLKNLEKNLKAKIFGQDEAIDSLVSSIKRSR--------AG--L---GNPNKP  483 (731)
T ss_pred             cCHHHHHHHHHHHhCCChhhhhhHHHHHHHHHHHHHhcceeCcHHHHHHHHHHHHHHh--------cC--C---CCCCCC
Confidence            5566667776666554432222221111111222335678999999999988876431        00  0   00 123


Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh-----hhchhH----HHHHHHHHHHhcCCCCcEE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK-----YYGESE----RLLGKVFSLANELPNGAII  392 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~-----~~G~~~----~~l~~~f~~A~~~a~~~IL  392 (567)
                      ..++||+||||||||++|+++|+.+      +.+++.++++++...     ++|...    ..-...+..+....|.+||
T Consensus       484 ~~~~lf~Gp~GvGKT~lA~~la~~l------~~~~~~~d~se~~~~~~~~~lig~~~gyvg~~~~~~l~~~~~~~p~~Vv  557 (731)
T TIGR02639       484 VGSFLFTGPTGVGKTELAKQLAEAL------GVHLERFDMSEYMEKHTVSRLIGAPPGYVGFEQGGLLTEAVRKHPHCVL  557 (731)
T ss_pred             ceeEEEECCCCccHHHHHHHHHHHh------cCCeEEEeCchhhhcccHHHHhcCCCCCcccchhhHHHHHHHhCCCeEE
Confidence            3458999999999999999999999      567888887776432     222211    0011223333344567999


Q ss_pred             EEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---------cCCcEEEEEeeCCC----------------------
Q 047219          393 FLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---------QDKKVVVIAATNRK----------------------  441 (567)
Q Consensus       393 fIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---------~~~~viVIaaTN~~----------------------  441 (567)
                      +|||||++.+.           +.+.|++.++...         .-.++++|+|||.-                      
T Consensus       558 llDEieka~~~-----------~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~  626 (731)
T TIGR02639       558 LLDEIEKAHPD-----------IYNILLQVMDYATLTDNNGRKADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDK  626 (731)
T ss_pred             EEechhhcCHH-----------HHHHHHHhhccCeeecCCCcccCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHH
Confidence            99999998654           3445555555321         12468899999862                      


Q ss_pred             ---CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-------------CHHHHHHHHHh--ccCCCHHHHHHHHHH
Q 047219          442 ---QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-------------TKAELAELATA--TEEMSGRDIRDVCQQ  503 (567)
Q Consensus       442 ---~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-------------~~~~l~~la~~--t~g~s~~dL~~L~~~  503 (567)
                         ..|.|+|+.|++.++.|.+.+.++..+|++..++.+             .++..+.++..  ...+..+.|+.+++.
T Consensus       627 ~~~~~f~pef~~Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l~~~~~~l~i~~~a~~~La~~~~~~~~GaR~l~r~i~~  706 (731)
T TIGR02639       627 AIKKLFSPEFRNRLDAIIHFNPLSEEVLEKIVQKFVDELSKQLNEKNIKLELTDDAKKYLAEKGYDEEFGARPLARVIQE  706 (731)
T ss_pred             HHHhhcChHHHhcCCeEEEcCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEeCHHHHHHHHHhCCCcccCchHHHHHHHH
Confidence               137889999999999999999999999999877642             23344455542  334556666666666


Q ss_pred             HHHHH
Q 047219          504 AERSW  508 (567)
Q Consensus       504 a~~~a  508 (567)
                      .....
T Consensus       707 ~~~~~  711 (731)
T TIGR02639       707 EIKKP  711 (731)
T ss_pred             HhHHH
Confidence            55444

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.60  E-value=3e-14  Score=166.22  Aligned_cols=237  Identities=20%  Similarity=0.231  Sum_probs=153.3

Q ss_pred             cCCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhc---cChhhHHhhhhccccccc
Q 047219          242 SLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSL---QSPEVYDDIARGTRCKFE  318 (567)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l---~~pelf~~l~~~~~~~~~  318 (567)
                      .++..++..+++.++..++.....++............+.|+|++.+++.+.+.+....   ..|               
T Consensus       530 ~v~~~~i~~vv~~~tgip~~~~~~~~~~~l~~l~~~l~~~viGQ~~ai~~l~~~i~~~~~gl~~~---------------  594 (857)
T PRK10865        530 KVTDAEIAEVLARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDP---------------  594 (857)
T ss_pred             ccCHHHHHHHHHHHHCCCchhhhhhHHHHHHHHHHHhCCeEeCCHHHHHHHHHHHHHHHhcccCC---------------
Confidence            46778888899988887765433333322223344556789999999999999987541   111               


Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh-----hhchhHH----HHHHHHHHHhcCCCC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK-----YYGESER----LLGKVFSLANELPNG  389 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~-----~~G~~~~----~l~~~f~~A~~~a~~  389 (567)
                      ..+..++||+||||||||++|++||+.+...   +.+++.++++++...     ++|....    .-...+..+....|+
T Consensus       595 ~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~---~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~  671 (857)
T PRK10865        595 NRPIGSFLFLGPTGVGKTELCKALANFMFDS---DDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPY  671 (857)
T ss_pred             CCCCceEEEECCCCCCHHHHHHHHHHHhhcC---CCcEEEEEhHHhhhhhhHHHHhCCCCcccccchhHHHHHHHHhCCC
Confidence            1223478999999999999999999988543   346788888766432     3322100    011233444444567


Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc---------ccCCcEEEEEeeCCC-------------------
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF---------EQDKKVVVIAATNRK-------------------  441 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~---------~~~~~viVIaaTN~~-------------------  441 (567)
                      ++||||||+.+.+..+           +.|+..++.-         ..-.++++|+|||..                   
T Consensus       672 ~vLllDEieka~~~v~-----------~~Ll~ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~  740 (857)
T PRK10865        672 SVILLDEVEKAHPDVF-----------NILLQVLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKEL  740 (857)
T ss_pred             CeEEEeehhhCCHHHH-----------HHHHHHHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHH
Confidence            9999999999875533           3344444321         112356799999861                   


Q ss_pred             ------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-------------CHHHHHHHHHhc--cCCCHHHHHHH
Q 047219          442 ------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-------------TKAELAELATAT--EEMSGRDIRDV  500 (567)
Q Consensus       442 ------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-------------~~~~l~~la~~t--~g~s~~dL~~L  500 (567)
                            ..|.|+|++|++.++.|.+++.++..+|+...+..+             ..+.++.++...  ..+..+.|+.+
T Consensus       741 ~~~~~~~~f~PELlnRld~iivF~PL~~edl~~Iv~~~L~~l~~rl~~~gi~l~is~~al~~L~~~gy~~~~GARpL~r~  820 (857)
T PRK10865        741 VLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYKRLEERGYEIHISDEALKLLSENGYDPVYGARPLKRA  820 (857)
T ss_pred             HHHHHcccccHHHHHhCCeeEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCcCcCCHHHHHHHHHcCCCccCChHHHHHH
Confidence                  247789999999999999999999999888776542             233444454421  12335566666


Q ss_pred             HHHHHHH
Q 047219          501 CQQAERS  507 (567)
Q Consensus       501 ~~~a~~~  507 (567)
                      ++.....
T Consensus       821 I~~~i~~  827 (857)
T PRK10865        821 IQQQIEN  827 (857)
T ss_pred             HHHHHHH
Confidence            6665544

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.60  E-value=7.7e-14  Score=137.90  Aligned_cols=186  Identities=15%  Similarity=0.206  Sum_probs=124.1

Q ss_pred             CCCCccccc--CcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          275 SEISWENIA--GYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       275 ~~~~~~dIi--G~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ...+|++.+  +...+++.+++.+.                     ...+.+++|+||+|||||++|+++++++...   
T Consensus        10 ~~~~~~~~~~~~~~~~~~~l~~~~~---------------------~~~~~~lll~G~~G~GKT~la~~~~~~~~~~---   65 (226)
T TIGR03420        10 DDPTFDNFYAGGNAELLAALRQLAA---------------------GKGDRFLYLWGESGSGKSHLLQAACAAAEER---   65 (226)
T ss_pred             CchhhcCcCcCCcHHHHHHHHHHHh---------------------cCCCCeEEEECCCCCCHHHHHHHHHHHHHhc---
Confidence            346777776  35556666666542                     3457899999999999999999999988533   


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +.+++++++..+....        ..++....   ...+|+|||+|.+......         ...+...++....... 
T Consensus        66 ~~~~~~i~~~~~~~~~--------~~~~~~~~---~~~lLvIDdi~~l~~~~~~---------~~~L~~~l~~~~~~~~-  124 (226)
T TIGR03420        66 GKSAIYLPLAELAQAD--------PEVLEGLE---QADLVCLDDVEAIAGQPEW---------QEALFHLYNRVREAGG-  124 (226)
T ss_pred             CCcEEEEeHHHHHHhH--------HHHHhhcc---cCCEEEEeChhhhcCChHH---------HHHHHHHHHHHHHcCC-
Confidence            4578899998876532        12222222   2469999999998654210         1122222222112223 


Q ss_pred             EEEEeeC-CCCCC---ChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          433 VVIAATN-RKQDL---DPALISRFD--SMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       433 iVIaaTN-~~~~L---d~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .+|.+++ .+..+   .+.|.+||.  ..+.++.|+.+++..+++.++.+    +..+.+..++.. ++-+.++++.+++
T Consensus       125 ~iIits~~~~~~~~~~~~~L~~r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~-~~gn~r~L~~~l~  203 (226)
T TIGR03420       125 RLLIAGRAAPAQLPLRLPDLRTRLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRH-GSRDMGSLMALLD  203 (226)
T ss_pred             eEEEECCCChHHCCcccHHHHHHHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHHHHHHHH
Confidence            3444554 33333   288998873  68899999999999999877653    567778888885 6678999999988


Q ss_pred             HHHH
Q 047219          503 QAER  506 (567)
Q Consensus       503 ~a~~  506 (567)
                      .+..
T Consensus       204 ~~~~  207 (226)
T TIGR03420       204 ALDR  207 (226)
T ss_pred             HHHH
Confidence            8664

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.59  E-value=2.9e-14  Score=162.61  Aligned_cols=176  Identities=23%  Similarity=0.341  Sum_probs=120.3

Q ss_pred             CCCCCcccccCcHHHHH---HHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          274 KSEISWENIAGYDQQKR---EIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~---~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      ..+.+|++++|++..+.   .+++++.                     .....+++||||||||||++|+++|+.+    
T Consensus        22 ~RP~tldd~vGQe~ii~~~~~L~~~i~---------------------~~~~~slLL~GPpGtGKTTLA~aIA~~~----   76 (725)
T PRK13341         22 LRPRTLEEFVGQDHILGEGRLLRRAIK---------------------ADRVGSLILYGPPGVGKTTLARIIANHT----   76 (725)
T ss_pred             cCCCcHHHhcCcHHHhhhhHHHHHHHh---------------------cCCCceEEEECCCCCCHHHHHHHHHHHh----
Confidence            34578999999999885   4544443                     3345689999999999999999999988    


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHH----hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA----NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF  426 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A----~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~  426 (567)
                        ..++..+++.....       +.++..++.+    .......+|||||||.|....|           +.|+..++  
T Consensus        77 --~~~f~~lna~~~~i-------~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~~qQ-----------daLL~~lE--  134 (725)
T PRK13341         77 --RAHFSSLNAVLAGV-------KDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQ-----------DALLPWVE--  134 (725)
T ss_pred             --cCcceeehhhhhhh-------HHHHHHHHHHHHHhhhcCCceEEEEeChhhCCHHHH-----------HHHHHHhc--
Confidence              44566666542111       1122222222    1222357999999999975433           33444444  


Q ss_pred             ccCCcEEEEEee--CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh-----------hCHHHHHHHHHhccCCC
Q 047219          427 EQDKKVVVIAAT--NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH-----------LTKAELAELATATEEMS  493 (567)
Q Consensus       427 ~~~~~viVIaaT--N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-----------~~~~~l~~la~~t~g~s  493 (567)
                        .+.+++|++|  |+...+++++++|+ ..+.|+.++.+++..+++..+..           +.++.++.++....|  
T Consensus       135 --~g~IiLI~aTTenp~~~l~~aL~SR~-~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~G--  209 (725)
T PRK13341        135 --NGTITLIGATTENPYFEVNKALVSRS-RLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANG--  209 (725)
T ss_pred             --CceEEEEEecCCChHhhhhhHhhccc-cceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCC--
Confidence              3567788776  34457899999998 78999999999999999988761           456677777776543  


Q ss_pred             HHHHHHHHHH
Q 047219          494 GRDIRDVCQQ  503 (567)
Q Consensus       494 ~~dL~~L~~~  503 (567)
                        |++.+.+.
T Consensus       210 --D~R~lln~  217 (725)
T PRK13341        210 --DARSLLNA  217 (725)
T ss_pred             --CHHHHHHH
Confidence              55555443

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.59  E-value=1.5e-14  Score=168.65  Aligned_cols=187  Identities=21%  Similarity=0.314  Sum_probs=141.4

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQG  353 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~  353 (567)
                      .++.++|.++.++++.+.+.                     ....++++|+||||||||++|+++|..+...    .+.+
T Consensus       177 ~~~~~igr~~ei~~~~~~L~---------------------r~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~  235 (821)
T CHL00095        177 NLDPVIGREKEIERVIQILG---------------------RRTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILED  235 (821)
T ss_pred             CCCCCCCcHHHHHHHHHHHc---------------------ccccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcC
Confidence            47889999999999988764                     3456789999999999999999999987432    2335


Q ss_pred             cCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          354 VPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..++.++...+.  .+|.|+.+.+++.+++.+.... ++||||||||.|.+........   ...+.|...+    .++.
T Consensus       236 ~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~-~~ILfiDEih~l~~~g~~~g~~---~~a~lLkp~l----~rg~  307 (821)
T CHL00095        236 KLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQENN-NIILVIDEVHTLIGAGAAEGAI---DAANILKPAL----ARGE  307 (821)
T ss_pred             CeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhcC-CeEEEEecHHHHhcCCCCCCcc---cHHHHhHHHH----hCCC
Confidence            778999988776  4788999999999999987654 5899999999998654322111   1122233333    3578


Q ss_pred             EEEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhccCCCH
Q 047219          432 VVVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATEEMSG  494 (567)
Q Consensus       432 viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~g~s~  494 (567)
                      +.+|++|+..+     ..+++|.+|| ..+.++.|+.++...|++.+...        +.++.+..+...+.+|.+
T Consensus       308 l~~IgaTt~~ey~~~ie~D~aL~rRf-~~I~v~ep~~~e~~aILr~l~~~~e~~~~v~i~deal~~i~~ls~~yi~  382 (821)
T CHL00095        308 LQCIGATTLDEYRKHIEKDPALERRF-QPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIA  382 (821)
T ss_pred             cEEEEeCCHHHHHHHHhcCHHHHhcc-eEEecCCCCHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhhccCc
Confidence            99999998753     5789999999 67899999999999998865432        456667777776666543

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.59  E-value=6.7e-14  Score=156.26  Aligned_cols=189  Identities=21%  Similarity=0.314  Sum_probs=136.8

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++..++.+++.+..                    ...++.+||+||+|||||++|+.+|+.+.+.. ..+
T Consensus        11 rP~~f~~viGq~~v~~~L~~~i~~--------------------~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~   70 (559)
T PRK05563         11 RPQTFEDVVGQEHITKTLKNAIKQ--------------------GKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDG   70 (559)
T ss_pred             CCCcHHhccCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            457899999999999999888752                    35677899999999999999999999986431 111


Q ss_pred             -----------------cCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 -----------------VPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 -----------------~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                                       .+++.+++..      +..-..++.+.+.+..   .+++.|+||||+|.|...          
T Consensus        71 ~pC~~C~~C~~i~~g~~~dv~eidaas------~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt~~----------  134 (559)
T PRK05563         71 EPCNECEICKAITNGSLMDVIEIDAAS------NNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLSTG----------  134 (559)
T ss_pred             CCCCccHHHHHHhcCCCCCeEEeeccc------cCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHH----------
Confidence                             1223332210      1123445566555542   334679999999998632          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.|++.++.  .+..+++|.+|+.+..+.+.+++|| ..+.|..|+.++....+...++.    +..+.+..++...
T Consensus       135 -a~naLLKtLEe--pp~~~ifIlatt~~~ki~~tI~SRc-~~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s  210 (559)
T PRK05563        135 -AFNALLKTLEE--PPAHVIFILATTEPHKIPATILSRC-QRFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAA  210 (559)
T ss_pred             -HHHHHHHHhcC--CCCCeEEEEEeCChhhCcHHHHhHh-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             45678888774  4667888888888899999999999 78999999999999988887764    3556777778776


Q ss_pred             cCCCHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQA  504 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a  504 (567)
                      .| +.++...++..+
T Consensus       211 ~G-~~R~al~~Ldq~  224 (559)
T PRK05563        211 EG-GMRDALSILDQA  224 (559)
T ss_pred             CC-CHHHHHHHHHHH
Confidence            65 555655555544

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.59  E-value=2.6e-14  Score=155.30  Aligned_cols=169  Identities=17%  Similarity=0.245  Sum_probs=111.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ..++++||||+|+|||+|++++++++...   +..+++++.+.+...+.......-...|......  ..+|+||||+.+
T Consensus       140 ~~npl~L~G~~G~GKTHLl~Ai~~~l~~~---~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~--~dvLiIDDiq~l  214 (445)
T PRK12422        140 PFNPIYLFGPEGSGKTHLMQAAVHALRES---GGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRN--VDALFIEDIEVF  214 (445)
T ss_pred             CCceEEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEeeHHHHHHHHHHHHhcchHHHHHHHccc--CCEEEEcchhhh
Confidence            34689999999999999999999988543   5678999988776654332211111223333332  469999999998


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC---CCChHHHhccc--eEEEecCCCHHHHHHHHHHHHH
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ---DLDPALISRFD--SMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~---~Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      .++..         ....|+..++.+...+..+|+++++.+.   .++++|++||.  ..+.+..|+.++|..|++..++
T Consensus       215 ~~k~~---------~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~  285 (445)
T PRK12422        215 SGKGA---------TQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAE  285 (445)
T ss_pred             cCChh---------hHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHH
Confidence            75421         1122333333222233445555544443   47899999995  6888999999999999999887


Q ss_pred             h----hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          476 H----LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       476 ~----~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .    ++.+.++.++....+ +.+.|...+...
T Consensus       286 ~~~~~l~~evl~~la~~~~~-dir~L~g~l~~l  317 (445)
T PRK12422        286 ALSIRIEETALDFLIEALSS-NVKSLLHALTLL  317 (445)
T ss_pred             HcCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHH
Confidence            5    567778888877654 344444444443

>PRK04195 replication factor C large subunit; Provisional

Probab=99.59  E-value=5.2e-14  Score=155.09  Aligned_cols=188  Identities=22%  Similarity=0.300  Sum_probs=133.7

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.++++|+|++.+++.+++.+....                 ...+++++||+||||||||++|+++|+++      +
T Consensus         8 yrP~~l~dlvg~~~~~~~l~~~l~~~~-----------------~g~~~~~lLL~GppG~GKTtla~ala~el------~   64 (482)
T PRK04195          8 YRPKTLSDVVGNEKAKEQLREWIESWL-----------------KGKPKKALLLYGPPGVGKTSLAHALANDY------G   64 (482)
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHHHHh-----------------cCCCCCeEEEECCCCCCHHHHHHHHHHHc------C
Confidence            345689999999999999999886432                 13457899999999999999999999999      6


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhc----C-CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANE----L-PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~----~-a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      .+++.+++++....      ..+..+...+..    . .++.+|+|||+|.|....+.       ..+..|+..++    
T Consensus        65 ~~~ielnasd~r~~------~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~d~-------~~~~aL~~~l~----  127 (482)
T PRK04195         65 WEVIELNASDQRTA------DVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNEDR-------GGARAILELIK----  127 (482)
T ss_pred             CCEEEEcccccccH------HHHHHHHHHhhccCcccCCCCeEEEEecCcccccccch-------hHHHHHHHHHH----
Confidence            67888887654321      122222222211    1 13579999999999753211       12234445444    


Q ss_pred             CCcEEEEEeeCCCCCCCh-HHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDP-ALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~-aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+..+|+++|.+..+.+ .|++|+ ..+.|+.|+.++...++...+..    +..+.++.++..+.|    |++.+++.
T Consensus       128 ~~~~~iIli~n~~~~~~~k~Lrsr~-~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~G----DlR~ain~  202 (482)
T PRK04195        128 KAKQPIILTANDPYDPSLRELRNAC-LMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERSGG----DLRSAIND  202 (482)
T ss_pred             cCCCCEEEeccCccccchhhHhccc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC----CHHHHHHH
Confidence            234567778888888887 788888 88999999999999999988764    456778888877654    66666665


Q ss_pred             HHH
Q 047219          504 AER  506 (567)
Q Consensus       504 a~~  506 (567)
                      ...
T Consensus       203 Lq~  205 (482)
T PRK04195        203 LQA  205 (482)
T ss_pred             HHH
Confidence            543

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=4.8e-14  Score=157.72  Aligned_cols=196  Identities=19%  Similarity=0.204  Sum_probs=135.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC---
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW---  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~---  351 (567)
                      .+.+|++|+|++..++.|++++..                    .+.++.+||+||+|||||++|+++|+.+++..-   
T Consensus        11 RP~~f~dviGQe~vv~~L~~~l~~--------------------~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~   70 (618)
T PRK14951         11 RPRSFSEMVGQEHVVQALTNALTQ--------------------QRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQ   70 (618)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccc
Confidence            347899999999999999987752                    456778899999999999999999999865210   


Q ss_pred             CC---cCeEEe-chhhHHhhh----------hchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          352 QG---VPLMYV-PLEVVMSKY----------YGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       352 ~~---~~~~~i-~~~~l~s~~----------~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      .+   .+|-.. +|..+....          ....-+.++.+.+.+...   +...|+||||+|.|...           
T Consensus        71 ~~~~~~pCg~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls~~-----------  139 (618)
T PRK14951         71 GGITATPCGVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLTNT-----------  139 (618)
T ss_pred             cCCCCCCCCccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCCHH-----------
Confidence            00   112111 111111100          001123455555544322   23579999999999643           


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhcc
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATE  490 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~  490 (567)
                      ..+.|++.++.  .+..+++|.+|+.+..+.+.+++|| ..++|..++.++..+.++..+..    +..+.+..++....
T Consensus       140 a~NaLLKtLEE--PP~~~~fIL~Ttd~~kil~TIlSRc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s~  216 (618)
T PRK14951        140 AFNAMLKTLEE--PPEYLKFVLATTDPQKVPVTVLSRC-LQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAAR  216 (618)
T ss_pred             HHHHHHHhccc--CCCCeEEEEEECCchhhhHHHHHhc-eeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            34677787774  5667888888888888999999999 89999999999988888877654    45667888888766


Q ss_pred             CCCHHHHHHHHHHHH
Q 047219          491 EMSGRDIRDVCQQAE  505 (567)
Q Consensus       491 g~s~~dL~~L~~~a~  505 (567)
                      | +.+++.+++..+.
T Consensus       217 G-slR~al~lLdq~i  230 (618)
T PRK14951        217 G-SMRDALSLTDQAI  230 (618)
T ss_pred             C-CHHHHHHHHHHHH
Confidence            5 5666666655443

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.59  E-value=4.3e-14  Score=143.77  Aligned_cols=146  Identities=21%  Similarity=0.281  Sum_probs=94.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh------hHHhhhhchhHHHH-HH--------------
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE------VVMSKYYGESERLL-GK--------------  378 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~------~l~s~~~G~~~~~l-~~--------------  378 (567)
                      ....++||+||||||||++|+++|+.+      +.+++.+++.      ++.+.+.+...... ..              
T Consensus        19 ~~g~~vLL~G~~GtGKT~lA~~la~~l------g~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~   92 (262)
T TIGR02640        19 KSGYPVHLRGPAGTGKTTLAMHVARKR------DRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQ   92 (262)
T ss_pred             hcCCeEEEEcCCCCCHHHHHHHHHHHh------CCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccce
Confidence            346789999999999999999999987      5667777553      33333332211111 10              


Q ss_pred             -----HHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHh---hcCcccCCcEEEEEeeCCCC-----CCC
Q 047219          379 -----VFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQ---IDGFEQDKKVVVIAATNRKQ-----DLD  445 (567)
Q Consensus       379 -----~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~---ld~~~~~~~viVIaaTN~~~-----~Ld  445 (567)
                           .+..|..  .+++|+||||+.+.++.+..+.+.+++-.-.+...   ...+..+.+++||+|+|+..     .++
T Consensus        93 ~~~~g~l~~A~~--~g~~lllDEi~r~~~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~  170 (262)
T TIGR02640        93 NWVDNRLTLAVR--EGFTLVYDEFTRSKPETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQ  170 (262)
T ss_pred             eecCchHHHHHH--cCCEEEEcchhhCCHHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceeccc
Confidence                 1111222  35899999999988665554444332200000000   00011335789999999753     579


Q ss_pred             hHHHhccceEEEecCCCHHHHHHHHHHHH
Q 047219          446 PALISRFDSMITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       446 ~aL~sRf~~~I~i~~P~~~eR~eIL~~~~  474 (567)
                      ++|++|| ..+.++.|+.++..+|+..++
T Consensus       171 ~aL~~R~-~~i~i~~P~~~~e~~Il~~~~  198 (262)
T TIGR02640       171 DALLDRL-ITIFMDYPDIDTETAILRAKT  198 (262)
T ss_pred             HHHHhhc-EEEECCCCCHHHHHHHHHHhh
Confidence            9999999 899999999999999999875

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.58  E-value=3.6e-14  Score=165.97  Aligned_cols=187  Identities=21%  Similarity=0.275  Sum_probs=137.6

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -.++.++|+++.++++.+.+.                     .+...+++|+||||||||+++++++..+...    ...
T Consensus       170 ~~~~~~igr~~ei~~~~~~l~---------------------r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~  228 (852)
T TIGR03346       170 GKLDPVIGRDEEIRRTIQVLS---------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLK  228 (852)
T ss_pred             CCCCcCCCcHHHHHHHHHHHh---------------------cCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhc
Confidence            357889999999888877654                     3455788999999999999999999987432    223


Q ss_pred             CcCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +.+++.++...+.  .+|.|+.+..+..+|+.+.....+.||||||||.|.+.......   ....+.|...+    ..+
T Consensus       229 ~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~---~d~~~~Lk~~l----~~g  301 (852)
T TIGR03346       229 NKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGA---MDAGNMLKPAL----ARG  301 (852)
T ss_pred             CCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcch---hHHHHHhchhh----hcC
Confidence            6678888877765  46889999999999998875544689999999999753221111   11223333322    467


Q ss_pred             cEEEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh--------CHHHHHHHHHhccCC
Q 047219          431 KVVVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL--------TKAELAELATATEEM  492 (567)
Q Consensus       431 ~viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~--------~~~~l~~la~~t~g~  492 (567)
                      .+.+|++|+..+     .+|++|.+|| ..+.++.|+.+++..|++.+...+        ....+...+..+.+|
T Consensus       302 ~i~~IgaTt~~e~r~~~~~d~al~rRf-~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~~d~~i~~~~~ls~~y  375 (852)
T TIGR03346       302 ELHCIGATTLDEYRKYIEKDAALERRF-QPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRY  375 (852)
T ss_pred             ceEEEEeCcHHHHHHHhhcCHHHHhcC-CEEEeCCCCHHHHHHHHHHHHHHhccccCCCCCHHHHHHHHHhcccc
Confidence            899999998753     5799999999 678999999999999999876542        344555555555554

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=7.4e-14  Score=161.06  Aligned_cols=189  Identities=19%  Similarity=0.186  Sum_probs=130.8

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--  351 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--  351 (567)
                      ....+|++|+|++.+++.|+.++..                    .+.++.+||+||+|||||++|++|++.+.+...  
T Consensus         9 yRP~~f~eiiGqe~v~~~L~~~i~~--------------------~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~   68 (824)
T PRK07764          9 YRPATFAEVIGQEHVTEPLSTALDS--------------------GRINHAYLFSGPRGCGKTSSARILARSLNCVEGPT   68 (824)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHh--------------------CCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCC
Confidence            3457899999999999999888752                    455677999999999999999999999965310  


Q ss_pred             ------------------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHH
Q 047219          352 ------------------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHE  410 (567)
Q Consensus       352 ------------------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~  410 (567)
                                        ....++.++....      ..-+.++.+.+.+.   ......|+||||+|.|...       
T Consensus        69 ~~pCg~C~sC~~~~~g~~~~~dv~eidaas~------~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt~~-------  135 (824)
T PRK07764         69 STPCGECDSCVALAPGGPGSLDVTEIDAASH------GGVDDARELRERAFFAPAESRYKIFIIDEAHMVTPQ-------  135 (824)
T ss_pred             CCCCcccHHHHHHHcCCCCCCcEEEeccccc------CCHHHHHHHHHHHHhchhcCCceEEEEechhhcCHH-------
Confidence                              0112233322110      01123333333222   2234689999999999633       


Q ss_pred             HHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHH
Q 047219          411 ATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELA  486 (567)
Q Consensus       411 ~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la  486 (567)
                          ..+.||+.++.  .+..++||++|+..+.|.+.|++|| ..++|..++.++..+.|...+++    +....+..++
T Consensus       136 ----a~NaLLK~LEE--pP~~~~fIl~tt~~~kLl~TIrSRc-~~v~F~~l~~~~l~~~L~~il~~EGv~id~eal~lLa  208 (824)
T PRK07764        136 ----GFNALLKIVEE--PPEHLKFIFATTEPDKVIGTIRSRT-HHYPFRLVPPEVMRGYLERICAQEGVPVEPGVLPLVI  208 (824)
T ss_pred             ----HHHHHHHHHhC--CCCCeEEEEEeCChhhhhHHHHhhe-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHH
Confidence                45678888874  4568888888888888999999999 89999999999998888887754    3445566666


Q ss_pred             HhccCCCHHHHHHHHHH
Q 047219          487 TATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       487 ~~t~g~s~~dL~~L~~~  503 (567)
                      ....| +.+++..+++.
T Consensus       209 ~~sgG-dlR~Al~eLEK  224 (824)
T PRK07764        209 RAGGG-SVRDSLSVLDQ  224 (824)
T ss_pred             HHcCC-CHHHHHHHHHH
Confidence            66544 44444444433

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=1.2e-13  Score=154.05  Aligned_cols=188  Identities=20%  Similarity=0.241  Sum_probs=132.2

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CC-
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQ-  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~-  352 (567)
                      .+.+|++|+|++.+++.|+.++..                    .+.++.+||+||+|||||++|+++|+.+.+.. .. 
T Consensus         8 RP~~f~eivGq~~i~~~L~~~i~~--------------------~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~   67 (584)
T PRK14952          8 RPATFAEVVGQEHVTEPLSSALDA--------------------GRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTA   67 (584)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCC
Confidence            447899999999999999988752                    35666789999999999999999999986421 10 


Q ss_pred             ------------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHH
Q 047219          353 ------------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEA  411 (567)
Q Consensus       353 ------------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~  411 (567)
                                        ...++.+++....      .-+.++.+.+.+.   ..++..|+||||+|.|...        
T Consensus        68 ~pCg~C~~C~~i~~~~~~~~dvieidaas~~------gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt~~--------  133 (584)
T PRK14952         68 TPCGVCESCVALAPNGPGSIDVVELDAASHG------GVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVTTA--------  133 (584)
T ss_pred             CcccccHHHHHhhcccCCCceEEEecccccc------CHHHHHHHHHHHHhhhhcCCceEEEEECCCcCCHH--------
Confidence                              1122333321100      1223344433332   2244679999999999633        


Q ss_pred             HHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHH
Q 047219          412 TRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELAT  487 (567)
Q Consensus       412 ~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~  487 (567)
                         .++.|++.++.  .+..+++|++|+.+..+.+.+++|| ..++|..++.++..+.+...+..    +..+.+..++.
T Consensus       134 ---A~NALLK~LEE--pp~~~~fIL~tte~~kll~TI~SRc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~al~~Ia~  207 (584)
T PRK14952        134 ---GFNALLKIVEE--PPEHLIFIFATTEPEKVLPTIRSRT-HHYPFRLLPPRTMRALIARICEQEGVVVDDAVYPLVIR  207 (584)
T ss_pred             ---HHHHHHHHHhc--CCCCeEEEEEeCChHhhHHHHHHhc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence               45678888874  5678899988888899999999998 89999999999988888877764    44556666666


Q ss_pred             hccCCCHHHHHHHHHH
Q 047219          488 ATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       488 ~t~g~s~~dL~~L~~~  503 (567)
                      ...| +.+++.+++..
T Consensus       208 ~s~G-dlR~aln~Ldq  222 (584)
T PRK14952        208 AGGG-SPRDTLSVLDQ  222 (584)
T ss_pred             HcCC-CHHHHHHHHHH
Confidence            5443 45555454444

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.58  E-value=1.5e-13  Score=137.52  Aligned_cols=186  Identities=13%  Similarity=0.158  Sum_probs=118.4

Q ss_pred             CCCCCCccccc-C-cHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          273 SKSEISWENIA-G-YDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       273 ~~~~~~~~dIi-G-~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      -.+..+|++.+ | ...+...++....                     .....+++||||||||||+|++++++++... 
T Consensus        15 ~~~~~~fd~f~~~~n~~a~~~l~~~~~---------------------~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~-   72 (235)
T PRK08084         15 LPDDETFASFYPGDNDSLLAALQNALR---------------------QEHSGYIYLWSREGAGRSHLLHAACAELSQR-   72 (235)
T ss_pred             CCCcCCccccccCccHHHHHHHHHHHh---------------------CCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-
Confidence            44567888877 4 4444554444332                     2234589999999999999999999987543 


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                        +..+.+++.+......        ..+++....   ..+|+||||+.+..+.+.         ...|...++.....+
T Consensus        73 --~~~v~y~~~~~~~~~~--------~~~~~~~~~---~dlliiDdi~~~~~~~~~---------~~~lf~l~n~~~e~g  130 (235)
T PRK08084         73 --GRAVGYVPLDKRAWFV--------PEVLEGMEQ---LSLVCIDNIECIAGDELW---------EMAIFDLYNRILESG  130 (235)
T ss_pred             --CCeEEEEEHHHHhhhh--------HHHHHHhhh---CCEEEEeChhhhcCCHHH---------HHHHHHHHHHHHHcC
Confidence              4556777776543211        112222221   258999999998755221         112222222222234


Q ss_pred             cE-EEEEeeCCCCC---CChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          431 KV-VVIAATNRKQD---LDPALISRFD--SMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       431 ~v-iVIaaTN~~~~---Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                      +. +++++++++..   +.++|++||.  .++.+..|+.+++.++++..+..    ++++.++.++....+ +.+.+..+
T Consensus       131 ~~~li~ts~~~p~~l~~~~~~L~SRl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v~~~L~~~~~~-d~r~l~~~  209 (235)
T PRK08084        131 RTRLLITGDRPPRQLNLGLPDLASRLDWGQIYKLQPLSDEEKLQALQLRARLRGFELPEDVGRFLLKRLDR-EMRTLFMT  209 (235)
T ss_pred             CCeEEEeCCCChHHcCcccHHHHHHHhCCceeeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhhcC-CHHHHHHH
Confidence            43 44445556555   6799999995  58999999999999999886653    567788888887665 45555555


Q ss_pred             HHH
Q 047219          501 CQQ  503 (567)
Q Consensus       501 ~~~  503 (567)
                      ++.
T Consensus       210 l~~  212 (235)
T PRK08084        210 LDQ  212 (235)
T ss_pred             HHH
Confidence            554

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=99.57  E-value=2.8e-13  Score=134.23  Aligned_cols=192  Identities=24%  Similarity=0.388  Sum_probs=141.2

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ....+.+++|+|.+.+++.|.+....++                 ...+.+++||||++|||||++++++.+++...   
T Consensus        20 ~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl-----------------~G~pannvLL~G~rGtGKSSlVkall~~y~~~---   79 (249)
T PF05673_consen   20 HPDPIRLDDLIGIERQKEALIENTEQFL-----------------QGLPANNVLLWGARGTGKSSLVKALLNEYADQ---   79 (249)
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHH-----------------cCCCCcceEEecCCCCCHHHHHHHHHHHHhhc---
Confidence            4567899999999999999988776542                 25688999999999999999999999998665   


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc--ccCC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF--EQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~--~~~~  430 (567)
                      ++.++.++...+..         +..+++.........|||+|++.. .  ..+.       -...|...+++-  ..+.
T Consensus        80 GLRlIev~k~~L~~---------l~~l~~~l~~~~~kFIlf~DDLsF-e--~~d~-------~yk~LKs~LeGgle~~P~  140 (249)
T PF05673_consen   80 GLRLIEVSKEDLGD---------LPELLDLLRDRPYKFILFCDDLSF-E--EGDT-------EYKALKSVLEGGLEARPD  140 (249)
T ss_pred             CceEEEECHHHhcc---------HHHHHHHHhcCCCCEEEEecCCCC-C--CCcH-------HHHHHHHHhcCccccCCC
Confidence            67889988877654         445566655555579999999752 1  1111       123444455553  4578


Q ss_pred             cEEEEEeeCCCC---------------CCCh--------HHHhccceEEEecCCCHHHHHHHHHHHHHhh----CHH---
Q 047219          431 KVVVIAATNRKQ---------------DLDP--------ALISRFDSMITFGLPDHENRQEIAAQYAKHL----TKA---  480 (567)
Q Consensus       431 ~viVIaaTN~~~---------------~Ld~--------aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~----~~~---  480 (567)
                      ||++.+|+|+-.               .+.+        +|..||+..+.|..|+.++..+|++.++..+    ..+   
T Consensus       141 NvliyATSNRRHLv~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~  220 (249)
T PF05673_consen  141 NVLIYATSNRRHLVPESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELR  220 (249)
T ss_pred             cEEEEEecchhhccchhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            999999999821               2221        3556999999999999999999999999753    222   


Q ss_pred             -HHHHHHHhccCCCHHHHHHHHHH
Q 047219          481 -ELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       481 -~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                       ...+.+..-.|.||+--++.+..
T Consensus       221 ~~Al~wa~~rg~RSGRtA~QF~~~  244 (249)
T PF05673_consen  221 QEALQWALRRGGRSGRTARQFIDD  244 (249)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHHH
Confidence             34556666677888877777664

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.57  E-value=5.1e-14  Score=151.37  Aligned_cols=220  Identities=20%  Similarity=0.340  Sum_probs=141.0

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccc-cccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRC-KFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~-~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      .|+|++++++.+...+....+.      +...... ........++||+||||||||++|+++|+.+      +.+|+.+
T Consensus        72 ~ViGq~~ak~~l~~av~~~~~r------~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l------~~pf~~i  139 (412)
T PRK05342         72 YVIGQERAKKVLSVAVYNHYKR------LRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL------DVPFAIA  139 (412)
T ss_pred             HeeChHHHHHHHHHHHHHHHHh------hhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh------CCCceec
Confidence            4899999999998777543222      2111000 0002345789999999999999999999998      7788988


Q ss_pred             chhhHHh-hhhchhH-HHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhh--hHHH-HHHHHHHHHHhhcCcc----
Q 047219          360 PLEVVMS-KYYGESE-RLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSE--MHEA-TRRILSVLLRQIDGFE----  427 (567)
Q Consensus       360 ~~~~l~s-~~~G~~~-~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~--l~~~-~~~vl~~LL~~ld~~~----  427 (567)
                      ++..+.. .|+|+.. ..+..++..+.   ..+.++||||||||.+..+....  ..++ ...+++.||+.|++..    
T Consensus       140 d~~~l~~~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~  219 (412)
T PRK05342        140 DATTLTEAGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVP  219 (412)
T ss_pred             chhhcccCCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeC
Confidence            8887653 5777643 33444443221   12347999999999998663211  0011 1235567777776431    


Q ss_pred             -------cCCcEEEEEeeCCCC----------------------------------------------------CCChHH
Q 047219          428 -------QDKKVVVIAATNRKQ----------------------------------------------------DLDPAL  448 (567)
Q Consensus       428 -------~~~~viVIaaTN~~~----------------------------------------------------~Ld~aL  448 (567)
                             ...++++|.|+|...                                                    .|.|+|
T Consensus       220 ~~gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEf  299 (412)
T PRK05342        220 PQGGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEF  299 (412)
T ss_pred             CCCCcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHH
Confidence                   123456666665400                                                    157889


Q ss_pred             HhccceEEEecCCCHHHHHHHHHH----HHHh-------------hCHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHH
Q 047219          449 ISRFDSMITFGLPDHENRQEIAAQ----YAKH-------------LTKAELAELATA--TEEMSGRDIRDVCQQAERSWA  509 (567)
Q Consensus       449 ~sRf~~~I~i~~P~~~eR~eIL~~----~~~~-------------~~~~~l~~la~~--t~g~s~~dL~~L~~~a~~~a~  509 (567)
                      +.|++.++.|...+.++...|+..    +++.             +.++.++.+++.  ...+-.+.|+.+++......+
T Consensus       300 lgRld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~~~~~~GAR~Lrriie~~l~~~~  379 (412)
T PRK05342        300 IGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVM  379 (412)
T ss_pred             hCCCCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhCCCCCCCCchHHHHHHHHhHHHH
Confidence            999999999999999999999973    2221             344556666663  445556777777776665555


Q ss_pred             HHH
Q 047219          510 SKI  512 (567)
Q Consensus       510 ~r~  512 (567)
                      ..+
T Consensus       380 ~~~  382 (412)
T PRK05342        380 FEL  382 (412)
T ss_pred             Hhc
Confidence            443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.57  E-value=4.2e-14  Score=156.78  Aligned_cols=170  Identities=18%  Similarity=0.284  Sum_probs=116.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      .++++|||++|||||+|+++|++++... ..+..++++++.++...+...........|......  ..+|+||||+.+.
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~~a~~~-~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~--~DLLlIDDIq~l~  390 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGHYARRL-YPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYRE--MDILLVDDIQFLE  390 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHh-CCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhc--CCEEEEehhcccc
Confidence            3569999999999999999999987431 125678999999888776544333222234433332  4799999999997


Q ss_pred             hhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CC---CCChHHHhccce--EEEecCCCHHHHHHHHHHHHH
Q 047219          402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQ---DLDPALISRFDS--MITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~---~Ld~aL~sRf~~--~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      .+...         ...|+..++.+...+..+|| |+|. +.   .++++|++||..  .+.|..|+.+.|.+||+.++.
T Consensus       391 gke~t---------qeeLF~l~N~l~e~gk~III-TSd~~P~eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~kka~  460 (617)
T PRK14086        391 DKEST---------QEEFFHTFNTLHNANKQIVL-SSDRPPKQLVTLEDRLRNRFEWGLITDVQPPELETRIAILRKKAV  460 (617)
T ss_pred             CCHHH---------HHHHHHHHHHHHhcCCCEEE-ecCCChHhhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHHHHHH
Confidence            65321         12333444433333344444 5554 33   578999999944  779999999999999999887


Q ss_pred             h----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          476 H----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       476 ~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .    ++.+.++.|+....+ +.++|..++....
T Consensus       461 ~r~l~l~~eVi~yLa~r~~r-nvR~LegaL~rL~  493 (617)
T PRK14086        461 QEQLNAPPEVLEFIASRISR-NIRELEGALIRVT  493 (617)
T ss_pred             hcCCCCCHHHHHHHHHhccC-CHHHHHHHHHHHH
Confidence            5    467788888887654 5666666666543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=1.6e-13  Score=150.98  Aligned_cols=190  Identities=18%  Similarity=0.204  Sum_probs=135.1

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC--
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ--  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~--  352 (567)
                      .+.+|++|+|++.+++.|...+..                    ...++.+|||||+|+|||++|+++++.+.+....  
T Consensus         9 RP~~fdeiiGqe~v~~~L~~~I~~--------------------grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~   68 (535)
T PRK08451          9 RPKHFDELIGQESVSKTLSLALDN--------------------NRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSS   68 (535)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHc--------------------CCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCC
Confidence            447899999999999999888752                    4567778999999999999999999998532110  


Q ss_pred             ----------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          353 ----------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       353 ----------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                                      ...++.+++..-      ..-+.++.+......   .++..|++|||+|.|...          
T Consensus        69 ~pC~~C~~C~~~~~~~h~dv~eldaas~------~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt~~----------  132 (535)
T PRK08451         69 TPCDTCIQCQSALENRHIDIIEMDAASN------RGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLTKE----------  132 (535)
T ss_pred             CCCcccHHHHHHhhcCCCeEEEeccccc------cCHHHHHHHHHHHhhCcccCCeEEEEEECcccCCHH----------
Confidence                            112222322110      012345555444321   234579999999999643          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.|++.++.  .+..+++|.+|+.+..+.+.+++|| ..++|..++.++....+...+..    +..+.+..++...
T Consensus       133 -A~NALLK~LEE--pp~~t~FIL~ttd~~kL~~tI~SRc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s  208 (535)
T PRK08451        133 -AFNALLKTLEE--PPSYVKFILATTDPLKLPATILSRT-QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSG  208 (535)
T ss_pred             -HHHHHHHHHhh--cCCceEEEEEECChhhCchHHHhhc-eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             44677777774  4567888888888899999999998 89999999999888888877764    4567788888876


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.+++..++..+.
T Consensus       209 ~G-dlR~alnlLdqai  223 (535)
T PRK08451        209 NG-SLRDTLTLLDQAI  223 (535)
T ss_pred             CC-cHHHHHHHHHHHH
Confidence            55 5666666665544

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=1.6e-13  Score=151.72  Aligned_cols=188  Identities=17%  Similarity=0.206  Sum_probs=130.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++.+++.|...+..                    .+.++.+||+||+|||||++|+.+|+.+.+.. ...
T Consensus        11 RP~~f~diiGq~~~v~~L~~~i~~--------------------~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~   70 (546)
T PRK14957         11 RPQSFAEVAGQQHALNSLVHALET--------------------QKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTA   70 (546)
T ss_pred             CcCcHHHhcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC
Confidence            447899999999999999887752                    35567799999999999999999999886421 111


Q ss_pred             c-----------------CeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 V-----------------PLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~-----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      -                 .++.++...    ..|  -..++.+.+.+.   ..+...|+||||+|.|...          
T Consensus        71 ~pCg~C~sC~~i~~~~~~dlieidaas----~~g--vd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls~~----------  134 (546)
T PRK14957         71 EPCNKCENCVAINNNSFIDLIEIDAAS----RTG--VEETKEILDNIQYMPSQGRYKVYLIDEVHMLSKQ----------  134 (546)
T ss_pred             CCCcccHHHHHHhcCCCCceEEeeccc----ccC--HHHHHHHHHHHHhhhhcCCcEEEEEechhhccHH----------
Confidence            1                 222222211    011  122334444333   2234679999999998643          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.|++.++.  .+..+++|++|+.+..+.+.+++|| ..++|..++.++....+...+..    +....+..++..+
T Consensus       135 -a~naLLK~LEe--pp~~v~fIL~Ttd~~kil~tI~SRc-~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~Al~~Ia~~s  210 (546)
T PRK14957        135 -SFNALLKTLEE--PPEYVKFILATTDYHKIPVTILSRC-IQLHLKHISQADIKDQLKIILAKENINSDEQSLEYIAYHA  210 (546)
T ss_pred             -HHHHHHHHHhc--CCCCceEEEEECChhhhhhhHHHhe-eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             44677777774  4567888888887888888999999 99999999999988888876654    4566677777776


Q ss_pred             cCCCHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQ  503 (567)
Q Consensus       490 ~g~s~~dL~~L~~~  503 (567)
                      .| +.+++-+++..
T Consensus       211 ~G-dlR~alnlLek  223 (546)
T PRK14957        211 KG-SLRDALSLLDQ  223 (546)
T ss_pred             CC-CHHHHHHHHHH
Confidence            54 44444444443

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.56  E-value=1.8e-13  Score=144.55  Aligned_cols=189  Identities=21%  Similarity=0.293  Sum_probs=132.7

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--  351 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--  351 (567)
                      ..+.+|++++|++.+++.+.+.+..                    ...++.+||+||||+|||++|+++++.+.....  
T Consensus         8 ~rp~~~~~iig~~~~~~~l~~~~~~--------------------~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~   67 (355)
T TIGR02397         8 YRPQTFEDVIGQEHIVQTLKNAIKN--------------------GRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPD   67 (355)
T ss_pred             hCCCcHhhccCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC
Confidence            3457899999999999999887742                    356678999999999999999999999853210  


Q ss_pred             ----------------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHH
Q 047219          352 ----------------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEAT  412 (567)
Q Consensus       352 ----------------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~  412 (567)
                                      ...+++.++...      ......++.+++.+...   ++..+++|||+|.+...         
T Consensus        68 ~~~c~~c~~c~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~~~---------  132 (355)
T TIGR02397        68 GEPCNECESCKEINSGSSLDVIEIDAAS------NNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLSKS---------  132 (355)
T ss_pred             CCCCCCCHHHHHHhcCCCCCEEEeeccc------cCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcCHH---------
Confidence                            012233333321      01123355566655432   33569999999998532         


Q ss_pred             HHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh
Q 047219          413 RRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATA  488 (567)
Q Consensus       413 ~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~  488 (567)
                        ..+.|+..++.  .+.++++|++|+.++.+.+.+++|| ..++|..|+.++..+++...++.    +..+.+..++..
T Consensus       133 --~~~~Ll~~le~--~~~~~~lIl~~~~~~~l~~~l~sr~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~  207 (355)
T TIGR02397       133 --AFNALLKTLEE--PPEHVVFILATTEPHKIPATILSRC-QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARA  207 (355)
T ss_pred             --HHHHHHHHHhC--CccceeEEEEeCCHHHHHHHHHhhe-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence              34567777764  4567888888888888899999999 78999999999999999987764    455677777776


Q ss_pred             ccCCCHHHHHHHHHH
Q 047219          489 TEEMSGRDIRDVCQQ  503 (567)
Q Consensus       489 t~g~s~~dL~~L~~~  503 (567)
                      +.| +.+.+.+.+..
T Consensus       208 ~~g-~~~~a~~~lek  221 (355)
T TIGR02397       208 ADG-SLRDALSLLDQ  221 (355)
T ss_pred             cCC-ChHHHHHHHHH
Confidence            654 44444444433

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.56  E-value=3.8e-14  Score=150.23  Aligned_cols=179  Identities=24%  Similarity=0.412  Sum_probs=125.2

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      +.|+|++++++.+..++....++..+...+.       ....|+++||+||||||||++|+++|+.+      +.+|+.+
T Consensus        12 ~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~-------~e~~p~~ILLiGppG~GKT~lAraLA~~l------~~~fi~v   78 (441)
T TIGR00390        12 KYIIGQDNAKKSVAIALRNRYRRSQLNEELK-------DEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKV   78 (441)
T ss_pred             hhccCHHHHHHHHHHHHHhhhhhhccccccc-------cccCCceEEEECCCCCCHHHHHHHHHHHh------CCeEEEe
Confidence            3589999999999887765422222111111       13457899999999999999999999999      6677777


Q ss_pred             chhhHHh-hhhc-hhHHHHHHHHHHH------------------------------------------------------
Q 047219          360 PLEVVMS-KYYG-ESERLLGKVFSLA------------------------------------------------------  383 (567)
Q Consensus       360 ~~~~l~s-~~~G-~~~~~l~~~f~~A------------------------------------------------------  383 (567)
                      ++..+.. .|+| +.+..++.+|..|                                                      
T Consensus        79 dat~~~e~g~vG~dvE~i~r~l~e~A~~~i~~d~i~~~r~~a~~~ae~riv~~Ll~~~~~~~~~~~~~~~~~~~r~~~~~  158 (441)
T TIGR00390        79 EATKFTEVGYVGRDVESMVRDLTDAAVKLVKEEAIEKVRDRAEELAEERIVDVLLPPAKNQWGQTEQQQEPESAREAFRK  158 (441)
T ss_pred             ecceeecCCcccCCHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCccccccccccccchHHHHHHHHH
Confidence            7665542 4555 3334444443333                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q 047219          384 --------------------------------------------------------------------------------  383 (567)
Q Consensus       384 --------------------------------------------------------------------------------  383 (567)
                                                                                                      
T Consensus       159 ~l~~g~ldd~~iei~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ea~~~l~~~e~~~lid~~~v~  238 (441)
T TIGR00390       159 KLREGELDDKEIEIDVSAKMPSGIEIMAPPGMEEMTMQLQSLFQNLGGQKKKKRKLKIKDAKKALIAEEAAKLVDPEEIK  238 (441)
T ss_pred             HHhcCCccCcEEEEeecCCCCCccccCCCcchhHHHhhHHHHHHhhcCCCCceEEeEHHHHHHHHHHHHHHhccChHHHH
Confidence                                                                                            


Q ss_pred             ---h-cCCCCcEEEEcCcchhhhhhhhhhHHHH-HHHHHHHHHhhcCcc--------cCCcEEEEEeeC----CCCCCCh
Q 047219          384 ---N-ELPNGAIIFLDEVDSFAVARDSEMHEAT-RRILSVLLRQIDGFE--------QDKKVVVIAATN----RKQDLDP  446 (567)
Q Consensus       384 ---~-~~a~~~ILfIDEID~L~~~~q~~l~~~~-~~vl~~LL~~ld~~~--------~~~~viVIaaTN----~~~~Ld~  446 (567)
                         . .....+|+||||||+++.+......++. ..++..||..+++..        ...++.+||+.-    .|.+|-|
T Consensus       239 ~~a~~~~e~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIP  318 (441)
T TIGR00390       239 QEAIDAVEQSGIIFIDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIP  318 (441)
T ss_pred             HHHHHHHHcCCEEEEEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccH
Confidence               0 0123589999999999876532222222 336678888888742        235788887763    4777999


Q ss_pred             HHHhccceEEEecCCCHHHHHHHHH
Q 047219          447 ALISRFDSMITFGLPDHENRQEIAA  471 (567)
Q Consensus       447 aL~sRf~~~I~i~~P~~~eR~eIL~  471 (567)
                      +|..||+..+.+..++.++...||.
T Consensus       319 El~GR~Pi~v~L~~L~~edL~rILt  343 (441)
T TIGR00390       319 ELQGRFPIRVELQALTTDDFERILT  343 (441)
T ss_pred             HHhCccceEEECCCCCHHHHHHHhc
Confidence            9999999999999999999999884

This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment), studied in PubMed:98389714, is Ser in other members of the seed alignment.

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.56  E-value=3.7e-14  Score=150.40  Aligned_cols=179  Identities=25%  Similarity=0.416  Sum_probs=126.5

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ..|+|++++++.+..++....++..+...+       .....|.++||+||||||||++|+++|+.+      +.+|+.+
T Consensus        15 ~~IiGQe~AkkalavAl~~~~~r~~l~~~~-------~~e~~~~~ILliGp~G~GKT~LAr~LAk~l------~~~fi~v   81 (443)
T PRK05201         15 KYIIGQDDAKRAVAIALRNRWRRMQLPEEL-------RDEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKV   81 (443)
T ss_pred             cccCCHHHHHHHHHHHHHHHHHHhcCCccc-------ccccCCceEEEECCCCCCHHHHHHHHHHHh------CChheee
Confidence            349999999999988875432221111100       012346899999999999999999999999      7778888


Q ss_pred             chhhHHh-hhhc-hhHHHHHHHHHHH------------------------------------------------------
Q 047219          360 PLEVVMS-KYYG-ESERLLGKVFSLA------------------------------------------------------  383 (567)
Q Consensus       360 ~~~~l~s-~~~G-~~~~~l~~~f~~A------------------------------------------------------  383 (567)
                      ++..+.. .|.| ..+..++.+|..|                                                      
T Consensus        82 D~t~f~e~GyvG~d~e~~ir~L~~~A~~~~~~~~~~~~~~~a~~~~e~ri~~~l~~~~~~~~~~~~~~~~~~~~r~~~~~  161 (443)
T PRK05201         82 EATKFTEVGYVGRDVESIIRDLVEIAVKMVREEKREKVREKAEEAAEERILDALLPPAKNNWGEEEEKEEISATRQKFRK  161 (443)
T ss_pred             cchhhccCCcccCCHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCccCCccccccchhhhHHHHHHHH
Confidence            8776664 5666 3344444444444                                                      


Q ss_pred             --------------------------------------------------------------------------------
Q 047219          384 --------------------------------------------------------------------------------  383 (567)
Q Consensus       384 --------------------------------------------------------------------------------  383 (567)
                                                                                                      
T Consensus       162 ~l~~g~ldd~~iei~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~eA~~~l~~~e~~~lid~~~v~~  241 (443)
T PRK05201        162 KLREGELDDKEIEIEVAEAAPMMEIMGPPGMEEMTIQLQDMFGNLGPKKKKKRKLKVKEARKILIEEEAAKLIDMEEIKQ  241 (443)
T ss_pred             HHHcCCcCCcEEEEEecCCCCcccCCCCcchhHHHHHHHHHHHhhCCCCCceEEeEHHHHHHHHHHHHHHhccChHHHHH
Confidence                                                                                            


Q ss_pred             --hc-CCCCcEEEEcCcchhhhhhhhhhHHHH-HHHHHHHHHhhcCcc--------cCCcEEEEEee----CCCCCCChH
Q 047219          384 --NE-LPNGAIIFLDEVDSFAVARDSEMHEAT-RRILSVLLRQIDGFE--------QDKKVVVIAAT----NRKQDLDPA  447 (567)
Q Consensus       384 --~~-~a~~~ILfIDEID~L~~~~q~~l~~~~-~~vl~~LL~~ld~~~--------~~~~viVIaaT----N~~~~Ld~a  447 (567)
                        .. ....||+||||||+++.+.+....++. +.++..||..+++..        ...++.+||+.    ..+.+|-|+
T Consensus       242 ~ai~~ae~~GIVfiDEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPE  321 (443)
T PRK05201        242 EAIERVEQNGIVFIDEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPE  321 (443)
T ss_pred             HHHHHHHcCCEEEEEcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHH
Confidence              01 013589999999999876532222222 336678888888742        23578888776    346778999


Q ss_pred             HHhccceEEEecCCCHHHHHHHHH
Q 047219          448 LISRFDSMITFGLPDHENRQEIAA  471 (567)
Q Consensus       448 L~sRf~~~I~i~~P~~~eR~eIL~  471 (567)
                      |..||+..+.+..++.++...||.
T Consensus       322 l~GR~Pi~v~L~~L~~~dL~~ILt  345 (443)
T PRK05201        322 LQGRFPIRVELDALTEEDFVRILT  345 (443)
T ss_pred             HhCccceEEECCCCCHHHHHHHhc
Confidence            999999999999999999999984

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.56  E-value=2.5e-13  Score=134.82  Aligned_cols=183  Identities=11%  Similarity=0.132  Sum_probs=120.5

Q ss_pred             CCCCCCccccc--CcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          273 SKSEISWENIA--GYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       273 ~~~~~~~~dIi--G~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      ..+..+|++.+  +.+.++..+++...                    +.....+++|+||+|||||++|+++++++... 
T Consensus        11 ~~~~~~~d~f~~~~~~~~~~~l~~~~~--------------------~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~-   69 (227)
T PRK08903         11 PPPPPTFDNFVAGENAELVARLRELAA--------------------GPVADRFFYLWGEAGSGRSHLLQALVADASYG-   69 (227)
T ss_pred             CCChhhhcccccCCcHHHHHHHHHHHh--------------------ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-
Confidence            34557889976  33445555544332                    02456789999999999999999999987433 


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                        +..+.++++..+....            .   ....+.+|+|||+|.+....+.           .|+..++.....+
T Consensus        70 --~~~~~~i~~~~~~~~~------------~---~~~~~~~liiDdi~~l~~~~~~-----------~L~~~~~~~~~~~  121 (227)
T PRK08903         70 --GRNARYLDAASPLLAF------------D---FDPEAELYAVDDVERLDDAQQI-----------ALFNLFNRVRAHG  121 (227)
T ss_pred             --CCcEEEEehHHhHHHH------------h---hcccCCEEEEeChhhcCchHHH-----------HHHHHHHHHHHcC
Confidence              5578888887654321            1   1112579999999998644322           2233333222334


Q ss_pred             cEEEEEeeCC-C--CCCChHHHhcc--ceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHH
Q 047219          431 KVVVIAATNR-K--QDLDPALISRF--DSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       431 ~viVIaaTN~-~--~~Ld~aL~sRf--~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ..++|.+++. +  ..+.++|++||  ...+++++|+.+++..++..++.+    +..+.++.++.. +.-+.+++..++
T Consensus       122 ~~~vl~~~~~~~~~~~l~~~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~-~~gn~~~l~~~l  200 (227)
T PRK08903        122 QGALLVAGPAAPLALPLREDLRTRLGWGLVYELKPLSDADKIAALKAAAAERGLQLADEVPDYLLTH-FRRDMPSLMALL  200 (227)
T ss_pred             CcEEEEeCCCCHHhCCCCHHHHHHHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHHHHHHH
Confidence            4444445443 2  24679999998  468899999998888888876654    567778888884 555778887777


Q ss_pred             HHHH
Q 047219          502 QQAE  505 (567)
Q Consensus       502 ~~a~  505 (567)
                      +...
T Consensus       201 ~~l~  204 (227)
T PRK08903        201 DALD  204 (227)
T ss_pred             HHHH
Confidence            7644

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=1e-13  Score=155.45  Aligned_cols=187  Identities=20%  Similarity=0.248  Sum_probs=133.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-C-
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-Q-  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~-  352 (567)
                      .+.+|++|+|++.+++.|.+.+..                    ...++.+||+||+|||||++|+++++.+.+... . 
T Consensus        11 RP~~f~~iiGq~~v~~~L~~~i~~--------------------~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~   70 (576)
T PRK14965         11 RPQTFSDLTGQEHVSRTLQNAIDT--------------------GRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTA   70 (576)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCC
Confidence            447899999999999999988752                    356778899999999999999999999864311 1 


Q ss_pred             ----------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          353 ----------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       353 ----------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                                      ..+++.+++..      ...-+.++.+.+.+..   .++..|+||||+|.|...          
T Consensus        71 ~~c~~c~~c~~i~~g~~~d~~eid~~s------~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt~~----------  134 (576)
T PRK14965         71 EPCNVCPPCVEITEGRSVDVFEIDGAS------NTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLSTN----------  134 (576)
T ss_pred             CCCCccHHHHHHhcCCCCCeeeeeccC------ccCHHHHHHHHHHHHhccccCCceEEEEEChhhCCHH----------
Confidence                            11223332211      0112345555554432   234579999999998633          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.|++.++.  .+.++++|.+|+.+..+.+.+++|| ..++|..++.++....+...++.    +..+.+..++...
T Consensus       135 -a~naLLk~LEe--pp~~~~fIl~t~~~~kl~~tI~SRc-~~~~f~~l~~~~i~~~L~~i~~~egi~i~~~al~~la~~a  210 (576)
T PRK14965        135 -AFNALLKTLEE--PPPHVKFIFATTEPHKVPITILSRC-QRFDFRRIPLQKIVDRLRYIADQEGISISDAALALVARKG  210 (576)
T ss_pred             -HHHHHHHHHHc--CCCCeEEEEEeCChhhhhHHHHHhh-hhhhcCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Confidence             34677888873  5678889989998999999999999 89999999998888877776654    4566777777776


Q ss_pred             cCCCHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQ  502 (567)
Q Consensus       490 ~g~s~~dL~~L~~  502 (567)
                      .| +.+++..++.
T Consensus       211 ~G-~lr~al~~Ld  222 (576)
T PRK14965        211 DG-SMRDSLSTLD  222 (576)
T ss_pred             CC-CHHHHHHHHH
Confidence            65 4444444443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=1.1e-13  Score=153.44  Aligned_cols=196  Identities=19%  Similarity=0.205  Sum_probs=135.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++|+|++.+++.+...+..                    .+.++.+||+||||||||++|+++++.+.+.. ...
T Consensus        11 rP~~f~divGq~~v~~~L~~~i~~--------------------~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~   70 (527)
T PRK14969         11 RPKSFSELVGQEHVVRALTNALEQ--------------------QRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTA   70 (527)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHHc--------------------CCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            346899999999999999887752                    35667789999999999999999999996531 111


Q ss_pred             cCeEEec-hhhHHhhh----------hchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHH
Q 047219          354 VPLMYVP-LEVVMSKY----------YGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL  419 (567)
Q Consensus       354 ~~~~~i~-~~~l~s~~----------~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~L  419 (567)
                      .+|...+ |..+....          .......++.+.+.+..   .++..|+||||+|.|...           ..+.|
T Consensus        71 ~pcg~C~~C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls~~-----------a~naL  139 (527)
T PRK14969         71 TPCGVCSACLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLSKS-----------AFNAM  139 (527)
T ss_pred             CCCCCCHHHHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCCHH-----------HHHHH
Confidence            2222211 11111000          01122345566555542   233579999999998632           44678


Q ss_pred             HHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHH
Q 047219          420 LRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGR  495 (567)
Q Consensus       420 L~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~  495 (567)
                      ++.++.  .+..+++|++|+.+..+.+.+++|| ..++|..++.++....+...+..    +....+..++..+.| +.+
T Consensus       140 LK~LEe--pp~~~~fIL~t~d~~kil~tI~SRc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s~G-slr  215 (527)
T PRK14969        140 LKTLEE--PPEHVKFILATTDPQKIPVTVLSRC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAAAG-SMR  215 (527)
T ss_pred             HHHHhC--CCCCEEEEEEeCChhhCchhHHHHH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHH
Confidence            888874  4578888888888888888999999 89999999999988888776653    355667777777654 556


Q ss_pred             HHHHHHHHHH
Q 047219          496 DIRDVCQQAE  505 (567)
Q Consensus       496 dL~~L~~~a~  505 (567)
                      +..+++..+.
T Consensus       216 ~al~lldqai  225 (527)
T PRK14969        216 DALSLLDQAI  225 (527)
T ss_pred             HHHHHHHHHH
Confidence            6666665544

>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]

Probab=99.56  E-value=1.3e-13  Score=152.47  Aligned_cols=197  Identities=38%  Similarity=0.569  Sum_probs=176.1

Q ss_pred             hccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHH
Q 047219          299 SLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGK  378 (567)
Q Consensus       299 ~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~  378 (567)
                      ++.+++.|+.++        ..++++++++||||||||+++++++++ .     ... ..+++....++++|+++..++.
T Consensus         3 ~~~~~~~~~~~~--------~~~~~~v~~~g~~~~~~t~~~~~~a~~-~-----~~~-~~~~~~~~~~~~~~~~~~~~~~   67 (494)
T COG0464           3 PLKEPELFKKLG--------IEPPKGVLLHGPPGTGKTLLARALANE-G-----AEF-LSINGPEILSKYVGESELRLRE   67 (494)
T ss_pred             CccCHHHHHHhC--------CCCCCCceeeCCCCCchhHHHHHHHhc-c-----Ccc-cccCcchhhhhhhhHHHHHHHH
Confidence            466788888776        889999999999999999999999998 2     334 7888999999999999999999


Q ss_pred             HHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh--ccceEE
Q 047219          379 VFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS--RFDSMI  456 (567)
Q Consensus       379 ~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I  456 (567)
                      .|..+....+ +++++||+|.+.+.+.........+++.+++..+++.. ...+.+++.+|.+..+++++++  ||+..+
T Consensus        68 ~~~~a~~~~~-~ii~~d~~~~~~~~~~~~~~~~~~~v~~~l~~~~d~~~-~~~v~~~~~~~~~~~~~~a~~~~~~~~~~~  145 (494)
T COG0464          68 LFEEAEKLAP-SIIFIDEIDALAPKRSSDQGEVERRVVAQLLALMDGLK-RGQVIVIGATNRPDGLDPAKRRPGRFDREI  145 (494)
T ss_pred             HHHHHHHhCC-CeEeechhhhcccCccccccchhhHHHHHHHHhccccc-CCceEEEeecCCccccChhHhCccccceee
Confidence            9999999886 99999999999999888666677889999999999988 5558889999999999999998  999999


Q ss_pred             EecCCCHHHHHHHHHHHHHhhCHH---HHHHHHHhccCCCHHHHHHHHHHHHHHHHHHH
Q 047219          457 TFGLPDHENRQEIAAQYAKHLTKA---ELAELATATEEMSGRDIRDVCQQAERSWASKI  512 (567)
Q Consensus       457 ~i~~P~~~eR~eIL~~~~~~~~~~---~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~  512 (567)
                      .+..|+...+.+++..+...+...   ....++..+.|+.++++..++.++...+..+.
T Consensus       146 ~~~~~~~~~~~ei~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~~~~~~~~~~r~  204 (494)
T COG0464         146 EVNLPDEAGRLEILQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRA  204 (494)
T ss_pred             ecCCCCHHHHHHHHHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHHHHHHHHHHHhh
Confidence            999999999999999988775443   78899999999999999999999998888886

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.55  E-value=9.3e-14  Score=161.73  Aligned_cols=237  Identities=19%  Similarity=0.227  Sum_probs=152.4

Q ss_pred             CCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCC
Q 047219          243 LTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRP  322 (567)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p  322 (567)
                      ++..++..+++.++..++.....++..........--+.|+|++++++.+.+.+......      +       .....|
T Consensus       529 v~~~~i~~vv~~~tgip~~~~~~~e~~~l~~l~~~L~~~v~GQ~~Av~~v~~~i~~~~~g------l-------~~~~~p  595 (852)
T TIGR03345       529 VDAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAG------L-------EDPRKP  595 (852)
T ss_pred             ecHHHHHHHHHHHHCCCchhhchhHHHHHHHHHHHhcCeEcChHHHHHHHHHHHHHHhcC------C-------CCCCCC
Confidence            567778888888887766443333322222222334467999999999999988754111      0       002234


Q ss_pred             c-eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh------------hhchhHHHHHHHHHHHhcCCCC
Q 047219          323 R-AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK------------YYGESERLLGKVFSLANELPNG  389 (567)
Q Consensus       323 ~-~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~------------~~G~~~~~l~~~f~~A~~~a~~  389 (567)
                      . .+||+||||||||.+|+++|..+...   ...++.++++++...            |+|+.+.   ..+..+....|.
T Consensus       596 ~~~~lf~Gp~GvGKT~lA~~La~~l~~~---~~~~~~~dmse~~~~~~~~~l~g~~~gyvg~~~~---g~L~~~v~~~p~  669 (852)
T TIGR03345       596 LGVFLLVGPSGVGKTETALALAELLYGG---EQNLITINMSEFQEAHTVSRLKGSPPGYVGYGEG---GVLTEAVRRKPY  669 (852)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhCC---CcceEEEeHHHhhhhhhhccccCCCCCccccccc---chHHHHHHhCCC
Confidence            4 48999999999999999999998543   346788888776543            3333221   123333344568


Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---------cCCcEEEEEeeCC-----------C--------
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---------QDKKVVVIAATNR-----------K--------  441 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---------~~~~viVIaaTN~-----------~--------  441 (567)
                      +||+||||+++.+.           +.+.|++.++...         .-.+++||+|||.           .        
T Consensus       670 svvllDEieka~~~-----------v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~  738 (852)
T TIGR03345       670 SVVLLDEVEKAHPD-----------VLELFYQVFDKGVMEDGEGREIDFKNTVILLTSNAGSDLIMALCADPETAPDPEA  738 (852)
T ss_pred             cEEEEechhhcCHH-----------HHHHHHHHhhcceeecCCCcEEeccccEEEEeCCCchHHHHHhccCcccCcchHH
Confidence            99999999987644           3344555554321         1257899999985           0        


Q ss_pred             ----------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh--------------CHHHHHHHHHhccC--CCHH
Q 047219          442 ----------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL--------------TKAELAELATATEE--MSGR  495 (567)
Q Consensus       442 ----------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~--------------~~~~l~~la~~t~g--~s~~  495 (567)
                                ..|.|+|++|++ ++.|..++.++...|+...+..+              .++..+.++....+  +-.+
T Consensus       739 ~~~~~~~~~~~~f~PEflnRi~-iI~F~pLs~e~l~~Iv~~~L~~l~~rl~~~~gi~l~i~d~a~~~La~~g~~~~~GAR  817 (852)
T TIGR03345       739 LLEALRPELLKVFKPAFLGRMT-VIPYLPLDDDVLAAIVRLKLDRIARRLKENHGAELVYSEALVEHIVARCTEVESGAR  817 (852)
T ss_pred             HHHHHHHHHHHhccHHHhccee-EEEeCCCCHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHHcCCCCCChH
Confidence                      127889999995 89999999999999998766532              23345555554432  4466


Q ss_pred             HHHHHHHHHHHHHHH
Q 047219          496 DIRDVCQQAERSWAS  510 (567)
Q Consensus       496 dL~~L~~~a~~~a~~  510 (567)
                      .|+.+++......+.
T Consensus       818 ~L~r~Ie~~i~~~la  832 (852)
T TIGR03345       818 NIDAILNQTLLPELS  832 (852)
T ss_pred             HHHHHHHHHHHHHHH
Confidence            666666654444433

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.55  E-value=4.5e-13  Score=142.06  Aligned_cols=208  Identities=25%  Similarity=0.318  Sum_probs=132.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC---C
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP---W  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~---~  351 (567)
                      +.+..+++.|.+++++.|...+...+.                 ...+.+++|+||||||||++++++++++....   -
T Consensus        10 ~~~~p~~l~gRe~e~~~l~~~l~~~~~-----------------~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~   72 (365)
T TIGR02928        10 PDYVPDRIVHRDEQIEELAKALRPILR-----------------GSRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRD   72 (365)
T ss_pred             CCCCCCCCCCcHHHHHHHHHHHHHHHc-----------------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccC
Confidence            344556899999999999988864321                 24567899999999999999999998763210   0


Q ss_pred             CCcCeEEechhhHH----------hhhh--ch--------hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHH
Q 047219          352 QGVPLMYVPLEVVM----------SKYY--GE--------SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEA  411 (567)
Q Consensus       352 ~~~~~~~i~~~~l~----------s~~~--G~--------~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~  411 (567)
                      ..+.+++++|....          ..+.  |.        ..+.+..+++......++.+|+|||+|.|....+      
T Consensus        73 ~~~~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~~~------  146 (365)
T TIGR02928        73 VRVVTVYVNCQILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGDDD------  146 (365)
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccCCc------
Confidence            01456777764321          1111  11        1223344555544444457999999999963211      


Q ss_pred             HHHHHHHHHHhhcCcc-cCCcEEEEEeeCCCC---CCChHHHhccc-eEEEecCCCHHHHHHHHHHHHHh------hCHH
Q 047219          412 TRRILSVLLRQIDGFE-QDKKVVVIAATNRKQ---DLDPALISRFD-SMITFGLPDHENRQEIAAQYAKH------LTKA  480 (567)
Q Consensus       412 ~~~vl~~LL~~ld~~~-~~~~viVIaaTN~~~---~Ld~aL~sRf~-~~I~i~~P~~~eR~eIL~~~~~~------~~~~  480 (567)
                        .++..|+...+... ...++.+|+++|.++   .+++.+.+||. ..++|++++.++..+|++..+..      +.++
T Consensus       147 --~~L~~l~~~~~~~~~~~~~v~lI~i~n~~~~~~~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~~~~~~~~~~  224 (365)
T TIGR02928       147 --DLLYQLSRARSNGDLDNAKVGVIGISNDLKFRENLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKAFYDGVLDDG  224 (365)
T ss_pred             --HHHHhHhccccccCCCCCeEEEEEEECCcchHhhcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhhccCCCCChh
Confidence              23345555422111 236789999998865   58889999985 57999999999999999998762      3344


Q ss_pred             HHHHHHH---hccCCCHHHHHHHHHHHHHHH
Q 047219          481 ELAELAT---ATEEMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       481 ~l~~la~---~t~g~s~~dL~~L~~~a~~~a  508 (567)
                      .++.++.   .+.| ..+....+|..|+..+
T Consensus       225 ~l~~i~~~~~~~~G-d~R~al~~l~~a~~~a  254 (365)
T TIGR02928       225 VIPLCAALAAQEHG-DARKAIDLLRVAGEIA  254 (365)
T ss_pred             HHHHHHHHHHHhcC-CHHHHHHHHHHHHHHH
Confidence            4443333   3334 2334444666666544

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.54  E-value=2.1e-13  Score=159.12  Aligned_cols=241  Identities=20%  Similarity=0.220  Sum_probs=155.6

Q ss_pred             CcCCHHHHHHHHHHHhhhcccccccCccccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCC
Q 047219          241 GSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESN  320 (567)
Q Consensus       241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~  320 (567)
                      ..++..++..+++.++..+......++..........--+.|+|++++++.+.+.+.....        |..    ....
T Consensus       470 ~~v~~~~i~~~~~~~tgip~~~~~~~~~~~l~~l~~~L~~~v~GQ~~ai~~l~~~i~~~~~--------gl~----~~~~  537 (821)
T CHL00095        470 PVVTEEDIAEIVSAWTGIPVNKLTKSESEKLLHMEETLHKRIIGQDEAVVAVSKAIRRARV--------GLK----NPNR  537 (821)
T ss_pred             CccCHHHHHHHHHHHHCCCchhhchhHHHHHHHHHHHhcCcCcChHHHHHHHHHHHHHHhh--------ccc----CCCC
Confidence            3467788888888888776654433333222222333446799999999999988864311        000    0023


Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh-----hhh-------chhHHHHHHHHHHHhcCCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS-----KYY-------GESERLLGKVFSLANELPN  388 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s-----~~~-------G~~~~~l~~~f~~A~~~a~  388 (567)
                      |...+||+||+|||||++|+++|+.+...   ..+++.++++++..     +++       |+.+  .+.+.+.. ...|
T Consensus       538 p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~---~~~~~~~d~s~~~~~~~~~~l~g~~~gyvg~~~--~~~l~~~~-~~~p  611 (821)
T CHL00095        538 PIASFLFSGPTGVGKTELTKALASYFFGS---EDAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNE--GGQLTEAV-RKKP  611 (821)
T ss_pred             CceEEEEECCCCCcHHHHHHHHHHHhcCC---ccceEEEEchhccccccHHHhcCCCCcccCcCc--cchHHHHH-HhCC
Confidence            33468999999999999999999998543   34677777766532     222       2221  11233333 3445


Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---------cCCcEEEEEeeCCCC-----------------
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---------QDKKVVVIAATNRKQ-----------------  442 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---------~~~~viVIaaTN~~~-----------------  442 (567)
                      .+||+|||||++.+.           +.+.|++.++...         .-.++++|+|||...                 
T Consensus       612 ~~VvllDeieka~~~-----------v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~  680 (821)
T CHL00095        612 YTVVLFDEIEKAHPD-----------IFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTSNLGSKVIETNSGGLGFELSEN  680 (821)
T ss_pred             CeEEEECChhhCCHH-----------HHHHHHHHhccCceecCCCcEEecCceEEEEeCCcchHHHHhhccccCCccccc
Confidence            799999999998644           4455556555421         135899999998410                 


Q ss_pred             --------------------CCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-------------CHHHHHHHHHh-
Q 047219          443 --------------------DLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-------------TKAELAELATA-  488 (567)
Q Consensus       443 --------------------~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-------------~~~~l~~la~~-  488 (567)
                                          .|.|+|++|+|.++.|.+.+.++...|+...+..+             .++..+.++.. 
T Consensus       681 ~~~~~~~~~~~~~~~~~~~~~f~peflnRid~ii~F~pL~~~~l~~Iv~~~l~~l~~rl~~~~i~l~~~~~~~~~La~~~  760 (821)
T CHL00095        681 QLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWEIAEIMLKNLFKRLNEQGIQLEVTERIKTLLIEEG  760 (821)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCHHHhccCCeEEEeCCCCHHHHHHHHHHHHHHHHHHHHHCCcEEEECHHHHHHHHHhc
Confidence                                15678999999999999999999999998877642             23445555553 


Q ss_pred             -ccCCCHHHHHHHHHHHHHHHHH
Q 047219          489 -TEEMSGRDIRDVCQQAERSWAS  510 (567)
Q Consensus       489 -t~g~s~~dL~~L~~~a~~~a~~  510 (567)
                       ...+-.+.|+.+++......+.
T Consensus       761 ~~~~~GAR~l~r~i~~~i~~~l~  783 (821)
T CHL00095        761 YNPLYGARPLRRAIMRLLEDPLA  783 (821)
T ss_pred             CCCCCChhhHHHHHHHHHHHHHH
Confidence             2345567777777665543333

>PRK06893 DNA replication initiation factor; Validated

Probab=99.54  E-value=4.1e-13  Score=133.95  Aligned_cols=157  Identities=15%  Similarity=0.185  Sum_probs=101.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                      ..++||||||||||+|++++++++...   +..+.+++.......        ...+++...   ...+|+||||+.+.+
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~---~~~~~y~~~~~~~~~--------~~~~~~~~~---~~dlLilDDi~~~~~  105 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLN---QRTAIYIPLSKSQYF--------SPAVLENLE---QQDLVCLDDLQAVIG  105 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHc---CCCeEEeeHHHhhhh--------hHHHHhhcc---cCCEEEEeChhhhcC
Confidence            458999999999999999999987433   345566665432110        112222222   246999999999865


Q ss_pred             hhhhhhHHHHHHHHHHHHHhhcCcccCCcEE-EEEeeCCCCCCC---hHHHhccc--eEEEecCCCHHHHHHHHHHHHHh
Q 047219          403 ARDSEMHEATRRILSVLLRQIDGFEQDKKVV-VIAATNRKQDLD---PALISRFD--SMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       403 ~~q~~l~~~~~~vl~~LL~~ld~~~~~~~vi-VIaaTN~~~~Ld---~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      ..+.      +   ..++..++.....+..+ +++++..+..++   ++|++|+.  ..+.++.|+.++|.++++..+..
T Consensus       106 ~~~~------~---~~l~~l~n~~~~~~~~illits~~~p~~l~~~~~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~~  176 (229)
T PRK06893        106 NEEW------E---LAIFDLFNRIKEQGKTLLLISADCSPHALSIKLPDLASRLTWGEIYQLNDLTDEQKIIVLQRNAYQ  176 (229)
T ss_pred             ChHH------H---HHHHHHHHHHHHcCCcEEEEeCCCChHHccccchhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHHH
Confidence            4321      1   22333333333334444 455555566554   89999873  48899999999999999988763


Q ss_pred             ----hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          477 ----LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       477 ----~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                          ++++.++.++....+ +.+.+..++..
T Consensus       177 ~~l~l~~~v~~~L~~~~~~-d~r~l~~~l~~  206 (229)
T PRK06893        177 RGIELSDEVANFLLKRLDR-DMHTLFDALDL  206 (229)
T ss_pred             cCCCCCHHHHHHHHHhccC-CHHHHHHHHHH
Confidence                567778888877654 44444444443

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.54  E-value=2.2e-14  Score=150.43  Aligned_cols=178  Identities=18%  Similarity=0.316  Sum_probs=119.0

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC--
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP--  350 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~--  350 (567)
                      ..+.+.|.+|+|+++.|+.|...+.                     .+...++||.|++|||||++||++++.+....  
T Consensus        10 ~~~~~pf~~ivGq~~~k~al~~~~~---------------------~p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~   68 (350)
T CHL00081         10 ERPVFPFTAIVGQEEMKLALILNVI---------------------DPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVV   68 (350)
T ss_pred             cCCCCCHHHHhChHHHHHHHHHhcc---------------------CCCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCcc
Confidence            3566899999999999998876654                     23446899999999999999999999885321  


Q ss_pred             ----CC----------------------------CcCeEEechhhHHhhhhchhHHHHHHHHHHH--------hcCCCCc
Q 047219          351 ----WQ----------------------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLA--------NELPNGA  390 (567)
Q Consensus       351 ----~~----------------------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A--------~~~a~~~  390 (567)
                          |.                            ..+|+.++...-.+.++|...  +...|...        ...+.++
T Consensus        69 ~~~pf~~~p~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD--~~~al~~g~~~~~~GlL~~A~~G  146 (350)
T CHL00081         69 KDDPFNSHPSDPELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTID--IEKALTEGVKAFEPGLLAKANRG  146 (350)
T ss_pred             CCCCCCCCCCChhhhchhhhhhhcccccccceeccccceecCCCCchhhccCccc--HHHHhhcCcccccCCeeeecCCC
Confidence                11                            123333333333344444210  01111111        1234479


Q ss_pred             EEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-CCChHHHhccceEEEecCCC-HHHHHH
Q 047219          391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-DLDPALISRFDSMITFGLPD-HENRQE  468 (567)
Q Consensus       391 ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-~Ld~aL~sRf~~~I~i~~P~-~~eR~e  468 (567)
                      +||||||+.+.++.|..+.+.+++-...+.+.......+.++++|+|.|+.+ .|+++|++||...+.+..|+ .+.+.+
T Consensus       147 iL~lDEInrL~~~~Q~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~eg~l~~~LldRf~l~i~l~~~~~~~~e~~  226 (350)
T CHL00081        147 ILYVDEVNLLDDHLVDILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGMHAEIRTVKDPELRVK  226 (350)
T ss_pred             EEEecChHhCCHHHHHHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCcccCCCCHHHHHHhCceeecCCCCChHHHHH
Confidence            9999999999988776655544321111111112223456899999999755 69999999999999999997 599999


Q ss_pred             HHHHH
Q 047219          469 IAAQY  473 (567)
Q Consensus       469 IL~~~  473 (567)
                      |++..
T Consensus       227 il~~~  231 (350)
T CHL00081        227 IVEQR  231 (350)
T ss_pred             HHHhh
Confidence            99875

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=4.2e-13  Score=149.60  Aligned_cols=196  Identities=20%  Similarity=0.233  Sum_probs=134.6

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQ  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~  352 (567)
                      ..+.+|++|+|++.+++.|+..+..                    ...++.+||+||+|+|||++|+++|+.+.+.. ..
T Consensus        10 yRP~~f~diiGqe~iv~~L~~~i~~--------------------~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~   69 (563)
T PRK06647         10 RRPRDFNSLEGQDFVVETLKHSIES--------------------NKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPT   69 (563)
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCC
Confidence            3457899999999999999988752                    35667899999999999999999999986431 11


Q ss_pred             CcCeEEec-hhhHHhh-------hhch---hHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHH
Q 047219          353 GVPLMYVP-LEVVMSK-------YYGE---SERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSV  418 (567)
Q Consensus       353 ~~~~~~i~-~~~l~s~-------~~G~---~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~  418 (567)
                      ..+|.... |..+...       +-|.   .-+.++.+.+.+..   .++..+++|||+|.|...           .++.
T Consensus        70 ~~pC~~C~~C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls~~-----------a~na  138 (563)
T PRK06647         70 PMPCGECSSCKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLSNS-----------AFNA  138 (563)
T ss_pred             CCCCccchHHHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcCHH-----------HHHH
Confidence            11222111 1010000       0011   11334444433332   234679999999998632           4567


Q ss_pred             HHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCH
Q 047219          419 LLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSG  494 (567)
Q Consensus       419 LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~  494 (567)
                      |++.++.  .+..+++|++|+.+..+.++|++|| ..++|..++.++....+...+..    +..+.+..++....| +.
T Consensus       139 LLK~LEe--pp~~~vfI~~tte~~kL~~tI~SRc-~~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s~G-dl  214 (563)
T PRK06647        139 LLKTIEE--PPPYIVFIFATTEVHKLPATIKSRC-QHFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKSTG-SV  214 (563)
T ss_pred             HHHhhcc--CCCCEEEEEecCChHHhHHHHHHhc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CH
Confidence            7888773  5678888888888888999999999 78999999999998888877653    456777778877655 55


Q ss_pred             HHHHHHHHHH
Q 047219          495 RDIRDVCQQA  504 (567)
Q Consensus       495 ~dL~~L~~~a  504 (567)
                      +++..++..+
T Consensus       215 R~alslLdkl  224 (563)
T PRK06647        215 RDAYTLFDQV  224 (563)
T ss_pred             HHHHHHHHHH
Confidence            5655555543

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=3.1e-13  Score=151.37  Aligned_cols=195  Identities=18%  Similarity=0.197  Sum_probs=136.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-CC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-QG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~~  353 (567)
                      .+.+|++|+|++..++.|.+.+..                    .+.++++||+||+|+|||++|+++|+.+.+... ..
T Consensus        19 RP~~f~dliGq~~~v~~L~~~~~~--------------------gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~   78 (598)
T PRK09111         19 RPQTFDDLIGQEAMVRTLTNAFET--------------------GRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGD   78 (598)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCCHHHHHHHHHHhhCcCCcccc
Confidence            446999999999999999887752                    466789999999999999999999999865311 00


Q ss_pred             -----cCeEE-echhhHHhhhh----------chhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          354 -----VPLMY-VPLEVVMSKYY----------GESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       354 -----~~~~~-i~~~~l~s~~~----------G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                           .+|.. -+|..+.....          ...-..++.+.+.+..   .+...|+||||+|.|...           
T Consensus        79 ~~~~~~~cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls~~-----------  147 (598)
T PRK09111         79 GGPTIDLCGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLSTA-----------  147 (598)
T ss_pred             CCCccccCcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCCHH-----------
Confidence                 01111 11111111000          0112345666555542   234689999999999632           


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhcc
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATE  490 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~  490 (567)
                      ..+.|++.++.  .+..+++|.+|+..+.+.+.+++|| ..++|..++.++....+...++.    +..+.++.++..+.
T Consensus       148 a~naLLKtLEe--Pp~~~~fIl~tte~~kll~tI~SRc-q~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~  224 (598)
T PRK09111        148 AFNALLKTLEE--PPPHVKFIFATTEIRKVPVTVLSRC-QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAAE  224 (598)
T ss_pred             HHHHHHHHHHh--CCCCeEEEEEeCChhhhhHHHHhhe-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcC
Confidence            34677777774  4567888888888888999999999 88999999999998888887764    45667777777765


Q ss_pred             CCCHHHHHHHHHHH
Q 047219          491 EMSGRDIRDVCQQA  504 (567)
Q Consensus       491 g~s~~dL~~L~~~a  504 (567)
                      | +.+++.+++..+
T Consensus       225 G-dlr~al~~Ldkl  237 (598)
T PRK09111        225 G-SVRDGLSLLDQA  237 (598)
T ss_pred             C-CHHHHHHHHHHH
Confidence            5 556665555544

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.54  E-value=9.6e-14  Score=151.32  Aligned_cols=171  Identities=14%  Similarity=0.242  Sum_probs=115.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHH---HHHHHHHHHhcCCCCcEEEEcCc
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER---LLGKVFSLANELPNGAIIFLDEV  397 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~---~l~~~f~~A~~~a~~~ILfIDEI  397 (567)
                      ..++++|||++|||||+|++++++++... ..+..+++++++++...+......   .+..+.... .  ...+|+|||+
T Consensus       140 ~~npl~i~G~~G~GKTHLl~Ai~~~l~~~-~~~~~v~yv~~~~f~~~~~~~l~~~~~~~~~~~~~~-~--~~dvLiIDDi  215 (450)
T PRK14087        140 SYNPLFIYGESGMGKTHLLKAAKNYIESN-FSDLKVSYMSGDEFARKAVDILQKTHKEIEQFKNEI-C--QNDVLIIDDV  215 (450)
T ss_pred             ccCceEEECCCCCcHHHHHHHHHHHHHHh-CCCCeEEEEEHHHHHHHHHHHHHHhhhHHHHHHHHh-c--cCCEEEEecc
Confidence            34679999999999999999999977421 115678899999888776543322   122221221 2  2469999999


Q ss_pred             chhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC---CCChHHHhccc--eEEEecCCCHHHHHHHHHH
Q 047219          398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ---DLDPALISRFD--SMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       398 D~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~---~Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~  472 (567)
                      +.+..+..         ....|...++.....+..+||++...|.   .++++|++||.  ..+.++.|+.++|.++++.
T Consensus       216 q~l~~k~~---------~~e~lf~l~N~~~~~~k~iIltsd~~P~~l~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~  286 (450)
T PRK14087        216 QFLSYKEK---------TNEIFFTIFNNFIENDKQLFFSSDKSPELLNGFDNRLITRFNMGLSIAIQKLDNKTATAIIKK  286 (450)
T ss_pred             ccccCCHH---------HHHHHHHHHHHHHHcCCcEEEECCCCHHHHhhccHHHHHHHhCCceeccCCcCHHHHHHHHHH
Confidence            99865421         1223333333333334434444444443   36899999994  4888899999999999999


Q ss_pred             HHHh------hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          473 YAKH------LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       473 ~~~~------~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .++.      ++++.++.++....| +.+.+..++..+.
T Consensus       287 ~~~~~gl~~~l~~evl~~Ia~~~~g-d~R~L~gaL~~l~  324 (450)
T PRK14087        287 EIKNQNIKQEVTEEAINFISNYYSD-DVRKIKGSVSRLN  324 (450)
T ss_pred             HHHhcCCCCCCCHHHHHHHHHccCC-CHHHHHHHHHHHH
Confidence            8864      567788888887765 6777777776655

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.54  E-value=1.8e-13  Score=152.34  Aligned_cols=181  Identities=17%  Similarity=0.227  Sum_probs=127.0

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQ  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~  352 (567)
                      ..+.+|++|+|++.+++.|.+++..                    .+.+..+||+||||||||++|+++|+.+.+.. ..
T Consensus        10 yRP~sf~dIiGQe~v~~~L~~ai~~--------------------~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~   69 (624)
T PRK14959         10 YRPQTFAEVAGQETVKAILSRAAQE--------------------NRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPT   69 (624)
T ss_pred             hCCCCHHHhcCCHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCCHHHHHHHHHHhccccCCCC
Confidence            3457899999999999999887752                    34567899999999999999999999996531 10


Q ss_pred             C-----------------cCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHH
Q 047219          353 G-----------------VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRI  415 (567)
Q Consensus       353 ~-----------------~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~v  415 (567)
                      +                 ..++.++...-  ..+... +.+...+..........||||||+|.|...           .
T Consensus        70 ~~pCg~C~sC~~i~~g~hpDv~eId~a~~--~~Id~i-R~L~~~~~~~p~~g~~kVIIIDEad~Lt~~-----------a  135 (624)
T PRK14959         70 GEPCNTCEQCRKVTQGMHVDVVEIDGASN--RGIDDA-KRLKEAIGYAPMEGRYKVFIIDEAHMLTRE-----------A  135 (624)
T ss_pred             CCCCcccHHHHHHhcCCCCceEEEecccc--cCHHHH-HHHHHHHHhhhhcCCceEEEEEChHhCCHH-----------H
Confidence            1                 12333332110  000111 122222222222334679999999999633           3


Q ss_pred             HHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccC
Q 047219          416 LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEE  491 (567)
Q Consensus       416 l~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g  491 (567)
                      ++.|++.++.  ....+++|++||.+..+.+.|++|| ..++|..++.++..++|...+..    +..+.++.++..+.|
T Consensus       136 ~naLLk~LEE--P~~~~ifILaTt~~~kll~TI~SRc-q~i~F~pLs~~eL~~~L~~il~~egi~id~eal~lIA~~s~G  212 (624)
T PRK14959        136 FNALLKTLEE--PPARVTFVLATTEPHKFPVTIVSRC-QHFTFTRLSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAG  212 (624)
T ss_pred             HHHHHHHhhc--cCCCEEEEEecCChhhhhHHHHhhh-hccccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            4667777774  4467889999988889999999999 78999999999999888876654    556777888877665

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.53  E-value=1.7e-13  Score=150.84  Aligned_cols=171  Identities=21%  Similarity=0.296  Sum_probs=122.9

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      .|=.|++++|+++.+.+.--        ++       .+.-...-++|+||||+|||+|++.||+.+      +..|+.+
T Consensus       323 ~dHYGLekVKeRIlEyLAV~--------~l-------~~~~kGpILcLVGPPGVGKTSLgkSIA~al------~RkfvR~  381 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQ--------KL-------TKKLKGPILCLVGPPGVGKTSLGKSIAKAL------GRKFVRI  381 (782)
T ss_pred             ccccCchhHHHHHHHHHHHH--------HH-------hccCCCcEEEEECCCCCCchhHHHHHHHHh------CCCEEEE
Confidence            45689999999999977421        11       013344668899999999999999999999      5557777


Q ss_pred             chh------hHHh---hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHH--HHhhcCc--
Q 047219          360 PLE------VVMS---KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL--LRQIDGF--  426 (567)
Q Consensus       360 ~~~------~l~s---~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~L--L~~ld~~--  426 (567)
                      +..      ++.+   .|+|....++-+-...|....|  +++|||||+|...-++.-..++-+++..=  -...|.+  
T Consensus       382 sLGGvrDEAEIRGHRRTYIGamPGrIiQ~mkka~~~NP--v~LLDEIDKm~ss~rGDPaSALLEVLDPEQN~~F~DhYLe  459 (782)
T COG0466         382 SLGGVRDEAEIRGHRRTYIGAMPGKIIQGMKKAGVKNP--VFLLDEIDKMGSSFRGDPASALLEVLDPEQNNTFSDHYLE  459 (782)
T ss_pred             ecCccccHHHhccccccccccCChHHHHHHHHhCCcCC--eEEeechhhccCCCCCChHHHHHhhcCHhhcCchhhcccc
Confidence            653      2322   3667766666666777776654  99999999998776554333322221100  0111111  


Q ss_pred             --ccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHH
Q 047219          427 --EQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       427 --~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~  474 (567)
                        -.-.+|+||+|+|..+.++..|+.|+ .+|++.-++.++..+|.+.|+
T Consensus       460 v~yDLS~VmFiaTANsl~tIP~PLlDRM-EiI~lsgYt~~EKl~IAk~~L  508 (782)
T COG0466         460 VPYDLSKVMFIATANSLDTIPAPLLDRM-EVIRLSGYTEDEKLEIAKRHL  508 (782)
T ss_pred             CccchhheEEEeecCccccCChHHhcce-eeeeecCCChHHHHHHHHHhc
Confidence              12368999999999999999999999 999999999999999999875

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.53  E-value=3.6e-13  Score=152.02  Aligned_cols=193  Identities=21%  Similarity=0.278  Sum_probs=134.0

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--  351 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--  351 (567)
                      ..+.+|++|+|++.+++.|+..+..                    .+.++.+||+||+|||||++|+++|+.+.+...  
T Consensus        12 yRP~~f~dIiGQe~~v~~L~~aI~~--------------------~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~   71 (725)
T PRK07133         12 YRPKTFDDIVGQDHIVQTLKNIIKS--------------------NKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTD   71 (725)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCC
Confidence            3557999999999999999988752                    456778999999999999999999999864311  


Q ss_pred             CCcCeEEechhhHHhh---hh---c---hhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHH
Q 047219          352 QGVPLMYVPLEVVMSK---YY---G---ESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVL  419 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~---~~---G---~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~L  419 (567)
                      ...+|..+.  .....   ++   +   .....++.+.+.+...   ++..|++|||+|.|...           .++.|
T Consensus        72 ~~~pC~~C~--~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~~-----------A~NAL  138 (725)
T PRK07133         72 LLEPCQECI--ENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSKS-----------AFNAL  138 (725)
T ss_pred             CCCchhHHH--HhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCHH-----------HHHHH
Confidence            001111110  00000   00   0   1123456665555432   34579999999998633           45678


Q ss_pred             HHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHH
Q 047219          420 LRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGR  495 (567)
Q Consensus       420 L~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~  495 (567)
                      +..++.  .+..+++|++|+.++.+.+.+++|| ..++|..++.++....+...+..    +..+.+..++..+.| +.+
T Consensus       139 LKtLEE--PP~~tifILaTte~~KLl~TI~SRc-q~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS~G-slR  214 (725)
T PRK07133        139 LKTLEE--PPKHVIFILATTEVHKIPLTILSRV-QRFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLSSG-SLR  214 (725)
T ss_pred             HHHhhc--CCCceEEEEEcCChhhhhHHHHhhc-eeEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHH
Confidence            888874  5678888888888899999999999 79999999999999888876654    345567777777654 444


Q ss_pred             HHHHHHHH
Q 047219          496 DIRDVCQQ  503 (567)
Q Consensus       496 dL~~L~~~  503 (567)
                      ++..++..
T Consensus       215 ~AlslLek  222 (725)
T PRK07133        215 DALSIAEQ  222 (725)
T ss_pred             HHHHHHHH
Confidence            44444443

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.53  E-value=4.8e-13  Score=145.91  Aligned_cols=177  Identities=19%  Similarity=0.244  Sum_probs=125.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC---
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW---  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~---  351 (567)
                      .+.+|++|+|++.+++.+...+..                    ...++.+|||||||+|||++|+++|+.+.....   
T Consensus        12 RP~~~~diiGq~~~v~~L~~~i~~--------------------~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~   71 (451)
T PRK06305         12 RPQTFSEILGQDAVVAVLKNALRF--------------------NRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTED   71 (451)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccC
Confidence            447999999999999999887752                    356788999999999999999999999854210   


Q ss_pred             ----------------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHH
Q 047219          352 ----------------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEAT  412 (567)
Q Consensus       352 ----------------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~  412 (567)
                                      ...+++.+++...    .|  -..++.+.+...   ..+...|+||||+|.|...         
T Consensus        72 ~~~c~~c~~C~~i~~~~~~d~~~i~g~~~----~g--id~ir~i~~~l~~~~~~~~~kvvIIdead~lt~~---------  136 (451)
T PRK06305         72 QEPCNQCASCKEISSGTSLDVLEIDGASH----RG--IEDIRQINETVLFTPSKSRYKIYIIDEVHMLTKE---------  136 (451)
T ss_pred             CCCCcccHHHHHHhcCCCCceEEeecccc----CC--HHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCHH---------
Confidence                            0112333332110    11  122333222222   2244689999999998633         


Q ss_pred             HHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh
Q 047219          413 RRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATA  488 (567)
Q Consensus       413 ~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~  488 (567)
                        ..+.|++.++.  .+..+++|++||.+..+.+.+++|| ..++|..++.++....+...++.    +..+.++.++..
T Consensus       137 --~~n~LLk~lEe--p~~~~~~Il~t~~~~kl~~tI~sRc-~~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~  211 (451)
T PRK06305        137 --AFNSLLKTLEE--PPQHVKFFLATTEIHKIPGTILSRC-QKMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARA  211 (451)
T ss_pred             --HHHHHHHHhhc--CCCCceEEEEeCChHhcchHHHHhc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence              34677888875  4567888888888889999999999 88999999999988888876653    456677778777


Q ss_pred             ccC
Q 047219          489 TEE  491 (567)
Q Consensus       489 t~g  491 (567)
                      +.|
T Consensus       212 s~g  214 (451)
T PRK06305        212 AQG  214 (451)
T ss_pred             cCC
Confidence            654

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.53  E-value=3.8e-13  Score=149.12  Aligned_cols=188  Identities=22%  Similarity=0.298  Sum_probs=133.1

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-C
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-G  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-~  353 (567)
                      .+.+|++++|++.+++.+.+.+..                    ...++++||+||+|||||++|+++|+.+.+..+. .
T Consensus        11 RP~~F~dIIGQe~iv~~L~~aI~~--------------------~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~   70 (605)
T PRK05896         11 RPHNFKQIIGQELIKKILVNAILN--------------------NKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDG   70 (605)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            457899999999999999887742                    4567889999999999999999999998653211 1


Q ss_pred             cC-----------------eEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 VP-----------------LMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .+                 ++.+++..    .  ..-..++.+.+.+..   .++..|++|||+|.|...          
T Consensus        71 ~~Cg~C~sCr~i~~~~h~DiieIdaas----~--igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~~----------  134 (605)
T PRK05896         71 DCCNSCSVCESINTNQSVDIVELDAAS----N--NGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLSTS----------  134 (605)
T ss_pred             CCCcccHHHHHHHcCCCCceEEecccc----c--cCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCHH----------
Confidence            12                 22222211    0  112234555444332   234579999999998633          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.|+..++.  .+..+++|++|+.+..+.+.+++|| ..++|..++.++....+...+..    +..+.+..++..+
T Consensus       135 -A~NaLLKtLEE--Pp~~tvfIL~Tt~~~KLl~TI~SRc-q~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS  210 (605)
T PRK05896        135 -AWNALLKTLEE--PPKHVVFIFATTEFQKIPLTIISRC-QRYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLA  210 (605)
T ss_pred             -HHHHHHHHHHh--CCCcEEEEEECCChHhhhHHHHhhh-hhcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             33667777773  4567888888888899999999999 78999999999998888877654    5567777777776


Q ss_pred             cCCCHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQ  503 (567)
Q Consensus       490 ~g~s~~dL~~L~~~  503 (567)
                      .| +.+++..++..
T Consensus       211 ~G-dlR~AlnlLek  223 (605)
T PRK05896        211 DG-SLRDGLSILDQ  223 (605)
T ss_pred             CC-cHHHHHHHHHH
Confidence            65 44444444443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.53  E-value=2.1e-13  Score=148.45  Aligned_cols=171  Identities=20%  Similarity=0.291  Sum_probs=114.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhH-HHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE-RLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~-~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      .++++||||||||||+|++++++++... ..+..+.+++++++...+..... ..... |...... ...+|+|||++.+
T Consensus       130 ~n~l~lyG~~G~GKTHLl~ai~~~l~~~-~~~~~v~yi~~~~f~~~~~~~~~~~~~~~-f~~~~~~-~~dvLlIDDi~~l  206 (440)
T PRK14088        130 YNPLFIYGGVGLGKTHLLQSIGNYVVQN-EPDLRVMYITSEKFLNDLVDSMKEGKLNE-FREKYRK-KVDVLLIDDVQFL  206 (440)
T ss_pred             CCeEEEEcCCCCcHHHHHHHHHHHHHHh-CCCCeEEEEEHHHHHHHHHHHHhcccHHH-HHHHHHh-cCCEEEEechhhh
Confidence            4679999999999999999999987432 11456889999887776543321 11222 2222221 2479999999988


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccc--eEEEecCCCHHHHHHHHHHHHH
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFD--SMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      .++..         ....|+..++.+...+..+||++.+.+..   +.+.|++||.  ..+.|+.|+.+.|.+|++..+.
T Consensus       207 ~~~~~---------~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~  277 (440)
T PRK14088        207 IGKTG---------VQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLE  277 (440)
T ss_pred             cCcHH---------HHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHH
Confidence            65421         11223333333333345566655555554   6688999993  3888999999999999999886


Q ss_pred             h----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          476 H----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       476 ~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .    ++++.++.++....+ +.++|..++....
T Consensus       278 ~~~~~l~~ev~~~Ia~~~~~-~~R~L~g~l~~l~  310 (440)
T PRK14088        278 IEHGELPEEVLNFVAENVDD-NLRRLRGAIIKLL  310 (440)
T ss_pred             hcCCCCCHHHHHHHHhcccc-CHHHHHHHHHHHH
Confidence            4    567788888887664 5666666666543

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.52  E-value=1.8e-13  Score=146.60  Aligned_cols=218  Identities=21%  Similarity=0.333  Sum_probs=137.1

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhh--ccccccc-CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIAR--GTRCKFE-SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~--~~~~~~~-~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      +.|+|++++++.+...+....+.      +..  ......+ .....++||+||||||||++|+++|+.+      +.+|
T Consensus        77 ~~ViGQe~A~~~l~~av~~h~~~------~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l------~~pf  144 (413)
T TIGR00382        77 EYVIGQEQAKKVLSVAVYNHYKR------LNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL------NVPF  144 (413)
T ss_pred             ceecCHHHHHHHHHHHHHHHHhh------hccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc------CCCe
Confidence            45799999999998777443222      110  0000000 1224689999999999999999999988      6778


Q ss_pred             EEechhhHH-hhhhchh-HHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhh--HHH-HHHHHHHHHHhhcCcc-
Q 047219          357 MYVPLEVVM-SKYYGES-ERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEM--HEA-TRRILSVLLRQIDGFE-  427 (567)
Q Consensus       357 ~~i~~~~l~-s~~~G~~-~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l--~~~-~~~vl~~LL~~ld~~~-  427 (567)
                      ..+++..+. ..|+|+. +..+..++..+.   ..+.++||||||||.+..+.....  ..+ -..+++.||+.+++.. 
T Consensus       145 ~~~da~~L~~~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~  224 (413)
T TIGR00382       145 AIADATTLTEAGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVA  224 (413)
T ss_pred             EEechhhccccccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchhHHHHHHHHhhccce
Confidence            888877664 3577774 344444443221   123468999999999987533210  011 1235566777765432 


Q ss_pred             ----------cCCcEEEEEeeCCC---------------------------C-----------------------CCChH
Q 047219          428 ----------QDKKVVVIAATNRK---------------------------Q-----------------------DLDPA  447 (567)
Q Consensus       428 ----------~~~~viVIaaTN~~---------------------------~-----------------------~Ld~a  447 (567)
                                ...++++|.|+|..                           .                       .|.|+
T Consensus       225 ~v~~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PE  304 (413)
T TIGR00382       225 NVPPQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPE  304 (413)
T ss_pred             ecccCCCccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHH
Confidence                      12467788887750                           0                       15688


Q ss_pred             HHhccceEEEecCCCHHHHHHHHHHHHHh-----------------hCHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHH
Q 047219          448 LISRFDSMITFGLPDHENRQEIAAQYAKH-----------------LTKAELAELATA--TEEMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       448 L~sRf~~~I~i~~P~~~eR~eIL~~~~~~-----------------~~~~~l~~la~~--t~g~s~~dL~~L~~~a~~~a  508 (567)
                      |+.|++.++.|...+.++..+|+......                 +.++.++.+++.  ...+-.+.|+.+++......
T Consensus       305 flgRld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~iie~~l~~~  384 (413)
T TIGR00382       305 FIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDV  384 (413)
T ss_pred             HhCCCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHHHHhhHHH
Confidence            88899999999999999999998863221                 234455555553  33455666666666555433


Q ss_pred             H
Q 047219          509 A  509 (567)
Q Consensus       509 ~  509 (567)
                      .
T Consensus       385 m  385 (413)
T TIGR00382       385 M  385 (413)
T ss_pred             H
Confidence            3

A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.52  E-value=2.2e-13  Score=157.03  Aligned_cols=203  Identities=19%  Similarity=0.272  Sum_probs=139.2

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++..|++++|+.+.+.+......               +...+..++|+||||||||++++.+++.+      +.+++.+
T Consensus       322 ~~~~g~~~vK~~i~~~l~~~~~~---------------~~~~g~~i~l~GppG~GKTtl~~~ia~~l------~~~~~~i  380 (784)
T PRK10787        322 TDHYGLERVKDRILEYLAVQSRV---------------NKIKGPILCLVGPPGVGKTSLGQSIAKAT------GRKYVRM  380 (784)
T ss_pred             hhccCHHHHHHHHHHHHHHHHhc---------------ccCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEE
Confidence            45899999999998877532111               12234579999999999999999999998      5567666


Q ss_pred             chhhHH---------hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc----
Q 047219          360 PLEVVM---------SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF----  426 (567)
Q Consensus       360 ~~~~l~---------s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~----  426 (567)
                      +.....         ..|.|.....+...+..+...  +.++||||||.+....+...       ...|+..+|.-    
T Consensus       381 ~~~~~~d~~~i~g~~~~~~g~~~G~~~~~l~~~~~~--~~villDEidk~~~~~~g~~-------~~aLlevld~~~~~~  451 (784)
T PRK10787        381 ALGGVRDEAEIRGHRRTYIGSMPGKLIQKMAKVGVK--NPLFLLDEIDKMSSDMRGDP-------ASALLEVLDPEQNVA  451 (784)
T ss_pred             EcCCCCCHHHhccchhccCCCCCcHHHHHHHhcCCC--CCEEEEEChhhcccccCCCH-------HHHHHHHhccccEEE
Confidence            544321         123444444444444443322  46999999999986644321       23444444421    


Q ss_pred             ---------ccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHH-h-------------hCHHHHH
Q 047219          427 ---------EQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK-H-------------LTKAELA  483 (567)
Q Consensus       427 ---------~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~-~-------------~~~~~l~  483 (567)
                               ..-+++++|+|+|.. .++++|++|| ..|.+..++.++..+|++.++. +             +..+...
T Consensus       452 ~~d~~~~~~~dls~v~~i~TaN~~-~i~~aLl~R~-~ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~  529 (784)
T PRK10787        452 FSDHYLEVDYDLSDVMFVATSNSM-NIPAPLLDRM-EVIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAII  529 (784)
T ss_pred             EecccccccccCCceEEEEcCCCC-CCCHHHhcce-eeeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHH
Confidence                     123689999999987 5999999999 7899999999999999988773 1             2344555


Q ss_pred             HHHH-hccCCCHHHHHHHHHHHHHHHHHHHHh
Q 047219          484 ELAT-ATEEMSGRDIRDVCQQAERSWASKIIR  514 (567)
Q Consensus       484 ~la~-~t~g~s~~dL~~L~~~a~~~a~~r~i~  514 (567)
                      .++. ++..+-.+.|+..+....+..+.+.+.
T Consensus       530 ~ii~~yt~e~GaR~LeR~I~~i~r~~l~~~~~  561 (784)
T PRK10787        530 GIIRYYTREAGVRSLEREISKLCRKAVKQLLL  561 (784)
T ss_pred             HHHHhCCcccCCcHHHHHHHHHHHHHHHHHHh
Confidence            5543 445566788888888877777766653

>PRK05642 DNA replication initiation factor; Validated

Probab=99.52  E-value=8.6e-13  Score=132.04  Aligned_cols=159  Identities=17%  Similarity=0.237  Sum_probs=109.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      ..+++||||+|||||+|++++++++...   +..+++++..++....        ..+.+....   ..+|+|||++.+.
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~---~~~v~y~~~~~~~~~~--------~~~~~~~~~---~d~LiiDDi~~~~  110 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQR---GEPAVYLPLAELLDRG--------PELLDNLEQ---YELVCLDDLDVIA  110 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEeeHHHHHhhh--------HHHHHhhhh---CCEEEEechhhhc
Confidence            4789999999999999999999987433   4678899988776531        122222222   3589999999886


Q ss_pred             hhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh
Q 047219          402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFD--SMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      ++.+         ....|+..++.....+..++|+++..+..   +.++|++||.  ..+.++.|+.+++.++++..+..
T Consensus       111 ~~~~---------~~~~Lf~l~n~~~~~g~~ilits~~~p~~l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~~ka~~  181 (234)
T PRK05642        111 GKAD---------WEEALFHLFNRLRDSGRRLLLAASKSPRELPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQLRASR  181 (234)
T ss_pred             CChH---------HHHHHHHHHHHHHhcCCEEEEeCCCCHHHcCccCccHHHHHhcCeeeecCCCCHHHHHHHHHHHHHH
Confidence            5522         12344555554445566677777765543   4699999994  57788999999999999966553


Q ss_pred             ----hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          477 ----LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       477 ----~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                          ++++.++.++....+ +.+.+..+++..
T Consensus       182 ~~~~l~~ev~~~L~~~~~~-d~r~l~~~l~~l  212 (234)
T PRK05642        182 RGLHLTDEVGHFILTRGTR-SMSALFDLLERL  212 (234)
T ss_pred             cCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHH
Confidence                566777777777654 555555555544

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.51  E-value=2.5e-13  Score=148.09  Aligned_cols=198  Identities=21%  Similarity=0.266  Sum_probs=151.0

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++++|++...+.|.+.+..                    .+..++.||+||.|||||++||.+|+.+++.. -.+
T Consensus        11 RP~~F~evvGQe~v~~~L~nal~~--------------------~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~   70 (515)
T COG2812          11 RPKTFDDVVGQEHVVKTLSNALEN--------------------GRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTA   70 (515)
T ss_pred             CcccHHHhcccHHHHHHHHHHHHh--------------------CcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCC
Confidence            446899999999999999998863                    56678899999999999999999999997653 222


Q ss_pred             cCeEEec-hhhHHhh-h---------hchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHH
Q 047219          354 VPLMYVP-LEVVMSK-Y---------YGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL  419 (567)
Q Consensus       354 ~~~~~i~-~~~l~s~-~---------~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~L  419 (567)
                      -+|.... |..+... +         ....-+.++.+.+.+..   .+...|++|||+|.|.           ...++.|
T Consensus        71 ePC~~C~~Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS-----------~~afNAL  139 (515)
T COG2812          71 EPCGKCISCKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLS-----------KQAFNAL  139 (515)
T ss_pred             CcchhhhhhHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhh-----------HHHHHHH
Confidence            3333221 1112111 0         11133456666665542   2346899999999986           3467889


Q ss_pred             HHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHH
Q 047219          420 LRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGR  495 (567)
Q Consensus       420 L~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~  495 (567)
                      |+.++  +++.+|.+|.+|..+..+++.++||| ..+.|...+.++...-|...+.+    +..+.+..++....| +.+
T Consensus       140 LKTLE--EPP~hV~FIlATTe~~Kip~TIlSRc-q~f~fkri~~~~I~~~L~~i~~~E~I~~e~~aL~~ia~~a~G-s~R  215 (515)
T COG2812         140 LKTLE--EPPSHVKFILATTEPQKIPNTILSRC-QRFDFKRLDLEEIAKHLAAILDKEGINIEEDALSLIARAAEG-SLR  215 (515)
T ss_pred             hcccc--cCccCeEEEEecCCcCcCchhhhhcc-ccccccCCCHHHHHHHHHHHHHhcCCccCHHHHHHHHHHcCC-Chh
Confidence            99888  57889999999999999999999999 89999999999988888888774    566778888888766 788


Q ss_pred             HHHHHHHHHHHH
Q 047219          496 DIRDVCQQAERS  507 (567)
Q Consensus       496 dL~~L~~~a~~~  507 (567)
                      |.-.++.++...
T Consensus       216 DalslLDq~i~~  227 (515)
T COG2812         216 DALSLLDQAIAF  227 (515)
T ss_pred             hHHHHHHHHHHc
Confidence            988888888743

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.51  E-value=6.6e-13  Score=145.81  Aligned_cols=195  Identities=21%  Similarity=0.291  Sum_probs=130.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-C
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-G  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-~  353 (567)
                      .+.+|++++|++.+++.++..+..                    ...++.+||+||+|+|||++|+.+|+.+.+.... .
T Consensus        11 RP~~f~diiGq~~i~~~L~~~i~~--------------------~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~   70 (486)
T PRK14953         11 RPKFFKEVIGQEIVVRILKNAVKL--------------------QRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEG   70 (486)
T ss_pred             CCCcHHHccChHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCC
Confidence            456899999999999999888752                    3456678999999999999999999998642100 1


Q ss_pred             cCeEEe-chhhHHhh----h------hchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHH
Q 047219          354 VPLMYV-PLEVVMSK----Y------YGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVL  419 (567)
Q Consensus       354 ~~~~~i-~~~~l~s~----~------~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~L  419 (567)
                      -+|-.. +|..+...    +      ....-..++.+.+.+..   .+...|++|||+|.|...           ..+.|
T Consensus        71 ~pc~~c~nc~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt~~-----------a~naL  139 (486)
T PRK14953         71 EPCGKCENCVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLTKE-----------AFNAL  139 (486)
T ss_pred             CCCCccHHHHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcCHH-----------HHHHH
Confidence            122211 11111110    0      00111233444443332   234579999999988632           34567


Q ss_pred             HHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHH
Q 047219          420 LRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGR  495 (567)
Q Consensus       420 L~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~  495 (567)
                      +..++.  .+..+++|.+|+..+.+.+++.+|| ..+.|..++.++....+...++.    +..+.+..++..+.| +.+
T Consensus       140 Lk~LEe--pp~~~v~Il~tt~~~kl~~tI~SRc-~~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s~G-~lr  215 (486)
T PRK14953        140 LKTLEE--PPPRTIFILCTTEYDKIPPTILSRC-QRFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQASEG-GMR  215 (486)
T ss_pred             HHHHhc--CCCCeEEEEEECCHHHHHHHHHHhc-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHH
Confidence            777764  4556777777877888999999999 78999999999999999988765    345677777777654 445


Q ss_pred             HHHHHHHHH
Q 047219          496 DIRDVCQQA  504 (567)
Q Consensus       496 dL~~L~~~a  504 (567)
                      ++.+++..+
T Consensus       216 ~al~~Ldkl  224 (486)
T PRK14953        216 DAASLLDQA  224 (486)
T ss_pred             HHHHHHHHH
Confidence            555555443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.50  E-value=1.6e-12  Score=139.33  Aligned_cols=207  Identities=23%  Similarity=0.324  Sum_probs=134.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +....+.++|.++++++|...+...+.                 ...+.+++|+||||||||++++.+++++.... .++
T Consensus        25 ~~~~P~~l~~Re~e~~~l~~~l~~~~~-----------------~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~-~~~   86 (394)
T PRK00411         25 PDYVPENLPHREEQIEELAFALRPALR-----------------GSRPLNVLIYGPPGTGKTTTVKKVFEELEEIA-VKV   86 (394)
T ss_pred             CCCcCCCCCCHHHHHHHHHHHHHHHhC-----------------CCCCCeEEEECCCCCCHHHHHHHHHHHHHHhc-CCc
Confidence            444567899999999999888754321                 24456799999999999999999999874321 135


Q ss_pred             CeEEechhhH----------Hhhhhch--------hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHH
Q 047219          355 PLMYVPLEVV----------MSKYYGE--------SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRIL  416 (567)
Q Consensus       355 ~~~~i~~~~l----------~s~~~G~--------~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl  416 (567)
                      .++++++...          ...+.+.        ....+..+.+.......+.+|+|||+|.+.....       ...+
T Consensus        87 ~~v~in~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~~~-------~~~l  159 (394)
T PRK00411         87 VYVYINCQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEKEG-------NDVL  159 (394)
T ss_pred             EEEEEECCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhccCC-------chHH
Confidence            6777776432          2222221        1223333444444334457999999999962111       1234


Q ss_pred             HHHHHhhcCcccCCcEEEEEeeCCCC---CCChHHHhccc-eEEEecCCCHHHHHHHHHHHHHh------hCHHHHHHHH
Q 047219          417 SVLLRQIDGFEQDKKVVVIAATNRKQ---DLDPALISRFD-SMITFGLPDHENRQEIAAQYAKH------LTKAELAELA  486 (567)
Q Consensus       417 ~~LL~~ld~~~~~~~viVIaaTN~~~---~Ld~aL~sRf~-~~I~i~~P~~~eR~eIL~~~~~~------~~~~~l~~la  486 (567)
                      ..|+..++... ..++.+|+++|..+   .+++.+.+||. ..+.|++++.++..++++..++.      +..+.++.++
T Consensus       160 ~~l~~~~~~~~-~~~v~vI~i~~~~~~~~~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~  238 (394)
T PRK00411        160 YSLLRAHEEYP-GARIGVIGISSDLTFLYILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEGFYPGVVDDEVLDLIA  238 (394)
T ss_pred             HHHHHhhhccC-CCeEEEEEEECCcchhhhcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhhcccCCCCHhHHHHHH
Confidence            55555554432 23788889888643   57888888884 47899999999999999988753      4556677777


Q ss_pred             HhccCCCHHHHH---HHHHHHHHHH
Q 047219          487 TATEEMSGRDIR---DVCQQAERSW  508 (567)
Q Consensus       487 ~~t~g~s~~dL~---~L~~~a~~~a  508 (567)
                      +.+.+.+ +|++   .+|..|+..+
T Consensus       239 ~~~~~~~-Gd~r~a~~ll~~a~~~a  262 (394)
T PRK00411        239 DLTAREH-GDARVAIDLLRRAGLIA  262 (394)
T ss_pred             HHHHHhc-CcHHHHHHHHHHHHHHH
Confidence            7664422 2444   5555555433

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.50  E-value=1.2e-12  Score=147.96  Aligned_cols=193  Identities=20%  Similarity=0.306  Sum_probs=125.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PW  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~  351 (567)
                      .+.+|++|+|++..++.+...+.                     ...+.+++|+||||||||++|+++++.....   ++
T Consensus       149 rp~~~~~iiGqs~~~~~l~~~ia---------------------~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~  207 (615)
T TIGR02903       149 RPRAFSEIVGQERAIKALLAKVA---------------------SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPF  207 (615)
T ss_pred             CcCcHHhceeCcHHHHHHHHHHh---------------------cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcc
Confidence            45789999999999998876553                     3446689999999999999999999877421   11


Q ss_pred             -CCcCeEEechhhHH-------hhhhchhHHH----HHHHHHH---------HhcCCCCcEEEEcCcchhhhhhhhhhHH
Q 047219          352 -QGVPLMYVPLEVVM-------SKYYGESERL----LGKVFSL---------ANELPNGAIIFLDEVDSFAVARDSEMHE  410 (567)
Q Consensus       352 -~~~~~~~i~~~~l~-------s~~~G~~~~~----l~~~f~~---------A~~~a~~~ILfIDEID~L~~~~q~~l~~  410 (567)
                       .+.+|+.+++..+.       ..++|.....    ....+..         ......+++|||||++.|....|..+..
T Consensus       208 ~~~~~fv~i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~~~Q~~Ll~  287 (615)
T TIGR02903       208 AEDAPFVEVDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDPLLQNKLLK  287 (615)
T ss_pred             cCCCCeEEEechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCHHHHHHHHH
Confidence             14567777775431       1223321110    0001110         0012246899999999998877766655


Q ss_pred             HHHHHHHH----------------HHHhhcCcccCCcEEEEEee-CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHH
Q 047219          411 ATRRILSV----------------LLRQIDGFEQDKKVVVIAAT-NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQY  473 (567)
Q Consensus       411 ~~~~vl~~----------------LL~~ld~~~~~~~viVIaaT-N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~  473 (567)
                      .+++....                +...++ ...+.++++|++| +.++.++++|++|| ..+.++.++.++..+|++..
T Consensus       288 ~Le~~~v~~~~~~~~~~~~~~~~~ik~~~~-~~~~~~~VLI~aTt~~~~~l~~aLrSR~-~~i~~~pls~edi~~Il~~~  365 (615)
T TIGR02903       288 VLEDKRVEFSSSYYDPDDPNVPKYIKKLFE-EGAPADFVLIGATTRDPEEINPALRSRC-AEVFFEPLTPEDIALIVLNA  365 (615)
T ss_pred             HHhhCeEEeecceeccCCcccchhhhhhcc-cCccceEEEEEeccccccccCHHHHhce-eEEEeCCCCHHHHHHHHHHH
Confidence            55431100                000011 1123457777665 55778999999999 67889999999999999998


Q ss_pred             HHh----hCHHHHHHHHHhcc
Q 047219          474 AKH----LTKAELAELATATE  490 (567)
Q Consensus       474 ~~~----~~~~~l~~la~~t~  490 (567)
                      +..    +..+.++.++.+++
T Consensus       366 a~~~~v~ls~eal~~L~~ys~  386 (615)
T TIGR02903       366 AEKINVHLAAGVEELIARYTI  386 (615)
T ss_pred             HHHcCCCCCHHHHHHHHHCCC
Confidence            775    44566667766655

Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.50  E-value=1.6e-12  Score=146.43  Aligned_cols=203  Identities=18%  Similarity=0.272  Sum_probs=135.8

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC----CCC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA----MPW  351 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~----~~~  351 (567)
                      .+.-+.|.|.++++++|...+...+..                ..+...++|+|+||||||++++.+.+++..    ...
T Consensus       751 DYVPD~LPhREeEIeeLasfL~paIkg----------------sgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~l  814 (1164)
T PTZ00112        751 DVVPKYLPCREKEIKEVHGFLESGIKQ----------------SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLL  814 (1164)
T ss_pred             ccCCCcCCChHHHHHHHHHHHHHHHhc----------------CCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccC
Confidence            344578999999999999888654321                233344579999999999999999988732    112


Q ss_pred             CCcCeEEechhhHHh----------hhhch-------hHHHHHHHHHHHhc-CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          352 QGVPLMYVPLEVVMS----------KYYGE-------SERLLGKVFSLANE-LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s----------~~~G~-------~~~~l~~~f~~A~~-~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      ..+.+++|+|..+..          .+++.       ....+..+|..... .....||+|||||.|....|        
T Consensus       815 p~f~vVYINCm~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK~Q--------  886 (1164)
T PTZ00112        815 PSFNVFEINGMNVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITKTQ--------  886 (1164)
T ss_pred             CCceEEEEeCCccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCccHH--------
Confidence            235678888843211          11111       23345566665432 22236999999999976532        


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCC---CCCCChHHHhccce-EEEecCCCHHHHHHHHHHHHHh----hCHHHHHHH
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNR---KQDLDPALISRFDS-MITFGLPDHENRQEIAAQYAKH----LTKAELAEL  485 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~---~~~Ld~aL~sRf~~-~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~l  485 (567)
                      .++..|+.+..  .....+.||+++|.   +..+++.+++||.. .+.|++++.+++.+||+..+..    +.++.++.+
T Consensus       887 DVLYnLFR~~~--~s~SKLiLIGISNdlDLperLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdAIELI  964 (1164)
T PTZ00112        887 KVLFTLFDWPT--KINSKLVLIAISNTMDLPERLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTAIQLC  964 (1164)
T ss_pred             HHHHHHHHHhh--ccCCeEEEEEecCchhcchhhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHHHHHH
Confidence            33444555433  23467999999986   55688999999854 4889999999999999998874    456666666


Q ss_pred             HHhccCCCHHHHHHHHHHHH
Q 047219          486 ATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       486 a~~t~g~s~~dL~~L~~~a~  505 (567)
                      ++..... .+|+|.++....
T Consensus       965 ArkVAq~-SGDARKALDILR  983 (1164)
T PTZ00112        965 ARKVANV-SGDIRKALQICR  983 (1164)
T ss_pred             HHhhhhc-CCHHHHHHHHHH
Confidence            6654433 347777665444

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=1.8e-13  Score=147.21  Aligned_cols=187  Identities=17%  Similarity=0.229  Sum_probs=128.5

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-  352 (567)
                      ..+.+|++|+|++.+++.|+..+..                    .+.++.+||+||||||||++|+++|+.+.+.... 
T Consensus        10 ~RP~~~~eiiGq~~~~~~L~~~~~~--------------------~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~   69 (397)
T PRK14955         10 YRPKKFADITAQEHITRTIQNSLRM--------------------GRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMID   69 (397)
T ss_pred             cCCCcHhhccChHHHHHHHHHHHHh--------------------CCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcC
Confidence            3457899999999999998887752                    4567789999999999999999999999653100 


Q ss_pred             -------------------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhh
Q 047219          353 -------------------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       353 -------------------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~  404 (567)
                                               ..++..+++...      ...+.++.+.+.+.   ..++..++||||+|.|... 
T Consensus        70 ~~~~~~~~~~~c~~c~~c~~~~~~~~~n~~~~~~~~~------~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~~-  142 (397)
T PRK14955         70 DADYLQEVTEPCGECESCRDFDAGTSLNISEFDAASN------NSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSIA-  142 (397)
T ss_pred             cccccccCCCCCCCCHHHHHHhcCCCCCeEeeccccc------CCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCHH-
Confidence                                     012222222110      01234444444442   2344679999999999643 


Q ss_pred             hhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHH
Q 047219          405 DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKA  480 (567)
Q Consensus       405 q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~  480 (567)
                                ..+.|+..++.  .+..+++|.+|+....+.+.+++|+ ..++|..++.++....+...++.    +..+
T Consensus       143 ----------~~~~LLk~LEe--p~~~t~~Il~t~~~~kl~~tl~sR~-~~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~  209 (397)
T PRK14955        143 ----------AFNAFLKTLEE--PPPHAIFIFATTELHKIPATIASRC-QRFNFKRIPLEEIQQQLQGICEAEGISVDAD  209 (397)
T ss_pred             ----------HHHHHHHHHhc--CCCCeEEEEEeCChHHhHHHHHHHH-HHhhcCCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence                      23456666663  4456777777777788999999999 78999999998888888877643    5667


Q ss_pred             HHHHHHHhccCCCHHHHHHHH
Q 047219          481 ELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       481 ~l~~la~~t~g~s~~dL~~L~  501 (567)
                      .++.++..+.| +.+.+.+.+
T Consensus       210 al~~l~~~s~g-~lr~a~~~L  229 (397)
T PRK14955        210 ALQLIGRKAQG-SMRDAQSIL  229 (397)
T ss_pred             HHHHHHHHcCC-CHHHHHHHH
Confidence            78888877655 333333333

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=1.3e-12  Score=147.31  Aligned_cols=183  Identities=20%  Similarity=0.299  Sum_probs=128.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC--
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ--  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~--  352 (567)
                      .+.+|++++|++.+++.|...+..                    .+.+.++||+||+|||||++|+++|+.+.+....  
T Consensus        11 RP~~f~~liGq~~i~~~L~~~l~~--------------------~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~   70 (620)
T PRK14948         11 RPQRFDELVGQEAIATTLKNALIS--------------------NRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKP   70 (620)
T ss_pred             CCCcHhhccChHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCC
Confidence            457899999999999999887752                    2446789999999999999999999998653111  


Q ss_pred             -CcCeEEech-hhHHh----------hhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHH
Q 047219          353 -GVPLMYVPL-EVVMS----------KYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILS  417 (567)
Q Consensus       353 -~~~~~~i~~-~~l~s----------~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~  417 (567)
                       ..+|..... ..+..          ...+..-+.++++.+.+...   +...|+||||+|.|...           ..+
T Consensus        71 ~~~~Cg~C~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt~~-----------a~n  139 (620)
T PRK14948         71 TPEPCGKCELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLSTA-----------AFN  139 (620)
T ss_pred             CCCCCcccHHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccCHH-----------HHH
Confidence             112221110 00100          00112234566666655432   34579999999999632           446


Q ss_pred             HHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccC
Q 047219          418 VLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEE  491 (567)
Q Consensus       418 ~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g  491 (567)
                      .|++.++.  .+..+++|++|+.+..+.+.|++|| ..++|..++.++....+...+.+    +..+.+..++..+.|
T Consensus       140 aLLK~LEe--Pp~~tvfIL~t~~~~~llpTIrSRc-~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s~G  214 (620)
T PRK14948        140 ALLKTLEE--PPPRVVFVLATTDPQRVLPTIISRC-QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRSQG  214 (620)
T ss_pred             HHHHHHhc--CCcCeEEEEEeCChhhhhHHHHhhe-eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC
Confidence            77888873  5667888888888888999999999 88999999988887777766654    445677777777665

>PRK08727 hypothetical protein; Validated

Probab=99.50  E-value=2.1e-12  Score=129.19  Aligned_cols=153  Identities=22%  Similarity=0.311  Sum_probs=102.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      ...++|+||+|||||+|++++++++...   +....+++..++...        +...++...   ...+|+|||++.+.
T Consensus        41 ~~~l~l~G~~G~GKThL~~a~~~~~~~~---~~~~~y~~~~~~~~~--------~~~~~~~l~---~~dlLiIDDi~~l~  106 (233)
T PRK08727         41 SDWLYLSGPAGTGKTHLALALCAAAEQA---GRSSAYLPLQAAAGR--------LRDALEALE---GRSLVALDGLESIA  106 (233)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEeHHHhhhh--------HHHHHHHHh---cCCEEEEeCccccc
Confidence            4569999999999999999999987544   456677776554432        222333332   24699999999987


Q ss_pred             hhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeC-CCCC---CChHHHhcc--ceEEEecCCCHHHHHHHHHHHHH
Q 047219          402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATN-RKQD---LDPALISRF--DSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN-~~~~---Ld~aL~sRf--~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      .+...         ...++..++.....+ ..+|.|+| .+..   +.++|++||  ...++++.|+.+++.++++.++.
T Consensus       107 ~~~~~---------~~~lf~l~n~~~~~~-~~vI~ts~~~p~~l~~~~~dL~SRl~~~~~~~l~~~~~e~~~~iL~~~a~  176 (233)
T PRK08727        107 GQRED---------EVALFDFHNRARAAG-ITLLYTARQMPDGLALVLPDLRSRLAQCIRIGLPVLDDVARAAVLRERAQ  176 (233)
T ss_pred             CChHH---------HHHHHHHHHHHHHcC-CeEEEECCCChhhhhhhhHHHHHHHhcCceEEecCCCHHHHHHHHHHHHH
Confidence            54321         122233333322223 33555554 5554   479999996  46889999999999999998765


Q ss_pred             h----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          476 H----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       476 ~----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .    ++.+.++.++..+.|    |++.+.+
T Consensus       177 ~~~l~l~~e~~~~La~~~~r----d~r~~l~  203 (233)
T PRK08727        177 RRGLALDEAAIDWLLTHGER----ELAGLVA  203 (233)
T ss_pred             HcCCCCCHHHHHHHHHhCCC----CHHHHHH
Confidence            3    567788888887653    5555533

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.50  E-value=2.6e-13  Score=144.07  Aligned_cols=172  Identities=18%  Similarity=0.262  Sum_probs=123.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ...++++|||+.|.|||+|++|++++..... ....+++++.+.+...++......-..-|+.-. .  -.+++||+|+.
T Consensus       111 ~~~nplfi~G~~GlGKTHLl~Aign~~~~~~-~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y-~--~dlllIDDiq~  186 (408)
T COG0593         111 GAYNPLFIYGGVGLGKTHLLQAIGNEALANG-PNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY-S--LDLLLIDDIQF  186 (408)
T ss_pred             CcCCcEEEECCCCCCHHHHHHHHHHHHHhhC-CCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh-c--cCeeeechHhH
Confidence            3568899999999999999999999985431 145688899988888776554443344555555 3  35999999999


Q ss_pred             hhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccce--EEEecCCCHHHHHHHHHHHH
Q 047219          400 FAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFDS--MITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       400 L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~~--~I~i~~P~~~eR~eIL~~~~  474 (567)
                      +.++.         +...+|...++.+...+..+|+.+...|..   +.++|++||.+  .+.+..|+.+.|..||...+
T Consensus       187 l~gk~---------~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~aiL~kka  257 (408)
T COG0593         187 LAGKE---------RTQEEFFHTFNALLENGKQIVLTSDRPPKELNGLEDRLRSRLEWGLVVEIEPPDDETRLAILRKKA  257 (408)
T ss_pred             hcCCh---------hHHHHHHHHHHHHHhcCCEEEEEcCCCchhhccccHHHHHHHhceeEEeeCCCCHHHHHHHHHHHH
Confidence            98762         223455555555555566666666666665   55999999955  77889999999999999977


Q ss_pred             Hh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          475 KH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       475 ~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      +.    ++++....++..... +.++|..+++...
T Consensus       258 ~~~~~~i~~ev~~~la~~~~~-nvReLegaL~~l~  291 (408)
T COG0593         258 EDRGIEIPDEVLEFLAKRLDR-NVRELEGALNRLD  291 (408)
T ss_pred             HhcCCCCCHHHHHHHHHHhhc-cHHHHHHHHHHHH
Confidence            64    567777777777543 4555555554443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=1.9e-12  Score=137.82  Aligned_cols=187  Identities=20%  Similarity=0.324  Sum_probs=129.3

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--  351 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--  351 (567)
                      ..+.+|++++|++.+++.+.+.+..                    ...+.++|||||||+|||++|+++++.+.....  
T Consensus        11 ~rP~~~~~iig~~~~~~~l~~~i~~--------------------~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~   70 (367)
T PRK14970         11 YRPQTFDDVVGQSHITNTLLNAIEN--------------------NHLAQALLFCGPRGVGKTTCARILARKINQPGYDD   70 (367)
T ss_pred             HCCCcHHhcCCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCC
Confidence            3457899999999999999887752                    356778999999999999999999999854211  


Q ss_pred             --C--CcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhc
Q 047219          352 --Q--GVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQID  424 (567)
Q Consensus       352 --~--~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld  424 (567)
                        .  ...++.++...      ......++.+++.+..   .++..+++|||+|.+...           .++.|+..++
T Consensus        71 ~~~~~~~~~~~l~~~~------~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~~-----------~~~~ll~~le  133 (367)
T PRK14970         71 PNEDFSFNIFELDAAS------NNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSSA-----------AFNAFLKTLE  133 (367)
T ss_pred             CCCCCCcceEEecccc------CCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCHH-----------HHHHHHHHHh
Confidence              1  12222232211      1112345555655432   233579999999988633           2355666665


Q ss_pred             CcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          425 GFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       425 ~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                      .  .+..+++|.+++....+.+++.+|| ..+++..|+.++...++...+..    +..+.++.++..+.| +.+.+...
T Consensus       134 ~--~~~~~~~Il~~~~~~kl~~~l~sr~-~~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~~~~g-dlr~~~~~  209 (367)
T PRK14970        134 E--PPAHAIFILATTEKHKIIPTILSRC-QIFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQKADG-ALRDALSI  209 (367)
T ss_pred             C--CCCceEEEEEeCCcccCCHHHHhcc-eeEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCC-CHHHHHHH
Confidence            4  3456777777887889999999999 78999999999998888876654    456777777776544 33433333


Q ss_pred             H
Q 047219          501 C  501 (567)
Q Consensus       501 ~  501 (567)
                      +
T Consensus       210 l  210 (367)
T PRK14970        210 F  210 (367)
T ss_pred             H
Confidence            3

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=1.6e-12  Score=145.85  Aligned_cols=178  Identities=15%  Similarity=0.218  Sum_probs=126.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-  352 (567)
                      ..+.+|++|+|++.+++.|+..+..                    ...++++||+||+|||||++|+++|+.+.+.... 
T Consensus        10 yRP~~f~eivGQe~i~~~L~~~i~~--------------------~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~   69 (620)
T PRK14954         10 YRPSKFADITAQEHITHTIQNSLRM--------------------DRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMID   69 (620)
T ss_pred             HCCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCC
Confidence            3457899999999999999887752                    4667889999999999999999999999653100 


Q ss_pred             -------------------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhh
Q 047219          353 -------------------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       353 -------------------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~  404 (567)
                                               ..++..+++...      ...+.++.+.+.+.   ..++..|++|||+|.|... 
T Consensus        70 ~~~~~~~~~~~Cg~C~sC~~~~~g~~~n~~~~d~~s~------~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~~-  142 (620)
T PRK14954         70 DPVYLQEVTEPCGECESCRDFDAGTSLNISEFDAASN------NSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLSTA-  142 (620)
T ss_pred             ccccccccCCCCccCHHHHHHhccCCCCeEEeccccc------CCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCHH-
Confidence                                     012222222100      01234444444442   2344679999999999633 


Q ss_pred             hhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHH
Q 047219          405 DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKA  480 (567)
Q Consensus       405 q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~  480 (567)
                                ..+.|++.++.  .+..+++|.+|+....+.+.+.+|+ ..++|..++.++....+...+..    +..+
T Consensus       143 ----------a~naLLK~LEe--Pp~~tv~IL~t~~~~kLl~TI~SRc-~~vef~~l~~~ei~~~L~~i~~~egi~I~~e  209 (620)
T PRK14954        143 ----------AFNAFLKTLEE--PPPHAIFIFATTELHKIPATIASRC-QRFNFKRIPLDEIQSQLQMICRAEGIQIDAD  209 (620)
T ss_pred             ----------HHHHHHHHHhC--CCCCeEEEEEeCChhhhhHHHHhhc-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence                      34677777774  4456777777777888999999999 89999999999888888776653    5677


Q ss_pred             HHHHHHHhccC
Q 047219          481 ELAELATATEE  491 (567)
Q Consensus       481 ~l~~la~~t~g  491 (567)
                      .++.++..+.|
T Consensus       210 al~~La~~s~G  220 (620)
T PRK14954        210 ALQLIARKAQG  220 (620)
T ss_pred             HHHHHHHHhCC
Confidence            78888877765

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=1.5e-12  Score=146.67  Aligned_cols=189  Identities=22%  Similarity=0.317  Sum_probs=129.4

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--  351 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--  351 (567)
                      ..+.+|++|+|++.+++.|+..+..                    ...++.+||+||+|+|||++|+++++.+.+...  
T Consensus        10 yRP~~~~eiiGq~~~~~~L~~~i~~--------------------~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~   69 (585)
T PRK14950         10 WRSQTFAELVGQEHVVQTLRNAIAE--------------------GRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDP   69 (585)
T ss_pred             hCCCCHHHhcCCHHHHHHHHHHHHh--------------------CCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCC
Confidence            3457899999999999999887752                    345677899999999999999999999854211  


Q ss_pred             CCcC-----------------eEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHH
Q 047219          352 QGVP-----------------LMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEA  411 (567)
Q Consensus       352 ~~~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~  411 (567)
                      ...+                 ++.++...    .  ...+.++.+.+.+.   ..+...|+||||+|.|...        
T Consensus        70 ~~~~c~~c~~c~~i~~~~~~d~~~i~~~~----~--~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~~~--------  135 (585)
T PRK14950         70 KGRPCGTCEMCRAIAEGSAVDVIEMDAAS----H--TSVDDAREIIERVQFRPALARYKVYIIDEVHMLSTA--------  135 (585)
T ss_pred             CCCCCccCHHHHHHhcCCCCeEEEEeccc----c--CCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCCHH--------
Confidence            0111                 22222210    0  11223344433332   2234679999999998632        


Q ss_pred             HHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHH
Q 047219          412 TRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELAT  487 (567)
Q Consensus       412 ~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~  487 (567)
                         .++.|++.++.  .+..++||.+++..+.+.+.+++|| ..++|..++..+....+...+..    +..+.+..++.
T Consensus       136 ---a~naLLk~LEe--pp~~tv~Il~t~~~~kll~tI~SR~-~~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~  209 (585)
T PRK14950        136 ---AFNALLKTLEE--PPPHAIFILATTEVHKVPATILSRC-QRFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIAR  209 (585)
T ss_pred             ---HHHHHHHHHhc--CCCCeEEEEEeCChhhhhHHHHhcc-ceeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence               34567777774  3456788888887888889999999 78999999999988888877654    45667777777


Q ss_pred             hccCCCHHHHHHHHHH
Q 047219          488 ATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       488 ~t~g~s~~dL~~L~~~  503 (567)
                      .+.| +.+++.+.++.
T Consensus       210 ~s~G-dlr~al~~Lek  224 (585)
T PRK14950        210 AATG-SMRDAENLLQQ  224 (585)
T ss_pred             HcCC-CHHHHHHHHHH
Confidence            7655 55555444443

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.48  E-value=1.8e-12  Score=134.53  Aligned_cols=180  Identities=20%  Similarity=0.256  Sum_probs=120.2

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++++++.++..+.                     .....+++|+||||||||++++++++++....+ .
T Consensus        11 yrP~~~~~~~g~~~~~~~l~~~i~---------------------~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~-~   68 (319)
T PRK00440         11 YRPRTLDEIVGQEEIVERLKSYVK---------------------EKNMPHLLFAGPPGTGKTTAALALARELYGEDW-R   68 (319)
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHh---------------------CCCCCeEEEECCCCCCHHHHHHHHHHHHcCCcc-c
Confidence            344789999999999999988774                     222346899999999999999999999854322 2


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcC-CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~-a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      .+++.+++......  ......+.......... .+..+|+|||+|.+....           ...|+..++..  ...+
T Consensus        69 ~~~i~~~~~~~~~~--~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~~~-----------~~~L~~~le~~--~~~~  133 (319)
T PRK00440         69 ENFLELNASDERGI--DVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDA-----------QQALRRTMEMY--SQNT  133 (319)
T ss_pred             cceEEeccccccch--HHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCHHH-----------HHHHHHHHhcC--CCCC
Confidence            34555544321110  00011111111111011 234699999999986432           23445555543  3356


Q ss_pred             EEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccC
Q 047219          433 VVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEE  491 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g  491 (567)
                      .+|.++|....+.+.+.+|+ ..++|+.++.++...++..++..    +..+.++.++..+.|
T Consensus       134 ~lIl~~~~~~~l~~~l~sr~-~~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~g  195 (319)
T PRK00440        134 RFILSCNYSSKIIDPIQSRC-AVFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYVSEG  195 (319)
T ss_pred             eEEEEeCCccccchhHHHHh-heeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            67778888888889999999 67999999999999999988764    556778888777654

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=99.46  E-value=1.2e-12  Score=143.54  Aligned_cols=171  Identities=24%  Similarity=0.335  Sum_probs=122.1

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      +|=.|++++|+++.|.|.--               ...+.-.++-++|+||||+|||++++.||..+++      .|+.+
T Consensus       411 eDHYgm~dVKeRILEfiAV~---------------kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnR------kFfRf  469 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVG---------------KLRGSVQGKILCFVGPPGVGKTSIAKSIARALNR------KFFRF  469 (906)
T ss_pred             ccccchHHHHHHHHHHHHHH---------------hhcccCCCcEEEEeCCCCCCcccHHHHHHHHhCC------ceEEE
Confidence            56689999999999987421               1223556778999999999999999999999955      46655


Q ss_pred             chh------hHHh---hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHH-----HHHHH-hhc
Q 047219          360 PLE------VVMS---KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRIL-----SVLLR-QID  424 (567)
Q Consensus       360 ~~~------~l~s---~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl-----~~LL~-~ld  424 (567)
                      +..      ++.+   .|+|....++-+.++......  .+++|||||++...-|+.-..++-+++     ..|+. .++
T Consensus       470 SvGG~tDvAeIkGHRRTYVGAMPGkiIq~LK~v~t~N--PliLiDEvDKlG~g~qGDPasALLElLDPEQNanFlDHYLd  547 (906)
T KOG2004|consen  470 SVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKVKTEN--PLILIDEVDKLGSGHQGDPASALLELLDPEQNANFLDHYLD  547 (906)
T ss_pred             eccccccHHhhcccceeeeccCChHHHHHHHhhCCCC--ceEEeehhhhhCCCCCCChHHHHHHhcChhhccchhhhccc
Confidence            532      2222   366776666666667666554  499999999998555543222221111     11221 111


Q ss_pred             CcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHH
Q 047219          425 GFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       425 ~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~  474 (567)
                      ---.-..|++|||.|..+.+++.|+.|+ .+|++.-+..++...|.+.|+
T Consensus       548 Vp~DLSkVLFicTAN~idtIP~pLlDRM-EvIelsGYv~eEKv~IA~~yL  596 (906)
T KOG2004|consen  548 VPVDLSKVLFICTANVIDTIPPPLLDRM-EVIELSGYVAEEKVKIAERYL  596 (906)
T ss_pred             cccchhheEEEEeccccccCChhhhhhh-heeeccCccHHHHHHHHHHhh
Confidence            1112358999999999999999999999 899999999999999998876

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.45  E-value=4.2e-12  Score=132.42  Aligned_cols=181  Identities=15%  Similarity=0.198  Sum_probs=128.7

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--CCcC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--QGVP  355 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--~~~~  355 (567)
                      +|++|+|++.+++.+...+..                    ...++.+||+||+|+|||++|+++++.+.+...  ....
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~--------------------~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D   61 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIK--------------------NRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVD   61 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHc--------------------CCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCC
Confidence            689999999999999887742                    466788999999999999999999998754311  1123


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +..+...  .+...  .-+.++.+.+.+..   .+...|++||++|.|...           ..+.|++.++.  ++.++
T Consensus        62 ~~~~~~~--~~~~i--~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~~~-----------a~naLLK~LEe--pp~~t  124 (313)
T PRK05564         62 IIEFKPI--NKKSI--GVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMTEQ-----------AQNAFLKTIEE--PPKGV  124 (313)
T ss_pred             eEEeccc--cCCCC--CHHHHHHHHHHHhcCcccCCceEEEEechhhcCHH-----------HHHHHHHHhcC--CCCCe
Confidence            3333321  11111  12335555443332   234579999999998633           44678888884  56778


Q ss_pred             EEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHH
Q 047219          433 VVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRD  496 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~d  496 (567)
                      ++|.+|+.++.+.+.+++|| ..++|..|+.++....+.........+.++.++..+.|-.+..
T Consensus       125 ~~il~~~~~~~ll~TI~SRc-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~l~~~~~g~~~~a  187 (313)
T PRK05564        125 FIILLCENLEQILDTIKSRC-QIYKLNRLSKEEIEKFISYKYNDIKEEEKKSAIAFSDGIPGKV  187 (313)
T ss_pred             EEEEEeCChHhCcHHHHhhc-eeeeCCCcCHHHHHHHHHHHhcCCCHHHHHHHHHHcCCCHHHH
Confidence            88888888899999999999 8999999999998888776655566677777777766644333

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.45  E-value=1.4e-13  Score=144.08  Aligned_cols=178  Identities=24%  Similarity=0.358  Sum_probs=109.2

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      ..+.|++|+|++++++.+.-.+.                     .....++||+|+||||||++|+++++.++... ..+
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~---------------------~~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~   61 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAI---------------------DPGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEG   61 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHh---------------------ccCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcc
Confidence            45789999999999988765332                     12236899999999999999999999985310 001


Q ss_pred             c--------------------------CeEEechhhHHhhhhchh--HHHH--H-HHHH-HHhcCCCCcEEEEcCcchhh
Q 047219          354 V--------------------------PLMYVPLEVVMSKYYGES--ERLL--G-KVFS-LANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       354 ~--------------------------~~~~i~~~~l~s~~~G~~--~~~l--~-~~f~-~A~~~a~~~ILfIDEID~L~  401 (567)
                      .                          ++..++...-...++|..  +..+  + ..|. .....+.+++||||||+.+.
T Consensus        62 ~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~  141 (334)
T PRK13407         62 CPVNSARPEDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLE  141 (334)
T ss_pred             cccccCcccCCcccccccCCcccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCC
Confidence            1                          111122111111233310  0000  0 0111 01122446899999999998


Q ss_pred             hhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-CCChHHHhccceEEEecCCCH-HHHHHHHHHH
Q 047219          402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-DLDPALISRFDSMITFGLPDH-ENRQEIAAQY  473 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-~Ld~aL~sRf~~~I~i~~P~~-~eR~eIL~~~  473 (567)
                      ++.|..+.+.+++-...+.........+.++++|+++|+.+ .++++|++||...+.++.|.. ++|.+++...
T Consensus       142 ~~~q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLldRF~~~v~v~~~~~~~e~~~il~~~  215 (334)
T PRK13407        142 DHIVDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLDRFGLSVEVRSPRDVETRVEVIRRR  215 (334)
T ss_pred             HHHHHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHh
Confidence            77555544443221000001111123456899999999744 699999999998999988866 9999999874

>PHA02244 ATPase-like protein

Probab=99.44  E-value=8.6e-13  Score=138.17  Aligned_cols=140  Identities=21%  Similarity=0.279  Sum_probs=90.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhH--HHH-HHHHHHHhcCCCCcEEEEc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE--RLL-GKVFSLANELPNGAIIFLD  395 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~--~~l-~~~f~~A~~~a~~~ILfID  395 (567)
                      .....+|||+||||||||++|+++|+.+      +.+|+.++...-.....|...  ... ..-|..+.  ..+++|+||
T Consensus       116 l~~~~PVLL~GppGtGKTtLA~aLA~~l------g~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~--~~GgvLiLD  187 (383)
T PHA02244        116 VNANIPVFLKGGAGSGKNHIAEQIAEAL------DLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAF--KKGGLFFID  187 (383)
T ss_pred             HhcCCCEEEECCCCCCHHHHHHHHHHHh------CCCEEEEecChHHHhhcccccccccccchHHHHHh--hcCCEEEEe
Confidence            3456789999999999999999999998      667887774321122222110  011 01122222  247899999


Q ss_pred             CcchhhhhhhhhhHHHHHHHHHHHHHhhc-CcccCCcEEEEEeeCCC-----------CCCChHHHhccceEEEecCCCH
Q 047219          396 EVDSFAVARDSEMHEATRRILSVLLRQID-GFEQDKKVVVIAATNRK-----------QDLDPALISRFDSMITFGLPDH  463 (567)
Q Consensus       396 EID~L~~~~q~~l~~~~~~vl~~LL~~ld-~~~~~~~viVIaaTN~~-----------~~Ld~aL~sRf~~~I~i~~P~~  463 (567)
                      ||+.+.+..+..++.....   .++...+ ....+.++++|+|+|+.           ..+++++++|| ..++++.|+ 
T Consensus       188 EId~a~p~vq~~L~~lLd~---r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllDRF-v~I~~dyp~-  262 (383)
T PHA02244        188 EIDASIPEALIIINSAIAN---KFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRF-APIEFDYDE-  262 (383)
T ss_pred             CcCcCCHHHHHHHHHHhcc---CeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHHhhc-EEeeCCCCc-
Confidence            9999987755554444322   1111122 22345789999999973           46899999999 789999998 


Q ss_pred             HHHHHHHH
Q 047219          464 ENRQEIAA  471 (567)
Q Consensus       464 ~eR~eIL~  471 (567)
                      +....|+.
T Consensus       263 ~~E~~i~~  270 (383)
T PHA02244        263 KIEHLISN  270 (383)
T ss_pred             HHHHHHhh
Confidence            43344443

>PRK06620 hypothetical protein; Validated

Probab=99.43  E-value=4.1e-12  Score=125.48  Aligned_cols=140  Identities=16%  Similarity=0.299  Sum_probs=93.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                      .+++||||||||||+|++++++...      .  ..++.....           ...+    ..  ..+|+|||||.+. 
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~~------~--~~~~~~~~~-----------~~~~----~~--~d~lliDdi~~~~-   98 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLSN------A--YIIKDIFFN-----------EEIL----EK--YNAFIIEDIENWQ-   98 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhccC------C--EEcchhhhc-----------hhHH----hc--CCEEEEeccccch-
Confidence            6799999999999999999998762      2  222211110           0111    11  3699999999551 


Q ss_pred             hhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC--CChHHHhccce--EEEecCCCHHHHHHHHHHHHHh--
Q 047219          403 ARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD--LDPALISRFDS--MITFGLPDHENRQEIAAQYAKH--  476 (567)
Q Consensus       403 ~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~--Ld~aL~sRf~~--~I~i~~P~~~eR~eIL~~~~~~--  476 (567)
                         +          ..|...++.+...+..++|+++..+..  + ++|++||..  ++.++.|+.+++..+++..+..  
T Consensus        99 ---~----------~~lf~l~N~~~e~g~~ilits~~~p~~l~l-~~L~SRl~~gl~~~l~~pd~~~~~~~l~k~~~~~~  164 (214)
T PRK06620         99 ---E----------PALLHIFNIINEKQKYLLLTSSDKSRNFTL-PDLSSRIKSVLSILLNSPDDELIKILIFKHFSISS  164 (214)
T ss_pred             ---H----------HHHHHHHHHHHhcCCEEEEEcCCCccccch-HHHHHHHhCCceEeeCCCCHHHHHHHHHHHHHHcC
Confidence               1          123333333344566788888765554  6 899999942  7999999999999999988763  


Q ss_pred             --hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          477 --LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       477 --~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                        ++++.++.++....+ +.+.+..+++.
T Consensus       165 l~l~~ev~~~L~~~~~~-d~r~l~~~l~~  192 (214)
T PRK06620        165 VTISRQIIDFLLVNLPR-EYSKIIEILEN  192 (214)
T ss_pred             CCCCHHHHHHHHHHccC-CHHHHHHHHHH
Confidence              567788888887654 44455444444

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.43  E-value=7.3e-12  Score=141.14  Aligned_cols=186  Identities=19%  Similarity=0.301  Sum_probs=131.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC---
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW---  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~---  351 (567)
                      .+.+|++|+|++.+++.|...+..                    ...++.+|||||+|+|||++|+++|+.+.+...   
T Consensus        12 RP~~f~~viGq~~~~~~L~~~i~~--------------------~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~   71 (614)
T PRK14971         12 RPSTFESVVGQEALTTTLKNAIAT--------------------NKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTAD   71 (614)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc--------------------CCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCC
Confidence            447899999999999999888752                    456778999999999999999999999853210   


Q ss_pred             ----------------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHH
Q 047219          352 ----------------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEAT  412 (567)
Q Consensus       352 ----------------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~  412 (567)
                                      ...++..+++...      .....++.+.+.+..   .+...|++|||+|.|...         
T Consensus        72 ~~~Cg~C~sC~~~~~~~~~n~~~ld~~~~------~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls~~---------  136 (614)
T PRK14971         72 GEACNECESCVAFNEQRSYNIHELDAASN------NSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLSQA---------  136 (614)
T ss_pred             CCCCCcchHHHHHhcCCCCceEEeccccc------CCHHHHHHHHHHHhhCcccCCcEEEEEECcccCCHH---------
Confidence                            0123333333210      112345555554432   234579999999999633         


Q ss_pred             HHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh
Q 047219          413 RRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATA  488 (567)
Q Consensus       413 ~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~  488 (567)
                        ..+.|+..++.  .+..+++|++|+....+.+.|++|| ..++|..++.++....+...+..    +..+.+..++..
T Consensus       137 --a~naLLK~LEe--pp~~tifIL~tt~~~kIl~tI~SRc-~iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~  211 (614)
T PRK14971        137 --AFNAFLKTLEE--PPSYAIFILATTEKHKILPTILSRC-QIFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQK  211 (614)
T ss_pred             --HHHHHHHHHhC--CCCCeEEEEEeCCchhchHHHHhhh-heeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence              34677787774  4567888888887889999999999 88999999999988888876654    345567777777


Q ss_pred             ccCCCHHHHHHHH
Q 047219          489 TEEMSGRDIRDVC  501 (567)
Q Consensus       489 t~g~s~~dL~~L~  501 (567)
                      +.| +.+++..++
T Consensus       212 s~g-dlr~al~~L  223 (614)
T PRK14971        212 ADG-GMRDALSIF  223 (614)
T ss_pred             cCC-CHHHHHHHH
Confidence            654 444444433

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.41  E-value=9.8e-12  Score=131.35  Aligned_cols=194  Identities=16%  Similarity=0.160  Sum_probs=128.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC---
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP---  350 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~---  350 (567)
                      ..+..+++|+|++++++.+...+..                    .+.+..+||+||+|+|||++|+.+++.+.+..   
T Consensus        17 ~~P~~~~~l~Gh~~a~~~L~~a~~~--------------------grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~   76 (351)
T PRK09112         17 PSPSENTRLFGHEEAEAFLAQAYRE--------------------GKLHHALLFEGPEGIGKATLAFHLANHILSHPDPA   76 (351)
T ss_pred             CCCCchhhccCcHHHHHHHHHHHHc--------------------CCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccc
Confidence            3456899999999999999987752                    56678899999999999999999999986521   


Q ss_pred             CC----CcCeEEe-chhhHHhh----h--h-------------chhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhh
Q 047219          351 WQ----GVPLMYV-PLEVVMSK----Y--Y-------------GESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVA  403 (567)
Q Consensus       351 ~~----~~~~~~i-~~~~l~s~----~--~-------------G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~  403 (567)
                      ..    ..+|... .|..+...    +  +             .-.-+.++.+.+...   ......|++|||+|.|...
T Consensus        77 ~~~~~~~~~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~~~  156 (351)
T PRK09112         77 EAPETLADPDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMNRN  156 (351)
T ss_pred             cCccccCCCCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcCHH
Confidence            00    0111000 01111000    0  0             001122333322222   2334579999999999643


Q ss_pred             hhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--hCHHH
Q 047219          404 RDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--LTKAE  481 (567)
Q Consensus       404 ~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--~~~~~  481 (567)
                                 ..+.|++.++.  .+.++++|..|+.++.+.+.+++|| ..+.|+.|+.++..+++......  +....
T Consensus       157 -----------aanaLLk~LEE--pp~~~~fiLit~~~~~llptIrSRc-~~i~l~pl~~~~~~~~L~~~~~~~~~~~~~  222 (351)
T PRK09112        157 -----------AANAILKTLEE--PPARALFILISHSSGRLLPTIRSRC-QPISLKPLDDDELKKALSHLGSSQGSDGEI  222 (351)
T ss_pred             -----------HHHHHHHHHhc--CCCCceEEEEECChhhccHHHHhhc-cEEEecCCCHHHHHHHHHHhhcccCCCHHH
Confidence                       34667787774  4567777777888899999999999 89999999999999999875432  33566


Q ss_pred             HHHHHHhccCCCHHHHHHHHH
Q 047219          482 LAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       482 l~~la~~t~g~s~~dL~~L~~  502 (567)
                      +..++..+.|- ++....++.
T Consensus       223 ~~~i~~~s~G~-pr~Al~ll~  242 (351)
T PRK09112        223 TEALLQRSKGS-VRKALLLLN  242 (351)
T ss_pred             HHHHHHHcCCC-HHHHHHHHh
Confidence            77777776664 444344443

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.41  E-value=6.1e-12  Score=133.60  Aligned_cols=192  Identities=17%  Similarity=0.141  Sum_probs=128.0

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC-
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG-  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~-  353 (567)
                      .+.++++|+|++.+++.+.+.+..                    .+.+..+||+||+|+||+++|.++|+.+.+....+ 
T Consensus        14 ~P~~~~~iiGq~~~~~~L~~~~~~--------------------~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~   73 (365)
T PRK07471         14 HPRETTALFGHAAAEAALLDAYRS--------------------GRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGG   73 (365)
T ss_pred             CCCchhhccChHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCC
Confidence            456889999999999999987752                    46788899999999999999999999985432100 


Q ss_pred             c---------------------------CeEEechh--hHHhhhhc-hhHHHHHHHHHHHhc---CCCCcEEEEcCcchh
Q 047219          354 V---------------------------PLMYVPLE--VVMSKYYG-ESERLLGKVFSLANE---LPNGAIIFLDEVDSF  400 (567)
Q Consensus       354 ~---------------------------~~~~i~~~--~l~s~~~G-~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L  400 (567)
                      .                           .+..+...  +-..+... -.-+.++.+.+.+..   ...+.|++|||+|.|
T Consensus        74 ~~~~~~~~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m  153 (365)
T PRK07471         74 DGAVPPPTSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEM  153 (365)
T ss_pred             CccccccccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhc
Confidence            0                           11111110  00000000 012334444443332   233579999999998


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHH
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKA  480 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~  480 (567)
                      ...           ..+.|++.++.  .+.++++|.+|+.++.+.+.+++|| ..+.|..|+.++-.+.+..........
T Consensus       154 ~~~-----------aanaLLK~LEe--pp~~~~~IL~t~~~~~llpti~SRc-~~i~l~~l~~~~i~~~L~~~~~~~~~~  219 (365)
T PRK07471        154 NAN-----------AANALLKVLEE--PPARSLFLLVSHAPARLLPTIRSRC-RKLRLRPLAPEDVIDALAAAGPDLPDD  219 (365)
T ss_pred             CHH-----------HHHHHHHHHhc--CCCCeEEEEEECCchhchHHhhccc-eEEECCCCCHHHHHHHHHHhcccCCHH
Confidence            633           44677777773  4567888889999999999999999 899999999999998888765434444


Q ss_pred             HHHHHHHhccCCCHHHHHHHH
Q 047219          481 ELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       481 ~l~~la~~t~g~s~~dL~~L~  501 (567)
                      .+..++..+.| ++.....++
T Consensus       220 ~~~~l~~~s~G-sp~~Al~ll  239 (365)
T PRK07471        220 PRAALAALAEG-SVGRALRLA  239 (365)
T ss_pred             HHHHHHHHcCC-CHHHHHHHh
Confidence            44556666555 344333333

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.40  E-value=7.8e-13  Score=137.02  Aligned_cols=147  Identities=21%  Similarity=0.248  Sum_probs=100.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh--hhchhHHH----------HHHHHHHHhcCCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK--YYGESERL----------LGKVFSLANELPN  388 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~--~~G~~~~~----------l~~~f~~A~~~a~  388 (567)
                      ..+++||.||||||||++++.+|+.+      +.+++.++++...+.  ++|...-.          ....+..|..  .
T Consensus        63 ~~~~ilL~G~pGtGKTtla~~lA~~l------~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~--~  134 (327)
T TIGR01650        63 YDRRVMVQGYHGTGKSTHIEQIAARL------NWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQ--H  134 (327)
T ss_pred             cCCcEEEEeCCCChHHHHHHHHHHHH------CCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHh--C
Confidence            35789999999999999999999999      778888887665543  55542110          0112333333  2


Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHH-HHHHHHHhhcCcccCCcEEEEEeeCCCC------------CCChHHHhccceE
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRR-ILSVLLRQIDGFEQDKKVVVIAATNRKQ------------DLDPALISRFDSM  455 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~-vl~~LL~~ld~~~~~~~viVIaaTN~~~------------~Ld~aL~sRf~~~  455 (567)
                      +++|++||||...++.+..+...++. -.-.+......+....+++||||+|+.+            .++++++.||..+
T Consensus       135 g~illlDEin~a~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lDRF~i~  214 (327)
T TIGR01650       135 NVALCFDEYDAGRPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMDRWSIV  214 (327)
T ss_pred             CeEEEechhhccCHHHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHhheeeE
Confidence            57899999999877755544333321 0000011112223456899999999854            4799999999667


Q ss_pred             EEecCCCHHHHHHHHHHHHH
Q 047219          456 ITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       456 I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +.++.|+.++..+|+.....
T Consensus       215 ~~~~Yp~~e~E~~Il~~~~~  234 (327)
T TIGR01650       215 TTLNYLEHDNEAAIVLAKAK  234 (327)
T ss_pred             eeCCCCCHHHHHHHHHhhcc
Confidence            78999999999999987653

This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.40  E-value=9.3e-12  Score=120.08  Aligned_cols=152  Identities=17%  Similarity=0.231  Sum_probs=103.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcCe-----------------EEechhhHHhhhhchhHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVPL-----------------MYVPLEVVMSKYYGESERLLGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~~-----------------~~i~~~~l~s~~~G~~~~~l~~~f  380 (567)
                      ...+..+||+||+|+|||++|+.+++.+... ...+.+|                 ..+....   ...  ..+.++.+.
T Consensus        11 ~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~---~~~--~~~~i~~i~   85 (188)
T TIGR00678        11 GRLAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEG---QSI--KVDQVRELV   85 (188)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEecccc---CcC--CHHHHHHHH
Confidence            4567889999999999999999999998542 1111111                 1111110   001  123444455


Q ss_pred             HHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEE
Q 047219          381 SLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMIT  457 (567)
Q Consensus       381 ~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~  457 (567)
                      +.+..   .+...+++|||+|.|...           ..+.|+..++.  .+..+.+|.+||.+..+.+++++|+ ..++
T Consensus        86 ~~~~~~~~~~~~kviiide~~~l~~~-----------~~~~Ll~~le~--~~~~~~~il~~~~~~~l~~~i~sr~-~~~~  151 (188)
T TIGR00678        86 EFLSRTPQESGRRVVIIEDAERMNEA-----------AANALLKTLEE--PPPNTLFILITPSPEKLLPTIRSRC-QVLP  151 (188)
T ss_pred             HHHccCcccCCeEEEEEechhhhCHH-----------HHHHHHHHhcC--CCCCeEEEEEECChHhChHHHHhhc-EEee
Confidence            54443   234579999999998643           33567777775  4456777777877789999999999 7999


Q ss_pred             ecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccC
Q 047219          458 FGLPDHENRQEIAAQYAKHLTKAELAELATATEE  491 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g  491 (567)
                      |..|+.++..+++...  .+..+.+..++..+.|
T Consensus       152 ~~~~~~~~~~~~l~~~--gi~~~~~~~i~~~~~g  183 (188)
T TIGR00678       152 FPPLSEEALLQWLIRQ--GISEEAAELLLALAGG  183 (188)
T ss_pred             CCCCCHHHHHHHHHHc--CCCHHHHHHHHHHcCC
Confidence            9999999998888776  3555566666655544

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.39  E-value=1.4e-11  Score=129.46  Aligned_cols=170  Identities=18%  Similarity=0.242  Sum_probs=117.6

Q ss_pred             CcccccC-cHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCCcC
Q 047219          278 SWENIAG-YDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQGVP  355 (567)
Q Consensus       278 ~~~dIiG-~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~~~  355 (567)
                      .|+.|.| ++.+++.++..+..                    .+.++.+||+||+|+||+++|+++++.+.... ..+.+
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~~--------------------~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~   62 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIAK--------------------NRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEP   62 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHHc--------------------CCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCC
Confidence            4888888 88899988887742                    56788899999999999999999999985431 11111


Q ss_pred             -----------------eEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHHHHH
Q 047219          356 -----------------LMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEATRRI  415 (567)
Q Consensus       356 -----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~~~v  415 (567)
                                       +..+..+   ++..  .-+.++.+.+.+.   ..+...|++|||+|.|...           .
T Consensus        63 cg~C~~c~~~~~~~hpD~~~i~~~---~~~i--~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~~~-----------a  126 (329)
T PRK08058         63 CGTCTNCKRIDSGNHPDVHLVAPD---GQSI--KKDQIRYLKEEFSKSGVESNKKVYIIEHADKMTAS-----------A  126 (329)
T ss_pred             CCcCHHHHHHhcCCCCCEEEeccc---cccC--CHHHHHHHHHHHhhCCcccCceEEEeehHhhhCHH-----------H
Confidence                             2222111   0000  1234455544433   2334579999999998633           4


Q ss_pred             HHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHh
Q 047219          416 LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATA  488 (567)
Q Consensus       416 l~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~  488 (567)
                      .+.|++.++.  ++.++++|.+|+.+..+.+.++||| ..++|..|+.++..+.+...  .+.......++..
T Consensus       127 ~NaLLK~LEE--Pp~~~~~Il~t~~~~~ll~TIrSRc-~~i~~~~~~~~~~~~~L~~~--gi~~~~~~~l~~~  194 (329)
T PRK08058        127 ANSLLKFLEE--PSGGTTAILLTENKHQILPTILSRC-QVVEFRPLPPESLIQRLQEE--GISESLATLLAGL  194 (329)
T ss_pred             HHHHHHHhcC--CCCCceEEEEeCChHhCcHHHHhhc-eeeeCCCCCHHHHHHHHHHc--CCChHHHHHHHHH
Confidence            5778888884  6778888889988899999999999 99999999999887777642  3444433334433

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.38  E-value=2.6e-12  Score=134.84  Aligned_cols=175  Identities=23%  Similarity=0.358  Sum_probs=107.4

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC------CC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM------PW  351 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~------~~  351 (567)
                      .|..|+|+++.|..+.-.+.                     .+...+++|.|+||+|||+++++++..+...      ++
T Consensus         2 pf~~ivgq~~~~~al~~~~~---------------------~~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~   60 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVI---------------------DPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPF   60 (337)
T ss_pred             CccccccHHHHHHHHHHHhc---------------------CCCCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCC
Confidence            47889999999988755442                     2335689999999999999999999887421      11


Q ss_pred             C---C-------------------------cCeEEechhhHHhhhhchhH--HHHH---HHHH-HHhcCCCCcEEEEcCc
Q 047219          352 Q---G-------------------------VPLMYVPLEVVMSKYYGESE--RLLG---KVFS-LANELPNGAIIFLDEV  397 (567)
Q Consensus       352 ~---~-------------------------~~~~~i~~~~l~s~~~G~~~--~~l~---~~f~-~A~~~a~~~ILfIDEI  397 (567)
                      .   .                         .++..++.......++|...  ..+.   ..|. .....+.+++||||||
T Consensus        61 ~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi  140 (337)
T TIGR02030        61 NSSPSDPEMMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEV  140 (337)
T ss_pred             CCCCCCccccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecCh
Confidence            0   0                         01111111111112333211  0000   0001 0112244699999999


Q ss_pred             chhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-CCChHHHhccceEEEecCCCH-HHHHHHHHHH
Q 047219          398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-DLDPALISRFDSMITFGLPDH-ENRQEIAAQY  473 (567)
Q Consensus       398 D~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-~Ld~aL~sRf~~~I~i~~P~~-~eR~eIL~~~  473 (567)
                      +.|.++.|..+.+++++-...+.........+.++++|+++|..+ .|+++|++||...+.++.|.. ++|.+|++..
T Consensus       141 ~~L~~~~Q~~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~eg~l~~~LldRf~l~i~l~~p~~~eer~eIL~~~  218 (337)
T TIGR02030       141 NLLEDHLVDVLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEEGELRPQLLDRFGLHAEIRTVRDVELRVEIVERR  218 (337)
T ss_pred             HhCCHHHHHHHHHHHHhCCeEEEECCEEEEcCCCEEEEeccccccCCCCHHHHhhcceEEECCCCCCHHHHHHHHHhh
Confidence            999877666555544321000111111122346789999999755 799999999998999998865 8889998873

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=99.38  E-value=5.5e-13  Score=122.41  Aligned_cols=130  Identities=22%  Similarity=0.411  Sum_probs=87.2

Q ss_pred             cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          283 AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       283 iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      +|.+..++++++.+...                   .....+|||+|++||||+++|++||......   ..+++.+++.
T Consensus         1 vG~S~~~~~l~~~l~~~-------------------a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~---~~~~~~~~~~   58 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERL-------------------AKSSSPVLITGEPGTGKSLLARALHRYSGRA---NGPFIVIDCA   58 (138)
T ss_dssp             --SCHHHHHHHHHHHHH-------------------HCSSS-EEEECCTTSSHHHHHHCCHHTTTTC---CS-CCCCCHH
T ss_pred             CCCCHHHHHHHHHHHHH-------------------hCCCCcEEEEcCCCCCHHHHHHHHHhhcCcc---CCCeEEechh
Confidence            58889999999988765                   5677899999999999999999999988643   3345555555


Q ss_pred             hHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC--
Q 047219          363 VVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR--  440 (567)
Q Consensus       363 ~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~--  440 (567)
                      .+.           .++++.+    .+++|||+|||.|....|..+           +..+... ...++++|+++..  
T Consensus        59 ~~~-----------~~~l~~a----~~gtL~l~~i~~L~~~~Q~~L-----------~~~l~~~-~~~~~RlI~ss~~~l  111 (138)
T PF14532_consen   59 SLP-----------AELLEQA----KGGTLYLKNIDRLSPEAQRRL-----------LDLLKRQ-ERSNVRLIASSSQDL  111 (138)
T ss_dssp             CTC-----------HHHHHHC----TTSEEEEECGCCS-HHHHHHH-----------HHHHHHC-TTTTSEEEEEECC-C
T ss_pred             hCc-----------HHHHHHc----CCCEEEECChHHCCHHHHHHH-----------HHHHHhc-CCCCeEEEEEeCCCH
Confidence            433           2244443    379999999999986644333           2222222 2456788888864  


Q ss_pred             -----CCCCChHHHhccceEEEecCCC
Q 047219          441 -----KQDLDPALISRFDSMITFGLPD  462 (567)
Q Consensus       441 -----~~~Ld~aL~sRf~~~I~i~~P~  462 (567)
                           .+.++++|++|| ..+.+.+|+
T Consensus       112 ~~l~~~~~~~~~L~~~l-~~~~i~lPp  137 (138)
T PF14532_consen  112 EELVEEGRFSPDLYYRL-SQLEIHLPP  137 (138)
T ss_dssp             CCHHHHSTHHHHHHHHC-STCEEEE--
T ss_pred             HHHhhccchhHHHHHHh-CCCEEeCCC
Confidence                 235889999999 445566565

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.38  E-value=2e-12  Score=146.76  Aligned_cols=175  Identities=26%  Similarity=0.359  Sum_probs=112.0

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC------C-
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM------P-  350 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~------~-  350 (567)
                      .|.+|+|++.++..+.-.+.                     .....+|||+|++|||||++|++|++.+...      + 
T Consensus         2 pf~~ivGq~~~~~al~~~av---------------------~~~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~   60 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAV---------------------DPRIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPF   60 (633)
T ss_pred             CcchhcChHHHHHHHHHHhh---------------------CCCCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcC
Confidence            47899999999977754443                     2223579999999999999999999998410      0 


Q ss_pred             ----------------------CCCcCeEEechhhHHhhhhchh--HHHHH---HHH-HHHhcCCCCcEEEEcCcchhhh
Q 047219          351 ----------------------WQGVPLMYVPLEVVMSKYYGES--ERLLG---KVF-SLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       351 ----------------------~~~~~~~~i~~~~l~s~~~G~~--~~~l~---~~f-~~A~~~a~~~ILfIDEID~L~~  402 (567)
                                            ....+|+.++++.....++|..  +..+.   ..+ ......+.++|||||||+.|..
T Consensus        61 ~c~p~~~~~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~~  140 (633)
T TIGR02442        61 SCDPDDPEEWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLDD  140 (633)
T ss_pred             CCCCCCccccChhhhhcccccccCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCCH
Confidence                                  0135677777766666666642  11110   000 0111234568999999999987


Q ss_pred             hhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCC-CCCChHHHhccceEEEecCC-CHHHHHHHHHHH
Q 047219          403 ARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK-QDLDPALISRFDSMITFGLP-DHENRQEIAAQY  473 (567)
Q Consensus       403 ~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~-~~Ld~aL~sRf~~~I~i~~P-~~~eR~eIL~~~  473 (567)
                      ..|..+...+++-...+.........+.++++|+|+|+. +.|+++|++||+..+.+..+ +.+++.+++...
T Consensus       141 ~~q~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~dR~~l~i~v~~~~~~~~~~~il~~~  213 (633)
T TIGR02442       141 HLVDVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLDRFGLCVDVAAPRDPEERVEIIRRR  213 (633)
T ss_pred             HHHHHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHhhcceEEEccCCCchHHHHHHHHHH
Confidence            755554443322100011111112334679999999974 47999999999888888766 467777887653

A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.

>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=99.38  E-value=1.3e-11  Score=111.04  Aligned_cols=125  Identities=36%  Similarity=0.543  Sum_probs=80.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHH---HHHHHHHHhcCCCCcEEEEcC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERL---LGKVFSLANELPNGAIIFLDE  396 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~---l~~~f~~A~~~a~~~ILfIDE  396 (567)
                      ....+++|+||||||||++++.+++.+...   +.+++++++..............   ....+... ....+++|+|||
T Consensus        17 ~~~~~v~i~G~~G~GKT~l~~~i~~~~~~~---~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~lilDe   92 (151)
T cd00009          17 PPPKNLLLYGPPGTGKTTLARAIANELFRP---GAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA-EKAKPGVLFIDE   92 (151)
T ss_pred             CCCCeEEEECCCCCCHHHHHHHHHHHhhcC---CCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhh-ccCCCeEEEEeC
Confidence            356789999999999999999999998532   45677887776555432221111   01111122 223468999999


Q ss_pred             cchhhhhhhhhhHHHHHHHHHHHHHhhcCcc----cCCcEEEEEeeCCCC--CCChHHHhccceEEEec
Q 047219          397 VDSFAVARDSEMHEATRRILSVLLRQIDGFE----QDKKVVVIAATNRKQ--DLDPALISRFDSMITFG  459 (567)
Q Consensus       397 ID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~----~~~~viVIaaTN~~~--~Ld~aL~sRf~~~I~i~  459 (567)
                      ++.+.....           ..++..+....    ...++.+|+++|...  .+++.+.+||+..+.++
T Consensus        93 ~~~~~~~~~-----------~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~r~~~~i~~~  150 (151)
T cd00009          93 IDSLSRGAQ-----------NALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIP  150 (151)
T ss_pred             hhhhhHHHH-----------HHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHhhhccEeecC
Confidence            998833211           22222222221    246789999998877  78899999997666654

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.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.37  E-value=3.3e-11  Score=117.90  Aligned_cols=194  Identities=25%  Similarity=0.336  Sum_probs=139.5

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      +..+.+.+.+|+|.+.+++.+.+.-+.+                 ....+.++|||||..|||||++++|+.+++...  
T Consensus        52 ~~~~~i~L~~l~Gvd~qk~~L~~NT~~F-----------------~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~--  112 (287)
T COG2607          52 PDPDPIDLADLVGVDRQKEALVRNTEQF-----------------AEGLPANNVLLWGARGTGKSSLVKALLNEYADE--  112 (287)
T ss_pred             CCCCCcCHHHHhCchHHHHHHHHHHHHH-----------------HcCCcccceEEecCCCCChHHHHHHHHHHHHhc--
Confidence            4556789999999999999887755443                 236778999999999999999999999999765  


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc--ccC
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF--EQD  429 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~--~~~  429 (567)
                       +..++.|+-+++..         +..+++..+......|||+|++-.=.   .+       .....|...+++-  ..+
T Consensus       113 -glrLVEV~k~dl~~---------Lp~l~~~Lr~~~~kFIlFcDDLSFe~---gd-------~~yK~LKs~LeG~ve~rP  172 (287)
T COG2607         113 -GLRLVEVDKEDLAT---------LPDLVELLRARPEKFILFCDDLSFEE---GD-------DAYKALKSALEGGVEGRP  172 (287)
T ss_pred             -CCeEEEEcHHHHhh---------HHHHHHHHhcCCceEEEEecCCCCCC---Cc-------hHHHHHHHHhcCCcccCC
Confidence             56689998887754         45567777776667999999984311   11       1122333444443  357


Q ss_pred             CcEEEEEeeCCCCCCC--------------h--------HHHhccceEEEecCCCHHHHHHHHHHHHHhhC----HH---
Q 047219          430 KKVVVIAATNRKQDLD--------------P--------ALISRFDSMITFGLPDHENRQEIAAQYAKHLT----KA---  480 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld--------------~--------aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~----~~---  480 (567)
                      .+|+|.+|+|+-..++              +        .|-.||+..+.|.+++.++...|+..+++++.    .+   
T Consensus       173 ~NVl~YATSNRRHLl~e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~~e~l~  252 (287)
T COG2607         173 ANVLFYATSNRRHLLPEDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDISDEELH  252 (287)
T ss_pred             CeEEEEEecCCcccccHhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCCHHHHH
Confidence            7999999999833222              1        23349999999999999999999999998753    22   


Q ss_pred             -HHHHHHHhccCCCHHHHHHHHHHH
Q 047219          481 -ELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       481 -~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                       ...+.+..-.|-||+--.+.+++.
T Consensus       253 ~eAl~WAt~rg~RSGR~A~QF~~~~  277 (287)
T COG2607         253 AEALQWATTRGGRSGRVAWQFIRDL  277 (287)
T ss_pred             HHHHHHHHhcCCCccHhHHHHHHHH
Confidence             233445555567777666665543

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.36  E-value=4.9e-11  Score=124.32  Aligned_cols=189  Identities=15%  Similarity=0.210  Sum_probs=126.7

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-------
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-------  350 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-------  350 (567)
                      .|++|+|++.+++.+.+.+..                    .+.+..+||+||+|+||+++|.++++.+.+..       
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~--------------------~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~   61 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQ--------------------NRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIR   61 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHh--------------------CCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHh
Confidence            589999999999999998853                    46688999999999999999999999985431       


Q ss_pred             -----CCCcCeEEechhhHH-hh--------hhc-------h-hHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhh
Q 047219          351 -----WQGVPLMYVPLEVVM-SK--------YYG-------E-SERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARD  405 (567)
Q Consensus       351 -----~~~~~~~~i~~~~l~-s~--------~~G-------~-~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q  405 (567)
                           ...-.+..+...... ++        ..|       . .-+.++.+.+.+..   .+...|++||++|.|...  
T Consensus        62 ~~~~~~~hPDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~~~--  139 (314)
T PRK07399         62 RRLEEGNHPDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMNEA--  139 (314)
T ss_pred             cccccCCCCCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcCHH--
Confidence                 011112222221000 00        001       0 01234455444332   345689999999999633  


Q ss_pred             hhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhC-HHHHHH
Q 047219          406 SEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLT-KAELAE  484 (567)
Q Consensus       406 ~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~-~~~l~~  484 (567)
                               ..+.||+.++.  .+ ++++|..|+.++.+-+.++||| ..++|..++.++..+.+......-. ......
T Consensus       140 ---------aaNaLLK~LEE--Pp-~~~fILi~~~~~~Ll~TI~SRc-q~i~f~~l~~~~~~~~L~~~~~~~~~~~~~~~  206 (314)
T PRK07399        140 ---------AANALLKTLEE--PG-NGTLILIAPSPESLLPTIVSRC-QIIPFYRLSDEQLEQVLKRLGDEEILNINFPE  206 (314)
T ss_pred             ---------HHHHHHHHHhC--CC-CCeEEEEECChHhCcHHHHhhc-eEEecCCCCHHHHHHHHHHhhccccchhHHHH
Confidence                     44778888874  33 6678888888999999999999 8999999999999988887643211 122456


Q ss_pred             HHHhccCCCHHHHHHHHH
Q 047219          485 LATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       485 la~~t~g~s~~dL~~L~~  502 (567)
                      ++....| +++....+++
T Consensus       207 l~~~a~G-s~~~al~~l~  223 (314)
T PRK07399        207 LLALAQG-SPGAAIANIE  223 (314)
T ss_pred             HHHHcCC-CHHHHHHHHH
Confidence            6666555 4444444444

>smart00350 MCM minichromosome maintenance proteins

Probab=99.33  E-value=1.5e-12  Score=144.21  Aligned_cols=181  Identities=19%  Similarity=0.224  Sum_probs=105.4

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC---cCeE
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG---VPLM  357 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~---~~~~  357 (567)
                      +|.|++.+|..+.-++..--. +..        ..........+|||+|+||||||++|+++|+.+.+..|..   ..+.
T Consensus       204 ~i~G~~~~k~~l~l~l~gg~~-~~~--------~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~  274 (509)
T smart00350      204 SIYGHEDIKKAILLLLFGGVH-KNL--------PDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAV  274 (509)
T ss_pred             cccCcHHHHHHHHHHHhCCCc-ccc--------CCCccccccceEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcC
Confidence            588999987766544321100 000        0000123445899999999999999999999886542221   1111


Q ss_pred             EechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEe
Q 047219          358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAA  437 (567)
Q Consensus       358 ~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaa  437 (567)
                      .+....+.....|+..     +-..+...+.+++++|||++.|....|..+++++++..-.+.+.......+.++.||||
T Consensus       275 ~l~~~~~~~~~~g~~~-----~~~G~l~~A~~Gil~iDEi~~l~~~~q~~L~e~me~~~i~i~k~G~~~~l~~~~~viAa  349 (509)
T smart00350      275 GLTAAVTRDPETREFT-----LEGGALVLADNGVCCIDEFDKMDDSDRTAIHEAMEQQTISIAKAGITTTLNARCSVLAA  349 (509)
T ss_pred             CccccceEccCcceEE-----ecCccEEecCCCEEEEechhhCCHHHHHHHHHHHhcCEEEEEeCCEEEEecCCcEEEEE
Confidence            1111111111111100     00011233457999999999998776665555442200000011111123568999999


Q ss_pred             eCCCC-------------CCChHHHhccceEEEe-cCCCHHHHHHHHHHHHH
Q 047219          438 TNRKQ-------------DLDPALISRFDSMITF-GLPDHENRQEIAAQYAK  475 (567)
Q Consensus       438 TN~~~-------------~Ld~aL~sRf~~~I~i-~~P~~~eR~eIL~~~~~  475 (567)
                      +|+.+             .|++++++|||..+.+ +.|+.+...+|.+..+.
T Consensus       350 ~NP~~g~y~~~~~~~~n~~l~~~lLsRFdLi~~~~d~~~~~~d~~i~~~i~~  401 (509)
T smart00350      350 ANPIGGRYDPKLTPEENIDLPAPILSRFDLLFVVLDEVDEERDRELAKHVVD  401 (509)
T ss_pred             eCCCCcccCCCcChhhccCCChHHhCceeeEEEecCCCChHHHHHHHHHHHH
Confidence            99842             5999999999886655 78999999999887653

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=99.32  E-value=9.1e-11  Score=124.59  Aligned_cols=174  Identities=24%  Similarity=0.368  Sum_probs=123.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +.+.-+.+.+.+++++++...+...+.                 ...|.+++++|+||||||.+++.+.+++....- ..
T Consensus        12 ~~~iP~~l~~Re~ei~~l~~~l~~~~~-----------------~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~-~~   73 (366)
T COG1474          12 EDYIPEELPHREEEINQLASFLAPALR-----------------GERPSNIIIYGPTGTGKTATVKFVMEELEESSA-NV   73 (366)
T ss_pred             CCCCcccccccHHHHHHHHHHHHHHhc-----------------CCCCccEEEECCCCCCHhHHHHHHHHHHHhhhc-cC
Confidence            334445699999999999987654322                 456667999999999999999999999854310 22


Q ss_pred             CeEEechhhHHhhh------h---------ch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHH
Q 047219          355 PLMYVPLEVVMSKY------Y---------GE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSV  418 (567)
Q Consensus       355 ~~~~i~~~~l~s~~------~---------G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~  418 (567)
                      .+++++|....+.+      +         |. ....+..+++.........|++|||+|.|..+.+        +++..
T Consensus        74 ~~~yINc~~~~t~~~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~--------~~LY~  145 (366)
T COG1474          74 EVVYINCLELRTPYQVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDG--------EVLYS  145 (366)
T ss_pred             ceEEEeeeeCCCHHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccc--------hHHHH
Confidence            26777775433221      1         11 2223334444444444468999999999976643        45667


Q ss_pred             HHHhhcCcccCCcEEEEEeeCCC---CCCChHHHhcc-ceEEEecCCCHHHHHHHHHHHHHh
Q 047219          419 LLRQIDGFEQDKKVVVIAATNRK---QDLDPALISRF-DSMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       419 LL~~ld~~~~~~~viVIaaTN~~---~~Ld~aL~sRf-~~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      |++..+..  ..++.+|+.+|..   +.+++.+.++| ...|.|++++.+|..+|+...++.
T Consensus       146 L~r~~~~~--~~~v~vi~i~n~~~~~~~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~  205 (366)
T COG1474         146 LLRAPGEN--KVKVSIIAVSNDDKFLDYLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEE  205 (366)
T ss_pred             HHhhcccc--ceeEEEEEEeccHHHHHHhhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHh
Confidence            77766644  5678999999874   46899999987 347899999999999999998874

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=99.31  E-value=1e-11  Score=130.63  Aligned_cols=179  Identities=22%  Similarity=0.329  Sum_probs=121.9

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCc
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGV  354 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~  354 (567)
                      .+.|.-++|++..+..|.-...                     ...-.++||.|+.|||||+++|+|+..++.. ...++
T Consensus        13 ~~pf~aivGqd~lk~aL~l~av---------------------~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc   71 (423)
T COG1239          13 NLPFTAIVGQDPLKLALGLNAV---------------------DPQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGC   71 (423)
T ss_pred             ccchhhhcCchHHHHHHhhhhc---------------------ccccceeEEecCCCccHHHHHHHHHHhCCccceecCC
Confidence            4678889999998877653322                     3345789999999999999999999998643 11122


Q ss_pred             C---------------------------------eEEechhhHHhhhhch--hHHHHH---HHHH-HHhcCCCCcEEEEc
Q 047219          355 P---------------------------------LMYVPLEVVMSKYYGE--SERLLG---KVFS-LANELPNGAIIFLD  395 (567)
Q Consensus       355 ~---------------------------------~~~i~~~~l~s~~~G~--~~~~l~---~~f~-~A~~~a~~~ILfID  395 (567)
                      +                                 ++.++.......++|.  .++.+.   ..|+ .....++.+||++|
T Consensus        72 ~f~cdP~~P~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvD  151 (423)
T COG1239          72 PFNCDPDDPEEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVD  151 (423)
T ss_pred             CCCCCCCChhhhhHHHHhhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEe
Confidence            1                                 1111111111112222  111111   0111 01123457999999


Q ss_pred             CcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CCCCChHHHhccceEEEecCC-CHHHHHHHHHHH
Q 047219          396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQDLDPALISRFDSMITFGLP-DHENRQEIAAQY  473 (567)
Q Consensus       396 EID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~~Ld~aL~sRf~~~I~i~~P-~~~eR~eIL~~~  473 (567)
                      |+..|....++.++.+...-.+........+..+.++++|+|+|+ .+.|.+.|+.||...+.+..| +.++|.+|++..
T Consensus       152 EvnlL~d~lvd~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEeGeLrpqLlDRfg~~v~~~~~~~~~~rv~Ii~r~  231 (423)
T COG1239         152 EVNLLDDHLVDALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEEGELRPQLLDRFGLEVDTHYPLDLEERVEIIRRR  231 (423)
T ss_pred             ccccccHHHHHHHHHHHHhCCceeeeCceeeccCccEEEEeecCccccccchhhHhhhcceeeccCCCCHHHHHHHHHHH
Confidence            999999888877777766655555555555667889999999998 457999999999999999766 789999999986


Q ss_pred             HH
Q 047219          474 AK  475 (567)
Q Consensus       474 ~~  475 (567)
                      ..
T Consensus       232 ~~  233 (423)
T COG1239         232 LA  233 (423)
T ss_pred             HH
Confidence            65

>PRK09087 hypothetical protein; Validated

Probab=99.29  E-value=5.5e-11  Score=118.45  Aligned_cols=142  Identities=17%  Similarity=0.265  Sum_probs=96.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      ...++|+||+|+|||||++++++..        .+.+++...+...+           +....    ..+|+|||++.+.
T Consensus        44 ~~~l~l~G~~GsGKThLl~~~~~~~--------~~~~i~~~~~~~~~-----------~~~~~----~~~l~iDDi~~~~  100 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLASIWREKS--------DALLIHPNEIGSDA-----------ANAAA----EGPVLIEDIDAGG  100 (226)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhc--------CCEEecHHHcchHH-----------HHhhh----cCeEEEECCCCCC
Confidence            3459999999999999999999875        23466654333221           11111    2589999999874


Q ss_pred             hhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh
Q 047219          402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFD--SMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      .. +           ..|+..++.....+..+||+++..+..   ..++|++||.  ..++++.|+.++|.++++.+++.
T Consensus       101 ~~-~-----------~~lf~l~n~~~~~g~~ilits~~~p~~~~~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~~~~  168 (226)
T PRK09087        101 FD-E-----------TGLFHLINSVRQAGTSLLMTSRLWPSSWNVKLPDLKSRLKAATVVEIGEPDDALLSQVIFKLFAD  168 (226)
T ss_pred             CC-H-----------HHHHHHHHHHHhCCCeEEEECCCChHHhccccccHHHHHhCCceeecCCCCHHHHHHHHHHHHHH
Confidence            22 1           123344443334456677776655443   3689999995  58999999999999999998875


Q ss_pred             ----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          477 ----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       477 ----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                          ++++.++.++....    ++++.+..
T Consensus       169 ~~~~l~~ev~~~La~~~~----r~~~~l~~  194 (226)
T PRK09087        169 RQLYVDPHVVYYLVSRME----RSLFAAQT  194 (226)
T ss_pred             cCCCCCHHHHHHHHHHhh----hhHHHHHH
Confidence                56777888887765    34444443

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.29  E-value=3.2e-11  Score=125.32  Aligned_cols=157  Identities=20%  Similarity=0.264  Sum_probs=109.3

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--------
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--------  351 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--------  351 (567)
                      +++.|.+.....+...+...                   .+.+..+||+||||||||++|.++|+.+.....        
T Consensus         1 ~~~~~~~~~~~~l~~~~~~~-------------------~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~   61 (325)
T COG0470           1 DELVPWQEAVKRLLVQALES-------------------GRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGH   61 (325)
T ss_pred             CCcccchhHHHHHHHHHHhc-------------------CCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccc
Confidence            35778888888777766532                   345557999999999999999999999964321        


Q ss_pred             ----------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHH
Q 047219          352 ----------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSV  418 (567)
Q Consensus       352 ----------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~  418 (567)
                                ...++..++.++....-  .....++.+-+.....   .+..|++|||+|.|...           ..+.
T Consensus        62 ~~~~~~~~~~~~~d~lel~~s~~~~~~--i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~~-----------A~na  128 (325)
T COG0470          62 CRSCKLIPAGNHPDFLELNPSDLRKID--IIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTED-----------AANA  128 (325)
T ss_pred             hhhhhHHhhcCCCceEEecccccCCCc--chHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhHH-----------HHHH
Confidence                      12356666665543321  1223444444433332   34689999999999753           4467


Q ss_pred             HHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHH
Q 047219          419 LLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAA  471 (567)
Q Consensus       419 LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~  471 (567)
                      +++.++  ..+.+.++|.+||.+..+-+.+++|| ..+.|..|+........+
T Consensus       129 llk~lE--ep~~~~~~il~~n~~~~il~tI~SRc-~~i~f~~~~~~~~i~~~e  178 (325)
T COG0470         129 LLKTLE--EPPKNTRFILITNDPSKILPTIRSRC-QRIRFKPPSRLEAIAWLE  178 (325)
T ss_pred             HHHHhc--cCCCCeEEEEEcCChhhccchhhhcc-eeeecCCchHHHHHHHhh
Confidence            777777  46788999999999999999999999 889998765554444333

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=99.29  E-value=5.9e-13  Score=129.29  Aligned_cols=147  Identities=23%  Similarity=0.378  Sum_probs=68.9

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-------
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-------  350 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-------  350 (567)
                      .|++|+|++.+|+.+.-.+.                       ...++||+||||||||++|+.++..++.-.       
T Consensus         1 Df~dI~GQe~aKrAL~iAAa-----------------------G~h~lLl~GppGtGKTmlA~~l~~lLP~l~~~e~le~   57 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAA-----------------------GGHHLLLIGPPGTGKTMLARRLPSLLPPLTEEEALEV   57 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHH-----------------------CC--EEEES-CCCTHHHHHHHHHHCS--CCEECCESS
T ss_pred             ChhhhcCcHHHHHHHHHHHc-----------------------CCCCeEEECCCCCCHHHHHHHHHHhCCCCchHHHhhh
Confidence            37899999999998876542                       257999999999999999999998875210       


Q ss_pred             ---------------CCCcCeEEechhhHHhhhhchhHH-HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          351 ---------------WQGVPLMYVPLEVVMSKYYGESER-LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       351 ---------------~~~~~~~~i~~~~l~s~~~G~~~~-~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                                     ....+|.....+.-...++|.... .-+.     ...+.++||||||+..+...           
T Consensus        58 ~~i~s~~~~~~~~~~~~~~Pfr~phhs~s~~~liGgg~~~~PGe-----islAh~GVLflDE~~ef~~~-----------  121 (206)
T PF01078_consen   58 SKIYSVAGLGPDEGLIRQRPFRAPHHSASEAALIGGGRPPRPGE-----ISLAHRGVLFLDELNEFDRS-----------  121 (206)
T ss_dssp             --S-TT---S---EEEE---EEEE-TT--HHHHHEEGGGEEE-C-----GGGGTTSEEEECETTTS-HH-----------
T ss_pred             ccccccccCCCCCceecCCCcccCCCCcCHHHHhCCCcCCCcCH-----HHHhcCCEEEechhhhcCHH-----------
Confidence                           001122222222112222222110 0011     13445799999999988533           


Q ss_pred             HHHHHHHhhcC-----------cccCCcEEEEEeeCC-----------------------CCCCChHHHhccceEEEecC
Q 047219          415 ILSVLLRQIDG-----------FEQDKKVVVIAATNR-----------------------KQDLDPALISRFDSMITFGL  460 (567)
Q Consensus       415 vl~~LL~~ld~-----------~~~~~~viVIaaTN~-----------------------~~~Ld~aL~sRf~~~I~i~~  460 (567)
                      +++.|+.-++.           ...+.++.+|+|+|+                       ...+...|+.|||..+.++.
T Consensus       122 vld~Lr~ple~g~v~i~R~~~~~~~Pa~f~lv~a~NPcpCG~~~~~~~~C~Cs~~~~~~Y~~rlsgpllDRiDi~v~~~~  201 (206)
T PF01078_consen  122 VLDALRQPLEDGEVTISRAGGSVTYPARFLLVAAMNPCPCGYYGDPDNRCRCSPRQIRRYQSRLSGPLLDRIDIHVEVPR  201 (206)
T ss_dssp             HHHHHHHHHHHSBEEEEETTEEEEEB--EEEEEEE-S-------------------------------------------
T ss_pred             HHHHHHHHHHCCeEEEEECCceEEEecccEEEEEeccccccccccccccccccccccccccccccccccccccccccccc
Confidence            44444444432           234678999999997                       22456667778877666655


Q ss_pred             CCH
Q 047219          461 PDH  463 (567)
Q Consensus       461 P~~  463 (567)
                      .+.
T Consensus       202 ~~~  204 (206)
T PF01078_consen  202 VSY  204 (206)
T ss_dssp             ---
T ss_pred             ccc
Confidence            443

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.28  E-value=3.1e-11  Score=117.47  Aligned_cols=189  Identities=16%  Similarity=0.227  Sum_probs=120.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+..+.||+|.++.+..+.-+..                     ...-.+++|.|||||||||-+.++|+++-...+ .
T Consensus        21 YrP~~l~dIVGNe~tv~rl~via~---------------------~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~-k   78 (333)
T KOG0991|consen   21 YRPSVLQDIVGNEDTVERLSVIAK---------------------EGNMPNLIISGPPGTGKTTSILCLARELLGDSY-K   78 (333)
T ss_pred             hCchHHHHhhCCHHHHHHHHHHHH---------------------cCCCCceEeeCCCCCchhhHHHHHHHHHhChhh-h
Confidence            344678999999999998876554                     345568999999999999999999999843211 1


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      -.+..+++++-.+-  ......+ +.|.+-+-.   ..+.|++|||.|+|....|..+           .+.|+-  ...
T Consensus        79 e~vLELNASdeRGI--DvVRn~I-K~FAQ~kv~lp~grhKIiILDEADSMT~gAQQAl-----------RRtMEi--yS~  142 (333)
T KOG0991|consen   79 EAVLELNASDERGI--DVVRNKI-KMFAQKKVTLPPGRHKIIILDEADSMTAGAQQAL-----------RRTMEI--YSN  142 (333)
T ss_pred             hHhhhccCcccccc--HHHHHHH-HHHHHhhccCCCCceeEEEeeccchhhhHHHHHH-----------HHHHHH--Hcc
Confidence            12444555433221  0111222 234333322   2347999999999975544333           233332  235


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ..+++.+||..+.+-+.+.+|| ..+.+...+..+...-+....+.    +..+.++.+.-...|    |+++.++...
T Consensus       143 ttRFalaCN~s~KIiEPIQSRC-AiLRysklsd~qiL~Rl~~v~k~Ekv~yt~dgLeaiifta~G----DMRQalNnLQ  216 (333)
T KOG0991|consen  143 TTRFALACNQSEKIIEPIQSRC-AILRYSKLSDQQILKRLLEVAKAEKVNYTDDGLEAIIFTAQG----DMRQALNNLQ  216 (333)
T ss_pred             cchhhhhhcchhhhhhhHHhhh-HhhhhcccCHHHHHHHHHHHHHHhCCCCCcchHHHhhhhccc----hHHHHHHHHH
Confidence            6788899999999999999999 77888777766655544444432    455556655554444    6666655543

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=1.1e-10  Score=122.27  Aligned_cols=158  Identities=19%  Similarity=0.249  Sum_probs=108.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCCcC-----------------eEEechhhHHhhhhchhHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQGVP-----------------LMYVPLEVVMSKYYGESERLLGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f  380 (567)
                      .+.++.+||+||+|+|||++|+++|+.+.+.. ....+                 +..+....- ++.  -.-+.++.+.
T Consensus        19 ~r~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~-~~~--i~id~iR~l~   95 (328)
T PRK05707         19 GRHPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEA-DKT--IKVDQVRELV   95 (328)
T ss_pred             CCcceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCC-CCC--CCHHHHHHHH
Confidence            46688899999999999999999999986531 11112                 222221100 000  1224555555


Q ss_pred             HHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEE
Q 047219          381 SLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMIT  457 (567)
Q Consensus       381 ~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~  457 (567)
                      +.+..   .+...|++||++|.|...           ..+.||+.++.  ++.++++|.+|+.++.+.|.++||| ..+.
T Consensus        96 ~~~~~~~~~~~~kv~iI~~a~~m~~~-----------aaNaLLK~LEE--Pp~~~~fiL~t~~~~~ll~TI~SRc-~~~~  161 (328)
T PRK05707         96 SFVVQTAQLGGRKVVLIEPAEAMNRN-----------AANALLKSLEE--PSGDTVLLLISHQPSRLLPTIKSRC-QQQA  161 (328)
T ss_pred             HHHhhccccCCCeEEEECChhhCCHH-----------HHHHHHHHHhC--CCCCeEEEEEECChhhCcHHHHhhc-eeee
Confidence            54442   234579999999999733           55788888884  5678999999999999999999999 7899


Q ss_pred             ecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCC
Q 047219          458 FGLPDHENRQEIAAQYAKHLTKAELAELATATEEMS  493 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s  493 (567)
                      |..|+.++-.+.+.........+....++....|-.
T Consensus       162 ~~~~~~~~~~~~L~~~~~~~~~~~~~~~l~la~Gsp  197 (328)
T PRK05707        162 CPLPSNEESLQWLQQALPESDERERIELLTLAGGSP  197 (328)
T ss_pred             CCCcCHHHHHHHHHHhcccCChHHHHHHHHHcCCCH
Confidence            999999988887776543344445555555555533

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.26  E-value=6.1e-11  Score=134.15  Aligned_cols=171  Identities=22%  Similarity=0.271  Sum_probs=131.6

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -.++-++|.++.++++.+.+.+                     +..++-+|.|+||+|||.++..+|...-..    .+.
T Consensus       167 gklDPvIGRd~EI~r~iqIL~R---------------------R~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~  225 (786)
T COG0542         167 GKLDPVIGRDEEIRRTIQILSR---------------------RTKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLK  225 (786)
T ss_pred             CCCCCCcChHHHHHHHHHHHhc---------------------cCCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHc
Confidence            3577899999999999887752                     345566788999999999999999987543    234


Q ss_pred             CcCeEEechhhHHh--hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~s--~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +..++.++...+..  +|.|+.+.++..+.++..... +.||||||||.+.+.-..... . -+..+-|...+    .++
T Consensus       226 ~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~-~vILFIDEiHtiVGAG~~~G~-a-~DAaNiLKPaL----ARG  298 (786)
T COG0542         226 DKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSK-NVILFIDEIHTIVGAGATEGG-A-MDAANLLKPAL----ARG  298 (786)
T ss_pred             CCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcCC-CeEEEEechhhhcCCCccccc-c-cchhhhhHHHH----hcC
Confidence            66788888877764  789999999999999999877 699999999999776443211 1 11223333333    357


Q ss_pred             cEEEEEeeCC-----CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh
Q 047219          431 KVVVIAATNR-----KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       431 ~viVIaaTN~-----~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      .+.+|++|..     .-.-|++|-+|| ..+.+..|+.++-..||+-+...
T Consensus       299 eL~~IGATT~~EYRk~iEKD~AL~RRF-Q~V~V~EPs~e~ti~ILrGlk~~  348 (786)
T COG0542         299 ELRCIGATTLDEYRKYIEKDAALERRF-QKVLVDEPSVEDTIAILRGLKER  348 (786)
T ss_pred             CeEEEEeccHHHHHHHhhhchHHHhcC-ceeeCCCCCHHHHHHHHHHHHHH
Confidence            8899999964     224689999999 88999999999999999977653

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=99.26  E-value=5.9e-11  Score=112.21  Aligned_cols=141  Identities=20%  Similarity=0.277  Sum_probs=93.2

Q ss_pred             CcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-----------
Q 047219          284 GYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-----------  352 (567)
Q Consensus       284 G~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-----------  352 (567)
                      |++++++.|.+.+..                    .+.|..+||+||+|+||+++|+++++.+......           
T Consensus         1 gq~~~~~~L~~~~~~--------------------~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~   60 (162)
T PF13177_consen    1 GQEEIIELLKNLIKS--------------------GRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCR   60 (162)
T ss_dssp             S-HHHHHHHHHHHHC--------------------TC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHH
T ss_pred             CcHHHHHHHHHHHHc--------------------CCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHH
Confidence            778888888877642                    5678889999999999999999999998654211           


Q ss_pred             ------CcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhh
Q 047219          353 ------GVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQI  423 (567)
Q Consensus       353 ------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~l  423 (567)
                            ..++..+.......   .-..+.++.+.+.+..   .++..|++|||+|.|...           ..+.||+.|
T Consensus        61 ~~~~~~~~d~~~~~~~~~~~---~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l~~~-----------a~NaLLK~L  126 (162)
T PF13177_consen   61 RIEEGNHPDFIIIKPDKKKK---SIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKLTEE-----------AQNALLKTL  126 (162)
T ss_dssp             HHHTT-CTTEEEEETTTSSS---SBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS-HH-----------HHHHHHHHH
T ss_pred             HHHhccCcceEEEecccccc---hhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhhhHH-----------HHHHHHHHh
Confidence                  22333333222100   0122445555554432   234579999999999733           557888888


Q ss_pred             cCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCC
Q 047219          424 DGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       424 d~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                      +  +.+.++++|.+|+.++.+.+.++||| ..+.|...
T Consensus       127 E--epp~~~~fiL~t~~~~~il~TI~SRc-~~i~~~~l  161 (162)
T PF13177_consen  127 E--EPPENTYFILITNNPSKILPTIRSRC-QVIRFRPL  161 (162)
T ss_dssp             H--STTTTEEEEEEES-GGGS-HHHHTTS-EEEEE---
T ss_pred             c--CCCCCEEEEEEECChHHChHHHHhhc-eEEecCCC
Confidence            8  46789999999999999999999999 78887654

...

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.26  E-value=1.5e-10  Score=124.38  Aligned_cols=148  Identities=20%  Similarity=0.312  Sum_probs=94.0

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcCeE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVPLM  357 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~~~  357 (567)
                      ++++.+.++..+.+...+.                       ..++++|+||||||||++|+.+|+.+... .+..+.++
T Consensus       174 l~d~~i~e~~le~l~~~L~-----------------------~~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~V  230 (459)
T PRK11331        174 LNDLFIPETTIETILKRLT-----------------------IKKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMV  230 (459)
T ss_pred             hhcccCCHHHHHHHHHHHh-----------------------cCCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEE
Confidence            5677777777766655442                       35789999999999999999999988532 22223344


Q ss_pred             EechhhHHhhhh--------ch--hHHHHHHHHHHHhcCC-CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhh---
Q 047219          358 YVPLEVVMSKYY--------GE--SERLLGKVFSLANELP-NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQI---  423 (567)
Q Consensus       358 ~i~~~~l~s~~~--------G~--~~~~l~~~f~~A~~~a-~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~l---  423 (567)
                      .+..+--...++        |.  ....+..+...|.... .+.+||||||+.-....          ++.+++..+   
T Consensus       231 tFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~k----------iFGel~~lLE~~  300 (459)
T PRK11331        231 QFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSK----------VFGEVMMLMEHD  300 (459)
T ss_pred             eecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHHH----------hhhhhhhhcccc
Confidence            443222111221        11  1122334455565432 46899999999865432          112222222   


Q ss_pred             -----------------cCcccCCcEEEEEeeCCCC----CCChHHHhccceEEEecC
Q 047219          424 -----------------DGFEQDKKVVVIAATNRKQ----DLDPALISRFDSMITFGL  460 (567)
Q Consensus       424 -----------------d~~~~~~~viVIaaTN~~~----~Ld~aL~sRf~~~I~i~~  460 (567)
                                       +.+..+.++.||||+|..+    .+|.+|+||| ..+++.+
T Consensus       301 ~rg~~~~v~l~y~e~d~e~f~iP~Nl~IIgTMNt~Drs~~~lD~AlrRRF-~fi~i~p  357 (459)
T PRK11331        301 KRGENWSVPLTYSENDEERFYVPENVYIIGLMNTADRSLAVVDYALRRRF-SFIDIEP  357 (459)
T ss_pred             ccccccceeeeccccccccccCCCCeEEEEecCccccchhhccHHHHhhh-heEEecC
Confidence                             2345678999999999877    6999999999 7788865

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.25  E-value=3.6e-10  Score=116.10  Aligned_cols=90  Identities=29%  Similarity=0.404  Sum_probs=67.2

Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC------------CCCCChHHHhccceEE
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR------------KQDLDPALISRFDSMI  456 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~------------~~~Ld~aL~sRf~~~I  456 (567)
                      ++||||||+|.|.-.           .+..|-+.|+.   .---++|+|||+            |.-++.+|+.|+ .+|
T Consensus       292 pGVLFIDEvHmLDIE-----------~FsFlnrAlEs---e~aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLDRl-lII  356 (450)
T COG1224         292 PGVLFIDEVHMLDIE-----------CFSFLNRALES---ELAPIIILATNRGMTKIRGTDIESPHGIPLDLLDRL-LII  356 (450)
T ss_pred             cceEEEechhhhhHH-----------HHHHHHHHhhc---ccCcEEEEEcCCceeeecccCCcCCCCCCHhhhhhe-eEE
Confidence            389999999988533           23333344442   233488888987            777999999999 899


Q ss_pred             EecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCC
Q 047219          457 TFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMS  493 (567)
Q Consensus       457 ~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s  493 (567)
                      ...+++.++.++|++..++.    +.++.++.++..-..-|
T Consensus       357 ~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etS  397 (450)
T COG1224         357 STRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETS  397 (450)
T ss_pred             ecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhh
Confidence            99999999999999998874    56677787777644333

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.25  E-value=2.2e-11  Score=123.29  Aligned_cols=135  Identities=24%  Similarity=0.395  Sum_probs=89.4

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      +-++|++.+|+.|-=++-.      -|+++...-....-.-.-.++||.||+|+|||+||+.+|+.+      ++||.--
T Consensus        61 ~YVIGQe~AKKvLsVAVYN------HYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~L------nVPFaiA  128 (408)
T COG1219          61 EYVIGQEQAKKVLSVAVYN------HYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKIL------NVPFAIA  128 (408)
T ss_pred             hheecchhhhceeeeeehh------HHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHh------CCCeeec
Confidence            4589999999877544432      244443221100001234679999999999999999999999      8999988


Q ss_pred             chhhHHh-hhhchhH-HHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhh--hHHH-HHHHHHHHHHhhcCc
Q 047219          360 PLEVVMS-KYYGESE-RLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSE--MHEA-TRRILSVLLRQIDGF  426 (567)
Q Consensus       360 ~~~~l~s-~~~G~~~-~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~--l~~~-~~~vl~~LL~~ld~~  426 (567)
                      ++..+.. .|+|+.- ..+-.++..|.   +.+..+|++|||||+++.+..+.  ..++ -+.++..||+.+++.
T Consensus       129 DATtLTEAGYVGEDVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALLKiiEGT  203 (408)
T COG1219         129 DATTLTEAGYVGEDVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEGT  203 (408)
T ss_pred             cccchhhccccchhHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHHHHHHcCc
Confidence            8877754 6888753 34445554443   22346999999999998775432  1111 134556788888774

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.24  E-value=2.1e-11  Score=131.97  Aligned_cols=162  Identities=16%  Similarity=0.153  Sum_probs=94.4

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcCeEEe
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVPLMYV  359 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~~~~i  359 (567)
                      .|+|.+++++.+...+                       ....+|||+||||||||++|+++|..+... +|....+...
T Consensus        21 ~i~gre~vI~lll~aa-----------------------lag~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~ft   77 (498)
T PRK13531         21 GLYERSHAIRLCLLAA-----------------------LSGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFS   77 (498)
T ss_pred             hccCcHHHHHHHHHHH-----------------------ccCCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeec
Confidence            4788888887765543                       456799999999999999999999988542 3322222221


Q ss_pred             chhhHHhhhhchh-HHHH--HHHHHHHhc--CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEE
Q 047219          360 PLEVVMSKYYGES-ERLL--GKVFSLANE--LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVV  434 (567)
Q Consensus       360 ~~~~l~s~~~G~~-~~~l--~~~f~~A~~--~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viV  434 (567)
                      ..    +.++|.. -...  ...|.....  .....+||+|||+.+.++.|..+.+++++  .++.........+..++ 
T Consensus        78 tp----~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~rasp~~QsaLLeam~E--r~~t~g~~~~~lp~rfi-  150 (498)
T PRK13531         78 TP----EEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIWKAGPAILNTLLTAINE--RRFRNGAHEEKIPMRLL-  150 (498)
T ss_pred             Cc----HHhcCcHHHhhhhhcCchhhhcCCccccccEEeecccccCCHHHHHHHHHHHHh--CeEecCCeEEeCCCcEE-
Confidence            22    2344431 0000  111221110  00123899999999988877766665533  11111111112222333 


Q ss_pred             EEeeCCCC---CCChHHHhccceEEEecCCC-HHHHHHHHHH
Q 047219          435 IAATNRKQ---DLDPALISRFDSMITFGLPD-HENRQEIAAQ  472 (567)
Q Consensus       435 IaaTN~~~---~Ld~aL~sRf~~~I~i~~P~-~~eR~eIL~~  472 (567)
                      ++|||...   .+.+++++||-..+.+++|+ .++..+++..
T Consensus       151 v~ATN~LPE~g~~leAL~DRFliri~vp~l~~~~~e~~lL~~  192 (498)
T PRK13531        151 VTASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSMLTS  192 (498)
T ss_pred             EEECCCCcccCCchHHhHhhEEEEEECCCCCchHHHHHHHHc
Confidence            44447522   46679999997688888886 4555777764

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=99.23  E-value=2.1e-11  Score=137.13  Aligned_cols=149  Identities=19%  Similarity=0.262  Sum_probs=97.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhH--HHHH-H--HHH-HHhcCCCCcEEEEc
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE--RLLG-K--VFS-LANELPNGAIIFLD  395 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~--~~l~-~--~f~-~A~~~a~~~ILfID  395 (567)
                      -.+|||.|+||||||++|+++|+.+...    .+|+.++.+.....++|...  ..+. .  .|. .....+++++||||
T Consensus        16 ~g~vLl~G~~GtgKs~lar~l~~~~~~~----~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lD   91 (589)
T TIGR02031        16 LGGVAIRARAGTGKTALARALAEILPPI----MPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVD   91 (589)
T ss_pred             cceEEEEcCCCcHHHHHHHHHHHhCCcC----CCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEecc
Confidence            4689999999999999999999988642    24666665444445555421  0000 0  000 01122456899999


Q ss_pred             CcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC---CCChHHHhccceEEEec-CCCHHHHHHHHH
Q 047219          396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ---DLDPALISRFDSMITFG-LPDHENRQEIAA  471 (567)
Q Consensus       396 EID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~---~Ld~aL~sRf~~~I~i~-~P~~~eR~eIL~  471 (567)
                      ||+.+.+..|..+.+++++-...+.+.......+.+++||+|+|..+   .|+++|++||...+.+. +|+.++|.+|++
T Consensus        92 Ei~rl~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g~L~~~LldRf~l~v~~~~~~~~~er~eil~  171 (589)
T TIGR02031        92 MANLLDDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGGGLPDHLLDRLALHVSLEDVASQDLRVEIVR  171 (589)
T ss_pred             chhhCCHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccCCCCHHHHHhccCeeecCCCCCHHHHHHHHH
Confidence            99999877665555444321100111111223356899999999865   79999999998877774 668888999998


Q ss_pred             HHH
Q 047219          472 QYA  474 (567)
Q Consensus       472 ~~~  474 (567)
                      ...
T Consensus       172 ~~~  174 (589)
T TIGR02031       172 RER  174 (589)
T ss_pred             HHH
Confidence            765

This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.21  E-value=2.7e-11  Score=127.30  Aligned_cols=144  Identities=26%  Similarity=0.316  Sum_probs=93.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH--hhhhchhHHHHH----HHHHHHhcCCCC---cE
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM--SKYYGESERLLG----KVFSLANELPNG---AI  391 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~--s~~~G~~~~~l~----~~f~~A~~~a~~---~I  391 (567)
                      ...++||.||||||||++|+.+|..+      +.+|..+.|....  +..+|...-...    ..|.....--..   ++
T Consensus        42 ~~~~vll~G~PG~gKT~la~~lA~~l------~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~i  115 (329)
T COG0714          42 AGGHVLLEGPPGVGKTLLARALARAL------GLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVI  115 (329)
T ss_pred             cCCCEEEECCCCccHHHHHHHHHHHh------CCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceE
Confidence            46789999999999999999999999      6778888876332  233443221111    001000000001   49


Q ss_pred             EEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC-cccCCcEEEEEeeCC-----CCCCChHHHhccceEEEecCC-CHH
Q 047219          392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG-FEQDKKVVVIAATNR-----KQDLDPALISRFDSMITFGLP-DHE  464 (567)
Q Consensus       392 LfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~-~~~~~~viVIaaTN~-----~~~Ld~aL~sRf~~~I~i~~P-~~~  464 (567)
                      +++|||+...++.|..+++.+++....+  .... +..+..+++|+|+|+     ...+++++++||...+.++.| +..
T Consensus       116 ll~DEInra~p~~q~aLl~~l~e~~vtv--~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ldRf~~~~~v~yp~~~~  193 (329)
T COG0714         116 LLLDEINRAPPEVQNALLEALEERQVTV--PGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSEE  193 (329)
T ss_pred             EEEeccccCCHHHHHHHHHHHhCcEEEE--CCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHhhEEEEEecCCCCchH
Confidence            9999999998876666655554411111  1112 445678999999994     556899999999889999999 444


Q ss_pred             HHHHHHHH
Q 047219          465 NRQEIAAQ  472 (567)
Q Consensus       465 eR~eIL~~  472 (567)
                      +...++..
T Consensus       194 e~~~i~~~  201 (329)
T COG0714         194 EERIILAR  201 (329)
T ss_pred             HHHHHHHh
Confidence            44444443

>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins

Probab=99.20  E-value=9.3e-10  Score=114.68  Aligned_cols=86  Identities=24%  Similarity=0.371  Sum_probs=55.2

Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC------------CCCCChHHHhccceEE
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR------------KQDLDPALISRFDSMI  456 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~------------~~~Ld~aL~sRf~~~I  456 (567)
                      +|||||||+|.|...           -+..|-+.++.   .-.-+||.+||+            |.-++.+|+.|| ..|
T Consensus       279 pGVLFIDEvHmLDiE-----------cFsfLnralEs---~~sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRl-lII  343 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIE-----------CFSFLNRALES---ELSPIIILATNRGITKIRGTDIISPHGIPLDLLDRL-LII  343 (398)
T ss_dssp             E-EEEEESGGGSBHH-----------HHHHHHHHHTS---TT--EEEEEES-SEEE-BTTS-EEETT--HHHHTTE-EEE
T ss_pred             cceEEecchhhccHH-----------HHHHHHHHhcC---CCCcEEEEecCceeeeccCccCcCCCCCCcchHhhc-EEE
Confidence            389999999998633           33444445542   334588888986            567899999999 999


Q ss_pred             EecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          457 TFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       457 ~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                      ...+++.++..+|++..++.    +..+.++.+....
T Consensus       344 ~t~py~~~ei~~Il~iR~~~E~v~i~~~al~~L~~ig  380 (398)
T PF06068_consen  344 RTKPYSEEEIKQILKIRAKEEDVEISEDALDLLTKIG  380 (398)
T ss_dssp             EE----HHHHHHHHHHHHHHCT--B-HHHHHHHHHHH
T ss_pred             ECCCCCHHHHHHHHHhhhhhhcCcCCHHHHHHHHHHh
Confidence            99999999999999999875    4455555555443

The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.20  E-value=1.8e-12  Score=118.64  Aligned_cols=109  Identities=30%  Similarity=0.489  Sum_probs=66.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH--hhhhchhHHH-------HHHHHHHHhcCCCCcEEEE
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM--SKYYGESERL-------LGKVFSLANELPNGAIIFL  394 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~--s~~~G~~~~~-------l~~~f~~A~~~a~~~ILfI  394 (567)
                      +|||+||||||||++|+.+|+.+      +.++..+.++...  ..++|...-.       -..+.... .  .++++||
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~------~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~-~--~~~il~l   71 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL------GRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAM-R--KGGILVL   71 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH------TCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTH-H--EEEEEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh------hcceEEEEeccccccccceeeeeecccccccccccccccc-c--ceeEEEE
Confidence            58999999999999999999999      5567666665422  2333321100       00000001 1  3689999


Q ss_pred             cCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc-----------ccCC------cEEEEEeeCCCC----CCChHHHhcc
Q 047219          395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGF-----------EQDK------KVVVIAATNRKQ----DLDPALISRF  452 (567)
Q Consensus       395 DEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~-----------~~~~------~viVIaaTN~~~----~Ld~aL~sRf  452 (567)
                      |||+...+....           .|+..++..           ....      ++++|+|+|+.+    .++++|++||
T Consensus        72 DEin~a~~~v~~-----------~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~Rf  139 (139)
T PF07728_consen   72 DEINRAPPEVLE-----------SLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLDRF  139 (139)
T ss_dssp             SSCGG--HHHHH-----------TTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHTT-
T ss_pred             CCcccCCHHHHH-----------HHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHhhC
Confidence            999987644333           333333321           1112      499999999988    8999999998

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of this ATPase AAA domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. This ATPase domain includes some proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 3NBX_X 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>TIGR00368 Mg chelatase-related protein

Probab=99.19  E-value=6.6e-11  Score=130.26  Aligned_cols=191  Identities=19%  Similarity=0.244  Sum_probs=113.1

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-----
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-----  350 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-----  350 (567)
                      ...|+++.|++.+++.+.-.                       .....+++|.||||||||++|++++..+....     
T Consensus       188 ~~d~~dv~Gq~~~~~al~~a-----------------------a~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~l  244 (499)
T TIGR00368       188 DLDLKDIKGQQHAKRALEIA-----------------------AAGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAI  244 (499)
T ss_pred             CCCHHHhcCcHHHHhhhhhh-----------------------ccCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEE
Confidence            35899999999987665432                       34557899999999999999999997653210     


Q ss_pred             -----------------CCCcCeEEechhhHHhhhhchhH-HHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHH
Q 047219          351 -----------------WQGVPLMYVPLEVVMSKYYGESE-RLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEAT  412 (567)
Q Consensus       351 -----------------~~~~~~~~i~~~~l~s~~~G~~~-~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~  412 (567)
                                       +...+|....++......+|... ...+ .+    ..+.+++|||||++.|....+..+.+.+
T Consensus       245 e~~~i~s~~g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG-~i----~lA~~GvLfLDEi~e~~~~~~~~L~~~L  319 (499)
T TIGR00368       245 ETARIWSLVGKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPG-EI----SLAHNGVLFLDELPEFKRSVLDALREPI  319 (499)
T ss_pred             eccccccchhhhccccccccCCccccccccchhhhhCCccccchh-hh----hccCCCeEecCChhhCCHHHHHHHHHHH
Confidence                             01123333332222222233211 1111 12    3345799999999998755443332222


Q ss_pred             HHHHHHHHHhhcCcccCCcEEEEEeeCCC-----C------------------CCChHHHhccceEEEecCCCHHHHHHH
Q 047219          413 RRILSVLLRQIDGFEQDKKVVVIAATNRK-----Q------------------DLDPALISRFDSMITFGLPDHENRQEI  469 (567)
Q Consensus       413 ~~vl~~LL~~ld~~~~~~~viVIaaTN~~-----~------------------~Ld~aL~sRf~~~I~i~~P~~~eR~eI  469 (567)
                      +.-.-.+.+.......+.++.+|+++|+-     +                  .+...|+.|||..+.++.++.++.   
T Consensus       320 E~~~v~i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllDR~dl~~~~~~~~~~~l---  396 (499)
T TIGR00368       320 EDGSISISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLDRIDLSVEVPLLPPEKL---  396 (499)
T ss_pred             HcCcEEEEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHhhCCEEEEEcCCCHHHH---
Confidence            11000000000011234689999999962     1                  488889999999999987765421   


Q ss_pred             HHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHH
Q 047219          470 AAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKII  513 (567)
Q Consensus       470 L~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~i  513 (567)
                                      .....+-+.++++.-+..|.....+|+.
T Consensus       397 ----------------~~~~~~e~s~~ir~rV~~Ar~~q~~R~~  424 (499)
T TIGR00368       397 ----------------LSTGSGESSAEVKQRVIKAREIQNIRYE  424 (499)
T ss_pred             ----------------hccCCCCCHHHHHHHHHHHHHHHHHHhc
Confidence                            1122345677777777777766666653

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=99.18  E-value=1e-09  Score=123.84  Aligned_cols=55  Identities=24%  Similarity=0.316  Sum_probs=46.3

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      ...|...+++++|++++++.++..+..                       ..+++|+||||||||++++++++.++..
T Consensus        10 ~~~~~~~~~~viG~~~a~~~l~~a~~~-----------------------~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        10 IPVPERLIDQVIGQEEAVEIIKKAAKQ-----------------------KRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             cCcchhhHhhccCHHHHHHHHHHHHHc-----------------------CCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            355778899999999999988876641                       2489999999999999999999998654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.17  E-value=1.6e-10  Score=117.92  Aligned_cols=116  Identities=22%  Similarity=0.298  Sum_probs=76.5

Q ss_pred             cEEEEcCcchhhhhhhhhhHHHH-HHHHHHHHHhhcCccc--------CCcEEEEEee----CCCCCCChHHHhccceEE
Q 047219          390 AIIFLDEVDSFAVARDSEMHEAT-RRILSVLLRQIDGFEQ--------DKKVVVIAAT----NRKQDLDPALISRFDSMI  456 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~-~~vl~~LL~~ld~~~~--------~~~viVIaaT----N~~~~Ld~aL~sRf~~~I  456 (567)
                      ||+||||||+++.+......++. +.++..||...++...        ...+++||+.    ..|.+|-|.|..||+..+
T Consensus       252 GIvFIDEIDKIa~~~~~g~~dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~sKPSDLiPELQGRfPIRV  331 (444)
T COG1220         252 GIVFIDEIDKIAKRGGSGGPDVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHVAKPSDLIPELQGRFPIRV  331 (444)
T ss_pred             CeEEEehhhHHHhcCCCCCCCcchhhhcccccccccCceeeccccccccceEEEEecCceecCChhhcChhhcCCCceEE
Confidence            99999999999877653322333 3455678888777532        2467788776    358899999999999999


Q ss_pred             EecCCCHHHHHHHHHHHHHhhCHHHH--HHHHHhccCCCHHHHHHHHHHHH
Q 047219          457 TFGLPDHENRQEIAAQYAKHLTKAEL--AELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       457 ~i~~P~~~eR~eIL~~~~~~~~~~~l--~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ++...+.++-..||..--..+..+..  -+--...-.|+...|..+...||
T Consensus       332 EL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~  382 (444)
T COG1220         332 ELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAY  382 (444)
T ss_pred             EcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHH
Confidence            99999999988887642211111111  00001112366677777777666

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.16  E-value=1e-10  Score=111.61  Aligned_cols=115  Identities=20%  Similarity=0.330  Sum_probs=72.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC-CCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG-AMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDE  396 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~-~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDE  396 (567)
                      |-.++||.||+|||||.+|+++++.+. ..   ..+++.++++.+....  +.+..+..++..+.   ...+.+||||||
T Consensus         2 p~~~~ll~GpsGvGKT~la~~la~~l~~~~---~~~~~~~d~s~~~~~~--~~~~~~~~l~~~~~~~v~~~~~gVVllDE   76 (171)
T PF07724_consen    2 PKSNFLLAGPSGVGKTELAKALAELLFVGS---ERPLIRIDMSEYSEGD--DVESSVSKLLGSPPGYVGAEEGGVVLLDE   76 (171)
T ss_dssp             -SEEEEEESSTTSSHHHHHHHHHHHHT-SS---CCEEEEEEGGGHCSHH--HCSCHCHHHHHHTTCHHHHHHHTEEEEET
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHhccCC---ccchHHHhhhcccccc--hHHhhhhhhhhcccceeeccchhhhhhHH
Confidence            345799999999999999999999995 22   3479999988876611  00111111111110   111246999999


Q ss_pred             cchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---------cCCcEEEEEeeCC
Q 047219          397 VDSFAVARDSEMHEATRRILSVLLRQIDGFE---------QDKKVVVIAATNR  440 (567)
Q Consensus       397 ID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---------~~~~viVIaaTN~  440 (567)
                      ||+..+.....-.-.-..+++.||+.+++-.         .-.++++|+|+|-
T Consensus        77 idKa~~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~  129 (171)
T PF07724_consen   77 IDKAHPSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNF  129 (171)
T ss_dssp             GGGCSHTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESS
T ss_pred             HhhccccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccc
Confidence            9999874222222222356667777765431         2358999999996

The highly conserved nature of this module across taxa suggests that it has a key cellular role. Members of the family are involved in diverse cellular functions including gene expression, peroxisome assembly and vesicle mediated transport. Although the role of ATPase AAA-2 domain is not, as yet, clear, the AAA+ superfamily of proteins to which the AAA ATPases belong has a chaperone-like function in the assembly, operation or disassembly of proteins []. Some of these ATPases function as a chaperone subunit of a proteasome-like degradation complex. This ATPase family includes some proteins not detected by IPR003959 from INTERPRO.; GO: 0005524 ATP binding; PDB: 1R6B_X 1KSF_X 3PXI_C 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 1HQY_E ....

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=99.16  E-value=1.3e-09  Score=113.67  Aligned_cols=165  Identities=16%  Similarity=0.140  Sum_probs=109.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC---------------cCeEEec--hhhHHhhh-hchhHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG---------------VPLMYVP--LEVVMSKY-YGESERLLGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~---------------~~~~~i~--~~~l~s~~-~G~~~~~l~~~f  380 (567)
                      .+.+..+||+||+|+||+++|.++|+.+.+..-..               -.+..+.  .+.-..+. ..-.-+.++++.
T Consensus        23 ~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~  102 (319)
T PRK08769         23 GRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREIS  102 (319)
T ss_pred             CCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHH
Confidence            56788999999999999999999999885431111               1122221  10000000 001134455555


Q ss_pred             HHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEE
Q 047219          381 SLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMIT  457 (567)
Q Consensus       381 ~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~  457 (567)
                      +.+...   +...|++||++|.|...           ..+.||+.++  +.+.++++|.+|+.++.+.|.++||| ..+.
T Consensus       103 ~~~~~~p~~g~~kV~iI~~ae~m~~~-----------AaNaLLKtLE--EPp~~~~fiL~~~~~~~lLpTIrSRC-q~i~  168 (319)
T PRK08769        103 QKLALTPQYGIAQVVIVDPADAINRA-----------ACNALLKTLE--EPSPGRYLWLISAQPARLPATIRSRC-QRLE  168 (319)
T ss_pred             HHHhhCcccCCcEEEEeccHhhhCHH-----------HHHHHHHHhh--CCCCCCeEEEEECChhhCchHHHhhh-eEee
Confidence            544432   23479999999999633           5578888888  46778999999999999999999999 8999


Q ss_pred             ecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHH
Q 047219          458 FGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRD  499 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~  499 (567)
                      |..|+.++-.+.+...  .........++....|-.+..+..
T Consensus       169 ~~~~~~~~~~~~L~~~--~~~~~~a~~~~~l~~G~p~~A~~~  208 (319)
T PRK08769        169 FKLPPAHEALAWLLAQ--GVSERAAQEALDAARGHPGLAAQW  208 (319)
T ss_pred             CCCcCHHHHHHHHHHc--CCChHHHHHHHHHcCCCHHHHHHH
Confidence            9999998877777642  345455555666665544444433

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.14  E-value=4.6e-10  Score=99.82  Aligned_cols=131  Identities=31%  Similarity=0.417  Sum_probs=83.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh--------------hchhHHHHHHHHHHHhcCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY--------------YGESERLLGKVFSLANELP  387 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~--------------~G~~~~~l~~~f~~A~~~a  387 (567)
                      +..++|+||||||||++++.+++.+...   ...+++++++......              ...........+..+....
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPP---GGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLK   78 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCC---CCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcC
Confidence            4689999999999999999999998543   1247777776543321              1234445666777777654


Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CCCCChHHHhccceEEEecCC
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                       +.+|||||++.+..............     ..............+|+++|. ....+..+..|++..+.+..+
T Consensus        79 -~~viiiDei~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~  147 (148)
T smart00382       79 -PDVLILDEITSLLDAEQEALLLLLEE-----LRLLLLLKSEKNLTVILTTNDEKDLGPALLRRRFDRRIVLLLI  147 (148)
T ss_pred             -CCEEEEECCcccCCHHHHHHHHhhhh-----hHHHHHHHhcCCCEEEEEeCCCccCchhhhhhccceEEEecCC
Confidence             48999999999976644332211100     000011123456788999986 344555566688777777544

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.

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=99.14  E-value=1.7e-09  Score=113.69  Aligned_cols=161  Identities=14%  Similarity=0.150  Sum_probs=109.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcC-----------------eEEechhhHHhhhhchhHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVP-----------------LMYVPLEVVMSKYYGESERLLGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f  380 (567)
                      .+.+..+||+||+|+||+++|.++|+.+.+. +-.+.+                 +..+..+.- ...  -.-+.++.+.
T Consensus        21 ~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~-~~~--I~idqiR~l~   97 (334)
T PRK07993         21 GRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKG-KSS--LGVDAVREVT   97 (334)
T ss_pred             CCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccc-ccc--CCHHHHHHHH
Confidence            5778899999999999999999999998542 111111                 222221100 000  1123455554


Q ss_pred             HHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEE
Q 047219          381 SLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMIT  457 (567)
Q Consensus       381 ~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~  457 (567)
                      +.+..   .+...|++||++|.|..           ...+.||+.++  +++.++++|..|+.++.+.|.++||| ..+.
T Consensus        98 ~~~~~~~~~g~~kV~iI~~ae~m~~-----------~AaNaLLKtLE--EPp~~t~fiL~t~~~~~lLpTIrSRC-q~~~  163 (334)
T PRK07993         98 EKLYEHARLGGAKVVWLPDAALLTD-----------AAANALLKTLE--EPPENTWFFLACREPARLLATLRSRC-RLHY  163 (334)
T ss_pred             HHHhhccccCCceEEEEcchHhhCH-----------HHHHHHHHHhc--CCCCCeEEEEEECChhhChHHHHhcc-cccc
Confidence            44332   23457999999999963           35588999998  47889999999999999999999999 6889


Q ss_pred             ecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHH
Q 047219          458 FGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDI  497 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL  497 (567)
                      |+.|+.++..+.+.... ....+....++....|-.+..+
T Consensus       164 ~~~~~~~~~~~~L~~~~-~~~~~~a~~~~~la~G~~~~Al  202 (334)
T PRK07993        164 LAPPPEQYALTWLSREV-TMSQDALLAALRLSAGAPGAAL  202 (334)
T ss_pred             CCCCCHHHHHHHHHHcc-CCCHHHHHHHHHHcCCCHHHHH
Confidence            99999888777665431 3444455555556555444433

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=99.13  E-value=3.1e-09  Score=110.98  Aligned_cols=137  Identities=13%  Similarity=0.187  Sum_probs=99.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCCcC-----------------eEEechhhHHhhhhchhHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQGVP-----------------LMYVPLEVVMSKYYGESERLLGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f  380 (567)
                      .+.++.+||+||+|+||+++|+++|+.+.+.. ....+                 +..+...  .++..  .-+.++.+.
T Consensus        21 ~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~--~~~~I--~id~iR~l~   96 (325)
T PRK06871         21 GLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPI--DNKDI--GVDQVREIN   96 (325)
T ss_pred             CCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccc--cCCCC--CHHHHHHHH
Confidence            46788999999999999999999999985431 11112                 2223211  01111  234455554


Q ss_pred             HHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEE
Q 047219          381 SLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMIT  457 (567)
Q Consensus       381 ~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~  457 (567)
                      +.+..   .+...|++||++|.|...           ..+.||+.++  +++.++++|.+|+.++.+.|.++||| ..+.
T Consensus        97 ~~~~~~~~~g~~KV~iI~~a~~m~~~-----------AaNaLLKtLE--EPp~~~~fiL~t~~~~~llpTI~SRC-~~~~  162 (325)
T PRK06871         97 EKVSQHAQQGGNKVVYIQGAERLTEA-----------AANALLKTLE--EPRPNTYFLLQADLSAALLPTIYSRC-QTWL  162 (325)
T ss_pred             HHHhhccccCCceEEEEechhhhCHH-----------HHHHHHHHhc--CCCCCeEEEEEECChHhCchHHHhhc-eEEe
Confidence            44432   234579999999999633           5578899888  47889999999999999999999999 8999


Q ss_pred             ecCCCHHHHHHHHHHH
Q 047219          458 FGLPDHENRQEIAAQY  473 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~  473 (567)
                      |..|+.++..+.+...
T Consensus       163 ~~~~~~~~~~~~L~~~  178 (325)
T PRK06871        163 IHPPEEQQALDWLQAQ  178 (325)
T ss_pred             CCCCCHHHHHHHHHHH
Confidence            9999999888777654

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=99.12  E-value=1.5e-10  Score=132.82  Aligned_cols=153  Identities=19%  Similarity=0.208  Sum_probs=91.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      +...+|||+|+||||||.+|+++|+...+..+ .+.++..+.+..... ..+...... .+-..+...+.+|+++|||++
T Consensus       490 RgdihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s~vgLTa~~~-~~d~~tG~~-~le~GaLvlAdgGtL~IDEid  567 (915)
T PTZ00111        490 RGIINVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSSSVGLTASIK-FNESDNGRA-MIQPGAVVLANGGVCCIDELD  567 (915)
T ss_pred             cCCceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCccccccchhh-hcccccCcc-cccCCcEEEcCCCeEEecchh
Confidence            44569999999999999999999998765421 233444444333211 010000000 000112234557999999999


Q ss_pred             hhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-------------CCChHHHhccceEEEe-cCCCHH
Q 047219          399 SFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-------------DLDPALISRFDSMITF-GLPDHE  464 (567)
Q Consensus       399 ~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-------------~Ld~aL~sRf~~~I~i-~~P~~~  464 (567)
                      .|....|..+++++++..-.+-+.......+.++.||||+|+..             .|++.|++|||.++.+ +.|+.+
T Consensus       568 kms~~~Q~aLlEaMEqqtIsI~KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLSRFDLIf~l~D~~d~~  647 (915)
T PTZ00111        568 KCHNESRLSLYEVMEQQTVTIAKAGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQD  647 (915)
T ss_pred             hCCHHHHHHHHHHHhCCEEEEecCCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhhhhcEEEEecCCCChH
Confidence            99877666655554321000111111123457899999999832             4889999999887655 667665


Q ss_pred             HHHHHHHHHH
Q 047219          465 NRQEIAAQYA  474 (567)
Q Consensus       465 eR~eIL~~~~  474 (567)
                      .=..|..+.+
T Consensus       648 ~D~~lA~hI~  657 (915)
T PTZ00111        648 TDQLISLSIA  657 (915)
T ss_pred             HHHHHHHHHH
Confidence            5555544433

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.11  E-value=1.3e-11  Score=111.00  Aligned_cols=121  Identities=24%  Similarity=0.302  Sum_probs=64.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh--hHHhhhhchhHHHH-HHHHHHHhcCCCCcEEEEcCcchh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE--VVMSKYYGESERLL-GKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~--~l~s~~~G~~~~~l-~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ||||+|+||+|||++|+++|+.+      +..|..|.+.  .+-+...|..--.. ...|+..+--.-..|+++|||...
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~------~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNra   74 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSL------GLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRA   74 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHT------T--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS
T ss_pred             CEeeECCCccHHHHHHHHHHHHc------CCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccC
Confidence            68999999999999999999999      6667776653  22333333210000 000000000001369999999999


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-----CCChHHHhcc
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-----DLDPALISRF  452 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-----~Ld~aL~sRf  452 (567)
                      .++.|+.+++++++  .+.--....+..+..+.||||.|+.+     .|+++++.||
T Consensus        75 ppktQsAlLeam~E--r~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF  129 (131)
T PF07726_consen   75 PPKTQSALLEAMEE--RQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRF  129 (131)
T ss_dssp             -HHHHHHHHHHHHH--SEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTS
T ss_pred             CHHHHHHHHHHHHc--CeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhccc
Confidence            99988877776654  11111112334567899999999865     6999999998

AAA ATPases form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules. AAA ATPases contain a P-loop NTPase domain, which is the most abundant class of NTP-binding protein fold, and is found throughout all kingdoms of life []. P-loop NTPase domains act to hydrolyse the beta-gamma phosphate bond of bound nucleoside triphosphate. There are two classes of P-loop domains: the KG (kinase-GTPase) division, and the ASCE division, the latter including the AAA+ group as well as several other ATPases. There are at least six major clades of AAA domains (metalloproteases, meiotic proteins, D1 and D2 domains of ATPases with two AAA domains, proteasome subunits, and BSC1), as well as several minor clades, some of which consist of hypothetical proteins []. The domain organisation of AAA ATPases consists of a non-ATPase N-terminal domain that acts in substrate recognition, followed by one or two AAA domains (D1 and D2), one of which may be degenerate.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2R44_A.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=99.07  E-value=4.7e-10  Score=126.49  Aligned_cols=52  Identities=25%  Similarity=0.360  Sum_probs=44.2

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..|++++|++++++.|...+..                       ..+++|+||||||||++|+++++.++
T Consensus        24 ~~~~~~~~~vigq~~a~~~L~~~~~~-----------------------~~~~l~~G~~G~GKttla~~l~~~l~   75 (637)
T PRK13765         24 EVPERLIDQVIGQEHAVEVIKKAAKQ-----------------------RRHVMMIGSPGTGKSMLAKAMAELLP   75 (637)
T ss_pred             ccCcccHHHcCChHHHHHHHHHHHHh-----------------------CCeEEEECCCCCcHHHHHHHHHHHcC
Confidence            45678999999999999988776641                       24799999999999999999998875

>PRK04132 replication factor C small subunit; Provisional

Probab=99.06  E-value=2.4e-09  Score=123.55  Aligned_cols=150  Identities=17%  Similarity=0.136  Sum_probs=112.6

Q ss_pred             CCceEEeeC--CCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCC-----CCcEEE
Q 047219          321 RPRAVLFEG--PPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELP-----NGAIIF  393 (567)
Q Consensus       321 ~p~~VLL~G--ppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a-----~~~ILf  393 (567)
                      |.-+-+..|  |++.||||+|+++|+++.... .+.+++.+++++..+.      +.++.+...+....     +..|+|
T Consensus       563 ~~~~~~~~G~lPh~lGKTT~A~ala~~l~g~~-~~~~~lElNASd~rgi------d~IR~iIk~~a~~~~~~~~~~KVvI  635 (846)
T PRK04132        563 PGYHNFIGGNLPTVLHNTTAALALARELFGEN-WRHNFLELNASDERGI------NVIREKVKEFARTKPIGGASFKIIF  635 (846)
T ss_pred             CchhhhhcCCCCCcccHHHHHHHHHHhhhccc-ccCeEEEEeCCCcccH------HHHHHHHHHHHhcCCcCCCCCEEEE
Confidence            445567779  999999999999999984332 1457899998874321      23444443322111     236999


Q ss_pred             EcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHH
Q 047219          394 LDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQY  473 (567)
Q Consensus       394 IDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~  473 (567)
                      |||+|.|...           .++.|++.|+.  .+.++++|++||.+..+.+.|+||| ..+.|..|+.++....+...
T Consensus       636 IDEaD~Lt~~-----------AQnALLk~lEe--p~~~~~FILi~N~~~kIi~tIrSRC-~~i~F~~ls~~~i~~~L~~I  701 (846)
T PRK04132        636 LDEADALTQD-----------AQQALRRTMEM--FSSNVRFILSCNYSSKIIEPIQSRC-AIFRFRPLRDEDIAKRLRYI  701 (846)
T ss_pred             EECcccCCHH-----------HHHHHHHHhhC--CCCCeEEEEEeCChhhCchHHhhhc-eEEeCCCCCHHHHHHHHHHH
Confidence            9999999744           34567777773  4578999999999999999999999 89999999999999888887


Q ss_pred             HHh----hCHHHHHHHHHhccC
Q 047219          474 AKH----LTKAELAELATATEE  491 (567)
Q Consensus       474 ~~~----~~~~~l~~la~~t~g  491 (567)
                      +.+    +..+.+..++..+.|
T Consensus       702 ~~~Egi~i~~e~L~~Ia~~s~G  723 (846)
T PRK04132        702 AENEGLELTEEGLQAILYIAEG  723 (846)
T ss_pred             HHhcCCCCCHHHHHHHHHHcCC
Confidence            764    457778888887776

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.05  E-value=8e-11  Score=117.90  Aligned_cols=153  Identities=21%  Similarity=0.273  Sum_probs=114.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC-----CCCCCCcCeEEechhhHHhhhhchhHHHHHHHH---HHHhcCCCCc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG-----AMPWQGVPLMYVPLEVVMSKYYGESERLLGKVF---SLANELPNGA  390 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~-----~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f---~~A~~~a~~~  390 (567)
                      .....++||.||+|.||+.||+.|...-.     ..+|+.+||..+.+..-|+.+||+....+...-   ......+.++
T Consensus       205 ~rsr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadgg  284 (531)
T COG4650         205 IRSRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGG  284 (531)
T ss_pred             hhccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCc
Confidence            45567899999999999999999875432     236777888888888888989887554332211   1122456789


Q ss_pred             EEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCH
Q 047219          391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDH  463 (567)
Q Consensus       391 ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~  463 (567)
                      .||||||..|....|..++..+++  ..|+......+...++-+|+-|.+       .+.+.++|+-|+ +...|.+|.+
T Consensus       285 mlfldeigelgadeqamllkaiee--krf~pfgsdr~v~sdfqliagtvrdlrq~vaeg~fredl~ari-nlwtf~lpgl  361 (531)
T COG4650         285 MLFLDEIGELGADEQAMLLKAIEE--KRFYPFGSDRQVSSDFQLIAGTVRDLRQLVAEGKFREDLYARI-NLWTFTLPGL  361 (531)
T ss_pred             eEehHhhhhcCccHHHHHHHHHHh--hccCCCCCccccccchHHhhhhHHHHHHHHhccchHHHHHHhh-heeeeecccc
Confidence            999999999988877766666554  445555555556678888888854       667999999999 8899999999


Q ss_pred             HHHHHHHHHHH
Q 047219          464 ENRQEIAAQYA  474 (567)
Q Consensus       464 ~eR~eIL~~~~  474 (567)
                      .+|.++++..+
T Consensus       362 ~qr~ediepnl  372 (531)
T COG4650         362 RQRQEDIEPNL  372 (531)
T ss_pred             ccCccccCCCc
Confidence            99999987543

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=99.05  E-value=5.7e-09  Score=109.81  Aligned_cols=141  Identities=21%  Similarity=0.280  Sum_probs=99.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-C-CCcC-----------------eEEechhhHH--------------
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-W-QGVP-----------------LMYVPLEVVM--------------  365 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~-~~~~-----------------~~~i~~~~l~--------------  365 (567)
                      .+.++.+||+||+|+||+++|+++|+.+.+.. . .+.+                 +..+......              
T Consensus        18 ~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~   97 (342)
T PRK06964         18 ARLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEAD   97 (342)
T ss_pred             CCcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccch
Confidence            57789999999999999999999999986531 1 0112                 2222211000              


Q ss_pred             ----hh----h-hchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEE
Q 047219          366 ----SK----Y-YGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVV  433 (567)
Q Consensus       366 ----s~----~-~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~vi  433 (567)
                          ++    . -.-.-+.++.+.+.+..   .+...|++||++|.|...           ..+.||+.++  +++.+++
T Consensus        98 ~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~~~-----------AaNaLLKtLE--EPp~~t~  164 (342)
T PRK06964         98 ADEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALNVA-----------AANALLKTLE--EPPPGTV  164 (342)
T ss_pred             hhcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhcCHH-----------HHHHHHHHhc--CCCcCcE
Confidence                00    0 00112345555544432   233579999999999633           5578899888  5788999


Q ss_pred             EEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHH
Q 047219          434 VIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQY  473 (567)
Q Consensus       434 VIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~  473 (567)
                      +|.+|+.++.+.|.++||| ..+.|..|+.++..+.+...
T Consensus       165 fiL~t~~~~~LLpTI~SRc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        165 FLLVSARIDRLLPTILSRC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             EEEEECChhhCcHHHHhcC-EEEEecCCCHHHHHHHHHHc
Confidence            9999999999999999999 89999999999888887653

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=99.03  E-value=1.2e-09  Score=116.86  Aligned_cols=152  Identities=23%  Similarity=0.343  Sum_probs=95.4

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC------
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM------  349 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~------  349 (567)
                      ...|.||+|++.+|+.+.-..                       -..+++|++||||||||++|+.+...++.-      
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAA-----------------------AGgHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~l  231 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAA-----------------------AGGHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEAL  231 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHH-----------------------hcCCcEEEecCCCCchHHhhhhhcccCCCCChHHHH
Confidence            468999999999999887543                       457899999999999999999998776421      


Q ss_pred             -----------------CCCCcCeEEechhhHHhhhhchh-HHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHH
Q 047219          350 -----------------PWQGVPLMYVPLEVVMSKYYGES-ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEA  411 (567)
Q Consensus       350 -----------------~~~~~~~~~i~~~~l~s~~~G~~-~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~  411 (567)
                                       .+...+|..-..+.-+..++|.. ....+++     ..+++|||||||+-.+.          
T Consensus       232 E~s~I~s~~g~~~~~~~~~~~rPFr~PHHsaS~~aLvGGG~~p~PGeI-----sLAH~GVLFLDElpef~----------  296 (490)
T COG0606         232 EVSAIHSLAGDLHEGCPLKIHRPFRAPHHSASLAALVGGGGVPRPGEI-----SLAHNGVLFLDELPEFK----------  296 (490)
T ss_pred             HHHHHhhhcccccccCccceeCCccCCCccchHHHHhCCCCCCCCCce-----eeecCCEEEeeccchhh----------
Confidence                             01112222211111122222211 1111111     34557999999997764          


Q ss_pred             HHHHHHHHHHhhcCc-----------ccCCcEEEEEeeCC-----------------------CCCCChHHHhccceEEE
Q 047219          412 TRRILSVLLRQIDGF-----------EQDKKVVVIAATNR-----------------------KQDLDPALISRFDSMIT  457 (567)
Q Consensus       412 ~~~vl~~LL~~ld~~-----------~~~~~viVIaaTN~-----------------------~~~Ld~aL~sRf~~~I~  457 (567)
                       +.+++.|..-+++-           ..+.++.+|+++|+                       ...+...|+.|+|..++
T Consensus       297 -~~iLe~LR~PLE~g~i~IsRa~~~v~ypa~Fqlv~AmNpcpcG~~~~~~~~C~c~~~~~~~Y~~klSgp~lDRiDl~ve  375 (490)
T COG0606         297 -RSILEALREPLENGKIIISRAGSKVTYPARFQLVAAMNPCPCGNLGAPLRRCPCSPRQIKRYLNKLSGPFLDRIDLMVE  375 (490)
T ss_pred             -HHHHHHHhCccccCcEEEEEcCCeeEEeeeeEEhhhcCCCCccCCCCCCCCcCCCHHHHHHHHHHhhHHHHhhhhheec
Confidence             34555555555442           23467899999997                       12356677778888888


Q ss_pred             ecCCCHHHH
Q 047219          458 FGLPDHENR  466 (567)
Q Consensus       458 i~~P~~~eR  466 (567)
                      ++.++..++
T Consensus       376 v~~~~~~e~  384 (490)
T COG0606         376 VPRLSAGEL  384 (490)
T ss_pred             ccCCCHHHh
Confidence            877664433

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=99.03  E-value=5.5e-09  Score=108.89  Aligned_cols=137  Identities=18%  Similarity=0.248  Sum_probs=97.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC-----------------cCeEEechhhHHhhhhchhHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG-----------------VPLMYVPLEVVMSKYYGESERLLGKVFS  381 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~-----------------~~~~~i~~~~l~s~~~G~~~~~l~~~f~  381 (567)
                      .+.+..+||+||.|+||+++|+++|+.+.+....+                 -.+..+.... .++.+  .-+.++.+.+
T Consensus        22 ~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~-~~~~I--~vdqiR~l~~   98 (319)
T PRK06090         22 GRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEK-EGKSI--TVEQIRQCNR   98 (319)
T ss_pred             CCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCc-CCCcC--CHHHHHHHHH
Confidence            57788999999999999999999999885431111                 1223332211 00111  1234454444


Q ss_pred             HHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEe
Q 047219          382 LANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITF  458 (567)
Q Consensus       382 ~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i  458 (567)
                      .+..   .+...|++||++|.|...           ..+.||+.++  +++.++++|..|+.++.+.|.++||| ..+.|
T Consensus        99 ~~~~~~~~~~~kV~iI~~ae~m~~~-----------AaNaLLKtLE--EPp~~t~fiL~t~~~~~lLpTI~SRC-q~~~~  164 (319)
T PRK06090         99 LAQESSQLNGYRLFVIEPADAMNES-----------ASNALLKTLE--EPAPNCLFLLVTHNQKRLLPTIVSRC-QQWVV  164 (319)
T ss_pred             HHhhCcccCCceEEEecchhhhCHH-----------HHHHHHHHhc--CCCCCeEEEEEECChhhChHHHHhcc-eeEeC
Confidence            3332   233579999999999633           5578889888  47788999999999999999999999 89999


Q ss_pred             cCCCHHHHHHHHHH
Q 047219          459 GLPDHENRQEIAAQ  472 (567)
Q Consensus       459 ~~P~~~eR~eIL~~  472 (567)
                      ..|+.++..+.+..
T Consensus       165 ~~~~~~~~~~~L~~  178 (319)
T PRK06090        165 TPPSTAQAMQWLKG  178 (319)
T ss_pred             CCCCHHHHHHHHHH
Confidence            99999888777654

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.02  E-value=1.6e-08  Score=112.12  Aligned_cols=207  Identities=20%  Similarity=0.243  Sum_probs=128.9

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHH----hhh-----------hcccccccCCCCceEEeeCCCCCcHH
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYD----DIA-----------RGTRCKFESNRPRAVLFEGPPGTGKT  336 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~----~l~-----------~~~~~~~~~~~p~~VLL~GppGTGKT  336 (567)
                      ....+-.|.|+.|.+..-+.+..++...  .|-+|.    ++.           .......+-++.+-+||+||||-|||
T Consensus       263 dky~Pk~FtdLLsDe~tNR~~L~WLK~W--D~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKT  340 (877)
T KOG1969|consen  263 DKYRPKKFTDLLSDEKTNRRMLGWLKQW--DPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKT  340 (877)
T ss_pred             cccChhHHHHHhcchhHHHHHHHHHHhh--cHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCChh
Confidence            3445568999999999999888887754  222332    220           00011112234466889999999999


Q ss_pred             HHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHh-c--CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN-E--LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       337 ~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~-~--~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      |||+.||++.      |+.++.|++++-.+..  .....+..+...-. .  ...|.+|+|||||--...          
T Consensus       341 TLAHViAkqa------GYsVvEINASDeRt~~--~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~~~----------  402 (877)
T KOG1969|consen  341 TLAHVIAKQA------GYSVVEINASDERTAP--MVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAPRA----------  402 (877)
T ss_pred             HHHHHHHHhc------CceEEEecccccccHH--HHHHHHHHHHhhccccccCCCcceEEEecccCCcHH----------
Confidence            9999999999      8899999998754421  11122222211111 1  134689999999964311          


Q ss_pred             HHHHHHHHhhc-------Cccc------------CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHH
Q 047219          414 RILSVLLRQID-------GFEQ------------DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       414 ~vl~~LL~~ld-------~~~~------------~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~  472 (567)
                       .++.++..+.       +.+.            .-.--|||.||.  ..-|+|+-  -|..++.|..|...-..+-|+.
T Consensus       403 -~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNd--LYaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~  479 (877)
T KOG1969|consen  403 -AVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICND--LYAPALRPLRPFAEIIAFVPPSQSRLVERLNE  479 (877)
T ss_pred             -HHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecC--ccchhhhhcccceEEEEecCCChhHHHHHHHH
Confidence             1222222222       1111            012467888884  45678875  5678999999988877777777


Q ss_pred             HHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          473 YAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       473 ~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .+..    .....+..+++.+.+    ||+..++...
T Consensus       480 IC~rE~mr~d~~aL~~L~el~~~----DIRsCINtLQ  512 (877)
T KOG1969|consen  480 ICHRENMRADSKALNALCELTQN----DIRSCINTLQ  512 (877)
T ss_pred             HHhhhcCCCCHHHHHHHHHHhcc----hHHHHHHHHH
Confidence            7654    344567777776654    8888887765

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=99.01  E-value=1.2e-08  Score=103.45  Aligned_cols=179  Identities=16%  Similarity=0.172  Sum_probs=104.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE--echhhHHhh---hhchh------HH---HHHHHHHHHhcCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY--VPLEVVMSK---YYGES------ER---LLGKVFSLANELP  387 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~--i~~~~l~s~---~~G~~------~~---~l~~~f~~A~~~a  387 (567)
                      +..++|+||+|+|||++++.+++.+.........+..  .+..++...   .+|..      ..   .+...+.......
T Consensus        43 ~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~  122 (269)
T TIGR03015        43 EGFILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAG  122 (269)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCC
Confidence            4468899999999999999999988532110000110  111222211   12211      11   1222222222233


Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC--CCCC----ChHHHhccceEEEecCC
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR--KQDL----DPALISRFDSMITFGLP  461 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~--~~~L----d~aL~sRf~~~I~i~~P  461 (567)
                      ...+|+|||++.+....        .+.+..+.....  .....+.|+.+...  .+.+    ...+.+|+...++++..
T Consensus       123 ~~~vliiDe~~~l~~~~--------~~~l~~l~~~~~--~~~~~~~vvl~g~~~~~~~l~~~~~~~l~~r~~~~~~l~~l  192 (269)
T TIGR03015       123 KRALLVVDEAQNLTPEL--------LEELRMLSNFQT--DNAKLLQIFLVGQPEFRETLQSPQLQQLRQRIIASCHLGPL  192 (269)
T ss_pred             CCeEEEEECcccCCHHH--------HHHHHHHhCccc--CCCCeEEEEEcCCHHHHHHHcCchhHHHHhheeeeeeCCCC
Confidence            45799999999985331        111222222111  11223334444432  1111    23577788788999999


Q ss_pred             CHHHHHHHHHHHHH--------hhCHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          462 DHENRQEIAAQYAK--------HLTKAELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       462 ~~~eR~eIL~~~~~--------~~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      +.++..+++...+.        .+..+.++.+.+.+.|. ++.+..+|..++..+...
T Consensus       193 ~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~-p~~i~~l~~~~~~~a~~~  249 (269)
T TIGR03015       193 DREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGI-PRLINILCDRLLLSAFLE  249 (269)
T ss_pred             CHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCc-ccHHHHHHHHHHHHHHHc
Confidence            99999999988775        25677899999999887 556999999999776553

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.

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=99.00  E-value=4.7e-09  Score=110.19  Aligned_cols=99  Identities=30%  Similarity=0.485  Sum_probs=72.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh-hhhchh-HHHHHHHHHHHh---cCCCCcEEEEcC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS-KYYGES-ERLLGKVFSLAN---ELPNGAIIFLDE  396 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s-~~~G~~-~~~l~~~f~~A~---~~a~~~ILfIDE  396 (567)
                      -.+|||.||+|+|||+||+.+|+.+      ++||.-.+|..+.. .|+|+. +..+..++..|.   +.+..+|+||||
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~l------dVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDE  299 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVL------DVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDE  299 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHh------CCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEeh
Confidence            3679999999999999999999999      89999999988765 688874 455666666654   223469999999


Q ss_pred             cchhhhhhhhh-hH-HH-HHHHHHHHHHhhcCc
Q 047219          397 VDSFAVARDSE-MH-EA-TRRILSVLLRQIDGF  426 (567)
Q Consensus       397 ID~L~~~~q~~-l~-~~-~~~vl~~LL~~ld~~  426 (567)
                      +|+|..+.... .. ++ -+-++..||+.+++.
T Consensus       300 vDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGt  332 (564)
T KOG0745|consen  300 VDKITKKAESIHTSRDVSGEGVQQALLKLLEGT  332 (564)
T ss_pred             hhhhcccCccccccccccchhHHHHHHHHhccc
Confidence            99998543221 11 11 133556677777763

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.99  E-value=8.5e-10  Score=121.23  Aligned_cols=161  Identities=24%  Similarity=0.326  Sum_probs=94.7

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC------
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP------  350 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~------  350 (567)
                      ..|.++.|+..+++.+.-.                       .....+++|.||||+|||++++.++..+....      
T Consensus       188 ~d~~~v~Gq~~~~~al~la-----------------------a~~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le  244 (506)
T PRK09862        188 HDLSDVIGQEQGKRGLEIT-----------------------AAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALE  244 (506)
T ss_pred             cCeEEEECcHHHHhhhhee-----------------------ccCCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEe
Confidence            4788899988777654211                       45668999999999999999999998764210      


Q ss_pred             ----------------CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          351 ----------------WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       351 ----------------~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                                      +...||..-..+.-...++|.....-...+    ..+.+++|||||++.+....+..+.+.+++
T Consensus       245 ~~~i~s~~g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~l----~~A~gGvLfLDEi~e~~~~~~~~L~~~LE~  320 (506)
T PRK09862        245 SAAILSLVNAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEI----SLAHNGVLFLDELPEFERRTLDALREPIES  320 (506)
T ss_pred             cchhhhhhccccccCCcCCCCccCCCccchHHHHhCCCceehhhHh----hhccCCEEecCCchhCCHHHHHHHHHHHHc
Confidence                            001112111111111122332111111122    344579999999999876544433332221


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCC---------------------CCChHHHhccceEEEecCCCHH
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQ---------------------DLDPALISRFDSMITFGLPDHE  464 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~---------------------~Ld~aL~sRf~~~I~i~~P~~~  464 (567)
                      -.-.+.+.......+.++.+|+|+|+..                     .++..++.|||..+.++.|+.+
T Consensus       321 g~v~I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLDRfdL~v~v~~~~~~  391 (506)
T PRK09862        321 GQIHLSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSLEIPLPPPG  391 (506)
T ss_pred             CcEEEecCCcceeccCCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHhhccEEEEeCCCCHH
Confidence            0000011111122357899999999742                     4778999999999999988654

>TIGR00602 rad24 checkpoint protein rad24

Probab=98.96  E-value=2.7e-08  Score=112.14  Aligned_cols=203  Identities=15%  Similarity=0.225  Sum_probs=115.5

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC--
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP--  350 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~--  350 (567)
                      ...+.++++|+|+++.++.++.++....                ++..+...++|+||||||||++++.+++++....  
T Consensus        77 KyrP~~ldel~~~~~ki~~l~~~l~~~~----------------~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~E  140 (637)
T TIGR00602        77 KYKPETQHELAVHKKKIEEVETWLKAQV----------------LENAPKRILLITGPSGCGKSTTIKILSKELGIQVQE  140 (637)
T ss_pred             HhCCCCHHHhcCcHHHHHHHHHHHHhcc----------------cccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHH
Confidence            4456789999999999999888775320                1133445699999999999999999999884320  


Q ss_pred             C-CCcCeEEech-----hhHHhh--hhchhHHHHHHHHHHHhc---------CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          351 W-QGVPLMYVPL-----EVVMSK--YYGESERLLGKVFSLANE---------LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       351 ~-~~~~~~~i~~-----~~l~s~--~~G~~~~~l~~~f~~A~~---------~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      | ..+++....-     ..+...  .+......+..++..+..         .....||||||++.+.....        
T Consensus       141 w~npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r~~--------  212 (637)
T TIGR00602       141 WSNPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYRDT--------  212 (637)
T ss_pred             HhhhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchhhH--------
Confidence            0 0011111000     000000  011122334444444431         12357999999987753211        


Q ss_pred             HHHHHHHH-hhcCcccCCcEEEEEeeC--CC------C-C------CChHHHh--ccceEEEecCCCHHHHHHHHHHHHH
Q 047219          414 RILSVLLR-QIDGFEQDKKVVVIAATN--RK------Q-D------LDPALIS--RFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       414 ~vl~~LL~-~ld~~~~~~~viVIaaTN--~~------~-~------Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +.+..++. ...   ..+.+.+|++++  ..      + .      +.+++++  |+ .+|.|++.+.......|...+.
T Consensus       213 ~~lq~lLr~~~~---e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t~l~K~L~rIl~  288 (637)
T TIGR00602       213 RALHEILRWKYV---SIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPTIMKKFLNRIVT  288 (637)
T ss_pred             HHHHHHHHHHhh---cCCCceEEEEecCCccccccccccccchhcccCHhHhcccce-eEEEeCCCCHHHHHHHHHHHHH
Confidence            12233333 111   123344444443  11      0 1      3478987  55 5799999999997777776665


Q ss_pred             hh-----------CHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Q 047219          476 HL-----------TKAELAELATATEEMSGRDIRDVCQQAERS  507 (567)
Q Consensus       476 ~~-----------~~~~l~~la~~t~g~s~~dL~~L~~~a~~~  507 (567)
                      ..           ..+.+..++...    .+|+|.+++.....
T Consensus       289 ~E~~~~~~~~~~p~~~~l~~I~~~s----~GDiRsAIn~LQf~  327 (637)
T TIGR00602       289 IEAKKNGEKIKVPKKTSVELLCQGC----SGDIRSAINSLQFS  327 (637)
T ss_pred             hhhhccccccccCCHHHHHHHHHhC----CChHHHHHHHHHHH
Confidence            31           124566666644    45888877766544

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

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.96  E-value=9.7e-09  Score=117.96  Aligned_cols=167  Identities=22%  Similarity=0.302  Sum_probs=115.4

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      --+.|+|+++++..|-++|...-..      +    .   ...+...+||.||.|+|||-||+++|..+...   .-.++
T Consensus       560 L~~~V~gQ~eAv~aIa~AI~~sr~g------l----~---~~~~~awflflGpdgvGKt~lAkaLA~~~Fgs---e~~~I  623 (898)
T KOG1051|consen  560 LHERVIGQDEAVAAIAAAIRRSRAG------L----K---DPNPDAWFLFLGPDGVGKTELAKALAEYVFGS---EENFI  623 (898)
T ss_pred             HHhhccchHHHHHHHHHHHHhhhcc------c----C---CCCCCeEEEEECCCchhHHHHHHHHHHHHcCC---ccceE
Confidence            3467999999999999999764111      1    0   01367789999999999999999999998654   55789


Q ss_pred             EechhhHHh--h-------hhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-
Q 047219          358 YVPLEVVMS--K-------YYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-  427 (567)
Q Consensus       358 ~i~~~~l~s--~-------~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-  427 (567)
                      .+++++++.  +       |.|+.+   ...+.++....|.+||+|||||.-.+.           +++.|++.+|..+ 
T Consensus       624 riDmse~~evskligsp~gyvG~e~---gg~LteavrrrP~sVVLfdeIEkAh~~-----------v~n~llq~lD~Grl  689 (898)
T KOG1051|consen  624 RLDMSEFQEVSKLIGSPPGYVGKEE---GGQLTEAVKRRPYSVVLFEEIEKAHPD-----------VLNILLQLLDRGRL  689 (898)
T ss_pred             EechhhhhhhhhccCCCcccccchh---HHHHHHHHhcCCceEEEEechhhcCHH-----------HHHHHHHHHhcCcc
Confidence            999887543  2       344332   234445555667899999999986433           4555666655432 


Q ss_pred             --------cCCcEEEEEeeCC------------------------------------C----CCCChHHHhccceEEEec
Q 047219          428 --------QDKKVVVIAATNR------------------------------------K----QDLDPALISRFDSMITFG  459 (567)
Q Consensus       428 --------~~~~viVIaaTN~------------------------------------~----~~Ld~aL~sRf~~~I~i~  459 (567)
                              .-.+++||+|+|.                                    .    ..+.+++.+|.+..+.+.
T Consensus       690 tDs~Gr~Vd~kN~I~IMTsn~~~~~i~~~~~~~~~l~~~~~~~~~~~~~k~~v~~~~~~~~~~~~r~Ef~nrid~i~lf~  769 (898)
T KOG1051|consen  690 TDSHGREVDFKNAIFIMTSNVGSSAIANDASLEEKLLDMDEKRGSYRLKKVQVSDAVRIYNKQFFRKEFLNRIDELDLNL  769 (898)
T ss_pred             ccCCCcEeeccceEEEEecccchHhhhcccccccccccchhhhhhhhhhhhhhhhhhhcccccccChHHhcccceeeeec
Confidence                    2358999999875                                    1    234566666777777777


Q ss_pred             CCCHHHHHHHHHHHH
Q 047219          460 LPDHENRQEIAAQYA  474 (567)
Q Consensus       460 ~P~~~eR~eIL~~~~  474 (567)
                      ..+.++..++.....
T Consensus       770 ~l~~~~~~~i~~~~~  784 (898)
T KOG1051|consen  770 PLDRDELIEIVNKQL  784 (898)
T ss_pred             ccchhhHhhhhhhHH
Confidence            778777666665544

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.96  E-value=3.5e-09  Score=107.73  Aligned_cols=192  Identities=20%  Similarity=0.171  Sum_probs=121.6

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      +...+-++++++++++....+.+...                     ...-.++|+|||||||||+...+.|..+...  
T Consensus        33 ekyrP~~l~dv~~~~ei~st~~~~~~---------------------~~~lPh~L~YgPPGtGktsti~a~a~~ly~~--   89 (360)
T KOG0990|consen   33 EKYRPPFLGIVIKQEPIWSTENRYSG---------------------MPGLPHLLFYGPPGTGKTSTILANARDFYSP--   89 (360)
T ss_pred             cCCCCchhhhHhcCCchhhHHHHhcc---------------------CCCCCcccccCCCCCCCCCchhhhhhhhcCC--
Confidence            34566788999999998888877532                     2333499999999999999999999998541  


Q ss_pred             CCcCeEEechhhHHhhhhch-hHHHHHHHHHHHhc------CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhc
Q 047219          352 QGVPLMYVPLEVVMSKYYGE-SERLLGKVFSLANE------LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQID  424 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~-~~~~l~~~f~~A~~------~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld  424 (567)
                        .+..+.......+.-.|- ....-...|..+..      ++....++|||.|.|....|..+.           +..+
T Consensus        90 --~~~~~m~lelnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~~AQnALR-----------Rvie  156 (360)
T KOG0990|consen   90 --HPTTSMLLELNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTRDAQNALR-----------RVIE  156 (360)
T ss_pred             --CCchhHHHHhhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhhHHHHHHHH-----------HHHH
Confidence              111111111111111111 01111123333331      234579999999999866554433           3333


Q ss_pred             CcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHH----HHHHHHHhccCCCHHHHHHH
Q 047219          425 GFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKA----ELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       425 ~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~----~l~~la~~t~g~s~~dL~~L  500 (567)
                      .  ...+++++..+|++..+.|++++|| ..+.|...+...-...+..+++.-..+    ....++.    .+.+|++..
T Consensus       157 k--~t~n~rF~ii~n~~~ki~pa~qsRc-trfrf~pl~~~~~~~r~shi~e~e~~~~~~~~~~a~~r----~s~gDmr~a  229 (360)
T KOG0990|consen  157 K--YTANTRFATISNPPQKIHPAQQSRC-TRFRFAPLTMAQQTERQSHIRESEQKETNPEGYSALGR----LSVGDMRVA  229 (360)
T ss_pred             H--hccceEEEEeccChhhcCchhhccc-ccCCCCCCChhhhhhHHHHHHhcchhhcCHHHHHHHHH----HhHHHHHHH
Confidence            2  3457788888899999999999999 778888888777777777776643222    2222333    345577777


Q ss_pred             HHHHHH
Q 047219          501 CQQAER  506 (567)
Q Consensus       501 ~~~a~~  506 (567)
                      +++...
T Consensus       230 ~n~Lqs  235 (360)
T KOG0990|consen  230 LNYLQS  235 (360)
T ss_pred             HHHHHH
Confidence            776553

>PRK08116 hypothetical protein; Validated

Probab=98.94  E-value=6.3e-09  Score=106.32  Aligned_cols=135  Identities=22%  Similarity=0.268  Sum_probs=80.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch----hHHHHHHHHHHHhcCCCCcEEEEcC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE----SERLLGKVFSLANELPNGAIIFLDE  396 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~----~~~~l~~~f~~A~~~a~~~ILfIDE  396 (567)
                      .+.+++|+|++|||||+||.+|++++...   +.++++++..++...+...    .......+++...   ...+|+|||
T Consensus       113 ~~~gl~l~G~~GtGKThLa~aia~~l~~~---~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~---~~dlLviDD  186 (268)
T PRK08116        113 ENVGLLLWGSVGTGKTYLAACIANELIEK---GVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLV---NADLLILDD  186 (268)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhc---CCCEEEEec
Confidence            34679999999999999999999998543   5678889888877654321    1111222333222   246999999


Q ss_pred             cchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCC-CC----CChHHHhcc---ceEEEecCCCHHHHHH
Q 047219          397 VDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK-QD----LDPALISRF---DSMITFGLPDHENRQE  468 (567)
Q Consensus       397 ID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~-~~----Ld~aL~sRf---~~~I~i~~P~~~eR~e  468 (567)
                      ++.....      +..   ...|...++.... ....+|.|||.+ ..    ++..+++|+   ...+.+.-++.  |..
T Consensus       187 lg~e~~t------~~~---~~~l~~iin~r~~-~~~~~IiTsN~~~~eL~~~~~~ri~sRl~e~~~~v~~~g~d~--R~~  254 (268)
T PRK08116        187 LGAERDT------EWA---REKVYNIIDSRYR-KGLPTIVTTNLSLEELKNQYGKRIYDRILEMCTPVENEGKSY--RKE  254 (268)
T ss_pred             ccCCCCC------HHH---HHHHHHHHHHHHH-CCCCEEEECCCCHHHHHHHHhHHHHHHHHHcCEEEEeeCcCh--hHH
Confidence            9653211      111   2334444443222 234577777763 22    577888885   24566666554  545


Q ss_pred             HHHHH
Q 047219          469 IAAQY  473 (567)
Q Consensus       469 IL~~~  473 (567)
                      +.+..
T Consensus       255 ~~~ek  259 (268)
T PRK08116        255 IAKEK  259 (268)
T ss_pred             HHHHH
Confidence            54443

>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 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=98.92  E-value=6.5e-10  Score=94.14  Aligned_cols=70  Identities=21%  Similarity=0.371  Sum_probs=59.3

Q ss_pred             hhhcchhhhH-HHHHHHhCCCCCCccceEEEEecceEEEEEEecC-C----CCcchHHHHHHHhhCceecccCCCceeEE
Q 047219          107 EIAKKERQRI-EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPP-A----CEIPQLIANLVSHLGLKVEEHGGGSDMGL  180 (567)
Q Consensus       107 ~~~~~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~~~~~~~~~~-~----~~~~~~~~~~~~~~~~~~~~~~~~~~v~v  180 (567)
                      +.+++++++| ++.|++||+.+||+    |.|.|.++|+|+|||. +    .+.+++++.+|+|+|+++||     .|+|
T Consensus        11 ~~~~~n~v~v~~~~m~~l~l~~gd~----v~i~g~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd-----~V~V   81 (87)
T PF02359_consen   11 EDAGTNCVRVSPEDMEELGLFPGDV----VLISGKRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGD-----RVTV   81 (87)
T ss_dssp             HHHCTTEEEEEHHHHHCTTT-TTEE----EEEETTTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTS-----EEEE
T ss_pred             HhCCCCEEEEcHHHHHHcCCCCccE----EEEeCCceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCC-----EEEE
Confidence            4589999999 79999999999999    9999998999999985 2    25689999999999999999     9999


Q ss_pred             Eeecc
Q 047219          181 RAWDS  185 (567)
Q Consensus       181 ~~~~~  185 (567)
                      ++++.
T Consensus        82 ~~~~~   86 (87)
T PF02359_consen   82 RPYDP   86 (87)
T ss_dssp             EEETT
T ss_pred             EECCC
Confidence            99764

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 VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.91  E-value=6.7e-08  Score=97.18  Aligned_cols=85  Identities=25%  Similarity=0.371  Sum_probs=62.8

Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-------------CCCCChHHHhccceE
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-------------KQDLDPALISRFDSM  455 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-------------~~~Ld~aL~sRf~~~  455 (567)
                      +++|||||++.|.-.           -+..|.+.++   .+-.-+||.+||+             |.-++++|+.|+ .+
T Consensus       297 PGVLFIDEVhMLDiE-----------cFTyL~kalE---S~iaPivifAsNrG~~~irGt~d~~sPhGip~dllDRl-~I  361 (456)
T KOG1942|consen  297 PGVLFIDEVHMLDIE-----------CFTYLHKALE---SPIAPIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRL-LI  361 (456)
T ss_pred             CcceEeeehhhhhhH-----------HHHHHHHHhc---CCCCceEEEecCCcceeecCCcCCCCCCCCCHHHhhhe-eE
Confidence            499999999988522           2334444444   3445578888887             667899999999 88


Q ss_pred             EEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh
Q 047219          456 ITFGLPDHENRQEIAAQYAKH----LTKAELAELATA  488 (567)
Q Consensus       456 I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~  488 (567)
                      |..-.++.++.++|++..++.    +.++.+..++..
T Consensus       362 irt~~y~~~e~r~Ii~~Ra~~E~l~~~e~a~~~l~~~  398 (456)
T KOG1942|consen  362 IRTLPYDEEEIRQIIKIRAQVEGLQVEEEALDLLAEI  398 (456)
T ss_pred             EeeccCCHHHHHHHHHHHHhhhcceecHHHHHHHHhh
Confidence            888899999999999988764    455566666654

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.91  E-value=6.8e-08  Score=96.63  Aligned_cols=175  Identities=14%  Similarity=0.179  Sum_probs=118.6

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC---
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG---  353 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~---  353 (567)
                      -+++.+.+.++....++....                     ...-.++++|||+|+||.|.+-++-+++.......   
T Consensus        10 ksl~~l~~~~e~~~~Lksl~~---------------------~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki   68 (351)
T KOG2035|consen   10 KSLDELIYHEELANLLKSLSS---------------------TGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKI   68 (351)
T ss_pred             chhhhcccHHHHHHHHHHhcc---------------------cCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheee
Confidence            456778888888777765432                     12236899999999999999999999985310000   


Q ss_pred             ------------c--------CeEEechhhHHhhhhch-hHHHHHHHHHHHh--------cCCCCcEEEEcCcchhhhhh
Q 047219          354 ------------V--------PLMYVPLEVVMSKYYGE-SERLLGKVFSLAN--------ELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       354 ------------~--------~~~~i~~~~l~s~~~G~-~~~~l~~~f~~A~--------~~a~~~ILfIDEID~L~~~~  404 (567)
                                  +        ..+.++.++     .|. ..--+.++.++..        ...+..+++|.|+|.|..+.
T Consensus        69 ~~~t~~tpS~kklEistvsS~yHlEitPSD-----aG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~dA  143 (351)
T KOG2035|consen   69 ETRTFTTPSKKKLEISTVSSNYHLEITPSD-----AGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDA  143 (351)
T ss_pred             eeEEEecCCCceEEEEEecccceEEeChhh-----cCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHHH
Confidence                        0        112222222     121 1122233333221        11235799999999997664


Q ss_pred             hhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHH
Q 047219          405 DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKA  480 (567)
Q Consensus       405 q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~  480 (567)
                      |..           |-+.|+.  ..+++++|..+|....+-+.+++|| ..+.++.|+.++...++...+.+    ++.+
T Consensus       144 Q~a-----------LRRTMEk--Ys~~~RlIl~cns~SriIepIrSRC-l~iRvpaps~eeI~~vl~~v~~kE~l~lp~~  209 (351)
T KOG2035|consen  144 QHA-----------LRRTMEK--YSSNCRLILVCNSTSRIIEPIRSRC-LFIRVPAPSDEEITSVLSKVLKKEGLQLPKE  209 (351)
T ss_pred             HHH-----------HHHHHHH--HhcCceEEEEecCcccchhHHhhhe-eEEeCCCCCHHHHHHHHHHHHHHhcccCcHH
Confidence            443           4444553  3568899999999999999999999 89999999999999999988775    4666


Q ss_pred             HHHHHHHhccC
Q 047219          481 ELAELATATEE  491 (567)
Q Consensus       481 ~l~~la~~t~g  491 (567)
                      .+.++++...|
T Consensus       210 ~l~rIa~kS~~  220 (351)
T KOG2035|consen  210 LLKRIAEKSNR  220 (351)
T ss_pred             HHHHHHHHhcc
Confidence            77777777654

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.89  E-value=1.3e-08  Score=106.91  Aligned_cols=84  Identities=15%  Similarity=0.066  Sum_probs=54.6

Q ss_pred             CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc--ccCCcEEEEEeeCCC-------CCCChHHHhccceEEE
Q 047219          387 PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF--EQDKKVVVIAATNRK-------QDLDPALISRFDSMIT  457 (567)
Q Consensus       387 a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~--~~~~~viVIaaTN~~-------~~Ld~aL~sRf~~~I~  457 (567)
                      ++.||+-|+|+.+...+.+..++.+.++..-.    +.+.  ..+.+.+||+++|..       ....++|++|| ..+.
T Consensus       235 aNrGi~~f~Ei~K~~~~~l~~LL~~~qE~~v~----~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~dR~-~~i~  309 (361)
T smart00763      235 ANRGILEFVEMFKADIKFLHPLLTATQEGNIK----GTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLDRI-IKVK  309 (361)
T ss_pred             ccCceEEEeehhcCCHHHHHHHhhhhhcceEe----cCCcccccccceEEEEeCCHHHHhhhhccccchhhhhce-EEEe
Confidence            34589999999988755444443333321000    1111  233467899999985       35689999999 5888


Q ss_pred             ecCC-CHHHHHHHHHHHHH
Q 047219          458 FGLP-DHENRQEIAAQYAK  475 (567)
Q Consensus       458 i~~P-~~~eR~eIL~~~~~  475 (567)
                      ++.| +.++-.+|.+..+.
T Consensus       310 vpY~l~~~~E~~Iy~k~~~  328 (361)
T smart00763      310 VPYCLRVSEEAQIYEKLLR  328 (361)
T ss_pred             CCCcCCHHHHHHHHHHHhc
Confidence            8866 66777778776665

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK12377 putative replication protein; Provisional

Probab=98.89  E-value=1e-08  Score=103.34  Aligned_cols=125  Identities=24%  Similarity=0.261  Sum_probs=74.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhH--HHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE--RLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~--~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ..+++|+||||||||+||.+|++++...   +..+.+++..++...+.....  .....+++...   ...+|+|||++.
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~---g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l~---~~dLLiIDDlg~  174 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAK---GRSVIVVTVPDVMSRLHESYDNGQSGEKFLQELC---KVDLLVLDEIGI  174 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHc---CCCeEEEEHHHHHHHHHHHHhccchHHHHHHHhc---CCCEEEEcCCCC
Confidence            4689999999999999999999998644   567888888887775432110  01122333322   247999999976


Q ss_pred             hhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-----CCChHHHhccc----eEEEecCCC
Q 047219          400 FAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-----DLDPALISRFD----SMITFGLPD  462 (567)
Q Consensus       400 L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-----~Ld~aL~sRf~----~~I~i~~P~  462 (567)
                      ....      +..++   .|...++.. .....-+|.|||...     .+...+++|+-    ..+.|.-++
T Consensus       175 ~~~s------~~~~~---~l~~ii~~R-~~~~~ptiitSNl~~~~l~~~~~~ri~dRl~~~~~~~v~~~g~s  236 (248)
T PRK12377        175 QRET------KNEQV---VLNQIIDRR-TASMRSVGMLTNLNHEAMSTLLGERVMDRMTMNGGRWVNFNWES  236 (248)
T ss_pred             CCCC------HHHHH---HHHHHHHHH-HhcCCCEEEEcCCCHHHHHHHhhHHHHHHHhhCCCeEEEeCCcC
Confidence            5322      12222   333333322 122334567788632     35667777762    235555444

>PRK08181 transposase; Validated

Probab=98.84  E-value=3.1e-08  Score=101.11  Aligned_cols=127  Identities=17%  Similarity=0.257  Sum_probs=76.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch-hHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE-SERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ...+++|+||||||||+||.++++++...   +..+.+++..++...+... ........+....   ...+|+|||++.
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~---g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~---~~dLLIIDDlg~  178 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIEN---GWRVLFTRTTDLVQKLQVARRELQLESAIAKLD---KFDLLILDDLAY  178 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHc---CCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHh---cCCEEEEecccc
Confidence            45689999999999999999999987543   6678888888887765321 1112223333333   246999999998


Q ss_pred             hhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC----------CCChHHHhcc---ceEEEecCCCHH
Q 047219          400 FAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ----------DLDPALISRF---DSMITFGLPDHE  464 (567)
Q Consensus       400 L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~----------~Ld~aL~sRf---~~~I~i~~P~~~  464 (567)
                      +....+.      .   ..|+..++.....  --+|.|||.+.          .+..++++|+   ...+.+.-.+.+
T Consensus       179 ~~~~~~~------~---~~Lf~lin~R~~~--~s~IiTSN~~~~~w~~~~~D~~~a~aildRL~h~~~~i~~~g~s~R  245 (269)
T PRK08181        179 VTKDQAE------T---SVLFELISARYER--RSILITANQPFGEWNRVFPDPAMTLAAVDRLVHHATIFEMNVESYR  245 (269)
T ss_pred             ccCCHHH------H---HHHHHHHHHHHhC--CCEEEEcCCCHHHHHHhcCCccchhhHHHhhhcCceEEecCCccch
Confidence            7654221      1   2333333322222  24677777622          1335566665   235555554444

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.83  E-value=2.4e-08  Score=100.50  Aligned_cols=125  Identities=19%  Similarity=0.264  Sum_probs=78.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchh---HHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES---ERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~---~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ..+++|+|+||||||+|+.+|++++...   +..+.+++..++...+....   ......+++...   ...+|+|||++
T Consensus        99 ~~~~~l~G~~GtGKThLa~aia~~l~~~---g~~v~~it~~~l~~~l~~~~~~~~~~~~~~l~~l~---~~dlLvIDDig  172 (244)
T PRK07952         99 IASFIFSGKPGTGKNHLAAAICNELLLR---GKSVLIITVADIMSAMKDTFSNSETSEEQLLNDLS---NVDLLVIDEIG  172 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEHHHHHHHHHHHHhhccccHHHHHHHhc---cCCEEEEeCCC
Confidence            3589999999999999999999998554   56788888888877554321   111223444333   24699999999


Q ss_pred             hhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-----CCChHHHhccc----eEEEecCCC
Q 047219          399 SFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-----DLDPALISRFD----SMITFGLPD  462 (567)
Q Consensus       399 ~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-----~Ld~aL~sRf~----~~I~i~~P~  462 (567)
                      .....      +....++..++.   . .......+|.+||...     .+.+.+.+|+.    ..+.|.-++
T Consensus       173 ~~~~s------~~~~~~l~~Ii~---~-Ry~~~~~tiitSNl~~~~l~~~~g~ri~sRl~~~~~~~i~f~~~s  235 (244)
T PRK07952        173 VQTES------RYEKVIINQIVD---R-RSSSKRPTGMLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFNWDS  235 (244)
T ss_pred             CCCCC------HHHHHHHHHHHH---H-HHhCCCCEEEeCCCCHHHHHHHhChHHHHHHHHCCceEEEeeCCc
Confidence            86422      222233333332   2 1223446777888632     36677777762    256665544

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.83  E-value=2.2e-08  Score=105.05  Aligned_cols=127  Identities=21%  Similarity=0.271  Sum_probs=75.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch---hHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE---SERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~---~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ..+++|+||+|||||+||.+||+++...   +..+++++..++...+...   ........++...   ..-+|+|||++
T Consensus       183 ~~~Lll~G~~GtGKThLa~aIa~~l~~~---g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~---~~DLLIIDDlG  256 (329)
T PRK06835        183 NENLLFYGNTGTGKTFLSNCIAKELLDR---GKSVIYRTADELIEILREIRFNNDKELEEVYDLLI---NCDLLIIDDLG  256 (329)
T ss_pred             CCcEEEECCCCCcHHHHHHHHHHHHHHC---CCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhc---cCCEEEEeccC
Confidence            4789999999999999999999998544   6678899988887755221   0011111123322   24699999998


Q ss_pred             hhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CC----CCChHHHhccc---eEEEecCCCHH
Q 047219          399 SFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQ----DLDPALISRFD---SMITFGLPDHE  464 (567)
Q Consensus       399 ~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~----~Ld~aL~sRf~---~~I~i~~P~~~  464 (567)
                      ......      .   ....|...++..... +-.+|.|||. +.    .+++.+.+|+.   ..+.|.-.+.+
T Consensus       257 ~e~~t~------~---~~~~Lf~iin~R~~~-~k~tIiTSNl~~~el~~~~~eri~SRL~~~~~~i~~~G~d~R  320 (329)
T PRK06835        257 TEKITE------F---SKSELFNLINKRLLR-QKKMIISTNLSLEELLKTYSERISSRLLGNFTLLKFYGEDIR  320 (329)
T ss_pred             CCCCCH------H---HHHHHHHHHHHHHHC-CCCEEEECCCCHHHHHHHHhHHHHHHHHcCCEEEEecCcChh
Confidence            764331      1   113333443332222 2246667775 22    35678888872   24555444433

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.80  E-value=4.5e-08  Score=95.95  Aligned_cols=184  Identities=20%  Similarity=0.316  Sum_probs=96.6

Q ss_pred             cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec--
Q 047219          283 AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP--  360 (567)
Q Consensus       283 iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~--  360 (567)
                      +|.+...+.|.+.+.                     ......++|+||.|+|||++++.+.+......+   ..+++.  
T Consensus         2 ~gR~~el~~l~~~l~---------------------~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~---~~~y~~~~   57 (234)
T PF01637_consen    2 FGREKELEKLKELLE---------------------SGPSQHILLYGPRGSGKTSLLKEFINELKEKGY---KVVYIDFL   57 (234)
T ss_dssp             -S-HHHHHHHHHCHH---------------------H--SSEEEEEESTTSSHHHHHHHHHHHCT--EE---CCCHHCCT
T ss_pred             CCHHHHHHHHHHHHH---------------------hhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCC---cEEEEecc
Confidence            577778887777654                     345688999999999999999999998843211   111111  


Q ss_pred             ----hhhHHhh------------hh-----------------chhHHHHHHHHHHHhcCCCCcEEEEcCcchhh-hhhhh
Q 047219          361 ----LEVVMSK------------YY-----------------GESERLLGKVFSLANELPNGAIIFLDEVDSFA-VARDS  406 (567)
Q Consensus       361 ----~~~l~s~------------~~-----------------G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~-~~~q~  406 (567)
                          .......            .+                 ......+..+++.........+|+|||++.+. .....
T Consensus        58 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~  137 (234)
T PF01637_consen   58 EESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEED  137 (234)
T ss_dssp             TBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTT
T ss_pred             cchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccch
Confidence                0000000            00                 11234456666666665545899999999998 22111


Q ss_pred             hhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCC------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh---
Q 047219          407 EMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL---  477 (567)
Q Consensus       407 ~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~---  477 (567)
                            ...+..|...++......++.+|.++...      ..-...+..|+.. +.++..+.++-.+++...+...   
T Consensus       138 ------~~~~~~l~~~~~~~~~~~~~~~v~~~S~~~~~~~~~~~~~~~~~~~~~-~~l~~l~~~e~~~~~~~~~~~~~~~  210 (234)
T PF01637_consen  138 ------KDFLKSLRSLLDSLLSQQNVSIVITGSSDSLMEEFLDDKSPLFGRFSH-IELKPLSKEEAREFLKELFKELIKL  210 (234)
T ss_dssp             ------HHHHHHHHHHHHH----TTEEEEEEESSHHHHHHTT-TTSTTTT---E-EEE----HHHHHHHHHHHHHCC---
T ss_pred             ------HHHHHHHHHHHhhccccCCceEEEECCchHHHHHhhcccCccccccce-EEEeeCCHHHHHHHHHHHHHHhhcc
Confidence                  12223333333332233444444443321      1223456778855 9999999999999999876543   


Q ss_pred             --CHHHHHHHHHhccCCCHHHHH
Q 047219          478 --TKAELAELATATEEMSGRDIR  498 (567)
Q Consensus       478 --~~~~l~~la~~t~g~s~~dL~  498 (567)
                        ....++.+...+.|. |+-|.
T Consensus       211 ~~~~~~~~~i~~~~gG~-P~~l~  232 (234)
T PF01637_consen  211 PFSDEDIEEIYSLTGGN-PRYLQ  232 (234)
T ss_dssp             ---HHHHHHHHHHHTT--HHHHH
T ss_pred             cCCHHHHHHHHHHhCCC-HHHHh
Confidence              556777777776653 44443

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.79  E-value=1.2e-07  Score=97.27  Aligned_cols=126  Identities=15%  Similarity=0.131  Sum_probs=87.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC----------CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP----------WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---  385 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~----------~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---  385 (567)
                      ...++.+||+||.|+||+.+|.++|+.+.+..          ...-.+..+.... .+..+  .-+.++.+.+.+..   
T Consensus        16 ~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~-~~~~I--~idqiR~l~~~~~~~p~   92 (290)
T PRK05917         16 QKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQG-KGRLH--SIETPRAIKKQIWIHPY   92 (290)
T ss_pred             CCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCC-CCCcC--cHHHHHHHHHHHhhCcc
Confidence            57788999999999999999999999985421          0011222221110 00001  12334444444332   


Q ss_pred             CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCC
Q 047219          386 LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       386 ~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                      .++..|++||++|.|...           ..+.||+.++  +++.++++|..|+.++.+.|.++||| ..+.|+.+
T Consensus        93 e~~~kv~ii~~ad~mt~~-----------AaNaLLK~LE--EPp~~~~fiL~~~~~~~ll~TI~SRc-q~~~~~~~  154 (290)
T PRK05917         93 ESPYKIYIIHEADRMTLD-----------AISAFLKVLE--DPPQHGVIILTSAKPQRLPPTIRSRS-LSIHIPME  154 (290)
T ss_pred             CCCceEEEEechhhcCHH-----------HHHHHHHHhh--cCCCCeEEEEEeCChhhCcHHHHhcc-eEEEccch
Confidence            234579999999999743           4578888888  47789999999999999999999999 78888654

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.75  E-value=1e-07  Score=99.93  Aligned_cols=140  Identities=18%  Similarity=0.203  Sum_probs=94.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC-C------------------CcCeEEechhhH---Hhhh-hchhHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW-Q------------------GVPLMYVPLEVV---MSKY-YGESERL  375 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~-~------------------~~~~~~i~~~~l---~s~~-~G~~~~~  375 (567)
                      .+.+..+||+||+|+|||++|+.+|+.+.+..- .                  .-.++.+....-   .++. -.-.-+.
T Consensus        18 ~r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~   97 (325)
T PRK08699         18 ERRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDA   97 (325)
T ss_pred             CCcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHH
Confidence            477889999999999999999999999854210 0                  122344432110   0000 0012345


Q ss_pred             HHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhcc
Q 047219          376 LGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRF  452 (567)
Q Consensus       376 l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf  452 (567)
                      ++.+.+.+..   .+...|++||+++.|...           ..+.+++.++..  +.++.+|.+|+.++.+.+.+++||
T Consensus        98 iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~-----------a~naLLk~LEep--~~~~~~Ilvth~~~~ll~ti~SRc  164 (325)
T PRK08699         98 VREIIDNVYLTSVRGGLRVILIHPAESMNLQ-----------AANSLLKVLEEP--PPQVVFLLVSHAADKVLPTIKSRC  164 (325)
T ss_pred             HHHHHHHHhhCcccCCceEEEEechhhCCHH-----------HHHHHHHHHHhC--cCCCEEEEEeCChHhChHHHHHHh
Confidence            6666555543   234579999999999744           335666666643  345778888888899999999999


Q ss_pred             ceEEEecCCCHHHHHHHHHH
Q 047219          453 DSMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       453 ~~~I~i~~P~~~eR~eIL~~  472 (567)
                       ..+.|..|+.++..+.+..
T Consensus       165 -~~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        165 -RKMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             -hhhcCCCCCHHHHHHHHHh
Confidence             8999999999887777654

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.75  E-value=5.4e-08  Score=107.15  Aligned_cols=145  Identities=23%  Similarity=0.283  Sum_probs=90.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-CcC------eEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEE
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-GVP------LMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIF  393 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-~~~------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILf  393 (567)
                      ..-+|||+|.||||||.+.+++|+.+++..+. |.-      ..++.-.--...++-+         ..|.-.+.+|+.+
T Consensus       461 ~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVtrd~dtkqlVLe---------sGALVLSD~GiCC  531 (804)
T KOG0478|consen  461 GDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVTKDPDTRQLVLE---------SGALVLSDNGICC  531 (804)
T ss_pred             ccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEEecCccceeeee---------cCcEEEcCCceEE
Confidence            34689999999999999999999999764221 000      0011000000001111         1122345579999


Q ss_pred             EcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-------------CCChHHHhccceEEEe-c
Q 047219          394 LDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-------------DLDPALISRFDSMITF-G  459 (567)
Q Consensus       394 IDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-------------~Ld~aL~sRf~~~I~i-~  459 (567)
                      |||+|+|....++.++++++...-.+-+.+--...+.+.-|||++|+.+             .|+|.|++|||.++-+ +
T Consensus       532 IDEFDKM~dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp~k~i~eNI~LpptLLSRFDLIylllD  611 (804)
T KOG0478|consen  532 IDEFDKMSDSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNPNKSIIENINLPPTLLSRFDLIFLLLD  611 (804)
T ss_pred             chhhhhhhHHHHHHHHHHHHHhhhhHhhcceeeeccccceeeeeeccccccCCCCCchhhccCCChhhhhhhcEEEEEec
Confidence            9999999888888888887653323322222123467889999999622             4889999999876544 6


Q ss_pred             CCCHHHHHHHHHHHH
Q 047219          460 LPDHENRQEIAAQYA  474 (567)
Q Consensus       460 ~P~~~eR~eIL~~~~  474 (567)
                      .||...-+.+..++.
T Consensus       612 ~~DE~~Dr~La~Hiv  626 (804)
T KOG0478|consen  612 KPDERSDRRLADHIV  626 (804)
T ss_pred             CcchhHHHHHHHHHH
Confidence            777664444444433

>PRK06526 transposase; Provisional

Probab=98.72  E-value=2.8e-08  Score=100.72  Aligned_cols=78  Identities=23%  Similarity=0.322  Sum_probs=52.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch-hHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE-SERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~-~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ..+.+++|+||||||||++|.+|+.++...   +..+.+++..++...+... ....+...+..   .....+|+|||++
T Consensus        96 ~~~~nlll~Gp~GtGKThLa~al~~~a~~~---g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~---l~~~dlLIIDD~g  169 (254)
T PRK06526         96 TGKENVVFLGPPGTGKTHLAIGLGIRACQA---GHRVLFATAAQWVARLAAAHHAGRLQAELVK---LGRYPLLIVDEVG  169 (254)
T ss_pred             hcCceEEEEeCCCCchHHHHHHHHHHHHHC---CCchhhhhHHHHHHHHHHHHhcCcHHHHHHH---hccCCEEEEcccc
Confidence            346789999999999999999999987543   5566677777766654321 11122222222   2235799999999


Q ss_pred             hhhhh
Q 047219          399 SFAVA  403 (567)
Q Consensus       399 ~L~~~  403 (567)
                      .+...
T Consensus       170 ~~~~~  174 (254)
T PRK06526        170 YIPFE  174 (254)
T ss_pred             cCCCC
Confidence            87543

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.71  E-value=7.9e-07  Score=92.13  Aligned_cols=151  Identities=12%  Similarity=0.092  Sum_probs=101.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-------CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC----C
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-------WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL----P  387 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-------~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~----a  387 (567)
                      ...++.+||+|+.|+||+.+|+.+++.+.+..       ....++..++...   ...  .-+.++.+.+.....    +
T Consensus        15 ~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g---~~i--~vd~Ir~l~~~~~~~~~~~~   89 (299)
T PRK07132         15 NKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFD---KDL--SKSEFLSAINKLYFSSFVQS   89 (299)
T ss_pred             CCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCC---CcC--CHHHHHHHHHHhccCCcccC
Confidence            45677889999999999999999999984311       0011334443100   101  113445554444322    2


Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHH
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQ  467 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~  467 (567)
                      +..|++||++|.|...           ..+.|++.++.  ++..+++|.+|+.++.+-+.+++|| ..++|..++.++..
T Consensus        90 ~~KvvII~~~e~m~~~-----------a~NaLLK~LEE--Pp~~t~~il~~~~~~kll~TI~SRc-~~~~f~~l~~~~l~  155 (299)
T PRK07132         90 QKKILIIKNIEKTSNS-----------LLNALLKTIEE--PPKDTYFLLTTKNINKVLPTIVSRC-QVFNVKEPDQQKIL  155 (299)
T ss_pred             CceEEEEecccccCHH-----------HHHHHHHHhhC--CCCCeEEEEEeCChHhChHHHHhCe-EEEECCCCCHHHHH
Confidence            5689999999998532           44678888884  6778888888888899999999999 89999999988877


Q ss_pred             HHHHHHHHhhCHHHHHHHHHhcc
Q 047219          468 EIAAQYAKHLTKAELAELATATE  490 (567)
Q Consensus       468 eIL~~~~~~~~~~~l~~la~~t~  490 (567)
                      +.+...  ....+....++....
T Consensus       156 ~~l~~~--~~~~~~a~~~a~~~~  176 (299)
T PRK07132        156 AKLLSK--NKEKEYNWFYAYIFS  176 (299)
T ss_pred             HHHHHc--CCChhHHHHHHHHcC
Confidence            766543  344444444444433

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=98.70  E-value=2e-08  Score=109.67  Aligned_cols=208  Identities=16%  Similarity=0.163  Sum_probs=125.7

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe-
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL-  356 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~-  356 (567)
                      .|-.|.|++.+|.-|.-++-         -...+-.......+...+|+|.|.||||||-+.+++++.+++..+..-+. 
T Consensus       343 l~PsIyGhe~VK~GilL~Lf---------GGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaS  413 (764)
T KOG0480|consen  343 LFPSIYGHELVKAGILLSLF---------GGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKAS  413 (764)
T ss_pred             hCccccchHHHHhhHHHHHh---------CCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCCcceEecCccc
Confidence            35568888888887754332         11111111122245567899999999999999999999987652221111 


Q ss_pred             ------EEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          357 ------MYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       357 ------~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                            ..+.-.+....|.-+         ..|.-.+.+||.+|||+|+|..+.|..+++++++..-.+-+.+-....+.
T Consensus       414 SaAGLTaaVvkD~esgdf~iE---------AGALmLADnGICCIDEFDKMd~~dqvAihEAMEQQtISIaKAGv~aTLnA  484 (764)
T KOG0480|consen  414 SAAGLTAAVVKDEESGDFTIE---------AGALMLADNGICCIDEFDKMDVKDQVAIHEAMEQQTISIAKAGVVATLNA  484 (764)
T ss_pred             ccccceEEEEecCCCCceeee---------cCcEEEccCceEEechhcccChHhHHHHHHHHHhheehheecceEEeecc
Confidence                  001001111111111         11224456899999999999988788888877653333333222223456


Q ss_pred             cEEEEEeeCCCC-------------CCChHHHhccceEEEe-cCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHH
Q 047219          431 KVVVIAATNRKQ-------------DLDPALISRFDSMITF-GLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRD  496 (567)
Q Consensus       431 ~viVIaaTN~~~-------------~Ld~aL~sRf~~~I~i-~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~d  496 (567)
                      +.-||||+|+..             .+++.+++|||..+-+ +-|+...-..|-++.+....  ..+........|+..+
T Consensus       485 RtSIlAAANPv~GhYdR~ktl~eNi~msApimSRFDL~FiLlD~~nE~~D~~ia~hIld~h~--~i~~~~~~~~~~~~e~  562 (764)
T KOG0480|consen  485 RTSILAAANPVGGHYDRKKTLRENINMSAPIMSRFDLFFILLDDCNEVVDYAIARHILDLHR--GIDDATERVCVYTLEQ  562 (764)
T ss_pred             hhhhhhhcCCcCCccccccchhhhcCCCchhhhhhcEEEEEecCCchHHHHHHHHHHHHHhc--cccccccccccccHHH
Confidence            778999999833             5889999999885544 78888877777776665311  1111112224567777


Q ss_pred             HHHHHHHHH
Q 047219          497 IRDVCQQAE  505 (567)
Q Consensus       497 L~~L~~~a~  505 (567)
                      ++..+.+|.
T Consensus       563 vrkYi~yAR  571 (764)
T KOG0480|consen  563 VRKYIRYAR  571 (764)
T ss_pred             HHHHHHHHH
Confidence            777777665

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.66  E-value=1.3e-07  Score=95.87  Aligned_cols=77  Identities=22%  Similarity=0.405  Sum_probs=55.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHH-HHH-HHHHHHhcCCCCcEEEEcCcc
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER-LLG-KVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~-~l~-~~f~~A~~~a~~~ILfIDEID  398 (567)
                      .+.+++|+||||||||+||-||++++...   +..+.+++.++++.++-..... ... .+.... .  ..-+|+|||+.
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~---g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~~~l-~--~~dlLIiDDlG  177 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKA---GISVLFITAPDLLSKLKAAFDEGRLEEKLLREL-K--KVDLLIIDDIG  177 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEEHHHHHHHHHHHHhcCchHHHHHHHh-h--cCCEEEEeccc
Confidence            67899999999999999999999998643   7789999999998876433221 111 111112 2  24699999999


Q ss_pred             hhhhh
Q 047219          399 SFAVA  403 (567)
Q Consensus       399 ~L~~~  403 (567)
                      .....
T Consensus       178 ~~~~~  182 (254)
T COG1484         178 YEPFS  182 (254)
T ss_pred             CccCC
Confidence            87544

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.65  E-value=1.3e-07  Score=98.28  Aligned_cols=75  Identities=15%  Similarity=0.255  Sum_probs=52.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhH-HHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE-RLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~-~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ..++++|+|++|||||+||.|+++++...   +..+.++..+++...+..... ..+...++...   ...+|+|||+..
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~---g~~v~~~~~~~l~~~lk~~~~~~~~~~~l~~l~---~~dlLiIDDiG~  228 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKK---GVSSTLLHFPEFIRELKNSISDGSVKEKIDAVK---EAPVLMLDDIGA  228 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEEEHHHHHHHHHHHHhcCcHHHHHHHhc---CCCEEEEecCCC
Confidence            46799999999999999999999998644   667788888777665432211 11223333332   246999999986


Q ss_pred             hh
Q 047219          400 FA  401 (567)
Q Consensus       400 L~  401 (567)
                      -.
T Consensus       229 e~  230 (306)
T PRK08939        229 EQ  230 (306)
T ss_pred             cc
Confidence            54

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.64  E-value=1.6e-06  Score=89.38  Aligned_cols=163  Identities=17%  Similarity=0.208  Sum_probs=100.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCCcCeEEec-hhhHHhh------hh---ch--hHHHHHHHHHHHhc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQGVPLMYVP-LEVVMSK------YY---GE--SERLLGKVFSLANE  385 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~~~~~~i~-~~~l~s~------~~---G~--~~~~l~~~f~~A~~  385 (567)
                      .+.+..+||+||  +||+++|+++|+.+.+.. ....+|-... |..+...      ++   |.  .-+.++.+.+.+..
T Consensus        21 ~rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~   98 (290)
T PRK07276         21 DRLNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQ   98 (290)
T ss_pred             CCcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhh
Confidence            577889999996  689999999999885431 1111221110 1111100      00   11  12445555444332


Q ss_pred             ---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCC
Q 047219          386 ---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPD  462 (567)
Q Consensus       386 ---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~  462 (567)
                         .++..|++||++|.|...           ..+.||+.++  +++.++++|.+|+.++.+-|.++||| ..+.|+. +
T Consensus        99 ~p~~~~~kV~II~~ad~m~~~-----------AaNaLLKtLE--EPp~~t~~iL~t~~~~~lLpTI~SRc-q~i~f~~-~  163 (290)
T PRK07276         99 SGYEGKQQVFIIKDADKMHVN-----------AANSLLKVIE--EPQSEIYIFLLTNDENKVLPTIKSRT-QIFHFPK-N  163 (290)
T ss_pred             CcccCCcEEEEeehhhhcCHH-----------HHHHHHHHhc--CCCCCeEEEEEECChhhCchHHHHcc-eeeeCCC-c
Confidence               234579999999999633           4578888888  46678999999999999999999999 8888965 5


Q ss_pred             HHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          463 HENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       463 ~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      .+...+++..  ..........++. ..| +++....+..
T Consensus       164 ~~~~~~~L~~--~g~~~~~a~~la~-~~~-s~~~A~~l~~  199 (290)
T PRK07276        164 EAYLIQLLEQ--KGLLKTQAELLAK-LAQ-STSEAEKLAQ  199 (290)
T ss_pred             HHHHHHHHHH--cCCChHHHHHHHH-HCC-CHHHHHHHhC
Confidence            5544444432  1233333333333 334 5555555553

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.64  E-value=9.7e-07  Score=90.53  Aligned_cols=207  Identities=18%  Similarity=0.287  Sum_probs=117.0

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPL  356 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~  356 (567)
                      +.-+|+..+.+.+.. ++..+.+|.              .....++||+|++|.|||++++.+.+.....   ....+|+
T Consensus        34 ~rWIgY~~A~~~L~~-L~~Ll~~P~--------------~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PV   98 (302)
T PF05621_consen   34 DRWIGYPRAKEALDR-LEELLEYPK--------------RHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPV   98 (302)
T ss_pred             CCeecCHHHHHHHHH-HHHHHhCCc--------------ccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccE
Confidence            456899988877755 445555663              4556789999999999999999999876432   1123566


Q ss_pred             EEechhh--HHhhhh-------c-------hhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHH
Q 047219          357 MYVPLEV--VMSKYY-------G-------ESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL  420 (567)
Q Consensus       357 ~~i~~~~--l~s~~~-------G-------~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL  420 (567)
                      +++..+.  -...+|       |       ...+....+....+... .-+|+|||+|.+.....    ...+.+++.|-
T Consensus        99 v~vq~P~~p~~~~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~-vrmLIIDE~H~lLaGs~----~~qr~~Ln~LK  173 (302)
T PF05621_consen   99 VYVQMPPEPDERRFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLG-VRMLIIDEFHNLLAGSY----RKQREFLNALK  173 (302)
T ss_pred             EEEecCCCCChHHHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcC-CcEEEeechHHHhcccH----HHHHHHHHHHH
Confidence            6665531  111111       1       01111222233333443 47999999999753321    11223333333


Q ss_pred             HhhcCcccCCcEEEEEeeCC--CCCCChHHHhccceEEEecCCCH-HHHHHHHHHHHHhhC---------HHHHHHHHHh
Q 047219          421 RQIDGFEQDKKVVVIAATNR--KQDLDPALISRFDSMITFGLPDH-ENRQEIAAQYAKHLT---------KAELAELATA  488 (567)
Q Consensus       421 ~~ld~~~~~~~viVIaaTN~--~~~Ld~aL~sRf~~~I~i~~P~~-~eR~eIL~~~~~~~~---------~~~l~~la~~  488 (567)
                      ...+.+  .-.++.++|-..  .-.-|+.|.+|| ..+.++.... ++...++..+-..++         .+....+...
T Consensus       174 ~L~NeL--~ipiV~vGt~~A~~al~~D~QLa~RF-~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~  250 (302)
T PF05621_consen  174 FLGNEL--QIPIVGVGTREAYRALRTDPQLASRF-EPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHER  250 (302)
T ss_pred             HHhhcc--CCCeEEeccHHHHHHhccCHHHHhcc-CCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHH
Confidence            333222  233444444322  224578999999 6677765543 333444444433322         2345677778


Q ss_pred             ccCCCHHHHHHHHHHHHHHHHH
Q 047219          489 TEEMSGRDIRDVCQQAERSWAS  510 (567)
Q Consensus       489 t~g~s~~dL~~L~~~a~~~a~~  510 (567)
                      +.|..| ++..+++.|+..|.+
T Consensus       251 s~G~iG-~l~~ll~~aA~~AI~  271 (302)
T PF05621_consen  251 SEGLIG-ELSRLLNAAAIAAIR  271 (302)
T ss_pred             cCCchH-HHHHHHHHHHHHHHh
Confidence            777655 788888887765544

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.64  E-value=2.2e-07  Score=104.67  Aligned_cols=177  Identities=24%  Similarity=0.292  Sum_probs=105.7

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC-------
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-------  352 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~-------  352 (567)
                      -.|-|++.+|+.|.-++--         ......-.....+..-+|||.|.||||||.|.+.+++.+++..+.       
T Consensus       286 PsIyG~e~VKkAilLqLfg---------Gv~k~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~  356 (682)
T COG1241         286 PSIYGHEDVKKAILLQLFG---------GVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSA  356 (682)
T ss_pred             ccccCcHHHHHHHHHHhcC---------CCcccCCCCcccccceeEEEcCCCchhHHHHHHHHHhhCCceEEEccccccc
Confidence            4578898888776533311         111000000013345789999999999999999999998764221       


Q ss_pred             -CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          353 -GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       353 -~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                       +.....+.... .++|+-+.         .|.-.+.+||++|||+|+|.......+++++++..-.+-+..-....+..
T Consensus       357 ~GLTAav~rd~~-tge~~Lea---------GALVlAD~Gv~cIDEfdKm~~~dr~aihEaMEQQtIsIaKAGI~atLnAR  426 (682)
T COG1241         357 AGLTAAVVRDKV-TGEWVLEA---------GALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAKAGITATLNAR  426 (682)
T ss_pred             cCceeEEEEccC-CCeEEEeC---------CEEEEecCCEEEEEeccCCChHHHHHHHHHHHhcEeeecccceeeecchh
Confidence             11111111111 11121111         12234568999999999998877777777765522222222211134567


Q ss_pred             EEEEEeeCCCC-------------CCChHHHhccceEEEe-cCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQ-------------DLDPALISRFDSMITF-GLPDHENRQEIAAQYAK  475 (567)
Q Consensus       432 viVIaaTN~~~-------------~Ld~aL~sRf~~~I~i-~~P~~~eR~eIL~~~~~  475 (567)
                      +-|+||+|+..             +|++.|++|||..+.+ ..|+.+.-.++..+.+.
T Consensus       427 csvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRFDLifvl~D~~d~~~D~~ia~hil~  484 (682)
T COG1241         427 CSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDLIFVLKDDPDEEKDEEIAEHILD  484 (682)
T ss_pred             hhhhhhhCCCCCcCCCCCCHHHhcCCChhHHhhCCeeEEecCCCCccchHHHHHHHHH
Confidence            88999999843             4889999999987766 57776655555555443

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.63  E-value=1e-06  Score=94.00  Aligned_cols=197  Identities=17%  Similarity=0.238  Sum_probs=127.5

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ..+.|.+..+..+++++..++                 ..+.+.++.+.|-||||||.+..-+-....... .....+++
T Consensus       150 ~~l~gRe~e~~~v~~F~~~hl-----------------e~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~-~~~~~v~i  211 (529)
T KOG2227|consen  150 GTLKGRELEMDIVREFFSLHL-----------------ELNTSGSLYVSGQPGTGKTALLSRVLDSLSKSS-KSPVTVYI  211 (529)
T ss_pred             CCccchHHHHHHHHHHHHhhh-----------------hcccCcceEeeCCCCcchHHHHHHHHHhhhhhc-ccceeEEE
Confidence            568999999999999887542                 256788999999999999999887766553221 02234566


Q ss_pred             chhh------HHhhhhch---------hHHHHHHHHHH-HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhh
Q 047219          360 PLEV------VMSKYYGE---------SERLLGKVFSL-ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQI  423 (567)
Q Consensus       360 ~~~~------l~s~~~G~---------~~~~l~~~f~~-A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~l  423 (567)
                      +|..      ++.+.++.         .+......|+. .......-++++||+|.|....+..+        ..+..+-
T Consensus       212 nc~sl~~~~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~vL--------y~lFewp  283 (529)
T KOG2227|consen  212 NCTSLTEASAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQTVL--------YTLFEWP  283 (529)
T ss_pred             eeccccchHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhccccee--------eeehhcc
Confidence            6653      22222221         11122233332 22233457999999999985544332        3333222


Q ss_pred             cCcccCCcEEEEEeeCCCCC---CChHHHhcc---ceEEEecCCCHHHHHHHHHHHHHhh-----CHHHHHHHHHhccCC
Q 047219          424 DGFEQDKKVVVIAATNRKQD---LDPALISRF---DSMITFGLPDHENRQEIAAQYAKHL-----TKAELAELATATEEM  492 (567)
Q Consensus       424 d~~~~~~~viVIaaTN~~~~---Ld~aL~sRf---~~~I~i~~P~~~eR~eIL~~~~~~~-----~~~~l~~la~~t~g~  492 (567)
                      .  ..+..+++|+.+|..+.   +-+.|..|+   ...+.|++++.++..+|+...+...     ....++-.|+...+.
T Consensus       284 ~--lp~sr~iLiGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~  361 (529)
T KOG2227|consen  284 K--LPNSRIILIGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAP  361 (529)
T ss_pred             c--CCcceeeeeeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccC
Confidence            2  24568899999997554   444444443   4589999999999999999988753     234566777777776


Q ss_pred             CHHHHHHHHHHHH
Q 047219          493 SGRDIRDVCQQAE  505 (567)
Q Consensus       493 s~~dL~~L~~~a~  505 (567)
                      +| |++.++....
T Consensus       362 SG-DlRkaLdv~R  373 (529)
T KOG2227|consen  362 SG-DLRKALDVCR  373 (529)
T ss_pred             ch-hHHHHHHHHH
Confidence            66 8887766544

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.63  E-value=1.6e-06  Score=96.31  Aligned_cols=182  Identities=23%  Similarity=0.299  Sum_probs=114.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCC----CCCCCcCeEEechhhHHh----------hhhch------hHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGA----MPWQGVPLMYVPLEVVMS----------KYYGE------SERLLGKVF  380 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~----~~~~~~~~~~i~~~~l~s----------~~~G~------~~~~l~~~f  380 (567)
                      ....+++.|-||||||.+++.+.+++..    .......++.|++-.+.+          .+-|+      .-..+..-|
T Consensus       421 ~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f  500 (767)
T KOG1514|consen  421 LGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRF  500 (767)
T ss_pred             CceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhh
Confidence            3457999999999999999999997742    223355677777644322          11222      122334444


Q ss_pred             HHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC----CChHHHhccc-eE
Q 047219          381 SLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD----LDPALISRFD-SM  455 (567)
Q Consensus       381 ~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~----Ld~aL~sRf~-~~  455 (567)
                      .......+.+||+|||+|.|....|        .++..|+.|-.  ..+..++||+..|..+.    |....-+|++ ..
T Consensus       501 ~~~k~~~~~~VvLiDElD~Lvtr~Q--------dVlYn~fdWpt--~~~sKLvvi~IaNTmdlPEr~l~nrvsSRlg~tR  570 (767)
T KOG1514|consen  501 TVPKPKRSTTVVLIDELDILVTRSQ--------DVLYNIFDWPT--LKNSKLVVIAIANTMDLPERLLMNRVSSRLGLTR  570 (767)
T ss_pred             ccCCCCCCCEEEEeccHHHHhcccH--------HHHHHHhcCCc--CCCCceEEEEecccccCHHHHhccchhhhcccee
Confidence            4333445579999999999976543        45555666544  34568888888886432    2333334653 48


Q ss_pred             EEecCCCHHHHHHHHHHHHHhh---CHHHHHHHHHhccCCCHHHHH---HHHHHHHHHHHHHHH
Q 047219          456 ITFGLPDHENRQEIAAQYAKHL---TKAELAELATATEEMSGRDIR---DVCQQAERSWASKII  513 (567)
Q Consensus       456 I~i~~P~~~eR~eIL~~~~~~~---~~~~l~~la~~t~g~s~~dL~---~L~~~a~~~a~~r~i  513 (567)
                      +.|.+++..+..+|+...+...   ..+..+-+++.....+| |.+   .+|+.|...+-.+..
T Consensus       571 i~F~pYth~qLq~Ii~~RL~~~~~f~~~aielvarkVAavSG-DaRraldic~RA~Eia~~~~~  633 (767)
T KOG1514|consen  571 ICFQPYTHEQLQEIISARLKGLDAFENKAIELVARKVAAVSG-DARRALDICRRAAEIAEERNV  633 (767)
T ss_pred             eecCCCCHHHHHHHHHHhhcchhhcchhHHHHHHHHHHhccc-cHHHHHHHHHHHHHHhhhhcc
Confidence            8999999999999999887653   34444444555544444 333   345555554444444

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.63  E-value=1.5e-06  Score=87.86  Aligned_cols=108  Identities=22%  Similarity=0.266  Sum_probs=69.8

Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC------------CCCCChHHHhccceEE
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR------------KQDLDPALISRFDSMI  456 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~------------~~~Ld~aL~sRf~~~I  456 (567)
                      +++|||||+|.|.-..-+           .|-+.+++   .-.-++|++||+            |.-++-+|+.|+ ..|
T Consensus       289 pGVLFIDEvHMLDIEcFs-----------FlNrAlE~---d~~PiiimaTNrgit~iRGTn~~SphGiP~D~lDR~-lII  353 (454)
T KOG2680|consen  289 PGVLFIDEVHMLDIECFS-----------FLNRALEN---DMAPIIIMATNRGITRIRGTNYRSPHGIPIDLLDRM-LII  353 (454)
T ss_pred             cceEEEeeehhhhhHHHH-----------HHHHHhhh---ccCcEEEEEcCCceEEeecCCCCCCCCCcHHHhhhh-hee
Confidence            499999999988543222           22222221   223367777776            667999999999 888


Q ss_pred             EecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          457 TFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       457 ~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      ...+++.++.++||+..+..    +..+.++.+......-+-+---.|+..+...+.+|
T Consensus       354 ~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~kr  412 (454)
T KOG2680|consen  354 STQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKR  412 (454)
T ss_pred             ecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHh
Confidence            99999999999999998875    45555665555444333333344444444444443

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.62  E-value=3.5e-08  Score=94.73  Aligned_cols=76  Identities=21%  Similarity=0.370  Sum_probs=51.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchh-HHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES-ERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~-~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ....+++|+||||||||+||.++++++-..   +..+.+++.+++...+.... .......+.....   ..+|+|||+.
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~ai~~~~~~~---g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~---~dlLilDDlG  118 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVAIANEAIRK---GYSVLFITASDLLDELKQSRSDGSYEELLKRLKR---VDLLILDDLG  118 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHHHHHHHHHT---T--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHT---SSCEEEETCT
T ss_pred             ccCeEEEEEhhHhHHHHHHHHHHHHHhccC---CcceeEeecCceeccccccccccchhhhcCcccc---ccEecccccc
Confidence            456799999999999999999999987543   77889999998887654321 1112233333332   4699999998


Q ss_pred             hhh
Q 047219          399 SFA  401 (567)
Q Consensus       399 ~L~  401 (567)
                      ...
T Consensus       119 ~~~  121 (178)
T PF01695_consen  119 YEP  121 (178)
T ss_dssp             SS-
T ss_pred             eee
Confidence            654

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.

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=98.60  E-value=8.9e-07  Score=95.31  Aligned_cols=144  Identities=25%  Similarity=0.318  Sum_probs=95.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhH--HHHHHHHHHHhcCCCCcEEEEcCc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE--RLLGKVFSLANELPNGAIIFLDEV  397 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~--~~l~~~f~~A~~~a~~~ILfIDEI  397 (567)
                      .+-.++||+||||+|||+||-.+|..+      +.||+.+-.++-+..+- ++.  ..+...|+.|++.. -+||++|+|
T Consensus       536 s~lvSvLl~Gp~~sGKTaLAA~iA~~S------~FPFvKiiSpe~miG~s-EsaKc~~i~k~F~DAYkS~-lsiivvDdi  607 (744)
T KOG0741|consen  536 SPLVSVLLEGPPGSGKTALAAKIALSS------DFPFVKIISPEDMIGLS-ESAKCAHIKKIFEDAYKSP-LSIIVVDDI  607 (744)
T ss_pred             CcceEEEEecCCCCChHHHHHHHHhhc------CCCeEEEeChHHccCcc-HHHHHHHHHHHHHHhhcCc-ceEEEEcch
Confidence            455789999999999999999999998      88898876555443221 222  34778999998775 599999999


Q ss_pred             chhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC-cEEEEEeeCCCCCCC-hHHHhccceEEEecCCCH-HHHHHHHHH
Q 047219          398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDK-KVVVIAATNRKQDLD-PALISRFDSMITFGLPDH-ENRQEIAAQ  472 (567)
Q Consensus       398 D~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~-~viVIaaTN~~~~Ld-~aL~sRf~~~I~i~~P~~-~eR~eIL~~  472 (567)
                      +.|..-. .-..++..-++..|+-.+....+.+ +..|++||....-|. -.++..|+..++++..+. ++..+++..
T Consensus       608 ErLiD~v-pIGPRfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~~m~i~~~F~~~i~Vpnl~~~~~~~~vl~~  684 (744)
T KOG0741|consen  608 ERLLDYV-PIGPRFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQEMGILDCFSSTIHVPNLTTGEQLLEVLEE  684 (744)
T ss_pred             hhhhccc-ccCchhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHHHcCHHHhhhheeecCccCchHHHHHHHHH
Confidence            9985221 1112334445555665665544443 456666666543332 356678988888866544 555555553

>PF13173 AAA_14: AAA domain

Probab=98.57  E-value=4.5e-07  Score=82.08  Aligned_cols=120  Identities=18%  Similarity=0.308  Sum_probs=70.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                      +.++|+||+|||||++++.+++.+.    ..-++++++..+..........  +...+...... ...+||||||+.+..
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~----~~~~~~yi~~~~~~~~~~~~~~--~~~~~~~~~~~-~~~~i~iDEiq~~~~   75 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL----PPENILYINFDDPRDRRLADPD--LLEYFLELIKP-GKKYIFIDEIQYLPD   75 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc----ccccceeeccCCHHHHHHhhhh--hHHHHHHhhcc-CCcEEEEehhhhhcc
Confidence            5689999999999999999998874    1245677776655442211111  22222222111 358999999998841


Q ss_pred             hhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCC----CCCChHHHhccceEEEecCCCHHH
Q 047219          403 ARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK----QDLDPALISRFDSMITFGLPDHEN  465 (567)
Q Consensus       403 ~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~----~~Ld~aL~sRf~~~I~i~~P~~~e  465 (567)
                      -         ...+..+.   +.   ..++.+|.|+...    ......|..|. ..+++.+.+.+|
T Consensus        76 ~---------~~~lk~l~---d~---~~~~~ii~tgS~~~~l~~~~~~~l~gr~-~~~~l~Plsf~E  126 (128)
T PF13173_consen   76 W---------EDALKFLV---DN---GPNIKIILTGSSSSLLSKDIAESLAGRV-IEIELYPLSFRE  126 (128)
T ss_pred             H---------HHHHHHHH---Hh---ccCceEEEEccchHHHhhcccccCCCeE-EEEEECCCCHHH
Confidence            1         12222222   21   1344555544332    23456677787 678888888765

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.56  E-value=2.4e-07  Score=103.96  Aligned_cols=139  Identities=14%  Similarity=0.129  Sum_probs=91.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchh--HHHHHH---HHH-HHhcCCCCcEEEEcC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES--ERLLGK---VFS-LANELPNGAIIFLDE  396 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~--~~~l~~---~f~-~A~~~a~~~ILfIDE  396 (567)
                      .+|+|.|++|||||+++++++..++.    ..+|..++.+.-...++|..  +..+..   .++ .....++++||||||
T Consensus        26 gGv~i~g~~G~~ks~~~r~l~~llp~----~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGlla~Ah~GvL~lDe  101 (584)
T PRK13406         26 GGVVLRARAGPVRDRWLAALRALLPA----GTPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLLAEADGGVLVLAM  101 (584)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhcCC----CCCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCceeeccCCEEEecC
Confidence            68999999999999999999999864    34566666655555666642  111100   010 111234579999999


Q ss_pred             cchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCC---CCCChHHHhccceEEEecCCCHHH
Q 047219          397 VDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK---QDLDPALISRFDSMITFGLPDHEN  465 (567)
Q Consensus       397 ID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~---~~Ld~aL~sRf~~~I~i~~P~~~e  465 (567)
                      +..+.++.++.+.+.+++-...+.+....+..+.++.+|++.|..   +.|++.|+.||+..+.+..|+..+
T Consensus       102 ~n~~~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~~~L~~~lLDRf~l~v~v~~~~~~~  173 (584)
T PRK13406        102 AERLEPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEEDERAPAALADRLAFHLDLDGLALRD  173 (584)
T ss_pred             cccCCHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcccCCCHHhHhheEEEEEcCCCChHH
Confidence            999987755554444433222222222233456789999985543   459999999999999999887554

>PRK06921 hypothetical protein; Provisional

Probab=98.54  E-value=3.2e-07  Score=93.71  Aligned_cols=73  Identities=25%  Similarity=0.432  Sum_probs=48.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ...+++|+|+||||||+|+.+|++++....  +..+++++..++...+.... ......+....   ...+|+|||++.
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~--g~~v~y~~~~~l~~~l~~~~-~~~~~~~~~~~---~~dlLiIDDl~~  188 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKK--GVPVLYFPFVEGFGDLKDDF-DLLEAKLNRMK---KVEVLFIDDLFK  188 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhc--CceEEEEEHHHHHHHHHHHH-HHHHHHHHHhc---CCCEEEEecccc
Confidence            467899999999999999999999885321  45677888766655432211 11122222222   246999999954

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=98.52  E-value=4.3e-07  Score=92.99  Aligned_cols=146  Identities=17%  Similarity=0.267  Sum_probs=82.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHh----------cCCCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN----------ELPNG  389 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~----------~~a~~  389 (567)
                      ...+++||+||+|||||++++..-+.+....   .-...++.+....      ...+..+.+...          .....
T Consensus        31 ~~~~pvLl~G~~GtGKT~li~~~l~~l~~~~---~~~~~~~~s~~Tt------s~~~q~~ie~~l~k~~~~~~gP~~~k~  101 (272)
T PF12775_consen   31 SNGRPVLLVGPSGTGKTSLIQNFLSSLDSDK---YLVITINFSAQTT------SNQLQKIIESKLEKRRGRVYGPPGGKK  101 (272)
T ss_dssp             HCTEEEEEESSTTSSHHHHHHHHHHCSTTCC---EEEEEEES-TTHH------HHHHHHCCCTTECECTTEEEEEESSSE
T ss_pred             HcCCcEEEECCCCCchhHHHHhhhccCCccc---cceeEeeccCCCC------HHHHHHHHhhcEEcCCCCCCCCCCCcE
Confidence            3468999999999999999998877664331   1123333332111      111111111100          11224


Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-------cCCcEEEEEeeCCCC---CCChHHHhccceEEEec
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-------QDKKVVVIAATNRKQ---DLDPALISRFDSMITFG  459 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-------~~~~viVIaaTN~~~---~Ld~aL~sRf~~~I~i~  459 (567)
                      .|+||||++.-.++.-+...  .-+.+.+++....-+.       .-.++.+|||+|+..   .+++.|.+.| .++.++
T Consensus       102 lv~fiDDlN~p~~d~ygtq~--~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r~f-~i~~~~  178 (272)
T PF12775_consen  102 LVLFIDDLNMPQPDKYGTQP--PIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLRHF-NILNIP  178 (272)
T ss_dssp             EEEEEETTT-S---TTS--H--HHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHTTE-EEEE--
T ss_pred             EEEEecccCCCCCCCCCCcC--HHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhhhe-EEEEec
Confidence            69999999865444322221  1244555554432221       124788899998743   4788999999 899999


Q ss_pred             CCCHHHHHHHHHHHHHhh
Q 047219          460 LPDHENRQEIAAQYAKHL  477 (567)
Q Consensus       460 ~P~~~eR~eIL~~~~~~~  477 (567)
                      .|+.+....|+..++..+
T Consensus       179 ~p~~~sl~~If~~il~~~  196 (272)
T PF12775_consen  179 YPSDESLNTIFSSILQSH  196 (272)
T ss_dssp             --TCCHHHHHHHHHHHHH
T ss_pred             CCChHHHHHHHHHHHhhh
Confidence            999999999988877643

>PRK09183 transposase/IS protein; Provisional

Probab=98.52  E-value=3e-07  Score=93.50  Aligned_cols=79  Identities=15%  Similarity=0.285  Sum_probs=53.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch-hHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE-SERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~-~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ....+++|+||||||||+||.+++......   +..+.+++..++...+... ....+...+.....  ...+++|||++
T Consensus       100 ~~~~~v~l~Gp~GtGKThLa~al~~~a~~~---G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~--~~dlLiiDdlg  174 (259)
T PRK09183        100 ERNENIVLLGPSGVGKTHLAIALGYEAVRA---GIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVM--APRLLIIDEIG  174 (259)
T ss_pred             hcCCeEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhc--CCCEEEEcccc
Confidence            446789999999999999999998875332   5667788877776544221 11223344443222  24699999998


Q ss_pred             hhhhh
Q 047219          399 SFAVA  403 (567)
Q Consensus       399 ~L~~~  403 (567)
                      .+...
T Consensus       175 ~~~~~  179 (259)
T PRK09183        175 YLPFS  179 (259)
T ss_pred             cCCCC
Confidence            86544

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.51  E-value=6.4e-06  Score=91.41  Aligned_cols=201  Identities=16%  Similarity=0.208  Sum_probs=114.3

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      +...+.+.+||..+...+++++..++..+.                +....+-+||+||||||||++++.+|+++...  
T Consensus        11 ~ky~P~~~~eLavhkkKv~eV~~wl~~~~~----------------~~~~~~iLlLtGP~G~GKtttv~~La~elg~~--   72 (519)
T PF03215_consen   11 EKYAPKTLDELAVHKKKVEEVRSWLEEMFS----------------GSSPKRILLLTGPSGCGKTTTVKVLAKELGFE--   72 (519)
T ss_pred             hhcCCCCHHHhhccHHHHHHHHHHHHHHhc----------------cCCCcceEEEECCCCCCHHHHHHHHHHHhCCe--
Confidence            445667889999999999999988874311                13345578899999999999999999999432  


Q ss_pred             CCcCeEEe-chh----------hHHh------hhhchhHHHHHHH-HHHHhc----------CCCCcEEEEcCcchhhhh
Q 047219          352 QGVPLMYV-PLE----------VVMS------KYYGESERLLGKV-FSLANE----------LPNGAIIFLDEVDSFAVA  403 (567)
Q Consensus       352 ~~~~~~~i-~~~----------~l~s------~~~G~~~~~l~~~-f~~A~~----------~a~~~ILfIDEID~L~~~  403 (567)
                          +.+- +..          +..+      .+... ...+..+ +..++.          .....||+|||+-.+...
T Consensus        73 ----v~Ew~np~~~~~~~~~~~d~~s~~~~~~~f~sq-~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~  147 (519)
T PF03215_consen   73 ----VQEWINPVSFRESDNQEDDFESDFNKFDEFLSQ-SDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHR  147 (519)
T ss_pred             ----eEEecCCCCccccccccccccccccccccccch-hhhhccccccccccccccccCCCcCCCceEEEeeccccccch
Confidence                2211 000          0000      00000 0111111 111111          123579999999765433


Q ss_pred             hhhhhHHHHHHHHHHHHHhhcCcccCC-cEEEEEe-e------CCC--------CCCChHHHh--ccceEEEecCCCHHH
Q 047219          404 RDSEMHEATRRILSVLLRQIDGFEQDK-KVVVIAA-T------NRK--------QDLDPALIS--RFDSMITFGLPDHEN  465 (567)
Q Consensus       404 ~q~~l~~~~~~vl~~LL~~ld~~~~~~-~viVIaa-T------N~~--------~~Ld~aL~s--Rf~~~I~i~~P~~~e  465 (567)
                      ..    ...++.+..++..     ... .+++|.+ +      |..        ..|+++++.  ++ ..|.|.+-...-
T Consensus       148 ~~----~~f~~~L~~~l~~-----~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i-~~I~FNpIa~T~  217 (519)
T PF03215_consen  148 DT----SRFREALRQYLRS-----SRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGI-TRIKFNPIAPTF  217 (519)
T ss_pred             hH----HHHHHHHHHHHHc-----CCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCc-eEEEecCCCHHH
Confidence            22    2223333333332     122 6666666 1      111        146788877  44 688998877766


Q ss_pred             HHHHHHHHHHhh----------C--HHHHHHHHHhccCCCHHHHHHHHHHHHHHHH
Q 047219          466 RQEIAAQYAKHL----------T--KAELAELATATEEMSGRDIRDVCQQAERSWA  509 (567)
Q Consensus       466 R~eIL~~~~~~~----------~--~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~  509 (567)
                      .+..|...+...          +  ...++.++..+    .+|||.+++.....+.
T Consensus       218 mkKaL~rI~~~E~~~~~~~~~~p~~~~~l~~I~~~s----~GDIRsAIn~LQf~~~  269 (519)
T PF03215_consen  218 MKKALKRILKKEARSSSGKNKVPDKQSVLDSIAESS----NGDIRSAINNLQFWCL  269 (519)
T ss_pred             HHHHHHHHHHHHhhhhcCCccCCChHHHHHHHHHhc----CchHHHHHHHHHHHhc
Confidence            666666555432          1  12356666554    4599998887775554

>PF12774 AAA_6: Hydrolytic ATP binding site of dynein motor region D1; PDB: 3VKH_A 3VKG_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A

Probab=98.49  E-value=1.2e-06  Score=87.64  Aligned_cols=136  Identities=19%  Similarity=0.238  Sum_probs=84.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ...+..++||+|||||.+++.+|+.+      +.+++.++|++.++-      ..+..+|..+...  ++.+++||++.|
T Consensus        31 ~~~~~~~~GpagtGKtetik~La~~l------G~~~~vfnc~~~~~~------~~l~ril~G~~~~--GaW~cfdefnrl   96 (231)
T PF12774_consen   31 LNLGGALSGPAGTGKTETIKDLARAL------GRFVVVFNCSEQMDY------QSLSRILKGLAQS--GAWLCFDEFNRL   96 (231)
T ss_dssp             TTTEEEEESSTTSSHHHHHHHHHHCT------T--EEEEETTSSS-H------HHHHHHHHHHHHH--T-EEEEETCCCS
T ss_pred             cCCCCCCcCCCCCCchhHHHHHHHHh------CCeEEEecccccccH------HHHHHHHHHHhhc--Cchhhhhhhhhh
Confidence            34667789999999999999999999      788999999876542      4556677666554  789999999999


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcC-------cccCCcEEEEEeeCC----CCCCChHHHhccceEEEecCCCHHHHHHH
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDG-------FEQDKKVVVIAATNR----KQDLDPALISRFDSMITFGLPDHENRQEI  469 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~-------~~~~~~viVIaaTN~----~~~Ld~aL~sRf~~~I~i~~P~~~eR~eI  469 (567)
                      ....-+......+.+...+......       +..+.++-++.|.|+    ...|++.|+.-| +.+.+..||.....++
T Consensus        97 ~~~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~lF-Rpvam~~PD~~~I~ei  175 (231)
T PF12774_consen   97 SEEVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKALF-RPVAMMVPDLSLIAEI  175 (231)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCTTE-EEEE--S--HHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHHHh-heeEEeCCCHHHHHHH
Confidence            7654333333333333332221111       122345667777775    347999999999 8999999998877776


Q ss_pred             HH
Q 047219          470 AA  471 (567)
Q Consensus       470 L~  471 (567)
                      +-
T Consensus       176 ~L  177 (231)
T PF12774_consen  176 LL  177 (231)
T ss_dssp             HH
T ss_pred             HH
Confidence            54

>PF05729 NACHT: NACHT domain

Probab=98.45  E-value=3e-06  Score=78.68  Aligned_cols=147  Identities=17%  Similarity=0.251  Sum_probs=79.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCC---cCeEEechhhHHhh------------hhchhHHHHHHHHHHHhcCCC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQG---VPLMYVPLEVVMSK------------YYGESERLLGKVFSLANELPN  388 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~---~~~~~i~~~~l~s~------------~~G~~~~~l~~~f~~A~~~a~  388 (567)
                      -++|+|+||+|||++++.++..+.......   .-.+++........            .+..........+.......+
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   81 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKNK   81 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcCC
Confidence            478999999999999999998875432111   11223333222111            111111222222333333445


Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccc--eEEEecCCCHHHH
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFD--SMITFGLPDHENR  466 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~--~~I~i~~P~~~eR  466 (567)
                      ..+|+||.+|.+....+....   ......+...+.. ....++.+|.++.+.. .. .+.+.+.  ..+.+...+.++.
T Consensus        82 ~~llilDglDE~~~~~~~~~~---~~~~~~l~~l~~~-~~~~~~~liit~r~~~-~~-~~~~~~~~~~~~~l~~~~~~~~  155 (166)
T PF05729_consen   82 RVLLILDGLDELEEQDQSQER---QRLLDLLSQLLPQ-ALPPGVKLIITSRPRA-FP-DLRRRLKQAQILELEPFSEEDI  155 (166)
T ss_pred             ceEEEEechHhcccchhhhHH---HHHHHHHHHHhhh-ccCCCCeEEEEEcCCh-HH-HHHHhcCCCcEEEECCCCHHHH
Confidence            689999999999764332111   1122222233332 1234556666665322 21 1444332  4688899999999


Q ss_pred             HHHHHHHHHh
Q 047219          467 QEIAAQYAKH  476 (567)
Q Consensus       467 ~eIL~~~~~~  476 (567)
                      .++++.++++
T Consensus       156 ~~~~~~~f~~  165 (166)
T PF05729_consen  156 KQYLRKYFSN  165 (166)
T ss_pred             HHHHHHHhhc
Confidence            9998877653

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.42  E-value=2.3e-06  Score=86.39  Aligned_cols=128  Identities=11%  Similarity=0.041  Sum_probs=85.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec-hhhHHhh------h-h----chhHHHHHHHHHHHhc-
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP-LEVVMSK------Y-Y----GESERLLGKVFSLANE-  385 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~-~~~l~s~------~-~----G~~~~~l~~~f~~A~~-  385 (567)
                      ..+|..+||+||.|+||..+|.++|+.+.+..- ..+|-... |..+...      + +    .-..+.++++.+.... 
T Consensus         4 ~~~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~-~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~   82 (261)
T PRK05818          4 KNKTHPLLLIERKGSFLKPFLYEYLTSIVCTKA-NGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRP   82 (261)
T ss_pred             CCCCcceeeeCCCCCcHHHHHHHHHHHHcCCCC-CCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccC
Confidence            467899999999999999999999998854310 11121111 1111000      0 0    0112334444433322 


Q ss_pred             ---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCC
Q 047219          386 ---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       386 ---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                         .+...|++||++|.|..           ...+.||+.++  +++.++++|..|+.++.+.+.++||| ..+.++.+
T Consensus        83 s~e~~~~KV~II~~ae~m~~-----------~AaNaLLK~LE--EPp~~t~fiLit~~~~~lLpTI~SRC-q~~~~~~~  147 (261)
T PRK05818         83 SVESNGKKIYIIYGIEKLNK-----------QSANSLLKLIE--EPPKNTYGIFTTRNENNILNTILSRC-VQYVVLSK  147 (261)
T ss_pred             chhcCCCEEEEeccHhhhCH-----------HHHHHHHHhhc--CCCCCeEEEEEECChHhCchHhhhhe-eeeecCCh
Confidence               22357999999999963           35588899888  47889999999999999999999999 66777655

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=98.37  E-value=3.2e-08  Score=104.15  Aligned_cols=147  Identities=26%  Similarity=0.379  Sum_probs=73.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--------CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcE
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--------QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI  391 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--------~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~I  391 (567)
                      +..-++||.|.||||||.|.+++++..++..+        .+.. ..+.-+....+|.-+...     +    -.+.+||
T Consensus        55 r~~ihiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLt-a~~~~d~~~~~~~leaGa-----l----vlad~Gi  124 (331)
T PF00493_consen   55 RGNIHILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLT-ASVSRDPVTGEWVLEAGA-----L----VLADGGI  124 (331)
T ss_dssp             --S--EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCC-EEECCCGGTSSECEEE-H-----H----HHCTTSE
T ss_pred             ccccceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCcc-ceeccccccceeEEeCCc-----h----hcccCce
Confidence            45579999999999999999999877754211        1111 122222222223222221     1    2234799


Q ss_pred             EEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-------------CCChHHHhccceEEEe
Q 047219          392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-------------DLDPALISRFDSMITF  458 (567)
Q Consensus       392 LfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-------------~Ld~aL~sRf~~~I~i  458 (567)
                      ++|||+|.|.......++++++...-.+-+..-....+.++.|+|++|+..             .+++.|++|||..+.+
T Consensus       125 ccIDe~dk~~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~l~~~LLSRFDLif~l  204 (331)
T PF00493_consen  125 CCIDEFDKMKEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENINLPPPLLSRFDLIFLL  204 (331)
T ss_dssp             EEECTTTT--CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-S-CCCHCC-SEEECC
T ss_pred             eeecccccccchHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhcccchhhHhhcCEEEEe
Confidence            999999999765444443333220000000000012356889999999844             4788999999988776


Q ss_pred             -cCCCHHHHHHHHHHHHHh
Q 047219          459 -GLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       459 -~~P~~~eR~eIL~~~~~~  476 (567)
                       +.|+.+.-..+.+..++.
T Consensus       205 ~D~~d~~~D~~la~~il~~  223 (331)
T PF00493_consen  205 RDKPDEEEDERLAEHILDS  223 (331)
T ss_dssp             --TTT-HHHHHHHHHHHTT
T ss_pred             ccccccccccccceEEEec
Confidence             666766555666655543

; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=98.36  E-value=3.8e-07  Score=97.52  Aligned_cols=179  Identities=20%  Similarity=0.251  Sum_probs=111.3

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC---CcCeE
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ---GVPLM  357 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~---~~~~~  357 (567)
                      +|.|++++|+.|.-++.-....     ..+    .-+..+..-+|+|.|.||+-||-|.++|.+...+..+.   +..=+
T Consensus       343 EIyGheDVKKaLLLlLVGgvd~-----~~~----dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYTTGrGSSGV  413 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLVGGVDK-----SPG----DGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYTTGRGSSGV  413 (721)
T ss_pred             hhccchHHHHHHHHHhhCCCCC-----CCC----CCceeecceeEEecCCCchhHHHHHHHHHhcCcccceecCCCCCcc
Confidence            5889999998886655421110     011    11235566789999999999999999999988664221   11111


Q ss_pred             EechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEe
Q 047219          358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAA  437 (567)
Q Consensus       358 ~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaa  437 (567)
                      -+.+.-.....-|+.-     +--.|.-.+.++|.+|||+|+|........+++++...-.+-+..-....+.++-|+|+
T Consensus       414 GLTAAVmkDpvTgEM~-----LEGGALVLAD~GICCIDEfDKM~e~DRtAIHEVMEQQTISIaKAGI~TtLNAR~sILaA  488 (721)
T KOG0482|consen  414 GLTAAVMKDPVTGEMV-----LEGGALVLADGGICCIDEFDKMDESDRTAIHEVMEQQTISIAKAGINTTLNARTSILAA  488 (721)
T ss_pred             ccchhhhcCCCCCeeE-----eccceEEEccCceEeehhhhhhhhhhhHHHHHHHHhhhhhhhhhccccchhhhHHhhhh
Confidence            1112211111222210     00112244568999999999998877777788776544444444333345678889999


Q ss_pred             eCCCC-------------CCChHHHhccceEEEe-cCCCHHHHHHHHHHH
Q 047219          438 TNRKQ-------------DLDPALISRFDSMITF-GLPDHENRQEIAAQY  473 (567)
Q Consensus       438 TN~~~-------------~Ld~aL~sRf~~~I~i-~~P~~~eR~eIL~~~  473 (567)
                      .|+..             .|+.+|++|||..+-+ +.|+.+.-..+.++.
T Consensus       489 ANPayGRYnprrs~e~NI~LPaALLSRFDll~Li~D~pdrd~D~~LA~Hi  538 (721)
T KOG0482|consen  489 ANPAYGRYNPRRSPEQNINLPAALLSRFDLLWLIQDRPDRDNDLRLAQHI  538 (721)
T ss_pred             cCccccccCcccChhHhcCCcHHHHHhhhhhhhhccCCcccchHHHHHHh
Confidence            99722             5899999999875554 678777666655543

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=98.31  E-value=2.6e-05  Score=79.33  Aligned_cols=136  Identities=21%  Similarity=0.288  Sum_probs=81.8

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCCcC
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQGVP  355 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~~~  355 (567)
                      ..|.|+.-+++.+...+...+.++.              ...|..+=|+|+|||||..+++.||+.+.+.    +++..-
T Consensus        82 ~~lfGQHla~~~Vv~alk~~~~n~~--------------p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~f  147 (344)
T KOG2170|consen   82 RALFGQHLAKQLVVNALKSHWANPN--------------PRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHF  147 (344)
T ss_pred             HHhhchHHHHHHHHHHHHHHhcCCC--------------CCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHh
Confidence            3488999999999999988777653              4556666789999999999999999998543    222111


Q ss_pred             eEEe--chhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHh---hcCcccCC
Q 047219          356 LMYV--PLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQ---IDGFEQDK  430 (567)
Q Consensus       356 ~~~i--~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~---ld~~~~~~  430 (567)
                      +...  +...-...|-.+-...   +...+.... .++.++||+|+|.+..    .    +++..+|..   .++ ....
T Consensus       148 vat~hFP~~~~ie~Yk~eL~~~---v~~~v~~C~-rslFIFDE~DKmp~gL----l----d~lkpfLdyyp~v~g-v~fr  214 (344)
T KOG2170|consen  148 VATLHFPHASKIEDYKEELKNR---VRGTVQACQ-RSLFIFDEVDKLPPGL----L----DVLKPFLDYYPQVSG-VDFR  214 (344)
T ss_pred             hhhccCCChHHHHHHHHHHHHH---HHHHHHhcC-CceEEechhhhcCHhH----H----HHHhhhhcccccccc-cccc
Confidence            1111  1122222232222222   333333444 5899999999997441    1    122233321   111 1235


Q ss_pred             cEEEEEeeCCCC
Q 047219          431 KVVVIAATNRKQ  442 (567)
Q Consensus       431 ~viVIaaTN~~~  442 (567)
                      +.++|.-+|.-+
T Consensus       215 kaIFIfLSN~gg  226 (344)
T KOG2170|consen  215 KAIFIFLSNAGG  226 (344)
T ss_pred             ceEEEEEcCCcc
Confidence            678888888633

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=98.28  E-value=5.4e-07  Score=98.35  Aligned_cols=160  Identities=22%  Similarity=0.266  Sum_probs=92.4

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC---CCcCeE
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW---QGVPLM  357 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~---~~~~~~  357 (567)
                      .|.|+..+|..+--.+-.-         ..++....-..+...+|||+|.|||||+-+.|++++...+..|   .|..-+
T Consensus       450 sIyGh~~VK~AvAlaLfGG---------v~kn~~~khkvRGDinvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASav  520 (854)
T KOG0477|consen  450 SIYGHEDVKRAVALALFGG---------VPKNPGGKHKVRGDINVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASAV  520 (854)
T ss_pred             hhhchHHHHHHHHHHHhcC---------CccCCCCCceeccceeEEEecCCCccHHHHHHHHHhcCcceeEeccCCcccc
Confidence            4778888887765433211         1111111111344568999999999999999999999865422   121111


Q ss_pred             Eechh----hHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEE
Q 047219          358 YVPLE----VVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVV  433 (567)
Q Consensus       358 ~i~~~----~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~vi  433 (567)
                      -+.+.    -+..+|.-+.         .|.-.+.+||.+|||+|+|........+++++..--.+-+..--......+.
T Consensus       521 GLTa~v~KdPvtrEWTLEa---------GALVLADkGvClIDEFDKMndqDRtSIHEAMEQQSISISKAGIVtsLqArct  591 (854)
T KOG0477|consen  521 GLTAYVRKDPVTREWTLEA---------GALVLADKGVCLIDEFDKMNDQDRTSIHEAMEQQSISISKAGIVTSLQARCT  591 (854)
T ss_pred             ceeEEEeeCCccceeeecc---------CeEEEccCceEEeehhhhhcccccchHHHHHHhcchhhhhhhHHHHHHhhhh
Confidence            11111    1111221111         1224456799999999999876666677766442222222111112246789


Q ss_pred             EEEeeCCCC-------------CCChHHHhccceEEEe
Q 047219          434 VIAATNRKQ-------------DLDPALISRFDSMITF  458 (567)
Q Consensus       434 VIaaTN~~~-------------~Ld~aL~sRf~~~I~i  458 (567)
                      +|+|+|+.+             .+.+.+++|||....+
T Consensus       592 vIAAanPigGRY~~s~tFaqNV~ltePIlSRFDiLcVv  629 (854)
T KOG0477|consen  592 VIAAANPIGGRYNPSLTFAQNVDLTEPILSRFDILCVV  629 (854)
T ss_pred             hheecCCCCCccCCccchhhccccccchhhhcceeeee
Confidence            999999822             4678899999875555

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=98.24  E-value=2.2e-05  Score=83.52  Aligned_cols=127  Identities=21%  Similarity=0.278  Sum_probs=71.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchh------HHHHHHHHHHHhcCCCCcEE
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES------ERLLGKVFSLANELPNGAII  392 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~------~~~l~~~f~~A~~~a~~~IL  392 (567)
                      ..+|+|++|||++|+|||+|+-...+.++......++|     ..++.......      ..-+..+.+.....  ..+|
T Consensus        59 ~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HF-----h~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~--~~lL  131 (362)
T PF03969_consen   59 PPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHF-----HEFMLDVHSRLHQLRGQDDPLPQVADELAKE--SRLL  131 (362)
T ss_pred             CCCCceEEEECCCCCchhHHHHHHHHhCCccccccccc-----cHHHHHHHHHHHHHhCCCccHHHHHHHHHhc--CCEE
Confidence            56899999999999999999999999886432222233     23333322221      11122232222222  2499


Q ss_pred             EEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CCC-----CC--------hHHHhccceEEEe
Q 047219          393 FLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQD-----LD--------PALISRFDSMITF  458 (567)
Q Consensus       393 fIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~~-----Ld--------~aL~sRf~~~I~i  458 (567)
                      +|||++--...      +  ..++..|+..+-    ..++++|+|+|+ |++     +.        ..|.++| .++++
T Consensus       132 cfDEF~V~Dia------D--Amil~rLf~~l~----~~gvvlVaTSN~~P~~Ly~~gl~r~~Flp~I~~l~~~~-~vv~l  198 (362)
T PF03969_consen  132 CFDEFQVTDIA------D--AMILKRLFEALF----KRGVVLVATSNRPPEDLYKNGLQRERFLPFIDLLKRRC-DVVEL  198 (362)
T ss_pred             EEeeeeccchh------H--HHHHHHHHHHHH----HCCCEEEecCCCChHHHcCCcccHHHHHHHHHHHHhce-EEEEe
Confidence            99999753211      1  113333433332    357899999997 222     22        2233466 67777


Q ss_pred             cCC-CHHH
Q 047219          459 GLP-DHEN  465 (567)
Q Consensus       459 ~~P-~~~e  465 (567)
                      +-+ |.+.
T Consensus       199 d~~~DyR~  206 (362)
T PF03969_consen  199 DGGVDYRR  206 (362)
T ss_pred             cCCCchhh
Confidence            666 4443

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.20  E-value=6.6e-06  Score=73.78  Aligned_cols=79  Identities=23%  Similarity=0.380  Sum_probs=44.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCC--CCCcCeEEechhhHHh--hhh------------c--hhHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMP--WQGVPLMYVPLEVVMS--KYY------------G--ESERLLGKVFSLA  383 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~--~~~~~~~~i~~~~l~s--~~~------------G--~~~~~l~~~f~~A  383 (567)
                      ...++++||||+|||++++.+++......  ....+++.+++.....  .++            .  ........+.+..
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            46799999999999999999999873210  0034466666654331  111            1  1222233333333


Q ss_pred             hcCCCCcEEEEcCcchhh
Q 047219          384 NELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~  401 (567)
                      .... ..+|+|||+|.+.
T Consensus        84 ~~~~-~~~lviDe~~~l~  100 (131)
T PF13401_consen   84 DRRR-VVLLVIDEADHLF  100 (131)
T ss_dssp             HHCT-EEEEEEETTHHHH
T ss_pred             HhcC-CeEEEEeChHhcC
Confidence            3333 2699999999985

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.19  E-value=1.2e-05  Score=74.11  Aligned_cols=35  Identities=37%  Similarity=0.586  Sum_probs=27.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ++|+|+||+|||+++..++......   +.++++++.+
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~---~~~v~~~~~e   36 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATK---GGKVVYVDIE   36 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhc---CCEEEEEECC
Confidence            6899999999999999999987432   3445555544

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.

>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]

Probab=98.14  E-value=2e-05  Score=84.81  Aligned_cols=173  Identities=21%  Similarity=0.282  Sum_probs=100.5

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC---CcCeE
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ---GVPLM  357 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~---~~~~~  357 (567)
                      .|.|.++.|+.+.-++---- .    +.+.    ..+-.+..-+|||.|.|||-|+-|.+.+-+-++-..+.   +..-.
T Consensus       332 SIfG~~DiKkAiaClLFgGs-r----K~Lp----Dg~~lRGDINVLLLGDPgtAKSQlLKFvEkvsPIaVYTSGKGSSAA  402 (729)
T KOG0481|consen  332 SIFGHEDIKKAIACLLFGGS-R----KRLP----DGVTLRGDINVLLLGDPGTAKSQLLKFVEKVSPIAVYTSGKGSSAA  402 (729)
T ss_pred             hhcCchhHHHHHHHHhhcCc-c----ccCC----CcceeccceeEEEecCCchhHHHHHHHHHhcCceEEEecCCCcccc
Confidence            47788888887765442110 0    0010    01113445689999999999999999998876321000   00000


Q ss_pred             EechhhHH---h-hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEE
Q 047219          358 YVPLEVVM---S-KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVV  433 (567)
Q Consensus       358 ~i~~~~l~---s-~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~vi  433 (567)
                      -+.++-+.   + .++-+.         .|.-.+.++|++|||+|+|-....-..+++++...-.+-+..-....+.++-
T Consensus       403 GLTASV~RD~~tReFylEG---------GAMVLADgGVvCIDEFDKMre~DRVAIHEAMEQQTISIAKAGITT~LNSRtS  473 (729)
T KOG0481|consen  403 GLTASVIRDPSTREFYLEG---------GAMVLADGGVVCIDEFDKMREDDRVAIHEAMEQQTISIAKAGITTTLNSRTS  473 (729)
T ss_pred             cceeeEEecCCcceEEEec---------ceEEEecCCEEEeehhhccCchhhhHHHHHHHhhhHHHhhhcceeeecchhh
Confidence            00000000   0 111111         1224566899999999999877666677776654444444433334567888


Q ss_pred             EEEeeCCCC-------------CCChHHHhccceEEEecCCCHHHHHHHHH
Q 047219          434 VIAATNRKQ-------------DLDPALISRFDSMITFGLPDHENRQEIAA  471 (567)
Q Consensus       434 VIaaTN~~~-------------~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~  471 (567)
                      |+|+.|+..             +|-+.+++|||.++-+.--..++|-..|.
T Consensus       474 VLAAANpvfGRyDd~Kt~~dNIDf~~TILSRFDmIFIVKD~h~~~~D~~lA  524 (729)
T KOG0481|consen  474 VLAAANPVFGRYDDTKTGEDNIDFMPTILSRFDMIFIVKDEHDEERDITLA  524 (729)
T ss_pred             hhhhcCCccccccccCCcccccchhhhHhhhccEEEEEeccCcchhhhHHH
Confidence            999999722             36689999999888776544444443333

>PF00931 NB-ARC: NB-ARC domain; InterPro: IPR002182 This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals []

Probab=98.10  E-value=5.4e-05  Score=77.31  Aligned_cols=165  Identities=18%  Similarity=0.210  Sum_probs=87.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC-CCCCCCcCeEEechh----hHHhhh---hc----------hhHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG-AMPWQGVPLMYVPLE----VVMSKY---YG----------ESERLLGKVFS  381 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~-~~~~~~~~~~~i~~~----~l~s~~---~G----------~~~~~l~~~f~  381 (567)
                      .....|.|+|++|+|||+||+.+++... ...|..+-++.+...    .+....   .+          ..+.....+.+
T Consensus        17 ~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~   96 (287)
T PF00931_consen   17 NEVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLRE   96 (287)
T ss_dssp             TSSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHH
T ss_pred             CCeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchh
Confidence            5667899999999999999999998732 222322222222211    111111   11          12223333333


Q ss_pred             HHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCC
Q 047219          382 LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       382 ~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                      .... . +++|+||+++...             .+..+...+.  ....+..||.||.... +-..+... ...++++..
T Consensus        97 ~L~~-~-~~LlVlDdv~~~~-------------~~~~l~~~~~--~~~~~~kilvTTR~~~-v~~~~~~~-~~~~~l~~L  157 (287)
T PF00931_consen   97 LLKD-K-RCLLVLDDVWDEE-------------DLEELREPLP--SFSSGSKILVTTRDRS-VAGSLGGT-DKVIELEPL  157 (287)
T ss_dssp             HHCC-T-SEEEEEEEE-SHH-------------HH-------H--CHHSS-EEEEEESCGG-GGTTHHSC-EEEEECSS-
T ss_pred             hhcc-c-cceeeeeeecccc-------------cccccccccc--cccccccccccccccc-cccccccc-ccccccccc
Confidence            3333 2 6999999998753             1111221111  1223567777776432 21222212 368899999


Q ss_pred             CHHHHHHHHHHHHHhhC-------HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          462 DHENRQEIAAQYAKHLT-------KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       462 ~~~eR~eIL~~~~~~~~-------~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      +.++-.+++...+....       .+...++++.+.| .|-.|+.+....
T Consensus       158 ~~~ea~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c~g-lPLal~~~a~~l  206 (287)
T PF00931_consen  158 SEEEALELFKKRAGRKESESPEDLEDLAKEIVEKCGG-LPLALKLIASYL  206 (287)
T ss_dssp             -HHHHHHHHHHHHTSHS----TTSCTHHHHHHHHTTT--HHHHHHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccccccccc-cccccccccccc
Confidence            99999999998865433       3356778888765 466666655443

This domain has been structurally characterised in the human protein apoptotic protease-activating factor 1 (Apaf-1) []. It contains the three-layered alpha-beta fold and subsequent short alpha-helical region characteristic of the AAA+ ATPase domain superfamily. While this domain is thought to bind and hyrolyse ATP, only ADP binding has been experimentally verified. It is proposed that binding and hydrolysis of ATP by this domain induces conformational changes the the overall protein, leading to formation of the apoptosome.; GO: 0043531 ADP binding; PDB: 3IZA_E 1Z6T_D 3SFZ_A 3SHF_A 1VT4_M 3IZ8_G 3LQR_A 2A5Y_C 3LQQ_A.

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.09  E-value=3.8e-05  Score=71.66  Aligned_cols=30  Identities=27%  Similarity=0.411  Sum_probs=25.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      .....++++|+||+||||++.-+++.+...
T Consensus         3 ~~~mki~ITG~PGvGKtTl~~ki~e~L~~~   32 (179)
T COG1618           3 KMAMKIFITGRPGVGKTTLVLKIAEKLREK   32 (179)
T ss_pred             CcceEEEEeCCCCccHHHHHHHHHHHHHhc
Confidence            345679999999999999999999988543

>PHA00729 NTP-binding motif containing protein

Probab=98.06  E-value=0.00019  Score=71.29  Aligned_cols=112  Identities=14%  Similarity=0.072  Sum_probs=64.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCC--C--------CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAM--P--------WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI  391 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~--~--------~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~I  391 (567)
                      ..+++|+|+||||||++|.+|++.+...  .        ..+..+..++.+++...+        ...+..   .....+
T Consensus        17 f~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L--------~~a~~~---~~~~dl   85 (226)
T PHA00729         17 FVSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKI--------QDAIDN---DYRIPL   85 (226)
T ss_pred             eEEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHH--------HHHHhc---CCCCCE
Confidence            3589999999999999999999986310  0        012345556555554432        112211   111358


Q ss_pred             EEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHH
Q 047219          392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAA  471 (567)
Q Consensus       392 LfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~  471 (567)
                      |+|||+..-..+-.     ...+                .  +    .....+.+++++|+ ..+.|..++.++..+.++
T Consensus        86 LIIDd~G~~~~~~~-----wh~~----------------~--~----~~yf~L~~aLrSR~-~l~il~~ls~edL~~~Lr  137 (226)
T PHA00729         86 IIFDDAGIWLSKYV-----WYED----------------Y--M----KTFYKIYALIRTRV-SAVIFTTPSPEDLAFYLR  137 (226)
T ss_pred             EEEeCCchhhcccc-----hhhh----------------c--c----chHHHHHHHHHhhC-cEEEEecCCHHHHHHHHH
Confidence            99999754321100     0000                0  0    01223567788888 567777777777777666


Q ss_pred             H
Q 047219          472 Q  472 (567)
Q Consensus       472 ~  472 (567)
                      .
T Consensus       138 ~  138 (226)
T PHA00729        138 E  138 (226)
T ss_pred             h
Confidence            5

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.06  E-value=3.3e-05  Score=89.44  Aligned_cols=168  Identities=21%  Similarity=0.298  Sum_probs=117.1

Q ss_pred             cccccCc-HHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCC
Q 047219          279 WENIAGY-DQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQG  353 (567)
Q Consensus       279 ~~dIiG~-~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~  353 (567)
                      .+-++|. ++.++.+.+.+.                     ....++-+|.|+||+|||.++.-+++.....    +...
T Consensus       185 ldPvigr~deeirRvi~iL~---------------------Rrtk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~  243 (898)
T KOG1051|consen  185 LDPVIGRHDEEIRRVIEILS---------------------RKTKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKD  243 (898)
T ss_pred             CCCccCCchHHHHHHHHHHh---------------------ccCCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccc
Confidence            4556676 777877777664                     2333788899999999999999999988543    2235


Q ss_pred             cCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          354 VPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..++.++...+.  .++.|+.+.++..+.+++.....+.||||||++.+.+......   .-...+ +|..+-   ..+.
T Consensus       244 ~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigelh~lvg~g~~~~---~~d~~n-lLkp~L---~rg~  316 (898)
T KOG1051|consen  244 KKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGELHWLVGSGSNYG---AIDAAN-LLKPLL---ARGG  316 (898)
T ss_pred             cceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecceeeeecCCCcch---HHHHHH-hhHHHH---hcCC
Confidence            567777766443  3567889999999999888666678999999999976654411   112222 222221   2345


Q ss_pred             EEEEEeeCCC-----CCCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRK-----QDLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       432 viVIaaTN~~-----~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +.+|+||...     -.-+|+|-+|| ..+.+..|+...-..|+..+..
T Consensus       317 l~~IGatT~e~Y~k~iekdPalErrw-~l~~v~~pS~~~~~~iL~~l~~  364 (898)
T KOG1051|consen  317 LWCIGATTLETYRKCIEKDPALERRW-QLVLVPIPSVENLSLILPGLSE  364 (898)
T ss_pred             eEEEecccHHHHHHHHhhCcchhhCc-ceeEeccCcccchhhhhhhhhh
Confidence            8999988632     24589999999 6778899998776666665544

>PF14516 AAA_35: AAA-like domain

Probab=98.05  E-value=0.00025  Score=74.83  Aligned_cols=178  Identities=17%  Similarity=0.200  Sum_probs=107.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch----------------------------
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE----------------------------  371 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~----------------------------  371 (567)
                      .++..+.++||..+|||++...+.+.+...   +..++++++..+.+..+..                            
T Consensus        29 ~~G~~~~I~apRq~GKTSll~~l~~~l~~~---~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~  105 (331)
T PF14516_consen   29 QPGSYIRIKAPRQMGKTSLLLRLLERLQQQ---GYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDE  105 (331)
T ss_pred             cCCCEEEEECcccCCHHHHHHHHHHHHHHC---CCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHH
Confidence            457789999999999999999998888554   5567777665432211000                            


Q ss_pred             ---hHHHHHHHHHH--HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---cCCcEEEEEeeCCCCC
Q 047219          372 ---SERLLGKVFSL--ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---QDKKVVVIAATNRKQD  443 (567)
Q Consensus       372 ---~~~~l~~~f~~--A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---~~~~viVIaaTN~~~~  443 (567)
                         ........|+.  ......+-||+|||||.+....+     ...+.+..|..+.+...   ....+++|.+......
T Consensus       106 ~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~-----~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~  180 (331)
T PF14516_consen  106 EIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQ-----IADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDY  180 (331)
T ss_pred             hcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcc-----hHHHHHHHHHHHHHhcccCcccceEEEEEecCcccc
Confidence               11123333443  22333468999999999975321     22233333333333211   1234445444432222


Q ss_pred             CChHHH-h--ccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          444 LDPALI-S--RFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       444 Ld~aL~-s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +..+.. +  .+...+.++..+.++-..+++.+-..+....++.+-..+.| -|-=++.+|...+.
T Consensus       181 ~~~~~~~SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~~~~~~~~l~~~tgG-hP~Lv~~~~~~l~~  245 (331)
T PF14516_consen  181 IILDINQSPFNIGQPIELPDFTPEEVQELAQRYGLEFSQEQLEQLMDWTGG-HPYLVQKACYLLVE  245 (331)
T ss_pred             cccCCCCCCcccccceeCCCCCHHHHHHHHHhhhccCCHHHHHHHHHHHCC-CHHHHHHHHHHHHH
Confidence            222221 1  22357778888999998888887666777789999988877 46777777777664

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=98.03  E-value=1.8e-05  Score=93.81  Aligned_cols=139  Identities=24%  Similarity=0.406  Sum_probs=95.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh--hhhch-----hHHHH---HHHHHHHhcCCCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS--KYYGE-----SERLL---GKVFSLANELPNG  389 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s--~~~G~-----~~~~l---~~~f~~A~~~a~~  389 (567)
                      ...+++||.|.||+|||++..++|+..      |..++.|+.++...  .+||.     ....+   ..-|-.|.+  .+
T Consensus      1541 qv~kpilLEGsPGVGKTSlItaLAr~t------G~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr--~G 1612 (4600)
T COG5271        1541 QVGKPILLEGSPGVGKTSLITALARKT------GKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMR--DG 1612 (4600)
T ss_pred             hcCCceeecCCCCccHHHHHHHHHHHh------cCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhh--cC
Confidence            457899999999999999999999999      66788888765332  23432     11111   011222222  47


Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC------------cccCCcEEEEEeeCCCC------CCChHHHhc
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG------------FEQDKKVVVIAATNRKQ------DLDPALISR  451 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~------------~~~~~~viVIaaTN~~~------~Ld~aL~sR  451 (567)
                      +.++|||+..-.           +.++..|-..+|.            +....+++|+||-|+.+      .|+..+..|
T Consensus      1613 ~WVlLDEiNLaS-----------QSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq~qggGRKgLPkSF~nR 1681 (4600)
T COG5271        1613 GWVLLDEINLAS-----------QSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQDQGGGRKGLPKSFLNR 1681 (4600)
T ss_pred             CEEEeehhhhhH-----------HHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCchhcCCCcccCCHHHhhh
Confidence            899999997643           2333333333332            23467899999999844      599999999


Q ss_pred             cceEEEecCCCHHHHHHHHHHHHHhhC
Q 047219          452 FDSMITFGLPDHENRQEIAAQYAKHLT  478 (567)
Q Consensus       452 f~~~I~i~~P~~~eR~eIL~~~~~~~~  478 (567)
                      | .++.++..+.++...|.........
T Consensus      1682 F-svV~~d~lt~dDi~~Ia~~~yp~v~ 1707 (4600)
T COG5271        1682 F-SVVKMDGLTTDDITHIANKMYPQVN 1707 (4600)
T ss_pred             h-heEEecccccchHHHHHHhhCCccC
Confidence            9 8899999998888888776655433

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.03  E-value=0.00013  Score=79.57  Aligned_cols=208  Identities=16%  Similarity=0.221  Sum_probs=105.6

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC--
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP--  350 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~--  350 (567)
                      ...+-+.+++.-+..-+.++++++...    ..|.          ..-..+-+||+||+||||||.++.++++++-..  
T Consensus        75 Ky~P~t~eeLAVHkkKI~eVk~WL~~~----~~~~----------~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~E  140 (634)
T KOG1970|consen   75 KYKPRTLEELAVHKKKISEVKQWLKQV----AEFT----------PKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIE  140 (634)
T ss_pred             hcCcccHHHHhhhHHhHHHHHHHHHHH----HHhc----------cCCCceEEEEeCCCCCCchhHHHHHHHhhCceeee
Confidence            334467788888888888887776521    1111          123446788999999999999999999994220  


Q ss_pred             CC-CcCeEEech----hhHHhhhhchhHHHHHHHHHHHh-----------cCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          351 WQ-GVPLMYVPL----EVVMSKYYGESERLLGKVFSLAN-----------ELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       351 ~~-~~~~~~i~~----~~l~s~~~G~~~~~l~~~f~~A~-----------~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      |. .+++...+-    +......+...-..+..+...+.           ....+.+|++||+=......   ..+..++
T Consensus       141 w~Npi~~~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d---~~~~f~e  217 (634)
T KOG1970|consen  141 WSNPINLKEPENLHNETSFLMFPYQSQLAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRD---DSETFRE  217 (634)
T ss_pred             ecCCccccccccccccchhcccchhhHHHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhh---hHHHHHH
Confidence            00 111111100    01111111111111111222221           11224689999997665331   1223334


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEe-eCCCCCCC------hHHHh--ccceEEEecCCCHHHHHHHHHHHHHhh----C---
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAA-TNRKQDLD------PALIS--RFDSMITFGLPDHENRQEIAAQYAKHL----T---  478 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaa-TN~~~~Ld------~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~----~---  478 (567)
                      ++..+...     ....+++|.| ++..+..+      .++.-  |. ..|.|.+-..--.+..|...+...    .   
T Consensus       218 vL~~y~s~-----g~~PlIf~iTd~~~~g~nnq~rlf~~d~q~~~ri-~~IsFNPIa~T~MKK~L~ric~~e~~~~s~~k  291 (634)
T KOG1970|consen  218 VLRLYVSI-----GRCPLIFIITDSLSNGNNNQDRLFPKDIQEEPRI-SNISFNPIAPTIMKKFLKRICRIEANKKSGIK  291 (634)
T ss_pred             HHHHHHhc-----CCCcEEEEEeccccCCCcchhhhchhhhhhccCc-ceEeecCCcHHHHHHHHHHHHHHhcccccCCc
Confidence            33322221     1122333332 22233322      23322  55 578888777777777777666542    1   


Q ss_pred             ---HHHHHHHHHhccCCCHHHHHHHHHHHHHH
Q 047219          479 ---KAELAELATATEEMSGRDIRDVCQQAERS  507 (567)
Q Consensus       479 ---~~~l~~la~~t~g~s~~dL~~L~~~a~~~  507 (567)
                         ...++.++..    +++||+.+++.....
T Consensus       292 ~~~~~~v~~i~~~----s~GDIRsAInsLQls  319 (634)
T KOG1970|consen  292 VPDTAEVELICQG----SGGDIRSAINSLQLS  319 (634)
T ss_pred             CchhHHHHHHHHh----cCccHHHHHhHhhhh
Confidence               2244445444    455898888776644

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.99  E-value=0.00019  Score=77.13  Aligned_cols=70  Identities=19%  Similarity=0.242  Sum_probs=44.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh-CCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA-GAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l-~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ....++++.||+|||||+++.+++... -..   +   ..++...+......   +.++       ......+|+|||+.
T Consensus       207 e~~~Nli~lGp~GTGKThla~~l~~~~a~~s---G---~f~T~a~Lf~~L~~---~~lg-------~v~~~DlLI~DEvg  270 (449)
T TIGR02688       207 EPNYNLIELGPKGTGKSYIYNNLSPYVILIS---G---GTITVAKLFYNIST---RQIG-------LVGRWDVVAFDEVA  270 (449)
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHhHHHHHHc---C---CcCcHHHHHHHHHH---HHHh-------hhccCCEEEEEcCC
Confidence            456899999999999999999998872 111   1   22333444332211   1111       22235799999999


Q ss_pred             hhhhhhh
Q 047219          399 SFAVARD  405 (567)
Q Consensus       399 ~L~~~~q  405 (567)
                      .+....+
T Consensus       271 ylp~~~~  277 (449)
T TIGR02688       271 TLKFAKP  277 (449)
T ss_pred             CCcCCch
Confidence            9775533

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.96  E-value=3.8e-05  Score=75.13  Aligned_cols=42  Identities=31%  Similarity=0.513  Sum_probs=32.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~  363 (567)
                      .....-++|+||||+|||+++..++......   +..+++++.+.
T Consensus         9 i~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~---g~~v~yi~~e~   50 (209)
T TIGR02237         9 VERGTITQIYGPPGSGKTNICMILAVNAARQ---GKKVVYIDTEG   50 (209)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCC
Confidence            4556779999999999999999988766332   45677777754

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

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.95  E-value=0.00067  Score=67.92  Aligned_cols=176  Identities=14%  Similarity=0.148  Sum_probs=103.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH-----Hhhhhch------------hHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV-----MSKYYGE------------SERLLGKVFSLA  383 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l-----~s~~~G~------------~~~~l~~~f~~A  383 (567)
                      ...-+.++|+-|+|||.+.|++...++..   .+..++++...+     ...++.+            .+..-+.+....
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s~~~d---~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~  126 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLASLNED---QVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALV  126 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHhcCCC---ceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHH
Confidence            33467899999999999999877777543   222235554322     2222211            122223333444


Q ss_pred             hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCC----hHHHhccceEEEec
Q 047219          384 NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLD----PALISRFDSMITFG  459 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld----~aL~sRf~~~I~i~  459 (567)
                      +....+.++++||.+.+....-.        .+.-|...-+.....-.+++|+-..-...+.    ..+.+|++..|+++
T Consensus       127 ~~g~r~v~l~vdEah~L~~~~le--------~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~  198 (269)
T COG3267         127 KKGKRPVVLMVDEAHDLNDSALE--------ALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELP  198 (269)
T ss_pred             HhCCCCeEEeehhHhhhChhHHH--------HHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecC
Confidence            44444589999999998754211        1122222222222223355555432211111    23334886668888


Q ss_pred             CCCHHHHHHHHHHHHHh-------hCHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Q 047219          460 LPDHENRQEIAAQYAKH-------LTKAELAELATATEEMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       460 ~P~~~eR~eIL~~~~~~-------~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a  508 (567)
                      +.+.++-...++.+++.       +..+.+..+...+.| -|..+.++|..|...+
T Consensus       199 P~~~~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~lin~~~~~Al~~a  253 (269)
T COG3267         199 PLTEAETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRLINNLATLALDAA  253 (269)
T ss_pred             CcChHHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHHHHHHHHHHHHHH
Confidence            88988888888888875       456677888888887 5778888887776543

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.94  E-value=3.6e-05  Score=69.38  Aligned_cols=55  Identities=27%  Similarity=0.391  Sum_probs=46.1

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..|.|+.-+.+.+.+++...+..+.              .+.|.-+-|+|+||||||.+++.||+.+..
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~--------------p~KpLVlSfHG~tGtGKn~v~~liA~~ly~   79 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPN--------------PRKPLVLSFHGWTGTGKNFVSRLIAEHLYK   79 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCC--------------CCCCEEEEeecCCCCcHHHHHHHHHHHHHh
Confidence            4689999999999999998876642              455666779999999999999999999744

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>PLN03210 Resistant to P

Probab=97.94  E-value=0.00029  Score=86.05  Aligned_cols=54  Identities=26%  Similarity=0.404  Sum_probs=43.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +...+++++|.+..++++...+..                   +....+-+-|+|++|+||||+|+++++.+.
T Consensus       179 ~~~~~~~~vG~~~~l~~l~~lL~l-------------------~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~  232 (1153)
T PLN03210        179 PSNDFEDFVGIEDHIAKMSSLLHL-------------------ESEEVRMVGIWGSSGIGKTTIARALFSRLS  232 (1153)
T ss_pred             cCcccccccchHHHHHHHHHHHcc-------------------ccCceEEEEEEcCCCCchHHHHHHHHHHHh
Confidence            345678999999999998876632                   134567788999999999999999988763

syringae 6; Provisional

>KOG0479 consensus DNA replication licensing factor, MCM3 component [Replication, recombination and repair]

Probab=97.93  E-value=2.1e-05  Score=85.63  Aligned_cols=159  Identities=22%  Similarity=0.245  Sum_probs=95.2

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--------CCC
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--------PWQ  352 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--------~~~  352 (567)
                      .|-|++.+|+.|.-++.-   --|.  .+    .+--..+..-++|+.|.|.|-|+-|.|++-+..+..        .-+
T Consensus       302 SI~GH~~vKkAillLLlG---GvEk--~L----~NGshlRGDINiLlvGDPSvAKSQLLRyVLntAplAI~TTGRGSSGV  372 (818)
T KOG0479|consen  302 SIYGHDYVKKAILLLLLG---GVEK--NL----ENGSHLRGDINILLVGDPSVAKSQLLRYVLNTAPLAIATTGRGSSGV  372 (818)
T ss_pred             ccccHHHHHHHHHHHHhc---ccee--cc----CCCceeccceeEEEecCchHHHHHHHHHHHhcccccccccCCCCCCc
Confidence            478999999988655431   1111  11    111113456789999999999999999999987531        111


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      ++.-. +.    ..+--|+     +.+-..|.-.+..||++|||+|+|..-.....+++++...-.+-+..-....+.+|
T Consensus       373 GLTAA-VT----tD~eTGE-----RRLEAGAMVLADRGVVCIDEFDKMsDiDRvAIHEVMEQqtVTIaKAGIHasLNARC  442 (818)
T KOG0479|consen  373 GLTAA-VT----TDQETGE-----RRLEAGAMVLADRGVVCIDEFDKMSDIDRVAIHEVMEQQTVTIAKAGIHASLNARC  442 (818)
T ss_pred             cceeE-Ee----eccccch-----hhhhcCceEEccCceEEehhcccccchhHHHHHHHHhcceEEeEeccchhhhccce
Confidence            11111 11    1111111     22323344556679999999999975544455555543222222222222346789


Q ss_pred             EEEEeeCCCC-------------CCChHHHhccceEEEe
Q 047219          433 VVIAATNRKQ-------------DLDPALISRFDSMITF  458 (567)
Q Consensus       433 iVIaaTN~~~-------------~Ld~aL~sRf~~~I~i  458 (567)
                      -|+|+.|+..             .|++.|++|||..+.+
T Consensus       443 SVlAAANPvyG~Yd~~k~P~eNIgLpDSLLSRFDLlFv~  481 (818)
T KOG0479|consen  443 SVLAAANPVYGQYDQSKTPMENIGLPDSLLSRFDLLFVV  481 (818)
T ss_pred             eeeeecCccccccCCCCChhhccCCcHHHHhhhcEEEEE
Confidence            9999999832             4889999999876555

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.91  E-value=0.00075  Score=67.40  Aligned_cols=144  Identities=11%  Similarity=0.088  Sum_probs=100.3

Q ss_pred             CCCCceEEeeCCCC-CcHHHHHHHHHHHhCCC---CCCCcCeEEechhhHH---hhhhchhHHHHHHHHHHHh---cCCC
Q 047219          319 SNRPRAVLFEGPPG-TGKTSCARVIANQAGAM---PWQGVPLMYVPLEVVM---SKYYGESERLLGKVFSLAN---ELPN  388 (567)
Q Consensus       319 ~~~p~~VLL~GppG-TGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~l~---s~~~G~~~~~l~~~f~~A~---~~a~  388 (567)
                      ....+..||.|..+ +||..++..+++.+...   ....-.+..+..+.-.   ++..  .-+.++++.+.+.   ..++
T Consensus        12 ~kLshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I--~IdqIReL~~~l~~~p~~g~   89 (263)
T PRK06581         12 NKLYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNI--SIEQIRKLQDFLSKTSAISG   89 (263)
T ss_pred             CcchheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcc--cHHHHHHHHHHHhhCcccCC
Confidence            45567899999998 99999999988877432   1112234444322100   0111  2234555544443   2334


Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHH
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQE  468 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~e  468 (567)
                      ..|++|+++|.|..           ...+.||+.++  +++.++++|..|..+..+.+.++||| ..+.+..|+...-.+
T Consensus        90 ~KViII~~ae~mt~-----------~AANALLKtLE--EPP~~t~fILit~~~~~LLpTIrSRC-q~i~~~~p~~~~~~e  155 (263)
T PRK06581         90 YKVAIIYSAELMNL-----------NAANSCLKILE--DAPKNSYIFLITSRAASIISTIRSRC-FKINVRSSILHAYNE  155 (263)
T ss_pred             cEEEEEechHHhCH-----------HHHHHHHHhhc--CCCCCeEEEEEeCChhhCchhHhhce-EEEeCCCCCHHHHHH
Confidence            67999999999963           35588899888  47788999999999999999999999 899999999987777


Q ss_pred             HHHHHHHhhC
Q 047219          469 IAAQYAKHLT  478 (567)
Q Consensus       469 IL~~~~~~~~  478 (567)
                      .....+..+.
T Consensus       156 ~~~~~~~p~~  165 (263)
T PRK06581        156 LYSQFIQPIA  165 (263)
T ss_pred             HHHHhccccc
Confidence            7766655443

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.86  E-value=9.6e-05  Score=88.01  Aligned_cols=136  Identities=24%  Similarity=0.297  Sum_probs=93.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH--Hhhhhch----hHH---HHHHHHHHHhcCCCC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV--MSKYYGE----SER---LLGKVFSLANELPNG  389 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l--~s~~~G~----~~~---~l~~~f~~A~~~a~~  389 (567)
                      ....-++||.||+.+|||++..++|++.      +..|+.|+-.+-  ...|.|.    ...   .-..++-+|.+.  +
T Consensus       885 s~~~fP~LiQGpTSSGKTSMI~yla~~t------ghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~--G  956 (4600)
T COG5271         885 SLSNFPLLIQGPTSSGKTSMILYLARET------GHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRR--G  956 (4600)
T ss_pred             hhcCCcEEEecCCCCCcchHHHHHHHHh------CccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHHhc--C
Confidence            3455689999999999999999999999      667888886543  2344443    111   011233334443  6


Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC------------cccCCcEEEEEeeCCCC------CCChHHHhc
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG------------FEQDKKVVVIAATNRKQ------DLDPALISR  451 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~------------~~~~~~viVIaaTN~~~------~Ld~aL~sR  451 (567)
                      -.|+|||+..-+..           ++..|-+.+|.            ..+..+++++||-|+|.      .|..+++.|
T Consensus       957 yWIVLDELNLApTD-----------VLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrAFRNR 1025 (4600)
T COG5271         957 YWIVLDELNLAPTD-----------VLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRAFRNR 1025 (4600)
T ss_pred             cEEEeeccccCcHH-----------HHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHHHHhh
Confidence            79999999765422           22333333332            13457899999999876      488999999


Q ss_pred             cceEEEecCCCHHHHHHHHHHHH
Q 047219          452 FDSMITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       452 f~~~I~i~~P~~~eR~eIL~~~~  474 (567)
                      | ..++|.--+.++..+|+...+
T Consensus      1026 F-lE~hFddipedEle~ILh~rc 1047 (4600)
T COG5271        1026 F-LEMHFDDIPEDELEEILHGRC 1047 (4600)
T ss_pred             h-HhhhcccCcHHHHHHHHhccC
Confidence            9 889998888888888887654

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=97.80  E-value=0.00021  Score=68.15  Aligned_cols=34  Identities=44%  Similarity=0.595  Sum_probs=25.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      +|++||||||||+++..++.+....   +.++.+++.
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~---g~~v~~~s~   35 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR---GEPGLYVTL   35 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC---CCcEEEEEC
Confidence            7899999999999999887765332   445666654

A related protein is found in archaea.

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=97.78  E-value=3.3e-05  Score=67.77  Aligned_cols=23  Identities=35%  Similarity=0.642  Sum_probs=21.1

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhC
Q 047219          325 VLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      |+|+||||+|||++|+.|++.+.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~   23 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLL   23 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHH
Confidence            57999999999999999998874

All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses [, ]. Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated. In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues []. Several structures of SF3 helicases have been solved []. They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins []. The SF3 helicase proteins assemble into a hexameric ring. Some proteins known to contain an SF3 helicase domain are listed below: Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein. The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.76  E-value=0.00018  Score=74.36  Aligned_cols=168  Identities=20%  Similarity=0.273  Sum_probs=97.6

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      -.+.|..+..+.+.+.+.....                 ....++|++.||.|+|||.+....-...... -.+.-.+.+
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~-----------------~gEsnsviiigprgsgkT~li~~~Ls~~q~~-~E~~l~v~L   85 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTIL-----------------HGESNSVIIIGPRGSGKTILIDTRLSDIQEN-GENFLLVRL   85 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHH-----------------hcCCCceEEEccCCCCceEeeHHHHhhHHhc-CCeEEEEEE
Confidence            4578888888888888775422                 3456899999999999998766554442111 001123334


Q ss_pred             chhhHHhh-------------------hhchhHHHHHHHHHHHhc---CCCC-cEEEEcCcchhhhhhhhhhHHHHHHHH
Q 047219          360 PLEVVMSK-------------------YYGESERLLGKVFSLANE---LPNG-AIIFLDEVDSFAVARDSEMHEATRRIL  416 (567)
Q Consensus       360 ~~~~l~s~-------------------~~G~~~~~l~~~f~~A~~---~a~~-~ILfIDEID~L~~~~q~~l~~~~~~vl  416 (567)
                      ++.....+                   .+|.....+..++...+.   .... .|.++||||.+++..       .+..+
T Consensus        86 ng~~~~dk~al~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~-------rQtll  158 (408)
T KOG2228|consen   86 NGELQTDKIALKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHS-------RQTLL  158 (408)
T ss_pred             CccchhhHHHHHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccch-------hhHHH
Confidence            43322211                   133333344444443331   2222 344577999987542       12222


Q ss_pred             HHHHHhhcCcccCCcEEEEEeeCCCC---CCChHHHhccceE-EEe-cCCCHHHHHHHHHHHH
Q 047219          417 SVLLRQIDGFEQDKKVVVIAATNRKQ---DLDPALISRFDSM-ITF-GLPDHENRQEIAAQYA  474 (567)
Q Consensus       417 ~~LL~~ld~~~~~~~viVIaaTN~~~---~Ld~aL~sRf~~~-I~i-~~P~~~eR~eIL~~~~  474 (567)
                      ..++..-.  ....++.||+.|.+-+   .|...+.+||... |++ +..++++...+++.++
T Consensus       159 YnlfDisq--s~r~Piciig~Ttrld~lE~LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  159 YNLFDISQ--SARAPICIIGVTTRLDILELLEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             HHHHHHHh--hcCCCeEEEEeeccccHHHHHHHHHHhhcccceeeccCCCChHHHHHHHHHHh
Confidence            33333222  2356888888887644   5678888999654 555 4447888888888776

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.74  E-value=0.00017  Score=71.49  Aligned_cols=41  Identities=32%  Similarity=0.503  Sum_probs=32.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      .....-++|+|+||+|||+++..++.+....   +.++++++.+
T Consensus        20 i~~g~i~~i~G~~GsGKT~l~~~la~~~~~~---~~~v~yi~~e   60 (225)
T PRK09361         20 FERGTITQIYGPPGSGKTNICLQLAVEAAKN---GKKVIYIDTE   60 (225)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEECC
Confidence            4556678999999999999999999866332   4567777776

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.72  E-value=0.00089  Score=70.40  Aligned_cols=201  Identities=17%  Similarity=0.213  Sum_probs=113.7

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ..+.+.+.+++.+...+-.   .+               -..|..+.|+|..|||||.+.|.+-+.+      +.+.+++
T Consensus         6 ~~v~~Re~qi~~L~~Llg~---~~---------------~~~PS~~~iyG~sgTGKT~~~r~~l~~~------n~~~vw~   61 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGN---NS---------------CTIPSIVHIYGHSGTGKTYLVRQLLRKL------NLENVWL   61 (438)
T ss_pred             cCccchHHHHHHHHHHhCC---CC---------------cccceeEEEeccCCCchhHHHHHHHhhc------CCcceee
Confidence            3567888888888765521   11               2357788999999999999999999998      3445555


Q ss_pred             chhhHH----------hhh-----hchh----HHHH---HHHHHH---HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          360 PLEVVM----------SKY-----YGES----ERLL---GKVFSL---ANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       360 ~~~~l~----------s~~-----~G~~----~~~l---~~~f~~---A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      ++-+..          .+.     -|..    ...+   -..|..   +.+......|++|.+|.+... ..       -
T Consensus        62 n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~-~a-------~  133 (438)
T KOG2543|consen   62 NCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDM-DA-------I  133 (438)
T ss_pred             ehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhcc-ch-------H
Confidence            543211          111     0110    0111   112222   223333578899999998522 11       1


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh----cc-ceEEEecCCCHHHHHHHHHHHHH-hhC--------HH
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS----RF-DSMITFGLPDHENRQEIAAQYAK-HLT--------KA  480 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s----Rf-~~~I~i~~P~~~eR~eIL~~~~~-~~~--------~~  480 (567)
                      .+..+++.-+-...+ .+.+|...-.    .+..+.    .+ -.+++|+.|+.++-..|+..--. ...        .-
T Consensus       134 ll~~l~~L~el~~~~-~i~iils~~~----~e~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~~~p~~r~~~~ya~fl~v  208 (438)
T KOG2543|consen  134 LLQCLFRLYELLNEP-TIVIILSAPS----CEKQYLINTGTLEIVVLHFPQYSVEETQVILSRDNPGKRKLDVYAQFLHV  208 (438)
T ss_pred             HHHHHHHHHHHhCCC-ceEEEEeccc----cHHHhhcccCCCCceEEecCCCCHHHHHHHHhcCCccccchHHHHHHHHH
Confidence            233333333322222 3444433322    122221    11 24788999999999998874322 111        12


Q ss_pred             HHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHhccccc
Q 047219          481 ELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITK  519 (567)
Q Consensus       481 ~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~i~~~i~~  519 (567)
                      .+.-+...+.  ...+++.+...+|...++++..+.++.
T Consensus       209 ~l~vF~~~cr--d~~eL~~~~~~~wpky~epi~~~~i~~  245 (438)
T KOG2543|consen  209 LLQVFYMACR--DVNELRSLISLAWPKYCEPITKGKIDP  245 (438)
T ss_pred             HHHHHHHHhC--CHHHHHHHHHHHHHhhccccccCCCCh
Confidence            2333444443  678888999999988888877766543

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.67  E-value=0.00029  Score=71.31  Aligned_cols=88  Identities=23%  Similarity=0.238  Sum_probs=51.9

Q ss_pred             ccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech------hhHHhhh--------hchh-HH---HHHH
Q 047219          317 FESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL------EVVMSKY--------YGES-ER---LLGK  378 (567)
Q Consensus       317 ~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~------~~l~s~~--------~G~~-~~---~l~~  378 (567)
                      +....+.-++|.||+|||||++++.+++......|...-++++..      .++....        .++. ..   ....
T Consensus        11 ~~i~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~~~fdv~~~v~vI~er~~ev~el~~~I~~~~v~~~~~~~~~~~~~~~~~   90 (249)
T cd01128          11 APIGKGQRGLIVAPPKAGKTTLLQSIANAITKNHPEVYLIVLLIDERPEEVTDMQRSVKGEVIASTFDEPPERHVQVAEM   90 (249)
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhccccccCCeEEEEEEccCCCccHHHHHHHhccEEEEecCCCCHHHHHHHHHH
Confidence            345677889999999999999999999988654221222333222      2222222        1211 11   1122


Q ss_pred             HHHHHh---cCCCCcEEEEcCcchhhhhh
Q 047219          379 VFSLAN---ELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       379 ~f~~A~---~~a~~~ILfIDEID~L~~~~  404 (567)
                      +.+.|+   ......+||+||+++++...
T Consensus        91 ~~~~a~~~~~~G~~vll~iDei~r~a~a~  119 (249)
T cd01128          91 VLEKAKRLVEHGKDVVILLDSITRLARAY  119 (249)
T ss_pred             HHHHHHHHHHCCCCEEEEEECHHHhhhhh
Confidence            233333   23446899999999997654

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.

>TIGR02012 tigrfam_recA protein RecA

Probab=97.66  E-value=0.00025  Score=74.15  Aligned_cols=117  Identities=22%  Similarity=0.267  Sum_probs=66.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh----hc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY----YG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~----~G------------~~~~~l~~~f~~  382 (567)
                      .+....++|+||||||||+||..++.+....   +..+++++.+......    +|            ..+..+..+...
T Consensus        52 lp~G~iteI~G~~GsGKTtLaL~~~~~~~~~---g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~l  128 (321)
T TIGR02012        52 LPRGRIIEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETL  128 (321)
T ss_pred             CcCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHH
Confidence            4566779999999999999988877665433   5567777765433211    11            122222222222


Q ss_pred             HhcCCCCcEEEEcCcchhhhhh--hhh----hHHHHHHHHHHHHHhhcCcccCCcEEEEEeeC
Q 047219          383 ANELPNGAIIFLDEVDSFAVAR--DSE----MHEATRRILSVLLRQIDGFEQDKKVVVIAATN  439 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~--q~~----l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN  439 (567)
                      .+.. ...+|+||-+..+.+..  +..    ......+.+..++..+...-...++.+|.+..
T Consensus       129 i~~~-~~~lIVIDSv~al~~~~E~e~~~g~~~~~~~aR~m~~~lr~L~~~l~~~~~tvi~tNQ  190 (321)
T TIGR02012       129 VRSG-AVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALSKSNTTAIFINQ  190 (321)
T ss_pred             hhcc-CCcEEEEcchhhhccchhhcccccccchhHHHHHHHHHHHHHHHHHHhCCCEEEEEec
Confidence            2233 35899999999887531  111    01112233344444444444456677776653

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.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.59  E-value=0.00018  Score=71.42  Aligned_cols=25  Identities=40%  Similarity=0.631  Sum_probs=21.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..|..+||||+||+|||++|+.++.
T Consensus        10 ~~~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        10 RIPNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CCCcEEEEECCCCCCHHHHHHhcCC
Confidence            3467799999999999999999874

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.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.58  E-value=0.0002  Score=69.84  Aligned_cols=38  Identities=29%  Similarity=0.482  Sum_probs=26.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..+..++.|+||||||++++.+...+...   +..++.+..
T Consensus        17 ~~~~~~l~G~aGtGKT~~l~~~~~~~~~~---g~~v~~~ap   54 (196)
T PF13604_consen   17 GDRVSVLQGPAGTGKTTLLKALAEALEAA---GKRVIGLAP   54 (196)
T ss_dssp             TCSEEEEEESTTSTHHHHHHHHHHHHHHT---T--EEEEES
T ss_pred             CCeEEEEEECCCCCHHHHHHHHHHHHHhC---CCeEEEECC
Confidence            34568889999999999999998877543   334444443

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.58  E-value=0.00055  Score=71.45  Aligned_cols=102  Identities=20%  Similarity=0.252  Sum_probs=59.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh-------hhchhHHHHHHHHHHHhcCCCCcE
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK-------YYGESERLLGKVFSLANELPNGAI  391 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~-------~~G~~~~~l~~~f~~A~~~a~~~I  391 (567)
                      ..+++++.|||+-|+|||.|.-.....++.......+|     ..+|..       +.|++ .-+..+-.+....  ..+
T Consensus        62 ~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HF-----h~FM~~vH~~l~~l~g~~-dpl~~iA~~~~~~--~~v  133 (367)
T COG1485          62 HGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHF-----HRFMARVHQRLHTLQGQT-DPLPPIADELAAE--TRV  133 (367)
T ss_pred             CCCCceEEEECCCCccHHHHHHHHHhhCCccccccccH-----HHHHHHHHHHHHHHcCCC-CccHHHHHHHHhc--CCE
Confidence            56889999999999999999999999885432112222     233332       23433 2222222222222  369


Q ss_pred             EEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC
Q 047219          392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR  440 (567)
Q Consensus       392 LfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~  440 (567)
                      |+|||++-=.      ..++  -++..|+..+-    ..+|++++|+|.
T Consensus       134 LCfDEF~VtD------I~DA--MiL~rL~~~Lf----~~GV~lvaTSN~  170 (367)
T COG1485         134 LCFDEFEVTD------IADA--MILGRLLEALF----ARGVVLVATSNT  170 (367)
T ss_pred             EEeeeeeecC------hHHH--HHHHHHHHHHH----HCCcEEEEeCCC
Confidence            9999996421      1111  13333333322    247899999997

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.58  E-value=0.00033  Score=74.70  Aligned_cols=86  Identities=27%  Similarity=0.278  Sum_probs=50.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE-Eechh------hHHhhhhc---------hhHHHHH---HH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM-YVPLE------VVMSKYYG---------ESERLLG---KV  379 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~-~i~~~------~l~s~~~G---------~~~~~l~---~~  379 (567)
                      ...+.-.+|+||||||||+|++.|++......+ ++.++ .+..+      ++.....|         ......+   .+
T Consensus       166 IGkGQR~lIvgppGvGKTTLaK~Ian~I~~nhF-Dv~~~VvLIgER~~EVtdiqrsIlg~vv~st~d~~~~~~~~~a~~~  244 (416)
T PRK09376        166 IGKGQRGLIVAPPKAGKTVLLQNIANSITTNHP-EVHLIVLLIDERPEEVTDMQRSVKGEVVASTFDEPAERHVQVAEMV  244 (416)
T ss_pred             cccCceEEEeCCCCCChhHHHHHHHHHHHhhcC-CeEEEEEEeCCchhHHHHHHHHhcCcEEEECCCCCHHHHHHHHHHH
Confidence            455667899999999999999999998854322 23322 22221      11111111         1222222   23


Q ss_pred             HHHHh---cCCCCcEEEEcCcchhhhhhh
Q 047219          380 FSLAN---ELPNGAIIFLDEVDSFAVARD  405 (567)
Q Consensus       380 f~~A~---~~a~~~ILfIDEID~L~~~~q  405 (567)
                      ++.|+   ......+||||||++++....
T Consensus       245 ie~Ae~~~e~G~dVlL~iDsItR~arAqr  273 (416)
T PRK09376        245 IEKAKRLVEHGKDVVILLDSITRLARAYN  273 (416)
T ss_pred             HHHHHHHHHcCCCEEEEEEChHHHHHHHH
Confidence            33333   334568999999999986543

>PRK14700 recombination factor protein RarA; Provisional

Probab=97.54  E-value=0.00057  Score=70.20  Aligned_cols=122  Identities=17%  Similarity=0.215  Sum_probs=87.9

Q ss_pred             cCCcEEEEEee--CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----------hCHHHHHHHHHhccCCCHH
Q 047219          428 QDKKVVVIAAT--NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----------LTKAELAELATATEEMSGR  495 (567)
Q Consensus       428 ~~~~viVIaaT--N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----------~~~~~l~~la~~t~g~s~~  495 (567)
                      .++.+++|+||  |+...++++|+||| +++.+..++.++...+++..+..          +.++.++.++....|    
T Consensus         5 E~G~i~LIGATTENP~f~vn~ALlSR~-~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~G----   79 (300)
T PRK14700          5 ESGKIILIGATTENPTYYLNDALVSRL-FILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEG----   79 (300)
T ss_pred             cCCcEEEEeecCCCccceecHhhhhhh-heeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCC----
Confidence            36789999988  78889999999999 99999999999999999987752          345566666665554    


Q ss_pred             HHHHHHHHHHHHHHHHHHhccccccCcccCCCcHHHHHHHHHHHHHHHHHHHHHHHhhH-----HhhhhccCC
Q 047219          496 DIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNI-----NNHRTKKQP  563 (567)
Q Consensus       496 dL~~L~~~a~~~a~~r~i~~~i~~~~~~~~~~~l~e~le~~e~~~~~li~~al~~~~~~-----~s~~~~~~~  563 (567)
                      |.|.+++.......  ...   ...  .  .....+.++.....+...+++..+.||++     ||+|+.++|
T Consensus        80 DaR~aLN~LE~a~~--~~~---~~~--~--~~it~~~~~~~~~~~~~~yDk~gd~HYd~iSAf~KSiRGSDpD  143 (300)
T PRK14700         80 DCRKILNLLERMFL--IST---RGD--E--IYLNKELFDQAVGETSRDFHREGKEFYEQLSAFHKSVRGTDPD  143 (300)
T ss_pred             HHHHHHHHHHHHHh--hcc---ccC--C--CccCHHHHHHHHhHHHhcccCCcchhHHHHHHHHHHhhcCCcc
Confidence            88887776654321  000   000  0  01223566666666677899999999986     888887766

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=97.50  E-value=0.00017  Score=70.03  Aligned_cols=68  Identities=13%  Similarity=0.179  Sum_probs=38.9

Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCC
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                      ++++|+|||++.+.+.+....... ..    .+..+.. ....+.-||.+|..+..+++.++...+..+++..+
T Consensus        79 ~~~liviDEa~~~~~~r~~~~~~~-~~----~~~~l~~-hRh~g~diiliTQ~~~~id~~ir~lve~~~~~~k~  146 (193)
T PF05707_consen   79 KGSLIVIDEAQNFFPSRSWKGKKV-PE----IIEFLAQ-HRHYGWDIILITQSPSQIDKFIRDLVEYHYHCRKL  146 (193)
T ss_dssp             TT-EEEETTGGGTSB---T-T-----H----HHHGGGG-CCCTT-EEEEEES-GGGB-HHHHCCEEEEEEEEE-
T ss_pred             CCcEEEEECChhhcCCCccccccc-hH----HHHHHHH-hCcCCcEEEEEeCCHHHHhHHHHHHHheEEEEEee
Confidence            479999999999988876532111 12    2233322 23456788889999999999999877666665433

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.47  E-value=0.00099  Score=72.05  Aligned_cols=121  Identities=17%  Similarity=0.213  Sum_probs=71.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVA  403 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~  403 (567)
                      .++|+||.+|||||+++.+.+.....      .++++..+.......- .+.+ ..+..+... ....+|||||+.+.. 
T Consensus        39 i~~i~GpR~~GKTtll~~l~~~~~~~------~iy~~~~d~~~~~~~l-~d~~-~~~~~~~~~-~~~yifLDEIq~v~~-  108 (398)
T COG1373          39 IILILGPRQVGKTTLLKLLIKGLLEE------IIYINFDDLRLDRIEL-LDLL-RAYIELKER-EKSYIFLDEIQNVPD-  108 (398)
T ss_pred             EEEEECCccccHHHHHHHHHhhCCcc------eEEEEecchhcchhhH-HHHH-HHHHHhhcc-CCceEEEecccCchh-
Confidence            89999999999999998888887331      4555544443322111 1111 122222222 347999999998742 


Q ss_pred             hhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC--CCCCChHHHhccceEEEecCCCHHHHHH
Q 047219          404 RDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR--KQDLDPALISRFDSMITFGLPDHENRQE  468 (567)
Q Consensus       404 ~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~--~~~Ld~aL~sRf~~~I~i~~P~~~eR~e  468 (567)
                                 +...+-...|....  ++++.+++..  .....+.|..|. ..+++.+.+..+...
T Consensus       109 -----------W~~~lk~l~d~~~~--~v~itgsss~ll~~~~~~~L~GR~-~~~~l~PlSF~Efl~  161 (398)
T COG1373         109 -----------WERALKYLYDRGNL--DVLITGSSSSLLSKEISESLAGRG-KDLELYPLSFREFLK  161 (398)
T ss_pred             -----------HHHHHHHHHccccc--eEEEECCchhhhccchhhhcCCCc-eeEEECCCCHHHHHh
Confidence                       22222223332111  3444443322  445667777896 888899999999865

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=97.45  E-value=0.00015  Score=84.65  Aligned_cols=160  Identities=24%  Similarity=0.252  Sum_probs=102.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch-------hHHHHHHHH---HHHh-cCCCCcEE
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE-------SERLLGKVF---SLAN-ELPNGAII  392 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~-------~~~~l~~~f---~~A~-~~a~~~IL  392 (567)
                      .++++||||+|||+.++++|.++      +..++..+.+...+++...       ....+...|   .... ......+|
T Consensus       359 ~~l~~G~pGigKT~~~h~~~k~~------g~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vi  432 (871)
T KOG1968|consen  359 ALLLSGPPGIGKTTAAHKAAKEL------GFKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLI  432 (871)
T ss_pred             HHHhcCCCCCCchhhHhhhhhhc------ccceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEE
Confidence            46999999999999999999999      7778888887665543221       111122222   0000 11234699


Q ss_pred             EEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHH
Q 047219          393 FLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       393 fIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~  472 (567)
                      ++||+|-+.....+        .+..+-....    ....-+|+++|...........|-+..++|..|+...+..-+..
T Consensus       433 l~devD~~~~~dRg--------~v~~l~~l~~----ks~~Piv~~cndr~~p~sr~~~~~~~~l~f~kP~~~~i~~ri~s  500 (871)
T KOG1968|consen  433 LMDEVDGMFGEDRG--------GVSKLSSLCK----KSSRPLVCTCNDRNLPKSRALSRACSDLRFSKPSSELIRSRIMS  500 (871)
T ss_pred             EEeccccccchhhh--------hHHHHHHHHH----hccCCeEEEecCCCCccccchhhhcceeeecCCcHHHHHhhhhh
Confidence            99999998752111        1122222221    23456788888766666555555446899999999888877776


Q ss_pred             HHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          473 YAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       473 ~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .+..    +....++++...+    ++||++.+.+..
T Consensus       501 i~~se~~ki~~~~l~~~s~~~----~~DiR~~i~~lq  533 (871)
T KOG1968|consen  501 ICKSEGIKISDDVLEEISKLS----GGDIRQIIMQLQ  533 (871)
T ss_pred             hhcccceecCcHHHHHHHHhc----ccCHHHHHHHHh
Confidence            6543    4555677776655    668888877654

>PF07693 KAP_NTPase: KAP family P-loop domain; InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals

Probab=97.45  E-value=0.0088  Score=62.28  Aligned_cols=30  Identities=20%  Similarity=0.298  Sum_probs=26.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      ..+..+.|+|+=|+|||++.+.+-+.+...
T Consensus        18 ~~~~~IgL~G~WGsGKSs~l~~l~~~L~~~   47 (325)
T PF07693_consen   18 DDPFVIGLYGEWGSGKSSFLNMLKEELKED   47 (325)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            678889999999999999999999888543

Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side [].

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.41  E-value=0.00018  Score=79.75  Aligned_cols=56  Identities=20%  Similarity=0.342  Sum_probs=44.1

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      -|+|+.|+++++.++.+.+......      +         ......++|.||||+|||+||+.|++.+..
T Consensus        74 fF~d~yGlee~ieriv~~l~~Aa~g------l---------~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         74 AFEEFYGMEEAIEQIVSYFRHAAQG------L---------EEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             chhcccCcHHHHHHHHHHHHHHHHh------c---------CCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            4889999999999998877533111      1         234467899999999999999999998753

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.41  E-value=0.0011  Score=71.09  Aligned_cols=80  Identities=21%  Similarity=0.332  Sum_probs=51.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh------hch--------hHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY------YGE--------SERLLGKVFSLAN  384 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~------~G~--------~~~~l~~~f~~A~  384 (567)
                      ..+..-++|+|+||+|||+++..++......   +.++++++.++-....      +|.        .+..+..+++.+.
T Consensus        79 i~~GslvLI~G~pG~GKStLllq~a~~~a~~---g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~  155 (372)
T cd01121          79 LVPGSVILIGGDPGIGKSTLLLQVAARLAKR---GGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASIE  155 (372)
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHH
Confidence            4566779999999999999999998876432   3457777654322211      111        1122344555554


Q ss_pred             cCCCCcEEEEcCcchhhh
Q 047219          385 ELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       385 ~~a~~~ILfIDEID~L~~  402 (567)
                      ... +.+|+||+|..+..
T Consensus       156 ~~~-~~lVVIDSIq~l~~  172 (372)
T cd01121         156 ELK-PDLVIIDSIQTVYS  172 (372)
T ss_pred             hcC-CcEEEEcchHHhhc
Confidence            444 58999999998853

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.

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

Probab=97.41  E-value=0.00096  Score=69.94  Aligned_cols=117  Identities=23%  Similarity=0.302  Sum_probs=64.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh----hc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY----YG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~----~G------------~~~~~l~~~f~~  382 (567)
                      .+...-+.++||||||||+||-.++.+....   +..+++++.+.-...-    +|            ..+..+..+...
T Consensus        52 lp~G~iteI~Gp~GsGKTtLal~~~~~~~~~---g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~l  128 (325)
T cd00983          52 YPKGRIIEIYGPESSGKTTLALHAIAEAQKL---GGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSL  128 (325)
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHH
Confidence            4556678999999999999999888765432   5567777765422210    11            122222222222


Q ss_pred             HhcCCCCcEEEEcCcchhhhhhh--hhh----HHHHHHHHHHHHHhhcCcccCCcEEEEEeeC
Q 047219          383 ANELPNGAIIFLDEVDSFAVARD--SEM----HEATRRILSVLLRQIDGFEQDKKVVVIAATN  439 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~q--~~l----~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN  439 (567)
                      ++.. ...+|+||-+..+.+..+  ...    .....+.+.+++..+...-...++.+|.+..
T Consensus       129 i~s~-~~~lIVIDSvaal~~~~E~~~~~~~~~~~~qaR~l~~~Lr~L~~~~~k~~~~vI~tNQ  190 (325)
T cd00983         129 VRSG-AVDLIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGSINKSNTTVIFINQ  190 (325)
T ss_pred             Hhcc-CCCEEEEcchHhhcccccccccccccchHHHHHHHHHHHHHHHHHHHhCCCEEEEEEc
Confidence            2233 358999999998875311  111    0111233344444443333445666666543

RecA couples ATP hydrolysis to DNA strand exchange.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.39  E-value=0.0011  Score=66.07  Aligned_cols=41  Identities=27%  Similarity=0.338  Sum_probs=30.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      .+.+..++++|+||||||+++..++......   +..+.+++.+
T Consensus        22 ~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~---g~~~~y~~~e   62 (234)
T PRK06067         22 IPFPSLILIEGDHGTGKSVLSQQFVYGALKQ---GKKVYVITTE   62 (234)
T ss_pred             CcCCcEEEEECCCCCChHHHHHHHHHHHHhC---CCEEEEEEcC
Confidence            5667789999999999999999997654222   4456666543

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.39  E-value=0.0012  Score=66.07  Aligned_cols=40  Identities=25%  Similarity=0.273  Sum_probs=27.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      .+....+++.|+||||||+++..++......   +..+.+++.
T Consensus        21 i~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~---g~~~~yi~~   60 (230)
T PRK08533         21 IPAGSLILIEGDESTGKSILSQRLAYGFLQN---GYSVSYVST   60 (230)
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHHHhC---CCcEEEEeC
Confidence            4556789999999999999975555444211   344555554

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.37  E-value=0.0019  Score=70.83  Aligned_cols=80  Identities=24%  Similarity=0.338  Sum_probs=52.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh------hch--------hHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY------YGE--------SERLLGKVFSLAN  384 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~------~G~--------~~~~l~~~f~~A~  384 (567)
                      ..+..-++|+|+||+|||+++..++......   +.++++++.++-....      +|.        .+..+..+++...
T Consensus        77 i~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~---g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~  153 (446)
T PRK11823         77 LVPGSVVLIGGDPGIGKSTLLLQVAARLAAA---GGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATIE  153 (446)
T ss_pred             ccCCEEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHH
Confidence            4556779999999999999999998876432   4567777765433322      111        1122344555554


Q ss_pred             cCCCCcEEEEcCcchhhh
Q 047219          385 ELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       385 ~~a~~~ILfIDEID~L~~  402 (567)
                      +.. +.+|+||+|..+..
T Consensus       154 ~~~-~~lVVIDSIq~l~~  170 (446)
T PRK11823        154 EEK-PDLVVIDSIQTMYS  170 (446)
T ss_pred             hhC-CCEEEEechhhhcc
Confidence            444 48999999998854

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.36  E-value=0.0021  Score=60.69  Aligned_cols=29  Identities=21%  Similarity=0.449  Sum_probs=25.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++-.++|.||+|||||+|.|++|....
T Consensus        26 v~~Ge~iaitGPSG~GKStllk~va~Lis   54 (223)
T COG4619          26 VRAGEFIAITGPSGCGKSTLLKIVASLIS   54 (223)
T ss_pred             ecCCceEEEeCCCCccHHHHHHHHHhccC
Confidence            46677899999999999999999998764

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.33  E-value=0.0021  Score=68.80  Aligned_cols=101  Identities=15%  Similarity=0.230  Sum_probs=56.8

Q ss_pred             HHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH-
Q 047219          286 DQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV-  364 (567)
Q Consensus       286 ~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l-  364 (567)
                      .+.++.+.+.+...+..+..+            ...+..++|.||+|+||||++..||..+...   +..+..+++... 
T Consensus       217 ~~~~~~l~~~l~~~l~~~~~~------------~~~~~vI~LVGptGvGKTTTiaKLA~~L~~~---GkkVglI~aDt~R  281 (436)
T PRK11889        217 EEVIEYILEDMRSHFNTENVF------------EKEVQTIALIGPTGVGKTTTLAKMAWQFHGK---KKTVGFITTDHSR  281 (436)
T ss_pred             HHHHHHHHHHHHHHhcccccc------------ccCCcEEEEECCCCCcHHHHHHHHHHHHHHc---CCcEEEEecCCcc
Confidence            455666666555443332111            2345789999999999999999999887432   223333333211 


Q ss_pred             ------Hhhh---------hchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          365 ------MSKY---------YGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       365 ------~s~~---------~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                            ...|         .......+...+..+.......+||||-.....
T Consensus       282 iaAvEQLk~yae~lgipv~v~~d~~~L~~aL~~lk~~~~~DvVLIDTaGRs~  333 (436)
T PRK11889        282 IGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFKEEARVDYILIDTAGKNY  333 (436)
T ss_pred             hHHHHHHHHHhhhcCCcEEecCCHHHHHHHHHHHHhccCCCEEEEeCccccC
Confidence                  1111         012333444455444432224799999887754

>PHA02624 large T antigen; Provisional

Probab=97.32  E-value=0.0026  Score=71.09  Aligned_cols=120  Identities=18%  Similarity=0.254  Sum_probs=65.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      .+..+.++|+||||||||+++.+|.+.+.      -..+.++++.-.+.+          .+.-+.   ...+.+||++.
T Consensus       428 iPKk~~il~~GPpnTGKTtf~~sLl~~L~------G~vlsVNsPt~ks~F----------wL~pl~---D~~~~l~dD~t  488 (647)
T PHA02624        428 VPKRRYWLFKGPVNSGKTTLAAALLDLCG------GKSLNVNCPPDKLNF----------ELGCAI---DQFMVVFEDVK  488 (647)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHcC------CeEEEeeCCcchhHH----------Hhhhhh---hceEEEeeecc
Confidence            34456899999999999999999999994      234555543322211          111111   24688888885


Q ss_pred             hhhhhhhh-hhHHHHHHHHHHHHHhhcCc-c-------cC-Cc---EEEEEeeCCCCCCChHHHhccceEEEec
Q 047219          399 SFAVARDS-EMHEATRRILSVLLRQIDGF-E-------QD-KK---VVVIAATNRKQDLDPALISRFDSMITFG  459 (567)
Q Consensus       399 ~L~~~~q~-~l~~~~~~vl~~LL~~ld~~-~-------~~-~~---viVIaaTN~~~~Ld~aL~sRf~~~I~i~  459 (567)
                      .-.....+ ..+..+. -+..|...+||- .       .+ ..   --+|.||| ...++..+.-||..++.|.
T Consensus       489 ~~~~~~~~Lp~G~~~d-Nl~~lRn~LDG~V~v~ld~KH~n~~q~~~PPlliT~N-ey~iP~T~~~Rf~~~~~F~  560 (647)
T PHA02624        489 GQPADNKDLPSGQGMN-NLDNLRDYLDGSVPVNLEKKHLNKRSQIFPPGIVTMN-EYLIPQTVKARFAKVLDFK  560 (647)
T ss_pred             ccccccccCCcccccc-hhhHHHhhcCCCCccccchhccCchhccCCCeEEeec-CcccchhHHHHHHHhcccc
Confidence            32210000 0000000 012333344543 1       11 01   13466777 5678889999998888874

>PRK06762 hypothetical protein; Provisional

Probab=97.30  E-value=0.00096  Score=62.71  Aligned_cols=41  Identities=24%  Similarity=0.447  Sum_probs=32.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      |.-++|+|+||+||||+|+.+++.+      +.++..++...+...+
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l------~~~~~~i~~D~~r~~l   42 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERL------GRGTLLVSQDVVRRDM   42 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh------CCCeEEecHHHHHHHh
Confidence            4568899999999999999999998      3346667766665543

>PRK10536 hypothetical protein; Provisional

Probab=97.30  E-value=0.002  Score=65.20  Aligned_cols=48  Identities=17%  Similarity=0.182  Sum_probs=35.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ....+..|-+.......+...+.                      . ..-+++.||+|||||+||.+++.+
T Consensus        50 ~~~~~~~i~p~n~~Q~~~l~al~----------------------~-~~lV~i~G~aGTGKT~La~a~a~~   97 (262)
T PRK10536         50 DSRDTSPILARNEAQAHYLKAIE----------------------S-KQLIFATGEAGCGKTWISAAKAAE   97 (262)
T ss_pred             hhcCCccccCCCHHHHHHHHHHh----------------------c-CCeEEEECCCCCCHHHHHHHHHHH
Confidence            34556667777777766665442                      1 247999999999999999999985

>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=97.29  E-value=0.00022  Score=63.19  Aligned_cols=22  Identities=36%  Similarity=0.877  Sum_probs=21.2

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|.|+||+||||+|+.+++.+
T Consensus         2 I~I~G~~gsGKST~a~~La~~~   23 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL   23 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999999998

...

>PRK04296 thymidine kinase; Provisional

Probab=97.29  E-value=0.0016  Score=63.09  Aligned_cols=25  Identities=16%  Similarity=0.102  Sum_probs=21.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .-.+++||+|+|||+++..++..+.
T Consensus         3 ~i~litG~~GsGKTT~~l~~~~~~~   27 (190)
T PRK04296          3 KLEFIYGAMNSGKSTELLQRAYNYE   27 (190)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHH
Confidence            3578999999999999988887763

>PF13671 AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1_A 1RRC_A 1RPZ_A 3ZVM_A 1YJ5_A 3ZVL_A 3U7E_B

Probab=97.27  E-value=0.00099  Score=60.58  Aligned_cols=38  Identities=26%  Similarity=0.635  Sum_probs=30.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      +++.|+||+||||+|+.+++.+      +  +..++...+...+.+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~------~--~~~i~~D~~~~~~~~   39 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRL------G--AVVISQDEIRRRLAG   39 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHS------T--EEEEEHHHHHHHHCC
T ss_pred             EEEECCCCCCHHHHHHHHHHHC------C--CEEEeHHHHHHHHcc
Confidence            6899999999999999999988      3  556777776665544

...

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.27  E-value=0.0061  Score=72.35  Aligned_cols=155  Identities=19%  Similarity=0.251  Sum_probs=80.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh-----HHhhh---h-----ch---------------
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV-----VMSKY---Y-----GE---------------  371 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~-----l~s~~---~-----G~---------------  371 (567)
                      ...+-++++||+|.|||+++...++...     .+..++++..+     +...+   +     +.               
T Consensus        30 ~~~~~~~v~apaG~GKTtl~~~~~~~~~-----~~~w~~l~~~d~~~~~f~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~  104 (903)
T PRK04841         30 NNYRLVLVTSPAGYGKTTLISQWAAGKN-----NLGWYSLDESDNQPERFASYLIAALQQATNGHCSKSEALAQKRQYAS  104 (903)
T ss_pred             cCCCeEEEECCCCCCHHHHHHHHHHhCC-----CeEEEecCcccCCHHHHHHHHHHHHHHhcCcccchhhhhhccCCcCC
Confidence            3456699999999999999998876542     11222332211     10000   0     00               


Q ss_pred             hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCC-hHHHh
Q 047219          372 SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLD-PALIS  450 (567)
Q Consensus       372 ~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld-~aL~s  450 (567)
                      ....+..++........+.+|+|||+|.+...       ...+.+..|+..     .+.++.+|.++.....+. ..++-
T Consensus       105 ~~~~~~~~~~~l~~~~~~~~lvlDD~h~~~~~-------~~~~~l~~l~~~-----~~~~~~lv~~sR~~~~~~~~~l~~  172 (903)
T PRK04841        105 LSSLFAQLFIELADWHQPLYLVIDDYHLITNP-------EIHEAMRFFLRH-----QPENLTLVVLSRNLPPLGIANLRV  172 (903)
T ss_pred             HHHHHHHHHHHHhcCCCCEEEEEeCcCcCCCh-------HHHHHHHHHHHh-----CCCCeEEEEEeCCCCCCchHhHHh
Confidence            01112233333333344689999999998422       222333444432     244555555664422232 12221


Q ss_pred             ccceEEEec----CCCHHHHHHHHHHHHH-hhCHHHHHHHHHhccCC
Q 047219          451 RFDSMITFG----LPDHENRQEIAAQYAK-HLTKAELAELATATEEM  492 (567)
Q Consensus       451 Rf~~~I~i~----~P~~~eR~eIL~~~~~-~~~~~~l~~la~~t~g~  492 (567)
                       -+..+++.    ..+.++-.+.+...+. .+..+....+.+.|.|.
T Consensus       173 -~~~~~~l~~~~l~f~~~e~~~ll~~~~~~~~~~~~~~~l~~~t~Gw  218 (903)
T PRK04841        173 -RDQLLEIGSQQLAFDHQEAQQFFDQRLSSPIEAAESSRLCDDVEGW  218 (903)
T ss_pred             -cCcceecCHHhCCCCHHHHHHHHHhccCCCCCHHHHHHHHHHhCCh
Confidence             12234454    6688888887765432 35566667777777664

>cd01394 radB RadB

Probab=97.27  E-value=0.0016  Score=64.10  Aligned_cols=41  Identities=34%  Similarity=0.516  Sum_probs=31.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      .....-++++|+||+|||+++..++.+....   +.++++++.+
T Consensus        16 i~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~---g~~v~yi~~e   56 (218)
T cd01394          16 VERGTVTQVYGPPGTGKTNIAIQLAVETAGQ---GKKVAYIDTE   56 (218)
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEECC
Confidence            4455669999999999999999999877432   4556666543

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

>PRK08118 topology modulation protein; Reviewed

Probab=97.25  E-value=0.00065  Score=64.53  Aligned_cols=31  Identities=23%  Similarity=0.540  Sum_probs=26.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .+++.||||+||||+|+.|++.+      +++++.++
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l------~~~~~~lD   33 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL------NIPVHHLD   33 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCCceecc
Confidence            58999999999999999999998      55666554

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.24  E-value=0.0025  Score=56.11  Aligned_cols=25  Identities=36%  Similarity=0.434  Sum_probs=21.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++++++||+|+|||+++-.++....
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~   25 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELL   25 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHH
Confidence            3689999999999998888887764

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

>PRK05973 replicative DNA helicase; Provisional

Probab=97.23  E-value=0.0027  Score=63.81  Aligned_cols=41  Identities=29%  Similarity=0.314  Sum_probs=29.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ..+...++|.|+||+|||+++-.++.+....   +.++++++.+
T Consensus        61 l~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---Ge~vlyfSlE  101 (237)
T PRK05973         61 LKPGDLVLLGARPGHGKTLLGLELAVEAMKS---GRTGVFFTLE  101 (237)
T ss_pred             CCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEEEEe
Confidence            5666789999999999999999887765322   4445555543

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.22  E-value=0.00029  Score=66.73  Aligned_cols=49  Identities=27%  Similarity=0.508  Sum_probs=31.7

Q ss_pred             ccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          282 IAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       282 IiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ++|.+++++++...+. .                 .....++.++|+|++|+|||++++++...+..
T Consensus         2 fvgR~~e~~~l~~~l~-~-----------------~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~   50 (185)
T PF13191_consen    2 FVGREEEIERLRDLLD-A-----------------AQSGSPRNLLLTGESGSGKTSLLRALLDRLAE   50 (185)
T ss_dssp             -TT-HHHHHHHHHTTG-G-----------------TSS-----EEE-B-TTSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH-H-----------------HHcCCCcEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            5788998888887663 1                 12456789999999999999999998887743

>PRK07261 topology modulation protein; Provisional

Probab=97.22  E-value=0.0017  Score=61.79  Aligned_cols=23  Identities=26%  Similarity=0.466  Sum_probs=21.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -+++.|+||+||||+|+.++..+
T Consensus         2 ri~i~G~~GsGKSTla~~l~~~~   24 (171)
T PRK07261          2 KIAIIGYSGSGKSTLARKLSQHY   24 (171)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999887

>PHA02774 E1; Provisional

Probab=97.18  E-value=0.0024  Score=71.16  Aligned_cols=26  Identities=23%  Similarity=0.403  Sum_probs=24.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      -+.++|+||||||||++|-+|++.+.
T Consensus       434 knciv~~GPP~TGKS~fa~sL~~~L~  459 (613)
T PHA02774        434 KNCLVIYGPPDTGKSMFCMSLIKFLK  459 (613)
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHhC
Confidence            46899999999999999999999984

>TIGR00767 rho transcription termination factor Rho

Probab=97.17  E-value=0.0012  Score=70.63  Aligned_cols=86  Identities=21%  Similarity=0.192  Sum_probs=50.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh------hHHhhh--------hchhHHH----HHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE------VVMSKY--------YGESERL----LGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~------~l~s~~--------~G~~~~~----l~~~f  380 (567)
                      ...+..++|.||||+|||++++.|++......+...-++.+..+      ++....        +++....    ...+.
T Consensus       165 ig~Gq~~~IvG~~g~GKTtL~~~i~~~I~~nhfdv~v~VlLIgER~~EVtDLqrsIlg~Vvast~d~p~~~~~~va~~v~  244 (415)
T TIGR00767       165 IGKGQRGLIVAPPKAGKTVLLQKIAQAITRNHPEVELIVLLIDERPEEVTDMQRSVKGEVVASTFDEPASRHVQVAEMVI  244 (415)
T ss_pred             eCCCCEEEEECCCCCChhHHHHHHHHhhcccCCceEEEEEEcCCCCccHHHHHHHhhceEEEecCCCChHHHHHHHHHHH
Confidence            56778899999999999999999999875432211123333322      111111        1211111    11222


Q ss_pred             HHHh---cCCCCcEEEEcCcchhhhhh
Q 047219          381 SLAN---ELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       381 ~~A~---~~a~~~ILfIDEID~L~~~~  404 (567)
                      +.|+   ......+|||||++.++...
T Consensus       245 e~Ae~~~~~GkdVVLlIDEitR~arAq  271 (415)
T TIGR00767       245 EKAKRLVEHKKDVVILLDSITRLARAY  271 (415)
T ss_pred             HHHHHHHHcCCCeEEEEEChhHHHHHH
Confidence            2222   33446899999999997654

Members of this family differ in the specificity of RNA binding.

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.17  E-value=0.0027  Score=68.25  Aligned_cols=139  Identities=16%  Similarity=0.241  Sum_probs=71.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechhhHHh----hhhc----------hhHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLEVVMS----KYYG----------ESERLLGKVFSL  382 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~l~s----~~~G----------~~~~~l~~~f~~  382 (567)
                      ..|..++|+||+|+||||++..+|..+...   .-..+.++.+++-....    +.++          .....+...+..
T Consensus       172 ~~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL~~~a~~lgvpv~~~~~~~~l~~~L~~  251 (388)
T PRK12723        172 LKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQIQTYGDIMGIPVKAIESFKDLKEEITQ  251 (388)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHHHHHhhcCCcceEeeCcHHHHHHHHHH
Confidence            346789999999999999999999876321   00123334444321111    1111          122223333332


Q ss_pred             HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC-CcEEEEEeeCCCCCCChHHHhcc----ceEEE
Q 047219          383 ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD-KKVVVIAATNRKQDLDPALISRF----DSMIT  457 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~-~~viVIaaTN~~~~Ld~aL~sRf----~~~I~  457 (567)
                      .   ....+|+||++..+...     ..    .+..+...++....+ ..++|+.+|.....+.. ...+|    -..+-
T Consensus       252 ~---~~~DlVLIDTaGr~~~~-----~~----~l~el~~~l~~~~~~~e~~LVlsat~~~~~~~~-~~~~~~~~~~~~~I  318 (388)
T PRK12723        252 S---KDFDLVLVDTIGKSPKD-----FM----KLAEMKELLNACGRDAEFHLAVSSTTKTSDVKE-IFHQFSPFSYKTVI  318 (388)
T ss_pred             h---CCCCEEEEcCCCCCccC-----HH----HHHHHHHHHHhcCCCCeEEEEEcCCCCHHHHHH-HHHHhcCCCCCEEE
Confidence            2   33579999999987532     11    123333333333223 34566666666555553 33433    12455


Q ss_pred             ecCCCHHHHHHHHH
Q 047219          458 FGLPDHENRQEIAA  471 (567)
Q Consensus       458 i~~P~~~eR~eIL~  471 (567)
                      |...|...+.-.+-
T Consensus       319 ~TKlDet~~~G~~l  332 (388)
T PRK12723        319 FTKLDETTCVGNLI  332 (388)
T ss_pred             EEeccCCCcchHHH
Confidence            65666555544333

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

Probab=97.15  E-value=0.0024  Score=63.03  Aligned_cols=44  Identities=23%  Similarity=0.141  Sum_probs=30.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC---CCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP---WQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~---~~~~~~~~i~~~  362 (567)
                      .....-+.|+||||+|||+++..++.......   -....+++++.+
T Consensus        16 ~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e   62 (226)
T cd01393          16 IPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTE   62 (226)
T ss_pred             CcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecC
Confidence            45667799999999999999999987653210   001456666654

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.

>PRK09354 recA recombinase A; Provisional

Probab=97.15  E-value=0.0022  Score=67.78  Aligned_cols=80  Identities=25%  Similarity=0.315  Sum_probs=49.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh-h---hc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK-Y---YG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~-~---~G------------~~~~~l~~~f~~  382 (567)
                      .+...-++|+||||||||+||-.++.+....   +-.+++++.+.-... +   +|            ..+..+..+-..
T Consensus        57 ip~G~IteI~G~~GsGKTtLal~~~~~~~~~---G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l~i~~~l  133 (349)
T PRK09354         57 LPRGRIVEIYGPESSGKTTLALHAIAEAQKA---GGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIADTL  133 (349)
T ss_pred             CcCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHH
Confidence            4566778999999999999999887665433   556777776542221 1   11            112222222222


Q ss_pred             HhcCCCCcEEEEcCcchhhh
Q 047219          383 ANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~  402 (567)
                      .+. ....+|+||-+-.|.+
T Consensus       134 i~s-~~~~lIVIDSvaaL~~  152 (349)
T PRK09354        134 VRS-GAVDLIVVDSVAALVP  152 (349)
T ss_pred             hhc-CCCCEEEEeChhhhcc
Confidence            223 3358999999998875

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.14  E-value=0.00049  Score=64.60  Aligned_cols=32  Identities=22%  Similarity=0.451  Sum_probs=27.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      ++..++|+|+||||||++|+.+++.+      +.+++.
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l------~~~~~d   34 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRL------GYDFID   34 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHh------CCCEEE
Confidence            46789999999999999999999998      555554

>PF01583 APS_kinase: Adenylylsulphate kinase; InterPro: IPR002891 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases

Probab=97.10  E-value=0.00059  Score=64.08  Aligned_cols=43  Identities=21%  Similarity=0.292  Sum_probs=34.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK  367 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~  367 (567)
                      +..|+|+|.||+|||++|+++.+.+...   +.+++.+++..+...
T Consensus         2 g~vIwltGlsGsGKtTlA~~L~~~L~~~---g~~~~~LDgD~lR~~   44 (156)
T PF01583_consen    2 GFVIWLTGLSGSGKTTLARALERRLFAR---GIKVYLLDGDNLRHG   44 (156)
T ss_dssp             -EEEEEESSTTSSHHHHHHHHHHHHHHT---TS-EEEEEHHHHCTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEecCcchhhc
Confidence            4568999999999999999999998654   677888888776543

Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain contains an ATP binding P-loop motif [].; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 1M7H_B 1M7G_B 3CR7_B 1D6J_A 2OFW_G 1X6V_B 1XNJ_A 1XJQ_B 2PEY_A 2PEZ_B ....

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.08  E-value=0.003  Score=62.76  Aligned_cols=45  Identities=18%  Similarity=0.097  Sum_probs=30.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCC--CcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQ--GVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~--~~~~~~i~~~~  363 (567)
                      .....-+.|+||||||||+++..++...... .+.  +..+++++.+.
T Consensus        16 i~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          16 IETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            4556678999999999999999998653211 110  24566666543

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 .

>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]

Probab=97.08  E-value=0.0011  Score=62.90  Aligned_cols=47  Identities=19%  Similarity=0.297  Sum_probs=40.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      ...+..++|+|.+|+||||+|.++.+.+...   +..++.+++..+...+
T Consensus        20 ~~~~~viW~TGLSGsGKSTiA~ale~~L~~~---G~~~y~LDGDnvR~gL   66 (197)
T COG0529          20 GQKGAVIWFTGLSGSGKSTIANALEEKLFAK---GYHVYLLDGDNVRHGL   66 (197)
T ss_pred             CCCCeEEEeecCCCCCHHHHHHHHHHHHHHc---CCeEEEecChhHhhcc
Confidence            5667889999999999999999999999766   7789999988776543

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.07  E-value=0.0015  Score=62.24  Aligned_cols=22  Identities=32%  Similarity=0.498  Sum_probs=21.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|.|+||+||||+|+.+++.+
T Consensus         2 i~i~G~pGsGKst~a~~la~~~   23 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENF   23 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            6899999999999999999988

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=97.07  E-value=0.0054  Score=57.51  Aligned_cols=25  Identities=28%  Similarity=0.412  Sum_probs=20.3

Q ss_pred             ceEEeeCCCCCcHHH-HHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTS-CARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~-LAraIA~~l~  347 (567)
                      ..+++.||+|+|||+ ++..+.+...
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~~   50 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEALK   50 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHhc
Confidence            789999999999999 6666666553

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.07  E-value=0.004  Score=61.61  Aligned_cols=80  Identities=19%  Similarity=0.192  Sum_probs=49.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcCeEEechh-hHHhhhhchhH-------------HHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVPLMYVPLE-VVMSKYYGESE-------------RLLGKVFSLA  383 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~~~~i~~~-~l~s~~~G~~~-------------~~l~~~f~~A  383 (567)
                      ....+.|+.|||||||||+.|-||+.+...  .|....+.-++.. ++..-..|...             -+-..+....
T Consensus       135 ~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaI  214 (308)
T COG3854         135 NGWLNTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAI  214 (308)
T ss_pred             cCceeeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHH
Confidence            445678999999999999999999987432  3444455555543 33333322211             1112233344


Q ss_pred             hcCCCCcEEEEcCcchh
Q 047219          384 NELPNGAIIFLDEVDSF  400 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L  400 (567)
                      +.+. |-++++|||...
T Consensus       215 rsm~-PEViIvDEIGt~  230 (308)
T COG3854         215 RSMS-PEVIIVDEIGTE  230 (308)
T ss_pred             HhcC-CcEEEEeccccH
Confidence            4555 489999999875

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.02  E-value=0.0017  Score=63.20  Aligned_cols=26  Identities=31%  Similarity=0.581  Sum_probs=23.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      -++|+|+||+|||++|+.+++++...
T Consensus         3 LiIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           3 LIILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             eEEEecCCCCCchHHHHHHHHHHHHh
Confidence            37899999999999999999998543

>PRK13949 shikimate kinase; Provisional

Probab=97.02  E-value=0.0075  Score=57.35  Aligned_cols=32  Identities=22%  Similarity=0.475  Sum_probs=27.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +.++|.|+||+|||++++.+|+.+      +.+++..+
T Consensus         2 ~~I~liG~~GsGKstl~~~La~~l------~~~~id~D   33 (169)
T PRK13949          2 ARIFLVGYMGAGKTTLGKALAREL------GLSFIDLD   33 (169)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc------CCCeeccc
Confidence            368999999999999999999999      55666554

>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=97.02  E-value=0.018  Score=57.92  Aligned_cols=134  Identities=18%  Similarity=0.289  Sum_probs=73.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhh---------c-----hhHHH-------HHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY---------G-----ESERL-------LGK  378 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~---------G-----~~~~~-------l~~  378 (567)
                      ..+-.+.+.|++|+|||+++..+-..+... +   ..+.+-.+.....+.         .     +.+..       +..
T Consensus        11 ~~~fr~viIG~sGSGKT~li~~lL~~~~~~-f---~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k   86 (241)
T PF04665_consen   11 KDPFRMVIIGKSGSGKTTLIKSLLYYLRHK-F---DHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEK   86 (241)
T ss_pred             CCCceEEEECCCCCCHHHHHHHHHHhhccc-C---CEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHH
Confidence            445678999999999999999998776432 1   122222211111111         0     00101       111


Q ss_pred             HHHHHh-c-CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEE
Q 047219          379 VFSLAN-E-LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMI  456 (567)
Q Consensus       379 ~f~~A~-~-~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I  456 (567)
                      ...... . ..+..+|+||++..-.         ...+.+..++..    ...-++.+|.++.....+++.++.-.+..+
T Consensus        87 ~~~k~~~~k~~~~~LiIlDD~~~~~---------~k~~~l~~~~~~----gRH~~is~i~l~Q~~~~lp~~iR~n~~y~i  153 (241)
T PF04665_consen   87 YIKKSPQKKNNPRFLIILDDLGDKK---------LKSKILRQFFNN----GRHYNISIIFLSQSYFHLPPNIRSNIDYFI  153 (241)
T ss_pred             HhhhhcccCCCCCeEEEEeCCCCch---------hhhHHHHHHHhc----ccccceEEEEEeeecccCCHHHhhcceEEE
Confidence            111111 1 1346899999985310         112233444432    234568888888888999999988776666


Q ss_pred             EecCCCHHHHHHHHH
Q 047219          457 TFGLPDHENRQEIAA  471 (567)
Q Consensus       457 ~i~~P~~~eR~eIL~  471 (567)
                      -+. -+.++..-+++
T Consensus       154 ~~~-~s~~dl~~i~~  167 (241)
T PF04665_consen  154 IFN-NSKRDLENIYR  167 (241)
T ss_pred             Eec-CcHHHHHHHHH
Confidence            564 35555444433

This is thought to be an ATPase involved in viral DNA packaging [].

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=97.00  E-value=0.0066  Score=60.84  Aligned_cols=41  Identities=37%  Similarity=0.528  Sum_probs=29.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ..++..+|++||||||||+++..++.+....   +-++++++.+
T Consensus        18 ~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~---ge~~lyvs~e   58 (237)
T TIGR03877        18 IPERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGIYVALE   58 (237)
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEEee
Confidence            5667889999999999999998776553221   4456665543

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.

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.94  E-value=0.0024  Score=68.22  Aligned_cols=27  Identities=30%  Similarity=0.512  Sum_probs=23.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..++|.||+|+||||++..++..+
T Consensus       135 ~~g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722        135 ERGGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            446789999999999999999999875

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=96.94  E-value=0.0055  Score=60.58  Aligned_cols=23  Identities=26%  Similarity=0.557  Sum_probs=20.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ++.++|+||.|+|||++.+.++.
T Consensus        29 ~~~~~itGpNg~GKStlLk~i~~   51 (213)
T cd03281          29 PSIMVITGPNSSGKSVYLKQVAL   51 (213)
T ss_pred             ceEEEEECCCCCChHHHHHHHHH
Confidence            37799999999999999999984

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

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=96.93  E-value=0.0025  Score=67.45  Aligned_cols=29  Identities=21%  Similarity=0.361  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+|++++|||.-|||||+|.-.....+.
T Consensus       111 ~~~PkGlYlYG~VGcGKTmLMDlFy~~~~  139 (467)
T KOG2383|consen  111 PGPPKGLYLYGSVGCGKTMLMDLFYDALP  139 (467)
T ss_pred             CCCCceEEEecccCcchhHHHHHHhhcCC
Confidence            45699999999999999999998886663

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=96.93  E-value=0.0024  Score=65.24  Aligned_cols=97  Identities=12%  Similarity=0.138  Sum_probs=56.6

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      .++++++-..+..+.+.+++.                      .....++|.||+|+||||+++++...+...   +..+
T Consensus        57 ~~l~~lg~~~~~~~~l~~~~~----------------------~~~GlilisG~tGSGKTT~l~all~~i~~~---~~~i  111 (264)
T cd01129          57 LDLEKLGLKPENLEIFRKLLE----------------------KPHGIILVTGPTGSGKTTTLYSALSELNTP---EKNI  111 (264)
T ss_pred             CCHHHcCCCHHHHHHHHHHHh----------------------cCCCEEEEECCCCCcHHHHHHHHHhhhCCC---CCeE
Confidence            456777666666666655442                      234568999999999999999998877532   2223


Q ss_pred             EEechh-hHH-----h-hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          357 MYVPLE-VVM-----S-KYYGESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       357 ~~i~~~-~l~-----s-~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      +.+..+ ++.     . .+..+...........+.+.. +.+|+++||..
T Consensus       112 itiEdp~E~~~~~~~q~~v~~~~~~~~~~~l~~~lR~~-PD~i~vgEiR~  160 (264)
T cd01129         112 ITVEDPVEYQIPGINQVQVNEKAGLTFARGLRAILRQD-PDIIMVGEIRD  160 (264)
T ss_pred             EEECCCceecCCCceEEEeCCcCCcCHHHHHHHHhccC-CCEEEeccCCC
Confidence            333211 100     0 000111112344555555655 48999999965

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.93  E-value=0.0077  Score=65.82  Aligned_cols=29  Identities=28%  Similarity=0.472  Sum_probs=25.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..|..++|+|++|+||||++..+|..+..
T Consensus        93 ~~p~vI~lvG~~GsGKTTtaakLA~~L~~  121 (437)
T PRK00771         93 LKPQTIMLVGLQGSGKTTTAAKLARYFKK  121 (437)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            45788999999999999999999988754

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.92  E-value=0.0051  Score=62.05  Aligned_cols=37  Identities=16%  Similarity=0.527  Sum_probs=28.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      |+|+|.||+||||+|+.+++.+...   +.++..++...+
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~---~~~v~~i~~D~l   38 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEK---NIDVIILGTDLI   38 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHc---CCceEEEccHHH
Confidence            6899999999999999999988533   345666665544

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.

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.91  E-value=0.011  Score=64.59  Aligned_cols=26  Identities=31%  Similarity=0.452  Sum_probs=22.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +..++|.||+|+||||++..+|..+.
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~  246 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYA  246 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            46789999999999999999887663

>PRK14974 cell division protein FtsY; Provisional

Probab=96.90  E-value=0.011  Score=62.45  Aligned_cols=29  Identities=31%  Similarity=0.477  Sum_probs=24.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..|.-++|.|+||+||||++..+|..+..
T Consensus       138 ~~~~vi~~~G~~GvGKTTtiakLA~~l~~  166 (336)
T PRK14974        138 GKPVVIVFVGVNGTGKTTTIAKLAYYLKK  166 (336)
T ss_pred             CCCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            34678999999999999999999887743

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.89  E-value=0.0056  Score=65.18  Aligned_cols=30  Identities=30%  Similarity=0.370  Sum_probs=25.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ...+...+|+||||||||++++.+++.+..
T Consensus       130 iGkGQR~LIvG~pGtGKTTLl~~la~~i~~  159 (380)
T PRK12608        130 IGKGQRGLIVAPPRAGKTVLLQQIAAAVAA  159 (380)
T ss_pred             cCCCceEEEECCCCCCHHHHHHHHHHHHHh
Confidence            345567899999999999999999998744

>cd01131 PilT Pilus retraction ATPase PilT

Probab=96.87  E-value=0.0013  Score=64.08  Aligned_cols=24  Identities=29%  Similarity=0.570  Sum_probs=21.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      -++|.||+|+||||+++++...+.
T Consensus         3 lilI~GptGSGKTTll~~ll~~~~   26 (198)
T cd01131           3 LVLVTGPTGSGKSTTLAAMIDYIN   26 (198)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            478999999999999999998875

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.86  E-value=0.004  Score=66.24  Aligned_cols=23  Identities=39%  Similarity=0.534  Sum_probs=21.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -+++.|.||||||.||-.++..+
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh
Confidence            47899999999999999999998

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=96.86  E-value=0.0031  Score=61.67  Aligned_cols=111  Identities=20%  Similarity=0.266  Sum_probs=62.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ......++|.|+-|+|||++.+.|+.+....     .....+           ..+....+    .   ..-++.|||++
T Consensus        49 ~k~d~~lvl~G~QG~GKStf~~~L~~~~~~d-----~~~~~~-----------~kd~~~~l----~---~~~iveldEl~  105 (198)
T PF05272_consen   49 CKNDTVLVLVGKQGIGKSTFFRKLGPEYFSD-----SINDFD-----------DKDFLEQL----Q---GKWIVELDELD  105 (198)
T ss_pred             CcCceeeeEecCCcccHHHHHHHHhHHhccC-----ccccCC-----------CcHHHHHH----H---HhHheeHHHHh
Confidence            3445678899999999999999997664211     001000           01111111    1   13689999999


Q ss_pred             hhhhhhhhhhHHHHHHHHHHHHHhhcCc---------ccCCcEEEEEeeCCCCCCCh-HHHhccceEEEecC
Q 047219          399 SFAVARDSEMHEATRRILSVLLRQIDGF---------EQDKKVVVIAATNRKQDLDP-ALISRFDSMITFGL  460 (567)
Q Consensus       399 ~L~~~~q~~l~~~~~~vl~~LL~~ld~~---------~~~~~viVIaaTN~~~~Ld~-aL~sRf~~~I~i~~  460 (567)
                      .+..+..+.       +.+.+-...+.+         ..+...++|+|||..+-|.. .=-||| ..+++..
T Consensus       106 ~~~k~~~~~-------lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnRRf-~~v~v~~  169 (198)
T PF05272_consen  106 GLSKKDVEA-------LKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNRRF-WPVEVSK  169 (198)
T ss_pred             hcchhhHHH-------HHHHhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCeEE-EEEEEcC
Confidence            986332221       112222222222         12356889999998765543 344688 7777754

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=96.86  E-value=0.0014  Score=66.86  Aligned_cols=101  Identities=15%  Similarity=0.192  Sum_probs=56.8

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      ..++++++-.....+.+.+.+...                   .....++++.|++|+||||+++++...++..   ...
T Consensus       100 ~~sle~l~~~~~~~~~~~~~l~~~-------------------v~~~~~ili~G~tGSGKTT~l~all~~i~~~---~~~  157 (270)
T PF00437_consen  100 PFSLEDLGESGSIPEEIAEFLRSA-------------------VRGRGNILISGPTGSGKTTLLNALLEEIPPE---DER  157 (270)
T ss_dssp             --CHCCCCHTHHCHHHHHHHHHHC-------------------HHTTEEEEEEESTTSSHHHHHHHHHHHCHTT---TSE
T ss_pred             cccHhhccCchhhHHHHHHHHhhc-------------------cccceEEEEECCCccccchHHHHHhhhcccc---ccc
Confidence            346666665555555555555432                   2346889999999999999999999988543   122


Q ss_pred             eEEechh-hHHhh------hh-chhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          356 LMYVPLE-VVMSK------YY-GESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       356 ~~~i~~~-~l~s~------~~-G~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      ++.+... ++.-.      +. .........++..+.+.. +.+|+++||-.
T Consensus       158 iv~iEd~~E~~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~-pD~iiigEiR~  208 (270)
T PF00437_consen  158 IVTIEDPPELRLPGPNQIQIQTRRDEISYEDLLKSALRQD-PDVIIIGEIRD  208 (270)
T ss_dssp             EEEEESSS-S--SCSSEEEEEEETTTBSHHHHHHHHTTS---SEEEESCE-S
T ss_pred             eEEeccccceeecccceEEEEeecCcccHHHHHHHHhcCC-CCcccccccCC
Confidence            2222211 11000      00 011223445566666665 48999999975

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.85  E-value=0.0046  Score=63.38  Aligned_cols=27  Identities=30%  Similarity=0.352  Sum_probs=24.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..+++|.||+|+||||+.++++..+..
T Consensus       111 ~~~~~i~g~~g~GKttl~~~l~~~~~~  137 (270)
T TIGR02858       111 VLNTLIISPPQCGKTTLLRDLARILST  137 (270)
T ss_pred             eeEEEEEcCCCCCHHHHHHHHhCccCC
Confidence            368999999999999999999998753

Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation.

>PRK13695 putative NTPase; Provisional

Probab=96.85  E-value=0.011  Score=56.08  Aligned_cols=24  Identities=38%  Similarity=0.549  Sum_probs=21.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .++|.|++|+|||++++.+++.+.
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~   25 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLK   25 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999988763

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=96.81  E-value=0.011  Score=56.42  Aligned_cols=23  Identities=30%  Similarity=0.458  Sum_probs=21.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+|+.|+||+|||++|..++..+
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~   25 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQS   25 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHc
Confidence            58999999999999999999887

>PF13479 AAA_24: AAA domain

Probab=96.79  E-value=0.0039  Score=61.52  Aligned_cols=21  Identities=48%  Similarity=0.888  Sum_probs=19.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVI  342 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraI  342 (567)
                      +..++|||+||+|||++|..+
T Consensus         3 ~~~~lIyG~~G~GKTt~a~~~   23 (213)
T PF13479_consen    3 PIKILIYGPPGSGKTTLAASL   23 (213)
T ss_pred             ceEEEEECCCCCCHHHHHHhC
Confidence            467999999999999999988

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.79  E-value=0.0058  Score=70.80  Aligned_cols=116  Identities=22%  Similarity=0.246  Sum_probs=61.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh-h---hhch------------hHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS-K---YYGE------------SERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s-~---~~G~------------~~~~l~~~f~~  382 (567)
                      ......++|+||||||||+|+..++......   +-.+++++.+.-.. .   -+|-            .+..+..+-..
T Consensus        57 ip~GsiteI~G~~GsGKTtLal~~~~~a~~~---G~~v~yId~E~t~~~~~A~~lGvDl~~llv~~~~~~E~~l~~i~~l  133 (790)
T PRK09519         57 LPRGRVIEIYGPESSGKTTVALHAVANAQAA---GGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADML  133 (790)
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEECCccchhHHHHHHcCCChhHeEEecCCCHHHHHHHHHHH
Confidence            4567789999999999999996655443222   45577777654222 1   1111            12222222222


Q ss_pred             HhcCCCCcEEEEcCcchhhhhhh------hhhHHHHHHHHHHHHHhhcCcccCCcEEEEEee
Q 047219          383 ANELPNGAIIFLDEVDSFAVARD------SEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT  438 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~q------~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaT  438 (567)
                      .... ...+|+||-|..|....+      +......++.+.+++..+..+-...++.+|.|-
T Consensus       134 v~~~-~~~LVVIDSI~aL~~r~E~~g~~g~~~~~~q~rl~~q~L~~L~~~l~~~nvtvi~TN  194 (790)
T PRK09519        134 IRSG-ALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFIN  194 (790)
T ss_pred             hhcC-CCeEEEEcchhhhcchhhccCCCCcccHHHHHHHHHHHHHHHHHHHHhCCCEEEEEe
Confidence            2222 358999999998875211      111112233334444444444334555666553

>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=96.79  E-value=0.018  Score=55.18  Aligned_cols=26  Identities=19%  Similarity=0.158  Sum_probs=23.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..++.-+.|.||+|+|||||.+++..
T Consensus        18 i~~G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          18 IPLNVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhh
Confidence            56777899999999999999999964

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.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.79  E-value=0.0023  Score=67.92  Aligned_cols=75  Identities=13%  Similarity=0.202  Sum_probs=43.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh-hHH---------hhhhchhHHHHHHHHHHHhcCCCCc
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE-VVM---------SKYYGESERLLGKVFSLANELPNGA  390 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~-~l~---------s~~~G~~~~~l~~~f~~A~~~a~~~  390 (567)
                      +...+++.||+|+||||+++++.+.+....  +..++.+..+ ++.         ..-.|.....+...+..+.... +.
T Consensus       121 ~~g~ili~G~tGSGKTT~l~al~~~i~~~~--~~~i~tiEdp~E~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr~~-pd  197 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTLASMIDYINKNA--AGHIITIEDPIEYVHRNKRSLINQREVGLDTLSFANALRAALRED-PD  197 (343)
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHhhCcCC--CCEEEEEcCChhhhccCccceEEccccCCCCcCHHHHHHHhhccC-CC
Confidence            346789999999999999999998875321  1222222211 110         0011221122344455555555 48


Q ss_pred             EEEEcCcc
Q 047219          391 IIFLDEVD  398 (567)
Q Consensus       391 ILfIDEID  398 (567)
                      +|++||+-
T Consensus       198 ~i~vgEir  205 (343)
T TIGR01420       198 VILIGEMR  205 (343)
T ss_pred             EEEEeCCC
Confidence            99999995

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.

>PRK13947 shikimate kinase; Provisional

Probab=96.78  E-value=0.0014  Score=61.75  Aligned_cols=31  Identities=23%  Similarity=0.357  Sum_probs=26.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +++|.|+||||||++++.+|+.+      +.+|+..+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~l------g~~~id~d   33 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTL------SFGFIDTD   33 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh------CCCEEECc
Confidence            68999999999999999999999      66665543

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=96.77  E-value=0.0033  Score=58.15  Aligned_cols=26  Identities=35%  Similarity=0.630  Sum_probs=23.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...++|++|-||||||+++..||..+
T Consensus         6 ~~PNILvtGTPG~GKstl~~~lae~~   31 (176)
T KOG3347|consen    6 ERPNILVTGTPGTGKSTLAERLAEKT   31 (176)
T ss_pred             cCCCEEEeCCCCCCchhHHHHHHHHh
Confidence            34679999999999999999999887

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.76  E-value=0.0046  Score=57.47  Aligned_cols=38  Identities=24%  Similarity=0.392  Sum_probs=28.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      ++|.|+||+|||++|+.++..+...   +.+.+.++...+.
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~---g~~~~~i~~d~~r   39 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQR---GRPVYVLDGDNVR   39 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHc---CCCEEEEcCHHHH
Confidence            6899999999999999999988432   3345666655444

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>PRK14532 adenylate kinase; Provisional

Probab=96.76  E-value=0.0026  Score=61.12  Aligned_cols=36  Identities=19%  Similarity=0.477  Sum_probs=27.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK  367 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~  367 (567)
                      .++|.|+||+||||+|+.+|+.+      +  +..++..++..+
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~------g--~~~is~~d~lr~   37 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEER------G--MVQLSTGDMLRA   37 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc------C--CeEEeCcHHHHH
Confidence            58999999999999999999988      3  444555444443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.74  E-value=0.011  Score=60.12  Aligned_cols=41  Identities=22%  Similarity=0.336  Sum_probs=29.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ......++++|+||||||+++..++......   +-++++++.+
T Consensus        33 ip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~---Ge~vlyis~E   73 (259)
T TIGR03878        33 IPAYSVINITGVSDTGKSLMVEQFAVTQASR---GNPVLFVTVE   73 (259)
T ss_pred             eECCcEEEEEcCCCCCHHHHHHHHHHHHHhC---CCcEEEEEec
Confidence            4566779999999999999999887654222   3455555543

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

>PRK03839 putative kinase; Provisional

Probab=96.74  E-value=0.0014  Score=62.60  Aligned_cols=30  Identities=27%  Similarity=0.604  Sum_probs=25.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      .++|.|+||+||||+++.+|+.+      +++++.+
T Consensus         2 ~I~l~G~pGsGKsT~~~~La~~~------~~~~id~   31 (180)
T PRK03839          2 IIAITGTPGVGKTTVSKLLAEKL------GYEYVDL   31 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCcEEeh
Confidence            48899999999999999999998      5556543

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.73  E-value=0.0061  Score=62.48  Aligned_cols=72  Identities=18%  Similarity=0.279  Sum_probs=39.6

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh--hhh--chhHHHHHHHHH----HHhcCCCCcEEEEcC
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS--KYY--GESERLLGKVFS----LANELPNGAIIFLDE  396 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s--~~~--G~~~~~l~~~f~----~A~~~a~~~ILfIDE  396 (567)
                      |+|+|-||+|||++|+.|+..+...   +..+..++.+.+.-  .-|  ...++..+..+.    .+..  ...|+++|+
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~---~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls--~~~iVI~Dd   78 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEK---GKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALS--KDTIVILDD   78 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHT---T--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHT--T-SEEEE-S
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhc---CCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhc--cCeEEEEeC
Confidence            7899999999999999999987543   45667777555541  112  123444444333    3322  247999999


Q ss_pred             cchhh
Q 047219          397 VDSFA  401 (567)
Q Consensus       397 ID~L~  401 (567)
                      ...+-
T Consensus        79 ~nYiK   83 (270)
T PF08433_consen   79 NNYIK   83 (270)
T ss_dssp             ---SH
T ss_pred             CchHH
Confidence            98874

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.72  E-value=0.0098  Score=57.94  Aligned_cols=25  Identities=24%  Similarity=0.473  Sum_probs=21.6

Q ss_pred             CCCC-ceEEeeCCCCCcHHHHHHHHH
Q 047219          319 SNRP-RAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       319 ~~~p-~~VLL~GppGTGKT~LAraIA  343 (567)
                      ...+ +.++|+||.|+|||++.+.|+
T Consensus        24 i~~~~~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          24 LGENKRVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             ECCCceEEEEECCCCCChHHHHHHHH
Confidence            4444 469999999999999999998

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 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, a

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=96.71  E-value=0.0094  Score=56.15  Aligned_cols=29  Identities=17%  Similarity=0.313  Sum_probs=25.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||+|.+.|+....
T Consensus        23 i~~Ge~~~l~G~nGsGKSTLl~~i~G~~~   51 (163)
T cd03216          23 VRRGEVHALLGENGAGKSTLMKILSGLYK   51 (163)
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            56778899999999999999999998763

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.

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=96.70  E-value=0.0077  Score=64.40  Aligned_cols=29  Identities=24%  Similarity=0.398  Sum_probs=25.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..+..+++.|+.|||||++.++|.+.+..
T Consensus        20 ~~~~~~fv~G~~GtGKs~l~~~i~~~~~~   48 (364)
T PF05970_consen   20 EEGLNFFVTGPAGTGKSFLIKAIIDYLRS   48 (364)
T ss_pred             cCCcEEEEEcCCCCChhHHHHHHHHHhcc
Confidence            56788999999999999999999998854

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK08233 hypothetical protein; Provisional

Probab=96.69  E-value=0.0091  Score=56.53  Aligned_cols=25  Identities=16%  Similarity=0.327  Sum_probs=22.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .-|.|.|+||+||||+|+.|+..+.
T Consensus         4 ~iI~I~G~~GsGKtTla~~L~~~l~   28 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLK   28 (182)
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4578899999999999999999884

>PRK04040 adenylate kinase; Provisional

Probab=96.68  E-value=0.011  Score=57.43  Aligned_cols=26  Identities=27%  Similarity=0.436  Sum_probs=23.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +.-++++|+|||||||+++.+++.+.
T Consensus         2 ~~~i~v~G~pG~GKtt~~~~l~~~l~   27 (188)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLK   27 (188)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHhc
Confidence            45789999999999999999999983

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=96.67  E-value=0.21  Score=54.01  Aligned_cols=79  Identities=15%  Similarity=0.154  Sum_probs=41.9

Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC---CCCCChHHHhccceEEEecCCCHHHH
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR---KQDLDPALISRFDSMITFGLPDHENR  466 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~---~~~Ld~aL~sRf~~~I~i~~P~~~eR  466 (567)
                      .||+||.+..-... ++...+.+-++...|..       +.---||..|+.   ...|..+|-+|--+.|.+.-.+.+.-
T Consensus       150 PVVVIdnF~~k~~~-~~~iy~~laeWAa~Lv~-------~nIAHVIFlT~dv~~~k~LskaLPn~vf~tI~L~Das~~~A  221 (431)
T PF10443_consen  150 PVVVIDNFLHKAEE-NDFIYDKLAEWAASLVQ-------NNIAHVIFLTDDVSYSKPLSKALPNRVFKTISLSDASPESA  221 (431)
T ss_pred             CEEEEcchhccCcc-cchHHHHHHHHHHHHHh-------cCccEEEEECCCCchhhhHHHhCCCCceeEEeecCCCHHHH
Confidence            69999999764322 22222222222222222       222233333332   33566777664337888887777777


Q ss_pred             HHHHHHHHHh
Q 047219          467 QEIAAQYAKH  476 (567)
Q Consensus       467 ~eIL~~~~~~  476 (567)
                      +..+..++..
T Consensus       222 k~yV~~~L~~  231 (431)
T PF10443_consen  222 KQYVLSQLDE  231 (431)
T ss_pred             HHHHHHHhcc
Confidence            6766666543

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>PRK00625 shikimate kinase; Provisional

Probab=96.66  E-value=0.0018  Score=61.92  Aligned_cols=31  Identities=26%  Similarity=0.472  Sum_probs=26.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +++|.|.||+|||++++.+++.+      +.+++.++
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l------~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFL------SLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------CCCEEEhh
Confidence            58999999999999999999999      66666554

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=96.66  E-value=0.0019  Score=59.52  Aligned_cols=39  Identities=28%  Similarity=0.604  Sum_probs=28.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      +++|+|+||+|||++|+.+++.+      +.+++  +...+.....|
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l------~~~~~--~~d~~~~~~~~   39 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKAL------GLPFV--DLDELIEQRAG   39 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHh------CCCEE--EchHHHHHHcC
Confidence            47899999999999999999998      55555  33344444333

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PLN02200 adenylate kinase family protein

Probab=96.64  E-value=0.0063  Score=61.07  Aligned_cols=28  Identities=25%  Similarity=0.407  Sum_probs=24.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+++.|+||+||||+|+.+++.+
T Consensus        40 ~~~~~ii~I~G~PGSGKsT~a~~La~~~   67 (234)
T PLN02200         40 EKTPFITFVLGGPGSGKGTQCEKIVETF   67 (234)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            3456678999999999999999999988

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

Probab=96.64  E-value=0.023  Score=56.25  Aligned_cols=27  Identities=37%  Similarity=0.580  Sum_probs=22.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+..+|+.||||||||+++..++.+
T Consensus        16 ip~gs~~li~G~~GsGKT~l~~q~l~~   42 (226)
T PF06745_consen   16 IPKGSVVLISGPPGSGKTTLALQFLYN   42 (226)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCcHHHHHHHHHH
Confidence            566778999999999999998876643

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 ....

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=96.61  E-value=0.0094  Score=57.41  Aligned_cols=20  Identities=30%  Similarity=0.512  Sum_probs=18.5

Q ss_pred             EEeeCCCCCcHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~  344 (567)
                      ++|+||.|.|||++.|.++.
T Consensus         2 ~~ltG~N~~GKst~l~~i~~   21 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGL   21 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHH
Confidence            68999999999999999983

>TIGR00416 sms DNA repair protein RadA

Probab=96.59  E-value=0.0059  Score=67.17  Aligned_cols=80  Identities=20%  Similarity=0.251  Sum_probs=51.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh------hch--------hHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY------YGE--------SERLLGKVFSLAN  384 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~------~G~--------~~~~l~~~f~~A~  384 (567)
                      ..+..-++|.|+||+|||+|+..++......   +.++++++.++-...+      +|.        .+..+..+...+.
T Consensus        91 i~~GsvilI~G~pGsGKTTL~lq~a~~~a~~---g~kvlYvs~EEs~~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~  167 (454)
T TIGR00416        91 IVPGSLILIGGDPGIGKSTLLLQVACQLAKN---QMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANIE  167 (454)
T ss_pred             ccCCeEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEECcCCHHHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHH
Confidence            4566779999999999999999998776432   3467777765433221      111        1112334444444


Q ss_pred             cCCCCcEEEEcCcchhhh
Q 047219          385 ELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       385 ~~a~~~ILfIDEID~L~~  402 (567)
                      +.. +.+++||.|..+..
T Consensus       168 ~~~-~~~vVIDSIq~l~~  184 (454)
T TIGR00416       168 EEN-PQACVIDSIQTLYS  184 (454)
T ss_pred             hcC-CcEEEEecchhhcc
Confidence            444 58999999998753

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)).

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

Probab=96.59  E-value=0.022  Score=55.88  Aligned_cols=134  Identities=19%  Similarity=0.317  Sum_probs=74.1

Q ss_pred             ccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhh----------
Q 047219          300 LQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY----------  369 (567)
Q Consensus       300 l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~----------  369 (567)
                      ..+.|+-+++|.+      .+.+.-+++.|+.|||||.|.+.++.-+-..   +....+++.+.-.-.+.          
T Consensus        12 ~gndelDkrLGGG------iP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~---g~~v~yvsTe~T~refi~qm~sl~ydv   82 (235)
T COG2874          12 SGNDELDKRLGGG------IPVGSLILIEGDNGTGKSVLSQRFAYGFLMN---GYRVTYVSTELTVREFIKQMESLSYDV   82 (235)
T ss_pred             CCcHHHHhhccCC------CccCeEEEEECCCCccHHHHHHHHHHHHHhC---CceEEEEEechhHHHHHHHHHhcCCCc
Confidence            4566666666522      3445568899999999999999998755322   33344443321111110          


Q ss_pred             -----------------------chhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc
Q 047219          370 -----------------------GESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF  426 (567)
Q Consensus       370 -----------------------G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~  426 (567)
                                             ......+..+.+..+... ..+++||-+..+....       ....+.+++..+..+
T Consensus        83 ~~~~l~G~l~~~~~~~~~~~~~~~~~~~~L~~l~~~~k~~~-~dViIIDSls~~~~~~-------~~~~vl~fm~~~r~l  154 (235)
T COG2874          83 SDFLLSGRLLFFPVNLEPVNWGRRSARKLLDLLLEFIKRWE-KDVIIIDSLSAFATYD-------SEDAVLNFMTFLRKL  154 (235)
T ss_pred             hHHHhcceeEEEEecccccccChHHHHHHHHHHHhhHHhhc-CCEEEEecccHHhhcc-------cHHHHHHHHHHHHHH
Confidence                                   112333444444444333 4799999998876432       111223333333333


Q ss_pred             ccCCcEEEEEeeCCCCCCChHHHhcc
Q 047219          427 EQDKKVVVIAATNRKQDLDPALISRF  452 (567)
Q Consensus       427 ~~~~~viVIaaTN~~~~Ld~aL~sRf  452 (567)
                      ...+++++ .|. ++..+++++..|+
T Consensus       155 ~d~gKvIi-lTv-hp~~l~e~~~~ri  178 (235)
T COG2874         155 SDLGKVII-LTV-HPSALDEDVLTRI  178 (235)
T ss_pred             HhCCCEEE-EEe-ChhhcCHHHHHHH
Confidence            33444443 344 4788898888765

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.59  E-value=0.007  Score=55.39  Aligned_cols=29  Identities=28%  Similarity=0.406  Sum_probs=25.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      .+...++|.|+.|+|||+++|.+++.++.
T Consensus        20 ~~~~~i~l~G~lGaGKTtl~~~l~~~lg~   48 (133)
T TIGR00150        20 DFGTVVLLKGDLGAGKTTLVQGLLQGLGI   48 (133)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHcCC
Confidence            45667999999999999999999999853

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=96.59  E-value=0.0024  Score=60.85  Aligned_cols=25  Identities=28%  Similarity=0.506  Sum_probs=22.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+-++|.|+||+||||+|+.+++.+
T Consensus         2 ~~~i~l~G~~gsGKst~a~~l~~~~   26 (175)
T cd00227           2 GRIIILNGGSSAGKSSIARALQSVL   26 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3568999999999999999999988

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>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=96.59  E-value=0.013  Score=56.16  Aligned_cols=29  Identities=31%  Similarity=0.485  Sum_probs=25.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+...+.|.||+|+|||||++.++....
T Consensus        22 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   50 (177)
T cd03222          22 VKEGEVIGIVGPNGTGKTTAVKILAGQLI   50 (177)
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            45677889999999999999999998763

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.

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=96.58  E-value=0.02  Score=56.66  Aligned_cols=41  Identities=29%  Similarity=0.337  Sum_probs=29.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ..+...+++.|+||+|||+++..++...-..   +.++.+++.+
T Consensus        13 i~~g~~~li~G~~G~GKt~~~~~~~~~~~~~---g~~~~y~s~e   53 (224)
T TIGR03880        13 FPEGHVIVVIGEYGTGKTTFSLQFLYQGLKN---GEKAMYISLE   53 (224)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECC
Confidence            4566789999999999999999887654222   3445555543

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.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=96.58  E-value=0.0082  Score=62.73  Aligned_cols=35  Identities=31%  Similarity=0.611  Sum_probs=30.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ..++..++|.|.||||||++++.++..+      +.+|+.+
T Consensus       130 ~~~~~~I~l~G~~GsGKStvg~~La~~L------g~~~id~  164 (309)
T PRK08154        130 AARRRRIALIGLRGAGKSTLGRMLAARL------GVPFVEL  164 (309)
T ss_pred             ccCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEeH
Confidence            5677899999999999999999999999      6677743

>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=96.58  E-value=0.015  Score=54.24  Aligned_cols=29  Identities=31%  Similarity=0.433  Sum_probs=25.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+...+.|.|++|+|||+++++|+....
T Consensus        22 i~~g~~~~i~G~nGsGKStll~~l~g~~~   50 (157)
T cd00267          22 LKAGEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            46677899999999999999999998764

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.

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.57  E-value=0.0068  Score=60.09  Aligned_cols=42  Identities=36%  Similarity=0.392  Sum_probs=31.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~  363 (567)
                      ...+..+++.|+||+|||+++..++......   +-++++++.+.
T Consensus        17 i~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---g~~~~~is~e~   58 (229)
T TIGR03881        17 IPRGFFVAVTGEPGTGKTIFCLHFAYKGLRD---GDPVIYVTTEE   58 (229)
T ss_pred             CcCCeEEEEECCCCCChHHHHHHHHHHHHhc---CCeEEEEEccC
Confidence            5667889999999999999999887654222   44567776644

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.

>PRK04328 hypothetical protein; Provisional

Probab=96.56  E-value=0.021  Score=57.80  Aligned_cols=40  Identities=35%  Similarity=0.504  Sum_probs=28.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..++..+|++|+||||||+++..++.+....   +-++++++.
T Consensus        20 ip~gs~ili~G~pGsGKT~l~~~fl~~~~~~---ge~~lyis~   59 (249)
T PRK04328         20 IPERNVVLLSGGPGTGKSIFSQQFLWNGLQM---GEPGVYVAL   59 (249)
T ss_pred             CcCCcEEEEEcCCCCCHHHHHHHHHHHHHhc---CCcEEEEEe
Confidence            4567789999999999999998876653221   344555554

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.55  E-value=0.0085  Score=56.93  Aligned_cols=42  Identities=17%  Similarity=0.268  Sum_probs=31.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ..+.-++|.|++|+||||+|+.+++.+...   +...+.++...+
T Consensus         5 ~~~~~I~i~G~~GsGKst~a~~l~~~l~~~---~~~~~~~~~d~~   46 (176)
T PRK05541          5 PNGYVIWITGLAGSGKTTIAKALYERLKLK---YSNVIYLDGDEL   46 (176)
T ss_pred             CCCCEEEEEcCCCCCHHHHHHHHHHHHHHc---CCcEEEEecHHH
Confidence            466789999999999999999999998432   233455555443

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.51  E-value=0.0077  Score=66.84  Aligned_cols=97  Identities=15%  Similarity=0.151  Sum_probs=57.2

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      .++++++-.++..+.++.++.                      .+..-++++||+|+||||+..++.+++...   +.++
T Consensus       219 ~~l~~Lg~~~~~~~~l~~~~~----------------------~~~GlilitGptGSGKTTtL~a~L~~l~~~---~~~i  273 (486)
T TIGR02533       219 LDLETLGMSPELLSRFERLIR----------------------RPHGIILVTGPTGSGKTTTLYAALSRLNTP---ERNI  273 (486)
T ss_pred             CCHHHcCCCHHHHHHHHHHHh----------------------cCCCEEEEEcCCCCCHHHHHHHHHhccCCC---CCcE
Confidence            567788767777777766552                      223357899999999999999888877532   2334


Q ss_pred             EEechhh------HHhhhhc-hhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          357 MYVPLEV------VMSKYYG-ESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       357 ~~i~~~~------l~s~~~G-~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      +++..+-      +....+. ............+.++. +.+|++.||-.
T Consensus       274 iTiEDpvE~~~~~~~q~~v~~~~g~~f~~~lr~~LR~d-PDvI~vGEiRd  322 (486)
T TIGR02533       274 LTVEDPVEYQIEGIGQIQVNPKIGLTFAAGLRAILRQD-PDIIMVGEIRD  322 (486)
T ss_pred             EEEcCCeeeecCCCceEEEccccCccHHHHHHHHHhcC-CCEEEEeCCCC
Confidence            4332210      0000000 11112333444445555 48999999965

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>PF13238 AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB_A 3IIM_A 2AXP_A 3KB2_A 1KHT_A 1NKS_A 3H86_C

Probab=96.51  E-value=0.0019  Score=57.22  Aligned_cols=22  Identities=36%  Similarity=0.635  Sum_probs=20.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      |+|.|+|||||||+|+.|++.+
T Consensus         1 I~i~G~~GsGKtTia~~L~~~~   22 (129)
T PF13238_consen    1 IGISGIPGSGKTTIAKELAERL   22 (129)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHHHHH
Confidence            6899999999999999999986

...

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=96.51  E-value=0.012  Score=56.16  Aligned_cols=22  Identities=27%  Similarity=0.447  Sum_probs=20.1

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +|+.|++|+|||++|..++...
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~   23 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAEL   23 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc
Confidence            6899999999999999998874

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.

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.50  E-value=0.0043  Score=59.78  Aligned_cols=28  Identities=21%  Similarity=0.372  Sum_probs=25.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .....++|.||+|+||||++++++....
T Consensus        23 ~~g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          23 EARKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             hCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            4567899999999999999999998875

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.47  E-value=0.0093  Score=59.45  Aligned_cols=41  Identities=24%  Similarity=0.420  Sum_probs=28.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..+..-++|.|+||+|||+++..++.......  +.++.+++.
T Consensus        10 l~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~--g~~vly~s~   50 (242)
T cd00984          10 LQPGDLIIIAARPSMGKTAFALNIAENIAKKQ--GKPVLFFSL   50 (242)
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhC--CCceEEEeC
Confidence            56677899999999999999998876652210  334555553

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.

>PRK13948 shikimate kinase; Provisional

Probab=96.46  E-value=0.0056  Score=59.09  Aligned_cols=44  Identities=16%  Similarity=0.166  Sum_probs=34.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      ..++..++|.|.+|+|||++++.+++.+      +.+|+..+  .+..+.+|
T Consensus         7 ~~~~~~I~LiG~~GsGKSTvg~~La~~l------g~~~iD~D--~~ie~~~g   50 (182)
T PRK13948          7 ERPVTWVALAGFMGTGKSRIGWELSRAL------MLHFIDTD--RYIERVTG   50 (182)
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHHc------CCCEEECC--HHHHHHHh
Confidence            3567899999999999999999999999      66676544  44444444

>PRK14737 gmk guanylate kinase; Provisional

Probab=96.45  E-value=0.0082  Score=58.08  Aligned_cols=27  Identities=15%  Similarity=0.393  Sum_probs=23.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .++-++|.||+|+|||+|++.+.+...
T Consensus         3 ~~~~ivl~GpsG~GK~tl~~~l~~~~~   29 (186)
T PRK14737          3 SPKLFIISSVAGGGKSTIIQALLEEHP   29 (186)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhcCC
Confidence            467799999999999999999988763

>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=96.45  E-value=0.017  Score=56.37  Aligned_cols=26  Identities=31%  Similarity=0.408  Sum_probs=22.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ...+.-++|+||.|+|||++.+.|+.
T Consensus        26 l~~~~~~~l~G~Ng~GKStll~~i~~   51 (202)
T cd03243          26 LGSGRLLLITGPNMGGKSTYLRSIGL   51 (202)
T ss_pred             EcCCeEEEEECCCCCccHHHHHHHHH
Confidence            34456799999999999999999993

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

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.44  E-value=0.0092  Score=61.62  Aligned_cols=38  Identities=26%  Similarity=0.387  Sum_probs=28.7

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK  367 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~  367 (567)
                      .-++|.|+|||||||+|+.+++.+.       ++..++...+...
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~-------~~~~l~~D~~r~~   40 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNP-------KAVNVNRDDLRQS   40 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCC-------CCEEEeccHHHHH
Confidence            4588999999999999999999872       2455555555443

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.42  E-value=0.019  Score=63.78  Aligned_cols=80  Identities=23%  Similarity=0.186  Sum_probs=52.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhh------ch---------------------
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY------GE---------------------  371 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~------G~---------------------  371 (567)
                      ..++..+|+.||||+|||+|+-.++......   +-++++++.++-...+.      |-                     
T Consensus       260 ~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~---ge~~~y~s~eEs~~~i~~~~~~lg~~~~~~~~~g~l~~~~~~p~~~  336 (484)
T TIGR02655       260 FFKDSIILATGATGTGKTLLVSKFLENACAN---KERAILFAYEESRAQLLRNAYSWGIDFEEMEQQGLLKIICAYPESA  336 (484)
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEEeeCCHHHHHHHHHHcCCChHHHhhCCcEEEEEcccccC
Confidence            5667789999999999999999888876332   44567776554322211      10                     


Q ss_pred             -hHHHHHHHHHHHhcCCCCcEEEEcCcchhhh
Q 047219          372 -SERLLGKVFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       372 -~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                       .+..+..+.+...... +.+++||-+..+..
T Consensus       337 ~~~~~~~~i~~~i~~~~-~~~vvIDsi~~~~~  367 (484)
T TIGR02655       337 GLEDHLQIIKSEIADFK-PARIAIDSLSALAR  367 (484)
T ss_pred             ChHHHHHHHHHHHHHcC-CCEEEEcCHHHHHH
Confidence             1334455555555544 47999999988753

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.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=96.41  E-value=0.025  Score=53.52  Aligned_cols=29  Identities=21%  Similarity=0.384  Sum_probs=26.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||+|.+.|+....
T Consensus        25 i~~G~~~~l~G~nGsGKstLl~~i~G~~~   53 (171)
T cd03228          25 IKPGEKVAIVGPSGSGKSTLLKLLLRLYD   53 (171)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcCCC
Confidence            56788899999999999999999998864

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.

>PRK06217 hypothetical protein; Validated

Probab=96.41  E-value=0.0032  Score=60.45  Aligned_cols=23  Identities=22%  Similarity=0.472  Sum_probs=21.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.|.||+||||+|++|++.+
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l   25 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERL   25 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            48999999999999999999998

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.41  E-value=0.019  Score=59.92  Aligned_cols=45  Identities=20%  Similarity=0.132  Sum_probs=31.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~  363 (567)
                      ...+.-++|+||||+|||+++-.++......   ...+-.+++++.+.
T Consensus        92 i~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~  139 (310)
T TIGR02236        92 IETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTEN  139 (310)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCC
Confidence            3456668899999999999999998775321   00122677777654

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.

>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=96.41  E-value=0.0097  Score=58.08  Aligned_cols=38  Identities=26%  Similarity=0.432  Sum_probs=26.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      |+-++|.||+|+||||.+-.+|..+... -..+-++..+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~-~~~v~lis~D   38 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLK-GKKVALISAD   38 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHT-T--EEEEEES
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhc-cccceeecCC
Confidence            5678999999999999888888877433 1133344444

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 ....

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=96.40  E-value=0.0032  Score=57.35  Aligned_cols=30  Identities=30%  Similarity=0.762  Sum_probs=25.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +.|.|+||+|||++|+.++..+      +++++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~------~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKL------GLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh------CCceeccc
Confidence            6799999999999999999998      66666554

>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.40  E-value=0.0089  Score=60.63  Aligned_cols=30  Identities=20%  Similarity=0.315  Sum_probs=26.6

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .......+-|.|++||||||++|.|.....
T Consensus        35 ~i~~ge~~glVGESG~GKSTlgr~i~~L~~   64 (268)
T COG4608          35 SIKEGETLGLVGESGCGKSTLGRLILGLEE   64 (268)
T ss_pred             EEcCCCEEEEEecCCCCHHHHHHHHHcCcC
Confidence            366778899999999999999999998775

>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=96.40  E-value=0.015  Score=53.70  Aligned_cols=29  Identities=24%  Similarity=0.352  Sum_probs=25.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||||+++++....
T Consensus        23 ~~~Ge~~~i~G~nGsGKStLl~~l~G~~~   51 (144)
T cd03221          23 INPGDRIGLVGRNGAGKSTLLKLIAGELE   51 (144)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHcCCCC
Confidence            56778899999999999999999998764

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.

>PRK14527 adenylate kinase; Provisional

Probab=96.39  E-value=0.01  Score=57.26  Aligned_cols=28  Identities=39%  Similarity=0.787  Sum_probs=24.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-+++.||||+||||+|+.+++.++
T Consensus         4 ~~~~~i~i~G~pGsGKsT~a~~La~~~~   31 (191)
T PRK14527          4 TKNKVVIFLGPPGAGKGTQAERLAQELG   31 (191)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4567799999999999999999999883

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.38  E-value=0.011  Score=56.07  Aligned_cols=41  Identities=34%  Similarity=0.509  Sum_probs=30.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      .+..+.|.|+||+|||++|+.++..+...   +..+..++...+
T Consensus         3 ~g~~i~~~G~~GsGKST~a~~la~~l~~~---g~~v~~id~D~~   43 (175)
T PRK00889          3 RGVTVWFTGLSGAGKTTIARALAEKLREA---GYPVEVLDGDAV   43 (175)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEcCccH
Confidence            45678999999999999999999988432   334555655443

>KOG3928 consensus Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis]

Probab=96.38  E-value=0.13  Score=55.09  Aligned_cols=51  Identities=12%  Similarity=0.148  Sum_probs=33.6

Q ss_pred             ccceEEEecCCCHHHHHHHHHHHHHh--h----C-HHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          451 RFDSMITFGLPDHENRQEIAAQYAKH--L----T-KAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       451 Rf~~~I~i~~P~~~eR~eIL~~~~~~--~----~-~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      -| ..|+++.++++|-.+++..+++.  +    + ++...++--. .+.+++.++.+|..
T Consensus       402 pf-~pi~v~nYt~~E~~~~i~YYl~~nwl~kkv~~Ee~~kql~fL-SngNP~l~~~lca~  459 (461)
T KOG3928|consen  402 PF-VPIEVENYTLDEFEALIDYYLQSNWLLKKVPGEENIKQLYFL-SNGNPSLMERLCAF  459 (461)
T ss_pred             Cc-CccccCCCCHHHHHHHHHHHHHhhHHHhhcCcccchhhhhhh-cCCCHHHHHHHHHh
Confidence            45 46788899999999999988764  1    1 2233333333 36788877777753

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=96.37  E-value=0.0032  Score=58.02  Aligned_cols=22  Identities=23%  Similarity=0.589  Sum_probs=20.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|+|+||+||||+|+.+++.+
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~   23 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERL   23 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhc
Confidence            6899999999999999999987

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.36  E-value=0.085  Score=54.38  Aligned_cols=77  Identities=16%  Similarity=0.322  Sum_probs=49.3

Q ss_pred             CCce-EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech----------hhHHhhhhchhHHHHHHHHHHHhcCCCC
Q 047219          321 RPRA-VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL----------EVVMSKYYGESERLLGKVFSLANELPNG  389 (567)
Q Consensus       321 ~p~~-VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~----------~~l~s~~~G~~~~~l~~~f~~A~~~a~~  389 (567)
                      .+++ ||++||+|+||||..-++-++++...  ..+.+.+..          +.+..+-+|..-..+...++.|.+.. |
T Consensus       123 ~~~GLILVTGpTGSGKSTTlAamId~iN~~~--~~HIlTIEDPIE~vh~skkslI~QREvG~dT~sF~~aLraALReD-P  199 (353)
T COG2805         123 SPRGLILVTGPTGSGKSTTLAAMIDYINKHK--AKHILTIEDPIEYVHESKKSLINQREVGRDTLSFANALRAALRED-P  199 (353)
T ss_pred             CCCceEEEeCCCCCcHHHHHHHHHHHHhccC--CcceEEecCchHhhhcchHhhhhHHHhcccHHHHHHHHHHHhhcC-C
Confidence            3444 77889999999999999999987542  122232221          22333445555455555566666665 4


Q ss_pred             cEEEEcCcchh
Q 047219          390 AIIFLDEVDSF  400 (567)
Q Consensus       390 ~ILfIDEID~L  400 (567)
                      .||++=|+-.+
T Consensus       200 DVIlvGEmRD~  210 (353)
T COG2805         200 DVILVGEMRDL  210 (353)
T ss_pred             CEEEEeccccH
Confidence            89999998654

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

Probab=96.36  E-value=0.0055  Score=62.22  Aligned_cols=45  Identities=38%  Similarity=0.533  Sum_probs=36.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      ......+|++|+||||||+++..++......   +-+|++++.++-..
T Consensus        20 ~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~---ge~vlyvs~~e~~~   64 (260)
T COG0467          20 LPRGSVVLITGPPGTGKTIFALQFLYEGARE---GEPVLYVSTEESPE   64 (260)
T ss_pred             CcCCcEEEEEcCCCCcHHHHHHHHHHHHHhc---CCcEEEEEecCCHH
Confidence            4667889999999999999999888877554   67788888765444

>TIGR01069 mutS2 MutS2 family protein

Probab=96.36  E-value=0.077  Score=62.19  Aligned_cols=23  Identities=26%  Similarity=0.413  Sum_probs=21.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..++|+||.|+|||++.+.++..
T Consensus       323 ~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       323 RVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             eEEEEECCCCCCchHHHHHHHHH
Confidence            67999999999999999999876

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=96.35  E-value=0.011  Score=54.85  Aligned_cols=34  Identities=26%  Similarity=0.497  Sum_probs=27.2

Q ss_pred             eeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          327 FEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       327 L~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      |.||||+|||++|+.||+.+        .+..++..++....
T Consensus         1 i~G~PgsGK~t~~~~la~~~--------~~~~is~~~llr~~   34 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRY--------GLVHISVGDLLREE   34 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHH--------TSEEEEHHHHHHHH
T ss_pred             CcCCCCCChHHHHHHHHHhc--------CcceechHHHHHHH
Confidence            57999999999999999988        35667766655543

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

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

Probab=96.35  E-value=0.017  Score=61.41  Aligned_cols=34  Identities=32%  Similarity=0.464  Sum_probs=29.0

Q ss_pred             ccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          315 CKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       315 ~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      .++....+..+|+-|.||||||++|--+-+.+..
T Consensus         3 ~FF~~~~G~TLLIKG~PGTGKTtfaLelL~~l~~   36 (484)
T PF07088_consen    3 RFFTQEPGQTLLIKGEPGTGKTTFALELLNSLKD   36 (484)
T ss_pred             hhhcCCCCcEEEEecCCCCCceeeehhhHHHHhc
Confidence            3455788999999999999999999988888754

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

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=96.35  E-value=0.066  Score=61.79  Aligned_cols=159  Identities=21%  Similarity=0.243  Sum_probs=87.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh-----HHhhhh----------ch------------
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV-----VMSKYY----------GE------------  371 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~-----l~s~~~----------G~------------  371 (567)
                      ....+-++|+-|.|.||||++-..+......  ..+..+.++.++     +.+.+.          |+            
T Consensus        34 ~~~~RL~li~APAGfGKttl~aq~~~~~~~~--~~v~Wlslde~dndp~rF~~yLi~al~~~~p~~~~~a~~l~q~~~~~  111 (894)
T COG2909          34 ANDYRLILISAPAGFGKTTLLAQWRELAADG--AAVAWLSLDESDNDPARFLSYLIAALQQATPTLGDEAQTLLQKHQYV  111 (894)
T ss_pred             CCCceEEEEeCCCCCcHHHHHHHHHHhcCcc--cceeEeecCCccCCHHHHHHHHHHHHHHhCccccHHHHHHHHhcccc
Confidence            4556789999999999999999988733221  122233333322     121111          11            


Q ss_pred             -hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CCCCChHHH
Q 047219          372 -SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQDLDPALI  449 (567)
Q Consensus       372 -~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~~Ld~aL~  449 (567)
                       ....+..+|.+......+..||||+.|.+...       +....+..|++.     .+.++.+|.+|.. |.---..++
T Consensus       112 ~l~~l~~~L~~Ela~~~~pl~LVlDDyHli~~~-------~l~~~l~fLl~~-----~P~~l~lvv~SR~rP~l~la~lR  179 (894)
T COG2909         112 SLESLLSSLLNELASYEGPLYLVLDDYHLISDP-------ALHEALRFLLKH-----APENLTLVVTSRSRPQLGLARLR  179 (894)
T ss_pred             cHHHHHHHHHHHHHhhcCceEEEeccccccCcc-------cHHHHHHHHHHh-----CCCCeEEEEEeccCCCCccccee
Confidence             12245566666666665689999999998632       444444555553     4678888888854 321111111


Q ss_pred             hccceEEEec----CCCHHHHHHHHHHHH-HhhCHHHHHHHHHhccCC
Q 047219          450 SRFDSMITFG----LPDHENRQEIAAQYA-KHLTKAELAELATATEEM  492 (567)
Q Consensus       450 sRf~~~I~i~----~P~~~eR~eIL~~~~-~~~~~~~l~~la~~t~g~  492 (567)
                      =| +..++++    ..+.+|-.+.+.... ..+...++..+...++|.
T Consensus       180 lr-~~llEi~~~~Lrf~~eE~~~fl~~~~~l~Ld~~~~~~L~~~teGW  226 (894)
T COG2909         180 LR-DELLEIGSEELRFDTEEAAAFLNDRGSLPLDAADLKALYDRTEGW  226 (894)
T ss_pred             eh-hhHHhcChHhhcCChHHHHHHHHHcCCCCCChHHHHHHHhhcccH
Confidence            00 0112221    225566666666544 234455666666666664

>PRK14531 adenylate kinase; Provisional

Probab=96.35  E-value=0.004  Score=59.79  Aligned_cols=24  Identities=38%  Similarity=0.688  Sum_probs=22.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++++||||+||||+++.+++.+
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~   26 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAH   26 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999998

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.34  E-value=0.019  Score=61.37  Aligned_cols=29  Identities=24%  Similarity=0.237  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+..++|.||+|+||||++..+|..+.
T Consensus       203 ~~~~~ii~lvGptGvGKTTt~akLA~~l~  231 (407)
T PRK12726        203 LSNHRIISLIGQTGVGKTTTLVKLGWQLL  231 (407)
T ss_pred             ecCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45577899999999999999999998763

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=96.33  E-value=0.0036  Score=60.05  Aligned_cols=22  Identities=41%  Similarity=0.759  Sum_probs=21.1

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      |+|.|+||+|||++|+.|++.+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~   23 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKY   23 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999999987

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=96.32  E-value=0.0048  Score=58.70  Aligned_cols=40  Identities=23%  Similarity=0.398  Sum_probs=30.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      .+++|.|++|+||||+.+++|+.+      +.+|+..+  .+..+..|
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L------~~~F~D~D--~~Ie~~~g   42 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKAL------NLPFIDTD--QEIEKRTG   42 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHc------CCCcccch--HHHHHHHC
Confidence            579999999999999999999999      66666544  44444333

>PRK14530 adenylate kinase; Provisional

Probab=96.31  E-value=0.0041  Score=61.31  Aligned_cols=24  Identities=29%  Similarity=0.535  Sum_probs=22.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++|.|+||+||||+++.|++.+
T Consensus         4 ~~I~i~G~pGsGKsT~~~~La~~~   27 (215)
T PRK14530          4 PRILLLGAPGAGKGTQSSNLAEEF   27 (215)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHh
Confidence            368999999999999999999998

>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=96.31  E-value=0.045  Score=51.93  Aligned_cols=29  Identities=28%  Similarity=0.453  Sum_probs=25.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||+|.+.|+....
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (173)
T cd03246          25 IEPGESLAIIGPSGSGKSTLARLILGLLR   53 (173)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHhccC
Confidence            46677899999999999999999998763

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

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=96.30  E-value=0.027  Score=57.74  Aligned_cols=92  Identities=21%  Similarity=0.230  Sum_probs=56.3

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      -+++-.+++++.+....+ .|                  ..+..+.||.|.+|+||.+++|..+...      +..++.+
T Consensus         8 m~lVlf~~ai~hi~ri~R-vL------------------~~~~Gh~LLvG~~GsGr~sl~rLaa~i~------~~~~~~i   62 (268)
T PF12780_consen    8 MNLVLFDEAIEHIARISR-VL------------------SQPRGHALLVGVGGSGRQSLARLAAFIC------GYEVFQI   62 (268)
T ss_dssp             ------HHHHHHHHHHHH-HH------------------CSTTEEEEEECTTTSCHHHHHHHHHHHT------TEEEE-T
T ss_pred             cceeeHHHHHHHHHHHHH-HH------------------cCCCCCeEEecCCCccHHHHHHHHHHHh------ccceEEE
Confidence            456777788887766443 22                  3455789999999999999999888877      5566666


Q ss_pred             chhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          360 PLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       360 ~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ....-.+  ..+....++.++..|--...+.+++|+|-+
T Consensus        63 ~~~~~y~--~~~f~~dLk~~~~~ag~~~~~~vfll~d~q   99 (268)
T PF12780_consen   63 EITKGYS--IKDFKEDLKKALQKAGIKGKPTVFLLTDSQ   99 (268)
T ss_dssp             TTSTTTH--HHHHHHHHHHHHHHHHCS-S-EEEEEECCC
T ss_pred             EeeCCcC--HHHHHHHHHHHHHHHhccCCCeEEEecCcc
Confidence            5432111  122345566777777655556788887754

The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four (D1 - D4) correspond to the ATP binding sites with P-loop signatures described previously, and two (D5, D6) are modules in which the P loop has been lost in evolution. This particular entry represents the D4 ATP-binding domain of the motor [].; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=96.30  E-value=0.031  Score=52.85  Aligned_cols=36  Identities=28%  Similarity=0.389  Sum_probs=26.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      -+++.|+||+|||++++.++..+...   +..+..++++
T Consensus         2 ~~~~~G~~G~GKTt~~~~la~~~~~~---g~~v~~i~~D   37 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKK---GKKVLLVAAD   37 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEEcC
Confidence            36889999999999999999876432   3344444443

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.

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=96.28  E-value=0.029  Score=67.65  Aligned_cols=144  Identities=15%  Similarity=0.203  Sum_probs=76.4

Q ss_pred             CCCCceEEeeCCCCCcHHHH-HHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHh-------------
Q 047219          319 SNRPRAVLFEGPPGTGKTSC-ARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN-------------  384 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~L-AraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~-------------  384 (567)
                      .+..++++++||||+|||.+ .-++-+++      ...+++++.+.-..     ++..+..+-+...             
T Consensus      1491 lnt~R~~i~cGppGSgK~mlM~~sLrs~~------~~ev~~~Nfs~~t~-----T~s~ls~Ler~t~yy~~tg~~~l~PK 1559 (3164)
T COG5245        1491 LNTLRSYIYCGPPGSGKEMLMCPSLRSEL------ITEVKYFNFSTCTM-----TPSKLSVLERETEYYPNTGVVRLYPK 1559 (3164)
T ss_pred             HhccceEEEECCCCCccchhcchhhhhhh------heeeeEEeeccccC-----CHHHHHHHHhhceeeccCCeEEEccC
Confidence            35678999999999999985 44555555      34455555432111     0111111111110             


Q ss_pred             cCCCCcEEEEcCcchhhhhhhhhhHHH---HHHHHHH--HHHhhcC-cccCCcEEEEEeeCCCCCC-----ChHHHhccc
Q 047219          385 ELPNGAIIFLDEVDSFAVARDSEMHEA---TRRILSV--LLRQIDG-FEQDKKVVVIAATNRKQDL-----DPALISRFD  453 (567)
Q Consensus       385 ~~a~~~ILfIDEID~L~~~~q~~l~~~---~~~vl~~--LL~~ld~-~~~~~~viVIaaTN~~~~L-----d~aL~sRf~  453 (567)
                      ..-...|||.|||+ |+....-....+   .+.++..  +...+.. ...-.++++.++||++.+.     ...+.++- 
T Consensus      1560 ~~vK~lVLFcDeIn-Lp~~~~y~~~~vI~FlR~l~e~QGfw~s~~~~wvTI~~i~l~Gacnp~td~gRv~~~eRf~r~~- 1637 (3164)
T COG5245        1560 PVVKDLVLFCDEIN-LPYGFEYYPPTVIVFLRPLVERQGFWSSIAVSWVTICGIILYGACNPGTDEGRVKYYERFIRKP- 1637 (3164)
T ss_pred             cchhheEEEeeccC-CccccccCCCceEEeeHHHHHhcccccchhhhHhhhcceEEEccCCCCCCcccCccHHHHhcCc-
Confidence            01113799999998 543321100000   0000000  1110000 0122578999999986543     34555544 


Q ss_pred             eEEEecCCCHHHHHHHHHHHHH
Q 047219          454 SMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       454 ~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      ..+.+..|.......|.+.++.
T Consensus      1638 v~vf~~ype~~SL~~Iyea~l~ 1659 (3164)
T COG5245        1638 VFVFCCYPELASLRNIYEAVLM 1659 (3164)
T ss_pred             eEEEecCcchhhHHHHHHHHHH
Confidence            5677889998888888887654

>PRK06547 hypothetical protein; Provisional

Probab=96.28  E-value=0.0046  Score=59.09  Aligned_cols=28  Identities=32%  Similarity=0.497  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-|++.|++|+|||++|+.+++.+
T Consensus        12 ~~~~~~i~i~G~~GsGKTt~a~~l~~~~   39 (172)
T PRK06547         12 GGGMITVLIDGRSGSGKTTLAGALAART   39 (172)
T ss_pred             cCCCEEEEEECCCCCCHHHHHHHHHHHh
Confidence            4567789999999999999999999987

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.28  E-value=0.1  Score=51.03  Aligned_cols=25  Identities=36%  Similarity=0.501  Sum_probs=23.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.-+++.|.||+|||++|+.++..+
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~   27 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHR   27 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            4578999999999999999999997

>PTZ00088 adenylate kinase 1; Provisional

Probab=96.28  E-value=0.0052  Score=61.45  Aligned_cols=26  Identities=27%  Similarity=0.636  Sum_probs=23.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|..++|.||||+||||+|+.+++.+
T Consensus         5 ~~mrIvl~G~PGsGK~T~a~~La~~~   30 (229)
T PTZ00088          5 GPLKIVLFGAPGVGKGTFAEILSKKE   30 (229)
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHh
Confidence            34559999999999999999999998

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=96.27  E-value=0.031  Score=54.61  Aligned_cols=27  Identities=22%  Similarity=0.427  Sum_probs=22.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....-++|.||+|+||||+.+.|+...
T Consensus        23 ~~g~~~~ltGpNg~GKSTllr~i~~~~   49 (199)
T cd03283          23 EKKNGILITGSNMSGKSTFLRTIGVNV   49 (199)
T ss_pred             cCCcEEEEECCCCCChHHHHHHHHHHH
Confidence            445778999999999999999998643

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

>PRK06696 uridine kinase; Validated

Probab=96.27  E-value=0.0065  Score=60.30  Aligned_cols=42  Identities=26%  Similarity=0.435  Sum_probs=30.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~  363 (567)
                      ...+.-|.+.|++|+||||+|+.|+..++..   +.+.+.++..+
T Consensus        19 ~~~~~iI~I~G~sgsGKSTlA~~L~~~l~~~---g~~v~~~~~Dd   60 (223)
T PRK06696         19 LTRPLRVAIDGITASGKTTFADELAEEIKKR---GRPVIRASIDD   60 (223)
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEecccc
Confidence            3456778999999999999999999998533   33445444433

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=96.27  E-value=0.011  Score=68.74  Aligned_cols=26  Identities=42%  Similarity=0.703  Sum_probs=22.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      +-++|.|+||||||++++++.+.+..
T Consensus       339 ~~~iitGgpGTGKTt~l~~i~~~~~~  364 (720)
T TIGR01448       339 KVVILTGGPGTGKTTITRAIIELAEE  364 (720)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHH
Confidence            46899999999999999999887743

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>TIGR00152 dephospho-CoA kinase

Probab=96.27  E-value=0.027  Score=54.18  Aligned_cols=39  Identities=15%  Similarity=0.271  Sum_probs=28.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE  371 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~  371 (567)
                      +.|+|.+|+|||++++.+++..      ++  ..+++..+....+..
T Consensus         2 i~itG~~gsGKst~~~~l~~~~------~~--~~i~~D~~~~~~~~~   40 (188)
T TIGR00152         2 IGLTGGIGSGKSTVANYLADKY------HF--PVIDADKIAHQVVEK   40 (188)
T ss_pred             EEEECCCCCCHHHHHHHHHHhc------CC--eEEeCCHHHHHHHhc
Confidence            6799999999999999999875      33  345566665554433

This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases.

>PLN02674 adenylate kinase

Probab=96.26  E-value=0.0099  Score=60.01  Aligned_cols=39  Identities=21%  Similarity=0.443  Sum_probs=30.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      ..+..++|.||||+||+|+|+.|++.+      +  +..++..++..
T Consensus        29 ~~~~~i~l~G~PGsGKgT~a~~La~~~------~--~~his~GdllR   67 (244)
T PLN02674         29 KPDKRLILIGPPGSGKGTQSPIIKDEY------C--LCHLATGDMLR   67 (244)
T ss_pred             ccCceEEEECCCCCCHHHHHHHHHHHc------C--CcEEchhHHHH
Confidence            445679999999999999999999988      3  45555555543

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

Probab=96.26  E-value=0.031  Score=56.83  Aligned_cols=28  Identities=21%  Similarity=0.298  Sum_probs=24.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+...++|.|+||+|||+++..++...
T Consensus        27 ~~~g~~~~i~g~~G~GKT~l~~~~~~~~   54 (271)
T cd01122          27 LRKGELIILTAGTGVGKTTFLREYALDL   54 (271)
T ss_pred             EcCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            5666789999999999999999888765

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

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=96.26  E-value=0.0037  Score=58.54  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=20.6

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|.||+|+||||+|+.+++.+
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l   22 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRL   22 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhc
Confidence            4789999999999999999998

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.26  E-value=0.02  Score=56.97  Aligned_cols=25  Identities=28%  Similarity=0.345  Sum_probs=22.1

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      .....++|.||.|+|||++.+.++.
T Consensus        29 ~~g~~~~itG~N~~GKStll~~i~~   53 (222)
T cd03287          29 EGGYCQIITGPNMGGKSSYIRQVAL   53 (222)
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHH
Confidence            4556789999999999999999987

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

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=96.24  E-value=0.018  Score=67.28  Aligned_cols=77  Identities=18%  Similarity=0.227  Sum_probs=44.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH----HhhhhchhHHHHHHHHH---HH-hcCCCCcEEE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV----MSKYYGESERLLGKVFS---LA-NELPNGAIIF  393 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l----~s~~~G~~~~~l~~~f~---~A-~~~a~~~ILf  393 (567)
                      ..-++|.|+||||||++++++...+...   +..+..+.....    +....|.....+..+..   .. ....+..+|+
T Consensus       368 ~~~~il~G~aGTGKTtll~~i~~~~~~~---g~~V~~~ApTg~Aa~~L~~~~g~~a~Ti~~~~~~~~~~~~~~~~~~llI  444 (744)
T TIGR02768       368 GDIAVVVGRAGTGKSTMLKAAREAWEAA---GYRVIGAALSGKAAEGLQAESGIESRTLASLEYAWANGRDLLSDKDVLV  444 (744)
T ss_pred             CCEEEEEecCCCCHHHHHHHHHHHHHhC---CCeEEEEeCcHHHHHHHHhccCCceeeHHHHHhhhccCcccCCCCcEEE
Confidence            3467899999999999999998776433   334444433222    22222221122222211   10 1123458999


Q ss_pred             EcCcchhh
Q 047219          394 LDEVDSFA  401 (567)
Q Consensus       394 IDEID~L~  401 (567)
                      |||+..+.
T Consensus       445 vDEasMv~  452 (744)
T TIGR02768       445 IDEAGMVG  452 (744)
T ss_pred             EECcccCC
Confidence            99998875

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK14730 coaE dephospho-CoA kinase; Provisional

Probab=96.23  E-value=0.038  Score=53.80  Aligned_cols=39  Identities=15%  Similarity=0.297  Sum_probs=30.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      -+.|+|++|+|||++++.+++.+      +  +..+++..+....+.
T Consensus         3 ~i~itG~~gsGKst~~~~l~~~~------g--~~~i~~D~~~~~~~~   41 (195)
T PRK14730          3 RIGLTGGIASGKSTVGNYLAQQK------G--IPILDADIYAREALA   41 (195)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh------C--CeEeeCcHHHHHHHh
Confidence            47899999999999999999876      3  444567666665553

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=96.23  E-value=0.059  Score=51.33  Aligned_cols=29  Identities=14%  Similarity=0.343  Sum_probs=25.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||+|++.++....
T Consensus        25 i~~Ge~~~i~G~nGsGKStLl~~l~G~~~   53 (178)
T cd03247          25 LKQGEKIALLGRSGSGKSTLLQLLTGDLK   53 (178)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            56778899999999999999999998764

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.

>PRK05537 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Validated

Probab=96.22  E-value=0.017  Score=65.35  Aligned_cols=95  Identities=22%  Similarity=0.308  Sum_probs=55.8

Q ss_pred             ccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhch-------h
Q 047219          300 LQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGE-------S  372 (567)
Q Consensus       300 l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~-------~  372 (567)
                      +..|+..+-|.......  ...+..++|+|.||+||||+|++++..+....  +.++..++...+...+.|+       .
T Consensus       372 f~rpeV~~iL~~~~~~r--~~~g~~Ivl~Gl~GSGKSTia~~La~~L~~~~--g~~~~~lD~D~vr~~l~ge~~f~~~er  447 (568)
T PRK05537        372 FSFPEVVAELRRTYPPR--HKQGFTVFFTGLSGAGKSTIAKALMVKLMEMR--GRPVTLLDGDVVRKHLSSELGFSKEDR  447 (568)
T ss_pred             hcHHHHHHHHHHHhccc--cCCCeEEEEECCCCChHHHHHHHHHHHhhhcc--CceEEEeCCcHHHHhccCCCCCCHHHH
Confidence            55566665554433332  34566799999999999999999999985411  3456777776665444332       1


Q ss_pred             HHHHHHHHHHHh-cCCCCcEEEEcCcc
Q 047219          373 ERLLGKVFSLAN-ELPNGAIIFLDEVD  398 (567)
Q Consensus       373 ~~~l~~~f~~A~-~~a~~~ILfIDEID  398 (567)
                      +.....+-..+. ....++++++|-+-
T Consensus       448 ~~~~~~l~~~a~~v~~~Gg~vI~~~~~  474 (568)
T PRK05537        448 DLNILRIGFVASEITKNGGIAICAPIA  474 (568)
T ss_pred             HHHHHHHHHHHHHHHhCCCEEEEEeCC
Confidence            111222211222 12236788888773

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.22  E-value=0.03  Score=54.95  Aligned_cols=26  Identities=27%  Similarity=0.387  Sum_probs=21.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ....-++|.||.|+|||++.+.++..
T Consensus        27 ~~~~~~~l~G~n~~GKstll~~i~~~   52 (204)
T cd03282          27 GSSRFHIITGPNMSGKSTYLKQIALL   52 (204)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHH
Confidence            34467999999999999999999743

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

>PTZ00202 tuzin; Provisional

Probab=96.21  E-value=0.21  Score=54.42  Aligned_cols=52  Identities=21%  Similarity=0.383  Sum_probs=41.3

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.+|.+.....|...+...                  ....+.-+.|.|++|||||++++.+...+.
T Consensus       260 ~~~~FVGReaEla~Lr~VL~~~------------------d~~~privvLtG~~G~GKTTLlR~~~~~l~  311 (550)
T PTZ00202        260 VIRQFVSREAEESWVRQVLRRL------------------DTAHPRIVVFTGFRGCGKSSLCRSAVRKEG  311 (550)
T ss_pred             CccCCCCcHHHHHHHHHHHhcc------------------CCCCceEEEEECCCCCCHHHHHHHHHhcCC
Confidence            4568899999999998877421                  123455788999999999999999998773

>PRK03846 adenylylsulfate kinase; Provisional

Probab=96.20  E-value=0.012  Score=57.12  Aligned_cols=44  Identities=20%  Similarity=0.360  Sum_probs=32.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      ...+.-+.|.|++|+||||+|+.++..+...   +...+.++...+.
T Consensus        21 ~~~~~~i~i~G~~GsGKSTla~~l~~~l~~~---~~~~~~ld~d~~~   64 (198)
T PRK03846         21 GHKGVVLWFTGLSGSGKSTVAGALEEALHEL---GVSTYLLDGDNVR   64 (198)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHhC---CCCEEEEcCEeHH
Confidence            3567789999999999999999999987432   3345666654443

>COG1124 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]

Probab=96.20  E-value=0.027  Score=56.30  Aligned_cols=28  Identities=29%  Similarity=0.459  Sum_probs=24.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..+=|.||+|||||||+|+++...
T Consensus        30 i~~Ge~lgivGeSGsGKSTL~r~l~Gl~   57 (252)
T COG1124          30 IERGETLGIVGESGSGKSTLARLLAGLE   57 (252)
T ss_pred             ecCCCEEEEEcCCCCCHHHHHHHHhccc
Confidence            5677788899999999999999999765

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.20  E-value=0.0043  Score=58.18  Aligned_cols=28  Identities=39%  Similarity=0.710  Sum_probs=24.4

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      +-+.|||||||||+|+.||+.+      ++++++
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~------gl~~vs   30 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHL------GLKLVS   30 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHh------CCceee
Confidence            5688999999999999999999      666664

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=96.19  E-value=0.034  Score=62.56  Aligned_cols=30  Identities=33%  Similarity=0.401  Sum_probs=26.8

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+++..+|+.||+|||||+|.|+||..-+
T Consensus       415 ~v~~G~~llI~G~SG~GKTsLlRaiaGLWP  444 (604)
T COG4178         415 EVRPGERLLITGESGAGKTSLLRALAGLWP  444 (604)
T ss_pred             eeCCCCEEEEECCCCCCHHHHHHHHhccCc
Confidence            367889999999999999999999998764

>PF13245 AAA_19: Part of AAA domain

Probab=96.19  E-value=0.005  Score=50.71  Aligned_cols=24  Identities=46%  Similarity=0.682  Sum_probs=17.4

Q ss_pred             ceEEeeCCCCCcHH-HHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKT-SCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT-~LAraIA~~l  346 (567)
                      .-+++.|||||||| ++++.++...
T Consensus        11 ~~~vv~g~pGtGKT~~~~~~i~~l~   35 (76)
T PF13245_consen   11 PLFVVQGPPGTGKTTTLAARIAELL   35 (76)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHH
Confidence            34556999999999 5566666555

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.18  E-value=0.0066  Score=58.38  Aligned_cols=23  Identities=39%  Similarity=0.793  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.||||+||||+|+.|++.+
T Consensus         2 riiilG~pGaGK~T~A~~La~~~   24 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKKL   24 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999987

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=96.15  E-value=0.011  Score=63.22  Aligned_cols=75  Identities=19%  Similarity=0.129  Sum_probs=43.6

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh-hH-----------HhhhhchhHHHHHHHHHHHhcCCCCc
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE-VV-----------MSKYYGESERLLGKVFSLANELPNGA  390 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~-~l-----------~s~~~G~~~~~l~~~f~~A~~~a~~~  390 (567)
                      ..+|++||+|+||||+++++.+++..... ....+.+..+ ++           ...-+|.....+...+..+.+.. +.
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i~~~~~-~~~IvtiEdp~E~~~~~~~~~~~~~q~evg~~~~~~~~~l~~aLR~~-PD  227 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHCGETYP-DRKIVTYEDPIEYILGSPDDLLPPAQSQIGRDVDSFANGIRLALRRA-PK  227 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcCC-CceEEEEecCchhccCCCceeecccccccCCCccCHHHHHHHhhccC-CC
Confidence            46899999999999999999988742110 1122332211 10           01111221123344555555665 58


Q ss_pred             EEEEcCcch
Q 047219          391 IIFLDEVDS  399 (567)
Q Consensus       391 ILfIDEID~  399 (567)
                      +|++.|+-.
T Consensus       228 ~I~vGEiRd  236 (372)
T TIGR02525       228 IIGVGEIRD  236 (372)
T ss_pred             EEeeCCCCC
Confidence            999999965

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=96.15  E-value=0.006  Score=57.57  Aligned_cols=40  Identities=18%  Similarity=0.324  Sum_probs=30.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      ..++|.|.+|+|||++++.+|+.+      +.+++..  ..+....+|
T Consensus         3 ~~i~~~G~~GsGKst~~~~la~~l------g~~~~d~--D~~~~~~~g   42 (171)
T PRK03731          3 QPLFLVGARGCGKTTVGMALAQAL------GYRFVDT--DQWLQSTSN   42 (171)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh------CCCEEEc--cHHHHHHhC
Confidence            468999999999999999999998      6666543  444444433

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.15  E-value=0.022  Score=59.61  Aligned_cols=45  Identities=20%  Similarity=0.132  Sum_probs=31.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~  363 (567)
                      ...+.-++|+||||||||+++..++......   ...+..+++++.+.
T Consensus        99 i~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~  146 (317)
T PRK04301         99 IETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEG  146 (317)
T ss_pred             ccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCC
Confidence            4556778899999999999999998764221   01123577777654

>PRK10436 hypothetical protein; Provisional

Probab=96.15  E-value=0.015  Score=64.01  Aligned_cols=97  Identities=13%  Similarity=0.178  Sum_probs=58.6

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      .++++++-.+...+.+++++.                      .+..-+|++||+|+||||+..++.+++...   ..++
T Consensus       195 ~~L~~LG~~~~~~~~l~~~~~----------------------~~~GliLvtGpTGSGKTTtL~a~l~~~~~~---~~~i  249 (462)
T PRK10436        195 LDLETLGMTPAQLAQFRQALQ----------------------QPQGLILVTGPTGSGKTVTLYSALQTLNTA---QINI  249 (462)
T ss_pred             CCHHHcCcCHHHHHHHHHHHH----------------------hcCCeEEEECCCCCChHHHHHHHHHhhCCC---CCEE
Confidence            467888777777777776553                      344568999999999999998888777543   2333


Q ss_pred             EEechh-hH-----Hhhhhc-hhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          357 MYVPLE-VV-----MSKYYG-ESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       357 ~~i~~~-~l-----~s~~~G-~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      +.+..+ ++     ...-++ .....+...+..+.++. +.+|++.||-.
T Consensus       250 ~TiEDPvE~~l~gi~Q~~v~~~~g~~f~~~lr~~LR~d-PDvI~vGEIRD  298 (462)
T PRK10436        250 CSVEDPVEIPLAGINQTQIHPKAGLTFQRVLRALLRQD-PDVIMVGEIRD  298 (462)
T ss_pred             EEecCCccccCCCcceEeeCCccCcCHHHHHHHHhcCC-CCEEEECCCCC
Confidence            333321 00     000011 11122344455555565 48999999965

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=96.14  E-value=0.15  Score=60.00  Aligned_cols=24  Identities=21%  Similarity=0.380  Sum_probs=20.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .+.++|+||.+.|||++.+.++-.
T Consensus       327 ~~~~iITGpN~gGKTt~lktigl~  350 (782)
T PRK00409        327 KTVLVITGPNTGGKTVTLKTLGLA  350 (782)
T ss_pred             ceEEEEECCCCCCcHHHHHHHHHH
Confidence            456899999999999999999754

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.14  E-value=0.071  Score=54.73  Aligned_cols=30  Identities=37%  Similarity=0.616  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ...++.++|.||+|+||||++..+|..+..
T Consensus        69 ~~~~~vi~l~G~~G~GKTTt~akLA~~l~~   98 (272)
T TIGR00064        69 ENKPNVILFVGVNGVGKTTTIAKLANKLKK   98 (272)
T ss_pred             CCCCeEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            345678889999999999999999987743

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.

>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars

Probab=96.14  E-value=0.0051  Score=49.46  Aligned_cols=22  Identities=32%  Similarity=0.608  Sum_probs=20.6

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.+.|+||+|||++++++++.+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999987

Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=96.14  E-value=0.0034  Score=65.35  Aligned_cols=77  Identities=14%  Similarity=0.168  Sum_probs=44.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh-hHHh---h----hhchhHHHHHHHHHHHhcCCCCcEE
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE-VVMS---K----YYGESERLLGKVFSLANELPNGAII  392 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~-~l~s---~----~~G~~~~~l~~~f~~A~~~a~~~IL  392 (567)
                      ...++++.|++|+||||+++++.+.+...+- ...++.+... ++.-   .    ..+.....+..++..+.+.. +..|
T Consensus       131 ~~~~ilI~G~tGSGKTTll~al~~~i~~~~~-~~ri~tiEd~~El~~~~~~~v~~~~~~~~~~~~~~l~~aLR~~-pD~i  208 (299)
T TIGR02782       131 ARKNILVVGGTGSGKTTLANALLAEIAKNDP-TDRVVIIEDTRELQCAAPNVVQLRTSDDAISMTRLLKATLRLR-PDRI  208 (299)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHhhccCC-CceEEEECCchhhcCCCCCEEEEEecCCCCCHHHHHHHHhcCC-CCEE
Confidence            3468999999999999999999988743100 1112222111 1000   0    00111113455666666666 4899


Q ss_pred             EEcCcch
Q 047219          393 FLDEVDS  399 (567)
Q Consensus       393 fIDEID~  399 (567)
                      ++.|+-.
T Consensus       209 ivGEiR~  215 (299)
T TIGR02782       209 IVGEVRG  215 (299)
T ss_pred             EEeccCC
Confidence            9999964

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=96.13  E-value=0.015  Score=60.62  Aligned_cols=117  Identities=21%  Similarity=0.277  Sum_probs=64.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ....+-++|+|+.|+|||++.+.|...++..      ...+..+..... ++..      -|..+.-.. .-+++.||++
T Consensus        73 ~~~~~~~~l~G~g~nGKStl~~~l~~l~G~~------~~~~~~~~~~~~-~~~~------~f~~a~l~g-k~l~~~~E~~  138 (304)
T TIGR01613        73 YTEQKLFFLYGNGGNGKSTFQNLLSNLLGDY------ATTAVASLKMNE-FQEH------RFGLARLEG-KRAVIGDEVQ  138 (304)
T ss_pred             CCceEEEEEECCCCCcHHHHHHHHHHHhChh------hccCCcchhhhh-ccCC------CchhhhhcC-CEEEEecCCC
Confidence            3456779999999999999999998887432      222122222221 1110      122222222 3688899987


Q ss_pred             hhhhhhhhhhHHHHHHHHHHHHHhhcCc----------ccCCcEEEEEeeCCCCC---CChHHHhccceEEEec
Q 047219          399 SFAVARDSEMHEATRRILSVLLRQIDGF----------EQDKKVVVIAATNRKQD---LDPALISRFDSMITFG  459 (567)
Q Consensus       399 ~L~~~~q~~l~~~~~~vl~~LL~~ld~~----------~~~~~viVIaaTN~~~~---Ld~aL~sRf~~~I~i~  459 (567)
                      .-... .       ...+..+. ..|.+          .......+|.+||..-.   -+.++.+|+ .+|.|+
T Consensus       139 ~~~~~-~-------~~~lK~lt-~gd~i~~~~k~k~~~~~~~~~~~i~~tN~~P~~~~~~~a~~RR~-~vi~f~  202 (304)
T TIGR01613       139 KGYRD-D-------ESTFKSLT-GGDTITARFKNKDPFEFTPKFTLVQSTNHLPRIRGFDGGIKRRL-RIIPFT  202 (304)
T ss_pred             CCccc-c-------HHhhhhhh-cCCeEEeecccCCcEEEEEeeEEEEEcCCCCccCCCChhheeeE-EEEecc
Confidence            42100 0       01112221 11111          22345778889987444   457899999 788874

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.13  E-value=0.3  Score=51.10  Aligned_cols=101  Identities=16%  Similarity=0.201  Sum_probs=55.9

Q ss_pred             HHHHHHHHhcCC--CCcEEEEcCcchhhhhhhhh------hHHHHHHHHHHHHHhhcCcc--cCCcEE-EEEeeCC---C
Q 047219          376 LGKVFSLANELP--NGAIIFLDEVDSFAVARDSE------MHEATRRILSVLLRQIDGFE--QDKKVV-VIAATNR---K  441 (567)
Q Consensus       376 l~~~f~~A~~~a--~~~ILfIDEID~L~~~~q~~------l~~~~~~vl~~LL~~ld~~~--~~~~vi-VIaaTN~---~  441 (567)
                      +..++++.....  .+.++.||++..+.....-.      .....-.+...|+..+.+..  .++.++ .+++|..   +
T Consensus       142 ~~~l~~EL~~~~~~~PVL~avD~~n~l~~~S~Y~~~~~~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t~~~~~~  221 (309)
T PF10236_consen  142 FQALIRELKAQSKRPPVLVAVDGFNALFGPSAYRDPDFKPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAATSVSNAP  221 (309)
T ss_pred             HHHHHHHHHhcccCCceEEEehhhHHhhCCccccCCCCccccHHHhhHHHHHHHHhcCccccCCCeEEEEEecccccccc
Confidence            455566655543  35788899999997653211      11222234455555533322  223332 2455432   2


Q ss_pred             C--CCChHHHhccc---------------------eEEEecCCCHHHHHHHHHHHHHh
Q 047219          442 Q--DLDPALISRFD---------------------SMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       442 ~--~Ld~aL~sRf~---------------------~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      .  .++.+|..+-.                     ..++++..+.+|-..+++.+.+.
T Consensus       222 ~~~~l~~~L~~~~~~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~~  279 (309)
T PF10236_consen  222 KSPTLPVALGGKEGFPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYADS  279 (309)
T ss_pred             CCccchhhhccccCCCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHHC
Confidence            2  45555554321                     16788888999998988887653

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis []. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix [] and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).

>PRK13764 ATPase; Provisional

Probab=96.13  E-value=0.01  Score=67.14  Aligned_cols=29  Identities=31%  Similarity=0.622  Sum_probs=25.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ....++|++||||+||||+++++++.+..
T Consensus       255 ~~~~~ILIsG~TGSGKTTll~AL~~~i~~  283 (602)
T PRK13764        255 ERAEGILIAGAPGAGKSTFAQALAEFYAD  283 (602)
T ss_pred             hcCCEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34578999999999999999999998864

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.12  E-value=0.024  Score=62.13  Aligned_cols=100  Identities=11%  Similarity=0.116  Sum_probs=60.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      ...++++++......+.+.+.+.                      .+..-+|++||+|+|||+...++.++++..   ..
T Consensus       233 ~~l~l~~Lg~~~~~~~~~~~~~~----------------------~p~GliLvTGPTGSGKTTTLY~~L~~ln~~---~~  287 (500)
T COG2804         233 VILDLEKLGMSPFQLARLLRLLN----------------------RPQGLILVTGPTGSGKTTTLYAALSELNTP---ER  287 (500)
T ss_pred             ccCCHHHhCCCHHHHHHHHHHHh----------------------CCCeEEEEeCCCCCCHHHHHHHHHHHhcCC---Cc
Confidence            34678888888888888877663                      344457788999999999999999998654   33


Q ss_pred             CeEEechh------hHHhhhhch-hHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          355 PLMYVPLE------VVMSKYYGE-SERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       355 ~~~~i~~~------~l~s~~~G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      +++.+.-+      .+..--+.. ..-.+...++...++. |.||++.||-..
T Consensus       288 nI~TiEDPVE~~~~gI~Q~qVN~k~gltfa~~LRa~LRqD-PDvImVGEIRD~  339 (500)
T COG2804         288 NIITIEDPVEYQLPGINQVQVNPKIGLTFARALRAILRQD-PDVIMVGEIRDL  339 (500)
T ss_pred             eEEEeeCCeeeecCCcceeecccccCCCHHHHHHHHhccC-CCeEEEeccCCH
Confidence            33333321      010000000 0001122233333454 599999999764

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.11  E-value=0.0044  Score=58.74  Aligned_cols=30  Identities=23%  Similarity=0.572  Sum_probs=25.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .++++|.|||||||+++.++ .+      +.+++.++
T Consensus         2 ~I~ITGTPGvGKTT~~~~L~-~l------g~~~i~l~   31 (180)
T COG1936           2 LIAITGTPGVGKTTVCKLLR-EL------GYKVIELN   31 (180)
T ss_pred             eEEEeCCCCCchHHHHHHHH-Hh------CCceeeHH
Confidence            47899999999999999999 77      66676654

>PRK14528 adenylate kinase; Provisional

Probab=96.11  E-value=0.0061  Score=58.85  Aligned_cols=24  Identities=33%  Similarity=0.872  Sum_probs=22.2

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.+++.||||+|||++|+.+++.+
T Consensus         2 ~~i~i~G~pGsGKtt~a~~la~~~   25 (186)
T PRK14528          2 KNIIFMGPPGAGKGTQAKILCERL   25 (186)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999988

>PRK08485 DNA polymerase III subunit delta'; Validated

Probab=96.11  E-value=0.05  Score=53.03  Aligned_cols=85  Identities=19%  Similarity=0.191  Sum_probs=62.8

Q ss_pred             HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccce
Q 047219          375 LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDS  454 (567)
Q Consensus       375 ~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~  454 (567)
                      .++.+.+.+...+..+-++|+++|.|..           ...+.||+.++  +++.++++|..|+.+..+.|.++|||..
T Consensus        41 ~iReii~~~~~~~~~~k~iI~~a~~l~~-----------~A~NaLLK~LE--EPp~~~~fiL~t~~~~~llpTI~SRc~~  107 (206)
T PRK08485         41 DAKEVIAEAYIAESEEKIIVIAAPSYGI-----------EAQNALLKILE--EPPKNICFIIVAKSKNLLLPTIRSRLII  107 (206)
T ss_pred             HHHHHHHHHhhCCCCcEEEEEchHhhCH-----------HHHHHHHHHhc--CCCCCeEEEEEeCChHhCchHHHhhhee
Confidence            4455555544333345567889998863           35588899888  4788999999999999999999999942


Q ss_pred             ------------EEEecCCCHHHHHHHHHH
Q 047219          455 ------------MITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       455 ------------~I~i~~P~~~eR~eIL~~  472 (567)
                                  .+.+...+.++..+.++.
T Consensus       108 ~~~~~~~~~~~l~l~l~~l~~~~i~~~L~~  137 (206)
T PRK08485        108 EKRKQKKPVKPLDLDLKKLDLKDIYEFLKE  137 (206)
T ss_pred             ccccccccccccccccCCCCHHHHHHHHHH
Confidence                        366777788887777766

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=96.09  E-value=0.0043  Score=60.56  Aligned_cols=23  Identities=48%  Similarity=0.749  Sum_probs=17.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -.+++||||||||+++..+...+
T Consensus        19 ~~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   19 ITLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             -EEEE-STTSSHHHHHHHHHHHH
T ss_pred             CEEEECCCCCChHHHHHHHHHHh
Confidence            48899999999997776666665

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=96.08  E-value=0.013  Score=72.66  Aligned_cols=131  Identities=25%  Similarity=0.351  Sum_probs=82.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh--hhhc----h----hHHHHHHHHHHHhcCCCCcE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS--KYYG----E----SERLLGKVFSLANELPNGAI  391 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s--~~~G----~----~~~~l~~~f~~A~~~a~~~I  391 (567)
                      -.++||.||.|+|||.+++.+|...      +.+++.++..+.+.  +|.|    .    ..-+-..+...++   +++.
T Consensus       440 ~~pillqG~tssGKtsii~~la~~~------g~~~vrinnhehtd~qeyig~y~~~~~g~l~freg~LV~Alr---~G~~  510 (1856)
T KOG1808|consen  440 KFPILLQGPTSSGKTSIIKELARAT------GKNIVRINNHEHTDLQEYIGTYVADDNGDLVFREGVLVQALR---NGDW  510 (1856)
T ss_pred             CCCeEEecCcCcCchhHHHHHHHHh------ccCceehhccccchHHHHHHhhhcCCCCCeeeehhHHHHHHH---hCCE
Confidence            3589999999999999999999999      66677776543322  3333    1    1111122333333   3789


Q ss_pred             EEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC------------cccCCcEEEEEeeCCCCC------CChHHHhccc
Q 047219          392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG------------FEQDKKVVVIAATNRKQD------LDPALISRFD  453 (567)
Q Consensus       392 LfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~------------~~~~~~viVIaaTN~~~~------Ld~aL~sRf~  453 (567)
                      +|+||++.-...           ++..|.+.++.            +....++++++|-|.+..      +..+|++|| 
T Consensus       511 ~vlD~lnla~~d-----------vL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn~~~~y~grk~lsRa~~~rf-  578 (1856)
T KOG1808|consen  511 IVLDELNLAPHD-----------VLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQNPPGTYGGRKILSRALRNRF-  578 (1856)
T ss_pred             EEeccccccchH-----------HHHHHHhhhhhhccccccccceeeccCcchhhhhhccCccccchhhhhhhcccccc-
Confidence            999999865422           22333333332            133456777888887643      567788888 


Q ss_pred             eEEEecCCCHHHHHHHHHHH
Q 047219          454 SMITFGLPDHENRQEIAAQY  473 (567)
Q Consensus       454 ~~I~i~~P~~~eR~eIL~~~  473 (567)
                      ..++|..-+.++..+|+...
T Consensus       579 ~e~~f~~~~e~e~~~i~~~~  598 (1856)
T KOG1808|consen  579 IELHFDDIGEEELEEILEHR  598 (1856)
T ss_pred             hhhhhhhcCchhhhhhhccc
Confidence            66677655666666666543

>PRK13946 shikimate kinase; Provisional

Probab=96.08  E-value=0.0059  Score=58.74  Aligned_cols=34  Identities=29%  Similarity=0.540  Sum_probs=28.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .++.|+|.|.+|+|||++++.+++.+      +.+|+..+
T Consensus         9 ~~~~I~l~G~~GsGKsti~~~LA~~L------g~~~id~D   42 (184)
T PRK13946          9 GKRTVVLVGLMGAGKSTVGRRLATML------GLPFLDAD   42 (184)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHc------CCCeECcC
Confidence            45789999999999999999999999      66666544

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=96.08  E-value=0.012  Score=57.72  Aligned_cols=133  Identities=18%  Similarity=0.261  Sum_probs=59.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh-hchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY-YGESERLLGKVFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~-~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                      -++|+||+|||||.+|-++|+..      +.+++..+.-.....+ .|.......++     ...  -=++|||-.--.+
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~------g~pvI~~Driq~y~~l~v~Sgrp~~~el-----~~~--~RiyL~~r~l~~G   69 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKT------GAPVISLDRIQCYPELSVGSGRPTPSEL-----KGT--RRIYLDDRPLSDG   69 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--------EEEEE-SGGG-GGGTTTTT---SGGG-----TT---EEEES----GGG-
T ss_pred             EEEEECCCCCChhHHHHHHHHHh------CCCEEEecceecccccccccCCCCHHHH-----ccc--ceeeeccccccCC
Confidence            46899999999999999999999      7788887765554433 22221111111     111  2377886543222


Q ss_pred             hhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh-----ccce-EEEecCCCHHHHHHHHHHHHHh
Q 047219          403 ARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS-----RFDS-MITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       403 ~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s-----Rf~~-~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      ...      ..+....|+..++.+...+.+++=+-+..  .+..=..+     .|.. +..+++|+.+.-..-.+...++
T Consensus        70 ~i~------a~ea~~~Li~~v~~~~~~~~~IlEGGSIS--Ll~~m~~~~~w~~~f~w~i~rl~l~d~~~f~~ra~~Rv~~  141 (233)
T PF01745_consen   70 IIN------AEEAHERLISEVNSYSAHGGLILEGGSIS--LLNCMAQDPYWSLDFRWHIRRLRLPDEEVFMARAKRRVRQ  141 (233)
T ss_dssp             S--------HHHHHHHHHHHHHTTTTSSEEEEEE--HH--HHHHHHH-TTTSSSSEEEEEE-----HHHHHHHHHHHHHH
T ss_pred             CcC------HHHHHHHHHHHHHhccccCceEEeCchHH--HHHHHHhcccccCCCeEEEEEEECCChHHHHHHHHHHHHH
Confidence            211      12233445555555555445555444421  11111111     2322 4555778877766666666555


Q ss_pred             h
Q 047219          477 L  477 (567)
Q Consensus       477 ~  477 (567)
                      |
T Consensus       142 M  142 (233)
T PF01745_consen  142 M  142 (233)
T ss_dssp             H
T ss_pred             h
Confidence            3

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=96.07  E-value=0.0069  Score=57.75  Aligned_cols=33  Identities=27%  Similarity=0.502  Sum_probs=27.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      ...++|.|++|+|||++++.+++.+      +.+++..+
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l------~~~~vd~D   36 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQL------NMEFYDSD   36 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHc------CCcEEECC
Confidence            4579999999999999999999998      55565544

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=96.07  E-value=0.012  Score=62.23  Aligned_cols=75  Identities=19%  Similarity=0.223  Sum_probs=45.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech-hhHH------------hh-hhchhHHHHHHHHHHHhc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL-EVVM------------SK-YYGESERLLGKVFSLANE  385 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~-~~l~------------s~-~~G~~~~~l~~~f~~A~~  385 (567)
                      ....++++.|++|+||||+++++....+..    ..++.+.. .++.            .+ -.|...-....++..+.+
T Consensus       158 ~~~~nili~G~tgSGKTTll~aL~~~ip~~----~ri~tiEd~~El~l~~~~n~~~~~~~~~~~~~~~~~~~~ll~~~LR  233 (332)
T PRK13900        158 ISKKNIIISGGTSTGKTTFTNAALREIPAI----ERLITVEDAREIVLSNHPNRVHLLASKGGQGRAKVTTQDLIEACLR  233 (332)
T ss_pred             HcCCcEEEECCCCCCHHHHHHHHHhhCCCC----CeEEEecCCCccccccCCCEEEEEecCCCCCcCcCcHHHHHHHHhc
Confidence            346789999999999999999999988642    11111110 0000            00 001112234556666666


Q ss_pred             CCCCcEEEEcCcch
Q 047219          386 LPNGAIIFLDEVDS  399 (567)
Q Consensus       386 ~a~~~ILfIDEID~  399 (567)
                      ..| ..|++.|+-.
T Consensus       234 ~~P-D~IivGEiR~  246 (332)
T PRK13900        234 LRP-DRIIVGELRG  246 (332)
T ss_pred             cCC-CeEEEEecCC
Confidence            664 8999999964

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=96.06  E-value=0.0061  Score=58.05  Aligned_cols=24  Identities=25%  Similarity=0.530  Sum_probs=21.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .-++|.|+||+||||+++.+++.+
T Consensus         4 ~ii~i~G~~GsGKsTl~~~l~~~~   27 (188)
T TIGR01360         4 KIIFIVGGPGSGKGTQCEKIVEKY   27 (188)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999999987

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=96.06  E-value=0.038  Score=52.00  Aligned_cols=26  Identities=23%  Similarity=0.423  Sum_probs=22.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++..++.||.|+|||++.++++-.+
T Consensus        20 ~~~~~~i~G~NgsGKS~~l~~i~~~~   45 (162)
T cd03227          20 EGSLTIITGPNGSGKSTILDAIGLAL   45 (162)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            34689999999999999999987654

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.

>TIGR00455 apsK adenylylsulfate kinase (apsK)

Probab=96.05  E-value=0.018  Score=55.18  Aligned_cols=44  Identities=18%  Similarity=0.314  Sum_probs=32.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      ..++.-++|.|+||+|||++|+.++..+...   +...+.++...+.
T Consensus        15 ~~~~~~i~i~G~~GsGKstla~~l~~~l~~~---~~~~~~l~~d~~r   58 (184)
T TIGR00455        15 GHRGVVIWLTGLSGSGKSTIANALEKKLESK---GYRVYVLDGDNVR   58 (184)
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEECChHHH
Confidence            4567789999999999999999999987432   3345666655443

Important residue (active site in E.coli) is residue 100 of the seed alignment.

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

Probab=96.05  E-value=0.047  Score=52.28  Aligned_cols=42  Identities=36%  Similarity=0.647  Sum_probs=28.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCC-CCC------CCcCeEEechh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGA-MPW------QGVPLMYVPLE  362 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~-~~~------~~~~~~~i~~~  362 (567)
                      ...-++|.||||+|||+++-.++..+.. .+|      ...++.+++.+
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~l~~~~~~g~~~~g~~~~~~~~Vl~i~~E   79 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQLAAALATGRPFLGELPPRPGRVLYISLE   79 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHHHHHHHHT---TT---------EEEEESS
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHhCCccCCcccccCceEEEEecc
Confidence            3456899999999999999999887643 122      24567777654

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.04  E-value=0.0095  Score=58.53  Aligned_cols=24  Identities=42%  Similarity=0.511  Sum_probs=19.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .-+.+.||.|||||++|-+.|.+.
T Consensus        20 ~~v~~~G~AGTGKT~LA~a~Al~~   43 (205)
T PF02562_consen   20 DLVIVNGPAGTGKTFLALAAALEL   43 (205)
T ss_dssp             SEEEEE--TTSSTTHHHHHHHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHH
Confidence            468899999999999999988765

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.03  E-value=0.017  Score=65.35  Aligned_cols=97  Identities=16%  Similarity=0.130  Sum_probs=57.7

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      .++++++-.++..+.+.+++.                      .+...+|++||+|+||||+..++.+.++..   ..++
T Consensus       293 ~~l~~lg~~~~~~~~l~~~~~----------------------~~~Glilv~G~tGSGKTTtl~a~l~~~~~~---~~~i  347 (564)
T TIGR02538       293 LDIDKLGFEPDQKALFLEAIH----------------------KPQGMVLVTGPTGSGKTVSLYTALNILNTE---EVNI  347 (564)
T ss_pred             CCHHHcCCCHHHHHHHHHHHH----------------------hcCCeEEEECCCCCCHHHHHHHHHHhhCCC---CceE
Confidence            467777767776777766553                      234568899999999999998888887532   2233


Q ss_pred             EEechh------hHHhhhhc-hhHHHHHHHHHHHhcCCCCcEEEEcCcch
Q 047219          357 MYVPLE------VVMSKYYG-ESERLLGKVFSLANELPNGAIIFLDEVDS  399 (567)
Q Consensus       357 ~~i~~~------~l~s~~~G-~~~~~l~~~f~~A~~~a~~~ILfIDEID~  399 (567)
                      +.+..+      .+...-+. .....+...+..+.++. +-+|++.||-.
T Consensus       348 ~tiEdpvE~~~~~~~q~~v~~~~g~~~~~~l~~~LR~d-PDvI~vGEiRd  396 (564)
T TIGR02538       348 STAEDPVEINLPGINQVNVNPKIGLTFAAALRSFLRQD-PDIIMVGEIRD  396 (564)
T ss_pred             EEecCCceecCCCceEEEeccccCCCHHHHHHHHhccC-CCEEEeCCCCC
Confidence            332221      00000000 11112334455555565 48999999975

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.99  E-value=0.008  Score=63.13  Aligned_cols=77  Identities=17%  Similarity=0.192  Sum_probs=43.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh-hHH---hh---hhchhHHHHHHHHHHHhcCCCCcEEE
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE-VVM---SK---YYGESERLLGKVFSLANELPNGAIIF  393 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~-~l~---s~---~~G~~~~~l~~~f~~A~~~a~~~ILf  393 (567)
                      ...++++.|++|+|||+++++++......+- ...++.+... ++.   ..   +....+-....++..+.+.. +..|+
T Consensus       147 ~~~~ilI~G~tGSGKTTll~aL~~~~~~~~~-~~rivtIEd~~El~~~~~~~v~~~~~~~~~~~~ll~~aLR~~-PD~Ii  224 (319)
T PRK13894        147 AHRNILVIGGTGSGKTTLVNAIINEMVIQDP-TERVFIIEDTGEIQCAAENYVQYHTSIDVNMTALLKTTLRMR-PDRIL  224 (319)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHhhhhcCC-CceEEEEcCCCccccCCCCEEEEecCCCCCHHHHHHHHhcCC-CCEEE
Confidence            4578999999999999999999987421000 0111111110 000   00   00011123455666666666 48999


Q ss_pred             EcCcch
Q 047219          394 LDEVDS  399 (567)
Q Consensus       394 IDEID~  399 (567)
                      +.|+-.
T Consensus       225 vGEiR~  230 (319)
T PRK13894        225 VGEVRG  230 (319)
T ss_pred             EeccCC
Confidence            999964

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=95.99  E-value=0.019  Score=59.31  Aligned_cols=26  Identities=27%  Similarity=0.460  Sum_probs=23.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.||+|+||||++..++..+
T Consensus       193 ~~~vi~~vGptGvGKTTt~~kLa~~~  218 (282)
T TIGR03499       193 QGGVIALVGPTGVGKTTTLAKLAARF  218 (282)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            46689999999999999999999877

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

Probab=95.99  E-value=0.064  Score=49.74  Aligned_cols=21  Identities=33%  Similarity=0.493  Sum_probs=17.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVI  342 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraI  342 (567)
                      .+++++.||+|+|||+.+...
T Consensus        14 ~~~~li~aptGsGKT~~~~~~   34 (169)
T PF00270_consen   14 GKNVLISAPTGSGKTLAYILP   34 (169)
T ss_dssp             TSEEEEECSTTSSHHHHHHHH
T ss_pred             CCCEEEECCCCCccHHHHHHH
Confidence            467999999999999988733

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 ....

>PRK13808 adenylate kinase; Provisional

Probab=95.98  E-value=0.032  Score=58.76  Aligned_cols=23  Identities=35%  Similarity=0.667  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|+||||+|||++++.|+..+
T Consensus         2 rIiv~GpPGSGK~T~a~~LA~~y   24 (333)
T PRK13808          2 RLILLGPPGAGKGTQAQRLVQQY   24 (333)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999988

>PF08303 tRNA_lig_kinase: tRNA ligase kinase domain; InterPro: IPR015966 This entry represents a kinase domain found in fungal tRNA ligases []

Probab=95.97  E-value=0.14  Score=48.35  Aligned_cols=131  Identities=18%  Similarity=0.187  Sum_probs=67.2

Q ss_pred             eCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh
Q 047219          328 EGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE  407 (567)
Q Consensus       328 ~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~  407 (567)
                      .+.+||||||++.++++.++.       +.-+.-.++.++   ...+.+....+.+.+.. ..++|.|-=..+...|   
T Consensus         5 IAtiGCGKTTva~aL~~LFg~-------wgHvQnDnI~~k---~~~~f~~~~l~~L~~~~-~~vViaDRNNh~~reR---   70 (168)
T PF08303_consen    5 IATIGCGKTTVALALSNLFGE-------WGHVQNDNITGK---RKPKFIKAVLELLAKDT-HPVVIADRNNHQKRER---   70 (168)
T ss_pred             ecCCCcCHHHHHHHHHHHcCC-------CCccccCCCCCC---CHHHHHHHHHHHHhhCC-CCEEEEeCCCchHHHH---
Confidence            478999999999999999841       223334444333   12233334444442222 4789998766654332   


Q ss_pred             hHHHHHHHHHHHHHhhc-CcccCCcEEEEEeeCCCCCCChHHHh--------ccce--EEEecCCCHHHHHHHHHHHHHh
Q 047219          408 MHEATRRILSVLLRQID-GFEQDKKVVVIAATNRKQDLDPALIS--------RFDS--MITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       408 l~~~~~~vl~~LL~~ld-~~~~~~~viVIaaTN~~~~Ld~aL~s--------Rf~~--~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                           ++++..+...-. .+....++.+||-.=..+.-.+.+++        |=|+  .|.....+...-..|+...++.
T Consensus        71 -----~ql~~~~~~~~~~yl~~~~~~r~VaL~fv~~~~~~~i~~it~~RV~~RGDNHQTika~~~~~~~~~~Im~gFi~r  145 (168)
T PF08303_consen   71 -----KQLFEDVSQLKPDYLPYDTNVRFVALNFVHDDDLDEIRRITQDRVLARGDNHQTIKADSKDEKKVEGIMEGFIKR  145 (168)
T ss_pred             -----HHHHHHHHHhcccccccCCCeEEEEEEccCCCCHHHHHHHHHHHHHhcCcCcceeecCCCCHHHHHHHHHHHHHh
Confidence                 222222222211 11234577888776333222233332        3333  4444444555666666665554


Q ss_pred             h
Q 047219          477 L  477 (567)
Q Consensus       477 ~  477 (567)
                      +
T Consensus       146 f  146 (168)
T PF08303_consen  146 F  146 (168)
T ss_pred             c
Confidence            3

Please see the following relevant references: [, ].; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation

>PRK02496 adk adenylate kinase; Provisional

Probab=95.97  E-value=0.0067  Score=58.07  Aligned_cols=23  Identities=43%  Similarity=0.795  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.||||+|||++|+.|+..+
T Consensus         3 ~i~i~G~pGsGKst~a~~la~~~   25 (184)
T PRK02496          3 RLIFLGPPGAGKGTQAVVLAEHL   25 (184)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48899999999999999999988

>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=95.97  E-value=0.053  Score=52.77  Aligned_cols=25  Identities=24%  Similarity=0.442  Sum_probs=19.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .++|+.|.+|+|||++.+.+...+-
T Consensus        39 ~h~li~G~tgsGKS~~l~~ll~~l~   63 (205)
T PF01580_consen   39 PHLLIAGATGSGKSTLLRTLLLSLA   63 (205)
T ss_dssp             -SEEEE--TTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEcCCCCCccHHHHHHHHHHH
Confidence            3999999999999999998887763

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.

>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1

Probab=95.96  E-value=0.034  Score=58.31  Aligned_cols=45  Identities=16%  Similarity=0.014  Sum_probs=30.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~  363 (567)
                      .....-+.|+||||+|||+++..++-.....   ...+..++|++.+.
T Consensus        93 i~~G~iteI~G~~GsGKTql~lqla~~~~~~~~~gg~~~~vvYIdtE~  140 (313)
T TIGR02238        93 IESMSITEVFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEG  140 (313)
T ss_pred             CcCCeEEEEECCCCCCcCHHHHHHHHHHhcchhhcCCCCeEEEEEcCC
Confidence            4556678899999999999998877533210   01134577777554

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.

>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]

Probab=95.96  E-value=0.037  Score=64.02  Aligned_cols=29  Identities=17%  Similarity=0.255  Sum_probs=25.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+++..+-|.|++|||||||+|.+.....
T Consensus       496 I~~Ge~vaIvG~SGsGKSTL~KLL~gly~  524 (709)
T COG2274         496 IPPGEKVAIVGRSGSGKSTLLKLLLGLYK  524 (709)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56677799999999999999999998763

>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=95.95  E-value=0.075  Score=50.14  Aligned_cols=29  Identities=34%  Similarity=0.453  Sum_probs=25.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||+|++.++....
T Consensus        24 i~~Ge~~~i~G~nGsGKSTLl~~l~G~~~   52 (166)
T cd03223          24 IKPGDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56778899999999999999999998764

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

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.94  E-value=0.0098  Score=62.49  Aligned_cols=75  Identities=16%  Similarity=0.156  Sum_probs=43.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech-hhHHh------hhhchhHHHHHHHHHHHhcCCCCcEEEE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL-EVVMS------KYYGESERLLGKVFSLANELPNGAIIFL  394 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~-~~l~s------~~~G~~~~~l~~~f~~A~~~a~~~ILfI  394 (567)
                      ..++++.|++|+||||+++++.......+. +...+.+.. .++.-      .+.....-....++..+.+.. +..|++
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i~~~~~-~~rivtiEd~~El~~~~~n~v~l~~~~~~~~~~lv~~aLR~~-PD~Iiv  221 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEIVASAP-EDRLVILEDTAEIQCAAENAVALHTSDTVDMARLLKSTMRLR-PDRIIV  221 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHhcCCC-CceEEEecCCcccccCCCCEEEeccCCCcCHHHHHHHHhCCC-CCEEEE
Confidence            468999999999999999999988731100 111222221 11110      000111122445666666665 489999


Q ss_pred             cCcc
Q 047219          395 DEVD  398 (567)
Q Consensus       395 DEID  398 (567)
                      .|+-
T Consensus       222 GEiR  225 (323)
T PRK13833        222 GEVR  225 (323)
T ss_pred             eecC
Confidence            9995

>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type

Probab=95.94  E-value=0.023  Score=59.88  Aligned_cols=37  Identities=16%  Similarity=0.123  Sum_probs=28.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ...+.|.|+||+|||||++.+++.+      +.+++.-.+.++
T Consensus       162 ~~~~~~~G~~~~gkstl~~~l~~~~------~~~~v~E~~R~~  198 (325)
T TIGR01526       162 VKTVAILGGESTGKSTLVNKLAAVF------NTTSAWEYAREY  198 (325)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhh------CCCEEeehhHHH
Confidence            4579999999999999999999988      445544444333

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.

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=95.88  E-value=0.07  Score=51.02  Aligned_cols=37  Identities=22%  Similarity=0.547  Sum_probs=27.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      +.|+|++|+||||+++.+++ +      +++  .+++..+....+.
T Consensus         2 i~itG~~gsGKst~~~~l~~-~------g~~--~i~~D~~~~~~~~   38 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-L------GIP--VIDADKIAHEVYE   38 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-C------CCC--EEecCHHHHhhhh
Confidence            67999999999999999998 5      443  4555566555443

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>TIGR01351 adk adenylate kinases

Probab=95.88  E-value=0.0075  Score=59.17  Aligned_cols=22  Identities=41%  Similarity=0.761  Sum_probs=21.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|.||||+||||+|+.|++.+
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~   23 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKY   23 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHc
Confidence            7899999999999999999987

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=95.88  E-value=0.016  Score=60.59  Aligned_cols=29  Identities=17%  Similarity=0.431  Sum_probs=25.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .....++++.||+|+||||+++++...+.
T Consensus       141 v~~~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHHHHHHHccCC
Confidence            45568999999999999999999998875

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=95.85  E-value=0.035  Score=66.23  Aligned_cols=75  Identities=19%  Similarity=0.184  Sum_probs=42.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh----hchhHHHHHHHHHHH---h-cCCCCcEEEEc
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY----YGESERLLGKVFSLA---N-ELPNGAIIFLD  395 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~----~G~~~~~l~~~f~~A---~-~~a~~~ILfID  395 (567)
                      -++|.|.+|||||++.+++...+...   +..++.+..+....+-    .|.....+..++...   . ...+..+|+||
T Consensus       364 v~vv~G~AGTGKTT~l~~~~~~~e~~---G~~V~~~ApTGkAA~~L~e~tGi~a~TI~sll~~~~~~~~~l~~~~vlIVD  440 (988)
T PRK13889        364 LGVVVGYAGTGKSAMLGVAREAWEAA---GYEVRGAALSGIAAENLEGGSGIASRTIASLEHGWGQGRDLLTSRDVLVID  440 (988)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEecCcHHHHHHHhhccCcchhhHHHHHhhhcccccccccCcEEEEE
Confidence            56799999999999999887765432   3334433332222211    222223333332111   1 12235799999


Q ss_pred             Ccchhh
Q 047219          396 EVDSFA  401 (567)
Q Consensus       396 EID~L~  401 (567)
                      |+..+.
T Consensus       441 EASMv~  446 (988)
T PRK13889        441 EAGMVG  446 (988)
T ss_pred             CcccCC
Confidence            998775

>PLN02459 probable adenylate kinase

Probab=95.84  E-value=0.014  Score=59.43  Aligned_cols=28  Identities=29%  Similarity=0.417  Sum_probs=24.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..++|.||||+||+|+++.+++.+
T Consensus        26 ~~~~~~ii~~G~PGsGK~T~a~~la~~~   53 (261)
T PLN02459         26 KGRNVNWVFLGCPGVGKGTYASRLSKLL   53 (261)
T ss_pred             ccCccEEEEECCCCCCHHHHHHHHHHHh
Confidence            3444568889999999999999999988

>PTZ00035 Rad51 protein; Provisional

Probab=95.83  E-value=0.051  Score=57.56  Aligned_cols=45  Identities=16%  Similarity=0.054  Sum_probs=29.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~  363 (567)
                      .....-+.|+||||+|||+++..++-.....   .-.+..+++++.+.
T Consensus       115 i~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~  162 (337)
T PTZ00035        115 IETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEG  162 (337)
T ss_pred             CCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccC
Confidence            4556668899999999999999988654310   00133566666543

>PRK00279 adk adenylate kinase; Reviewed

Probab=95.82  E-value=0.0091  Score=58.83  Aligned_cols=23  Identities=39%  Similarity=0.751  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+++|+||+||||+|+.||+.+
T Consensus         2 ~I~v~G~pGsGKsT~a~~la~~~   24 (215)
T PRK00279          2 RLILLGPPGAGKGTQAKFIAEKY   24 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            38999999999999999999988

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

Probab=95.81  E-value=0.073  Score=54.08  Aligned_cols=29  Identities=21%  Similarity=0.320  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+-|.||.|||||||.|+++..+.
T Consensus        25 i~~G~i~~iiGpNG~GKSTLLk~l~g~l~   53 (258)
T COG1120          25 IPKGEITGILGPNGSGKSTLLKCLAGLLK   53 (258)
T ss_pred             ecCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            45667788999999999999999999764

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=95.81  E-value=0.32  Score=52.78  Aligned_cols=55  Identities=20%  Similarity=0.309  Sum_probs=41.6

Q ss_pred             CCCCcccc-cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          275 SEISWENI-AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       275 ~~~~~~dI-iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      |....+.| +|.+..++.+.+.+...                  .......-++.|+-|+|||++.+.+.....
T Consensus        19 P~~Gl~~~~VGr~~e~~~l~~~l~~v------------------~~G~s~~kfi~G~YGsGKTf~l~~i~~~A~   74 (416)
T PF10923_consen   19 PRIGLDHIAVGREREIEALDRDLDRV------------------ADGGSSFKFIRGEYGSGKTFFLRLIRERAL   74 (416)
T ss_pred             CcccCcceeechHHHHHHHHHHHHHH------------------hCCCCeEEEEEeCCCCcHHHHHHHHHHHHH
Confidence            44555555 79999999998877543                  134455678899999999999999987653

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>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=95.78  E-value=0.036  Score=52.96  Aligned_cols=29  Identities=24%  Similarity=0.331  Sum_probs=25.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||+|++.|+....
T Consensus        22 i~~G~~~~l~G~nGsGKStLl~~i~G~~~   50 (180)
T cd03214          22 IEAGEIVGILGPNGAGKSTLLKTLAGLLK   50 (180)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            56778899999999999999999998763

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.

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=95.77  E-value=0.042  Score=56.36  Aligned_cols=78  Identities=17%  Similarity=0.241  Sum_probs=45.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH-------Hhhhh---------chhHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV-------MSKYY---------GESERLLGKVFSLAN  384 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l-------~s~~~---------G~~~~~l~~~f~~A~  384 (567)
                      ++..++|.|++|+|||++++.++..+...   +.....+++...       ...+.         ......+...+..+.
T Consensus        74 ~~~~i~~~G~~g~GKTtl~~~l~~~l~~~---~~~v~~i~~D~~ri~~~~ql~~~~~~~~~~~~~~~~~~~l~~~l~~l~  150 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGK---KKTVGFITTDHSRIGTVQQLQDYVKTIGFEVIAVRDEAAMTRALTYFK  150 (270)
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHHHHHHc---CCeEEEEecCCCCHHHHHHHHHHhhhcCceEEecCCHHHHHHHHHHHH
Confidence            55789999999999999999998876321   122322332111       01111         112333444444444


Q ss_pred             cCCCCcEEEEcCcchhh
Q 047219          385 ELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       385 ~~a~~~ILfIDEID~L~  401 (567)
                      ......+++||-.....
T Consensus       151 ~~~~~D~ViIDt~Gr~~  167 (270)
T PRK06731        151 EEARVDYILIDTAGKNY  167 (270)
T ss_pred             hcCCCCEEEEECCCCCc
Confidence            33335789999988764

>cd01125 repA Hexameric Replicative Helicase RepA

Probab=95.76  E-value=0.21  Score=49.97  Aligned_cols=39  Identities=26%  Similarity=0.233  Sum_probs=27.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCC-C--------CCCcCeEEechhh
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAM-P--------WQGVPLMYVPLEV  363 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~-~--------~~~~~~~~i~~~~  363 (567)
                      -+|.||||+|||+|+-.+|...... +        ..+.++++++.++
T Consensus         4 ~ll~g~~G~GKS~lal~la~~va~G~~~~g~~~~~~~~~~Vlyi~~Ed   51 (239)
T cd01125           4 SALVAPGGTGKSSLLLVLALAMALGKNLFGGGLKVTEPGRVVYLSAED   51 (239)
T ss_pred             eEEEcCCCCCHHHHHHHHHHHHhcCccccCCccccCCCceEEEEECCC
Confidence            5799999999999999998765321 1        1244677777653

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.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.75  E-value=0.058  Score=60.01  Aligned_cols=27  Identities=30%  Similarity=0.518  Sum_probs=23.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..+.|.||+|+|||+++..|+..+
T Consensus       348 ~~G~vIaLVGPtGvGKTTtaakLAa~l  374 (559)
T PRK12727        348 ERGGVIALVGPTGAGKTTTIAKLAQRF  374 (559)
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHHHH
Confidence            446788999999999999999998765

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=95.74  E-value=0.031  Score=51.19  Aligned_cols=23  Identities=22%  Similarity=0.596  Sum_probs=20.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhC
Q 047219          325 VLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++|.||+|+|||++++.+++...
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~   24 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFD   24 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCC
Confidence            67899999999999999999854

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

>TIGR02239 recomb_RAD51 DNA repair protein RAD51

Probab=95.74  E-value=0.035  Score=58.30  Aligned_cols=27  Identities=22%  Similarity=0.119  Sum_probs=23.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..+..-+.++||||+|||+++..++..
T Consensus        93 i~~g~i~~i~G~~g~GKT~l~~~~~~~  119 (316)
T TIGR02239        93 IETGSITEIFGEFRTGKTQLCHTLAVT  119 (316)
T ss_pred             CCCCeEEEEECCCCCCcCHHHHHHHHH
Confidence            456677889999999999999998863

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).

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=95.73  E-value=0.049  Score=57.78  Aligned_cols=45  Identities=16%  Similarity=0.003  Sum_probs=29.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~~  363 (567)
                      .....-..|+||||||||+|+..++-.....   .-.+..++|++.+.
T Consensus       123 i~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~  170 (344)
T PLN03187        123 IETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEG  170 (344)
T ss_pred             CCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCC
Confidence            4555668899999999999999887443210   00123567776643

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=95.71  E-value=0.012  Score=56.60  Aligned_cols=38  Identities=32%  Similarity=0.505  Sum_probs=29.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      |.+.|+||+|||++|+.++..+...   +.++..++..++.
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~---~~~~~~i~~Ddf~   39 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVN---GIGPVVISLDDYY   39 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEEehhhcc
Confidence            6789999999999999999998533   3456666655544

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.70  E-value=0.16  Score=55.13  Aligned_cols=26  Identities=35%  Similarity=0.658  Sum_probs=22.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.||+|+||||++..+|...
T Consensus       222 ~~~vi~lvGptGvGKTTtaaKLA~~~  247 (432)
T PRK12724        222 QRKVVFFVGPTGSGKTTSIAKLAAKY  247 (432)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            35568899999999999999999754

>PF00488 MutS_V: MutS domain V C-terminus

Probab=95.68  E-value=0.072  Score=53.52  Aligned_cols=109  Identities=17%  Similarity=0.228  Sum_probs=54.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh---CCCCCCCcC----------eEEechhh-HHh--hhhchhHHHHHHHHHHHhc
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA---GAMPWQGVP----------LMYVPLEV-VMS--KYYGESERLLGKVFSLANE  385 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l---~~~~~~~~~----------~~~i~~~~-l~s--~~~G~~~~~l~~~f~~A~~  385 (567)
                      .+.++|+||...|||++.|.|+...   ....++...          +..+...+ +..  ..|...-..+..+++.+. 
T Consensus        43 ~~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~-  121 (235)
T PF00488_consen   43 SRIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNAT-  121 (235)
T ss_dssp             SSEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH---
T ss_pred             eeEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeecccccccccccccHHHhHHHHHhhhhhcc-
Confidence            3679999999999999999998754   111111111          12222211 111  122233345556666544 


Q ss_pred             CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC
Q 047219          386 LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ  442 (567)
Q Consensus       386 ~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~  442 (567)
                        +.++++|||+.+=....+.  ......++..|..       ..+..+|.+|+..+
T Consensus       122 --~~sLvliDE~g~gT~~~eg--~ai~~aile~l~~-------~~~~~~i~~TH~~~  167 (235)
T PF00488_consen  122 --EKSLVLIDELGRGTNPEEG--IAIAIAILEYLLE-------KSGCFVIIATHFHE  167 (235)
T ss_dssp             --TTEEEEEESTTTTSSHHHH--HHHHHHHHHHHHH-------TTT-EEEEEES-GG
T ss_pred             --cceeeecccccCCCChhHH--HHHHHHHHHHHHH-------hccccEEEEeccch
Confidence              3689999999764322111  1112222222221       13567888888654

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>PF08298 AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 This is entry is found at the N terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length

Probab=95.67  E-value=0.021  Score=60.18  Aligned_cols=54  Identities=22%  Similarity=0.365  Sum_probs=41.8

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      +++.|+++.+.++.+.+...-+.-               ....+-++|.||+|+|||++++.+.+.+..
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~---------------~~~krIl~L~GPvg~GKSsl~~~Lk~~le~  114 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGL---------------EERKRILLLLGPVGGGKSSLAELLKRGLEE  114 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhcc---------------CccceEEEEECCCCCCHHHHHHHHHHHhhe
Confidence            389999999999988765431111               234567889999999999999999998854

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK14526 adenylate kinase; Provisional

Probab=95.67  E-value=0.013  Score=57.85  Aligned_cols=23  Identities=39%  Similarity=0.910  Sum_probs=21.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.||||+||||+++.++..+
T Consensus         2 ~i~l~G~pGsGKsT~a~~La~~~   24 (211)
T PRK14526          2 KLVFLGPPGSGKGTIAKILSNEL   24 (211)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999887

>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed

Probab=95.66  E-value=0.085  Score=59.89  Aligned_cols=28  Identities=25%  Similarity=0.357  Sum_probs=26.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+++..+.|.||+|+|||||++.+....
T Consensus       373 i~~G~~vaIvG~SGsGKSTL~~lL~g~~  400 (588)
T PRK11174        373 LPAGQRIALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            6788899999999999999999999876

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=95.66  E-value=0.012  Score=58.06  Aligned_cols=21  Identities=24%  Similarity=0.646  Sum_probs=19.4

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      ++++|+||+|||++++.+...
T Consensus         1 ~vv~G~pGsGKSt~i~~~~~~   21 (234)
T PF01443_consen    1 IVVHGVPGSGKSTLIKKLLKD   21 (234)
T ss_pred             CEEEcCCCCCHHHHHHHHHHh
Confidence            478999999999999999988

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	567
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		5e-29
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		5e-29
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		5e-29
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		7e-29
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		9e-29
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		1e-28
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		3e-26
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		8e-25
3vfd_A	389	Human Spastin Aaa Domain Length = 389		4e-24
4b4t_J	405	Near-Atomic Resolution Structural Model Of The Yeas		1e-23
3h4m_A	285	Aaa Atpase Domain Of The Proteasome- Activating Nuc		2e-23
3b9p_A	297	Spastin Length = 297		2e-23
4b4t_I	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-23
4b4t_H	467	Near-Atomic Resolution Structural Model Of The Yeas		5e-23
3d8b_A	357	Crystal Structure Of Human Fidgetin-Like Protein 1		5e-23
4b4t_M	434	Near-Atomic Resolution Structural Model Of The Yeas		1e-22
3cf0_A	301	Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH		1e-22
2rko_A	331	Crystal Structure Of The Vps4p-Dimer Length = 331		2e-22
2qp9_X	355	Crystal Structure Of S.Cerevisiae Vps4 Length = 355		4e-22
3eih_A	340	Crystal Structure Of S.Cerevisiae Vps4 In The Prese		5e-22
3eie_A	322	Crystal Structure Of S.Cerevisiae Vps4 In The So4-B		6e-22
2x8a_A	274	Human Nuclear Valosin Containing Protein Like (Nvl)		1e-21
1xwi_A	322	Crystal Structure Of Vps4b Length = 322		1e-20
2zam_A	444	Crystal Structure Of Mouse Skd1VPS4B APO-Form Lengt		1e-20
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		3e-20
2r62_A	268	Crystal Structure Of Helicobacter Pylori Atp Depend		2e-17
1iy2_A	278	Crystal Structure Of The Ftsh Atpase Domain From Th		4e-17
4eiw_A	508	Whole Cytosolic Region Of Atp-Dependent Metalloprot		5e-17
1ixz_A	254	Crystal Structure Of The Ftsh Atpase Domain From Th		5e-17
2dhr_A	499	Whole Cytosolic Region Of Atp-Dependent Metalloprot		6e-17
2ce7_A	476	Edta Treated Length = 476		6e-17
3kds_E	465	Apo-ftsh Crystal Structure Length = 465		2e-16
2qz4_A	262	Human Paraplegin, Aaa Domain In Complex With Adp Le		4e-14

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  125 bits (315), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 122/226 (53%), Gaps = 20/226 (8%)
Query: 253 SVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARG 312
           +V+   G  I   DE +   S +E+ +++I G  +Q  +I++ + L L+ P ++  I   
Sbjct: 180 TVIHCEGEPIKREDEEE---SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG-- 234
Query: 313 TRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES 372
                    PR +L  GPPGTGKT  AR +AN+ GA  +    L+  P   +MSK  GES
Sbjct: 235 ------VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----LINGP--EIMSKLAGES 282
Query: 373 ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV 432
           E  L K F  A E    AIIF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V
Sbjct: 283 ESNLRKAFEEA-EKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV 341
Query: 433 VVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAAQYAKH 476
           +V+AATNR   +DPAL    RFD  +  G+PD   R EI   + K+
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN 387

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  125 bits (315), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 122/226 (53%), Gaps = 20/226 (8%)
Query: 253 SVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARG 312
           +V+   G  I   DE +   S +E+ +++I G  +Q  +I++ + L L+ P ++  I   
Sbjct: 180 TVIHCEGEPIKREDEEE---SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG-- 234
Query: 313 TRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES 372
                    PR +L  GPPGTGKT  AR +AN+ GA  +    L+  P   +MSK  GES
Sbjct: 235 ------VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----LINGP--EIMSKLAGES 282
Query: 373 ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV 432
           E  L K F  A E    AIIF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V
Sbjct: 283 ESNLRKAFEEA-EKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV 341
Query: 433 VVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAAQYAKH 476
           +V+AATNR   +DPAL    RFD  +  G+PD   R EI   + K+
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN 387

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  125 bits (315), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 122/226 (53%), Gaps = 20/226 (8%)
Query: 253 SVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARG 312
           +V+   G  I   DE +   S +E+ +++I G  +Q  +I++ + L L+ P ++  I   
Sbjct: 180 TVIHCEGEPIKREDEEE---SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG-- 234
Query: 313 TRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES 372
                    PR +L  GPPGTGKT  AR +AN+ GA  +    L+  P   +MSK  GES
Sbjct: 235 ------VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----LINGP--EIMSKLAGES 282
Query: 373 ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV 432
           E  L K F  A E    AIIF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V
Sbjct: 283 ESNLRKAFEEA-EKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV 341
Query: 433 VVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAAQYAKH 476
           +V+AATNR   +DPAL    RFD  +  G+PD   R EI   + K+
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN 387

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  125 bits (314), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 122/226 (53%), Gaps = 20/226 (8%)
Query: 253 SVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARG 312
           +V+   G  I   DE +   S +E+ +++I G  +Q  +I++ + L L+ P ++  I   
Sbjct: 180 TVIHCEGEPIKREDEEE---SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG-- 234
Query: 313 TRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES 372
                    PR +L  GPPGTGKT  AR +AN+ GA  +    L+  P   +MSK  GES
Sbjct: 235 ------VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----LINGP--EIMSKLAGES 282
Query: 373 ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV 432
           E  L K F  A E    AIIF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V
Sbjct: 283 ESNLRKAFEEA-EKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV 341
Query: 433 VVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAAQYAKH 476
           +V+AATNR   +DPAL    RFD  +  G+PD   R EI   + K+
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN 387

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score =  125 bits (313), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 85/226 (37%), Positives = 122/226 (53%), Gaps = 20/226 (8%)
Query: 253 SVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARG 312
           +V+   G  I   DE +   S +E+ ++++ G  +Q  +I++ + L L+ P ++  I   
Sbjct: 180 TVIHCEGEPIKREDEEE---SLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIG-- 234
Query: 313 TRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES 372
                    PR +L  GPPGTGKT  AR +AN+ GA  +    L+  P   +MSK  GES
Sbjct: 235 ------VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----LINGP--EIMSKLAGES 282
Query: 373 ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV 432
           E  L K F  A E    AIIF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V
Sbjct: 283 ESNLRKAFEEA-EKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV 341
Query: 433 VVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAAQYAKH 476
           +V+AATNR   +DPAL    RFD  +  G+PD   R EI   + K+
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN 387

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  124 bits (312), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 85/226 (37%), Positives = 122/226 (53%), Gaps = 20/226 (8%)
Query: 253 SVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARG 312
           +V+   G  I   DE +   S +E+ ++++ G  +Q  +I++ + L L+ P ++  I   
Sbjct: 180 TVIHCEGEPIKREDEEE---SLNEVGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIG-- 234
Query: 313 TRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGES 372
                    PR +L  GPPGTGKT  AR +AN+ GA  +    L+  P   +MSK  GES
Sbjct: 235 ------VKPPRGILLYGPPGTGKTLIARAVANETGAFFF----LINGP--EIMSKLAGES 282
Query: 373 ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV 432
           E  L K F  A E    AIIF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V
Sbjct: 283 ESNLRKAFEEA-EKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHV 341
Query: 433 VVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAAQYAKH 476
           +V+AATNR   +DPAL    RFD  +  G+PD   R EI   + K+
Sbjct: 342 IVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKN 387

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  116 bits (291), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 80/237 (33%), Positives = 123/237 (51%), Gaps = 21/237 (8%)
Query: 238 IKKGSLTSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTIL 297
           +KKG   + ++  L +++++  R    L     +  + EI+++ I G  +Q RE+ + I 
Sbjct: 140 LKKGVRVTLDITTL-TIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIE 198
Query: 298 LSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM 357
           L L++PE++  +            P+ VL  GPPGTGKT  A+ +A   GA        +
Sbjct: 199 LPLKNPEIFQRVG--------IKPPKGVLLYGPPGTGKTLLAKAVAATIGAN------FI 244
Query: 358 YVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATR---R 414
           + P   ++ KY GES R++ ++F+ A E     IIF+DEVD+    R SE   A R   R
Sbjct: 245 FSPASGIVDKYIGESARIIREMFAYAKE-HEPCIIFMDEVDAIGGRRFSEGTSADREIQR 303
Query: 415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEI 469
            L  LL Q+DGF+   +  +I ATNR   LDPAL+   R D  +   LP+   R EI
Sbjct: 304 TLMELLTQMDGFDNLGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEI 360

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score =  112 bits (279), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 78/201 (38%), Positives = 105/201 (52%), Gaps = 24/201 (11%)
Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
           K ++++ ++ G D QK+EI + + L L   ++Y+ I          + PR VL  GPPGT
Sbjct: 166 KPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG--------IDPPRGVLLYGPPGT 217
Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG-AII 392
           GKT   + +AN   A        + V     + KY GE  R++  VF LA E  N  +II
Sbjct: 218 GKTMLVKAVANSTKA------AFIRVNGSEFVHKYLGEGPRMVRDVFRLARE--NAPSII 269
Query: 393 FLDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
           F+DEVDS A  R      + R   RIL  LL Q+DGF+Q   V VI ATNR   LDPAL+
Sbjct: 270 FIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIMATNRADTLDPALL 329
Query: 450 --SRFDSMITFGLPDHENRQE 468
              R D  I F  P   +R+E
Sbjct: 330 RPGRLDRKIEF--PSLRDRRE 348

>pdb|3VFD|A Chain A, Human Spastin Aaa Domain Length = 389

Iteration: 1
 Score =  109 bits (273), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 65/194 (33%), Positives = 107/194 (55%), Gaps = 18/194 (9%)
Query: 275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTG 334
           + + +++IAG D  K+ +++ ++L    PE++     G R        R +L  GPPG G
Sbjct: 110 TAVKFDDIAGQDLAKQALQEIVILPSLRPELFT----GLRAP-----ARGLLLFGPPGNG 160
Query: 335 KTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFL 394
           KT  A+ +A ++ A          +    + SKY GE E+L+  +F++A EL   +IIF+
Sbjct: 161 KTMLAKAVAAESNAT------FFNISAASLTSKYVGEGEKLVRALFAVAREL-QPSIIFI 213
Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ--DKKVVVIAATNRKQDLDPALISRF 452
           D+VDS    R    H+A+RR+ +  L + DG +   D +V+V+ ATNR Q+LD A++ RF
Sbjct: 214 DQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRF 273
Query: 453 DSMITFGLPDHENR 466
              +   LP+ E R
Sbjct: 274 IKRVYVSLPNEETR 287

>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 405

Iteration: 1
 Score =  107 bits (268), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 118/239 (49%), Gaps = 31/239 (12%)
Query: 278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTS 337
           +++ + G  +Q +EI++ I L ++ PE+++ +           +P+ V+  GPPGTGKT 
Sbjct: 146 TYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIA--------QPKGVILYGPPGTGKTL 197
Query: 338 CARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEV 397
            AR +A+            + V    ++ KY GE  R++ ++F +A E    +IIF+DE+
Sbjct: 198 LARAVAHHTDC------KFIRVSGAELVQKYIGEGSRMVRELFVMARE-HAPSIIFMDEI 250
Query: 398 DSFAVAR-------DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI- 449
           DS    R       DSE+    +R +  LL Q+DGFE  K + +I ATNR   LDPAL+ 
Sbjct: 251 DSIGSTRVEGSGGGDSEV----QRTMLELLNQLDGFETSKNIKIIMATNRLDILDPALLR 306
Query: 450 -SRFDSMITFGLPDHENRQEIAAQYAKHXXXXXXXXXXXXXXXM---SGRDIRDVCQQA 504
             R D  I F  P    R EI   +++                M   SG D++ VC +A
Sbjct: 307 PGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEA 365

>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating Nucleotidase Length = 285

Iteration: 1
 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 67/202 (33%), Positives = 105/202 (51%), Gaps = 20/202 (9%)
Query: 273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPG 332
            +  + +E+I G ++Q +EI + + L L+ PE+++ +            P+ +L  GPPG
Sbjct: 10  ERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVG--------IEPPKGILLYGPPG 61
Query: 333 TGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAII 392
           TGKT  A+ +A +  A        + V    ++ K+ GE   L+  +F LA E    +II
Sbjct: 62  TGKTLLAKAVATETNAT------FIRVVGSELVKKFIGEGASLVKDIFKLAKE-KAPSII 114
Query: 393 FLDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
           F+DE+D+ A  R   +    R   R L  LL ++DGF+    V +I ATNR   LDPA++
Sbjct: 115 FIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAIL 174
Query: 450 --SRFDSMITFGLPDHENRQEI 469
              RFD +I    PD + R EI
Sbjct: 175 RPGRFDRIIEVPAPDEKGRLEI 196

>pdb|3B9P|A Chain A, Spastin Length = 297

Iteration: 1
 Score =  107 bits (267), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 66/196 (33%), Positives = 107/196 (54%), Gaps = 19/196 (9%)
Query: 275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTG 334
           +++ W +IAG D  K+ +++ ++L    PE++     G R        + +L  GPPG G
Sbjct: 16  AKVEWTDIAGQDVAKQALQEMVILPSVRPELFT----GLRAP-----AKGLLLFGPPGNG 66
Query: 335 KTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFL 394
           KT  AR +A +  A        + +    + SKY G+ E+L+  +F++A  +   +IIF+
Sbjct: 67  KTLLARAVATECSAT------FLNISAASLTSKYVGDGEKLVRALFAVARHM-QPSIIFI 119
Query: 395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD---KKVVVIAATNRKQDLDPALISR 451
           DEVDS    R S  HEA+RR+ +  L + DG   +    ++VV+AATNR Q+LD A + R
Sbjct: 120 DEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAALRR 179
Query: 452 FDSMITFGLPDHENRQ 467
           F   +   LPD + R+
Sbjct: 180 FTKRVYVSLPDEQTRE 195

>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score =  107 bits (266), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 123/245 (50%), Gaps = 26/245 (10%)
Query: 269 QLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFE 328
           +++ S +E S+ +I G + Q +EI++++ L L  PE+Y+++            P+ V+  
Sbjct: 172 KMDKSPTE-SYSDIGGLESQIQEIKESVELPLTHPELYEEMG--------IKPPKGVILY 222
Query: 329 GPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPN 388
           G PGTGKT  A+ +ANQ  A        + +    ++ KY G+  RL  ++F +A E  N
Sbjct: 223 GAPGTGKTLLAKAVANQTSAT------FLRIVGSELIQKYLGDGPRLCRQIFKVAGE--N 274
Query: 389 G-AIIFLDEVDSFAVAR---DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDL 444
             +I+F+DE+D+    R   +S      +R +  LL Q+DGF+    V VI ATN+ + L
Sbjct: 275 APSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDDRGDVKVIMATNKIETL 334
Query: 445 DPALI--SRFDSMITFGLPDHENRQEIAAQYAKHXXXXXXXXXXXXXXX---MSGRDIRD 499
           DPALI   R D  I F  PD   +++I   +                     +SG DI+ 
Sbjct: 335 DPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQA 394
Query: 500 VCQQA 504
           +C +A
Sbjct: 395 MCTEA 399

>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 467

Iteration: 1
 Score =  105 bits (263), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 116/240 (48%), Gaps = 25/240 (10%)
Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
           K ++++ ++ G   Q  ++ + + L L SPE +  +          + P+ +L  GPPGT
Sbjct: 203 KPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG--------IDPPKGILLYGPPGT 254
Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIF 393
           GKT CAR +AN+  A        + V    ++ KY GE  R++ ++F +A       IIF
Sbjct: 255 GKTLCARAVANRTDAT------FIRVIGSELVQKYVGEGARMVRELFEMAR-TKKACIIF 307
Query: 394 LDEVDSFAVARDSEM----HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
            DE+D+   AR  +     +E  R +L  L+ Q+DGF+    + V+ ATNR   LDPAL+
Sbjct: 308 FDEIDAVGGARFDDGAGGDNEVQRTMLE-LITQLDGFDPRGNIKVMFATNRPNTLDPALL 366
Query: 450 --SRFDSMITFGLPDHENRQEIAAQYAKHXXXXXX---XXXXXXXXXMSGRDIRDVCQQA 504
              R D  + F LPD E R  I   ++K                    +G ++R VC +A
Sbjct: 367 RPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEA 426

>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In Complex With Adp Length = 357

Iteration: 1
 Score =  105 bits (263), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 107/196 (54%), Gaps = 18/196 (9%)
Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           ++WE+IAG +  K  I++ ++  +  P+++  + RG         P+ +L  GPPGTGKT
Sbjct: 81  VNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGL-RGP--------PKGILLFGPPGTGKT 131
Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDE 396
              + IA+Q+GA          +    + SK+ GE E+++  +F++A      A+IF+DE
Sbjct: 132 LIGKCIASQSGAT------FFSISASSLTSKWVGEGEKMVRALFAVAR-CQQPAVIFIDE 184
Query: 397 VDSFAVARDSEMHEATRRILSVLLRQIDG--FEQDKKVVVIAATNRKQDLDPALISRFDS 454
           +DS    R    HE++RRI +  L Q+DG     + +++V+ ATNR Q++D A   R   
Sbjct: 185 IDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAARRRLVK 244
Query: 455 MITFGLPDHENRQEIA 470
            +   LP+   R++I 
Sbjct: 245 RLYIPLPEASARKQIV 260

>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 434

Iteration: 1
 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 75/198 (37%), Positives = 105/198 (53%), Gaps = 22/198 (11%)
Query: 278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTS 337
           ++ ++ G D+Q  E+ + I+L ++  + + D+  G R       P+  L  GPPGTGKT 
Sbjct: 179 TYSDVGGLDKQIEELVEAIVLPMKRADKFKDM--GIRA------PKGALMYGPPGTGKTL 230
Query: 338 CARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEV 397
            AR  A Q  A   +    +  P  V M  Y GE  +L+   F+LA E     IIF+DE+
Sbjct: 231 LARACAAQTNATFLK----LAAPQLVQM--YIGEGAKLVRDAFALAKE-KAPTIIFIDEL 283
Query: 398 DSFAVAR-DSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SR 451
           D+    R DSE     E  R +L  LL Q+DGF  D +V V+AATNR   LDPAL+   R
Sbjct: 284 DAIGTKRFDSEKSGDREVQRTMLE-LLNQLDGFSSDDRVKVLAATNRVDVLDPALLRSGR 342
Query: 452 FDSMITFGLPDHENRQEI 469
            D  I F LP  ++R +I
Sbjct: 343 LDRKIEFPLPSEDSRAQI 360

>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP Length = 301

Iteration: 1
 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 119/239 (49%), Gaps = 27/239 (11%)
Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           +++WE+I G +  KRE+++ +   ++ P+ +         KF     + VLF GPPG GK
Sbjct: 11  QVTWEDIGGLEDVKRELQELVQYPVEHPDKF--------LKFGMTPSKGVLFYGPPGCGK 62
Query: 336 TSCARVIAN--QAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIF 393
           T  A+ IAN  QA  +  +G  L+        + ++GESE  + ++F  A +     ++F
Sbjct: 63  TLLAKAIANECQANFISIKGPELL--------TMWFGESEANVREIFDKARQ-AAPCVLF 113
Query: 394 LDEVDSFAVARDSEMHE---ATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI- 449
            DE+DS A AR   + +   A  R+++ +L ++DG    K V +I ATNR   +DPA++ 
Sbjct: 114 FDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILR 173
Query: 450 -SRFDSMITFGLPDHENRQEIAAQYAKHXXXXX---XXXXXXXXXXMSGRDIRDVCQQA 504
             R D +I   LPD ++R  I     +                    SG D+ ++CQ+A
Sbjct: 174 PGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRA 232

>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer Length = 331

Iteration: 1
 Score =  103 bits (258), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 66/197 (33%), Positives = 110/197 (55%), Gaps = 19/197 (9%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRA-VLFEGP 330
           + K  + WE++AG +  K  +++ ++L ++ P ++    +G R      +P + +L  GP
Sbjct: 19  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLF----KGNR------KPTSGILLYGP 68
Query: 331 PGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGA 390
           PGTGK+  A+ +A +A +          V    ++SK+ GESE+L+ ++F++A E    +
Sbjct: 69  PGTGKSYLAKAVATEANST------FFSVSSSDLVSKWMGESEKLVKQLFAMARE-NKPS 121
Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAATNRKQDLDPALI 449
           IIF+DEVD+    R     EA+RRI + LL Q++G   D + V+V+ ATN    LD A+ 
Sbjct: 122 IIFIDEVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIR 181
Query: 450 SRFDSMITFGLPDHENR 466
            RF+  I   LPD   R
Sbjct: 182 RRFERRIYIPLPDLAAR 198

>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4 Length = 355

Iteration: 1
 Score =  102 bits (255), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 64/193 (33%), Positives = 109/193 (56%), Gaps = 19/193 (9%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRA-VLFEGP 330
           + K  + WE++AG +  K  +++ ++L ++ P ++    +G R      +P + +L  GP
Sbjct: 43  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLF----KGNR------KPTSGILLYGP 92
Query: 331 PGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGA 390
           PGTGK+  A+ +A +A +          V    ++SK+ GESE+L+ ++F++A E    +
Sbjct: 93  PGTGKSYLAKAVATEANST------FFSVSSSDLVSKWMGESEKLVKQLFAMARE-NKPS 145
Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAATNRKQDLDPALI 449
           IIF+D+VD+    R     EA+RRI + LL Q++G   D + V+V+ ATN    LD A+ 
Sbjct: 146 IIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIR 205
Query: 450 SRFDSMITFGLPD 462
            RF+  I   LPD
Sbjct: 206 RRFERRIYIPLPD 218

>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of Atpgammas Length = 340

Iteration: 1
 Score =  102 bits (254), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 66/209 (31%), Positives = 115/209 (55%), Gaps = 19/209 (9%)
Query: 260 RRIYGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFES 319
           +++ G     + + K  + WE++AG +  K  +++ ++L ++ P ++    +G R     
Sbjct: 16  KKLRGALSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLF----KGNR----- 66
Query: 320 NRPRA-VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGK 378
            +P + +L  GPPGTGK+  A+ +A +A +          V    ++SK+ GESE+L+ +
Sbjct: 67  -KPTSGILLYGPPGTGKSYLAKAVATEANST------FFSVSSSDLVSKWMGESEKLVKQ 119
Query: 379 VFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAA 437
           +F++A E    +IIF+D+VD+    R     EA+RRI + LL Q++G   D + V+V+ A
Sbjct: 120 LFAMARE-NKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGA 178
Query: 438 TNRKQDLDPALISRFDSMITFGLPDHENR 466
           TN    LD A+  RF+  I   LPD   R
Sbjct: 179 TNIPWQLDSAIRRRFERRIYIPLPDLAAR 207

>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound State Length = 322

Iteration: 1
 Score =  102 bits (254), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 65/197 (32%), Positives = 110/197 (55%), Gaps = 19/197 (9%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRA-VLFEGP 330
           + K  + WE++AG +  K  +++ ++L ++ P ++    +G R      +P + +L  GP
Sbjct: 10  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLF----KGNR------KPTSGILLYGP 59
Query: 331 PGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGA 390
           PGTGK+  A+ +A +A +          V    ++SK+ GESE+L+ ++F++A E    +
Sbjct: 60  PGTGKSYLAKAVATEANST------FFSVSSSDLVSKWMGESEKLVKQLFAMARE-NKPS 112
Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAATNRKQDLDPALI 449
           IIF+D+VD+    R     EA+RRI + LL Q++G   D + V+V+ ATN    LD A+ 
Sbjct: 113 IIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIR 172
Query: 450 SRFDSMITFGLPDHENR 466
            RF+  I   LPD   R
Sbjct: 173 RRFERRIYIPLPDLAAR 189

>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C- Terminal Aaa-Atpase Domain Length = 274

Iteration: 1
 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 64/203 (31%), Positives = 105/203 (51%), Gaps = 19/203 (9%)
Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           ++W +I   +  + E+   IL  +++P+ +  +   T        P  VL  GPPG GKT
Sbjct: 7   VTWADIGALEDIREELTMAILAPVRNPDQFKALGLVT--------PAGVLLAGPPGCGKT 58
Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA-NELPNGAIIFLD 395
             A+ +AN++G      +  + V    +++ Y GESER + +VF  A N  P   +IF D
Sbjct: 59  LLAKAVANESG------LNFISVKGPELLNMYVGESERAVRQVFQRAKNSAP--CVIFFD 110
Query: 396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFD 453
           EVD+    R      A+ R+++ LL ++DG E  ++V ++AATNR   +DPA++   R D
Sbjct: 111 EVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPGRLD 170
Query: 454 SMITFGLPDHENRQEIAAQYAKH 476
             +  GLP   +R  I     K+
Sbjct: 171 KTLFVGLPPPADRLAILKTITKN 193

>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b Length = 322

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 64/204 (31%), Positives = 104/204 (50%), Gaps = 19/204 (9%)
Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
           +  + W ++AG +  K  +++ ++L ++ P ++     G R  +     R +L  GPPGT
Sbjct: 6   RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLF----TGKRTPW-----RGILLFGPPGT 56
Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIF 393
           GK+  A+ +A +A            +    ++SK+ GESE+L+  +F LA E    +IIF
Sbjct: 57  GKSYLAKAVATEA-----NNSTFFSISSSDLVSKWLGESEKLVKNLFQLARE-NKPSIIF 110
Query: 394 LDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAATNRKQDLDPALISRF 452
           +DE+DS   +R     EA RRI +  L Q+ G   D   ++V+ ATN    LD A+  RF
Sbjct: 111 IDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRF 170
Query: 453 DSMITFGLPDHENRQEIAAQYAKH 476
           +  I   LP+   R   AA +  H
Sbjct: 171 EKRIYIPLPEPHAR---AAMFKLH 191

>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form Length = 444

Iteration: 1
 Score = 97.8 bits (242), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 64/201 (31%), Positives = 103/201 (51%), Gaps = 19/201 (9%)
Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           + W ++AG +  K  +++ ++L ++ P ++     G R  +     R +L  GPPGTGK+
Sbjct: 131 VKWSDVAGLEGAKEALKEAVILPIKFPHLF----TGKRTPW-----RGILLFGPPGTGKS 181
Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDE 396
             A+ +A +A            +    ++SK+ GESE+L+  +F LA E    +IIF+DE
Sbjct: 182 YLAKAVATEA-----NNSTFFSISSSDLVSKWLGESEKLVKNLFQLARE-NKPSIIFIDE 235
Query: 397 VDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAATNRKQDLDPALISRFDSM 455
           +DS   +R     EA RRI +  L Q+ G   D   ++V+ ATN    LD A+  RF+  
Sbjct: 236 IDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIRRRFEKR 295
Query: 456 ITFGLPDHENRQEIAAQYAKH 476
           I   LP+   R   AA +  H
Sbjct: 296 IYIPLPEAHAR---AAMFRLH 313

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 96.7 bits (239), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 107/210 (50%), Gaps = 26/210 (12%)
Query: 265 LDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRA 324
           L E Q+ T+     + ++AG D+ K E+ + ++  L+ P  +         K     P+ 
Sbjct: 2   LTEDQIKTT-----FADVAGCDEAKEEVAE-LVEYLREPSRFQ--------KLGGKIPKG 47
Query: 325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN 384
           VL  GPPGTGKT  A+ IA +A       VP   +     +  + G     +  +F  A 
Sbjct: 48  VLMVGPPGTGKTLLAKAIAGEAK------VPFFTISGSDFVEMFVGVGASRVRDMFEQAK 101
Query: 385 ELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRK 441
           +     IIF+DE+D+    R + +   H+   + L+ +L ++DGFE ++ ++VIAATNR 
Sbjct: 102 KAAP-CIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRP 160
Query: 442 QDLDPALI--SRFDSMITFGLPDHENRQEI 469
             LDPAL+   RFD  +  GLPD   R++I
Sbjct: 161 DVLDPALLRPGRFDRQVVVGLPDVRGREQI 190

>pdb|2R62|A Chain A, Crystal Structure Of Helicobacter Pylori Atp Dependent Protease, Ftsh Length = 268

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 66/214 (30%), Positives = 111/214 (51%), Gaps = 25/214 (11%)
Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
           +N  K  + ++++AG ++ K E+ + I+  L+ PE Y ++  G +       P+ VL  G
Sbjct: 1   INAEKPNVRFKDMAGNEEAKEEVVE-IVDFLKYPERYANL--GAKI------PKGVLLVG 51
Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA-NELPN 388
           PPGTGKT  A+ +A +A       VP   +     +  + G     +  +F  A  + P 
Sbjct: 52  PPGTGKTLLAKAVAGEA------HVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQAP- 104
Query: 389 GAIIFLDEVDSFAVARDS----EMHEATRRILSVLLRQIDGF-EQDKKVVVIAATNRKQD 443
            +IIF+DE+D+   +R +      ++   + L+ LL ++DGF  ++  V+V+AATNR + 
Sbjct: 105 -SIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIVLAATNRPEI 163
Query: 444 LDPALI--SRFDSMITFGLPDHENRQEIAAQYAK 475
           LDPAL+   RFD  +    PD   R EI   + K
Sbjct: 164 LDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIK 197

>pdb|1IY2|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 278

Iteration: 1
 Score = 86.7 bits (213), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 110/209 (52%), Gaps = 21/209 (10%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           T   +++++++AG ++ K E++  I+  L++P  + ++  G R       P+ VL  GPP
Sbjct: 32  TEAPKVTFKDVAGAEEAKEELK-EIVEFLKNPSRFHEM--GARI------PKGVLLVGPP 82
Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI 391
           G GKT  AR +A +A       VP +       +  + G     +  +F  A       I
Sbjct: 83  GVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGVGAARVRDLFETAKRHAP-CI 135
Query: 392 IFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
           +F+DE+D+    R S +   ++   + L+ LL ++DGFE+D  +VV+AATNR   LDPAL
Sbjct: 136 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPAL 195
Query: 449 I--SRFDSMITFGLPDHENRQEIAAQYAK 475
           +   RFD  I    PD + R++I   +A+
Sbjct: 196 LRPGRFDRQIAIDAPDVKGREQILRIHAR 224

>pdb|4EIW|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 508

Iteration: 1
 Score = 85.9 bits (211), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 108/209 (51%), Gaps = 21/209 (10%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           T   +++++++AG ++ K E    I+  L++P  + ++  G R       P+ VL  GPP
Sbjct: 32  TEAPKVTFKDVAGAEEAK-EELKEIVEFLKNPSRFHEM--GARI------PKGVLLVGPP 82
Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI 391
           G GKT  AR +A +A       VP +       +  + G     +  +F  A       I
Sbjct: 83  GVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGVGAARVRDLFETAKRHAP-CI 135
Query: 392 IFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
           +F+DE+D+    R S +   ++   + L+ LL ++DGFE+D  +VV+AATNR   LDPAL
Sbjct: 136 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPAL 195
Query: 449 I--SRFDSMITFGLPDHENRQEIAAQYAK 475
           +   RFD  I    PD + R++I   +A+
Sbjct: 196 LRPGRFDRQIAIDAPDVKGREQILRIHAR 224

>pdb|1IXZ|A Chain A, Crystal Structure Of The Ftsh Atpase Domain From Thermus Thermophilus Length = 254

Iteration: 1
 Score = 85.9 bits (211), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 110/209 (52%), Gaps = 21/209 (10%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           T   +++++++AG ++ K E++  I+  L++P  + ++  G R       P+ VL  GPP
Sbjct: 8   TEAPKVTFKDVAGAEEAKEELK-EIVEFLKNPSRFHEM--GARI------PKGVLLVGPP 58
Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI 391
           G GKT  AR +A +A       VP +       +  + G     +  +F  A       I
Sbjct: 59  GVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGVGAARVRDLFETAKRHAP-CI 111
Query: 392 IFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
           +F+DE+D+    R S +   ++   + L+ LL ++DGFE+D  +VV+AATNR   LDPAL
Sbjct: 112 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPAL 171
Query: 449 I--SRFDSMITFGLPDHENRQEIAAQYAK 475
           +   RFD  I    PD + R++I   +A+
Sbjct: 172 LRPGRFDRQIAIDAPDVKGREQILRIHAR 200

>pdb|2DHR|A Chain A, Whole Cytosolic Region Of Atp-Dependent Metalloprotease Ftsh (G399l) Length = 499

Iteration: 1
 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 110/209 (52%), Gaps = 21/209 (10%)
Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           T   +++++++AG ++ K E++  I+  L++P  + ++  G R       P+ VL  GPP
Sbjct: 23  TEAPKVTFKDVAGAEEAKEELK-EIVEFLKNPSRFHEM--GARI------PKGVLLVGPP 73
Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI 391
           G GKT  AR +A +A       VP +       +  + G     +  +F  A       I
Sbjct: 74  GVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGVGAARVRDLFETAKRHAP-CI 126
Query: 392 IFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
           +F+DE+D+    R S +   ++   + L+ LL ++DGFE+D  +VV+AATNR   LDPAL
Sbjct: 127 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPAL 186
Query: 449 I--SRFDSMITFGLPDHENRQEIAAQYAK 475
           +   RFD  I    PD + R++I   +A+
Sbjct: 187 LRPGRFDRQIAIDAPDVKGREQILRIHAR 215

>pdb|2CE7|A Chain A, Edta Treated Length = 476

Iteration: 1
 Score = 85.9 bits (211), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 59/199 (29%), Positives = 104/199 (52%), Gaps = 23/199 (11%)
Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           ++++++ G ++   E+++ +   L+ P  ++ I  G R       P+ +L  GPPGTGKT
Sbjct: 13  VTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRI--GARM------PKGILLVGPPGTGKT 63
Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN-ELPNGAIIFLD 395
             AR +A +A       VP  ++     +  + G     +  +F+ A    P   I+F+D
Sbjct: 64  LLARAVAGEAN------VPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAP--CIVFID 115
Query: 396 EVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--S 450
           E+D+    R + +   H+   + L+ LL ++DGF+  + ++V+AATNR   LDPAL+   
Sbjct: 116 EIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPG 175
Query: 451 RFDSMITFGLPDHENRQEI 469
           RFD  I    PD   R++I
Sbjct: 176 RFDKKIVVDPPDMLGRKKI 194

>pdb|3KDS|E Chain E, Apo-ftsh Crystal Structure Length = 465

Iteration: 1
 Score = 83.6 bits (205), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 58/199 (29%), Positives = 103/199 (51%), Gaps = 23/199 (11%)
Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           ++++++ G ++   E+++ +   L+ P  ++ I  G R       P+ +L  GPPGTG T
Sbjct: 13  VTFKDVGGAEEAIEELKEVVEF-LKDPSKFNRI--GARM------PKGILLVGPPGTGAT 63
Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN-ELPNGAIIFLD 395
             AR +A +A       VP  ++     +  + G     +  +F+ A    P   I+F+D
Sbjct: 64  LLARAVAGEAN------VPFFHISGSDFVELFVGVGAARVRDLFAQAKAHAP--CIVFID 115
Query: 396 EVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--S 450
           E+D+    R + +   H+   + L+ LL ++DGF+  + ++V+AATNR   LDPAL+   
Sbjct: 116 EIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAATNRPDILDPALLRPG 175
Query: 451 RFDSMITFGLPDHENRQEI 469
           RFD  I    PD   R++I
Sbjct: 176 RFDKKIVVDPPDMLGRKKI 194

>pdb|2QZ4|A Chain A, Human Paraplegin, Aaa Domain In Complex With Adp Length = 262

Iteration: 1
 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 109/243 (44%), Gaps = 35/243 (14%)
Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           +S++++AG  + K E+ + +   L+SPE +         +  +  P+  L  GPPG GKT
Sbjct: 3   VSFKDVAGMHEAKLEVREFVDY-LKSPERF--------LQLGAKVPKGALLLGPPGCGKT 53
Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLG--KVFSLANELPNGA--II 392
             A+ +A +A            VP   +    + E    LG  +V SL  E    A  I+
Sbjct: 54  LLAKAVATEA-----------QVPFLAMAGAEFVEVIGGLGAARVRSLFKEARARAPCIV 102
Query: 393 FLDEVDSFAVARDSEM----HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
           ++DE+D+    R + M    +    + L+ LL ++DG      V+V+A+TNR   LD AL
Sbjct: 103 YIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNRADILDGAL 162
Query: 449 I--SRFDSMITFGLPDHENRQEIAAQYAKHXXXXXXXXXXXXXXX-----MSGRDIRDVC 501
           +   R D  +   LP  + R+EI  Q+ K                      SG DI ++C
Sbjct: 163 MRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANIC 222
Query: 502 QQA 504
            +A
Sbjct: 223 NEA 225

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	567
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	4e-58
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	3e-56
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	4e-56
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	5e-56
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	4e-55
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	2e-54
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	9e-53
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	3e-52
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	5e-52
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	7e-52
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	8e-51
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-47
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	2e-49
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	9e-33
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	1e-31
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	2e-27
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	3e-27
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	5e-27
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	5e-27
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	4e-25
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	1e-21
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	5e-21
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	2e-15
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-13
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	7e-12
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	9e-10
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	7e-09
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	3e-08
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	6e-08
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	2e-07
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	3e-07
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	6e-06
3pvs_A	447	Replication-associated recombination protein A; ma	2e-05
2chg_A	226	Replication factor C small subunit; DNA-binding pr	4e-05
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	9e-05
2krk_A	86	26S protease regulatory subunit 8; structural geno	1e-04
2chq_A	319	Replication factor C small subunit; DNA-binding pr	2e-04

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score =  195 bits (497), Expect = 4e-58
 Identities = 74/240 (30%), Positives = 122/240 (50%), Gaps = 25/240 (10%)

Query: 273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPG 332
             +++ W +IAG D  K+ +++ ++L    PE++  +             + +L  GPPG
Sbjct: 14  GGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAP---------AKGLLLFGPPG 64

Query: 333 TGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGAI 391
            GKT  AR +A +  A        + +    + SKY G+ E+L+  +F++A  + P  +I
Sbjct: 65  NGKTLLARAVATECSAT------FLNISAASLTSKYVGDGEKLVRALFAVARHMQP--SI 116

Query: 392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK---VVVIAATNRKQDLDPAL 448
           IF+DEVDS    R S  HEA+RR+ +  L + DG   +     +VV+AATNR Q+LD A 
Sbjct: 117 IFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELDEAA 176

Query: 449 ISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA 504
           + RF   +   LPD + R+ +  +  +     L    L  LA  T+  SG D+  + + A
Sbjct: 177 LRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDA 236

>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} Length = 357

 Score =  192 bits (489), Expect = 3e-56
 Identities = 68/239 (28%), Positives = 124/239 (51%), Gaps = 24/239 (10%)

Query: 273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPG 332
               ++WE+IAG +  K  I++ ++  +  P+++  +            P+ +L  GPPG
Sbjct: 77  HGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGP---------PKGILLFGPPG 127

Query: 333 TGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGAI 391
           TGKT   + IA+Q+GA          +    + SK+ GE E+++  +F++A    P  A+
Sbjct: 128 TGKTLIGKCIASQSGAT------FFSISASSLTSKWVGEGEKMVRALFAVARCQQP--AV 179

Query: 392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF--EQDKKVVVIAATNRKQDLDPALI 449
           IF+DE+DS    R    HE++RRI +  L Q+DG     + +++V+ ATNR Q++D A  
Sbjct: 180 IFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDRILVVGATNRPQEIDEAAR 239

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA 504
            R    +   LP+   R++I           L++ E+ ++   ++  SG D+  +C++A
Sbjct: 240 RRLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREA 298

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score =  192 bits (490), Expect = 4e-56
 Identities = 76/239 (31%), Positives = 127/239 (53%), Gaps = 24/239 (10%)

Query: 273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPG 332
           + + + +++IAG D  K+ +++ ++L    PE++  +             R +L  GPPG
Sbjct: 108 NGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAP---------ARGLLLFGPPG 158

Query: 333 TGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGAI 391
            GKT  A+ +A ++ A          +    + SKY GE E+L+  +F++A EL P  +I
Sbjct: 159 NGKTMLAKAVAAESNAT------FFNISAASLTSKYVGEGEKLVRALFAVARELQP--SI 210

Query: 392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE--QDKKVVVIAATNRKQDLDPALI 449
           IF+D+VDS    R    H+A+RR+ +  L + DG +   D +V+V+ ATNR Q+LD A++
Sbjct: 211 IFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVL 270

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA 504
            RF   +   LP+ E R  +           LT+ ELA+LA  T+  SG D+  + + A
Sbjct: 271 RRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDA 329

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score =  189 bits (481), Expect = 5e-56
 Identities = 79/240 (32%), Positives = 126/240 (52%), Gaps = 25/240 (10%)

Query: 274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGT 333
           +  + +E+I G ++Q +EI + + L L+ PE+++ +  G         P+ +L  GPPGT
Sbjct: 11  RPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKV--GIE------PPKGILLYGPPGT 62

Query: 334 GKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE-LPNGAII 392
           GKT  A+ +A +  A        + V    ++ K+ GE   L+  +F LA E  P  +II
Sbjct: 63  GKTLLAKAVATETNA------TFIRVVGSELVKKFIGEGASLVKDIFKLAKEKAP--SII 114

Query: 393 FLDEVDSFAVARDSEMHEATR---RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
           F+DE+D+ A  R   +    R   R L  LL ++DGF+    V +I ATNR   LDPA++
Sbjct: 115 FIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDARGDVKIIGATNRPDILDPAIL 174

Query: 450 --SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
              RFD +I    PD + R EI   + + +  AE   L E+A  TE   G +++ +C +A
Sbjct: 175 RPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEA 234

>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 Length = 322

 Score =  187 bits (478), Expect = 4e-55
 Identities = 75/239 (31%), Positives = 120/239 (50%), Gaps = 23/239 (9%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           + K  + WE++AG +  K  +++ ++L ++ P ++         K        +L  GPP
Sbjct: 10  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLF---------KGNRKPTSGILLYGPP 60

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGA 390
           GTGK+  A+ +A +A +          V    ++SK+ GESE+L+ ++F++A E  P  +
Sbjct: 61  GTGKSYLAKAVATEANST------FFSVSSSDLVSKWMGESEKLVKQLFAMARENKP--S 112

Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF-EQDKKVVVIAATNRKQDLDPALI 449
           IIF+D+VD+    R     EA+RRI + LL Q++G     + V+V+ ATN    LD A+ 
Sbjct: 113 IIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIR 172

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA 504
            RF+  I   LPD   R  +           LTK +   L   TE  SG DI  V + A
Sbjct: 173 RRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDA 231

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score =  186 bits (473), Expect = 2e-54
 Identities = 73/241 (30%), Positives = 117/241 (48%), Gaps = 26/241 (10%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNR--PRAVLFEG 329
             +  + W ++AG +  K  +++ ++L ++ P +           F   R   R +L  G
Sbjct: 4   IERPNVKWSDVAGLEGAKEALKEAVILPIKFPHL-----------FTGKRTPWRGILLFG 52

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PN 388
           PPGTGK+  A+ +A +A            +    ++SK+ GESE+L+  +F LA E  P 
Sbjct: 53  PPGTGKSYLAKAVATEAN-----NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKP- 106

Query: 389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK-VVVIAATNRKQDLDPA 447
            +IIF+DE+DS   +R     EA RRI +  L Q+ G   D   ++V+ ATN    LD A
Sbjct: 107 -SIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSA 165

Query: 448 LISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQ 503
           +  RF+  I   LP+   R  +   +       LT+A+  EL   T+  SG DI  + + 
Sbjct: 166 IRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRD 225

Query: 504 A 504
           A
Sbjct: 226 A 226

>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* Length = 355

 Score =  182 bits (464), Expect = 9e-53
 Identities = 76/239 (31%), Positives = 122/239 (51%), Gaps = 23/239 (9%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           + K  + WE++AG +  K  +++ ++L ++ P ++    +G R          +L  GPP
Sbjct: 43  SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLF----KGNRKP-----TSGILLYGPP 93

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGA 390
           GTGK+  A+ +A +A +          V    ++SK+ GESE+L+ ++F++A E  P  +
Sbjct: 94  GTGKSYLAKAVATEANST------FFSVSSSDLVSKWMGESEKLVKQLFAMARENKP--S 145

Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF-EQDKKVVVIAATNRKQDLDPALI 449
           IIF+D+VD+    R     EA+RRI + LL Q++G     + V+V+ ATN    LD A+ 
Sbjct: 146 IIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQGVLVLGATNIPWQLDSAIR 205

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA 504
            RF+  I   LPD   R  +           LTK +   L   TE  SG DI  V + A
Sbjct: 206 RRFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDA 264

>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 Length = 444

 Score =  184 bits (467), Expect = 3e-52
 Identities = 71/239 (29%), Positives = 116/239 (48%), Gaps = 22/239 (9%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
             +  + W ++AG +  K  +++ ++L ++ P ++                R +L  GPP
Sbjct: 126 IERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTP---------WRGILLFGPP 176

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGA 390
           GTGK+  A+ +A +A            +    ++SK+ GESE+L+  +F LA E  P  +
Sbjct: 177 GTGKSYLAKAVATEAN-----NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENKP--S 229

Query: 391 IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD-KKVVVIAATNRKQDLDPALI 449
           IIF+DE+DS   +R     EA RRI +  L Q+ G   D   ++V+ ATN    LD A+ 
Sbjct: 230 IIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDGILVLGATNIPWVLDSAIR 289

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA 504
            RF+  I   LP+   R  +   +       LT+A+  EL   T+  SG DI  + + A
Sbjct: 290 RRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDA 348

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score =  184 bits (468), Expect = 5e-52
 Identities = 88/238 (36%), Positives = 129/238 (54%), Gaps = 22/238 (9%)

Query: 273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPG 332
           S +E+ +++I G  +Q  +I++ + L L+ P ++  I  G +       PR +L  GPPG
Sbjct: 197 SLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAI--GVKP------PRGILLYGPPG 248

Query: 333 TGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL-PNGAI 391
           TGKT  AR +AN+ GA          +    +MSK  GESE  L K F  A +  P  AI
Sbjct: 249 TGKTLIARAVANETGA------FFFLINGPEIMSKLAGESESNLRKAFEEAEKNAP--AI 300

Query: 392 IFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI-- 449
           IF+DE+D+ A  R+    E  RRI+S LL  +DG +Q   V+V+AATNR   +DPAL   
Sbjct: 301 IFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRF 360

Query: 450 SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
            RFD  +  G+PD   R EI   + K++  A+   L ++A  T    G D+  +C +A
Sbjct: 361 GRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEA 418

>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} Length = 301

 Score =  178 bits (454), Expect = 7e-52
 Identities = 76/240 (31%), Positives = 125/240 (52%), Gaps = 29/240 (12%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           +++WE+I G +  KRE+++ +   ++ P+ +         KF     + VLF GPPG GK
Sbjct: 11  QVTWEDIGGLEDVKRELQELVQYPVEHPDKFL--------KFGMTPSKGVLFYGPPGCGK 62

Query: 336 TSCARVIANQAGA--MPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA-NELPNGAII 392
           T  A+ IAN+  A  +  +G  L+        + ++GESE  + ++F  A    P   ++
Sbjct: 63  TLLAKAIANECQANFISIKGPELL--------TMWFGESEANVREIFDKARQAAP--CVL 112

Query: 393 FLDEVDSFAVARDSEMHE---ATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI 449
           F DE+DS A AR   + +   A  R+++ +L ++DG    K V +I ATNR   +DPA++
Sbjct: 113 FFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAIL 172

Query: 450 S--RFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
              R D +I   LPD ++R  I     +    A+   L  LA  T   SG D+ ++CQ+A
Sbjct: 173 RPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRA 232

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score =  171 bits (436), Expect = 2e-49
 Identities = 71/242 (29%), Positives = 117/242 (48%), Gaps = 31/242 (12%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
            ++W +I   +  + E+   IL  +++P+ +               P  VL  GPPG GK
Sbjct: 6   NVTWADIGALEDIREELTMAILAPVRNPDQFK--------ALGLVTPAGVLLAGPPGCGK 57

Query: 336 TSCARVIANQAGA--MPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA-NELPNGAII 392
           T  A+ +AN++G   +  +G  L        ++ Y GESER + +VF  A N  P   +I
Sbjct: 58  TLLAKAVANESGLNFISVKGPEL--------LNMYVGESERAVRQVFQRAKNSAP--CVI 107

Query: 393 FLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--S 450
           F DEVD+    R      A+ R+++ LL ++DG E  ++V ++AATNR   +DPA++   
Sbjct: 108 FFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQVFIMAATNRPDIIDPAILRPG 167

Query: 451 RFDSMITFGLPDHENRQEIAAQYAKHLTKAELA------ELA--TATEEMSGRDIRDVCQ 502
           R D  +  GLP   +R  I     K+ TK  L        +A     +  +G D+  + +
Sbjct: 168 RLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVR 227

Query: 503 QA 504
           +A
Sbjct: 228 EA 229

>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* Length = 272

 Score =  125 bits (316), Expect = 9e-33
 Identities = 38/233 (16%), Positives = 87/233 (37%), Gaps = 30/233 (12%)

Query: 263 YGLDEPQLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRP 322
           +G ++    +         I  +      + D   L +Q  +             +    
Sbjct: 20  FGTNQEDYAS----YIMNGIIKWGDPVTRVLDDGELLVQQTKN-----------SDRTPL 64

Query: 323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE-RLLGKVFS 381
            +VL EGPP +GKT+ A  IA ++        P + +     M  +   ++ + + K+F 
Sbjct: 65  VSVLLEGPPHSGKTALAAKIAEESNF------PFIKICSPDKMIGFSETAKCQAMKKIFD 118

Query: 382 LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-QDKKVVVIAATNR 440
            A +    + + +D+++             +  +L  LL  +     Q +K+++I  T+R
Sbjct: 119 DAYKSQL-SCVVVDDIERLLDYVPIG-PRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSR 176

Query: 441 KQDLDPALI-SRFDSMITFGLPDHENRQEIAA--QYAKHLTKAELAELATATE 490
           K  L    + + F + I   +P+    +++    +   +    E   +A   +
Sbjct: 177 KDVLQEMEMLNAFSTTI--HVPNIATGEQLLEALELLGNFKDKERTTIAQQVK 227

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score =  122 bits (309), Expect = 1e-31
 Identities = 37/259 (14%), Positives = 84/259 (32%), Gaps = 38/259 (14%)

Query: 281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR 340
            + G+      ++  ++   ++     +I            P  +   G  G GK+    
Sbjct: 5   KLDGFYIAPAFMDKLVVHITKNFLKLPNI----------KVPLILGIWGGKGQGKSFQCE 54

Query: 341 VIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGA---IIFLDEV 397
           ++  + G       P+M    E+  S   GE  +L+ + +  A E+        +F++++
Sbjct: 55  LVFRKMGIN-----PIMMSAGELE-SGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDL 108

Query: 398 DSFAVARDSEMHE-ATRRILSVLLRQI------------DGFEQDKKVVVIAATNRKQDL 444
           D+ A             ++++  L  I               +++ +V +I   N    L
Sbjct: 109 DAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTL 168

Query: 445 DPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQ 502
              LI   R +       P  E+R  +     +        ++    +   G+ I     
Sbjct: 169 YAPLIRDGRMEKFYWA--PTREDRIGVCTGIFRT-DNVPAEDVVKIVDNFPGQSIDFFGA 225

Query: 503 QAERSWASKIIRGQITKDG 521
              R      +R  ++  G
Sbjct: 226 LRARV-YDDEVRKWVSGTG 243

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score =  110 bits (277), Expect = 2e-27
 Identities = 77/256 (30%), Positives = 128/256 (50%), Gaps = 48/256 (18%)

Query: 269 QLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFE 328
           ++ T   +++++++AG ++ K E+++ +   L++P  + ++  G R       P+ VL  
Sbjct: 29  RVLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEM--GARI------PKGVLLV 79

Query: 329 GPPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESERLLGK 378
           GPPG GKT  AR +A +A       VP           M+V +        G +     +
Sbjct: 80  GPPGVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGV--------GAA-----R 120

Query: 379 VFSLANELPNGA--IIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVV 433
           V  L       A  I+F+DE+D+    R S +   ++   + L+ LL ++DGFE+D  +V
Sbjct: 121 VRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIV 180

Query: 434 VIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATA 488
           V+AATNR   LDPAL+   RFD  I    PD + R++I   +A+    AE   LA LA  
Sbjct: 181 VMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKR 240

Query: 489 TEEMSGRDIRDVCQQA 504
           T    G D+ ++  +A
Sbjct: 241 TPGFVGADLENLLNEA 256

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score =  109 bits (275), Expect = 3e-27
 Identities = 71/251 (28%), Positives = 113/251 (45%), Gaps = 51/251 (20%)

Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           +S++++AG  + K E+ +  +  L+SPE +  +  G +       P+  L  GPPG GKT
Sbjct: 3   VSFKDVAGMHEAKLEVRE-FVDYLKSPERFLQL--GAKV------PKGALLLGPPGCGKT 53

Query: 337 SCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESE-RLLGKVFSLANE 385
             A+ +A +A       VP           +   L        G +  R L   F  A  
Sbjct: 54  LLAKAVATEAQ------VPFLAMAGAEFVEVIGGL--------GAARVRSL---FKEARA 96

Query: 386 -LPNGAIIFLDEVDSFAVARDSEM----HEATRRILSVLLRQIDGFEQDKKVVVIAATNR 440
             P   I+++DE+D+    R + M    +    + L+ LL ++DG      V+V+A+TNR
Sbjct: 97  RAP--CIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLASTNR 154

Query: 441 KQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE-----LAELATATEEMS 493
              LD AL+   R D  +   LP  + R+EI  Q+ K L   +        LA  T   S
Sbjct: 155 ADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFS 214

Query: 494 GRDIRDVCQQA 504
           G DI ++C +A
Sbjct: 215 GADIANICNEA 225

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score =  108 bits (273), Expect = 5e-27
 Identities = 78/255 (30%), Positives = 128/255 (50%), Gaps = 48/255 (18%)

Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
           + T   +++++++AG ++ K E+++ I+  L++P  + ++  G R       P+ VL  G
Sbjct: 6   VLTEAPKVTFKDVAGAEEAKEELKE-IVEFLKNPSRFHEM--GARI------PKGVLLVG 56

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESERLLGKV 379
           PPG GKT  AR +A +A       VP           M+V +        G +     +V
Sbjct: 57  PPGVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGV--------GAA-----RV 97

Query: 380 FSLANELPNGA--IIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVV 434
             L       A  I+F+DE+D+    R S +   ++   + L+ LL ++DGFE+D  +VV
Sbjct: 98  RDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVV 157

Query: 435 IAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATAT 489
           +AATNR   LDPAL+   RFD  I    PD + R++I   +A+    AE   LA LA  T
Sbjct: 158 MAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRT 217

Query: 490 EEMSGRDIRDVCQQA 504
               G D+ ++  +A
Sbjct: 218 PGFVGADLENLLNEA 232

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score =  108 bits (273), Expect = 5e-27
 Identities = 75/255 (29%), Positives = 124/255 (48%), Gaps = 48/255 (18%)

Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
           L   + + ++ ++AG D+ K E+ + +   L+ P  +  +  G +       P+ VL  G
Sbjct: 2   LTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKL--GGKI------PKGVLMVG 52

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESERLLGKV 379
           PPGTGKT  A+ IA +A       VP           M+V +        G S     +V
Sbjct: 53  PPGTGKTLLAKAIAGEAK------VPFFTISGSDFVEMFVGV--------GAS-----RV 93

Query: 380 FSLANELPNGA--IIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVV 434
             +  +    A  IIF+DE+D+    R + +   H+   + L+ +L ++DGFE ++ ++V
Sbjct: 94  RDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIV 153

Query: 435 IAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATAT 489
           IAATNR   LDPAL+   RFD  +  GLPD   R++I   + + +  A     A +A  T
Sbjct: 154 IAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGT 213

Query: 490 EEMSGRDIRDVCQQA 504
              SG D+ ++  +A
Sbjct: 214 PGFSGADLANLVNEA 228

>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* Length = 268

 Score =  104 bits (261), Expect = 4e-25
 Identities = 80/257 (31%), Positives = 128/257 (49%), Gaps = 50/257 (19%)

Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
           +N  K  + ++++AG ++ K E+ + I+  L+ PE Y ++  G +       P+ VL  G
Sbjct: 1   INAEKPNVRFKDMAGNEEAKEEVVE-IVDFLKYPERYANL--GAKI------PKGVLLVG 51

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESE-RLLGK 378
           PPGTGKT  A+ +A +A       VP           M+V L        G S  R L  
Sbjct: 52  PPGTGKTLLAKAVAGEAH------VPFFSMGGSSFIEMFVGL--------GASRVRDL-- 95

Query: 379 VFSLANE-LPNGAIIFLDEVDSFAVARDSEM----HEATRRILSVLLRQIDGFEQDKK-V 432
            F  A +  P  +IIF+DE+D+   +R +      ++   + L+ LL ++DGF  +   V
Sbjct: 96  -FETAKKQAP--SIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPV 152

Query: 433 VVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELAT 487
           +V+AATNR + LDPAL+   RFD  +    PD   R EI   + K +  A    L E+A 
Sbjct: 153 IVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAK 212

Query: 488 ATEEMSGRDIRDVCQQA 504
            T  ++G D+ ++  +A
Sbjct: 213 LTAGLAGADLANIINEA 229

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 97.3 bits (243), Expect = 1e-21
 Identities = 82/264 (31%), Positives = 126/264 (47%), Gaps = 66/264 (25%)

Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
           + T   +++++++AG ++ K E+++ +   L++P  + ++  G R       P+ VL  G
Sbjct: 21  VLTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEM--GARI------PKGVLLVG 71

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESE-RLLGK 378
           PPG GKT  AR +A +A       VP           M+V +        G +  R L  
Sbjct: 72  PPGVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGV--------GAARVRDL-- 115

Query: 379 VFSLANE-LPNGAIIFLDEVDSFAVARDSEMH------------EATRRILSVLLRQIDG 425
            F  A    P   I+F+DE+D  AV R                 E T   L+ LL ++DG
Sbjct: 116 -FETAKRHAP--CIVFIDEID--AVGR----KRGSGVGGGNDEREQT---LNQLLVEMDG 163

Query: 426 FEQDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE-- 481
           FE+D  +VV+AATNR   LDPAL+   RFD  I    PD + R++I   +A+    AE  
Sbjct: 164 FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDV 223

Query: 482 -LAELATATEEMSGRDIRDVCQQA 504
            LA LA  T    G D+ ++  +A
Sbjct: 224 DLALLAKRTPGFVGADLENLLNEA 247

>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* Length = 476

 Score = 95.3 bits (238), Expect = 5e-21
 Identities = 74/261 (28%), Positives = 121/261 (46%), Gaps = 66/261 (25%)

Query: 273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPG 332
               ++++++ G ++   E+++ ++  L+ P  ++ I  G R       P+ +L  GPPG
Sbjct: 9   GNKRVTFKDVGGAEEAIEELKE-VVEFLKDPSKFNRI--GARM------PKGILLVGPPG 59

Query: 333 TGKTSCARVIANQAGAMPWQGVPL----------MYVPLEVVMSKYYGESE-RLLGKVFS 381
           TGKT  AR +A +A       VP           ++V +        G +  R L   F+
Sbjct: 60  TGKTLLARAVAGEAN------VPFFHISGSDFVELFVGV--------GAARVRDL---FA 102

Query: 382 LANE-LPNGAIIFLDEVDSFAVARDSEMH------------EATRRILSVLLRQIDGFEQ 428
            A    P   I+F+DE+D  AV R    H            E T   L+ LL ++DGF+ 
Sbjct: 103 QAKAHAP--CIVFIDEID--AVGR----HRGAGLGGGHDEREQT---LNQLLVEMDGFDS 151

Query: 429 DKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LA 483
            + ++V+AATNR   LDPAL+   RFD  I    PD   R++I   + ++   AE   L 
Sbjct: 152 KEGIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLE 211

Query: 484 ELATATEEMSGRDIRDVCQQA 504
            +A  T    G D+ ++  +A
Sbjct: 212 IIAKRTPGFVGADLENLVNEA 232

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A* Length = 309

 Score = 76.3 bits (187), Expect = 2e-15
 Identities = 48/251 (19%), Positives = 88/251 (35%), Gaps = 27/251 (10%)

Query: 279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC 338
              + G    K  I +T  L      +  + AR             + F G PGTGKT+ 
Sbjct: 30  DRELIGLKPVKDRIRETAAL------LLVERARQKLGLAHETPTLHMSFTGNPGTGKTTV 83

Query: 339 ARVIANQAGAMPW-QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEV 397
           A  +A     + + +   L+ V  + ++ +Y G +     +V   A     G ++F+DE 
Sbjct: 84  ALKMAGLLHRLGYVRKGHLVSVTRDDLVGQYIGHTAPKTKEVLKRA----MGGVLFIDEA 139

Query: 398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDL---DPALISRFDS 454
                  +   +   +  + +LL+ ++    D  V++    +R ++    +P   SR   
Sbjct: 140 YYLYRPDNERDYG--QEAIEILLQVMENNRDDLVVILAGYADRMENFFQSNPGFRSRIAH 197

Query: 455 MITFGLPDHENRQEIAAQYAK----HLTKAELAELATATEEMS-------GRDIRDVCQQ 503
            I F     E   EIA          +T      L                R IR+   +
Sbjct: 198 HIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALDR 257

Query: 504 AERSWASKIIR 514
           A    A+++  
Sbjct: 258 ARLRQANRLFT 268

>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 = 73.0 bits (178), Expect = 1e-13
 Identities = 68/466 (14%), Positives = 137/466 (29%), Gaps = 123/466 (26%)

Query: 208 QSGDMNAREGDLCILIFRSLITSDK--PEIEFIKKGSLTSEELDALVS------------ 253
           ++G+   +  D+ + +F      +    +++ + K  L+ EE+D ++             
Sbjct: 10  ETGEHQYQYKDI-LSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLF 68

Query: 254 -VLQLAGRRIY-----GLDEPQLNTSKSEISWENIA------GYDQQK-REIEDTILLS- 299
             L      +       +         S I  E          Y +Q+ R   D  + + 
Sbjct: 69  WTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAK 128

Query: 300 --LQSPEVYDDIARGTRCKFESNRP-RAVLFEGPPGTGKTSCA-------RVIANQAGAM 349
             +   + Y  +    R      RP + VL +G  G+GKT  A       +V       +
Sbjct: 129 YNVSRLQPYLKL----RQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKI 184

Query: 350 PW---------QGVPLMYVPLEVVMSKYYGE----SERLLGKVFSLANEL---------P 387
            W         + V  M   L   +   +      S  +  ++ S+  EL          
Sbjct: 185 FWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYE 244

Query: 388 NGAIIFLDEV------DSFAVA-------RDSE----MHEATRRILSVLLRQIDGFEQDK 430
           N  ++ L  V      ++F ++       R  +    +  AT   +S+          D+
Sbjct: 245 NCLLV-LLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHS-MTLTPDE 302

Query: 431 KVVVIA--ATNRKQDL-------DPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAE 481
              ++      R QDL       +P  +    S+I   + D            KH+   +
Sbjct: 303 VKSLLLKYLDCRPQDLPREVLTTNPRRL----SIIAESIRDGLAT----WDNWKHVNCDK 354

Query: 482 LAE-LATATEEMSGRDIR-----------DV---CQQAERSWASKIIR--GQITKDGEQA 524
           L   + ++   +   + R                       W   I      +     + 
Sbjct: 355 LTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKY 414

Query: 525 CL-----PPLQEYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLD 565
            L           I S     +  L+     H++I +H    +  D
Sbjct: 415 SLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFD 460

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 67.6 bits (164), Expect = 7e-12
 Identities = 91/592 (15%), Positives = 159/592 (26%), Gaps = 206/592 (34%)

Query: 84  DQGAGTAKPSLPSESSSSYENL-EEIAKKERQRIEELLKRKGMHYGSC--PTFTVAVKGQ 140
            +     +  +      +Y+ L   I  ++RQ    ++ R    Y       +      Q
Sbjct: 73  SKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQP--SMMTRM---YIEQRDRLYND---NQ 124

Query: 141 KVTIKFQVPPACEIPQLIANLVSHL-GLKVEE----HG-GGS-----------DMGL-RA 182
               K+ V       Q    L   L  L+  +     G  GS              +   
Sbjct: 125 VFA-KYNVS----RLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCK 179

Query: 183 WDSAVAWQLTL---KPPEK-----QN---------ESGGDRAQSGDMNAREGDL------ 219
            D  + W L L     PE      Q           S  D + +  +             
Sbjct: 180 MDFKIFW-LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLL 238

Query: 220 -------CILI------------F----RSLITS-DKPEIEFIK------------KGSL 243
                  C+L+            F    + L+T+  K   +F+               +L
Sbjct: 239 KSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTL 298

Query: 244 TSEELDALVSVLQLAGRRIYGLDEPQLNTSKSEIS------------WENIA--GYDQQK 289
           T +E+ +L+   +    R   L    L T+   +S            W+N      D+  
Sbjct: 299 TPDEVKSLLL--KYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLT 356

Query: 290 REIEDTILLSLQSPEV---YDDIARGTRCKFESNR--PRAVLFEGPPGTGKTSCARVIAN 344
             IE + L  L+  E    +D ++      F  +   P  +L                  
Sbjct: 357 TIIESS-LNVLEPAEYRKMFDRLS-----VFPPSAHIPTILL------------------ 392

Query: 345 QAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD---SFA 401
              ++ W  V      + VV++K       L     SL  + P  + I +  +       
Sbjct: 393 ---SLIWFDVI--KSDVMVVVNK-------LHKY--SLVEKQPKESTISIPSIYLELKVK 438

Query: 402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLP 461
           +  +  +H   R I+          +            +  D D  +    D        
Sbjct: 439 LENEYALH---RSIV----------DHYNI-------PKTFDSDDLIPPYLDQYFYS--- 475

Query: 462 DHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSW-ASKIIRGQITKD 520
            H     I   +  HL   E  E  T    +   D R         +   KI       +
Sbjct: 476 -H-----IG--H--HLKNIEHPERMTLFRMVF-LDFR---------FLEQKIRHDSTAWN 515

Query: 521 GEQACLPPLQ------EYIESATNRRRSLLDAAEQSHQNINNHRTKKQPLDL 566
              + L  LQ       YI     +   L++A       I  +    +  DL
Sbjct: 516 ASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLICSKYTDL 567

>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 Length = 516

 Score = 60.3 bits (146), Expect = 9e-10
 Identities = 41/227 (18%), Positives = 69/227 (30%), Gaps = 45/227 (19%)

Query: 291 EIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP 350
                +   L + E     +     K  S   RA +  GPPG GKT+ A ++A + G   
Sbjct: 46  GSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELG--- 102

Query: 351 WQGVPLMYVPLE----------VVMS--KYYGESERLLGKVFSLANELPNGA---IIFLD 395
                  Y  LE          ++ +  K   ++  ++G                +I +D
Sbjct: 103 -------YDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMD 155

Query: 396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSM 455
           EVD         M    R  +    +      +    +++    R               
Sbjct: 156 EVDG--------MSGGDRGGVG---QLAQFCRKTSTPLILICNERNLPKMRPFDRVC-LD 203

Query: 456 ITFGLPDHE---NR-QEIAAQYAKHLTKAELAELATATEEMSGRDIR 498
           I F  PD     +R   IA +    L    +  L     + +  DIR
Sbjct: 204 IQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLI----QTTRGDIR 246

>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} Length = 386

 Score = 57.0 bits (137), Expect = 7e-09
 Identities = 50/274 (18%), Positives = 95/274 (34%), Gaps = 41/274 (14%)

Query: 306 YDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---------------- 349
              IA      +   +P  +   G  GTGKT+  + + ++                    
Sbjct: 29  IRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQID 88

Query: 350 -PWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEM 408
            P++ +  +   L+V +         L  ++     +  +  +I LDE+D+F    + + 
Sbjct: 89  TPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYNDD- 147

Query: 409 HEATRRILSVLLRQIDGFEQDKKVVVIAATNR---KQDLDPALISRFD-SMITFGLPDHE 464
                 IL  L R I+      K+  I  TN       LDP + S      I F   + E
Sbjct: 148 ------ILYKLSR-INSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAE 200

Query: 465 NRQEIAAQYAKH------LTKAELAELA--TATEEMSGRDIRDVCQQA----ERSWASKI 512
             ++I  + A+       L    +   A   A E    R   D+ + +    ER   +K+
Sbjct: 201 ELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDLLRVSGEIAERMKDTKV 260

Query: 513 IRGQITKDGEQACLPPLQEYIESATNRRRSLLDA 546
               +    E+     +++ I +     + +L A
Sbjct: 261 KEEYVYMAKEEIERDRVRDIILTLPFHSKLVLMA 294

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix} Length = 387

 Score = 54.8 bits (131), Expect = 3e-08
 Identities = 44/293 (15%), Positives = 86/293 (29%), Gaps = 42/293 (14%)

Query: 304 EVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-------------- 349
                +A          +P   L  G  GTGKT+ AR++  +  A               
Sbjct: 26  AELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVN 85

Query: 350 ------PWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVA 403
                 P++    +   + V +         +  ++    + L    II LDE+D     
Sbjct: 86  ARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLP-- 143

Query: 404 RDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR---KQDLDPALISRF-DSMITFG 459
                    + +L  + R          V ++  TN     ++L+P + S   +  + F 
Sbjct: 144 ----KRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFP 199

Query: 460 LPDHENRQEIAAQYAKHLTK--------AELAELATATEEMSGRDIRDVCQQA----ERS 507
                  ++I    A+              L     A E    R   D+ + A    ER 
Sbjct: 200 PYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDLLRVAGEIAERR 259

Query: 508 WASKIIRGQITKDGEQACLPPLQEYIESATNRRRSLLDAAEQSHQNINNHRTK 560
              ++ R  +     +     + E + +     + +L +            T 
Sbjct: 260 REERVRREHVYSARAEIERDRVSEVVRTLPLHAKLVLLSIMMLEDGGRPASTG 312

>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* Length = 412

 Score = 54.1 bits (129), Expect = 6e-08
 Identities = 36/319 (11%), Positives = 80/319 (25%), Gaps = 62/319 (19%)

Query: 280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA 339
             +     +   +    L         + +  G      S+        G  G GKT+ A
Sbjct: 22  PELRVRRGEAEALARIYL---------NRLLSGAGL---SDVNMIYGSIGRVGIGKTTLA 69

Query: 340 RVIANQAGAMPWQG---VPLMYVPLEVVMSKY--YGESERLLG---------------KV 379
           +    +      +    V   YV      + Y       R  G                +
Sbjct: 70  KFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKAL 129

Query: 380 FSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLR---QIDGFEQDKKVVVIA 436
                   +  ++ LDE  S                L  LLR   +I   +   ++  + 
Sbjct: 130 VDNLYVENHYLLVILDEFQSML-----SSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLL 184

Query: 437 ATN------RKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAE--------- 481
             +        ++  P + S+    +            I  Q A+   +           
Sbjct: 185 VASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLEL 244

Query: 482 LAELATATEEMSG--RDIRDVCQQ----AERSWASKIIRGQITKDGEQACLPPL-QEYIE 534
           ++++    +   G  R      +     AE      +    + K   +     +    +E
Sbjct: 245 ISDVYGEDKGGDGSARRAIVALKMACEMAEAMGRDSLSEDLVRKAVSENEAASIQTHELE 304

Query: 535 SATNRRRSLLDAAEQSHQN 553
           + +     +L    ++   
Sbjct: 305 ALSIHELIILRLIAEATLG 323

>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 Length = 389

 Score = 52.1 bits (124), Expect = 2e-07
 Identities = 37/270 (13%), Positives = 76/270 (28%), Gaps = 50/270 (18%)

Query: 316 KFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---------------PWQGVPLMYVP 360
           +   +        G PGTGKT   R +                          +  +   
Sbjct: 38  RNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARS 97

Query: 361 LEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL 420
           L +   +     +  L  +     E      + LD+  + A             ILS  +
Sbjct: 98  LNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLA-----------PDILSTFI 146

Query: 421 RQIDGFEQDK--KVVVIAATNR---KQDLDPALISRF-DSMITFGLPDHENRQEIAAQYA 474
           R     ++    ++ ++   +      +LDP+        +I F     +   +I    A
Sbjct: 147 RLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRA 206

Query: 475 KHLTK------------AELAELATATEEMSG--RDIRDVCQQ----AERSWASKIIRGQ 516
           K                A++    T  +   G  R   D+  +    A+++    I    
Sbjct: 207 KAGLAEGSYSEDILQMIADITGAQTPLDTNRGDARLAIDILYRSAYAAQQNGRKHIAPED 266

Query: 517 ITKDGEQACLPPLQEYIESATNRRRSLLDA 546
           + K  ++      +E +       +  L A
Sbjct: 267 VRKSSKEVLFGISEEVLIGLPLHEKLFLLA 296

>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} Length = 384

 Score = 51.7 bits (123), Expect = 3e-07
 Identities = 57/291 (19%), Positives = 105/291 (36%), Gaps = 47/291 (16%)

Query: 304 EVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ-----GVPLMY 358
           ++  D A   R   ++    + LF G  GTGKT  ++ I N+   +  +      V   Y
Sbjct: 27  DILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAY 86

Query: 359 VPLEVVMSKYYGESERLLGKVFS-----------------LANELPNGAIIFLDEVDSFA 401
           V    V          L GK+                           AII+LDEVD+  
Sbjct: 87  VNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTL- 145

Query: 402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR---KQDLDPALISRFDSMITF 458
                      RR   ++L Q+     D  + VI  +N    +  ++P ++S     + F
Sbjct: 146 ---------VKRRGGDIVLYQL--LRSDANISVIMISNDINVRDYMEPRVLSSLGPSVIF 194

Query: 459 GLPDHENRQEIAAQYAKH------LTKAELAELATATEEMSG--RDIRDVCQQA-ERSWA 509
              D E  + I ++YA++           L+ +A  + +  G  R   ++  +A + +  
Sbjct: 195 KPYDAEQLKFILSKYAEYGLIKGTYDDEILSYIAAISAKEHGDARKAVNLLFRAAQLASG 254

Query: 510 SKIIRGQITKDGEQACLP-PLQEYIESATNRRRSLLDAAEQSHQNINNHRT 559
             IIR +             L E +++     +  L +  +S   ++ H+ 
Sbjct: 255 GGIIRKEHVDKAIVDYEQERLIEAVKALPFHYKLALRSLIESEDVMSAHKM 305

>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* Length = 456

 Score = 48.1 bits (114), Expect = 6e-06
 Identities = 29/160 (18%), Positives = 52/160 (32%), Gaps = 28/160 (17%)

Query: 322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVF- 380
            RAVL  GPPGTGKT+ A  IA + G+     VP   +    V S    ++E L+     
Sbjct: 63  GRAVLLAGPPGTGKTALALAIAQELGS----KVPFCPMVGSEVYSTEIKKTEVLMENFRR 118

Query: 381 SLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQI----------------- 423
           ++   +     ++  EV                + +S ++  +                 
Sbjct: 119 AIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFE 178

Query: 424 ----DGFEQDKKVVVIAATNRKQDLDPALI--SRFDSMIT 457
               +  E    + + A +   +         + FD    
Sbjct: 179 SLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAE 218

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli} Length = 447

 Score = 46.4 bits (111), Expect = 2e-05
 Identities = 15/32 (46%), Positives = 20/32 (62%)

Query: 317 FESNRPRAVLFEGPPGTGKTSCARVIANQAGA 348
            E+    +++  GPPGTGKT+ A VIA  A A
Sbjct: 45  IEAGHLHSMILWGPPGTGKTTLAEVIARYANA 76

>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} Length = 226

 Score = 44.1 bits (105), Expect = 4e-05
 Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 18/82 (21%)

Query: 326 LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLG------KV 379
           LF GPPGTGKT+ A  +A       W+     +  +E+         ER +       K 
Sbjct: 42  LFSGPPGTGKTATAIALARDLFGENWRD---NF--IEM-----NASDERGIDVVRHKIKE 91

Query: 380 FSLANELPNGA--IIFLDEVDS 399
           F+    +      IIFLDE D+
Sbjct: 92  FARTAPIGGAPFKIIFLDEADA 113

>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 Length = 327

 Score = 43.5 bits (103), Expect = 9e-05
 Identities = 51/228 (22%), Positives = 84/228 (36%), Gaps = 44/228 (19%)

Query: 326 LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLG------KV 379
           LF GPPG GKT+ A  +A +     W+     +  LE+         ER +       K 
Sbjct: 50  LFAGPPGVGKTTAALALARELFGENWRH---NF--LEL-----NASDERGINVIREKVKE 99

Query: 380 FSLANELPNGA--IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAA 437
           F+    +   +  IIFLDE D+       +  +A RR        ++ F     V  I +
Sbjct: 100 FARTKPIGGASFKIIFLDEADAL----TQDAQQALRRT-------MEMFS--SNVRFILS 146

Query: 438 TNRKQDLDPALISRFDSMITFGLPDHE---NR-QEIAAQYAKHLTKAELAELATATEEMS 493
            N    +   + SR  ++  F     E    R + IA      LT+  L  +      ++
Sbjct: 147 CNYSSKIIEPIQSRC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAIL----YIA 201

Query: 494 GRDIR---DVCQQAERSWASKIIRGQITKDGEQACLPPLQEYIESATN 538
             D+R   ++ Q A      KI    +     +A    ++E +  A  
Sbjct: 202 EGDMRRAINILQAAAAL-DKKITDENVFMVASRARPEDIREMMLLALK 248

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens} Length = 86

 Score = 40.2 bits (95), Expect = 1e-04
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 3/52 (5%)

Query: 456 ITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQA 504
                P+ E R +I   +++ +       L ++A      SG +++ VC +A
Sbjct: 6   HHHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEA 57

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A Length = 319

 Score = 42.7 bits (101), Expect = 2e-04
 Identities = 25/82 (30%), Positives = 35/82 (42%), Gaps = 18/82 (21%)

Query: 326 LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLG------KV 379
           LF GPPGTGKT+ A  +A       W+     +  +E+         ER +       K 
Sbjct: 42  LFSGPPGTGKTATAIALARDLFGENWRD---NF--IEM-----NASDERGIDVVRHKIKE 91

Query: 380 FSLANELPNGA--IIFLDEVDS 399
           F+    +      IIFLDE D+
Sbjct: 92  FARTAPIGGAPFKIIFLDEADA 113

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	567
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	100.0
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	100.0
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	100.0
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	100.0
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.98
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.97
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.97
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.97
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.96
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.96
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.96
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.96
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.96
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.96
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.94
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.94
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.93
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.93
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.92
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.87
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.87
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.87
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.82
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.81
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.8
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.8
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.79
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.79
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.78
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.78
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.76
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.75
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.75
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.75
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.74
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.74
3pvs_A	447	Replication-associated recombination protein A; ma	99.73
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.73
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.73
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.72
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.71
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.71
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.71
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.7
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.7
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.69
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.69
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.68
3co5_A	143	Putative two-component system transcriptional RES	99.68
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	99.67
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.66
3bos_A	242	Putative DNA replication factor; P-loop containing	99.66
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.65
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.65
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.64
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.64
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.63
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.63
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.63
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.62
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.62
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	99.62
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.61
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.61
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.61
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.61
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.6
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	99.59
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.57
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.56
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.55
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.51
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.5
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.49
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.46
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.38
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.34
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.31
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.3
1wlf_A	179	PEX1, peroxisome biogenesis factor 1; N-terminal d	99.29
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.08
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.99
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.95
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.89
2fna_A	357	Conserved hypothetical protein; structural genomic	98.88
3f8t_A	506	Predicted ATPase involved in replication control,	98.88
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.86
2qgz_A	308	Helicase loader, putative primosome component; str	98.79
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.75
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.6
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.48
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.41
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.41
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.34
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.31
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.26
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.1
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	97.95
3kw6_A	78	26S protease regulatory subunit 8; structural geno	97.74
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.69
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.68
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	97.67
2krk_A	86	26S protease regulatory subunit 8; structural geno	97.64
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.56
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.5
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.5
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.49
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.46
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.43
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.43
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.42
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.39
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.39
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.35
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.3
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	97.23
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.23
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.21
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.18
4a74_A	231	DNA repair and recombination protein RADA; hydrola	97.14
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.12
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.11
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.1
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	97.06
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.04
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	96.99
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.97
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.93
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	96.92
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.91
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.9
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.89
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	96.85
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.82
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	96.81
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.79
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.79
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	96.78
3io5_A	333	Recombination and repair protein; storage dimer, i	96.76
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.73
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	96.7
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.69
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.66
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.65
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.64
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	96.62
1via_A	175	Shikimate kinase; structural genomics, transferase	96.61
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.6
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.57
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.52
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.5
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	96.49
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.49
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.48
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.44
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	96.4
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	96.39
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.38
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.36
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.34
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	96.34
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.34
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.33
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.32
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.31
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	96.3
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.29
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	96.28
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.28
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.27
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.27
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.27
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	96.26
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.25
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.24
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.24
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	96.23
2vli_A	183	Antibiotic resistance protein; transferase, tunica	96.23
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.19
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.18
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	96.16
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	96.16
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	96.15
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.14
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.13
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	96.12
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	96.12
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	96.11
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	96.11
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.1
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.08
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	96.08
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	96.08
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	96.05
3bor_A	237	Human initiation factor 4A-II; translation initiat	96.03
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	96.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	96.0
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.96
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	95.95
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.94
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	95.93
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	95.93
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	95.92
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.91
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	95.89
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	95.85
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	95.84
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.83
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.76
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	95.74
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.67
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.67
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	95.64
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	95.62
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	95.62
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	95.6
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	95.59
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	95.55
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.53
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	95.52
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	95.49
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.46
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.45
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	95.45
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	95.44
3b6e_A	216	Interferon-induced helicase C domain-containing P;	95.44
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.44
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.43
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.41
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.36
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.33
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	95.32
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	95.28
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	95.27
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	95.26
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	95.25
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	95.23
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	95.21
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	95.19
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	95.19
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.18
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.17
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	95.15
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	95.14
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	95.13
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	95.11
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	95.09
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	95.05
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.05
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	95.04
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.01
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	94.99
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.99
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.98
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.98
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	94.93
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	94.93
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	94.91
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	94.91
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.9
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	94.89
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	94.83
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	94.8
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	94.79
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.77
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.76
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	94.75
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	94.64
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.64
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	94.63
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	94.59
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	94.59
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	94.58
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.54
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.43
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	94.43
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	94.42
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.42
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	94.41
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	94.4
2eyu_A	261	Twitching motility protein PILT; pilus retraction	94.4
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	94.39
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	94.34
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	94.32
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.32
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.24
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.21
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	94.2
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	94.11
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.07
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.0
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.98
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	93.89
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	93.89
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	93.87
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	93.84
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.84
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	93.84
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.76
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	93.74
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.7
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	93.65
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	93.58
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	93.55
2ewv_A	372	Twitching motility protein PILT; pilus retraction	93.53
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	93.49
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	93.41
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	93.39
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	93.39
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	93.28
2ged_A	193	SR-beta, signal recognition particle receptor beta	93.24
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.21
3h1t_A	590	Type I site-specific restriction-modification syst	93.19
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	93.18
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	93.06
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	93.05
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	93.01
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	93.0
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	92.94
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	92.88
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	92.88
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	92.84
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.84
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	92.78
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	92.72
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	92.7
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	92.68
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	92.65
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	92.62
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	92.61
2og2_A	359	Putative signal recognition particle receptor; nuc	92.61
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	92.51
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	92.47
3kta_A	182	Chromosome segregation protein SMC; structural mai	92.39
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	92.37
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	92.33
1b0u_A	262	Histidine permease; ABC transporter, transport pro	92.31
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.23
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	92.21
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	92.2
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	92.15
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	92.15
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	92.13
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	92.07
3ch4_B	202	Pmkase, phosphomevalonate kinase; parallel beta-sh	92.05
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	91.99
1g6h_A	257	High-affinity branched-chain amino acid transport	91.99
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	91.94
1sgw_A	214	Putative ABC transporter; structural genomics, P p	91.94
2ghi_A	260	Transport protein; multidrug resistance protein, M	91.94
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	91.92
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	91.91
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	91.91
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	91.9
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	91.85
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	91.85
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	91.83
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	91.81
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	91.77
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	91.76
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	91.73
1ji0_A	240	ABC transporter; ATP binding protein, structural g	91.72
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	91.69
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	91.65
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	91.65
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.61
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.61
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.61
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	91.53
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	91.53
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	91.51
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	91.43
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	91.43
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	91.4
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.36
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	91.33
1nrj_B	218	SR-beta, signal recognition particle receptor beta	91.31
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	91.31
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	91.3
2hf9_A	226	Probable hydrogenase nickel incorporation protein	91.26
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	91.25
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	91.16
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	91.14
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	91.09
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	91.09
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	91.05
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	91.03
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	91.02
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	90.97
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	90.96
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	90.95
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	90.9
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	90.85
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	90.84
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	90.8
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	90.8
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	90.76
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	90.68
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	90.64
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	90.61
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	90.5
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	90.45
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	90.41
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	90.38
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	90.35
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	90.34
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	90.2
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	90.19
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	90.17
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	90.16
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	90.15
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	90.11
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	90.05
2wji_A	165	Ferrous iron transport protein B homolog; membrane	90.0
1yks_A	440	Genome polyprotein [contains: flavivirin protease	89.98
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	89.96
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	89.93
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	89.88
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	89.84
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	89.79
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	89.78
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	89.77
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	89.76
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	89.75
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	89.68
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	89.66
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	89.62
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	89.52
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	89.48
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	89.43
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	89.42
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	89.37
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	89.35
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	89.32
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	89.27
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	89.27
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	89.26
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	89.25
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	89.22
3ice_A	422	Transcription termination factor RHO; transcriptio	89.21
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	89.16
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	89.14
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	89.1
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	89.07
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	89.06
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	89.04
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	88.98
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	88.98
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	88.98
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	88.95
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	88.85
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	88.84
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	88.8
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	88.78
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	88.76
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	88.76
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	88.74
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	88.74
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	88.73
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	88.68
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	88.67
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	88.64
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	88.63
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	88.62
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	88.62
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	88.59
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	88.59
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	88.57
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	88.56
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	88.54
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	88.49
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	88.4
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	88.39
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	88.38
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	88.35
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	88.32
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	88.23
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	88.2
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	88.12
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	88.09
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	88.08
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	88.02
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	87.97
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	87.93
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	87.87
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	87.81
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	87.8
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	87.77
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	87.73
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	87.71

>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=100.00  E-value=2.2e-49  Score=452.29  Aligned_cols=368  Identities=27%  Similarity=0.389  Sum_probs=300.2

Q ss_pred             chhhhH-HHHHHHhCCCCCCccceEEEEecceEEEEEEecC-----CCCcchHHHHHHHhhCceecccCCCceeEEEee-
Q 047219          111 KERQRI-EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPP-----ACEIPQLIANLVSHLGLKVEEHGGGSDMGLRAW-  183 (567)
Q Consensus       111 ~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~-  183 (567)
                      ++++|| ++.|++||+.+||+    |+|+|++.+.|++|+.     ..+++++++.+|+|+|+++||     .|+|+++ 
T Consensus        36 ~~~~~~~~~~~~~l~~~~gd~----v~i~g~~~~~~~~~~~~~~~~~~~~i~~~~~~r~n~~v~~gd-----~V~v~~~~  106 (806)
T 3cf2_A           36 NSVVSLSQPKMDELQLFRGDT----VLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGD-----VISIQPCP  106 (806)
T ss_dssp             TTEEEECHHHHHHTTCCSSCE----EEEECGGGCBCCEEEEECTTSBTTBCEECHHHHHTTTCCTTC-----EEEEEECC
T ss_pred             CCEEEECHHHHHHcCCCCCCE----EEEEcCCCceEEEEEcCCCCCCCCEEEeCHHHHHhcCCCCCC-----EEEEEECC
Confidence            678999 69999999999999    9999999888888864     126789999999999999999     9999998 


Q ss_pred             cccccceeEecCCCCccccCCCccccCcccccccchhee--eeceeecCCCCceeeeccCcCCHHHHHHHHHHHhhhcc-
Q 047219          184 DSAVAWQLTLKPPEKQNESGGDRAQSGDMNAREGDLCIL--IFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAGR-  260 (567)
Q Consensus       184 ~~~~a~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  260 (567)
                      ++++|++|+++|....+.........      .+....+  .++|+..||.+.+.... +.+     .+.+..+.+.+. 
T Consensus       107 ~~~~a~~v~l~p~~~~~~~~~~~~~~------~~l~~~~~~~~~~v~~gd~~~v~~~~-~~~-----~f~V~~~~P~~~~  174 (806)
T 3cf2_A          107 DVKYGKRIHVLPIDDTVEGITGNLFE------VYLKPYFLEAYRPIRKGDIFLVRGGM-RAV-----EFKVVETDPSPYC  174 (806)
T ss_dssp             CCCBCSBEEEEEBTTTSTTCCSCHHH------HTHHHHHTTTCCEEETTCEEEECCTT-SCE-----EEEEEEESSSSEE
T ss_pred             CCCcCCEEEEeccccchhccchhHHH------HHHHHHHHhcCCcccCCCEEEEecCC-cEE-----EEEEEEEeCCCCe
Confidence            78999999999986644322221101      1112222  24788888876553221 000     000000111110 


Q ss_pred             ------cccccCcc----ccccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCC
Q 047219          261 ------RIYGLDEP----QLNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGP  330 (567)
Q Consensus       261 ------~~~~~~~~----~~~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~Gp  330 (567)
                            .+.....+    ......+.++|+||+|+++++++|++++.+|+++|++|+.++        ..+|++||||||
T Consensus       175 ~v~~~T~i~~~~~~~~~~~~~~~~~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g--------~~~p~GILL~GP  246 (806)
T 3cf2_A          175 IVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG--------VKPPRGILLYGP  246 (806)
T ss_dssp             ECCTTSBCCBCSCCBCCCTTSCCSSSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCC--------CCCCCEEEEECC
T ss_pred             EECCCcEEEEeccccCcccccccCCCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcC--------CCCCCeEEEECC
Confidence                  11111111    112356889999999999999999999999999999999876        789999999999


Q ss_pred             CCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHH
Q 047219          331 PGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHE  410 (567)
Q Consensus       331 pGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~  410 (567)
                      ||||||++|+++|+++      +.+++.++++++.++++|+++..++.+|..|+.++| +||||||||.|.++++....+
T Consensus       247 PGTGKT~LAraiA~el------g~~~~~v~~~~l~sk~~gese~~lr~lF~~A~~~~P-sIIfIDEiDal~~~r~~~~~~  319 (806)
T 3cf2_A          247 PGTGKTLIARAVANET------GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAP-AIIFIDELDAIAPKREKTHGE  319 (806)
T ss_dssp             TTSCHHHHHHHHHTTT------TCEEEEEEHHHHHSSCTTHHHHHHHHHHHHHTTSCS-EEEEEESGGGTCCTTTTCCCT
T ss_pred             CCCCHHHHHHHHHHHh------CCeEEEEEhHHhhcccchHHHHHHHHHHHHHHHcCC-eEEEEehhcccccccCCCCCh
Confidence            9999999999999999      888999999999999999999999999999998885 999999999999988877667


Q ss_pred             HHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHH
Q 047219          411 ATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAEL  485 (567)
Q Consensus       411 ~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~l  485 (567)
                      ..++++++|+..|+++....+|+||+|||+++.+|++|++  ||+..|+++.|+.++|.+||+.+++++.   +.++..+
T Consensus       320 ~~~riv~~LL~~mdg~~~~~~V~VIaaTN~~d~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~l  399 (806)
T 3cf2_A          320 VERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQV  399 (806)
T ss_dssp             THHHHHHHHHTHHHHCCGGGCEEEEEECSSTTTSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHH
T ss_pred             HHHHHHHHHHHHHhcccccCCEEEEEecCChhhcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHH
Confidence            7788999999999999888999999999999999999999  9999999999999999999999887643   3368999


Q ss_pred             HHhccCCCHHHHHHHHHHHHHHHHHHHHh
Q 047219          486 ATATEEMSGRDIRDVCQQAERSWASKIIR  514 (567)
Q Consensus       486 a~~t~g~s~~dL~~L~~~a~~~a~~r~i~  514 (567)
                      +..|+||+++||..+|++|.+.+.+|...
T Consensus       400 A~~T~GfsgaDL~~Lv~eA~~~A~~r~~~  428 (806)
T 3cf2_A          400 ANETHGHVGADLAALCSEAALQAIRKKMD  428 (806)
T ss_dssp             HHHCCSCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCCCHHHHHHHHHHHHHHHHHhccc
Confidence            99999999999999999999988887653

>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=100.00  E-value=2.1e-43  Score=386.10  Aligned_cols=370  Identities=28%  Similarity=0.415  Sum_probs=288.5

Q ss_pred             hhhhH-HHHHHHhCCCCCCccceEEEEecce--EEEEEEecCC-C--CcchHHHHHHHhhCceecccCCCceeEEEee-c
Q 047219          112 ERQRI-EELLKRKGMHYGSCPTFTVAVKGQK--VTIKFQVPPA-C--EIPQLIANLVSHLGLKVEEHGGGSDMGLRAW-D  184 (567)
Q Consensus       112 ~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~--~~~~~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~-~  184 (567)
                      |++|| ++.|.+||+.+||+    |+|+|++  .|+|++||.. +  +++++++.+|+|+|+++||     .|+|+++ +
T Consensus        37 ~~~~~~~~~~~~l~~~~gd~----v~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~r~n~~~~~gd-----~v~v~~~~~  107 (489)
T 3hu3_A           37 SVVSLSQPKMDELQLFRGDT----VLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGD-----VISIQPCPD  107 (489)
T ss_dssp             TEEEECHHHHHHHTCCTTCE----EEEECSTTCEEEEEEEECTTSCTTEEECCHHHHHHTTCCTTC-----EEEEEECTT
T ss_pred             CEEEECHHHHHHcCCCCCCE----EEEecCccCcEEEEEeeCCCCCCCEEEecHHHHhhcCCCCCC-----EEEEEECCC
Confidence            89999 69999999999999    9999988  6999999973 3  6799999999999999999     9999999 9


Q ss_pred             ccccceeEecCCCCcccc-CCCccccCcccccccchheeeeceeecCCCCceeeeccCcCC----HHHHHHHHHHHhhhc
Q 047219          185 SAVAWQLTLKPPEKQNES-GGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLT----SEELDALVSVLQLAG  259 (567)
Q Consensus       185 ~~~a~~v~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~  259 (567)
                      +++|++|+++|....+.. ..+.  .+|+.. .....  ...++..++.+.+.... ..+.    ..+...++. +.+ .
T Consensus       108 ~~~a~~v~~~~~~~av~a~~~ga--~d~~~K-p~~~~--~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~-~~~-~  179 (489)
T 3hu3_A          108 VKYGKRIHVLPIDDTVEGITGNL--FEVYLK-PYFLE--AYRPIRKGDIFLVHGGM-RAVEFKVVETDPSPYCI-VAP-D  179 (489)
T ss_dssp             CCBCSEEEEEEBGGGSSSCCSCH--HHHTHH-HHHTT--TCEEEETTCEEEEEETT-EEEEEEEEEEESSSEEE-ECT-T
T ss_pred             CCccCEEEEcCCCcccccccchh--HHHHhH-HHHhh--cCcccccCCEEEecCCC-ceEEEEEEeecCCCceE-EcC-C
Confidence            999999999997665542 2221  112110 10000  01233333332221100 0000    000000000 000 0


Q ss_pred             ccccccCcccc----ccCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcH
Q 047219          260 RRIYGLDEPQL----NTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK  335 (567)
Q Consensus       260 ~~~~~~~~~~~----~~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGK  335 (567)
                      ..+....++..    ....+.++|++|+|++.++++|++++..++.+|++|+.++        ..++.++||+|||||||
T Consensus       180 t~~~~~~~~~~~~~~~~~~~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g--------~~~~~~vLL~GppGtGK  251 (489)
T 3hu3_A          180 TVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIG--------VKPPRGILLYGPPGTGK  251 (489)
T ss_dssp             CEEECCSSCBCHHHHHHHHTCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHT--------CCCCCEEEEECSTTSSH
T ss_pred             eEEEEccCcccccccccccCCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcC--------CCCCCcEEEECcCCCCH
Confidence            00000001100    1123567899999999999999999999999999999886        78899999999999999


Q ss_pred             HHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHH
Q 047219          336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRI  415 (567)
Q Consensus       336 T~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~v  415 (567)
                      |++|+++|+++      +.+|+++++..+.+.++|+.+..++.+|+.+.... +++|||||||.|.++++....+...++
T Consensus       252 T~lAraia~~~------~~~fv~vn~~~l~~~~~g~~~~~~~~~f~~A~~~~-p~iLfLDEId~l~~~~~~~~~~~~~~~  324 (489)
T 3hu3_A          252 TLIARAVANET------GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNA-PAIIFIDELDAIAPKREKTHGEVERRI  324 (489)
T ss_dssp             HHHHHHHHHHC------SSEEEEEEHHHHHTSCTTHHHHHHHHHHHHHHHTC-SEEEEEESHHHHCBCTTSCCCHHHHHH
T ss_pred             HHHHHHHHHHh------CCCEEEEEchHhhhhhcchhHHHHHHHHHHHHhcC-CcEEEecchhhhccccccccchHHHHH
Confidence            99999999998      77899999999999999999999999999998876 499999999999998876666677788


Q ss_pred             HHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhcc
Q 047219          416 LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATE  490 (567)
Q Consensus       416 l~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~  490 (567)
                      +..|+..+++.....+++||+|||+++.+++++++  ||+..++|+.|+.++|.+||+.+++.+..   .++..++..+.
T Consensus       325 ~~~LL~~ld~~~~~~~v~vIaaTn~~~~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~  404 (489)
T 3hu3_A          325 VSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETH  404 (489)
T ss_dssp             HHHHHHHHHHSCTTSCEEEEEEESCGGGBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCT
T ss_pred             HHHHHHHhhccccCCceEEEEecCCccccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHcc
Confidence            89999999988888899999999999999999999  99999999999999999999999876532   35788999999


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHH
Q 047219          491 EMSGRDIRDVCQQAERSWASKII  513 (567)
Q Consensus       491 g~s~~dL~~L~~~a~~~a~~r~i  513 (567)
                      ||+++||..+|++|+..+.++..
T Consensus       405 g~s~~dL~~L~~~A~~~a~r~~~  427 (489)
T 3hu3_A          405 GHVGADLAALCSEAALQAIRKKM  427 (489)
T ss_dssp             TCCHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCcHHHHHHHHHHHHHHHHHhcc
Confidence            99999999999999988877654

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=6.7e-41  Score=354.82  Aligned_cols=225  Identities=32%  Similarity=0.560  Sum_probs=208.1

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|+++++++|++.+.+|+++|++|+++|        ..+|+++|||||||||||++|+|+|+++     
T Consensus       140 ~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~g--------i~~prGvLL~GPPGTGKTllAkAiA~e~-----  206 (405)
T 4b4t_J          140 EKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLG--------IAQPKGVILYGPPGTGKTLLARAVAHHT-----  206 (405)
T ss_dssp             ECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHT--------CCCCCCEEEESCSSSSHHHHHHHHHHHH-----
T ss_pred             cCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCC--------CCCCCceEEeCCCCCCHHHHHHHHHHhh-----
Confidence            356889999999999999999999999999999999987        8899999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+|+.++++++.++|+|++++.++.+|..|+..+| |||||||||.+.+++...   .....++++++||..||++..
T Consensus       207 -~~~f~~v~~s~l~sk~vGese~~vr~lF~~Ar~~aP-~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  284 (405)
T 4b4t_J          207 -DCKFIRVSGAELVQKYIGEGSRMVRELFVMAREHAP-SIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFET  284 (405)
T ss_dssp             -TCEEEEEEGGGGSCSSTTHHHHHHHHHHHHHHHTCS-EEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTC
T ss_pred             -CCCceEEEhHHhhccccchHHHHHHHHHHHHHHhCC-ceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCC
Confidence             889999999999999999999999999999999985 999999999999876432   234567889999999999998


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+++||+|||+++.||++|+|  |||..|+|++|+.++|.+||+.+++++..   .+++.++..++||||+||+++|++
T Consensus       285 ~~~V~vIaATNrpd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~e  364 (405)
T 4b4t_J          285 SKNIKIIMATNRLDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTE  364 (405)
T ss_dssp             CCCEEEEEEESCSSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHHH
T ss_pred             CCCeEEEeccCChhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHHH
Confidence            9999999999999999999998  99999999999999999999999987642   368999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |.+.++++
T Consensus       365 A~~~Air~  372 (405)
T 4b4t_J          365 AGMYALRE  372 (405)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHc
Confidence            99877653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=8.5e-40  Score=347.45  Aligned_cols=225  Identities=32%  Similarity=0.570  Sum_probs=207.5

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|+++++++|++.+.+|+++|++|+.+|        ..+|++||||||||||||++|+|+|+++     
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~G--------i~~prGvLLyGPPGTGKTlLAkAiA~e~-----  240 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMG--------IKPPKGVILYGAPGTGKTLLAKAVANQT-----  240 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHT--------CCCCSEEEEESSTTTTHHHHHHHHHHHH-----
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCC--------CCCCCCCceECCCCchHHHHHHHHHHHh-----
Confidence            467889999999999999999999999999999999987        8899999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+|+.++++++.++|+|++++.++.+|..|+..+| |||||||||.+..++...   ......+++.+||..+|++..
T Consensus       241 -~~~fi~v~~s~l~sk~vGesek~ir~lF~~Ar~~aP-~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~  318 (437)
T 4b4t_I          241 -SATFLRIVGSELIQKYLGDGPRLCRQIFKVAGENAP-SIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDD  318 (437)
T ss_dssp             -TCEEEEEESGGGCCSSSSHHHHHHHHHHHHHHHTCS-EEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCC
T ss_pred             -CCCEEEEEHHHhhhccCchHHHHHHHHHHHHHhcCC-cEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCC
Confidence             889999999999999999999999999999999985 999999999999887432   233456788999999999988


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+++||+|||+++.||++|+|  |||..|+|+.|+.++|.+||+.+++++..   .+++.++..++|||++||+++|++
T Consensus       319 ~~~ViVIaATNrpd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~e  398 (437)
T 4b4t_I          319 RGDVKVIMATNKIETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTE  398 (437)
T ss_dssp             SSSEEEEEEESCSTTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHHH
T ss_pred             CCCEEEEEeCCChhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHH
Confidence            8999999999999999999998  99999999999999999999999987642   368999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |.+.++++
T Consensus       399 A~~~Air~  406 (437)
T 4b4t_I          399 AGLLALRE  406 (437)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHc
Confidence            99877654

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.5e-39  Score=345.76  Aligned_cols=225  Identities=31%  Similarity=0.565  Sum_probs=207.9

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|++++|++|++.|.+|+.+|++|+++|        ..+|++||||||||||||++|+|||+++     
T Consensus       201 ~e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G--------i~pprGILLyGPPGTGKTlLAkAiA~e~-----  267 (467)
T 4b4t_H          201 EEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG--------IDPPKGILLYGPPGTGKTLCARAVANRT-----  267 (467)
T ss_dssp             ESSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT--------CCCCSEEEECSCTTSSHHHHHHHHHHHH-----
T ss_pred             cCCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC--------CCCCCceEeeCCCCCcHHHHHHHHHhcc-----
Confidence            467899999999999999999999999999999999987        8899999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+|+.++++++.++|+|++++.++.+|..|+..+| |||||||+|.+..++...   ......+++.++|..|+++..
T Consensus       268 -~~~fi~vs~s~L~sk~vGesek~ir~lF~~Ar~~aP-~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  345 (467)
T 4b4t_H          268 -DATFIRVIGSELVQKYVGEGARMVRELFEMARTKKA-CIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDP  345 (467)
T ss_dssp             -TCEEEEEEGGGGCCCSSSHHHHHHHHHHHHHHHTCS-EEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCC
T ss_pred             -CCCeEEEEhHHhhcccCCHHHHHHHHHHHHHHhcCC-ceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCC
Confidence             889999999999999999999999999999999985 999999999999877432   334556788999999999988


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+++||+|||+++.||++|+|  ||+..|+|++|+.++|.+||+.+++++..   .+++.++..+.||+++||+++|++
T Consensus       346 ~~~ViVIaATNrpd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~e  425 (467)
T 4b4t_H          346 RGNIKVMFATNRPNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTE  425 (467)
T ss_dssp             TTTEEEEEECSCTTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHHH
T ss_pred             CCcEEEEeCCCCcccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHH
Confidence            8999999999999999999998  99999999999999999999999987643   368999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |.+.++++
T Consensus       426 Aa~~Air~  433 (467)
T 4b4t_H          426 AGMFAIRA  433 (467)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHc
Confidence            99887765

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.5e-39  Score=347.11  Aligned_cols=225  Identities=33%  Similarity=0.560  Sum_probs=207.7

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|++++|+.|++.+.+|+++|++|+++|        ..+|++||||||||||||++|+|+|+++     
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g--------~~~prGvLLyGPPGTGKTllAkAiA~e~-----  239 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMG--------IRAPKGALMYGPPGTGKTLLARACAAQT-----  239 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHC--------CCCCCEEEEESCTTSSHHHHHHHHHHHH-----
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCC--------CCCCCeeEEECcCCCCHHHHHHHHHHHh-----
Confidence            467889999999999999999999999999999999987        8899999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhh---HHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l---~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+|+.++++++.++|+|++++.++.+|..|+..+| |||||||||.+..++....   .....+++.+||..|+++..
T Consensus       240 -~~~f~~v~~s~l~~~~vGese~~ir~lF~~A~~~aP-~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~  317 (434)
T 4b4t_M          240 -NATFLKLAAPQLVQMYIGEGAKLVRDAFALAKEKAP-TIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSS  317 (434)
T ss_dssp             -TCEEEEEEGGGGCSSCSSHHHHHHHHHHHHHHHHCS-EEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCS
T ss_pred             -CCCEEEEehhhhhhcccchHHHHHHHHHHHHHhcCC-eEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCC
Confidence             889999999999999999999999999999999885 9999999999998875432   34567788999999999988


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+|+||+|||+++.||++|++  ||+..|+|++|+.++|.+||+.+++++..   .+++.++..++||||+||+++|++
T Consensus       318 ~~~ViVIaaTNrp~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~e  397 (434)
T 4b4t_M          318 DDRVKVLAATNRVDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTVE  397 (434)
T ss_dssp             SCSSEEEEECSSCCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCchhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHH
Confidence            8999999999999999999988  99999999999999999999999988643   268999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |.+.++++
T Consensus       398 A~~~a~r~  405 (434)
T 4b4t_M          398 AGMIALRN  405 (434)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHc
Confidence            99887764

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.8e-39  Score=346.02  Aligned_cols=225  Identities=34%  Similarity=0.578  Sum_probs=206.8

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|++++++.|++.+.+|+++|++|+++|        ..+|+++|||||||||||++|+|||+++     
T Consensus       173 ~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g--------~~~prGvLL~GPPGtGKTllAkAiA~e~-----  239 (437)
T 4b4t_L          173 FEQGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVG--------IKPPKGVLLYGPPGTGKTLLAKAVAATI-----  239 (437)
T ss_dssp             EESCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHC--------CCCCCEEEEESCTTSSHHHHHHHHHHHH-----
T ss_pred             ccCCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCC--------CCCCCeEEEECCCCCcHHHHHHHHHHHh-----
Confidence            357889999999999999999999999999999999987        8899999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+|+.++++++.++|+|+++..++.+|..|...+| |||||||||.+..++...   ......+++++||..||++..
T Consensus       240 -~~~~~~v~~s~l~sk~~Gese~~ir~~F~~A~~~~P-~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~  317 (437)
T 4b4t_L          240 -GANFIFSPASGIVDKYIGESARIIREMFAYAKEHEP-CIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDN  317 (437)
T ss_dssp             -TCEEEEEEGGGTCCSSSSHHHHHHHHHHHHHHHSCS-EEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSC
T ss_pred             -CCCEEEEehhhhccccchHHHHHHHHHHHHHHhcCC-ceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccC
Confidence             889999999999999999999999999999999885 999999999999877432   234567788999999999988


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ..+++||+|||+++.||++|+|  ||+..|+|++|+.++|.+||+.+++++.   ..+++.++..|+||||+||+++|++
T Consensus       318 ~~~vivI~ATNrp~~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~e  397 (437)
T 4b4t_L          318 LGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATE  397 (437)
T ss_dssp             TTSSEEEEEESSTTSSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHHH
T ss_pred             CCCeEEEEecCCchhhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHHH
Confidence            8999999999999999999998  6999999999999999999999998764   3368999999999999999999999


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      |++.++++
T Consensus       398 A~~~air~  405 (437)
T 4b4t_L          398 AGFFAIRD  405 (437)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHc
Confidence            99877653

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.8e-38  Score=340.27  Aligned_cols=225  Identities=38%  Similarity=0.604  Sum_probs=207.0

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...|.++|+||+|++++|+.|++.+.+|+++|++|+++|        ..+|+++|||||||||||++|+|+|+++     
T Consensus       164 ~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g--------~~~prGiLL~GPPGtGKT~lakAiA~~~-----  230 (428)
T 4b4t_K          164 NEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG--------IDPPRGVLLYGPPGTGKTMLVKAVANST-----  230 (428)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC--------CCCCCEEEEESCTTTTHHHHHHHHHHHH-----
T ss_pred             CCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC--------CCCCceEEEECCCCCCHHHHHHHHHHHh-----
Confidence            357889999999999999999999999999999999987        8899999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+|+.++++++.++|+|+++..++.+|..|+..+| |||||||+|.+...+...   .....++++++||..||++..
T Consensus       231 -~~~~~~v~~~~l~~~~~Ge~e~~ir~lF~~A~~~aP-~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~  308 (428)
T 4b4t_K          231 -KAAFIRVNGSEFVHKYLGEGPRMVRDVFRLARENAP-SIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQ  308 (428)
T ss_dssp             -TCEEEEEEGGGTCCSSCSHHHHHHHHHHHHHHHTCS-EEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCS
T ss_pred             -CCCeEEEecchhhccccchhHHHHHHHHHHHHHcCC-CeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCC
Confidence             889999999999999999999999999999999885 999999999999887432   234567889999999999988


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEec-CCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFG-LPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~-~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      ..+++||+|||+++.||++|+|  ||+..|+|+ +|+.++|.+|++.+++++.   ..+++.++..++||||+||+++|+
T Consensus       309 ~~~v~vI~aTN~~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~  388 (428)
T 4b4t_K          309 STNVKVIMATNRADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQ  388 (428)
T ss_dssp             SCSEEEEEEESCSSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHH
T ss_pred             CCCEEEEEecCChhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHH
Confidence            8999999999999999999998  999999995 8999999999999998764   336899999999999999999999


Q ss_pred             HHHHHHHHH
Q 047219          503 QAERSWASK  511 (567)
Q Consensus       503 ~a~~~a~~r  511 (567)
                      +|.+.++++
T Consensus       389 eA~~~a~r~  397 (428)
T 4b4t_K          389 EAGLRAVRK  397 (428)
T ss_dssp             HHHHHHHHT
T ss_pred             HHHHHHHHC
Confidence            999877654

>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=100.00  E-value=9.8e-37  Score=348.10  Aligned_cols=228  Identities=31%  Similarity=0.566  Sum_probs=182.9

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|.++|++|+|++++++.|.+.+.+++++|++|.+++        ..+++++|||||||||||++|+++|+++      
T Consensus       470 ~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g--------~~~~~gvLl~GPPGtGKT~lAkaiA~e~------  535 (806)
T 3cf2_A          470 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG--------MTPSKGVLFYGPPGCGKTLLAKAIANEC------  535 (806)
T ss_dssp             BCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSC--------CCCCSCCEEESSTTSSHHHHHHHHHHTT------
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcC--------CCCCceEEEecCCCCCchHHHHHHHHHh------
Confidence            45889999999999999999999999999999998776        7889999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+|+.++.+++.++|+|++++.++.+|+.|+..+| |||||||||.+.+.+...   .....++++++||.+||++...
T Consensus       536 ~~~f~~v~~~~l~s~~vGese~~vr~lF~~Ar~~~P-~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~  614 (806)
T 3cf2_A          536 QANFISIKGPELLTMWFGESEANVREIFDKARQAAP-CVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK  614 (806)
T ss_dssp             TCEEEECCHHHHHTTTCSSCHHHHHHHHHHHHTTCS-EEEECSCGGGCC--------------CHHHHHHHHHHHSSCSS
T ss_pred             CCceEEeccchhhccccchHHHHHHHHHHHHHHcCC-ceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCC
Confidence            889999999999999999999999999999998875 999999999999887532   3446678999999999999988


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+|+||+|||+++.||++|+|  ||+..|+|++|+.++|.+||+.++++++   ..+++.+++.+.||||+||.++|++|
T Consensus       615 ~~V~vi~aTN~p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~~A  694 (806)
T 3cf2_A          615 KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRA  694 (806)
T ss_dssp             SSEEEECC-CCSSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHHHH
T ss_pred             CCEEEEEeCCCchhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHHHH
Confidence            999999999999999999999  9999999999999999999999987754   34789999999999999999999999


Q ss_pred             HHHHHHHHHhc
Q 047219          505 ERSWASKIIRG  515 (567)
Q Consensus       505 ~~~a~~r~i~~  515 (567)
                      ++.++++.+..
T Consensus       695 ~~~a~r~~~~~  705 (806)
T 3cf2_A          695 CKLAIRESIES  705 (806)
T ss_dssp             HHHHHHHHHC-
T ss_pred             HHHHHHHHHHh
Confidence            99999887653

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=100.00  E-value=1.9e-33  Score=292.13  Aligned_cols=227  Identities=30%  Similarity=0.509  Sum_probs=204.6

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|+||+|++++++.|++.+.+++++|++|...         ..+++++||+||||||||++|+++|+++.     
T Consensus         5 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~---------~~~~~~iLL~GppGtGKT~la~ala~~~~-----   70 (322)
T 1xwi_A            5 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGK---------RTPWRGILLFGPPGTGKSYLAKAVATEAN-----   70 (322)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTT---------CCCCSEEEEESSSSSCHHHHHHHHHHHTT-----
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCC---------CCCCceEEEECCCCccHHHHHHHHHHHcC-----
Confidence            4578999999999999999999999999999998632         45779999999999999999999999983     


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-cCCc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-QDKK  431 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-~~~~  431 (567)
                      +.+|+.++++++.+++.|+.+..++.+|..+.... ++||||||||.+.+.++........+++++|+..++++. ...+
T Consensus        71 ~~~~~~i~~~~l~~~~~g~~~~~~~~lf~~a~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~~~~  149 (322)
T 1xwi_A           71 NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENK-PSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  149 (322)
T ss_dssp             SCEEEEEECCSSCCSSCCSCHHHHHHHHHHHHHTS-SEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSCCTT
T ss_pred             CCcEEEEEhHHHHhhhhhHHHHHHHHHHHHHHhcC-CcEEEeecHHHhccccccccchHHHHHHHHHHHHHhcccccCCC
Confidence            45789999999999999999999999999998776 499999999999988776666677888899999999875 3678


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh----CHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL----TKAELAELATATEEMSGRDIRDVCQQAERS  507 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~----~~~~l~~la~~t~g~s~~dL~~L~~~a~~~  507 (567)
                      ++||+|||+++.+++++++||+..++++.|+.++|.+|++.++...    ...++..++..+.||+++||..+|++|++.
T Consensus       150 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~A~~~  229 (322)
T 1xwi_A          150 ILVLGATNIPWVLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQ  229 (322)
T ss_dssp             EEEEEEESCTTTSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHHHHTH
T ss_pred             EEEEEecCCcccCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999998753    577899999999999999999999999999


Q ss_pred             HHHHHHh
Q 047219          508 WASKIIR  514 (567)
Q Consensus       508 a~~r~i~  514 (567)
                      +.++...
T Consensus       230 a~r~~~~  236 (322)
T 1xwi_A          230 PVRKVQS  236 (322)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9888763

>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=100.00  E-value=6.7e-33  Score=287.51  Aligned_cols=227  Identities=33%  Similarity=0.529  Sum_probs=201.3

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ...++++|++|+|++++++.|++.+..++.+|++|...         ..+++++||+||||||||++|+++|+++     
T Consensus        10 ~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~---------~~~~~~vLl~GppGtGKT~la~aia~~~-----   75 (322)
T 3eie_A           10 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGN---------RKPTSGILLYGPPGTGKSYLAKAVATEA-----   75 (322)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTT---------CCCCCEEEEECSSSSCHHHHHHHHHHHH-----
T ss_pred             ecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcC---------CCCCCeEEEECCCCCcHHHHHHHHHHHH-----
Confidence            35678999999999999999999999999999988653         4678899999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-cCC
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-QDK  430 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-~~~  430 (567)
                       +.+++.++++++.++++|+.+..++.+|..+.... ++||||||||.|..++.........+++++++..+++.. ...
T Consensus        76 -~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  153 (322)
T 3eie_A           76 -NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENK-PSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQ  153 (322)
T ss_dssp             -TCEEEEEEHHHHHTTTGGGHHHHHHHHHHHHHHTS-SEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTSCC
T ss_pred             -CCCEEEEchHHHhhcccchHHHHHHHHHHHHHhcC-CeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhccccccCC
Confidence             77899999999999999999999999999998876 499999999999887765544556677889999998874 567


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +++||+|||.++.++++|++||+..++++.|+.++|.+|++.++..    +....+..++..+.||+++||+.+|++|++
T Consensus       154 ~v~vi~atn~~~~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~a~~  233 (322)
T 3eie_A          154 GVLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALM  233 (322)
T ss_dssp             CEEEEEEESCGGGSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHHHTT
T ss_pred             ceEEEEecCChhhCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            8999999999999999999999999999999999999999999875    357789999999999999999999999999


Q ss_pred             HHHHHHHh
Q 047219          507 SWASKIIR  514 (567)
Q Consensus       507 ~a~~r~i~  514 (567)
                      .+.++...
T Consensus       234 ~a~r~~~~  241 (322)
T 3eie_A          234 QPIRKIQS  241 (322)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHhh
Confidence            99888764

>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=100.00  E-value=9.5e-32  Score=282.92  Aligned_cols=226  Identities=33%  Similarity=0.529  Sum_probs=193.7

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++.|++.+.+++.+|++|...         ..+++++||+||||||||++|+++|+++      
T Consensus        44 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~---------~~~~~~iLL~GppGtGKT~la~ala~~~------  108 (355)
T 2qp9_X           44 EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGN---------RKPTSGILLYGPPGTGKSYLAKAVATEA------  108 (355)
T ss_dssp             ---CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSS---------CCCCCCEEEECSTTSCHHHHHHHHHHHH------
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcC---------CCCCceEEEECCCCCcHHHHHHHHHHHh------
Confidence            4567899999999999999999999999999998742         5678899999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc-CCc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ-DKK  431 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~-~~~  431 (567)
                      +.+++.+++.++.+.++|+.+..++.+|..+.... ++||||||||.|...+.........+++++|+..+++... ..+
T Consensus       109 ~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~-~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~~~~  187 (355)
T 2qp9_X          109 NSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENK-PSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGNDSQG  187 (355)
T ss_dssp             TCEEEEEEHHHHHSCC---CHHHHHHHHHHHHHTS-SEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC---CC
T ss_pred             CCCEEEeeHHHHhhhhcchHHHHHHHHHHHHHHcC-CeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhcccccCCC
Confidence            77899999999999999999999999999998766 5999999999998876655555667788899999987753 568


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAERS  507 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~  507 (567)
                      ++||++||.++.+++++++||+..++++.|+.++|.+|++.++..    +...+++.++..+.||+++||+.+|++|.+.
T Consensus       188 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~~A~~~  267 (355)
T 2qp9_X          188 VLVLGATNIPWQLDSAIRRRFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQ  267 (355)
T ss_dssp             EEEEEEESCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHHH
T ss_pred             eEEEeecCCcccCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999875    3577899999999999999999999999999


Q ss_pred             HHHHHHh
Q 047219          508 WASKIIR  514 (567)
Q Consensus       508 a~~r~i~  514 (567)
                      +.++...
T Consensus       268 a~~~~~~  274 (355)
T 2qp9_X          268 PIRKIQS  274 (355)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8887653

>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=99.98  E-value=1.7e-31  Score=274.43  Aligned_cols=227  Identities=31%  Similarity=0.576  Sum_probs=200.2

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++.|++.+.+++.+|+.|..++        ..++.++||+||||||||++|+++|+++      
T Consensus         8 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~--------~~~~~~vLL~Gp~GtGKT~la~ala~~~------   73 (301)
T 3cf0_A            8 EVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG--------MTPSKGVLFYGPPGCGKTLLAKAIANEC------   73 (301)
T ss_dssp             ECCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC--------CCCCSEEEEECSSSSSHHHHHHHHHHHT------
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcC--------CCCCceEEEECCCCcCHHHHHHHHHHHh------
Confidence            45789999999999999999999999999999998876        6788999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhh---HHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l---~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+++..+.++++|+.+..++.+|..+.... +++|||||||.|...++...   .....+++++|+..++++...
T Consensus        74 ~~~~i~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~-p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~  152 (301)
T 3cf0_A           74 QANFISIKGPELLTMWFGESEANVREIFDKARQAA-PCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTK  152 (301)
T ss_dssp             TCEEEEECHHHHHHHHHTTCTTHHHHHHHHHHHTC-SEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTT
T ss_pred             CCCEEEEEhHHHHhhhcCchHHHHHHHHHHHHhcC-CeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCC
Confidence            67899999999999999999999999999998776 49999999999987764321   112345668889999888777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||+|||+++.+++++++  ||+..++++.|+.++|.+|++.+++...   ..+++.++..+.||+++||+++|+.|
T Consensus       153 ~~v~vi~atn~~~~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~~a  232 (301)
T 3cf0_A          153 KNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRA  232 (301)
T ss_dssp             SSEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHHHH
T ss_pred             CCEEEEEecCCccccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHHHH
Confidence            899999999999999999998  9999999999999999999999887643   23577888999999999999999999


Q ss_pred             HHHHHHHHHh
Q 047219          505 ERSWASKIIR  514 (567)
Q Consensus       505 ~~~a~~r~i~  514 (567)
                      ...+..+.+.
T Consensus       233 ~~~a~~~~~~  242 (301)
T 3cf0_A          233 CKLAIRESIE  242 (301)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9888877653

>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=99.97  E-value=6.2e-31  Score=284.69  Aligned_cols=227  Identities=31%  Similarity=0.518  Sum_probs=193.8

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++.|++.+.+++.+|++|...         ..+++++||+||||||||++|+++|+++.     
T Consensus       127 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~---------~~~~~~vLL~GppGtGKT~lA~aia~~~~-----  192 (444)
T 2zan_A          127 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGK---------RTPWRGILLFGPPGTGKSYLAKAVATEAN-----  192 (444)
T ss_dssp             CCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGG---------GCCCSEEEEECSTTSSHHHHHHHHHHHCC-----
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhcc---------CCCCceEEEECCCCCCHHHHHHHHHHHcC-----
Confidence            4678999999999999999999999999999988632         45779999999999999999999999983     


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-cCCc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-QDKK  431 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-~~~~  431 (567)
                      +.+|+.++++++.+.++|+.+..++.+|..+.... ++||||||||.|.+.+.........+++++|+..+++.. ...+
T Consensus       193 ~~~~~~v~~~~l~~~~~g~~~~~~~~~f~~a~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~  271 (444)
T 2zan_A          193 NSTFFSISSSDLVSKWLGESEKLVKNLFQLARENK-PSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVDNDG  271 (444)
T ss_dssp             SSEEEEECCC---------CCCTHHHHHHHHHHSC-SEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCCCSS
T ss_pred             CCCEEEEeHHHHHhhhcchHHHHHHHHHHHHHHcC-CeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccCCCC
Confidence            45799999999999999999899999999988766 499999999999877665555556778899999999875 3678


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAERS  507 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~  507 (567)
                      ++||+|||+++.++++|++||+..+.++.|+.++|.+|++.++..    +...++..++..+.||+++||..+|++|++.
T Consensus       272 v~vI~atn~~~~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a~~~  351 (444)
T 2zan_A          272 ILVLGATNIPWVLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQ  351 (444)
T ss_dssp             CEEEEEESCGGGSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHHHTH
T ss_pred             EEEEecCCCccccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999875    4677899999999999999999999999999


Q ss_pred             HHHHHHh
Q 047219          508 WASKIIR  514 (567)
Q Consensus       508 a~~r~i~  514 (567)
                      +.++...
T Consensus       352 a~r~~~~  358 (444)
T 2zan_A          352 PVRKVQS  358 (444)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHh
Confidence            9988764

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.97  E-value=1.4e-30  Score=264.58  Aligned_cols=227  Identities=29%  Similarity=0.535  Sum_probs=185.4

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|.++|+||+|++++++.|++.+.+++.+++.|+.++        ...+++++|+||||||||+++++|+.++      
T Consensus         3 ~~~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~--------l~~~~GvlL~Gp~GtGKTtLakala~~~------   68 (274)
T 2x8a_A            3 TVPNVTWADIGALEDIREELTMAILAPVRNPDQFKALG--------LVTPAGVLLAGPPGCGKTLLAKAVANES------   68 (274)
T ss_dssp             ---------CCHHHHHHHHHHHHHTHHHHSHHHHHHTT--------CCCCSEEEEESSTTSCHHHHHHHHHHHT------
T ss_pred             CCCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcC--------CCCCCeEEEECCCCCcHHHHHHHHHHHc------
Confidence            35779999999999999999999999999999999886        6778889999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +.+++.+++.++.+.+.|+.+..++.+|+.+.... ++++|+||+|.+...+.........+.+++++..|++......+
T Consensus        69 ~~~~i~i~g~~l~~~~~~~~~~~i~~vf~~a~~~~-p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~~~~~  147 (274)
T 2x8a_A           69 GLNFISVKGPELLNMYVGESERAVRQVFQRAKNSA-PCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEARQQV  147 (274)
T ss_dssp             TCEEEEEETTTTCSSTTHHHHHHHHHHHHHHHHTC-SEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCSTTCE
T ss_pred             CCCEEEEEcHHHHhhhhhHHHHHHHHHHHHHHhcC-CCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccccCCE
Confidence            56799999999988888999999999999987665 49999999999876543322223345678899999988888889


Q ss_pred             EEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHh---h---CHHHHHHHHHhc--cCCCHHHHHHHHH
Q 047219          433 VVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKH---L---TKAELAELATAT--EEMSGRDIRDVCQ  502 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~---~---~~~~l~~la~~t--~g~s~~dL~~L~~  502 (567)
                      +++++||+++.+|+++++  ||+..|+++.|+.++|.+|++.++++   .   ...+++.++..+  +||+++||..+|+
T Consensus       148 i~ia~tn~p~~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~  227 (274)
T 2x8a_A          148 FIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVR  227 (274)
T ss_dssp             EEEEEESCGGGSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHH
T ss_pred             EEEeecCChhhCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHH
Confidence            999999999999999998  99999999999999999999998753   1   133678888864  5999999999999


Q ss_pred             HHHHHHHHHHHh
Q 047219          503 QAERSWASKIIR  514 (567)
Q Consensus       503 ~a~~~a~~r~i~  514 (567)
                      +|...+.++.+.
T Consensus       228 ~a~~~a~~~~~~  239 (274)
T 2x8a_A          228 EASICALRQEMA  239 (274)
T ss_dssp             HHHHHHHHHHC-
T ss_pred             HHHHHHHHHHHh
Confidence            999988877643

>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=99.97  E-value=2.7e-29  Score=264.32  Aligned_cols=222  Identities=30%  Similarity=0.587  Sum_probs=193.5

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .+.++|++|+|++++++.|++.+.+++.++++|...         ..+++++||+||||||||++|+++|+++      +
T Consensus        78 ~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~---------~~~~~~vLl~GppGtGKT~la~aia~~~------~  142 (357)
T 3d8b_A           78 GPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGL---------RGPPKGILLFGPPGTGKTLIGKCIASQS------G  142 (357)
T ss_dssp             SCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGG---------GSCCSEEEEESSTTSSHHHHHHHHHHHT------T
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhc---------cCCCceEEEECCCCCCHHHHHHHHHHHc------C
Confidence            467899999999999999999999999999988755         3678899999999999999999999998      7


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc--cCCc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE--QDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~--~~~~  431 (567)
                      .+++.++++.+.+.+.|+.+..++.+|..+.... ++||||||||.|...++........++++.++..+++..  ...+
T Consensus       143 ~~~~~i~~~~l~~~~~g~~~~~~~~~~~~a~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~~~  221 (357)
T 3d8b_A          143 ATFFSISASSLTSKWVGEGEKMVRALFAVARCQQ-PAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSSEDR  221 (357)
T ss_dssp             CEEEEEEGGGGCCSSTTHHHHHHHHHHHHHHHTC-SEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC----CCCC
T ss_pred             CeEEEEehHHhhccccchHHHHHHHHHHHHHhcC-CeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccccCCCC
Confidence            7899999999999999999999999999888765 599999999999887665545556677888888888764  3468


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAERS  507 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~  507 (567)
                      ++||+|||.++.+++++++||+..++++.|+.++|.+|+..++++    +....++.++..+.||+++||+.+|+++|..
T Consensus       222 v~vI~atn~~~~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a~~~  301 (357)
T 3d8b_A          222 ILVVGATNRPQEIDEAARRRLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLG  301 (357)
T ss_dssp             EEEEEEESCGGGBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHTH
T ss_pred             EEEEEecCChhhCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999989999999999999999999875    5678899999999999999999999999987


Q ss_pred             HHHH
Q 047219          508 WASK  511 (567)
Q Consensus       508 a~~r  511 (567)
                      +.++
T Consensus       302 ~ir~  305 (357)
T 3d8b_A          302 PIRS  305 (357)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            7664

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.96  E-value=2.7e-29  Score=256.09  Aligned_cols=224  Identities=32%  Similarity=0.593  Sum_probs=191.8

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..++++|++|+|++++++.+++.+..++.+|++|..+         ..++.++||+||||||||++|+++|+++      
T Consensus        14 ~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~---------~~~~~~vll~Gp~GtGKT~la~~la~~~------   78 (297)
T 3b9p_A           14 GGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGL---------RAPAKGLLLFGPPGNGKTLLARAVATEC------   78 (297)
T ss_dssp             CSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGG---------GCCCSEEEEESSSSSCHHHHHHHHHHHT------
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcC---------CCCCCeEEEECcCCCCHHHHHHHHHHHh------
Confidence            4567899999999999999999999999999988765         3567899999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC---
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD---  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~---  429 (567)
                      +.+++.+++..+.+.+.|..+..++.+|..+.... +++|||||+|.+...++........+..+.++..+++....   
T Consensus        79 ~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  157 (297)
T 3b9p_A           79 SATFLNISAASLTSKYVGDGEKLVRALFAVARHMQ-PSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDG  157 (297)
T ss_dssp             TCEEEEEESTTTSSSSCSCHHHHHHHHHHHHHHTC-SEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC-----
T ss_pred             CCCeEEeeHHHHhhcccchHHHHHHHHHHHHHHcC-CcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCC
Confidence            67899999999999999999899999999888765 59999999999988766544444456667888888766432   


Q ss_pred             CcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      .+++||++||.++.+++++++||+..+.++.|+.++|.+|++.++++    +....+..++..+.|++++||+.+|+++|
T Consensus       158 ~~v~vi~~tn~~~~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~a~  237 (297)
T 3b9p_A          158 DRIVVLAATNRPQELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAA  237 (297)
T ss_dssp             -CEEEEEEESCGGGBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHT
T ss_pred             CcEEEEeecCChhhCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999998875    45778999999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          506 RSWASKI  512 (567)
Q Consensus       506 ~~a~~r~  512 (567)
                      ..+.++.
T Consensus       238 ~~a~r~~  244 (297)
T 3b9p_A          238 LEPIREL  244 (297)
T ss_dssp             THHHHTC
T ss_pred             HHHHHHH
Confidence            8776653

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.96  E-value=3.6e-29  Score=266.04  Aligned_cols=224  Identities=33%  Similarity=0.580  Sum_probs=186.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++.+++.|.+.+..++.++++|..++         .++.++||+||||||||++|++||+++      
T Consensus       108 ~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~---------~~~~~vLL~GppGtGKT~la~aia~~~------  172 (389)
T 3vfd_A          108 NGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLR---------APARGLLLFGPPGNGKTMLAKAVAAES------  172 (389)
T ss_dssp             CSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG---------CCCSEEEEESSTTSCHHHHHHHHHHHT------
T ss_pred             cCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccC---------CCCceEEEECCCCCCHHHHHHHHHHhh------
Confidence            45678999999999999999999999999999887653         567899999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc--CC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ--DK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~--~~  430 (567)
                      +.+|+.+++..+.+.+.|+.+..+..+|..+.... ++||||||||.|...++........+++..|+..+++...  ..
T Consensus       173 ~~~~~~v~~~~l~~~~~g~~~~~~~~~~~~a~~~~-~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~  251 (389)
T 3vfd_A          173 NATFFNISAASLTSKYVGEGEKLVRALFAVARELQ-PSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDD  251 (389)
T ss_dssp             TCEEEEECSCCC-------CHHHHHHHHHHHHHSS-SEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC-----
T ss_pred             cCcEEEeeHHHhhccccchHHHHHHHHHHHHHhcC-CeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccccCCC
Confidence            77899999999999999999999999999998776 4999999999998776655444566777888888887643  56


Q ss_pred             cEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +++||+|||.++.+++++++||+..++++.|+.++|.+|++.++..    +....+..++..+.|+++++|..+|+++|.
T Consensus       252 ~v~vI~atn~~~~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~a~~  331 (389)
T 3vfd_A          252 RVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAAL  331 (389)
T ss_dssp             CEEEEEEESCGGGCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTT
T ss_pred             CEEEEEecCCchhcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            7999999999999999999999889999999999999999998865    677889999999999999999999999998


Q ss_pred             HHHHHH
Q 047219          507 SWASKI  512 (567)
Q Consensus       507 ~a~~r~  512 (567)
                      .+.+++
T Consensus       332 ~~~rel  337 (389)
T 3vfd_A          332 GPIREL  337 (389)
T ss_dssp             HHHHTS
T ss_pred             HHHHhh
Confidence            877664

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.96  E-value=8.7e-29  Score=250.68  Aligned_cols=224  Identities=33%  Similarity=0.606  Sum_probs=196.9

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++.|++.+..++.++++|+.++        ...+.++||+||||||||++|+++++.+      
T Consensus        10 ~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~--------~~~~~~~ll~G~~GtGKT~la~~la~~~------   75 (285)
T 3h4m_A           10 ERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVG--------IEPPKGILLYGPPGTGKTLLAKAVATET------   75 (285)
T ss_dssp             SSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHC--------CCCCSEEEEESSSSSSHHHHHHHHHHHT------
T ss_pred             CCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC--------CCCCCeEEEECCCCCcHHHHHHHHHHHh------
Confidence            45779999999999999999999999999999999886        6788999999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+++..+...+.|.....+..+|..+.... ++||||||+|.+..++++.   .....++.+..++..+++....
T Consensus        76 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~  154 (285)
T 3h4m_A           76 NATFIRVVGSELVKKFIGEGASLVKDIFKLAKEKA-PSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDAR  154 (285)
T ss_dssp             TCEEEEEEGGGGCCCSTTHHHHHHHHHHHHHHHTC-SEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCSS
T ss_pred             CCCEEEEehHHHHHhccchHHHHHHHHHHHHHHcC-CeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCCC
Confidence            77899999999999999999999999999998776 4999999999998765432   1223456667778888777777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||+|||.++.+++++++  ||+..+.++.|+.++|.+|++.+++.+.   ..++..++..+.|++++||+.+|+.|
T Consensus       155 ~~~~vI~ttn~~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~~a  234 (285)
T 3h4m_A          155 GDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEA  234 (285)
T ss_dssp             SSEEEEEECSCGGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCchhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            899999999999999999999  9999999999999999999999887643   23688999999999999999999999


Q ss_pred             HHHHHHH
Q 047219          505 ERSWASK  511 (567)
Q Consensus       505 ~~~a~~r  511 (567)
                      ...+..+
T Consensus       235 ~~~a~~~  241 (285)
T 3h4m_A          235 GMNAIRE  241 (285)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            8776553

>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=99.96  E-value=8.5e-29  Score=269.12  Aligned_cols=221  Identities=29%  Similarity=0.519  Sum_probs=191.5

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .+.++|++|+|++++++++++.+. .+.+|+.|+.++        ...|+++||+||||||||++|+++|+++      +
T Consensus        10 ~~~~~f~di~G~~~~~~~l~e~v~-~l~~~~~~~~~g--------~~~p~gvLL~GppGtGKT~Laraia~~~------~   74 (476)
T 2ce7_A           10 NKRVTFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIG--------ARMPKGILLVGPPGTGKTLLARAVAGEA------N   74 (476)
T ss_dssp             SCCCCGGGCCSCHHHHHHHHHHHH-HHHCTHHHHTTT--------CCCCSEEEEECCTTSSHHHHHHHHHHHH------T
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHH-HhhChHHHhhcC--------CCCCCeEEEECCCCCCHHHHHHHHHHHc------C
Confidence            567899999999999999999875 478888898776        6788999999999999999999999999      7


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccCC
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      .+|+.++++++...++|.....++.+|..+...+ ++||||||||.+..+++..   ......+++++|+..++++....
T Consensus        75 ~~f~~is~~~~~~~~~g~~~~~~r~lf~~A~~~~-p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~  153 (476)
T 2ce7_A           75 VPFFHISGSDFVELFVGVGAARVRDLFAQAKAHA-PCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKE  153 (476)
T ss_dssp             CCEEEEEGGGTTTCCTTHHHHHHHHHHHHHHHTC-SEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGG
T ss_pred             CCeeeCCHHHHHHHHhcccHHHHHHHHHHHHhcC-CCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCC
Confidence            8899999999999999999999999999998876 4999999999998877643   22234567889999999877778


Q ss_pred             cEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      +++||++||+++.+++++++  ||+..+.++.|+.++|.+|++.+++...   ..++..++..+.|++++||.++|++|.
T Consensus       154 ~viVIaaTn~~~~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~~Aa  233 (476)
T 2ce7_A          154 GIIVMAATNRPDILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAA  233 (476)
T ss_dssp             TEEEEEEESCGGGSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             CEEEEEecCChhhhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            99999999999999999998  9999999999999999999999887643   225778999999999999999999998


Q ss_pred             HHHHH
Q 047219          506 RSWAS  510 (567)
Q Consensus       506 ~~a~~  510 (567)
                      ..+.+
T Consensus       234 l~A~~  238 (476)
T 2ce7_A          234 LLAAR  238 (476)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76653

>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=99.96  E-value=1.4e-28  Score=245.32  Aligned_cols=220  Identities=30%  Similarity=0.489  Sum_probs=173.8

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +.++|++|+|++++++.+++.+.. +.+++.|..++        ...+.++||+||||||||++|+++|+++      +.
T Consensus         1 ~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~g--------~~~~~~vll~G~~GtGKT~la~~la~~~------~~   65 (262)
T 2qz4_A            1 MGVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLG--------AKVPKGALLLGPPGCGKTLLAKAVATEA------QV   65 (262)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHHH-HHCCC--------------CCCCCEEEEESCTTSSHHHHHHHHHHHH------TC
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHH-HHCHHHHHHcC--------CCCCceEEEECCCCCCHHHHHHHHHHHh------CC
Confidence            458899999999999999998765 78888887765        6788999999999999999999999999      77


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhh----HHHHHHHHHHHHHhhcCcccCC
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEM----HEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l----~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +++.+++..+.+.+.|.....+..+|..+.... +++|||||+|.+..++....    ....+..+..++..+++.....
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~-~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~  144 (262)
T 2qz4_A           66 PFLAMAGAEFVEVIGGLGAARVRSLFKEARARA-PCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTD  144 (262)
T ss_dssp             CEEEEETTTTSSSSTTHHHHHHHHHHHHHHHTC-SEEEEEECC-------------------CHHHHHHHHHHHTCCTTC
T ss_pred             CEEEechHHHHhhccChhHHHHHHHHHHHHhcC-CeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCC
Confidence            899999999988888888888999999988765 59999999999977654322    2223456677888888776677


Q ss_pred             cEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC----HH-HHHHHHHhccCCCHHHHHHHHHH
Q 047219          431 KVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT----KA-ELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       431 ~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~----~~-~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      ++++|++||.++.+++++++  ||+..++++.|+.++|.++++.++..+.    .. ....++..+.|+++++|+.+|+.
T Consensus       145 ~~~vi~~tn~~~~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~~  224 (262)
T 2qz4_A          145 HVIVLASTNRADILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNE  224 (262)
T ss_dssp             CEEEEEEESCGGGGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             CEEEEecCCChhhcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHHH
Confidence            99999999999999999999  9999999999999999999999887642    22 45789999999999999999999


Q ss_pred             HHHHHHH
Q 047219          504 AERSWAS  510 (567)
Q Consensus       504 a~~~a~~  510 (567)
                      |+..+..
T Consensus       225 a~~~a~~  231 (262)
T 2qz4_A          225 AALHAAR  231 (262)
T ss_dssp             HHTC---
T ss_pred             HHHHHHH
Confidence            8866544

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.96  E-value=2.4e-28  Score=244.39  Aligned_cols=222  Identities=32%  Similarity=0.563  Sum_probs=186.9

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+..+|++|+|++++++.+.+.+.. +.+++.|+.++        ...+++++|+||||||||++|+++|+++      
T Consensus         5 ~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~--------~~~~~~vll~G~~GtGKT~la~~la~~~------   69 (257)
T 1lv7_A            5 DQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQKLG--------GKIPKGVLMVGPPGTGKTLLAKAIAGEA------   69 (257)
T ss_dssp             CSSCCCGGGSCSCHHHHHHTHHHHHH-HHCGGGC-------------CCCCEEEEECCTTSCHHHHHHHHHHHH------
T ss_pred             cCCCCCHHHhcCcHHHHHHHHHHHHH-HhCHHHHHHcC--------CCCCCeEEEECcCCCCHHHHHHHHHHHc------
Confidence            45678999999999999999998754 77888877665        5778899999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhh---HHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l---~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+++..+...+.|.....++.+|+.+.... ++++||||+|.+...++..+   .....+.++.++..++++..+
T Consensus        70 ~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~a~~~~-~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~  148 (257)
T 1lv7_A           70 KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAA-PCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGN  148 (257)
T ss_dssp             TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTTC-SEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSS
T ss_pred             CCCEEEEeHHHHHHHhhhhhHHHHHHHHHHHHHcC-CeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccC
Confidence            66799999999988889998899999999988665 48999999999988765432   122345678888889888777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||++||.++.+++++++  ||+..++++.|+.++|.+|++.+++.+.   ...+..++..+.||+++||..+|+.|
T Consensus       149 ~~~~vI~~tn~~~~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~~a  228 (257)
T 1lv7_A          149 EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEA  228 (257)
T ss_dssp             SCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CCEEEEEeeCCchhCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHHHH
Confidence            899999999999999999998  9999999999999999999999887643   23467788999999999999999999


Q ss_pred             HHHHHH
Q 047219          505 ERSWAS  510 (567)
Q Consensus       505 ~~~a~~  510 (567)
                      ...+..
T Consensus       229 ~~~a~~  234 (257)
T 1lv7_A          229 ALFAAR  234 (257)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876654

>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=99.94  E-value=5.6e-26  Score=226.76  Aligned_cols=222  Identities=32%  Similarity=0.546  Sum_probs=184.3

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++++|+++++.++++.+.. +.++..++.++        ...+++++|+||||||||++++++++.+      
T Consensus         9 ~~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~~~~~~--------~~~~~g~ll~G~~G~GKTtl~~~i~~~~------   73 (254)
T 1ixz_A            9 EAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMG--------ARIPKGVLLVGPPGVGKTHLARAVAGEA------   73 (254)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTT--------CCCCSEEEEECCTTSSHHHHHHHHHHHT------
T ss_pred             CCCCCCHHHhCCcHHHHHHHHHHHHH-HHCHHHHHHcC--------CCCCCeEEEECCCCCCHHHHHHHHHHHh------
Confidence            45779999999999999999987754 56777777665        5677889999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+++..+...+.+.....++.+|+.+.... ++++|+||||.+...+...   ......+.++.++..+++....
T Consensus        74 ~~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~  152 (254)
T 1ixz_A           74 RVPFITASGSDFVEMFVGVGAARVRDLFETAKRHA-PCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  152 (254)
T ss_dssp             TCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSS-SEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTT
T ss_pred             CCCEEEeeHHHHHHHHhhHHHHHHHHHHHHHHhcC-CeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCC
Confidence            56789999999888888888888899999887554 4899999999997665421   1223456678888888887777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      ..++++++||.++.+++++++  ||+..++++.|+.++|.+|++.+++.+.   ..++..++..+.|++++||+.+|+.|
T Consensus       153 ~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~~a  232 (254)
T 1ixz_A          153 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  232 (254)
T ss_dssp             CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CCEEEEEccCCchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            789999999999999999998  8999999999999999999998887643   22578899999999999999999998


Q ss_pred             HHHHHH
Q 047219          505 ERSWAS  510 (567)
Q Consensus       505 ~~~a~~  510 (567)
                      ...+..
T Consensus       233 ~~~a~~  238 (254)
T 1ixz_A          233 ALLAAR  238 (254)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876543

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.94  E-value=6.4e-27  Score=255.73  Aligned_cols=219  Identities=32%  Similarity=0.547  Sum_probs=188.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +.++|++|+|++++++++++.+. .+.+++.|+.++        ...++++||+||||||||+||++||.++      +.
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~-~l~~~~~~~~lg--------~~ip~GvLL~GppGtGKTtLaraIa~~~------~~   90 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMG--------ARIPKGVLLVGPPGVGKTHLARAVAGEA------RV   90 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHH-HHHCGGGTTTTS--------CCCCSEEEEECSSSSSHHHHHHHHHHHT------TC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHH-Hhhchhhhhhcc--------CCCCceEEEECCCCCCHHHHHHHHHHHh------CC
Confidence            67899999999999999999875 467788777665        6778899999999999999999999998      67


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccCCc
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ++++++++++...+.|.....++.+|+.+.... ++++||||||.+...++..   ......+.+++++..+++......
T Consensus        91 ~~i~i~g~~~~~~~~g~~~~~v~~lfq~a~~~~-p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~  169 (499)
T 2dhr_A           91 PFITASGSDFVEMFVGVGAARVRDLFETAKRHA-PCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTA  169 (499)
T ss_dssp             CEEEEEGGGGTSSCTTHHHHHHHHHTTTSSSSS-SCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCC
T ss_pred             CEEEEehhHHHHhhhhhHHHHHHHHHHHHHhcC-CCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCcc
Confidence            899999999998888988888999999887655 4999999999998766531   123445678899999998887788


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +++|++||+++.+|++|++  ||+..+.|+.|+.++|.+|++.+++.+.   ..++..++..+.|++++||+++|++|..
T Consensus       170 viviAatn~p~~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~Aa~  249 (499)
T 2dhr_A          170 IVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAAL  249 (499)
T ss_dssp             CEEEECCSCGGGSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHHHH
T ss_pred             EEEEEecCChhhcCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            9999999999999999998  8999999999999999999998876542   2357889999999999999999999886


Q ss_pred             HHH
Q 047219          507 SWA  509 (567)
Q Consensus       507 ~a~  509 (567)
                      .+.
T Consensus       250 ~A~  252 (499)
T 2dhr_A          250 LAA  252 (499)
T ss_dssp             HHT
T ss_pred             HHH
Confidence            554

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.93  E-value=1.3e-24  Score=220.32  Aligned_cols=222  Identities=32%  Similarity=0.546  Sum_probs=183.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++++++.+.. +..+..++.++        ...+++++|+||||||||+++++|+..+      
T Consensus        33 ~~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~l~~~~--------~~~~~gvll~Gp~GtGKTtl~~~i~~~~------   97 (278)
T 1iy2_A           33 EAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMG--------ARIPKGVLLVGPPGVGKTHLARAVAGEA------   97 (278)
T ss_dssp             CCCCCCGGGSSSCHHHHHHHHHHHHH-HHCHHHHHHTT--------CCCCCEEEEECCTTSSHHHHHHHHHHHT------
T ss_pred             CCCCCCHHHhCChHHHHHHHHHHHHH-HHCHHHHHHcC--------CCCCCeEEEECCCcChHHHHHHHHHHHc------
Confidence            34779999999999999999987754 56677777664        5667789999999999999999999998      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      ...++.+++..+...+.+.....+..+|+.+.... ++++|+||||.+...+...   ......+.+..++..+++....
T Consensus        98 ~~~~i~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~  176 (278)
T 1iy2_A           98 RVPFITASGSDFVEMFVGVGAARVRDLFETAKRHA-PCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  176 (278)
T ss_dssp             TCCEEEEEHHHHHHSTTTHHHHHHHHHHHHHHTSC-SEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTT
T ss_pred             CCCEEEecHHHHHHHHhhHHHHHHHHHHHHHHhcC-CcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCC
Confidence            56789999998888888888888889999887555 4899999999987654321   1223456677888888887777


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      ..++++++||.++.+++++++  ||+..++|+.|+.++|.+|++.+++.+.   ...+..++..+.|++++||+.+|+.|
T Consensus       177 ~~~i~~a~t~~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a  256 (278)
T 1iy2_A          177 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  256 (278)
T ss_dssp             CCEEEEEEESCTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CCEEEEEecCCchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            789999999999999999998  8999999999999999999998887642   23578899999999999999999998


Q ss_pred             HHHHHH
Q 047219          505 ERSWAS  510 (567)
Q Consensus       505 ~~~a~~  510 (567)
                      ...+..
T Consensus       257 ~~~a~~  262 (278)
T 1iy2_A          257 ALLAAR  262 (278)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            865543

>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=99.93  E-value=1.9e-27  Score=238.86  Aligned_cols=220  Identities=31%  Similarity=0.540  Sum_probs=177.2

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.++|++|+|++++++.+++.+.. +.+++.|..++        ...++++||+||||||||++|+++|+++      
T Consensus         4 ~~~~~~~~~i~G~~~~~~~l~~~~~~-~~~~~~~~~~~--------~~~~~~vll~G~~GtGKT~la~~la~~~------   68 (268)
T 2r62_A            4 EKPNVRFKDMAGNEEAKEEVVEIVDF-LKYPERYANLG--------AKIPKGVLLVGPPGTGKTLLAKAVAGEA------   68 (268)
T ss_dssp             CCCCCCSTTSSSCTTTHHHHHHHHHH-HHCHHHHHHHS--------CCCCSCCCCBCSSCSSHHHHHHHHHHHH------
T ss_pred             cCCCCCHHHhCCcHHHHHHHHHHHHH-HHChHHHHHCC--------CCCCceEEEECCCCCcHHHHHHHHHHHh------
Confidence            45678999999999999999998764 78999998876        6778899999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhH----HHHHHHHHHHHHhhcCccc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMH----EATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~----~~~~~vl~~LL~~ld~~~~  428 (567)
                      +.+++.+++..+.+.+.|.....++.+|..+.... +++|||||+|.|...++....    ....+.++.|+..+++...
T Consensus        69 ~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~a~~~~-~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~  147 (268)
T 2r62_A           69 HVPFFSMGGSSFIEMFVGLGASRVRDLFETAKKQA-PSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGS  147 (268)
T ss_dssp             TCCCCCCCSCTTTTSCSSSCSSSSSTTHHHHHHSC-SCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSC
T ss_pred             CCCEEEechHHHHHhhcchHHHHHHHHHHHHHhcC-CeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCccc
Confidence            66788888888888888877767777888887765 499999999999876432110    0011234566777766543


Q ss_pred             -CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHH
Q 047219          429 -DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       429 -~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                       ..+++||+|||.++.+++++++  ||+..++++.|+.++|.++++.+++.+.   ...+..++..+.|++++||+.+|+
T Consensus       148 ~~~~v~vi~ttn~~~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~  227 (268)
T 2r62_A          148 ENAPVIVLAATNRPEILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIIN  227 (268)
T ss_dssp             SCSCCEEEECBSCCTTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHH
T ss_pred             CCCCEEEEEecCCchhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHH
Confidence             3469999999999999999999  9999999999999999999998887642   224677888899999999999999


Q ss_pred             HHHHHH
Q 047219          503 QAERSW  508 (567)
Q Consensus       503 ~a~~~a  508 (567)
                      .|...+
T Consensus       228 ~a~~~a  233 (268)
T 2r62_A          228 EAALLA  233 (268)
T ss_dssp             HHHHTT
T ss_pred             HHHHHH
Confidence            987644

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.87  E-value=1.6e-21  Score=199.25  Aligned_cols=221  Identities=22%  Similarity=0.293  Sum_probs=171.7

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcCeEE
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVPLMY  358 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~~~~  358 (567)
                      .+|+|++++++.|.+.+..+. .+..++..|..     ...++.++||+||||||||++|+++++.+... .....++++
T Consensus        31 ~~i~G~~~~~~~l~~~~~~~~-~~~~~~~~g~~-----~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~  104 (309)
T 3syl_A           31 RELIGLKPVKDRIRETAALLL-VERARQKLGLA-----HETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVS  104 (309)
T ss_dssp             HHSSSCHHHHHHHHHHHHHHH-HHHHHHHHTCC-----SSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEE
T ss_pred             HHccChHHHHHHHHHHHHHHH-hHHHHHHcCCC-----CCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEE
Confidence            379999999999999887654 35666655422     13556789999999999999999999988433 222457999


Q ss_pred             echhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEee
Q 047219          359 VPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT  438 (567)
Q Consensus       359 i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaT  438 (567)
                      +++..+.+.++|.....+..+|..+.    +++|||||+|.|...++...  ...+.++.|+..++.  ...++++|++|
T Consensus       105 ~~~~~l~~~~~g~~~~~~~~~~~~~~----~~vl~iDEid~l~~~~~~~~--~~~~~~~~Ll~~l~~--~~~~~~~i~~~  176 (309)
T 3syl_A          105 VTRDDLVGQYIGHTAPKTKEVLKRAM----GGVLFIDEAYYLYRPDNERD--YGQEAIEILLQVMEN--NRDDLVVILAG  176 (309)
T ss_dssp             ECGGGTCCSSTTCHHHHHHHHHHHHT----TSEEEEETGGGSCCCC---C--CTHHHHHHHHHHHHH--CTTTCEEEEEE
T ss_pred             EcHHHhhhhcccccHHHHHHHHHhcC----CCEEEEEChhhhccCCCccc--ccHHHHHHHHHHHhc--CCCCEEEEEeC
Confidence            99999999999998888888888774    68999999999975543211  123455677777774  34678999999


Q ss_pred             CCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHh-------ccCCCHHHHHHHHH
Q 047219          439 NRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATA-------TEEMSGRDIRDVCQ  502 (567)
Q Consensus       439 N~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~-------t~g~s~~dL~~L~~  502 (567)
                      |...     .++++|++||+..++|+.|+.+++.+|++.++..    +..+.+..++..       .+..+.+++++++.
T Consensus       177 ~~~~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l~  256 (309)
T 3syl_A          177 YADRMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEAETALRAYIGLRRNQPHFANARSIRNALD  256 (309)
T ss_dssp             CHHHHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHHH
T ss_pred             ChHHHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Confidence            8643     3579999999999999999999999999998874    456666766665       34456899999999


Q ss_pred             HHHHHHHHHHHh
Q 047219          503 QAERSWASKIIR  514 (567)
Q Consensus       503 ~a~~~a~~r~i~  514 (567)
                      .+...+..+++.
T Consensus       257 ~a~~~~~~r~~~  268 (309)
T 3syl_A          257 RARLRQANRLFT  268 (309)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999888888775

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.87  E-value=7.9e-23  Score=210.50  Aligned_cols=245  Identities=18%  Similarity=0.223  Sum_probs=159.4

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC--CCCCcCeE
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM--PWQGVPLM  357 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~--~~~~~~~~  357 (567)
                      ++|+|.+..++.+.+.+...                   ...+.+|||+||||||||++|++||+.+.+.  +|+.++|.
T Consensus         2 ~~iig~s~~~~~~~~~~~~~-------------------a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~   62 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMV-------------------APSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCA   62 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHH-------------------CSTTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECS
T ss_pred             CCcEECCHHHHHHHHHHHHH-------------------hCCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCC
Confidence            46899999999999988765                   4567899999999999999999999988643  33333333


Q ss_pred             EechhhHHhhhhchhHH-------HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc----
Q 047219          358 YVPLEVVMSKYYGESER-------LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF----  426 (567)
Q Consensus       358 ~i~~~~l~s~~~G~~~~-------~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~----  426 (567)
                      .++...+.+.+||+...       .....|..+.    +++|||||||.|....|.           .|+..++..    
T Consensus        63 ~~~~~l~~~~lfg~~~g~~tg~~~~~~g~~~~a~----~g~L~LDEi~~l~~~~q~-----------~Ll~~l~~~~~~~  127 (304)
T 1ojl_A           63 ALNESLLESELFGHEKGAFTGADKRREGRFVEAD----GGTLFLDEIGDISPLMQV-----------RLLRAIQEREVQR  127 (304)
T ss_dssp             SCCHHHHHHHHTCCCSSCCC---CCCCCHHHHHT----TSEEEEESCTTCCHHHHH-----------HHHHHHHSSBCCB
T ss_pred             CCChHHHHHHhcCccccccCchhhhhcCHHHhcC----CCEEEEeccccCCHHHHH-----------HHHHHHhcCEeee
Confidence            33444455566665211       1112344443    689999999999765433           333333322    


Q ss_pred             -----ccCCcEEEEEeeCCC-------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh---------------CH
Q 047219          427 -----EQDKKVVVIAATNRK-------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL---------------TK  479 (567)
Q Consensus       427 -----~~~~~viVIaaTN~~-------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~---------------~~  479 (567)
                           ..+.+++||+|||..       +.|+++|++|| ..+.+..|++++|.+++..+++++               ..
T Consensus       128 ~g~~~~~~~~~riI~atn~~l~~~v~~g~fr~~L~~Rl-~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~  206 (304)
T 1ojl_A          128 VGSNQTISVDVRLIAATHRDLAEEVSAGRFRQDLYYRL-NVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTP  206 (304)
T ss_dssp             TTBCCCCBCCCEEEEEESSCHHHHHHHTSSCHHHHHHH-SSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCH
T ss_pred             cCCcccccCCeEEEEecCccHHHHHHhCCcHHHHHhhc-CeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCH
Confidence                 124579999999974       46899999999 588889999999888776655543               33


Q ss_pred             HHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHhccccccCcccC--------CCcHHH-HHHHHHHHHHHHHHHHHHH
Q 047219          480 AELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQAC--------LPPLQE-YIESATNRRRSLLDAAEQS  550 (567)
Q Consensus       480 ~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~i~~~i~~~~~~~~--------~~~l~e-~le~~e~~~~~li~~al~~  550 (567)
                      +.++.+..+.+..+.++|++++..+...+..    ..++.+.....        ...+.+ .++.+|   +.+|..++.+
T Consensus       207 ~a~~~L~~~~wpGnvReL~~~l~~~~~~~~~----~~i~~~~l~~~~~~~~~~~~~~l~~~~~~~~e---~~~i~~~l~~  279 (304)
T 1ojl_A          207 QAMDLLIHYDWPGNIRELENAIERAVVLLTG----EYISERELPLAIAATPIKTEYSGEIQPLVDVE---KEVILAALEK  279 (304)
T ss_dssp             HHHHHHHHCCCSSHHHHHHHHHHHHHHHCCS----SSBCGGGSCGGGC-------CCSSCCCHHHHH---HHHHHHHHHT
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHHHHHHhCCC----CcccHHhhhhhhccCCCccCCCcchhhHHHHH---HHHHHHHHHH
Confidence            4555555555555555666665555432111    11211110000        001111 344455   8999999999


Q ss_pred             HhhHHhhhhccCCCCC
Q 047219          551 HQNINNHRTKKQPLDL  566 (567)
Q Consensus       551 ~~~~~s~~~~~~~l~~  566 (567)
                      ++++++++++.+++|.
T Consensus       280 ~~gn~~~aA~~Lgi~r  295 (304)
T 1ojl_A          280 TGGNKTEAARQLGITR  295 (304)
T ss_dssp             TTTCHHHHHHHHTSCH
T ss_pred             cCCCHHHHHHHHCcCH
Confidence            9999999999888874

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.87  E-value=6.5e-21  Score=195.08  Aligned_cols=171  Identities=16%  Similarity=0.236  Sum_probs=126.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHH----hcCCCCcEEEE
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA----NELPNGAIIFL  394 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A----~~~a~~~ILfI  394 (567)
                      ...|.++|||||||||||++|++||+++      +.+++.++++.+.+++.|+.+..++.+|..+    +... ++||||
T Consensus        33 ~~~p~~lLl~GppGtGKT~la~aiA~~l------~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~-~~vl~i  105 (293)
T 3t15_A           33 IKVPLILGIWGGKGQGKSFQCELVFRKM------GINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGN-MCCLFI  105 (293)
T ss_dssp             CCCCSEEEEEECTTSCHHHHHHHHHHHH------TCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSS-CCCEEE
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHh------CCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCC-CeEEEE
Confidence            6778999999999999999999999999      7889999999999999999999999999988    3333 699999


Q ss_pred             cCcchhhhhhhhhhH--HHHHHHHHHHHHhhcCcc-----------cCCcEEEEEeeCCCCCCChHHHh--ccceEEEec
Q 047219          395 DEVDSFAVARDSEMH--EATRRILSVLLRQIDGFE-----------QDKKVVVIAATNRKQDLDPALIS--RFDSMITFG  459 (567)
Q Consensus       395 DEID~L~~~~q~~l~--~~~~~vl~~LL~~ld~~~-----------~~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~  459 (567)
                      ||||.+.+.......  ...+++.+.|+..+++..           ...+++||+|||.++.++++|++  ||+..+.  
T Consensus       106 DEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~--  183 (293)
T 3t15_A          106 NDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYW--  183 (293)
T ss_dssp             ECCC--------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEE--
T ss_pred             echhhhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEe--
Confidence            999999875442211  123456678888876332           45689999999999999999997  8977776  


Q ss_pred             CCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHH
Q 047219          460 LPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRD  499 (567)
Q Consensus       460 ~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~  499 (567)
                      .|+.++|.+|++.++.... -..+.++..+.+|++++|..
T Consensus       184 ~P~~~~r~~Il~~~~~~~~-~~~~~l~~~~~~~~~~~l~~  222 (293)
T 3t15_A          184 APTREDRIGVCTGIFRTDN-VPAEDVVKIVDNFPGQSIDF  222 (293)
T ss_dssp             CCCHHHHHHHHHHHHGGGC-CCHHHHHHHHHHSCSCCHHH
T ss_pred             CcCHHHHHHHHHHhccCCC-CCHHHHHHHhCCCCcccHHH
Confidence            5899999999998775421 12556667778888888764

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.82  E-value=8.8e-19  Score=181.51  Aligned_cols=191  Identities=18%  Similarity=0.283  Sum_probs=144.6

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++..++.+...+......                ..++.++||+||||||||++|+++|+.+      +
T Consensus        23 ~~p~~~~~iiG~~~~~~~l~~~l~~~~~~----------------~~~~~~vll~G~~GtGKT~la~~ia~~~------~   80 (338)
T 3pfi_A           23 LRPSNFDGYIGQESIKKNLNVFIAAAKKR----------------NECLDHILFSGPAGLGKTTLANIISYEM------S   80 (338)
T ss_dssp             CCCCSGGGCCSCHHHHHHHHHHHHHHHHT----------------TSCCCCEEEECSTTSSHHHHHHHHHHHT------T
T ss_pred             cCCCCHHHhCChHHHHHHHHHHHHHHHhc----------------CCCCCeEEEECcCCCCHHHHHHHHHHHh------C
Confidence            34458999999999999999988754211                3567789999999999999999999998      6


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc------
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE------  427 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~------  427 (567)
                      .+++.+++..+..      ...+...+.   ..+.+++|||||||.+....+..+           +..++...      
T Consensus        81 ~~~~~~~~~~~~~------~~~~~~~~~---~~~~~~vl~lDEi~~l~~~~~~~L-----------l~~l~~~~~~~~~~  140 (338)
T 3pfi_A           81 ANIKTTAAPMIEK------SGDLAAILT---NLSEGDILFIDEIHRLSPAIEEVL-----------YPAMEDYRLDIIIG  140 (338)
T ss_dssp             CCEEEEEGGGCCS------HHHHHHHHH---TCCTTCEEEEETGGGCCHHHHHHH-----------HHHHHTSCC-----
T ss_pred             CCeEEecchhccc------hhHHHHHHH---hccCCCEEEEechhhcCHHHHHHH-----------HHHHHhccchhhcc
Confidence            6788888875531      122333333   334579999999999975544333           33332211      


Q ss_pred             ----------cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCC
Q 047219          428 ----------QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMS  493 (567)
Q Consensus       428 ----------~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s  493 (567)
                                ...++++|++||....++++|++||+..++|+.|+.+++.+++...+..    +..+.++.++..+ +.+
T Consensus       141 ~~~~~~~~~~~~~~~~~i~atn~~~~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~-~G~  219 (338)
T 3pfi_A          141 SGPAAQTIKIDLPKFTLIGATTRAGMLSNPLRDRFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRS-RST  219 (338)
T ss_dssp             ----CCCCCCCCCCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTT-TTC
T ss_pred             cCccccceecCCCCeEEEEeCCCccccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH-CcC
Confidence                      0125899999999999999999999999999999999999999988875    5677888888854 456


Q ss_pred             HHHHHHHHHHHHHH
Q 047219          494 GRDIRDVCQQAERS  507 (567)
Q Consensus       494 ~~dL~~L~~~a~~~  507 (567)
                      .+.+.+++..++..
T Consensus       220 ~r~l~~~l~~~~~~  233 (338)
T 3pfi_A          220 PRIALRLLKRVRDF  233 (338)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            78888888877543

>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=99.81  E-value=1e-18  Score=179.42  Aligned_cols=189  Identities=20%  Similarity=0.310  Sum_probs=141.1

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      .+.+|++++|.+..++.+.+.+......                ...+.++||+||||||||++|+++|+.+      +.
T Consensus         7 ~p~~~~~~ig~~~~~~~l~~~l~~~~~~----------------~~~~~~vll~G~~GtGKT~la~~i~~~~------~~   64 (324)
T 1hqc_A            7 RPKTLDEYIGQERLKQKLRVYLEAAKAR----------------KEPLEHLLLFGPPGLGKTTLAHVIAHEL------GV   64 (324)
T ss_dssp             CCCSTTTCCSCHHHHHHHHHHHHHHHHH----------------CSCCCCCEEECCTTCCCHHHHHHHHHHH------TC
T ss_pred             CcccHHHhhCHHHHHHHHHHHHHHHHcc----------------CCCCCcEEEECCCCCCHHHHHHHHHHHh------CC
Confidence            4458999999999999999887643110                3456899999999999999999999999      66


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-------
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-------  427 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-------  427 (567)
                      +++.+++..+..      ...+...|..  ..+.+++|||||||.+....+..+           +..++...       
T Consensus        65 ~~~~~~~~~~~~------~~~l~~~l~~--~~~~~~~l~lDEi~~l~~~~~~~L-----------~~~l~~~~~~~v~~~  125 (324)
T 1hqc_A           65 NLRVTSGPAIEK------PGDLAAILAN--SLEEGDILFIDEIHRLSRQAEEHL-----------YPAMEDFVMDIVIGQ  125 (324)
T ss_dssp             CEEEECTTTCCS------HHHHHHHHTT--TCCTTCEEEETTTTSCCHHHHHHH-----------HHHHHHSEEEECCSS
T ss_pred             CEEEEeccccCC------hHHHHHHHHH--hccCCCEEEEECCcccccchHHHH-----------HHHHHhhhhHHhccc
Confidence            788888765532      1122222222  134579999999999975543332           22222211       


Q ss_pred             ---------cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCH
Q 047219          428 ---------QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSG  494 (567)
Q Consensus       428 ---------~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~  494 (567)
                               ...++++|++||.++.++++|++||+..+.++.|+.+++.+++..++..    +..+.++.++..+.| ++
T Consensus       126 ~~~~~~~~~~~~~~~~i~~t~~~~~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~  204 (324)
T 1hqc_A          126 GPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TM  204 (324)
T ss_dssp             SSSCCCEEEECCCCEEEEEESCCSSCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHSCS-CH
T ss_pred             cccccccccCCCCEEEEEeCCCcccCCHHHHhcccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHccC-CH
Confidence                     1136899999999999999999999889999999999999999988764    567788888888755 67


Q ss_pred             HHHHHHHHHHH
Q 047219          495 RDIRDVCQQAE  505 (567)
Q Consensus       495 ~dL~~L~~~a~  505 (567)
                      +.+..++..++
T Consensus       205 r~l~~~l~~~~  215 (324)
T 1hqc_A          205 RVAKRLFRRVR  215 (324)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHH
Confidence            88888887765

>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=99.80  E-value=1.4e-21  Score=212.08  Aligned_cols=203  Identities=21%  Similarity=0.243  Sum_probs=135.8

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+...|++|+|++++++.+.+.+.... .               +..+++++||+||||||||++|+++|++++.    
T Consensus        30 ~~~~~~~~~iiG~~~~~~~l~~~~~~~~-~---------------~~~~~~~iLl~GppGtGKT~la~ala~~l~~----   89 (456)
T 2c9o_A           30 GLAKQAASGLVGQENAREACGVIVELIK-S---------------KKMAGRAVLLAGPPGTGKTALALAIAQELGS----   89 (456)
T ss_dssp             SCBCSEETTEESCHHHHHHHHHHHHHHH-T---------------TCCTTCEEEEECCTTSSHHHHHHHHHHHHCT----
T ss_pred             cChhhchhhccCHHHHHHHHHHHHHHHH-h---------------CCCCCCeEEEECCCcCCHHHHHHHHHHHhCC----
Confidence            4566789999999999999988775431 1               1456789999999999999999999999943    


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHH---hcCCCCcEEEEcCcchhhhhhhhhhHHHH----HH-----------
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLA---NELPNGAIIFLDEVDSFAVARDSEMHEAT----RR-----------  414 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A---~~~a~~~ILfIDEID~L~~~~q~~l~~~~----~~-----------  414 (567)
                      ..+|+.++++++.++++|+++. +...|..+   +... +++|||||||.+.+++........    .+           
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~-~~~~f~~a~~~~~~~-~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~  167 (456)
T 2c9o_A           90 KVPFCPMVGSEVYSTEIKKTEV-LMENFRRAIGLRIKE-TKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGT  167 (456)
T ss_dssp             TSCEEEEEGGGGCCSSSCHHHH-HHHHHHHTEEEEEEE-EEEEEEEEEEEEEEC--------------CEEEEEEETTEE
T ss_pred             CceEEEEeHHHHHHHhhhhhHH-HHHHHHHHHhhhhcC-CcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccc
Confidence            2789999999999999999987 89999998   5454 599999999999988755421111    00           


Q ss_pred             ----HHHHHHHhhc--CcccCCcEEEEEeeCCCCCCChHHHh--ccce--EEEecCC--CHHHHHHHHHHHHHhhCHHHH
Q 047219          415 ----ILSVLLRQID--GFEQDKKVVVIAATNRKQDLDPALIS--RFDS--MITFGLP--DHENRQEIAAQYAKHLTKAEL  482 (567)
Q Consensus       415 ----vl~~LL~~ld--~~~~~~~viVIaaTN~~~~Ld~aL~s--Rf~~--~I~i~~P--~~~eR~eIL~~~~~~~~~~~l  482 (567)
                          +...++..++  +......++|++|||+++.+++++++  ||+.  .+.++.|  +.++|.+|++.++    ..++
T Consensus       168 ~~~~~~~~ll~~l~~~~~~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~----~~dl  243 (456)
T 2c9o_A          168 KQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVT----LHDL  243 (456)
T ss_dssp             EEEEECHHHHHHHHHTTCCTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEE----HHHH
T ss_pred             hhHhhhHHHHHHHhhccCCCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHH----HHHH
Confidence                1112333333  22233335555888999999999976  9988  5667777  4577888776443    3478


Q ss_pred             HHHHHhccCCCHHHHHHHHHH
Q 047219          483 AELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       483 ~~la~~t~g~s~~dL~~L~~~  503 (567)
                      +.++..+.|  ++|+.++|..
T Consensus       244 ~~~a~~t~g--gadl~~l~~~  262 (456)
T 2c9o_A          244 DVANARPQG--GQDILSMMGQ  262 (456)
T ss_dssp             HHTC-----------------
T ss_pred             HHHHHhCCC--hhHHHHHHhh
Confidence            888888888  9999999854

>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=99.80  E-value=6.9e-19  Score=179.03  Aligned_cols=216  Identities=20%  Similarity=0.350  Sum_probs=148.8

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++|+|++++++.+...+..+..++.+...+.       ....+.++||+||||||||++|+++|+.+      +.+++.+
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~-------~~~~~~~vll~G~~GtGKT~la~~la~~l------~~~~~~i   81 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLR-------HEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKV   81 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHH-------HHCCCCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEE
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhccccc-------ccCCCceEEEECCCCCCHHHHHHHHHHHh------CCCEEEE
Confidence            4699999999999998876544443332221       13467899999999999999999999999      6679999


Q ss_pred             chhhHHh-hhhchh-HHHHHHHHHHHh----cCCCCcEEEEcCcchhhhhhhhhhHHHH-HHHHHHHHHhhcCcc-----
Q 047219          360 PLEVVMS-KYYGES-ERLLGKVFSLAN----ELPNGAIIFLDEVDSFAVARDSEMHEAT-RRILSVLLRQIDGFE-----  427 (567)
Q Consensus       360 ~~~~l~s-~~~G~~-~~~l~~~f~~A~----~~a~~~ILfIDEID~L~~~~q~~l~~~~-~~vl~~LL~~ld~~~-----  427 (567)
                      ++..+.. .++|.. ...+..++..+.    ...+++||||||+|.+....+....... ..+.+.|+..+++..     
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~  161 (310)
T 1ofh_A           82 EATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKH  161 (310)
T ss_dssp             EGGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETT
T ss_pred             cchhcccCCccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEeccc
Confidence            9988765 455542 234555554220    0012589999999999876532222222 234567777777532     


Q ss_pred             ---cCCcEEEEEee----CCCCCCChHHHhccceEEEecCCCHHHHHHHHHH----HHH-------------hhCHHHHH
Q 047219          428 ---QDKKVVVIAAT----NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQ----YAK-------------HLTKAELA  483 (567)
Q Consensus       428 ---~~~~viVIaaT----N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~----~~~-------------~~~~~~l~  483 (567)
                         ...++++|+++    +.+..++++|++||+..++|+.|+.+++.+|++.    +..             .+..+.++
T Consensus       162 ~~~~~~~~~~i~~~~~~~~~~~~l~~~l~~R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~  241 (310)
T 1ofh_A          162 GMVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVK  241 (310)
T ss_dssp             EEEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHH
T ss_pred             ccccCCcEEEEEcCCcccCCcccCCHHHHhhCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHH
Confidence               23578889885    5677899999999988899999999999999983    111             14455566


Q ss_pred             HHHHhcc-------CCCHHHHHHHHHHHHHHH
Q 047219          484 ELATATE-------EMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       484 ~la~~t~-------g~s~~dL~~L~~~a~~~a  508 (567)
                      .++...+       +.+.+.+..++..+...+
T Consensus       242 ~l~~~~~~~~~~~~~g~~R~l~~~l~~~~~~~  273 (310)
T 1ofh_A          242 KIAEAAFRVNEKTENIGARRLHTVMERLMDKI  273 (310)
T ss_dssp             HHHHHHHHHHHHSCCCTTHHHHHHHHHHSHHH
T ss_pred             HHHHHhhhhcccccccCcHHHHHHHHHHHHhh
Confidence            6666553       355666666666655443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.79  E-value=3.3e-18  Score=178.91  Aligned_cols=203  Identities=18%  Similarity=0.213  Sum_probs=142.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..|..+|++++|++.+++.+...+... ..               +..+++++||+||||||||++|+++++.+..    
T Consensus        37 ~~p~~~~~~ivG~~~~~~~l~~l~~~~-~~---------------~~~~~~~vLl~GppGtGKT~la~~la~~l~~----   96 (368)
T 3uk6_A           37 LEPRQASQGMVGQLAARRAAGVVLEMI-RE---------------GKIAGRAVLIAGQPGTGKTAIAMGMAQALGP----   96 (368)
T ss_dssp             SCBCSEETTEESCHHHHHHHHHHHHHH-HT---------------TCCTTCEEEEEESTTSSHHHHHHHHHHHHCS----
T ss_pred             cCcCcchhhccChHHHHHHHHHHHHHH-Hc---------------CCCCCCEEEEECCCCCCHHHHHHHHHHHhcc----
Confidence            345567999999999998876655332 11               1344689999999999999999999999954    


Q ss_pred             CcCeEEechhhHHhhhhc-------------------------------------------------hhHHHHHHHHHHH
Q 047219          353 GVPLMYVPLEVVMSKYYG-------------------------------------------------ESERLLGKVFSLA  383 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G-------------------------------------------------~~~~~l~~~f~~A  383 (567)
                      ..+++.+++..+.+.+.+                                                 +....++..+..+
T Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~  176 (368)
T 3uk6_A           97 DTPFTAIAGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAK  176 (368)
T ss_dssp             SCCEEEEEGGGGSCSSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHH
T ss_pred             cCCcccccchhhhhcccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHH
Confidence            345666665443222211                                                 1122334444333


Q ss_pred             hc----CC----CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEee-----------CCCCCC
Q 047219          384 NE----LP----NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT-----------NRKQDL  444 (567)
Q Consensus       384 ~~----~a----~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaT-----------N~~~~L  444 (567)
                      ..    ..    .++||||||+|.|...           .++.|++.++..  ...++++++.           |.+..+
T Consensus       177 ~~~~~~~g~~~~~~~vl~IDEi~~l~~~-----------~~~~L~~~le~~--~~~~~ii~t~~~~~~i~~t~~~~~~~l  243 (368)
T 3uk6_A          177 VAEWREEGKAEIIPGVLFIDEVHMLDIE-----------SFSFLNRALESD--MAPVLIMATNRGITRIRGTSYQSPHGI  243 (368)
T ss_dssp             HHHHHHHTC---CBCEEEEESGGGSBHH-----------HHHHHHHHTTCT--TCCEEEEEESCSEEECBTSSCEEETTC
T ss_pred             HHHhhhhccccccCceEEEhhccccChH-----------HHHHHHHHhhCc--CCCeeeeecccceeeeeccCCCCcccC
Confidence            21    11    1379999999999633           345566666543  2345554443           347789


Q ss_pred             ChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHHHH
Q 047219          445 DPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAERSWA  509 (567)
Q Consensus       445 d~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~  509 (567)
                      +++|++|| ..+.|+.|+.+++.++++..+..    +..+.++.++..+.+.+++++..++..+...+.
T Consensus       244 ~~~l~sR~-~~i~~~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~a~~~A~  311 (368)
T 3uk6_A          244 PIDLLDRL-LIVSTTPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITAASLVCR  311 (368)
T ss_dssp             CHHHHTTE-EEEEECCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHH
T ss_pred             CHHHHhhc-cEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence            99999999 55899999999999999988875    677889999999886789999999998876543

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.79  E-value=1e-18  Score=178.39  Aligned_cols=208  Identities=22%  Similarity=0.274  Sum_probs=144.2

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++++|++.+++.+...+......-      .      ....+..++||+||||||||++|+++|+.+...   +.+++.+
T Consensus        17 ~~i~G~~~~~~~l~~~i~~~~~~~------~------~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~---~~~~~~~   81 (311)
T 4fcw_A           17 KRVVGQDEAIRAVADAIRRARAGL------K------DPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRI   81 (311)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTC------S------CTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC---GGGEEEE
T ss_pred             hhcCCHHHHHHHHHHHHHHHhcCC------C------CCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC---CcceEEe
Confidence            468999999999999887541110      0      002344689999999999999999999998543   4567888


Q ss_pred             chhhHH-----hhhhchhHH----HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc---
Q 047219          360 PLEVVM-----SKYYGESER----LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE---  427 (567)
Q Consensus       360 ~~~~l~-----s~~~G~~~~----~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~---  427 (567)
                      ++..+.     ..++|....    .....+..+....++++|||||+|.+....+           +.|+..++...   
T Consensus        82 ~~~~~~~~~~~~~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~~~~-----------~~Ll~~le~~~~~~  150 (311)
T 4fcw_A           82 DMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAHPDVF-----------NILLQMLDDGRLTD  150 (311)
T ss_dssp             EGGGCCSTTHHHHHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSCHHHH-----------HHHHHHHHHSEEEC
T ss_pred             ecccccccccHHHhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhcCHHHH-----------HHHHHHHhcCEEEc
Confidence            876543     233322100    0001222333334479999999999975433           34444443221   


Q ss_pred             ------cCCcEEEEEeeCC--------------------------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          428 ------QDKKVVVIAATNR--------------------------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       428 ------~~~~viVIaaTN~--------------------------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                            .-.++++|+|||.                          .+.++++|++||+..+.+.+|+.+++.+|+..+++
T Consensus       151 ~~~~~~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R~~~~~~~~p~~~~~~~~i~~~~l~  230 (311)
T 4fcw_A          151 SHGRTVDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQMS  230 (311)
T ss_dssp             TTSCEEECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHTH
T ss_pred             CCCCEEECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhcCCeEEEeCCCCHHHHHHHHHHHHH
Confidence                  1137789999998                          55799999999999999999999999999998765


Q ss_pred             h-------------hCHHHHHHHHHhcc--CCCHHHHHHHHHHHHHHHHHHHH
Q 047219          476 H-------------LTKAELAELATATE--EMSGRDIRDVCQQAERSWASKII  513 (567)
Q Consensus       476 ~-------------~~~~~l~~la~~t~--g~s~~dL~~L~~~a~~~a~~r~i  513 (567)
                      .             +..+.++.++...+  ..+.++|++++..+...+..+.+
T Consensus       231 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~gn~R~L~~~i~~~~~~~~~~~i  283 (311)
T 4fcw_A          231 YLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKI  283 (311)
T ss_dssp             HHHHHHHTTTCEEEECHHHHHHHHHHSCBTTTBTTTHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHhCCcEEEeCHHHHHHHHHhCCCccCCchhHHHHHHHHHHHHHHHHH
Confidence            4             45567788888776  67888899999888876555544

>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=99.78  E-value=2.2e-19  Score=180.01  Aligned_cols=191  Identities=19%  Similarity=0.233  Sum_probs=121.5

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      .+|++++|.+..++.+.+.+...                   ...+.++||+||||||||++|+++|+.+...   +.++
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~-------------------~~~~~~vll~G~~GtGKt~la~~i~~~~~~~---~~~~   60 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHL-------------------APLDKPVLIIGERGTGKELIASRLHYLSSRW---QGPF   60 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHH-------------------TTSCSCEEEECCTTSCHHHHHHHHHHTSTTT---TSCE
T ss_pred             cccccceeCCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCCcHHHHHHHHHHhcCcc---CCCe
Confidence            57899999999999999888754                   3456799999999999999999999998643   4678


Q ss_pred             EEechhhH-----HhhhhchhHHHHH-------HHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhc
Q 047219          357 MYVPLEVV-----MSKYYGESERLLG-------KVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQID  424 (567)
Q Consensus       357 ~~i~~~~l-----~s~~~G~~~~~l~-------~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld  424 (567)
                      ++++|+.+     .+.++|.......       ..+..    +.+++|||||||.+....|.           .|+..++
T Consensus        61 ~~v~~~~~~~~~~~~~l~g~~~~~~~g~~~~~~~~l~~----a~~~~l~lDEi~~l~~~~q~-----------~Ll~~l~  125 (265)
T 2bjv_A           61 ISLNCAALNENLLDSELFGHEAGAFTGAQKRHPGRFER----ADGGTLFLDELATAPMMVQE-----------KLLRVIE  125 (265)
T ss_dssp             EEEEGGGSCHHHHHHHHHCCC---------CCCCHHHH----TTTSEEEEESGGGSCHHHHH-----------HHHHHHH
T ss_pred             EEEecCCCChhHHHHHhcCCcccccccccccccchhhh----cCCcEEEEechHhcCHHHHH-----------HHHHHHH
Confidence            88888765     3334443221111       12222    23689999999999765433           3333333


Q ss_pred             Cc---------ccCCcEEEEEeeCCC-------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-----------
Q 047219          425 GF---------EQDKKVVVIAATNRK-------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-----------  477 (567)
Q Consensus       425 ~~---------~~~~~viVIaaTN~~-------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-----------  477 (567)
                      ..         ....++++|+|||..       ..++++|++|| ..+.+..|++++|.+++..+++++           
T Consensus       126 ~~~~~~~g~~~~~~~~~~iI~atn~~~~~~~~~~~~~~~L~~Rl-~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~  204 (265)
T 2bjv_A          126 YGELERVGGSQPLQVNVRLVCATNADLPAMVNEGTFRADLLDAL-AFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLP  204 (265)
T ss_dssp             HCEECCCCC--CEECCCEEEEEESSCHHHHHHHTSSCHHHHHHH-CSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCS
T ss_pred             hCCeecCCCcccccCCeEEEEecCcCHHHHHHcCCccHHHHHhh-cCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCC
Confidence            21         123578999999973       35899999999 457888899988877666554432           


Q ss_pred             -----CHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          478 -----TKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       478 -----~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                           ..+.++.+....+..+.++|++++..+.
T Consensus       205 ~~~~~~~~a~~~L~~~~~~gn~reL~~~l~~~~  237 (265)
T 2bjv_A          205 LFPGFTERARETLLNYRWPGNIRELKNVVERSV  237 (265)
T ss_dssp             SCCCBCHHHHHHHHHSCCTTHHHHHHHHHHHHH
T ss_pred             cccCcCHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence                 3334444544444444555555555543

>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=99.78  E-value=4e-18  Score=179.05  Aligned_cols=220  Identities=20%  Similarity=0.327  Sum_probs=151.0

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .|+|++.+++.+...+.......      ...........++.++||+||||||||++|++||+.+      +.+|+.++
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~------~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~------~~~~~~~~   83 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRL------RNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL------DVPFTMAD   83 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHH------HTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT------TCCEEEEE
T ss_pred             hccCHHHHHHHHHHHHHHHHhhh------ccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc------CCCEEEec
Confidence            47999999999999886432211      1000001112467899999999999999999999999      77899999


Q ss_pred             hhhHHh-hhhchh-HHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhh---HHHHHHHHHHHHHhhcCcc-----
Q 047219          361 LEVVMS-KYYGES-ERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFE-----  427 (567)
Q Consensus       361 ~~~l~s-~~~G~~-~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l---~~~~~~vl~~LL~~ld~~~-----  427 (567)
                      +..+.. .|+|+. ...+..+|..+.   ..++++||||||||.+...+....   ....+++++.|+..+++..     
T Consensus        84 ~~~l~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~  163 (363)
T 3hws_A           84 ATTLTEAGYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPP  163 (363)
T ss_dssp             HHHHTTCHHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC------
T ss_pred             hHHhcccccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccC
Confidence            998874 478875 556677776542   112368999999999987643321   1122346777888877421     


Q ss_pred             --------------cCCcEEEEEeeCCC----------CC-----------------------------------CChHH
Q 047219          428 --------------QDKKVVVIAATNRK----------QD-----------------------------------LDPAL  448 (567)
Q Consensus       428 --------------~~~~viVIaaTN~~----------~~-----------------------------------Ld~aL  448 (567)
                                    ...++++|+++|..          ..                                   |+++|
T Consensus       164 ~~~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l  243 (363)
T 3hws_A          164 QGGRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEF  243 (363)
T ss_dssp             ----------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHH
T ss_pred             ccccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHH
Confidence                          22455666666542          11                                   89999


Q ss_pred             HhccceEEEecCCCHHHHHHHHHH----HHHh-------------hCHHHHHHHHH--hccCCCHHHHHHHHHHHHHHHH
Q 047219          449 ISRFDSMITFGLPDHENRQEIAAQ----YAKH-------------LTKAELAELAT--ATEEMSGRDIRDVCQQAERSWA  509 (567)
Q Consensus       449 ~sRf~~~I~i~~P~~~eR~eIL~~----~~~~-------------~~~~~l~~la~--~t~g~s~~dL~~L~~~a~~~a~  509 (567)
                      ++||+..+.|.+|+.+++.+|+..    +.+.             +..+.++.++.  +.+.+..++|++++..+.....
T Consensus       244 ~~R~~~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~~~l  323 (363)
T 3hws_A          244 IGRLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALLDTM  323 (363)
T ss_dssp             HTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHHHHH
T ss_pred             hcccCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHHHHH
Confidence            999999999999999999999886    3221             34556666664  4455667788888887776655


Q ss_pred             HHH
Q 047219          510 SKI  512 (567)
Q Consensus       510 ~r~  512 (567)
                      .+.
T Consensus       324 ~~~  326 (363)
T 3hws_A          324 YDL  326 (363)
T ss_dssp             HST
T ss_pred             Hhc
Confidence            543

>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=99.76  E-value=4e-18  Score=188.76  Aligned_cols=209  Identities=22%  Similarity=0.273  Sum_probs=143.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      ....+++++|++++++.+.+.+.......               ..++.+++|+||||||||++|++||..+      +.
T Consensus        76 ~~~l~~di~G~~~vk~~i~~~~~l~~~~~---------------~~~g~~vll~Gp~GtGKTtlar~ia~~l------~~  134 (543)
T 3m6a_A           76 GRLLDEEHHGLEKVKERILEYLAVQKLTK---------------SLKGPILCLAGPPGVGKTSLAKSIAKSL------GR  134 (543)
T ss_dssp             GGTHHHHCSSCHHHHHHHHHHHHHHHHSS---------------SCCSCEEEEESSSSSSHHHHHHHHHHHH------TC
T ss_pred             HHHHHHHhccHHHHHHHHHHHHHHHHhcc---------------cCCCCEEEEECCCCCCHHHHHHHHHHhc------CC
Confidence            34556889999999999987665321111               2256789999999999999999999999      55


Q ss_pred             CeEEechhhHHh---------hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC
Q 047219          355 PLMYVPLEVVMS---------KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG  425 (567)
Q Consensus       355 ~~~~i~~~~l~s---------~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~  425 (567)
                      ++..+++..+..         .+.|.....+...|..+...  ++||||||||.+....+.       ..++.|+..++.
T Consensus       135 ~~~~i~~~~~~~~~~~~g~~~~~ig~~~~~~~~~~~~a~~~--~~vl~lDEid~l~~~~~~-------~~~~~LL~~ld~  205 (543)
T 3m6a_A          135 KFVRISLGGVRDESEIRGHRRTYVGAMPGRIIQGMKKAGKL--NPVFLLDEIDKMSSDFRG-------DPSSAMLEVLDP  205 (543)
T ss_dssp             EEEEECCCC--------------------CHHHHHHTTCSS--SEEEEEEESSSCC----------------CCGGGTCT
T ss_pred             CeEEEEecccchhhhhhhHHHHHhccCchHHHHHHHHhhcc--CCEEEEhhhhhhhhhhcc-------CHHHHHHHHHhh
Confidence            677776654322         45566556666677766544  359999999999876432       134556666654


Q ss_pred             ccc-------------CCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------------hC
Q 047219          426 FEQ-------------DKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------------LT  478 (567)
Q Consensus       426 ~~~-------------~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------------~~  478 (567)
                      ...             ..+++||+|||+++.++++|++|| ..++|+.|+.+++.+|+..++..              +.
T Consensus       206 ~~~~~~~~~~~~~~~~~~~v~iI~ttN~~~~l~~aL~~R~-~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~  284 (543)
T 3m6a_A          206 EQNSSFSDHYIEETFDLSKVLFIATANNLATIPGPLRDRM-EIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLR  284 (543)
T ss_dssp             TTTTBCCCSSSCCCCBCSSCEEEEECSSTTTSCHHHHHHE-EEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEEC
T ss_pred             hhcceeecccCCeeecccceEEEeccCccccCCHHHHhhc-ceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCC
Confidence            321             157899999999999999999999 68999999999999999987521              34


Q ss_pred             HHHHHHHHH-hccCCCHHHHHHHHHHHHHHHHHHHHh
Q 047219          479 KAELAELAT-ATEEMSGRDIRDVCQQAERSWASKIIR  514 (567)
Q Consensus       479 ~~~l~~la~-~t~g~s~~dL~~L~~~a~~~a~~r~i~  514 (567)
                      .+.+..+.. +++....++|++.+..+.+.++.+.+.
T Consensus       285 ~~~l~~l~~~~~~~~~vR~L~~~i~~~~~~aa~~~~~  321 (543)
T 3m6a_A          285 DQAILDIIRYYTREAGVRSLERQLAAICRKAAKAIVA  321 (543)
T ss_dssp             HHHHHHHHHHHCCCSSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHhCChhhchhHHHHHHHHHHHHHHHHHHh
Confidence            566777655 555567788888877777766666554

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.75  E-value=3e-18  Score=196.93  Aligned_cols=204  Identities=19%  Similarity=0.260  Sum_probs=145.2

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      .++++|++.+++.+.+.+......-.            ....+..++||+||||||||++|+++|+.+...   +.+|+.
T Consensus       490 ~~~viGq~~a~~~l~~~i~~~~~~~~------------~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~---~~~~i~  554 (758)
T 3pxi_A          490 HSRVIGQDEAVVAVAKAVRRARAGLK------------DPKRPIGSFIFLGPTGVGKTELARALAESIFGD---EESMIR  554 (758)
T ss_dssp             HTTSCSCHHHHHHHHHHHHHHTTTCS------------CTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC---TTCEEE
T ss_pred             hCcCcChHHHHHHHHHHHHHHHcccC------------CCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC---CcceEE
Confidence            46799999999999998875411100            001233479999999999999999999998543   568999


Q ss_pred             echhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc---------ccC
Q 047219          359 VPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF---------EQD  429 (567)
Q Consensus       359 i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~---------~~~  429 (567)
                      ++++++...+... ..    .+..+....+++||||||||.+.+..           ++.|++.++..         ...
T Consensus       555 i~~s~~~~~~~~~-~~----~l~~~~~~~~~~vl~lDEi~~~~~~~-----------~~~Ll~~le~g~~~~~~g~~~~~  618 (758)
T 3pxi_A          555 IDMSEYMEKHSTS-GG----QLTEKVRRKPYSVVLLDAIEKAHPDV-----------FNILLQVLEDGRLTDSKGRTVDF  618 (758)
T ss_dssp             EEGGGGCSSCCCC--------CHHHHHHCSSSEEEEECGGGSCHHH-----------HHHHHHHHHHSBCC-----CCBC
T ss_pred             Eechhcccccccc-cc----hhhHHHHhCCCeEEEEeCccccCHHH-----------HHHHHHHhccCeEEcCCCCEecc
Confidence            9999988776554 11    12222233457999999999987543           34444444432         134


Q ss_pred             CcEEEEEeeCCCCC------------CChHHHhccceEEEecCCCHHHHHHHHHHHHHh-------------hCHHHHHH
Q 047219          430 KKVVVIAATNRKQD------------LDPALISRFDSMITFGLPDHENRQEIAAQYAKH-------------LTKAELAE  484 (567)
Q Consensus       430 ~~viVIaaTN~~~~------------Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-------------~~~~~l~~  484 (567)
                      .++++|+|||....            |+|+|++||+..+.|++|+.+++.+|+..++..             +..+.++.
T Consensus       619 ~~~~iI~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~  698 (758)
T 3pxi_A          619 RNTILIMTSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAK  698 (758)
T ss_dssp             TTCEEEEEESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHH
T ss_pred             CCeEEEEeCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHH
Confidence            57899999996443            899999999999999999999999999987754             34556777


Q ss_pred             HHH--hccCCCHHHHHHHHHHHHHHHHHHHH
Q 047219          485 LAT--ATEEMSGRDIRDVCQQAERSWASKII  513 (567)
Q Consensus       485 la~--~t~g~s~~dL~~L~~~a~~~a~~r~i  513 (567)
                      ++.  +.+.+..++|+++++.+......+.+
T Consensus       699 l~~~~~~~~~~~R~L~~~i~~~v~~~l~~~~  729 (758)
T 3pxi_A          699 VAEEGVDLEYGARPLRRAIQKHVEDRLSEEL  729 (758)
T ss_dssp             HHGGGCCTTTTTTTHHHHHHHHTHHHHHHHH
T ss_pred             HHHhCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence            765  55667888899888887765554443

>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=99.75  E-value=1.2e-17  Score=171.97  Aligned_cols=171  Identities=19%  Similarity=0.259  Sum_probs=126.0

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|+++.++.+++.+..                    ...+..+|++||||||||++|+++++++      +
T Consensus        20 ~rP~~~~~ivg~~~~~~~l~~~l~~--------------------~~~~~~~L~~G~~G~GKT~la~~la~~l------~   73 (324)
T 3u61_B           20 YRPSTIDECILPAFDKETFKSITSK--------------------GKIPHIILHSPSPGTGKTTVAKALCHDV------N   73 (324)
T ss_dssp             SCCCSTTTSCCCHHHHHHHHHHHHT--------------------TCCCSEEEECSSTTSSHHHHHHHHHHHT------T
T ss_pred             hCCCCHHHHhCcHHHHHHHHHHHHc--------------------CCCCeEEEeeCcCCCCHHHHHHHHHHHh------C
Confidence            3456899999999999999887752                    4566788999999999999999999999      6


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHH-HhcC---CCCcEEEEcCcchhh-hhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSL-ANEL---PNGAIIFLDEVDSFA-VARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~-A~~~---a~~~ILfIDEID~L~-~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      .++++++++...       ...++..+.. +...   ..+.+|||||+|.+. ...           .+.|+..++.  .
T Consensus        74 ~~~~~i~~~~~~-------~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~~~~-----------~~~L~~~le~--~  133 (324)
T 3u61_B           74 ADMMFVNGSDCK-------IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGLAES-----------QRHLRSFMEA--Y  133 (324)
T ss_dssp             EEEEEEETTTCC-------HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGGHHH-----------HHHHHHHHHH--H
T ss_pred             CCEEEEcccccC-------HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCcHHH-----------HHHHHHHHHh--C
Confidence            778998876532       1223333332 2221   246899999999996 332           2344444442  2


Q ss_pred             CCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh-----------hCH-HHHHHHHHhccC
Q 047219          429 DKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH-----------LTK-AELAELATATEE  491 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-----------~~~-~~l~~la~~t~g  491 (567)
                      +.++++|++||.+..++++|++|| ..++|+.|+.+++.+|++.+...           +.. +.++.++..+.|
T Consensus       134 ~~~~~iI~~~n~~~~l~~~l~sR~-~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~g  207 (324)
T 3u61_B          134 SSNCSIIITANNIDGIIKPLQSRC-RVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFP  207 (324)
T ss_dssp             GGGCEEEEEESSGGGSCTTHHHHS-EEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCS
T ss_pred             CCCcEEEEEeCCccccCHHHHhhC-cEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCC
Confidence            357899999999999999999999 78999999999988877765443           233 566677776554

>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=99.75  E-value=6.3e-18  Score=170.18  Aligned_cols=202  Identities=18%  Similarity=0.247  Sum_probs=133.0

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      ....++|+++.++.+.+.....   .+.++..        +..++.++||+||||||||++|+++|+.+      +.+++
T Consensus        31 ~~~~~i~~~~~~~~i~~~~~~l---~~~l~~~--------~~~~~~~vLl~G~~GtGKT~la~~ia~~~------~~~~~   93 (272)
T 1d2n_A           31 IMNGIIKWGDPVTRVLDDGELL---VQQTKNS--------DRTPLVSVLLEGPPHSGKTALAAKIAEES------NFPFI   93 (272)
T ss_dssp             CTTCCCCCSHHHHHHHHHHHHH---HHHHHHC--------SSCSEEEEEEECSTTSSHHHHHHHHHHHH------TCSEE
T ss_pred             HhcCCCCccHHHHHHHHHHHHH---HHHHhcc--------CCCCCeEEEEECCCCCcHHHHHHHHHHHh------CCCEE
Confidence            3457899999888777742211   0011111        14667899999999999999999999998      67788


Q ss_pred             EechhhHHhhhhch----hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-cCCcE
Q 047219          358 YVPLEVVMSKYYGE----SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-QDKKV  432 (567)
Q Consensus       358 ~i~~~~l~s~~~G~----~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-~~~~v  432 (567)
                      .+++..   .++|.    ....++.+|..+.... +++|||||||.|...+... ......++..|...++... ...++
T Consensus        94 ~i~~~~---~~~g~~~~~~~~~~~~~~~~~~~~~-~~vl~iDEid~l~~~~~~~-~~~~~~~l~~L~~~~~~~~~~~~~~  168 (272)
T 1d2n_A           94 KICSPD---KMIGFSETAKCQAMKKIFDDAYKSQ-LSCVVVDDIERLLDYVPIG-PRFSNLVLQALLVLLKKAPPQGRKL  168 (272)
T ss_dssp             EEECGG---GCTTCCHHHHHHHHHHHHHHHHTSS-EEEEEECCHHHHTTCBTTT-TBCCHHHHHHHHHHTTCCCSTTCEE
T ss_pred             EEeCHH---HhcCCchHHHHHHHHHHHHHHHhcC-CcEEEEEChhhhhccCCCC-hhHHHHHHHHHHHHhcCccCCCCCE
Confidence            887764   33333    2355677888776544 5999999999995443211 0112334455666666543 34578


Q ss_pred             EEEEeeCCCCCCCh-HHHhccceEEEecCCCHHHHHHHHHHHH--HhhCHHHHHHHHHhccCC----CHHHHHHHHHH
Q 047219          433 VVIAATNRKQDLDP-ALISRFDSMITFGLPDHENRQEIAAQYA--KHLTKAELAELATATEEM----SGRDIRDVCQQ  503 (567)
Q Consensus       433 iVIaaTN~~~~Ld~-aL~sRf~~~I~i~~P~~~eR~eIL~~~~--~~~~~~~l~~la~~t~g~----s~~dL~~L~~~  503 (567)
                      ++|+|||.++.+++ .+++||+..++++  +..+|.++...+.  ..+..+.+..++..+.|+    +.+++.+++..
T Consensus       169 ~ii~ttn~~~~l~~~~l~~rf~~~i~~p--~l~~r~~i~~i~~~~~~~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~  244 (272)
T 1d2n_A          169 LIIGTTSRKDVLQEMEMLNAFSTTIHVP--NIATGEQLLEALELLGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEM  244 (272)
T ss_dssp             EEEEEESCHHHHHHTTCTTTSSEEEECC--CEEEHHHHHHHHHHHTCSCHHHHHHHHHHHTTSEEEECHHHHHHHHHH
T ss_pred             EEEEecCChhhcchhhhhcccceEEcCC--CccHHHHHHHHHHhcCCCCHHHHHHHHHHhcCCCccccHHHHHHHHHH
Confidence            89999999888887 6788997777774  4444444444333  236677888888888776    44455444443

>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=99.74  E-value=8.3e-17  Score=166.07  Aligned_cols=197  Identities=18%  Similarity=0.230  Sum_probs=134.3

Q ss_pred             CCCCCccccc-C--cHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          274 KSEISWENIA-G--YDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       274 ~~~~~~~dIi-G--~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      .+..+|++++ |  ...+...++..+..+                   ...+.+++|+||||||||++|+++++.+... 
T Consensus         5 ~~~~~f~~fv~g~~~~~a~~~~~~~~~~~-------------------~~~~~~lll~G~~GtGKT~la~~i~~~~~~~-   64 (324)
T 1l8q_A            5 NPKYTLENFIVGEGNRLAYEVVKEALENL-------------------GSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-   64 (324)
T ss_dssp             CTTCCSSSCCCCTTTHHHHHHHHHHHHTT-------------------TTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-
T ss_pred             CCCCCcccCCCCCcHHHHHHHHHHHHhCc-------------------CCCCCeEEEECCCCCcHHHHHHHHHHHHHHC-
Confidence            4567899997 4  444455554444321                   2356799999999999999999999988433 


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                        +.+++++++..+...+.+.........|......  +++|||||+|.+..+..         ....++..++.....+
T Consensus        65 --~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~vL~iDEi~~l~~~~~---------~~~~l~~~l~~~~~~~  131 (324)
T 1l8q_A           65 --GYRVIYSSADDFAQAMVEHLKKGTINEFRNMYKS--VDLLLLDDVQFLSGKER---------TQIEFFHIFNTLYLLE  131 (324)
T ss_dssp             --TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHHT--CSEEEEECGGGGTTCHH---------HHHHHHHHHHHHHHTT
T ss_pred             --CCEEEEEEHHHHHHHHHHHHHcCcHHHHHHHhcC--CCEEEEcCcccccCChH---------HHHHHHHHHHHHHHCC
Confidence              4578999998887766554332222223332222  58999999999975311         1112222222222334


Q ss_pred             cEEEEEeeCCCC---CCChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHH
Q 047219          431 KVVVIAATNRKQ---DLDPALISRFD--SMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       431 ~viVIaaTN~~~---~Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ..+|+++++.+.   .++++|++||.  ..+++++ +.+++.+++..++..    ++.+.++.++..+  .+.+++..++
T Consensus       132 ~~iii~~~~~~~~l~~l~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~--g~~r~l~~~l  208 (324)
T 1l8q_A          132 KQIILASDRHPQKLDGVSDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT--KNVREIEGKI  208 (324)
T ss_dssp             CEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC--SSHHHHHHHH
T ss_pred             CeEEEEecCChHHHHHhhhHhhhcccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC--CCHHHHHHHH
Confidence            566777777665   68999999996  5788988 999999999998864    5677888888888  4667777777


Q ss_pred             HHHHH
Q 047219          502 QQAER  506 (567)
Q Consensus       502 ~~a~~  506 (567)
                      ..+..
T Consensus       209 ~~~~~  213 (324)
T 1l8q_A          209 KLIKL  213 (324)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66553

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.74  E-value=5.3e-18  Score=158.63  Aligned_cols=166  Identities=20%  Similarity=0.289  Sum_probs=119.0

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PW  351 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~  351 (567)
                      +..|++++|.++.++.+.+.+.                     ...+.+++|+||||||||++|+++++.+...    ..
T Consensus        18 ~~~~~~~~g~~~~~~~l~~~l~---------------------~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~   76 (195)
T 1jbk_A           18 QGKLDPVIGRDEEIRRTIQVLQ---------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGL   76 (195)
T ss_dssp             TTCSCCCCSCHHHHHHHHHHHT---------------------SSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGG
T ss_pred             hccccccccchHHHHHHHHHHh---------------------cCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhh
Confidence            3578999999999998887653                     3456789999999999999999999987421    11


Q ss_pred             CCcCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC
Q 047219          352 QGVPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       352 ~~~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      .+.+++.+++..+.  ..+.+.....+..++..+.....+.+|||||+|.+...........   +.+.+...++    .
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~---~~~~l~~~~~----~  149 (195)
T 1jbk_A           77 KGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMD---AGNMLKPALA----R  149 (195)
T ss_dssp             TTCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCC---CHHHHHHHHH----T
T ss_pred             cCCcEEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHH---HHHHHHHhhc----c
Confidence            25678888888776  3455666677777877665554467999999999975432111001   1122222222    3


Q ss_pred             CcEEEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHH
Q 047219          430 KKVVVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIA  470 (567)
Q Consensus       430 ~~viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL  470 (567)
                      .++.+|++||.+.     .+++++++||. .++++.|+.+++.+++
T Consensus       150 ~~~~~i~~~~~~~~~~~~~~~~~l~~r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          150 GELHCVGATTLDEYRQYIEKDAALERRFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             TSCCEEEEECHHHHHHHTTTCHHHHTTEE-EEECCCCCHHHHHTTC
T ss_pred             CCeEEEEeCCHHHHHHHHhcCHHHHHHhc-eeecCCCCHHHHHHHh
Confidence            5678899998765     78999999995 7999999999998875

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.73  E-value=4.7e-17  Score=175.99  Aligned_cols=182  Identities=21%  Similarity=0.290  Sum_probs=130.5

Q ss_pred             CCCCCcccccCcHHHH---HHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          274 KSEISWENIAGYDQQK---REIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k---~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      ..+.+|++++|++..+   +.++..+..                     ....++||+||||||||++|++||+.+    
T Consensus        20 ~rP~~l~~ivGq~~~~~~~~~L~~~i~~---------------------~~~~~vLL~GppGtGKTtlAr~ia~~~----   74 (447)
T 3pvs_A           20 MRPENLAQYIGQQHLLAAGKPLPRAIEA---------------------GHLHSMILWGPPGTGKTTLAEVIARYA----   74 (447)
T ss_dssp             TCCCSTTTCCSCHHHHSTTSHHHHHHHH---------------------TCCCEEEEECSTTSSHHHHHHHHHHHT----
T ss_pred             hCCCCHHHhCCcHHHHhchHHHHHHHHc---------------------CCCcEEEEECCCCCcHHHHHHHHHHHh----
Confidence            3446899999999999   777776652                     233789999999999999999999999    


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~  427 (567)
                        +.++..+++....       .+.++.+++.+..   ...++||||||||.|....|+.           |+..++.  
T Consensus        75 --~~~f~~l~a~~~~-------~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~~q~~-----------LL~~le~--  132 (447)
T 3pvs_A           75 --NADVERISAVTSG-------VKEIREAIERARQNRNAGRRTILFVDEVHRFNKSQQDA-----------FLPHIED--  132 (447)
T ss_dssp             --TCEEEEEETTTCC-------HHHHHHHHHHHHHHHHTTCCEEEEEETTTCC------C-----------CHHHHHT--
T ss_pred             --CCCeEEEEeccCC-------HHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHHHHHH-----------HHHHHhc--
Confidence              5668877764322       1234444444332   3346999999999997664443           4444442  


Q ss_pred             cCCcEEEEEee--CCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh-----------hCHHHHHHHHHhccCCCH
Q 047219          428 QDKKVVVIAAT--NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH-----------LTKAELAELATATEEMSG  494 (567)
Q Consensus       428 ~~~~viVIaaT--N~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-----------~~~~~l~~la~~t~g~s~  494 (567)
                        +.+++|++|  |....++++|++|| .++.|+.|+.+++..++...+..           +..+.++.++..+.| +.
T Consensus       133 --~~v~lI~att~n~~~~l~~aL~sR~-~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~G-d~  208 (447)
T 3pvs_A          133 --GTITFIGATTENPSFELNSALLSRA-RVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNG-DA  208 (447)
T ss_dssp             --TSCEEEEEESSCGGGSSCHHHHTTE-EEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCS-CH
T ss_pred             --CceEEEecCCCCcccccCHHHhCce-eEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCC-CH
Confidence              457777777  55668999999999 68999999999999999998764           456778888888544 56


Q ss_pred             HHHHHHHHHHHH
Q 047219          495 RDIRDVCQQAER  506 (567)
Q Consensus       495 ~dL~~L~~~a~~  506 (567)
                      +.+.+++..+..
T Consensus       209 R~lln~Le~a~~  220 (447)
T 3pvs_A          209 RRALNTLEMMAD  220 (447)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            666666666553

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.73  E-value=1.6e-18  Score=184.13  Aligned_cols=198  Identities=22%  Similarity=0.280  Sum_probs=142.8

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      ++.++|.+..++++.+.+...                   .....+|||+|++||||+++|+++|..+.+.   ..+|+.
T Consensus       136 ~~~~ig~s~~m~~l~~~i~~~-------------------a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~---~~~fv~  193 (387)
T 1ny5_A          136 EEEYVFESPKMKEILEKIKKI-------------------SCAECPVLITGESGVGKEVVARLIHKLSDRS---KEPFVA  193 (387)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHH-------------------TTCCSCEEEECSTTSSHHHHHHHHHHHSTTT---TSCEEE
T ss_pred             chhhhhccHHhhHHHHHHHHh-------------------cCCCCCeEEecCCCcCHHHHHHHHHHhcCCC---CCCeEE
Confidence            457899999999998888754                   5566789999999999999999999998654   345666


Q ss_pred             echh-----hHHhhhhchhHHH-------HHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc
Q 047219          359 VPLE-----VVMSKYYGESERL-------LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF  426 (567)
Q Consensus       359 i~~~-----~l~s~~~G~~~~~-------l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~  426 (567)
                      ++|.     .+.+.+||+....       ....|+.|    .+|+||||||+.|+...|..+.+++++  ..+.......
T Consensus       194 v~~~~~~~~~~~~elfg~~~g~~tga~~~~~g~~~~a----~~gtlfldei~~l~~~~q~~Ll~~l~~--~~~~~~g~~~  267 (387)
T 1ny5_A          194 LNVASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELA----DGGTLFLDEIGELSLEAQAKLLRVIES--GKFYRLGGRK  267 (387)
T ss_dssp             EETTTSCHHHHHHHHHCBCTTSSTTCCSCBCCHHHHT----TTSEEEEESGGGCCHHHHHHHHHHHHH--SEECCBTCCS
T ss_pred             EecCCCCHHHHHHHhcCCCCCCCCCcccccCCceeeC----CCcEEEEcChhhCCHHHHHHHHHHHhc--CcEEeCCCCc
Confidence            6654     4566677753321       11234433    379999999999988766665554433  1111112222


Q ss_pred             ccCCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHH
Q 047219          427 EQDKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRD  499 (567)
Q Consensus       427 ~~~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~  499 (567)
                      ....++++|+|||.       .+.++++|++|+ ..+.+..|++++|.+++..+++++......++.....+++...+..
T Consensus       268 ~~~~~~rii~at~~~l~~~~~~g~fr~dl~~rl-~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~  346 (387)
T 1ny5_A          268 EIEVNVRILAATNRNIKELVKEGKFREDLYYRL-GVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQEL  346 (387)
T ss_dssp             BEECCCEEEEEESSCHHHHHHTTSSCHHHHHHH-TTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHH
T ss_pred             eeeccEEEEEeCCCCHHHHHHcCCccHHHHHhh-cCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHH
Confidence            33468999999997       567999999999 7888999999999999998888776555555554455677777777


Q ss_pred             HHHHHH
Q 047219          500 VCQQAE  505 (567)
Q Consensus       500 L~~~a~  505 (567)
                      |.++.|
T Consensus       347 l~~~~w  352 (387)
T 1ny5_A          347 LLSYPW  352 (387)
T ss_dssp             HHHSCC
T ss_pred             HHhCCC
Confidence            777776

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.73  E-value=3.8e-17  Score=187.59  Aligned_cols=205  Identities=20%  Similarity=0.332  Sum_probs=142.6

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++++|++++++.+...+.....        |  ..  ....+..++||+||||||||++|+++|+.+      +.+++.+
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~--------g--~~--~~~~p~~~~ll~G~~GtGKT~la~~la~~l------~~~~~~i  519 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARA--------G--LG--HEHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRF  519 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHT--------T--CS--CTTSCSEEEEEECSTTSSHHHHHHHHHHHH------TCEEEEE
T ss_pred             hhccCHHHHHHHHHHHHHHHhc--------c--cC--CCCCCceEEEEECCCCCcHHHHHHHHHHHh------cCCEEEE
Confidence            4689999999999887764310        0  00  002344579999999999999999999999      6679999


Q ss_pred             chhhHHhh------------hhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc
Q 047219          360 PLEVVMSK------------YYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       360 ~~~~l~s~------------~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~  427 (567)
                      +++++...            |+|..+.  +.+..... .++++||||||||.+.+.           +++.|++.++...
T Consensus       520 ~~s~~~~~~~~~~l~g~~~g~~g~~~~--~~l~~~~~-~~~~~vl~lDEi~~~~~~-----------~~~~Ll~~le~~~  585 (758)
T 1r6b_X          520 DMSEYMERHTVSRLIGAPPGYVGFDQG--GLLTDAVI-KHPHAVLLLDEIEKAHPD-----------VFNILLQVMDNGT  585 (758)
T ss_dssp             EGGGCSSSSCCSSSCCCCSCSHHHHHT--THHHHHHH-HCSSEEEEEETGGGSCHH-----------HHHHHHHHHHHSE
T ss_pred             echhhcchhhHhhhcCCCCCCcCcccc--chHHHHHH-hCCCcEEEEeCccccCHH-----------HHHHHHHHhcCcE
Confidence            99887653            3333221  11222222 345799999999998644           4455555555321


Q ss_pred             c---------CCcEEEEEeeCCCC-------------------------CCChHHHhccceEEEecCCCHHHHHHHHHHH
Q 047219          428 Q---------DKKVVVIAATNRKQ-------------------------DLDPALISRFDSMITFGLPDHENRQEIAAQY  473 (567)
Q Consensus       428 ~---------~~~viVIaaTN~~~-------------------------~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~  473 (567)
                      .         -.+++||+|||...                         .++++|++||+..+.|+.|+.+++..|+..+
T Consensus       586 ~~~~~g~~~~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~l~~~~~~~i~~~~  665 (758)
T 1r6b_X          586 LTDNNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKF  665 (758)
T ss_dssp             EEETTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHH
T ss_pred             EEcCCCCEEecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCCcceeeCCCCHHHHHHHHHHH
Confidence            1         25789999999743                         6899999999999999999999999999988


Q ss_pred             HHh-------------hCHHHHHHHHHhcc--CCCHHHHHHHHHHHHHH-HHHHHHhcc
Q 047219          474 AKH-------------LTKAELAELATATE--EMSGRDIRDVCQQAERS-WASKIIRGQ  516 (567)
Q Consensus       474 ~~~-------------~~~~~l~~la~~t~--g~s~~dL~~L~~~a~~~-a~~r~i~~~  516 (567)
                      +..             +..+.++.++...+  .+..++++++++.+... .++.++.+.
T Consensus       666 l~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~g~R~l~~~i~~~~~~~l~~~~l~~~  724 (758)
T 1r6b_X          666 IVELQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNLKKPLANELLFGS  724 (758)
T ss_dssp             HHHHHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHHTHHHHHHHHHST
T ss_pred             HHHHHHHHHHCCcEEEeCHHHHHHHHHhCCCcCCCchHHHHHHHHHHHHHHHHHHHcCc
Confidence            763             34556666766543  34577888888877755 334444443

>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=99.73  E-value=6.7e-17  Score=170.38  Aligned_cols=226  Identities=19%  Similarity=0.289  Sum_probs=137.6

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHH--------hhhhcc-cccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYD--------DIARGT-RCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~--------~l~~~~-~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      +.|+|++++++.|...+...++......        .-.... .......++.++||+||||||||++|+++|+.+    
T Consensus        21 ~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l----   96 (376)
T 1um8_A           21 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL----   96 (376)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT----
T ss_pred             hHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHh----
Confidence            3589999999999988854332221100        000000 000013467789999999999999999999999    


Q ss_pred             CCCcCeEEechhhHH-hhhhchh-HHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhH--H-HHHHHHHHHHHh
Q 047219          351 WQGVPLMYVPLEVVM-SKYYGES-ERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMH--E-ATRRILSVLLRQ  422 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~-s~~~G~~-~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~--~-~~~~vl~~LL~~  422 (567)
                        +.+|+.+++..+. ..++|+. +..+..++..+..   .+.++||||||+|.+...+.....  + ....+++.|+..
T Consensus        97 --~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~  174 (376)
T 1um8_A           97 --DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKI  174 (376)
T ss_dssp             --TCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHH
T ss_pred             --CCCEEEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCceecccchHHHHHHHHHH
Confidence              6789999888765 3555653 3445555543321   123699999999999866322110  0 111255677777


Q ss_pred             hcCcc-------------------cCCcEEEEEeeCC-----------------------------------------CC
Q 047219          423 IDGFE-------------------QDKKVVVIAATNR-----------------------------------------KQ  442 (567)
Q Consensus       423 ld~~~-------------------~~~~viVIaaTN~-----------------------------------------~~  442 (567)
                      +++..                   ...++++|+++|.                                         ..
T Consensus       175 le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~  254 (376)
T 1um8_A          175 VEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTY  254 (376)
T ss_dssp             HHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHT
T ss_pred             hhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhc
Confidence            76431                   1256788888772                                         12


Q ss_pred             CCChHHHhccceEEEecCCCHHHHHHHHHH----HHH-------------hhCHHHHHHHHHhcc--CCCHHHHHHHHHH
Q 047219          443 DLDPALISRFDSMITFGLPDHENRQEIAAQ----YAK-------------HLTKAELAELATATE--EMSGRDIRDVCQQ  503 (567)
Q Consensus       443 ~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~----~~~-------------~~~~~~l~~la~~t~--g~s~~dL~~L~~~  503 (567)
                      .+.++|++||+..+.|+.++.++..+++..    ++.             .+..+.++.++...+  ....+.|++++..
T Consensus       255 ~~~p~l~~R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~  334 (376)
T 1um8_A          255 GLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIED  334 (376)
T ss_dssp             TCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHH
T ss_pred             CCChHHhcCCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHHH
Confidence            478999999999999999999999998862    211             144556666666644  2456777777777


Q ss_pred             HHHHHHHH
Q 047219          504 AERSWASK  511 (567)
Q Consensus       504 a~~~a~~r  511 (567)
                      +...++.+
T Consensus       335 ~~~~~~~~  342 (376)
T 1um8_A          335 FCLDIMFD  342 (376)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhh
Confidence            66555444

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A

Probab=99.72  E-value=1.3e-18  Score=183.76  Aligned_cols=200  Identities=23%  Similarity=0.270  Sum_probs=146.0

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-CCCCcCeEE
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-PWQGVPLMY  358 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-~~~~~~~~~  358 (567)
                      .+++|.+..++++.+.+...                   .....++|++|++||||+++|+++|+.+.+. .|+.++|..
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~-------------------a~~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~  189 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKI-------------------AKSKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCAS  189 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHH-------------------HTSCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSS
T ss_pred             ccccccchHHHHHHhhhhhh-------------------hccchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEccc
Confidence            46899999999998877654                   4456779999999999999999999998654 244444444


Q ss_pred             echhhHHhhhhchhHHHH-------HHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          359 VPLEVVMSKYYGESERLL-------GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       359 i~~~~l~s~~~G~~~~~l-------~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ++.+.+.+.+||+....+       ...|+.|    .+++||||||+.|+...|..+.+++++  ..+...........+
T Consensus       190 ~~~~~~~~~lfg~~~g~~tga~~~~~g~~~~a----~~gtlfldei~~l~~~~Q~~Ll~~l~~--~~~~~~g~~~~~~~~  263 (368)
T 3dzd_A          190 IPQELAESELFGHEKGAFTGALTRKKGKLELA----DQGTLFLDEVGELDQRVQAKLLRVLET--GSFTRLGGNQKIEVD  263 (368)
T ss_dssp             SCTTTHHHHHHEECSCSSSSCCCCEECHHHHT----TTSEEEEETGGGSCHHHHHHHHHHHHH--SEECCBTCCCBEECC
T ss_pred             CChHHHHHHhcCccccccCCcccccCChHhhc----CCCeEEecChhhCCHHHHHHHHHHHHh--CCcccCCCCcceeee
Confidence            444556777777643221       1234443    379999999999998877666555443  111112222223457


Q ss_pred             EEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          432 VVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       432 viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      +++|+|||.       .+.|+++|++|+ ..+.+.+|++++|.+++..+++++......++.....+++...++.|+.+.
T Consensus       264 ~rii~at~~~l~~~v~~g~fr~dL~~rl-~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~~  342 (368)
T 3dzd_A          264 IRVISATNKNLEEEIKKGNFREDLYYRL-SVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQE  342 (368)
T ss_dssp             CEEEEEESSCHHHHHHTTSSCHHHHHHH-TSEEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHTCC
T ss_pred             eEEEEecCCCHHHHHHcCCccHHHHHHh-CCeEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhCC
Confidence            899999997       467999999999 789999999999999999998887766666665556678888888888888


Q ss_pred             H
Q 047219          505 E  505 (567)
Q Consensus       505 ~  505 (567)
                      |
T Consensus       343 w  343 (368)
T 3dzd_A          343 W  343 (368)
T ss_dssp             C
T ss_pred             C
Confidence            7

>1g8p_A Magnesium-chelatase 38 kDa subunit; parallel beta sheet, P-loop, rossman fold, AAA+, photosynthesis, metal transport; 2.10A {Rhodobacter capsulatus} SCOP: c.37.1.20 PDB: 2x31_G

Probab=99.71  E-value=2.2e-17  Score=171.12  Aligned_cols=178  Identities=21%  Similarity=0.320  Sum_probs=104.6

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCC----
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGA----  348 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~----  348 (567)
                      ..+..+|++++|++..++.+...+.                     .....++||+||||||||++|+++|+.+..    
T Consensus        17 ~~~~~~f~~i~G~~~~~~~l~~~~~---------------------~~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~   75 (350)
T 1g8p_A           17 TRPVFPFSAIVGQEDMKLALLLTAV---------------------DPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAV   75 (350)
T ss_dssp             -CCCCCGGGSCSCHHHHHHHHHHHH---------------------CGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEE
T ss_pred             CCCCCCchhccChHHHHHHHHHHhh---------------------CCCCceEEEECCCCccHHHHHHHHHHhCcccccc
Confidence            3466889999999997765433221                     123456999999999999999999999863    


Q ss_pred             --CCCC---------------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHh--------cCCCCcEEEEcCc
Q 047219          349 --MPWQ---------------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLAN--------ELPNGAIIFLDEV  397 (567)
Q Consensus       349 --~~~~---------------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~--------~~a~~~ILfIDEI  397 (567)
                        .++.                     ..+++.++.......++|...  +...+....        ..+.+++||||||
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~g~~~--~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi  153 (350)
T 1g8p_A           76 EGCPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALD--IERAISKGEKAFEPGLLARANRGYLYIDEC  153 (350)
T ss_dssp             TTCTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEEC--HHHHHHHCGGGEECCHHHHHTTEEEEETTG
T ss_pred             ccccccccccccccchhhhhccccccCCCcccccCCCcchhhheeech--hhhhhcCCceeecCceeeecCCCEEEEeCh
Confidence              1110                     011222222222223333210  011111110        0112689999999


Q ss_pred             chhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC-CCChHHHhccceEEEecCC-CHHHHHHHHHHH
Q 047219          398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ-DLDPALISRFDSMITFGLP-DHENRQEIAAQY  473 (567)
Q Consensus       398 D~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~-~Ld~aL~sRf~~~I~i~~P-~~~eR~eIL~~~  473 (567)
                      |.+....+..+...+++....+.........+.++++|+|||+.. .++++|++||+..++++.| +.+++.+|++..
T Consensus       154 ~~l~~~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~R~~~~~~l~~~~~~~~~~~il~~~  231 (350)
T 1g8p_A          154 NLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRR  231 (350)
T ss_dssp             GGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHH
Confidence            999765443332222110000000000111234899999999844 8999999999888999999 677777888763

>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=99.71  E-value=7.9e-16  Score=147.18  Aligned_cols=189  Identities=19%  Similarity=0.193  Sum_probs=130.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+..|++++|.++.++.+.+.+..                     ....+++|+||||||||++|+++++.+.... ..
T Consensus        11 ~~p~~~~~~~g~~~~~~~l~~~l~~---------------------~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~-~~   68 (226)
T 2chg_A           11 YRPRTLDEVVGQDEVIQRLKGYVER---------------------KNIPHLLFSGPPGTGKTATAIALARDLFGEN-WR   68 (226)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHT---------------------TCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-GG
T ss_pred             cCCCCHHHHcCcHHHHHHHHHHHhC---------------------CCCCeEEEECCCCCCHHHHHHHHHHHHhccc-cc
Confidence            3456799999999999999887752                     2334599999999999999999999863221 13


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHhc-----CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLANE-----LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~-----~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      ..++.+++......      ..+...+.....     ...+.+|||||+|.+....           ...|+..++.  .
T Consensus        69 ~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~-----------~~~l~~~l~~--~  129 (226)
T 2chg_A           69 DNFIEMNASDERGI------DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTADA-----------QAALRRTMEM--Y  129 (226)
T ss_dssp             GGEEEEETTCTTCH------HHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCHHH-----------HHHHHHHHHH--T
T ss_pred             cceEEeccccccCh------HHHHHHHHHHhcccCCCccCceEEEEeChhhcCHHH-----------HHHHHHHHHh--c
Confidence            44666665433221      111222222111     2346899999999986442           2234444442  2


Q ss_pred             CCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      ..++++|++||.+..+++++++|| ..+.++.|+.++..+++..++..    +..+.+..++..+.| +.+.+.+++..+
T Consensus       130 ~~~~~~i~~~~~~~~~~~~l~~r~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~l~~~  207 (226)
T 2chg_A          130 SKSCRFILSCNYVSRIIEPIQSRC-AVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRKAINALQGA  207 (226)
T ss_dssp             TTTEEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHHHH
T ss_pred             CCCCeEEEEeCChhhcCHHHHHhC-ceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHHH
Confidence            457889999999999999999999 49999999999999999988754    456777788776654 555555555544


Q ss_pred             H
Q 047219          505 E  505 (567)
Q Consensus       505 ~  505 (567)
                      +
T Consensus       208 ~  208 (226)
T 2chg_A          208 A  208 (226)
T ss_dssp             H
T ss_pred             H
Confidence            4

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=99.71  E-value=1.7e-16  Score=170.61  Aligned_cols=220  Identities=20%  Similarity=0.342  Sum_probs=153.7

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++|+|++++++.+...+..+.+++.++..+.       ...+++++||+||||||||++|+++|+.+      +.+|+.+
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~-------~~~~~~~iLl~GppGtGKT~lar~lA~~l------~~~~~~v   81 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLR-------HEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKV   81 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTT-------TTCCCCCEEEECCTTSSHHHHHHHHHHHT------TCCEEEE
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccc-------cccCCceEEEEcCCCCCHHHHHHHHHHHc------CCCceee
Confidence            4799999999999999987766666554332       12367899999999999999999999999      7789999


Q ss_pred             chhhHHh-hhhch-hHHHHHHHHHHHh-----------------------------------------------------
Q 047219          360 PLEVVMS-KYYGE-SERLLGKVFSLAN-----------------------------------------------------  384 (567)
Q Consensus       360 ~~~~l~s-~~~G~-~~~~l~~~f~~A~-----------------------------------------------------  384 (567)
                      +++.+.+ .|+|+ .+..++.+|..+.                                                     
T Consensus        82 ~~~~~~~~g~vG~d~e~~lr~lf~~a~~~~~~De~d~~~~~~~~~~e~rvl~~LL~~~dg~~~~~~v~a~~TN~~~~ld~  161 (444)
T 1g41_A           82 EATKFTEVGYVGKEVDSIIRDLTDSAMKLVRQQEIAKNRARAEDVAEERILDALLPPAKNQWGEVENHDSHSSTRQAFRK  161 (444)
T ss_dssp             EGGGGC----CCCCTHHHHHHHHHHHHHHHHHHHHHSCC-----------------------------------------
T ss_pred             cchhhcccceeeccHHHHHHHHHHHHHhcchhhhhhhhhccchhhHHHHHHHHHHHHhhccccccccccccccCHHHHHH
Confidence            9888777 47774 5555555554330                                                     


Q ss_pred             --------------------------------------------------------------------------------
Q 047219          385 --------------------------------------------------------------------------------  384 (567)
Q Consensus       385 --------------------------------------------------------------------------------  384 (567)
                                                                                                      
T Consensus       162 aL~rggr~D~~i~i~lP~~~~~~~ei~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~~a~~~l~~~e~~~l~~~~~~~  241 (444)
T 1g41_A          162 KLREGQLDDKEIEIDVSAGVSMGVEIMAPPGMEEMTNQLQSLFQNLGSDKTKKRKMKIKDALKALIDDEAAKLINPEELK  241 (444)
T ss_dssp             ----------------------------------------------------------------CCGGGSCSSCCHHHHH
T ss_pred             HHHcCCCcceEEEEcCCCCccchhhhhcCCChHHHHHHHHHHHHhhcCCCCcceeeeHHHHHHHHHHHHHHHccCHHHHH
Confidence                                                                                            


Q ss_pred             ----cCC-CCcEEEEcCcchhhhhhhhhhHHHH-HHHHHHHHHhhcCcc--------cCCcEEEEEee----CCCCCCCh
Q 047219          385 ----ELP-NGAIIFLDEVDSFAVARDSEMHEAT-RRILSVLLRQIDGFE--------QDKKVVVIAAT----NRKQDLDP  446 (567)
Q Consensus       385 ----~~a-~~~ILfIDEID~L~~~~q~~l~~~~-~~vl~~LL~~ld~~~--------~~~~viVIaaT----N~~~~Ld~  446 (567)
                          ..+ +++++|+||||+++.+......+.. +.++..||..+++..        ...++++|||.    +.+.++.|
T Consensus       242 ~~ai~~ae~~~il~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~dlip  321 (444)
T 1g41_A          242 QKAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIP  321 (444)
T ss_dssp             HHHHHHHHHHCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGGGSCH
T ss_pred             HHHHHHhccCCeeeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChhhcch
Confidence                011 3579999999999865332222332 335678888888742        34678999987    23455779


Q ss_pred             HHHhccceEEEecCCCHHHHHHHHHH----HHH-------------hhCHHHHHHHHH-------hccCCCHHHHHHHHH
Q 047219          447 ALISRFDSMITFGLPDHENRQEIAAQ----YAK-------------HLTKAELAELAT-------ATEEMSGRDIRDVCQ  502 (567)
Q Consensus       447 aL~sRf~~~I~i~~P~~~eR~eIL~~----~~~-------------~~~~~~l~~la~-------~t~g~s~~dL~~L~~  502 (567)
                      .|++||+.++.|+.++.++...|+..    +..             .+.++.+..+++       ++.....+.|+.++.
T Consensus       322 el~~R~~i~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~t~~~GaR~L~~~ie  401 (444)
T 1g41_A          322 ELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVME  401 (444)
T ss_dssp             HHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHHSCCCGGGHHHHHHH
T ss_pred             HHhcccceeeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccCCccCCchHHHHHHH
Confidence            99999988899999999999999941    111             144555555554       345566677777777


Q ss_pred             HHHHHHHHHH
Q 047219          503 QAERSWASKI  512 (567)
Q Consensus       503 ~a~~~a~~r~  512 (567)
                      ...+.....+
T Consensus       402 ~~~~~~~~~~  411 (444)
T 1g41_A          402 RLMDKISFSA  411 (444)
T ss_dssp             HHHHHHHHHG
T ss_pred             HHHHHHHhhc
Confidence            6666555443

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.70  E-value=1.2e-17  Score=152.91  Aligned_cols=136  Identities=15%  Similarity=0.194  Sum_probs=99.0

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +++|.+..++.+.+.+...                   ...+.+|||+||||||||++|+++|+.+.+.   +.+|+ ++
T Consensus         2 ~iiG~s~~~~~~~~~~~~~-------------------a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~---~~~~v-~~   58 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQL-------------------SETDIAVWLYGAPGTGRMTGARYLHQFGRNA---QGEFV-YR   58 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHH-------------------TTCCSCEEEESSTTSSHHHHHHHHHHSSTTT---TSCCE-EE
T ss_pred             CceeCCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCCCHHHHHHHHHHhCCcc---CCCEE-EE
Confidence            6899999999999988754                   4567889999999999999999999987554   45677 77


Q ss_pred             hhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC
Q 047219          361 LEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR  440 (567)
Q Consensus       361 ~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~  440 (567)
                      +..+...      ......|..+.    +++|||||||.+....|.           .|+..+.  ....++++|+|||.
T Consensus        59 ~~~~~~~------~~~~~~~~~a~----~g~l~ldei~~l~~~~q~-----------~Ll~~l~--~~~~~~~~I~~t~~  115 (145)
T 3n70_A           59 ELTPDNA------PQLNDFIALAQ----GGTLVLSHPEHLTREQQY-----------HLVQLQS--QEHRPFRLIGIGDT  115 (145)
T ss_dssp             ECCTTTS------SCHHHHHHHHT----TSCEEEECGGGSCHHHHH-----------HHHHHHH--SSSCSSCEEEEESS
T ss_pred             CCCCCcc------hhhhcHHHHcC----CcEEEEcChHHCCHHHHH-----------HHHHHHh--hcCCCEEEEEECCc
Confidence            7765543      12233455543    689999999999765443           3333332  23457889999996


Q ss_pred             -------CCCCChHHHhccceEEEecCCCH
Q 047219          441 -------KQDLDPALISRFDSMITFGLPDH  463 (567)
Q Consensus       441 -------~~~Ld~aL~sRf~~~I~i~~P~~  463 (567)
                             ...++++|++|+ ..+.+..|++
T Consensus       116 ~~~~~~~~~~~~~~L~~rl-~~~~i~lPpL  144 (145)
T 3n70_A          116 SLVELAASNHIIAELYYCF-AMTQIACLPL  144 (145)
T ss_dssp             CHHHHHHHSCCCHHHHHHH-HHHEEECCCC
T ss_pred             CHHHHHHcCCCCHHHHHHh-cCCEEeCCCC
Confidence                   346899999998 5566666764

>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=99.70  E-value=4.3e-17  Score=189.60  Aligned_cols=207  Identities=23%  Similarity=0.305  Sum_probs=145.6

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      .+++|+|++++++.+...+......      +.      ....+..++||+||||||||++|+++|+.+.+.   +.+++
T Consensus       556 l~~~viG~~~a~~~l~~~i~~~~~g------~~------~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~---~~~~i  620 (854)
T 1qvr_A          556 LHKRVVGQDEAIRAVADAIRRARAG------LK------DPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMI  620 (854)
T ss_dssp             HHHHSCSCHHHHHHHHHHHHHHGGG------CS------CSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS---GGGEE
T ss_pred             HhcccCCcHHHHHHHHHHHHHHhcc------cC------CCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC---CCcEE
Confidence            3578999999999999988653110      00      002334689999999999999999999998554   56788


Q ss_pred             EechhhHHhh-----hh-------chhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC
Q 047219          358 YVPLEVVMSK-----YY-------GESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG  425 (567)
Q Consensus       358 ~i~~~~l~s~-----~~-------G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~  425 (567)
                      .++++.+...     ++       |..+  .+ .|..+....+++||||||||.+.+.           +++.|++.++.
T Consensus       621 ~i~~~~~~~~~~~s~l~g~~~~~~G~~~--~g-~l~~~~~~~~~~vl~lDEi~~l~~~-----------~~~~Ll~~l~~  686 (854)
T 1qvr_A          621 RIDMTEYMEKHAVSRLIGAPPGYVGYEE--GG-QLTEAVRRRPYSVILFDEIEKAHPD-----------VFNILLQILDD  686 (854)
T ss_dssp             EECTTTCCSSGGGGGC-----------------CHHHHHHHCSSEEEEESSGGGSCHH-----------HHHHHHHHHTT
T ss_pred             EEechhccchhHHHHHcCCCCCCcCccc--cc-hHHHHHHhCCCeEEEEecccccCHH-----------HHHHHHHHhcc
Confidence            8888765432     33       3222  11 2233333345799999999998643           45666777664


Q ss_pred             cc---------cCCcEEEEEeeCC--------------------------CCCCChHHHhccceEEEecCCCHHHHHHHH
Q 047219          426 FE---------QDKKVVVIAATNR--------------------------KQDLDPALISRFDSMITFGLPDHENRQEIA  470 (567)
Q Consensus       426 ~~---------~~~~viVIaaTN~--------------------------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL  470 (567)
                      ..         .-.+++||+|||.                          ...|+++|++||+..+.|.+|+.++...|+
T Consensus       687 ~~~~~~~g~~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~Rl~~~i~~~pl~~edi~~i~  766 (854)
T 1qvr_A          687 GRLTDSHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIV  766 (854)
T ss_dssp             TEECCSSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHH
T ss_pred             CceECCCCCEeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHHhcCeEEeCCCCCHHHHHHHH
Confidence            32         1147889999997                          346899999999999999999999999999


Q ss_pred             HHHHHh-------------hCHHHHHHHHHhcc--CCCHHHHHHHHHHHHHHHHHHHH
Q 047219          471 AQYAKH-------------LTKAELAELATATE--EMSGRDIRDVCQQAERSWASKII  513 (567)
Q Consensus       471 ~~~~~~-------------~~~~~l~~la~~t~--g~s~~dL~~L~~~a~~~a~~r~i  513 (567)
                      ..++..             +..+.++.++...+  .++.++|+++++.+......+.+
T Consensus       767 ~~~l~~~~~~~~~~~~~~~~~~~a~~~L~~~~~~~~gn~R~L~~~i~~~~~~~~~~~i  824 (854)
T 1qvr_A          767 EIQLSYLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPLAQKI  824 (854)
T ss_dssp             HHHHHHHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCceEEECHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence            887652             45667777877766  67888888888887765555443

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.69  E-value=2.4e-16  Score=171.38  Aligned_cols=184  Identities=21%  Similarity=0.281  Sum_probs=129.7

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -++++|+|.++.++.+.+.+.                     .....++||+||||||||++|+++|+.+...    .+.
T Consensus       177 ~~ld~iiGr~~~i~~l~~~l~---------------------r~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~  235 (468)
T 3pxg_A          177 DSLDPVIGRSKEIQRVIEVLS---------------------RRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILR  235 (468)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHH---------------------CSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTS
T ss_pred             CCCCCccCcHHHHHHHHHHHh---------------------ccCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhc
Confidence            468899999999999888764                     2445789999999999999999999997432    123


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +.+++.+++.   ..+.|+.+..++.+|..+.... ++|||||    .  .         ....+.|+..++    .+.+
T Consensus       236 ~~~~~~l~~~---~~~~g~~e~~~~~~~~~~~~~~-~~iLfiD----~--~---------~~a~~~L~~~L~----~g~v  292 (468)
T 3pxg_A          236 DKRVMTLDMG---TKYRGEFEDRLKKVMDEIRQAG-NIILFID----A--A---------IDASNILKPSLA----RGEL  292 (468)
T ss_dssp             SCCEECC-------------CTTHHHHHHHHHTCC-CCEEEEC----C-------------------CCCTT----SSSC
T ss_pred             CCeEEEeeCC---ccccchHHHHHHHHHHHHHhcC-CeEEEEe----C--c---------hhHHHHHHHhhc----CCCE
Confidence            6678888877   6677887788888999888764 5999999    1  1         112234444443    5689


Q ss_pred             EEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhccCCC-----H
Q 047219          433 VVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATEEMS-----G  494 (567)
Q Consensus       433 iVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~g~s-----~  494 (567)
                      ++|++||...     .++++|++|| ..+.|+.|+.+++.+|++.++..        +.++.+..++..+.+|.     +
T Consensus       293 ~vI~at~~~e~~~~~~~~~al~~Rf-~~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~lp  371 (468)
T 3pxg_A          293 QCIGATTLDEYRKYIEKDAALERRF-QPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLP  371 (468)
T ss_dssp             EEEEECCTTTTHHHHTTCSHHHHSE-EEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTT
T ss_pred             EEEecCCHHHHHHHhhcCHHHHHhC-ccceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcCC
Confidence            9999999876     6999999999 57999999999999999987654        45666676666655544     3


Q ss_pred             HHHHHHHHHHH
Q 047219          495 RDIRDVCQQAE  505 (567)
Q Consensus       495 ~dL~~L~~~a~  505 (567)
                      .....++..+.
T Consensus       372 ~~ai~ll~~a~  382 (468)
T 3pxg_A          372 DKAIDLIDEAG  382 (468)
T ss_dssp             HHHHHHHHHHH
T ss_pred             cHHHHHHHHHH
Confidence            45666666655

>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=99.69  E-value=2.6e-15  Score=145.07  Aligned_cols=190  Identities=21%  Similarity=0.233  Sum_probs=135.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+..|++++|.+..++.+.+.+..                    ...+..++|+||||||||++++++++.+.... ...
T Consensus        18 ~p~~~~~~~g~~~~~~~l~~~l~~--------------------~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~   77 (250)
T 1njg_A           18 RPQTFADVVGQEHVLTALANGLSL--------------------GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA   77 (250)
T ss_dssp             CCCSGGGCCSCHHHHHHHHHHHHH--------------------TCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCS
T ss_pred             CCccHHHHhCcHHHHHHHHHHHHc--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCC
Confidence            345789999999999999887753                    34456899999999999999999999874321 111


Q ss_pred             c-----------------CeEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 V-----------------PLMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~-----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .                 .+..++...      ......+..++..+..   ...+.+|||||+|.+...          
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~~~----------  141 (250)
T 1njg_A           78 TPCGVCDNCREIEQGRFVDLIEIDAAS------RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH----------  141 (250)
T ss_dssp             SCCSCSHHHHHHHTTCCSSEEEEETTC------GGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHH----------
T ss_pred             CCCcccHHHHHHhccCCcceEEecCcc------cccHHHHHHHHHHhhhchhcCCceEEEEECcccccHH----------
Confidence            1                 112222111      0122334445544331   223589999999998533          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       .++.|+..++.  .+.++++|++||.+..+.+.+++|+ ..++++.|+.++..+++..++..    +..+.++.++..+
T Consensus       142 -~~~~l~~~l~~--~~~~~~~i~~t~~~~~~~~~l~~r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~  217 (250)
T 1njg_A          142 -SFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILSRC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAA  217 (250)
T ss_dssp             -HHHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHH
T ss_pred             -HHHHHHHHHhc--CCCceEEEEEeCChHhCCHHHHHHh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHc
Confidence             23445555553  3567899999999999999999998 89999999999999999988753    5677888899888


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +++.+..++..+.
T Consensus       218 ~G-~~~~~~~~~~~~~  232 (250)
T 1njg_A          218 EG-SLRDALSLTDQAI  232 (250)
T ss_dssp             TT-CHHHHHHHHHHHH
T ss_pred             CC-CHHHHHHHHHHHH
Confidence            66 7888888887664

>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=99.68  E-value=4.1e-16  Score=168.34  Aligned_cols=175  Identities=19%  Similarity=0.244  Sum_probs=121.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      +.+++|+||||||||++|+++++++... +.+.+++++++..+...+.+.........|...... .+.+|||||+|.+.
T Consensus       130 ~~~lll~Gp~G~GKTtLa~aia~~l~~~-~~~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~vL~IDEi~~l~  207 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLLQSIGNYVVQN-EPDLRVMYITSEKFLNDLVDSMKEGKLNEFREKYRK-KVDILLIDDVQFLI  207 (440)
T ss_dssp             SCCEEEECSSSSSHHHHHHHHHHHHHHH-CCSSCEEEEEHHHHHHHHHHHHHTTCHHHHHHHHTT-TCSEEEEECGGGGS
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHh-CCCCeEEEeeHHHHHHHHHHHHHcccHHHHHHHhcC-CCCEEEEeCccccc
Confidence            6799999999999999999999987321 115578999998877665544332211223332221 25899999999997


Q ss_pred             hhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCC---CChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh
Q 047219          402 VARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQD---LDPALISRFD--SMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~---Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      .+..         ....|+..++.....+..+||++.+.+..   ++++|++||.  ..+.++.|+.++|.+++...+..
T Consensus       208 ~~~~---------~q~~l~~~l~~l~~~~~~iIitt~~~~~~l~~l~~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~  278 (440)
T 2z4s_A          208 GKTG---------VQTELFHTFNELHDSGKQIVICSDREPQKLSEFQDRLVSRFQMGLVAKLEPPDEETRKSIARKMLEI  278 (440)
T ss_dssp             SCHH---------HHHHHHHHHHHHHTTTCEEEEEESSCGGGCSSCCHHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHH
T ss_pred             CChH---------HHHHHHHHHHHHHHCCCeEEEEECCCHHHHHHHHHHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHH
Confidence            5311         11233333333223445566666565554   8899999995  68999999999999999988763


Q ss_pred             ----hCHHHHHHHHHhccCCCHHHHHHHHHHHHHHH
Q 047219          477 ----LTKAELAELATATEEMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       477 ----~~~~~l~~la~~t~g~s~~dL~~L~~~a~~~a  508 (567)
                          ++.+.++.++..+.| +.+++..++..+...+
T Consensus       279 ~~~~i~~e~l~~la~~~~g-n~R~l~~~L~~~~~~a  313 (440)
T 2z4s_A          279 EHGELPEEVLNFVAENVDD-NLRRLRGAIIKLLVYK  313 (440)
T ss_dssp             HTCCCCTTHHHHHHHHCCS-CHHHHHHHHHHHHHHH
T ss_pred             cCCCCCHHHHHHHHHhcCC-CHHHHHHHHHHHHHHH
Confidence                456678888888764 7888888888776543

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.68  E-value=2.1e-17  Score=151.01  Aligned_cols=133  Identities=15%  Similarity=0.238  Sum_probs=95.8

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +++|.+++++++++.+...                   ...+.+|||+||||||||++|+++|+.+      . +++.++
T Consensus         5 ~~iG~s~~~~~l~~~~~~~-------------------~~~~~~vll~G~~GtGKt~lA~~i~~~~------~-~~~~~~   58 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAA-------------------AKRTSPVFLTGEAGSPFETVARYFHKNG------T-PWVSPA   58 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHH-------------------HTCSSCEEEEEETTCCHHHHHGGGCCTT------S-CEECCS
T ss_pred             CceeCCHHHHHHHHHHHHH-------------------hCCCCcEEEECCCCccHHHHHHHHHHhC------C-CeEEec
Confidence            5889999999999988754                   3456789999999999999999999987      3 788899


Q ss_pred             hhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC
Q 047219          361 LEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR  440 (567)
Q Consensus       361 ~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~  440 (567)
                      +..+...+       ....++.+.    +++|||||||.+....|..+.           ..++.. ...++++|+|||.
T Consensus        59 ~~~~~~~~-------~~~~~~~a~----~~~l~lDei~~l~~~~q~~Ll-----------~~l~~~-~~~~~~iI~~tn~  115 (143)
T 3co5_A           59 RVEYLIDM-------PMELLQKAE----GGVLYVGDIAQYSRNIQTGIT-----------FIIGKA-ERCRVRVIASCSY  115 (143)
T ss_dssp             STTHHHHC-------HHHHHHHTT----TSEEEEEECTTCCHHHHHHHH-----------HHHHHH-TTTTCEEEEEEEE
T ss_pred             hhhCChHh-------hhhHHHhCC----CCeEEEeChHHCCHHHHHHHH-----------HHHHhC-CCCCEEEEEecCC
Confidence            88776544       334555443    689999999999866544333           222221 1457889999985


Q ss_pred             C-CC----CChHHHhccceEEEecCCCH
Q 047219          441 K-QD----LDPALISRFDSMITFGLPDH  463 (567)
Q Consensus       441 ~-~~----Ld~aL~sRf~~~I~i~~P~~  463 (567)
                      + ..    ++++|++|| ..+.+.+|++
T Consensus       116 ~~~~~~~~~~~~L~~rl-~~~~i~lPpL  142 (143)
T 3co5_A          116 AAGSDGISCEEKLAGLF-SESVVRIPPL  142 (143)
T ss_dssp             CTTTC--CHHHHHHHHS-SSEEEEECCC
T ss_pred             CHHHHHhCccHHHHHHh-cCcEEeCCCC
Confidence            3 22    678899998 5556666664

>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding, transport protein; HET: MLY; 2.00A {Homo sapiens} PDB: 2pjh_B

Probab=99.67  E-value=4.8e-18  Score=164.88  Aligned_cols=110  Identities=13%  Similarity=0.198  Sum_probs=92.8

Q ss_pred             chhhhH-HHHHHHhCCCCCCccceEEEEecce--EEEEEEecC-CC--CcchHHHHHHHhhCceecccCCCceeEEEee-
Q 047219          111 KERQRI-EELLKRKGMHYGSCPTFTVAVKGQK--VTIKFQVPP-AC--EIPQLIANLVSHLGLKVEEHGGGSDMGLRAW-  183 (567)
Q Consensus       111 ~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~--~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~-  183 (567)
                      +|++|| ++.|++||+.+||+    |+|+|++  .|+|+|||+ .+  +++++++.+|+|+|+++||     .|+|+++ 
T Consensus        39 rgivrl~p~~m~~Lgl~~GD~----V~I~Gkr~k~Tva~v~~~~~~~~g~Irid~~~R~N~gV~iGD-----~V~V~~~~  109 (211)
T 3qwz_A           39 NSVVSLSQPKMDELQLFRGDT----VLLKGXKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGD-----VISIQPCP  109 (211)
T ss_dssp             TTEEEECHHHHHHHTCCBTCE----EEEECSTTCEEEEEEEECTTSCTTEEEECHHHHHHTTCCTTC-----EEEEEECT
T ss_pred             CcEEEECHHHHHHcCCCCCCE----EEEeCCCCCcEEEEEEeCCCCCCCEEEeCHHHHhhcCCCCCC-----EEEEEECC
Confidence            899999 69999999999999    9999998  899999997 33  6799999999999999999     9999999 


Q ss_pred             cccccceeEecCCCCccc-cCCCccccCcccccccchheee--eceeecCCCCcee
Q 047219          184 DSAVAWQLTLKPPEKQNE-SGGDRAQSGDMNAREGDLCILI--FRSLITSDKPEIE  236 (567)
Q Consensus       184 ~~~~a~~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~~~~  236 (567)
                      ++++|++|+|+|..+++. +.++.       ...+....+.  ++|+..||.+.+.
T Consensus       110 ~v~~A~~V~LaP~~~~i~~i~~~~-------~~~~lk~~l~~~~rPV~~GD~i~v~  158 (211)
T 3qwz_A          110 DVKYGKRIHVLPIDDTVEGITGNL-------FEVYLKPYFLEAYRPIRKGDIFLVR  158 (211)
T ss_dssp             TCCBCSEEEEEEBGGGCTTCCSCH-------HHHTTHHHHTTCCEEEETTCEEECC
T ss_pred             CCCCceEEEEeccCcchhccCchh-------HHHHHHHHHhhCCceeecCCEEEEc
Confidence            899999999999866554 33330       0134556675  7999999988665

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.66  E-value=2e-15  Score=157.54  Aligned_cols=210  Identities=20%  Similarity=0.218  Sum_probs=142.0

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC---C
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP---W  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~---~  351 (567)
                      +....++++|.++.++.+.+.+...+                 ....+.+++|+||||||||++|+++++.+....   .
T Consensus        14 ~~~~p~~~~gr~~~~~~l~~~l~~~~-----------------~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~   76 (387)
T 2v1u_A           14 PDYVPDVLPHREAELRRLAEVLAPAL-----------------RGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLG   76 (387)
T ss_dssp             TTCCCSCCTTCHHHHHHHHHTTGGGT-----------------SSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHT
T ss_pred             CccCCCCCCCHHHHHHHHHHHHHHHH-----------------cCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccC
Confidence            33455899999999999887664321                 135678999999999999999999999873210   0


Q ss_pred             CCcCeEEechhhHH------hhhh----------ch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          352 QGVPLMYVPLEVVM------SKYY----------GE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       352 ~~~~~~~i~~~~l~------s~~~----------G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      .+..++++++....      ..+.          |. ....+..++........+.+|||||+|.+....      ..++
T Consensus        77 ~~~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~------~~~~  150 (387)
T 2v1u_A           77 VLVKPIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRP------GGQD  150 (387)
T ss_dssp             CCEEEEEEETTTSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHST------THHH
T ss_pred             CCeEEEEEECCcCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccC------CCCh
Confidence            13467778765321      1111          11 223344455544444335799999999996542      0134


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCC---CCCChHHHhccce-EEEecCCCHHHHHHHHHHHHHh------hCHHHHHH
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRK---QDLDPALISRFDS-MITFGLPDHENRQEIAAQYAKH------LTKAELAE  484 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~---~~Ld~aL~sRf~~-~I~i~~P~~~eR~eIL~~~~~~------~~~~~l~~  484 (567)
                      .+..++..++......++.+|++||.+   +.+++.+++||.. .+.|+.|+.++..+++...+..      +..+.++.
T Consensus       151 ~l~~l~~~~~~~~~~~~~~~I~~t~~~~~~~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~  230 (387)
T 2v1u_A          151 LLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPL  230 (387)
T ss_dssp             HHHHHHHGGGCC-----CEEEEECSCSTTSSSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHH
T ss_pred             HHHhHhhchhhcCCCceEEEEEEECCCchHhhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHH
Confidence            455566665543225688999999987   7899999999975 8999999999999999988763      44556777


Q ss_pred             HHHhcc---CCCHHHHHHHHHHHHHHH
Q 047219          485 LATATE---EMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       485 la~~t~---g~s~~dL~~L~~~a~~~a  508 (567)
                      ++..+.   | .++.+..++..++..+
T Consensus       231 l~~~~~~~~G-~~r~~~~~l~~a~~~a  256 (387)
T 2v1u_A          231 CAALAAREHG-DARRALDLLRVAGEIA  256 (387)
T ss_dssp             HHHHHHSSSC-CHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcc-CHHHHHHHHHHHHHHH
Confidence            777776   5 5677778888777544

>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=99.66  E-value=1.7e-15  Score=147.48  Aligned_cols=190  Identities=15%  Similarity=0.170  Sum_probs=127.6

Q ss_pred             CCCCCcccccCc---HHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          274 KSEISWENIAGY---DQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       274 ~~~~~~~dIiG~---~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      .+..+|++++|.   ..+++.+...+.                     ...+.+++|+||||||||++|+++++++... 
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~l~~~~~---------------------~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~-   79 (242)
T 3bos_A           22 PDDETFTSYYPAAGNDELIGALKSAAS---------------------GDGVQAIYLWGPVKSGRTHLIHAACARANEL-   79 (242)
T ss_dssp             CTTCSTTTSCC--CCHHHHHHHHHHHH---------------------TCSCSEEEEECSTTSSHHHHHHHHHHHHHHT-
T ss_pred             CCCCChhhccCCCCCHHHHHHHHHHHh---------------------CCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-
Confidence            345789999972   355555554432                     2356899999999999999999999988543 


Q ss_pred             CCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          351 WQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                        +.++.++++..+...+...        +.   ....+.+|||||+|.+.....         ....++..++.....+
T Consensus        80 --~~~~~~~~~~~~~~~~~~~--------~~---~~~~~~vliiDe~~~~~~~~~---------~~~~l~~~l~~~~~~~  137 (242)
T 3bos_A           80 --ERRSFYIPLGIHASISTAL--------LE---GLEQFDLICIDDVDAVAGHPL---------WEEAIFDLYNRVAEQK  137 (242)
T ss_dssp             --TCCEEEEEGGGGGGSCGGG--------GT---TGGGSSEEEEETGGGGTTCHH---------HHHHHHHHHHHHHHHC
T ss_pred             --CCeEEEEEHHHHHHHHHHH--------HH---hccCCCEEEEeccccccCCHH---------HHHHHHHHHHHHHHcC
Confidence              4678888887766543111        11   112358999999999875531         0122223322222233


Q ss_pred             cEEEEEeeC-CCC---CCChHHHhccc--eEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          431 KVVVIAATN-RKQ---DLDPALISRFD--SMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       431 ~viVIaaTN-~~~---~Ld~aL~sRf~--~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                      .+.+|+++| .+.   .+.+++++||.  ..++++.|+.+++.+++..++..    +..+.++.++..+.| +.+++.++
T Consensus       138 ~~~ii~~~~~~~~~~~~~~~~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~l~~~  216 (242)
T 3bos_A          138 RGSLIVSASASPMEAGFVLPDLVSRMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRMAR-DLRTLFDV  216 (242)
T ss_dssp             SCEEEEEESSCTTTTTCCCHHHHHHHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHTTT-CHHHHHHH
T ss_pred             CCeEEEEcCCCHHHHHHhhhhhhhHhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHccC-CHHHHHHH
Confidence            443444554 333   45699999996  79999999999999999998764    567788888887754 67777777


Q ss_pred             HHHHHHHH
Q 047219          501 CQQAERSW  508 (567)
Q Consensus       501 ~~~a~~~a  508 (567)
                      +..+...+
T Consensus       217 l~~~~~~a  224 (242)
T 3bos_A          217 LDRLDKAS  224 (242)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77766543

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.65  E-value=5.7e-16  Score=144.66  Aligned_cols=157  Identities=22%  Similarity=0.303  Sum_probs=111.4

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      ..|++++|.+++++.+.+.+.                     ...+.+++|+||||||||++|+++++.+...    ...
T Consensus        19 ~~~~~~~g~~~~~~~l~~~l~---------------------~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~   77 (187)
T 2p65_A           19 GKLDPVIGRDTEIRRAIQILS---------------------RRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLK   77 (187)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHT---------------------SSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTT
T ss_pred             cccchhhcchHHHHHHHHHHh---------------------CCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhc
Confidence            468899999999988877653                     3446789999999999999999999987431    112


Q ss_pred             CcCeEEechhhHHh--hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhh-hhhHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARD-SEMHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s--~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q-~~l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.+++.+++..+..  .+.+.....+..++..+.....+.+|||||+|.+..... ....   ..+.+.+...++    .
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~---~~~~~~l~~~~~----~  150 (187)
T 2p65_A           78 GRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGA---LDAGNILKPMLA----R  150 (187)
T ss_dssp             TCEEEEECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSSCTTS---CCTHHHHHHHHH----T
T ss_pred             CCeEEEEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccccccc---hHHHHHHHHHHh----c
Confidence            56788888877653  245556667777777776654457999999999974432 1000   111222333332    3


Q ss_pred             CcEEEEEeeCCCC-----CCChHHHhccceEEEecCCC
Q 047219          430 KKVVVIAATNRKQ-----DLDPALISRFDSMITFGLPD  462 (567)
Q Consensus       430 ~~viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~  462 (567)
                      .++++|+++|.+.     .++++|++||. .++++.|+
T Consensus       151 ~~~~ii~~~~~~~~~~~~~~~~~l~~R~~-~i~i~~p~  187 (187)
T 2p65_A          151 GELRCIGATTVSEYRQFIEKDKALERRFQ-QILVEQPS  187 (187)
T ss_dssp             TCSCEEEEECHHHHHHHTTTCHHHHHHEE-EEECCSCC
T ss_pred             CCeeEEEecCHHHHHHHHhccHHHHHhcC-cccCCCCC
Confidence            5678999998765     68999999995 68898885

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.65  E-value=4e-16  Score=161.28  Aligned_cols=166  Identities=19%  Similarity=0.211  Sum_probs=105.9

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      +++++|++++++.+...+..                       +.++||+||||||||++|+++++.+      +.++..
T Consensus        26 ~~~i~g~~~~~~~l~~~l~~-----------------------~~~vll~G~pGtGKT~la~~la~~~------~~~~~~   76 (331)
T 2r44_A           26 GKVVVGQKYMINRLLIGICT-----------------------GGHILLEGVPGLAKTLSVNTLAKTM------DLDFHR   76 (331)
T ss_dssp             TTTCCSCHHHHHHHHHHHHH-----------------------TCCEEEESCCCHHHHHHHHHHHHHT------TCCEEE
T ss_pred             ccceeCcHHHHHHHHHHHHc-----------------------CCeEEEECCCCCcHHHHHHHHHHHh------CCCeEE
Confidence            46799999999888766531                       3589999999999999999999998      556776


Q ss_pred             echh--hHHhhhhchhHH-HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEE
Q 047219          359 VPLE--VVMSKYYGESER-LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVI  435 (567)
Q Consensus       359 i~~~--~l~s~~~G~~~~-~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVI  435 (567)
                      +++.  ...+.+.|.... .....|......-.+++|||||+|.+.+..+..+...+++....+  .......+.++++|
T Consensus        77 i~~~~~~~~~~l~g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~~~~~~Ll~~l~~~~~~~--~g~~~~~~~~~~vi  154 (331)
T 2r44_A           77 IQFTPDLLPSDLIGTMIYNQHKGNFEVKKGPVFSNFILADEVNRSPAKVQSALLECMQEKQVTI--GDTTYPLDNPFLVL  154 (331)
T ss_dssp             EECCTTCCHHHHHEEEEEETTTTEEEEEECTTCSSEEEEETGGGSCHHHHHHHHHHHHHSEEEE--TTEEEECCSSCEEE
T ss_pred             EecCCCCChhhcCCceeecCCCCceEeccCcccccEEEEEccccCCHHHHHHHHHHHhcCceee--CCEEEECCCCEEEE
Confidence            6652  111122221000 000000000000013799999999987664443333222100000  00011235678999


Q ss_pred             EeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          436 AATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       436 aaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +|+|+.+     .++++|++||+..+.++.|+.+++.+|++..+.
T Consensus       155 at~np~~~~~~~~l~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~  199 (331)
T 2r44_A          155 ATQNPVEQEGTYPLPEAQVDRFMMKIHLTYLDKESELEVMRRVSN  199 (331)
T ss_dssp             EEECTTCCSCCCCCCHHHHTTSSEEEECCCCCHHHHHHHHHHHHC
T ss_pred             EecCCCcccCcccCCHHHHhheeEEEEcCCCCHHHHHHHHHhccc
Confidence            9999654     389999999977899999999999999988764

>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=99.64  E-value=4.6e-15  Score=172.58  Aligned_cols=201  Identities=21%  Similarity=0.286  Sum_probs=133.5

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -+|++++|.++.++.+.+.+.                     .....+++|+||||||||++|+++|+.+...    ...
T Consensus       167 ~~ld~viGr~~~i~~l~~~l~---------------------~~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~  225 (854)
T 1qvr_A          167 GKLDPVIGRDEEIRRVIQILL---------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLK  225 (854)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHH---------------------CSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTST
T ss_pred             CCCcccCCcHHHHHHHHHHHh---------------------cCCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhc
Confidence            578999999999998887663                     3456789999999999999999999987321    122


Q ss_pred             CcCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +.+++++++..+.  .++.|+.+..+..+|..+.....++||||||+|.|.+.......   ....+.|...++    .+
T Consensus       226 ~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~---~~~~~~L~~~l~----~~  298 (854)
T 1qvr_A          226 GKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA---VDAGNMLKPALA----RG  298 (854)
T ss_dssp             TCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC----------------------HHHHH----TT
T ss_pred             CCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccch---HHHHHHHHHHHh----CC
Confidence            6678899988876  56788888999999998886544689999999999765432211   122233444443    35


Q ss_pred             cEEEEEeeCCCC----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhcc-----CCC
Q 047219          431 KVVVIAATNRKQ----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATE-----EMS  493 (567)
Q Consensus       431 ~viVIaaTN~~~----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~-----g~s  493 (567)
                      .+.+|++||.+.    .++++|.+||+ .+.|+.|+.+++.+|++.++..        +.++.+..++..+.     .+.
T Consensus       299 ~i~~I~at~~~~~~~~~~d~aL~rRf~-~i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~l  377 (854)
T 1qvr_A          299 ELRLIGATTLDEYREIEKDPALERRFQ-PVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRL  377 (854)
T ss_dssp             CCCEEEEECHHHHHHHTTCTTTCSCCC-CEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCT
T ss_pred             CeEEEEecCchHHhhhccCHHHHhCCc-eEEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccC
Confidence            778999998754    47999999995 5999999999999999877653        34556666655443     355


Q ss_pred             HHHHHHHHHHHHH
Q 047219          494 GRDIRDVCQQAER  506 (567)
Q Consensus       494 ~~dL~~L~~~a~~  506 (567)
                      +.....++.++..
T Consensus       378 p~kai~lldea~a  390 (854)
T 1qvr_A          378 PDKAIDLIDEAAA  390 (854)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHH
Confidence            6666677766653

>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=99.64  E-value=1.1e-14  Score=148.96  Aligned_cols=193  Identities=19%  Similarity=0.197  Sum_probs=131.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++++++.+...+..                     ....++||+||||||||++|+++++.+.... ..
T Consensus        19 ~~p~~~~~~~g~~~~~~~l~~~l~~---------------------~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~-~~   76 (327)
T 1iqp_A           19 YRPQRLDDIVGQEHIVKRLKHYVKT---------------------GSMPHLLFAGPPGVGKTTAALALARELFGEN-WR   76 (327)
T ss_dssp             TCCCSTTTCCSCHHHHHHHHHHHHH---------------------TCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-HH
T ss_pred             cCCCCHHHhhCCHHHHHHHHHHHHc---------------------CCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-cc
Confidence            4456899999999999999887752                     2233599999999999999999999863210 02


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHH-hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLA-NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A-~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      ..++.++++.....  ......+....... ...+.+.+|||||+|.+....           .+.|+..++.  .+.++
T Consensus        77 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~~-----------~~~L~~~le~--~~~~~  141 (327)
T 1iqp_A           77 HNFLELNASDERGI--NVIREKVKEFARTKPIGGASFKIIFLDEADALTQDA-----------QQALRRTMEM--FSSNV  141 (327)
T ss_dssp             HHEEEEETTCHHHH--HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHHH-----------HHHHHHHHHH--TTTTE
T ss_pred             CceEEeeccccCch--HHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCHHH-----------HHHHHHHHHh--cCCCC
Confidence            34666666543221  01111122211110 011346899999999996442           2344444542  34678


Q ss_pred             EEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          433 VVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       433 iVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      ++|++||.+..+.+++.+|| ..+.|+.|+.++..+++...+..    +..+.++.++..+.| +.+.+.++++.++
T Consensus       142 ~~i~~~~~~~~l~~~l~sr~-~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~g-~~r~~~~~l~~~~  216 (327)
T 1iqp_A          142 RFILSCNYSSKIIEPIQSRC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG-DMRRAINILQAAA  216 (327)
T ss_dssp             EEEEEESCGGGSCHHHHHTE-EEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT-CHHHHHHHHHHHH
T ss_pred             eEEEEeCCccccCHHHHhhC-cEEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHCCC-CHHHHHHHHHHHH
Confidence            89999999999999999999 58999999999999999887753    567778888887655 5555555555444

>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=99.63  E-value=3.5e-15  Score=154.58  Aligned_cols=192  Identities=19%  Similarity=0.180  Sum_probs=129.9

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++++++.+...+.                     .....++||+||||||||++|+++++.+.......
T Consensus        31 ~~p~~~~~i~g~~~~~~~l~~~l~---------------------~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~   89 (353)
T 1sxj_D           31 YRPKNLDEVTAQDHAVTVLKKTLK---------------------SANLPHMLFYGPPGTGKTSTILALTKELYGPDLMK   89 (353)
T ss_dssp             TCCSSTTTCCSCCTTHHHHHHHTT---------------------CTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHT
T ss_pred             cCCCCHHHhhCCHHHHHHHHHHHh---------------------cCCCCEEEEECCCCCCHHHHHHHHHHHhCCCcccc
Confidence            345689999999999988877653                     22234599999999999999999999863210002


Q ss_pred             cCeEEechhhHHh-hhhchhHHHHHHHHHH------------HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHH
Q 047219          354 VPLMYVPLEVVMS-KYYGESERLLGKVFSL------------ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL  420 (567)
Q Consensus       354 ~~~~~i~~~~l~s-~~~G~~~~~l~~~f~~------------A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL  420 (567)
                      ..+..+++..... ..+.   ..+.. +..            ......+.+|||||+|.+....+           +.|+
T Consensus        90 ~~~~~~~~~~~~~~~~~~---~~~~~-~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~~~~-----------~~Ll  154 (353)
T 1sxj_D           90 SRILELNASDERGISIVR---EKVKN-FARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQ-----------SALR  154 (353)
T ss_dssp             TSEEEECSSSCCCHHHHT---THHHH-HHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHHHH-----------HHHH
T ss_pred             cceEEEccccccchHHHH---HHHHH-HhhhcccccchhhcccCCCCCceEEEEECCCccCHHHH-----------HHHH
Confidence            3466666554211 1111   11111 111            11123457999999999975533           3444


Q ss_pred             HhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHH
Q 047219          421 RQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRD  496 (567)
Q Consensus       421 ~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~d  496 (567)
                      ..++.  ...++++|.+||.+..+.+++++|| ..+.+..|+.++...++...+..    +..+.++.++..+.| ..+.
T Consensus       155 ~~le~--~~~~~~~il~~~~~~~l~~~l~sR~-~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~r~  230 (353)
T 1sxj_D          155 RTMET--YSGVTRFCLICNYVTRIIDPLASQC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAG-DLRR  230 (353)
T ss_dssp             HHHHH--TTTTEEEEEEESCGGGSCHHHHHHS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS-CHHH
T ss_pred             HHHHh--cCCCceEEEEeCchhhCcchhhccC-ceEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHH
Confidence            44443  2346778888999999999999999 68999999999999999987753    567788888888876 3445


Q ss_pred             HHHHHHHHH
Q 047219          497 IRDVCQQAE  505 (567)
Q Consensus       497 L~~L~~~a~  505 (567)
                      +.+++..++
T Consensus       231 ~~~~l~~~~  239 (353)
T 1sxj_D          231 GITLLQSAS  239 (353)
T ss_dssp             HHHHHHHTH
T ss_pred             HHHHHHHHH
Confidence            445555444

>2chq_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATP ATP-binding, nucleotide-binding; HET: ANP; 3.5A {Archaeoglobus fulgidus} PDB: 2chv_A

Probab=99.63  E-value=2.7e-15  Score=152.85  Aligned_cols=192  Identities=19%  Similarity=0.216  Sum_probs=130.9

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ...+.+|++++|++..++.+.+.+.                     .....++||+||||||||++|+++++.+....+ 
T Consensus        10 k~~p~~~~~~~g~~~~~~~l~~~l~---------------------~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~~-   67 (319)
T 2chq_A           10 KYRPRTLDEVVGQDEVIQRLKGYVE---------------------RKNIPHLLFSGPPGTGKTATAIALARDLFGENW-   67 (319)
T ss_dssp             TTSCSSGGGSCSCHHHHHHHHTTTT---------------------TTCCCCEEEESSSSSSHHHHHHHHHHHHHTTCH-
T ss_pred             hcCCCCHHHHhCCHHHHHHHHHHHh---------------------CCCCCeEEEECcCCcCHHHHHHHHHHHhcCCcc-
Confidence            3455789999999999998876553                     122334999999999999999999998732211 


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHh-cCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLAN-ELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~-~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..+++.++++...+.  ......+........ ...++.+|||||+|.+...           ..+.|+..++.  .+.+
T Consensus        68 ~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~~-----------~~~~L~~~le~--~~~~  132 (319)
T 2chq_A           68 RDNFIEMNASDERGI--DVVRHKIKEFARTAPIGGAPFKIIFLDEADALTAD-----------AQAALRRTMEM--YSKS  132 (319)
T ss_dssp             HHHCEEEETTSTTCT--TTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCHH-----------HHHTTGGGTSS--SSSS
T ss_pred             cCCeEEEeCccccCh--HHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCHH-----------HHHHHHHHHHh--cCCC
Confidence            234666766543221  111112222211111 1134689999999998643           23455666663  3568


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      +++|++||.+..+.+++++|| ..+.|..|+.+++.+++...+..    +..+.++.++..+.| +.+.+.++++.
T Consensus       133 ~~~i~~~~~~~~l~~~l~sr~-~~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~r~~~~~l~~  206 (319)
T 2chq_A          133 CRFILSCNYVSRIIEPIQSRC-AVFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYISGG-DFRKAINALQG  206 (319)
T ss_dssp             EEEEEEESCGGGSCHHHHTTC-EEEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHTTTT-CHHHHHHHHHH
T ss_pred             CeEEEEeCChhhcchHHHhhC-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHH
Confidence            899999999999999999999 69999999999999999988764    467778888866544 34444444433

>1r6b_X CLPA protein; AAA+, N-terminal domain, CLPS, crystal, binding mechanism, hydrolase; HET: ADP; 2.25A {Escherichia coli} SCOP: a.174.1.1 c.37.1.20 c.37.1.20 PDB: 1ksf_X*

Probab=99.63  E-value=2.7e-15  Score=172.19  Aligned_cols=200  Identities=18%  Similarity=0.233  Sum_probs=143.5

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -.|++++|.++.++.+.+.+.                     ...+.++||+||||||||++|+++|+.+...    .+.
T Consensus       183 ~~~d~~iGr~~~i~~l~~~l~---------------------~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~  241 (758)
T 1r6b_X          183 GGIDPLIGREKELERAIQVLC---------------------RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMA  241 (758)
T ss_dssp             TCSCCCCSCHHHHHHHHHHHT---------------------SSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGT
T ss_pred             CCCCCccCCHHHHHHHHHHHh---------------------ccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhc
Confidence            468899999999999887663                     3456789999999999999999999987432    112


Q ss_pred             CcCeEEechhhHH--hhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          353 GVPLMYVPLEVVM--SKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       353 ~~~~~~i~~~~l~--s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                      +..++.++...+.  .++.|+.+..+..+|..+.... ++||||||+|.|.+.......  .....+.|...+    ..+
T Consensus       242 ~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~-~~iL~IDEi~~l~~~~~~~~~--~~~~~~~L~~~l----~~~  314 (758)
T 1r6b_X          242 DCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDT-NSILFIDEIHTIIGAGAASGG--QVDAANLIKPLL----SSG  314 (758)
T ss_dssp             TCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSS-CEEEEETTTTTTTTSCCSSSC--HHHHHHHHSSCS----SSC
T ss_pred             CCEEEEEcHHHHhccccccchHHHHHHHHHHHHHhcC-CeEEEEechHHHhhcCCCCcc--hHHHHHHHHHHH----hCC
Confidence            4556777766665  4577888889999999887654 599999999999765432111  111222333333    356


Q ss_pred             cEEEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhccC-----C
Q 047219          431 KVVVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATEE-----M  492 (567)
Q Consensus       431 ~viVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~g-----~  492 (567)
                      .+.+|++||.++     .++++|.+||. .+.|+.|+.+++.+|++.+..+        +..+.+..++..+.+     +
T Consensus       315 ~~~~I~at~~~~~~~~~~~d~aL~~Rf~-~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~~~~al~~~~~~s~~~i~~~~  393 (758)
T 1r6b_X          315 KIRVIGSTTYQEFSNIFEKDRALARRFQ-KIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRH  393 (758)
T ss_dssp             CCEEEEEECHHHHHCCCCCTTSSGGGEE-EEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSC
T ss_pred             CeEEEEEeCchHHhhhhhcCHHHHhCce-EEEcCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhccccc
Confidence            889999998643     57899999995 8999999999999999987754        345556666655544     4


Q ss_pred             CHHHHHHHHHHHH
Q 047219          493 SGRDIRDVCQQAE  505 (567)
Q Consensus       493 s~~dL~~L~~~a~  505 (567)
                      .+..+..++.++.
T Consensus       394 lp~~~i~lld~a~  406 (758)
T 1r6b_X          394 LPDKAIDVIDEAG  406 (758)
T ss_dssp             TTHHHHHHHHHHH
T ss_pred             CchHHHHHHHHHH
Confidence            4566777777665

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.62  E-value=2.5e-15  Score=172.58  Aligned_cols=185  Identities=21%  Similarity=0.278  Sum_probs=130.3

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ  352 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~  352 (567)
                      -.+++|+|.++.++.+.+.+.                     .....++||+||||||||++|+++|+.+...    ...
T Consensus       177 ~~ld~iiG~~~~i~~l~~~l~---------------------~~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~  235 (758)
T 3pxi_A          177 DSLDPVIGRSKEIQRVIEVLS---------------------RRTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILR  235 (758)
T ss_dssp             SCSCCCCCCHHHHHHHHHHHH---------------------CSSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTS
T ss_pred             CCCCCccCchHHHHHHHHHHh---------------------CCCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhc
Confidence            468899999999999988764                     3456789999999999999999999997332    123


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcE
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKV  432 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~v  432 (567)
                      +..++.+++   ..++.|+.+..++.+|..+.... ++|||||  ..             ....+.|+..++    .+.+
T Consensus       236 ~~~~~~~~~---g~~~~G~~e~~l~~~~~~~~~~~-~~iLfiD--~~-------------~~~~~~L~~~l~----~~~v  292 (758)
T 3pxi_A          236 DKRVMTLDM---GTKYRGEFEDRLKKVMDEIRQAG-NIILFID--AA-------------IDASNILKPSLA----RGEL  292 (758)
T ss_dssp             SCCEECC-------------CTTHHHHHHHHHTCC-CCEEEEC--C---------------------CCCTT----SSSC
T ss_pred             CCeEEEecc---cccccchHHHHHHHHHHHHHhcC-CEEEEEc--Cc-------------hhHHHHHHHHHh----cCCE
Confidence            556777766   56678888889999999988754 5999999  11             112234444443    5689


Q ss_pred             EEEEeeCCCC-----CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--------hCHHHHHHHHHhcc-----CCCH
Q 047219          433 VVIAATNRKQ-----DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--------LTKAELAELATATE-----EMSG  494 (567)
Q Consensus       433 iVIaaTN~~~-----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--------~~~~~l~~la~~t~-----g~s~  494 (567)
                      ++|++||...     .++++|++|| ..+.|+.|+.+++.+|++.+...        +....+..++..+.     ++.+
T Consensus       293 ~~I~at~~~~~~~~~~~d~al~rRf-~~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p  371 (758)
T 3pxi_A          293 QCIGATTLDEYRKYIEKDAALERRF-QPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLP  371 (758)
T ss_dssp             EEEEECCTTTTHHHHTTCSHHHHSE-EEEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTT
T ss_pred             EEEeCCChHHHHHHhhccHHHHhhC-cEEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCC
Confidence            9999999887     7999999999 77999999999999999977654        34555555555443     4456


Q ss_pred             HHHHHHHHHHHH
Q 047219          495 RDIRDVCQQAER  506 (567)
Q Consensus       495 ~dL~~L~~~a~~  506 (567)
                      .....++..+..
T Consensus       372 ~~ai~ll~~a~~  383 (758)
T 3pxi_A          372 DKAIDLIDEAGS  383 (758)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHH
Confidence            666677766654

>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=99.62  E-value=4e-14  Score=148.17  Aligned_cols=203  Identities=17%  Similarity=0.182  Sum_probs=142.0

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCc--eEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPR--AVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~--~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .+..++++|.+++++.+.+.+...+.                 ...+.  +++|+||||||||++++++++.+....  +
T Consensus        13 ~~~p~~l~gr~~~~~~l~~~l~~~~~-----------------~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~--~   73 (389)
T 1fnn_A           13 SYVPKRLPHREQQLQQLDILLGNWLR-----------------NPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT--T   73 (389)
T ss_dssp             TCCCSCCTTCHHHHHHHHHHHHHHHH-----------------STTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC--C
T ss_pred             ccCCCCCCChHHHHHHHHHHHHHHHc-----------------CCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhc--C
Confidence            34558899999999999988864321                 23344  899999999999999999999985431  3


Q ss_pred             cCeEEechhhHH------hhh---h-------ch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHH
Q 047219          354 VPLMYVPLEVVM------SKY---Y-------GE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRIL  416 (567)
Q Consensus       354 ~~~~~i~~~~l~------s~~---~-------G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl  416 (567)
                      ..++++++....      ..+   +       +. .......+.........+.+|||||+|.+.           ...+
T Consensus        74 ~~~~~i~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~-----------~~~~  142 (389)
T 1fnn_A           74 ARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLA-----------PDIL  142 (389)
T ss_dssp             CEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSC-----------HHHH
T ss_pred             eeEEEEeCccCCCHHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECccccc-----------hHHH
Confidence            457777754322      111   1       11 122222333333333335799999999983           1234


Q ss_pred             HHHHHhhcCccc--CCcEEEEEeeCCC---CCCChHHHhccce-EEEecCCCHHHHHHHHHHHHHh------hCHHHHHH
Q 047219          417 SVLLRQIDGFEQ--DKKVVVIAATNRK---QDLDPALISRFDS-MITFGLPDHENRQEIAAQYAKH------LTKAELAE  484 (567)
Q Consensus       417 ~~LL~~ld~~~~--~~~viVIaaTN~~---~~Ld~aL~sRf~~-~I~i~~P~~~eR~eIL~~~~~~------~~~~~l~~  484 (567)
                      ..|+..++....  ..++.+|++||.+   ..+++.+.+||.. .+.|++++.++..+++...+..      +..+.++.
T Consensus       143 ~~L~~~~~~~~~~~~~~~~iI~~~~~~~~~~~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~  222 (389)
T 1fnn_A          143 STFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQM  222 (389)
T ss_dssp             HHHHHHTTCHHHHSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHH
T ss_pred             HHHHHHHHhCCCCCcCCEEEEEEECCchHHHHhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHH
Confidence            556666654322  2588999999887   6789999999964 8999999999999999988764      66778888


Q ss_pred             HHHhcc--------CCCHHHHHHHHHHHHHHH
Q 047219          485 LATATE--------EMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       485 la~~t~--------g~s~~dL~~L~~~a~~~a  508 (567)
                      ++..++        +-..+.+..++..++..+
T Consensus       223 l~~~~~~~~~~~~~~G~~r~~~~~l~~a~~~a  254 (389)
T 1fnn_A          223 IADITGAQTPLDTNRGDARLAIDILYRSAYAA  254 (389)
T ss_dssp             HHHHHSBSSTTCTTSCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhcccCCCCCCcHHHHHHHHHHHHHHH
Confidence            988884        335777888888877544

>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate recognition DOM hydrolase; NMR {Thermoplasma acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A

Probab=99.62  E-value=1.6e-16  Score=151.74  Aligned_cols=112  Identities=17%  Similarity=0.171  Sum_probs=96.3

Q ss_pred             hcchhhhH-HHHHHHhCCCCCCccceEEEEecceEEEEEEecC-CC----CcchHHHHHHHhhCceecccCCCceeEEEe
Q 047219          109 AKKERQRI-EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPP-AC----EIPQLIANLVSHLGLKVEEHGGGSDMGLRA  182 (567)
Q Consensus       109 ~~~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~~~~~~~~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~  182 (567)
                      +|||++|| ++.|++||+.+||+    |+|+|++.++|++||+ ..    +++++++.+|+|+|+++||     .|+|++
T Consensus        19 ~gr~ivrl~p~~m~~Lgl~~GD~----V~I~G~r~t~a~v~~~~~ed~~~g~Irid~~~R~N~gv~iGD-----~V~V~~   89 (185)
T 1cz4_A           19 PGMSRVRLDESSRRLLDAEIGDV----VEIEKVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGD-----KVKVRK   89 (185)
T ss_dssp             CCSSEEEECHHHHHTTCCCTTCE----EEEESSSEEEEEEEECSSTTTTTSEEECCHHHHHHHTCCTTC-----EEEEEE
T ss_pred             cCCCEEEECHHHHHHcCCCCCCE----EEEEcCCeEEEEEEEcCcCcCCCCEEEeCHHHHhccCCCCCC-----EEEEEE
Confidence            79999999 69999999999999    9999999999999997 22    5789999999999999999     999999


Q ss_pred             ecccccceeEecCCC---CccccCCCccccCcccccccchheeeeceeecCCCCceee
Q 047219          183 WDSAVAWQLTLKPPE---KQNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEF  237 (567)
Q Consensus       183 ~~~~~a~~v~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  237 (567)
                      +++++|++|+|+|..   +.+.+.++.        .++....+.++|+..||.+.+..
T Consensus        90 ~~~~~A~~V~l~P~~~~~~~~~~~~~~--------~~~l~~~l~~rpv~~Gd~v~v~~  139 (185)
T 1cz4_A           90 VRTEIAKKVTLAPIIRKDQRLKFGEGI--------EEYVQRALIRRPMLEQDNISVPG  139 (185)
T ss_dssp             ECCCBCSEEEEEEECSTTCCSCCCSSH--------HHHHHHHHTTCEECTTCEECCSS
T ss_pred             CCCCCccEEEEecccccccccccccch--------HHHHHHHHCCCcccCCCEEEEee
Confidence            999999999999985   444443332        14556788899999999987654

>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=99.61  E-value=1.7e-14  Score=151.02  Aligned_cols=196  Identities=25%  Similarity=0.298  Sum_probs=134.1

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCC-C
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQ-G  353 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~-~  353 (567)
                      .++++|.+++++.+.+.+...+.                 ...+.+++|+||||||||++|+++++++...    .-. +
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~-----------------~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~   81 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVK-----------------NEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKD   81 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHT-----------------TCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTT
T ss_pred             CCCCCChHHHHHHHHHHHHHHHc-----------------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCC
Confidence            47899999999999988764311                 3456799999999999999999999987221    001 3


Q ss_pred             cCeEEechhhHH-h----------hhh-------ch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          354 VPLMYVPLEVVM-S----------KYY-------GE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       354 ~~~~~i~~~~l~-s----------~~~-------G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      .+++++++.... +          .+.       +. ....+..++..+...  +.+|||||+|.+.....       .+
T Consensus        82 ~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~--~~vlilDEi~~l~~~~~-------~~  152 (384)
T 2qby_B           82 VKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNI--RAIIYLDEVDTLVKRRG-------GD  152 (384)
T ss_dssp             CEEEEEEHHHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSS--CEEEEEETTHHHHHSTT-------SH
T ss_pred             ceEEEEECccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccC--CCEEEEECHHHhccCCC-------Cc
Confidence            467888876543 1          110       11 123344444444332  23999999999965421       11


Q ss_pred             H-HHHHHHhhcCcccCCcEEEEEeeCCC---CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh------hCHHHHHH
Q 047219          415 I-LSVLLRQIDGFEQDKKVVVIAATNRK---QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH------LTKAELAE  484 (567)
Q Consensus       415 v-l~~LL~~ld~~~~~~~viVIaaTN~~---~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~------~~~~~l~~  484 (567)
                      . +..|+...      .++.+|++||..   ..+++.+++||+..++|++|+.++..+++...+..      +..+.++.
T Consensus       153 ~~l~~l~~~~------~~~~iI~~t~~~~~~~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~  226 (384)
T 2qby_B          153 IVLYQLLRSD------ANISVIMISNDINVRDYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYGLIKGTYDDEILSY  226 (384)
T ss_dssp             HHHHHHHTSS------SCEEEEEECSSTTTTTTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHTSCTTSCCSHHHHH
T ss_pred             eeHHHHhcCC------cceEEEEEECCCchHhhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhhcccCCcCHHHHHH
Confidence            2 33343332      688999999986   67999999999789999999999999999988763      44566777


Q ss_pred             HHHhccC--CCHHHHHHHHHHHHH
Q 047219          485 LATATEE--MSGRDIRDVCQQAER  506 (567)
Q Consensus       485 la~~t~g--~s~~dL~~L~~~a~~  506 (567)
                      ++..+.+  -..+.+..++..++.
T Consensus       227 i~~~~~~~~G~~r~a~~~l~~a~~  250 (384)
T 2qby_B          227 IAAISAKEHGDARKAVNLLFRAAQ  250 (384)
T ss_dssp             HHHHHHTTCCCHHHHHHHHHHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHH
Confidence            7777662  234555566666654

>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=99.61  E-value=3.6e-14  Score=148.04  Aligned_cols=190  Identities=21%  Similarity=0.248  Sum_probs=136.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-CCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-WQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~~~  353 (567)
                      .+.+|++++|++++++.+.+.+..                    ...+..+||+||+|||||++|+++++.+.... ...
T Consensus        11 rp~~~~~~vg~~~~~~~L~~~l~~--------------------~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~   70 (373)
T 1jr3_A           11 RPQTFADVVGQEHVLTALANGLSL--------------------GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITA   70 (373)
T ss_dssp             CCCSTTTSCSCHHHHHHHHHHHHH--------------------TCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCS
T ss_pred             CCCchhhccCcHHHHHHHHHHHHh--------------------CCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCC
Confidence            345789999999999999887752                    34567899999999999999999999986431 111


Q ss_pred             cC-----------------eEEechhhHHhhhhchhHHHHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHH
Q 047219          354 VP-----------------LMYVPLEVVMSKYYGESERLLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATR  413 (567)
Q Consensus       354 ~~-----------------~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~  413 (567)
                      .+                 ++.++...      ......++.+++.+..   ...+.+|||||+|.+...          
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~~~----------  134 (373)
T 1jr3_A           71 TPCGVCDNCREIEQGRFVDLIEIDAAS------RTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH----------  134 (373)
T ss_dssp             SCCSSSHHHHHHHTSCCSSCEEEETTC------SCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSCHH----------
T ss_pred             CCCcccHHHHHHhccCCCceEEecccc------cCCHHHHHHHHHHHhhccccCCeEEEEEECcchhcHH----------
Confidence            11                 22222111      0011234455555442   223579999999998633          


Q ss_pred             HHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhc
Q 047219          414 RILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATAT  489 (567)
Q Consensus       414 ~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t  489 (567)
                       ..+.|+..++.  .+.++++|++|+.+..+.+.+++|| ..+++..|+.++..+++...++.    +..+.+..++..+
T Consensus       135 -~~~~Ll~~le~--~~~~~~~Il~~~~~~~l~~~l~sr~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~  210 (373)
T 1jr3_A          135 -SFNALLKTLEE--PPEHVKFLLATTDPQKLPVTILSRC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAA  210 (373)
T ss_dssp             -HHHHHHHHHHS--CCSSEEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHS
T ss_pred             -HHHHHHHHHhc--CCCceEEEEEeCChHhCcHHHHhhe-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHC
Confidence             23455666653  4568899999999999999999999 89999999999999999988754    4566788888887


Q ss_pred             cCCCHHHHHHHHHHHH
Q 047219          490 EEMSGRDIRDVCQQAE  505 (567)
Q Consensus       490 ~g~s~~dL~~L~~~a~  505 (567)
                      .| +.+++.+++..++
T Consensus       211 ~G-~~r~~~~~l~~~~  225 (373)
T 1jr3_A          211 EG-SLRDALSLTDQAI  225 (373)
T ss_dssp             SS-CHHHHHHHHHHHH
T ss_pred             CC-CHHHHHHHHHHHH
Confidence            65 6777777776654

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.61  E-value=8.1e-15  Score=151.37  Aligned_cols=167  Identities=11%  Similarity=0.082  Sum_probs=119.3

Q ss_pred             ccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCCcCeE
Q 047219          282 IAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQGVPLM  357 (567)
Q Consensus       282 IiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~~~~~  357 (567)
                      |.|.+++++.+...+...+                 ....+.+++|+||||||||++++++++++...    ....+.++
T Consensus        22 L~~Re~E~~~i~~~L~~~i-----------------~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v   84 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSL-----------------MSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYI   84 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHH-----------------HTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEE
T ss_pred             cCCHHHHHHHHHHHHHHHh-----------------cCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEE
Confidence            6778888888877665432                 25678999999999999999999999998422    11235678


Q ss_pred             EechhhHHh----------hhhc------hhHHHHHHHHHHH-hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHH
Q 047219          358 YVPLEVVMS----------KYYG------ESERLLGKVFSLA-NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL  420 (567)
Q Consensus       358 ~i~~~~l~s----------~~~G------~~~~~l~~~f~~A-~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL  420 (567)
                      +++|..+.+          ++.|      .....+...|... .....+.|+||||+|.|.  .        ++++..|+
T Consensus        85 ~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~--~--------q~~L~~l~  154 (318)
T 3te6_A           85 HIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL--S--------EKILQYFE  154 (318)
T ss_dssp             EEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC--C--------THHHHHHH
T ss_pred             EEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh--c--------chHHHHHH
Confidence            888754322          2222      3456677788765 122335899999999997  2        23445555


Q ss_pred             HhhcCcccCCcEEEEEeeCCCCC----CChHHHhccc-eEEEecCCCHHHHHHHHHHHHHhh
Q 047219          421 RQIDGFEQDKKVVVIAATNRKQD----LDPALISRFD-SMITFGLPDHENRQEIAAQYAKHL  477 (567)
Q Consensus       421 ~~ld~~~~~~~viVIaaTN~~~~----Ld~aL~sRf~-~~I~i~~P~~~eR~eIL~~~~~~~  477 (567)
                      .+..  ....++.||+++|..+.    +++++++||. ..|.|++++.++..+|++..++.+
T Consensus       155 ~~~~--~~~s~~~vI~i~n~~d~~~~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~~  214 (318)
T 3te6_A          155 KWIS--SKNSKLSIICVGGHNVTIREQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSL  214 (318)
T ss_dssp             HHHH--CSSCCEEEEEECCSSCCCHHHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             hccc--ccCCcEEEEEEecCcccchhhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHhh
Confidence            5443  24568999999998654    4556678996 589999999999999999988753

>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=99.61  E-value=5e-15  Score=162.92  Aligned_cols=203  Identities=19%  Similarity=0.215  Sum_probs=128.5

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhcc-ChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQ-SPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~-~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      ..+.+|++|+|++.+++.+++.+..... .+..|+..+     ..+...++++||+||||||||++|+++|+++      
T Consensus        33 yrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g-----~~~~~~~~~lLL~GppGtGKTtla~~la~~l------  101 (516)
T 1sxj_A           33 YAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAG-----KDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL------  101 (516)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCC-----TTSTTSCSEEEEECSTTSSHHHHHHHHHHHT------
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccC-----ccCCCCCcEEEEECCCCCCHHHHHHHHHHHc------
Confidence            3446899999999999999998874311 112222211     0112356899999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHH-------HHHHHHHHH----hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHH
Q 047219          353 GVPLMYVPLEVVMSKYYGESER-------LLGKVFSLA----NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLR  421 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~-------~l~~~f~~A----~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~  421 (567)
                      +.++++++++.+.+.......-       .+..+|..+    .....++||||||+|.|....+..        +..|+.
T Consensus       102 ~~~~i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~~~~--------l~~L~~  173 (516)
T 1sxj_A          102 GYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGG--------VGQLAQ  173 (516)
T ss_dssp             TCEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTH--------HHHHHH
T ss_pred             CCCEEEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhhHHH--------HHHHHH
Confidence            6788999887655433211100       011222222    112346899999999998654322        233444


Q ss_pred             hhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHH
Q 047219          422 QIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDI  497 (567)
Q Consensus       422 ~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL  497 (567)
                      .++.  ....+++|+++.....+ +.+++|+ ..+.|+.|+.+++.+++...+..    +..+.+..++..+.|    |+
T Consensus       174 ~l~~--~~~~iIli~~~~~~~~l-~~l~~r~-~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s~G----di  245 (516)
T 1sxj_A          174 FCRK--TSTPLILICNERNLPKM-RPFDRVC-LDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG----DI  245 (516)
T ss_dssp             HHHH--CSSCEEEEESCTTSSTT-GGGTTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT----CH
T ss_pred             HHHh--cCCCEEEEEcCCCCccc-hhhHhce-EEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC----cH
Confidence            4432  22344554444333344 3466666 79999999999999999887654    456677888877654    44


Q ss_pred             HHHHHH
Q 047219          498 RDVCQQ  503 (567)
Q Consensus       498 ~~L~~~  503 (567)
                      +.+++.
T Consensus       246 R~~i~~  251 (516)
T 1sxj_A          246 RQVINL  251 (516)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            444443

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=99.60  E-value=2.6e-14  Score=145.72  Aligned_cols=188  Identities=16%  Similarity=0.176  Sum_probs=130.3

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++..++.+.+.+..                    ...+ ++||+||||||||++|+++++.+.... ..
T Consensus        15 ~~p~~~~~~~g~~~~~~~l~~~l~~--------------------~~~~-~~ll~G~~G~GKt~la~~l~~~l~~~~-~~   72 (323)
T 1sxj_B           15 YRPQVLSDIVGNKETIDRLQQIAKD--------------------GNMP-HMIISGMPGIGKTTSVHCLAHELLGRS-YA   72 (323)
T ss_dssp             TCCSSGGGCCSCTHHHHHHHHHHHS--------------------CCCC-CEEEECSTTSSHHHHHHHHHHHHHGGG-HH
T ss_pred             cCCCCHHHHHCCHHHHHHHHHHHHc--------------------CCCC-eEEEECcCCCCHHHHHHHHHHHhcCCc-cc
Confidence            3446799999999999999887641                    2333 499999999999999999999863210 02


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHh----c--CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLAN----E--LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE  427 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~----~--~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~  427 (567)
                      .+++++++....+      ...++..+....    .  ..++.+|||||+|.+....+           +.|+..++.  
T Consensus        73 ~~~~~~~~~~~~~------~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~~~~-----------~~L~~~le~--  133 (323)
T 1sxj_B           73 DGVLELNASDDRG------IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTAGAQ-----------QALRRTMEL--  133 (323)
T ss_dssp             HHEEEECTTSCCS------HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCHHHH-----------HTTHHHHHH--
T ss_pred             CCEEEecCccccC------hHHHHHHHHHHHhccccCCCCCceEEEEECcccCCHHHH-----------HHHHHHHhc--
Confidence            3466666554211      123333333332    1  22358999999999965422           334444442  


Q ss_pred             cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          428 QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       428 ~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      .+.++++|++||.+..+.+++++|| ..+.|+.|+.++..+++...+..    +..+.+..++..+.| +.+.+.+++..
T Consensus       134 ~~~~~~~il~~~~~~~l~~~l~sr~-~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~r~a~~~l~~  211 (323)
T 1sxj_B          134 YSNSTRFAFACNQSNKIIEPLQSQC-AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG-DMRQAINNLQS  211 (323)
T ss_dssp             TTTTEEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT-CHHHHHHHHHH
T ss_pred             cCCCceEEEEeCChhhchhHHHhhc-eEEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC-CHHHHHHHHHH
Confidence            3467888999999999999999999 69999999999999999987753    456777888887765 34444444443


Q ss_pred             H
Q 047219          504 A  504 (567)
Q Consensus       504 a  504 (567)
                      +
T Consensus       212 ~  212 (323)
T 1sxj_B          212 T  212 (323)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A

Probab=99.59  E-value=5.6e-16  Score=147.73  Aligned_cols=111  Identities=12%  Similarity=0.138  Sum_probs=91.9

Q ss_pred             chhhhH-HHHHHHhCCCCCCccceEEEEecce--EEEEEEecCC---CCcchHHHHHHHhhCceecccCCCceeEEEee-
Q 047219          111 KERQRI-EELLKRKGMHYGSCPTFTVAVKGQK--VTIKFQVPPA---CEIPQLIANLVSHLGLKVEEHGGGSDMGLRAW-  183 (567)
Q Consensus       111 ~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~--~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~-  183 (567)
                      +|++|| ++.|++||+.+||+    |+|+|++  .|+|+|||+.   .+++++++.+|+|+|+++||     .|+|+++ 
T Consensus        36 ~givrl~p~~m~~Lgl~~GD~----V~I~Gkr~k~Tva~v~~~~~~~~g~Irid~~~R~N~gV~iGD-----~V~V~~~~  106 (187)
T 3tiw_A           36 NSVVSLSQPKMDELQLFRGDT----VLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGD-----VISIQPCP  106 (187)
T ss_dssp             TTEEEECHHHHHHHTCCTTCE----EEEECSTTCEEEEEEEECTTSCTTEEEECHHHHHHTTCCTTC-----EEEEEECT
T ss_pred             CcEEEECHHHHHHcCCCCCCE----EEEECCCCCeEEEEEEECCCCCCCEEEeCHHHHhhcCCCCCC-----EEEEEECC
Confidence            899999 69999999999999    9999998  8999999973   26799999999999999999     9999999 


Q ss_pred             cccccceeEecCCCCccc-cCCCccccCcccccccchheee--eceeecCCCCceee
Q 047219          184 DSAVAWQLTLKPPEKQNE-SGGDRAQSGDMNAREGDLCILI--FRSLITSDKPEIEF  237 (567)
Q Consensus       184 ~~~~a~~v~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~--~~~~~~~~~~~~~~  237 (567)
                      ++++|++|+|+|...++. +.++.       ...+....+.  ++|+..||.+.+..
T Consensus       107 ~v~~A~~V~LaP~~~~i~~i~~~~-------~~~~lk~~l~~~~rpV~~GD~i~v~~  156 (187)
T 3tiw_A          107 DVKYGKRIHVLPIDDTVEGITGNL-------FEVYLKPYFLEAYRPIRKGDIFLVRG  156 (187)
T ss_dssp             TCEECSEEEEEECCCC-----CCH-------HHHTHHHHHTTTCCEEETTCEEEEEC
T ss_pred             CCCCceEEEEeccccchhhccchh-------HHHHHHHHhccCCceeeCCCEEEEcc
Confidence            899999999999866554 43330       0134556776  59999999987654

>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=99.57  E-value=1.9e-13  Score=142.04  Aligned_cols=188  Identities=20%  Similarity=0.325  Sum_probs=131.9

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      ..+|++++|++.+++.+...+.....                ...++.+++|+|||||||||+|+++++++      +.+
T Consensus        21 ~~~l~~~~g~~~~~~~l~~~i~~~~~----------------~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l------~~~   78 (334)
T 1in4_A           21 PKSLDEFIGQENVKKKLSLALEAAKM----------------RGEVLDHVLLAGPPGLGKTTLAHIIASEL------QTN   78 (334)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHHHHH----------------HTCCCCCEEEESSTTSSHHHHHHHHHHHH------TCC
T ss_pred             CccHHHccCcHHHHHHHHHHHHHHHh----------------cCCCCCeEEEECCCCCcHHHHHHHHHHHh------CCC
Confidence            34789999999888888776643200                03456789999999999999999999999      555


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc--------
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE--------  427 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~--------  427 (567)
                      +...+++.+..      ...+..++..   .....|+||||++.+.+..++.+           +..++...        
T Consensus        79 ~~~~sg~~~~~------~~~l~~~~~~---~~~~~v~~iDE~~~l~~~~~e~L-----------~~~~~~~~~~i~~~~~  138 (334)
T 1in4_A           79 IHVTSGPVLVK------QGDMAAILTS---LERGDVLFIDEIHRLNKAVEELL-----------YSAIEDFQIDIMIGKG  138 (334)
T ss_dssp             EEEEETTTCCS------HHHHHHHHHH---CCTTCEEEEETGGGCCHHHHHHH-----------HHHHHTSCCCC-----
T ss_pred             EEEEechHhcC------HHHHHHHHHH---ccCCCEEEEcchhhcCHHHHHHH-----------HHHHHhcccceeeccC
Confidence            66555543321      1122233322   22358999999999875322221           11111110        


Q ss_pred             --------cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHH
Q 047219          428 --------QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGR  495 (567)
Q Consensus       428 --------~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~  495 (567)
                              ....+.++++|+.+..+++.+++||...+.++.|+.+++.++++..++.    +..+.+..++..+.| +++
T Consensus       139 ~~~~~i~~~l~~~~li~at~~~~~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~~G-~~R  217 (334)
T 1in4_A          139 PSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPR  217 (334)
T ss_dssp             ----------CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHH
T ss_pred             cccccccccCCCeEEEEecCCcccCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhcCC-ChH
Confidence                    1124778889999999999999999888999999999999999988764    467788888888776 567


Q ss_pred             HHHHHHHHHHH
Q 047219          496 DIRDVCQQAER  506 (567)
Q Consensus       496 dL~~L~~~a~~  506 (567)
                      .+..+++.+..
T Consensus       218 ~a~~ll~~~~~  228 (334)
T 1in4_A          218 IAIRLTKRVRD  228 (334)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            77777776654

>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=99.56  E-value=1.2e-13  Score=143.82  Aligned_cols=209  Identities=19%  Similarity=0.250  Sum_probs=139.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +....++++|.++.++.+.+.+...+                 ....+..++|+||||||||++++++++.+......+.
T Consensus        15 ~~~~p~~~~gr~~e~~~l~~~l~~~~-----------------~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~   77 (386)
T 2qby_A           15 PDYIPDELPHREDQIRKIASILAPLY-----------------REEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKF   77 (386)
T ss_dssp             SSCCCSCCTTCHHHHHHHHHSSGGGG-----------------GTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSC
T ss_pred             CccCCCCCCChHHHHHHHHHHHHHHH-----------------cCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCc
Confidence            34556899999999999887654221                 1355678999999999999999999998732100034


Q ss_pred             CeEEechhhHHh------hh----------hch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHH
Q 047219          355 PLMYVPLEVVMS------KY----------YGE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILS  417 (567)
Q Consensus       355 ~~~~i~~~~l~s------~~----------~G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~  417 (567)
                      .++++++.....      .+          .+. .......++........+.+|||||++.+......       ..+.
T Consensus        78 ~~~~i~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~~-------~~l~  150 (386)
T 2qby_A           78 KHVYINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYND-------DILY  150 (386)
T ss_dssp             EEEEEEHHHHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSCS-------THHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCcC-------HHHH
Confidence            577787654321      11          111 22334444444444443689999999998754211       2334


Q ss_pred             HHHHhhcCcccCCcEEEEEeeCCC---CCCChHHHhccc-eEEEecCCCHHHHHHHHHHHHHh------hCHHHHHHHHH
Q 047219          418 VLLRQIDGFEQDKKVVVIAATNRK---QDLDPALISRFD-SMITFGLPDHENRQEIAAQYAKH------LTKAELAELAT  487 (567)
Q Consensus       418 ~LL~~ld~~~~~~~viVIaaTN~~---~~Ld~aL~sRf~-~~I~i~~P~~~eR~eIL~~~~~~------~~~~~l~~la~  487 (567)
                      .++..++.. ...++.+|++||..   ..+++.+.+||. ..+.+++++.++..+++...+..      +..+.++.++.
T Consensus       151 ~l~~~~~~~-~~~~~~~I~~~~~~~~~~~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~  229 (386)
T 2qby_A          151 KLSRINSEV-NKSKISFIGITNDVKFVDLLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAA  229 (386)
T ss_dssp             HHHHHHHSC-CC--EEEEEEESCGGGGGGCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHH
T ss_pred             HHhhchhhc-CCCeEEEEEEECCCChHhhhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHH
Confidence            555555433 34678899999876   468899999985 48999999999999999987652      45667777777


Q ss_pred             hccC--CCHHHHHHHHHHHHHHH
Q 047219          488 ATEE--MSGRDIRDVCQQAERSW  508 (567)
Q Consensus       488 ~t~g--~s~~dL~~L~~~a~~~a  508 (567)
                      .+..  ..++.+..++..++..+
T Consensus       230 ~~~~~~G~~r~~~~ll~~a~~~a  252 (386)
T 2qby_A          230 LAAREHGDARRALDLLRVSGEIA  252 (386)
T ss_dssp             HHHHTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHHHH
Confidence            7661  35666667777776543

>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=99.55  E-value=1e-13  Score=144.06  Aligned_cols=192  Identities=14%  Similarity=0.161  Sum_probs=124.4

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC--
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW--  351 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~--  351 (567)
                      ..+.+|++++|++.+++.+++.+.   ..                ...+. ++|+||+|||||++++++++++.....  
T Consensus         8 yrP~~~~~~vg~~~~~~~l~~~~~---~~----------------~~~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~   67 (354)
T 1sxj_E            8 YRPKSLNALSHNEELTNFLKSLSD---QP----------------RDLPH-LLLYGPNGTGKKTRCMALLESIFGPGVYR   67 (354)
T ss_dssp             TCCCSGGGCCSCHHHHHHHHTTTT---CT----------------TCCCC-EEEECSTTSSHHHHHHTHHHHHSCTTCCC
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHh---hC----------------CCCCe-EEEECCCCCCHHHHHHHHHHHHcCCCCCe
Confidence            345689999999999888776541   00                23344 999999999999999999997532100  


Q ss_pred             ---C------------------CcCeEEechhhHHhhhhchhHHHHHHHHHHHhc-------------CCCCcEEEEcCc
Q 047219          352 ---Q------------------GVPLMYVPLEVVMSKYYGESERLLGKVFSLANE-------------LPNGAIIFLDEV  397 (567)
Q Consensus       352 ---~------------------~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~-------------~a~~~ILfIDEI  397 (567)
                         .                  ..+++.++......    .....++..++.+..             ..++.+++|||+
T Consensus        68 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~  143 (354)
T 1sxj_E           68 LKIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGN----NDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEA  143 (354)
T ss_dssp             ------------------CCEECSSEEEECCC--------CCHHHHHHHHHHHTTTTC------------CCEEEEEECT
T ss_pred             EEecceeecccccccceeeeecccceEEecHhhcCC----cchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCc
Confidence               0                  01122333221110    001123333333321             123569999999


Q ss_pred             chhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh-
Q 047219          398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH-  476 (567)
Q Consensus       398 D~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~-  476 (567)
                      +.|...           ..+.|++.++..  +.++.+|.+||.+..+.+.+++|| ..+.|+.|+.++..+++...+.. 
T Consensus       144 ~~L~~~-----------~~~~L~~~le~~--~~~~~~Il~t~~~~~l~~~l~sR~-~~~~~~~~~~~~~~~~l~~~~~~~  209 (354)
T 1sxj_E          144 NSLTKD-----------AQAALRRTMEKY--SKNIRLIMVCDSMSPIIAPIKSQC-LLIRCPAPSDSEISTILSDVVTNE  209 (354)
T ss_dssp             TSSCHH-----------HHHHHHHHHHHS--TTTEEEEEEESCSCSSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             cccCHH-----------HHHHHHHHHHhh--cCCCEEEEEeCCHHHHHHHHHhhc-eEEecCCcCHHHHHHHHHHHHHHc
Confidence            997533           223445555432  346889999999999999999999 89999999999999999988764 


Q ss_pred             ---hC-HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          477 ---LT-KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       477 ---~~-~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                         +. .+.++.++..+.| +.+++..+++.+
T Consensus       210 ~~~~~~~~~l~~i~~~~~G-~~r~a~~~l~~~  240 (354)
T 1sxj_E          210 RIQLETKDILKRIAQASNG-NLRVSLLMLESM  240 (354)
T ss_dssp             TCEECCSHHHHHHHHHHTT-CHHHHHHHHTHH
T ss_pred             CCCCCcHHHHHHHHHHcCC-CHHHHHHHHHHH
Confidence               45 6778888877655 444444444433

>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=99.51  E-value=2.2e-13  Score=141.45  Aligned_cols=176  Identities=21%  Similarity=0.236  Sum_probs=120.7

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      ..+.+|++++|++.+++.|...+..                    ...+ +++|+||||||||++|+++++.+....+ .
T Consensus        19 ~rp~~~~~~~g~~~~~~~L~~~i~~--------------------g~~~-~~ll~Gp~G~GKTtla~~la~~l~~~~~-~   76 (340)
T 1sxj_C           19 YRPETLDEVYGQNEVITTVRKFVDE--------------------GKLP-HLLFYGPPGTGKTSTIVALAREIYGKNY-S   76 (340)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHHT--------------------TCCC-CEEEECSSSSSHHHHHHHHHHHHHTTSH-H
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHhc--------------------CCCc-eEEEECCCCCCHHHHHHHHHHHHcCCCc-c
Confidence            3456899999999999988877652                    2333 4999999999999999999999743211 2


Q ss_pred             cCeEEechhhHHhhhhchhHHHHHHHHHHHh-c----CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          354 VPLMYVPLEVVMSKYYGESERLLGKVFSLAN-E----LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~-~----~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      ..+..++.+...    |  ...++..+.... .    .....+++|||+|.|....           .+.|+..++.  .
T Consensus        77 ~~~~~~~~~~~~----~--~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~~~-----------~~~L~~~le~--~  137 (340)
T 1sxj_C           77 NMVLELNASDDR----G--IDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTNAA-----------QNALRRVIER--Y  137 (340)
T ss_dssp             HHEEEECTTSCC----S--HHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCHHH-----------HHHHHHHHHH--T
T ss_pred             ceEEEEcCcccc----c--HHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCHHH-----------HHHHHHHHhc--C
Confidence            235555554321    1  112222222211 1    1225899999999996442           2345555553  3


Q ss_pred             CCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccC
Q 047219          429 DKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEE  491 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g  491 (567)
                      +..+.+|.+||.+..+.+++++|| ..+.|..++.++..+.+...++.    +....+..++..+.|
T Consensus       138 ~~~~~~il~~n~~~~i~~~i~sR~-~~~~~~~l~~~~~~~~l~~~~~~~~~~i~~~~~~~i~~~s~G  203 (340)
T 1sxj_C          138 TKNTRFCVLANYAHKLTPALLSQC-TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNG  203 (340)
T ss_dssp             TTTEEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT
T ss_pred             CCCeEEEEEecCccccchhHHhhc-eeEeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCC
Confidence            467788889999999999999999 68999999999999988887742    455666666666544

>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=99.50  E-value=3.5e-13  Score=140.00  Aligned_cols=163  Identities=14%  Similarity=0.132  Sum_probs=114.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC------------------cCeEEechhhHHhhhhchhHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG------------------VPLMYVPLEVVMSKYYGESERLLGKVF  380 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~------------------~~~~~i~~~~l~s~~~G~~~~~l~~~f  380 (567)
                      .+.++.+||+||||||||++|+++++.+.......                  .++..+....- +.  ....+.++.++
T Consensus        21 ~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~-~~--~~~i~~ir~l~   97 (334)
T 1a5t_A           21 GRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKG-KN--TLGVDAVREVT   97 (334)
T ss_dssp             TCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTT-CS--SBCHHHHHHHH
T ss_pred             CCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecccc-CC--CCCHHHHHHHH
Confidence            45677899999999999999999999986432100                  22333332200 00  01224466666


Q ss_pred             HHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEE
Q 047219          381 SLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMIT  457 (567)
Q Consensus       381 ~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~  457 (567)
                      +.+...   +...|++|||+|.|...           ..+.|++.++.  .+.++++|.+||.++.+.+.+++|| ..++
T Consensus        98 ~~~~~~~~~~~~kvviIdead~l~~~-----------a~naLLk~lEe--p~~~~~~Il~t~~~~~l~~ti~SRc-~~~~  163 (334)
T 1a5t_A           98 EKLNEHARLGGAKVVWVTDAALLTDA-----------AANALLKTLEE--PPAETWFFLATREPERLLATLRSRC-RLHY  163 (334)
T ss_dssp             HHTTSCCTTSSCEEEEESCGGGBCHH-----------HHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHHTTS-EEEE
T ss_pred             HHHhhccccCCcEEEEECchhhcCHH-----------HHHHHHHHhcC--CCCCeEEEEEeCChHhCcHHHhhcc-eeee
Confidence            665532   24589999999999633           34667777774  5568999999999999999999999 7899


Q ss_pred             ecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHH
Q 047219          458 FGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                      |+.|+.++..+++.... .+..+.+..++..+.| +.+.+..+
T Consensus       164 ~~~~~~~~~~~~L~~~~-~~~~~~~~~l~~~s~G-~~r~a~~~  204 (334)
T 1a5t_A          164 LAPPPEQYAVTWLSREV-TMSQDALLAALRLSAG-SPGAALAL  204 (334)
T ss_dssp             CCCCCHHHHHHHHHHHC-CCCHHHHHHHHHHTTT-CHHHHHHT
T ss_pred             CCCCCHHHHHHHHHHhc-CCCHHHHHHHHHHcCC-CHHHHHHH
Confidence            99999999999888765 4566677777777655 34444333

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.49  E-value=1.5e-14  Score=158.15  Aligned_cols=187  Identities=17%  Similarity=0.167  Sum_probs=111.9

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ..|+|++++++.+...+.                       ...++||+||||||||++|+++|+.+...    .+|..+
T Consensus        22 ~~ivGq~~~i~~l~~al~-----------------------~~~~VLL~GpPGtGKT~LAraLa~~l~~~----~~f~~~   74 (500)
T 3nbx_X           22 KGLYERSHAIRLCLLAAL-----------------------SGESVFLLGPPGIAKSLIARRLKFAFQNA----RAFEYL   74 (500)
T ss_dssp             TTCSSCHHHHHHHHHHHH-----------------------HTCEEEEECCSSSSHHHHHHHGGGGBSSC----CEEEEE
T ss_pred             hhhHHHHHHHHHHHHHHh-----------------------cCCeeEeecCchHHHHHHHHHHHHHHhhh----hHHHHH
Confidence            358899999887765543                       23689999999999999999999988532    223333


Q ss_pred             chhh-HHhhhhch----hHHHHHHHHHHHhcC--CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcC-------
Q 047219          360 PLEV-VMSKYYGE----SERLLGKVFSLANEL--PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDG-------  425 (567)
Q Consensus       360 ~~~~-l~s~~~G~----~~~~l~~~f~~A~~~--a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~-------  425 (567)
                      .+.. ..+.++|.    .... ...|..+...  +.++|||||||+.+.++.+.           .|+..|+.       
T Consensus        75 ~~~~~t~~dL~G~~~~~~~~~-~g~~~~~~~g~l~~~~IL~IDEI~r~~~~~q~-----------~LL~~lee~~v~i~G  142 (500)
T 3nbx_X           75 MTRFSTPEEVFGPLSIQALKD-EGRYERLTSGYLPEAEIVFLDEIWKAGPAILN-----------TLLTAINERQFRNGA  142 (500)
T ss_dssp             CCTTCCHHHHHCCBC-----------CBCCTTSGGGCSEEEEESGGGCCHHHHH-----------HHHHHHHSSEEECSS
T ss_pred             HHhcCCHHHhcCcccHHHHhh-chhHHhhhccCCCcceeeeHHhHhhhcHHHHH-----------HHHHHHHHHhccCCC
Confidence            3321 11233331    1111 1122211111  02468999999988755443           34444432       


Q ss_pred             --cccCCcEEEEEeeCCCC---CCChHHHhccceEEEecCCCH-HHHHHHHHHHHH------------------------
Q 047219          426 --FEQDKKVVVIAATNRKQ---DLDPALISRFDSMITFGLPDH-ENRQEIAAQYAK------------------------  475 (567)
Q Consensus       426 --~~~~~~viVIaaTN~~~---~Ld~aL~sRf~~~I~i~~P~~-~eR~eIL~~~~~------------------------  475 (567)
                        ...+.. ++|+|||+..   .+.+++++||...+.++.|+. +++.+|+.....                        
T Consensus       143 ~~~~~~~~-~iI~ATN~lpe~~~~~~aLldRF~~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~  221 (500)
T 3nbx_X          143 HVEKIPMR-LLVAASNELPEADSSLEALYDRMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEI  221 (500)
T ss_dssp             SEEECCCC-EEEEEESSCCCTTCTTHHHHTTCCEEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHH
T ss_pred             CcCCcchh-hhhhccccCCCccccHHHHHHHHHHHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcC
Confidence              112233 4577778532   366799999988899999987 678888865431                        


Q ss_pred             -h--hCHHHHHHHHHhc---------cCCCHHHHHHHHHHHHH
Q 047219          476 -H--LTKAELAELATAT---------EEMSGRDIRDVCQQAER  506 (567)
Q Consensus       476 -~--~~~~~l~~la~~t---------~g~s~~dL~~L~~~a~~  506 (567)
                       .  ++++..+.++...         .+.+++.+..+++.+..
T Consensus       222 ~~v~v~d~v~e~i~~l~~~lr~~r~~~~iS~R~~~~llr~A~A  264 (500)
T 3nbx_X          222 GEITLPDHVFELIFMLRQQLDKLPDAPYVSDRRWKKAIRLLQA  264 (500)
T ss_dssp             TTCBCCHHHHHHHHHHHHHHHHCSSSCCCCHHHHHHHHHHHHH
T ss_pred             CcccCchHHHHHHHHHHHHhhcCCCCCccchhHHHHHHHHHHH
Confidence             1  2333344444333         47788888888776653

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.46  E-value=1.6e-15  Score=169.46  Aligned_cols=180  Identities=24%  Similarity=0.282  Sum_probs=97.3

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC---cCe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG---VPL  356 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~---~~~  356 (567)
                      ..|+|++.+++.+...+..  ..+....       . .......++||+||||||||++|+++|+.+++..+..   ..+
T Consensus       295 ~~I~G~e~vk~al~~~l~~--g~~~~~~-------~-~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~  364 (595)
T 3f9v_A          295 PSIYGHWELKEALALALFG--GVPKVLE-------D-TRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTA  364 (595)
T ss_dssp             STTSCCHHHHHHHTTTTTC--CCCEETT-------T-TEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTT
T ss_pred             chhcChHHHHHHHHHHHhC--CCccccc-------C-CCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecCCCcccc
Confidence            4689999887766332210  0000000       0 0123445899999999999999999999885431110   111


Q ss_pred             EEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEE
Q 047219          357 MYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIA  436 (567)
Q Consensus       357 ~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIa  436 (567)
                      ..+.+........|..... ...+..|    .++|+||||||.+....+..+++++++..-.+.........+.++.||+
T Consensus       365 ~~l~~~~~~~~~~g~~~~~-~G~l~~A----~~gil~IDEid~l~~~~q~~Ll~~le~~~i~i~~~g~~~~~~~~~~vIa  439 (595)
T 3f9v_A          365 AGLTAAVVREKGTGEYYLE-AGALVLA----DGGIAVIDEIDKMRDEDRVAIHEAMEQQTVSIAKAGIVAKLNARAAVIA  439 (595)
T ss_dssp             TTSEEECSSGGGTSSCSEE-ECHHHHH----SSSEECCTTTTCCCSHHHHHHHHHHHSSSEEEESSSSEEEECCCCEEEE
T ss_pred             ccccceeeecccccccccc-CCeeEec----CCCcEEeehhhhCCHhHhhhhHHHHhCCEEEEecCCcEEEecCceEEEE
Confidence            1111111111111111000 0112222    3699999999999866544433332210000000011112346789999


Q ss_pred             eeCCCC-------------CCChHHHhccceEEEe-cCCCHHHHHHHHHHHHH
Q 047219          437 ATNRKQ-------------DLDPALISRFDSMITF-GLPDHENRQEIAAQYAK  475 (567)
Q Consensus       437 aTN~~~-------------~Ld~aL~sRf~~~I~i-~~P~~~eR~eIL~~~~~  475 (567)
                      |||+..             .++++|++|||..+.+ +.|+.+ ...+.+..+.
T Consensus       440 atNp~~G~~~~~~~~~~ni~l~~aLl~RFDl~~~~~~~~~~e-~~~i~~~il~  491 (595)
T 3f9v_A          440 AGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPGEQ-DRELANYILD  491 (595)
T ss_dssp             EECCTTCCSCTTSCSCTTTCSCSSSGGGCSCCEEECCTTHHH-HHHHHHHHHT
T ss_pred             EcCCcCCccCcccCchhccCCCHHHHhhCeEEEEeCCCCCHH-HHHHHHHHHH
Confidence            999876             8999999999865444 566666 7777666554

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=99.38  E-value=5.8e-12  Score=129.48  Aligned_cols=149  Identities=11%  Similarity=0.132  Sum_probs=106.8

Q ss_pred             CcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh
Q 047219          284 GYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV  363 (567)
Q Consensus       284 G~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~  363 (567)
                      |++++++.++..+..                    .. ..++||+||||||||++|+++++.+....-...++..++.+.
T Consensus         1 g~~~~~~~L~~~i~~--------------------~~-~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~   59 (305)
T 2gno_A            1 GAKDQLETLKRIIEK--------------------SE-GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEG   59 (305)
T ss_dssp             ---CHHHHHHHHHHT--------------------CS-SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSS
T ss_pred             ChHHHHHHHHHHHHC--------------------CC-CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCc
Confidence            567777777776652                    23 678999999999999999999987421100134567776542


Q ss_pred             HHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC
Q 047219          364 VMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR  440 (567)
Q Consensus       364 l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~  440 (567)
                         ..  ..-+.++.+.+.+...   +...|+||||+|.|...           ..+.|++.++.  .+.++++|.+||.
T Consensus        60 ---~~--~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~~-----------a~naLLk~LEe--p~~~t~fIl~t~~  121 (305)
T 2gno_A           60 ---EN--IGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQ-----------AANAFLKALEE--PPEYAVIVLNTRR  121 (305)
T ss_dssp             ---SC--BCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHH-----------HHHHTHHHHHS--CCTTEEEEEEESC
T ss_pred             ---CC--CCHHHHHHHHHHHhhccccCCceEEEeccHHHhCHH-----------HHHHHHHHHhC--CCCCeEEEEEECC
Confidence               01  1223466677766543   23579999999999643           34667777773  5678899999998


Q ss_pred             CCCCChHHHhccceEEEecCCCHHHHHHHHHHHH
Q 047219          441 KQDLDPALISRFDSMITFGLPDHENRQEIAAQYA  474 (567)
Q Consensus       441 ~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~  474 (567)
                      +..+.+++++|   .++|..|+.++..+.+...+
T Consensus       122 ~~kl~~tI~SR---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          122 WHYLLPTIKSR---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             GGGSCHHHHTT---SEEEECCCCHHHHHHHHHHH
T ss_pred             hHhChHHHHce---eEeCCCCCHHHHHHHHHHHh
Confidence            99999999999   89999999999998888766

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.34  E-value=3.2e-12  Score=143.20  Aligned_cols=116  Identities=20%  Similarity=0.287  Sum_probs=69.9

Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhc-----------CcccCCcEEEEEeeCCC--CCCChHHHhccc-
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQID-----------GFEQDKKVVVIAATNRK--QDLDPALISRFD-  453 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld-----------~~~~~~~viVIaaTN~~--~~Ld~aL~sRf~-  453 (567)
                      .+++|||||++.|.+..+..+.+.+++-  .+ ....           ....+.+++||++||+.  ..++++|++||. 
T Consensus       201 ~~gvL~LDEi~~l~~~~q~~Ll~~Le~~--~~-~~~g~~~~~~~~~l~~~~~p~~~~vI~atn~~~~~~l~~~l~~R~~v  277 (604)
T 3k1j_A          201 HKGVLFIDEIATLSLKMQQSLLTAMQEK--KF-PITGQSEMSSGAMVRTEPVPCDFVLVAAGNLDTVDKMHPALRSRIRG  277 (604)
T ss_dssp             TTSEEEETTGGGSCHHHHHHHHHHHHHS--EE-CCBCSCTTSGGGGCBCSCEECCCEEEEEECHHHHHHSCHHHHHHHHH
T ss_pred             CCCEEEEechhhCCHHHHHHHHHHHHcC--cE-EecccccccccccCCCCccceeEEEEEecCHHHHhhcCHHHHHHhhc
Confidence            4689999999999766554444333220  00 0000           11224588999999986  679999999995 


Q ss_pred             --eEEEecCC---CHHHHHHHHHHHHHh---------hCHHHHHHHHHhc---cCC------CHHHHHHHHHHHHH
Q 047219          454 --SMITFGLP---DHENRQEIAAQYAKH---------LTKAELAELATAT---EEM------SGRDIRDVCQQAER  506 (567)
Q Consensus       454 --~~I~i~~P---~~~eR~eIL~~~~~~---------~~~~~l~~la~~t---~g~------s~~dL~~L~~~a~~  506 (567)
                        ..+.|+..   ..+....++..+.+.         +..+.+..+....   .|.      +.+++.++++.|..
T Consensus       278 ~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r~~l~~~~R~l~~llr~A~~  353 (604)
T 3k1j_A          278 YGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRKGHLTLRLRDLGGIVRAAGD  353 (604)
T ss_dssp             HSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCSTTEEECCHHHHHHHHHHHHH
T ss_pred             cceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccccccccCHHHHHHHHHHHHH
Confidence              34454321   344555555444321         3455666665543   342      67888888887653

>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=99.31  E-value=3.2e-11  Score=127.19  Aligned_cols=211  Identities=15%  Similarity=0.106  Sum_probs=132.3

Q ss_pred             CCCcccccCcHHHHHHHHHHH-HHhccChhhHHhhhhcccccccCCCCceEEe--eCCCCCcHHHHHHHHHHHhCCC---
Q 047219          276 EISWENIAGYDQQKREIEDTI-LLSLQSPEVYDDIARGTRCKFESNRPRAVLF--EGPPGTGKTSCARVIANQAGAM---  349 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i-~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL--~GppGTGKT~LAraIA~~l~~~---  349 (567)
                      ....++++|.++.++.+.+.+ ......+               ...+..++|  +||||||||++++++++.+...   
T Consensus        18 ~~~p~~l~gR~~el~~l~~~l~~~~~~~~---------------~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~   82 (412)
T 1w5s_A           18 NYIPPELRVRRGEAEALARIYLNRLLSGA---------------GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAK   82 (412)
T ss_dssp             TCCCSSCSSSCHHHHHHHHHHHHHHHTSS---------------CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCCCCCChHHHHHHHHHHHhHHHhcCC---------------CCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhc
Confidence            344578999999999999887 5431110               135678999  9999999999999999887321   


Q ss_pred             CCCCcCeEEechhh------HHhhhh----------ch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHH
Q 047219          350 PWQGVPLMYVPLEV------VMSKYY----------GE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEAT  412 (567)
Q Consensus       350 ~~~~~~~~~i~~~~------l~s~~~----------G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~  412 (567)
                      ...+..++++++..      +...+.          +. ....+..+.........+.+|+|||+|.+...... .    
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~-~----  157 (412)
T 1w5s_A           83 EGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRI-A----  157 (412)
T ss_dssp             TTCCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTS-C----
T ss_pred             cCCceeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCc-c----
Confidence            00124566776532      111111          11 11222222222222223579999999998642100 0    


Q ss_pred             HHHHHHHHHhhcCcc-cC--CcEEEEEeeCCCC---CCC---hHHHhccceEEEecCCCHHHHHHHHHHHHH------hh
Q 047219          413 RRILSVLLRQIDGFE-QD--KKVVVIAATNRKQ---DLD---PALISRFDSMITFGLPDHENRQEIAAQYAK------HL  477 (567)
Q Consensus       413 ~~vl~~LL~~ld~~~-~~--~~viVIaaTN~~~---~Ld---~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~------~~  477 (567)
                      ...+..++..+.... ..  .++.+|++||.++   .++   +.+.++|...+.++.++.++..+++...+.      .+
T Consensus       158 ~~~l~~l~~~~~~~~~~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~  237 (412)
T 1w5s_A          158 AEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVW  237 (412)
T ss_dssp             HHHHHHHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSC
T ss_pred             hHHHHHHHHHHHhcccCCCCceEEEEEEeccccHHHHHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCC
Confidence            122333444443322 12  6788888887554   344   677788866799999999999999987765      25


Q ss_pred             CHHHHHHHHHhcc------CCCHHHHHHHHHHHHHH
Q 047219          478 TKAELAELATATE------EMSGRDIRDVCQQAERS  507 (567)
Q Consensus       478 ~~~~l~~la~~t~------g~s~~dL~~L~~~a~~~  507 (567)
                      ..+.+..+...+.      | .++.+..++..++..
T Consensus       238 ~~~~~~~i~~~~~~~~~~~G-~p~~~~~l~~~a~~~  272 (412)
T 1w5s_A          238 EPRHLELISDVYGEDKGGDG-SARRAIVALKMACEM  272 (412)
T ss_dssp             CHHHHHHHHHHHCGGGTSCC-CHHHHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHhccCCC-cHHHHHHHHHHHHHH
Confidence            5677888888877      5 577777888776643

>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=99.30  E-value=2.5e-12  Score=156.39  Aligned_cols=163  Identities=19%  Similarity=0.215  Sum_probs=113.7

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccC----------hhhHHh------hh-hccccccc-CCCCce--EEeeCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQS----------PEVYDD------IA-RGTRCKFE-SNRPRA--VLFEGPPG  332 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~----------pelf~~------l~-~~~~~~~~-~~~p~~--VLL~GppG  332 (567)
                      +...++|+++.|.+++++.+.+.+++++.+          ++.|+.      .| ...+..++ ..+|++  +|||||||
T Consensus      1013 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~glD~~lg~GG~p~g~~~l~~G~~g 1092 (1706)
T 3cmw_A         1013 SASGSSTGSMSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPES 1092 (1706)
T ss_dssp             -----------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTT
T ss_pred             ccCCceeeecCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhHHHHhccCCCCCCCEEEEEcCCC
Confidence            445689999999999999999999999854          556654      11 00112222 334444  99999999


Q ss_pred             CcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH------------hhhhch----hHHHHHHHHHHHhcCCCCcEEEEcC
Q 047219          333 TGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM------------SKYYGE----SERLLGKVFSLANELPNGAIIFLDE  396 (567)
Q Consensus       333 TGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~------------s~~~G~----~~~~l~~~f~~A~~~a~~~ILfIDE  396 (567)
                      ||||+||++++.+....   +-++++|+.++..            ++|+++    +++.++.+|..|+..+ ++++|+||
T Consensus      1093 ~GKT~la~~~~~~~~~~---g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~-~~~i~~d~ 1168 (1706)
T 3cmw_A         1093 SGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGA-VDVIVVDS 1168 (1706)
T ss_dssp             SSHHHHHHHHHHHHHHT---TCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTC-CSEEEESC
T ss_pred             CChHHHHHHHHHHhhhc---CCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcC-CeEEEeCc
Confidence            99999999999988443   4566666665433            566677    8999999999898877 49999999


Q ss_pred             cchhhhhhhhh------hHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC
Q 047219          397 VDSFAVARDSE------MHEATRRILSVLLRQIDGFEQDKKVVVIAATNR  440 (567)
Q Consensus       397 ID~L~~~~q~~------l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~  440 (567)
                      ++.|.+.+...      ......|++++++..+++.....+|+|| +||+
T Consensus      1169 ~~al~~~~~~~g~~~~~~~~~~~r~~~q~l~~~~~~~~~~~v~v~-~~n~ 1217 (1706)
T 3cmw_A         1169 VAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLI-FINQ 1217 (1706)
T ss_dssp             GGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHHTTCEEE-EEEC
T ss_pred             hHhcCcccccccccccccccHHHHHHHHHHHHHHhhhccCCeEEE-Eecc
Confidence            99999885321      1256678899999999988777888888 7776

>1wlf_A PEX1, peroxisome biogenesis factor 1; N-terminal domain, protein transport; 2.05A {Mus musculus} SCOP: b.52.2.3 d.31.1.1

Probab=99.29  E-value=3.7e-13  Score=127.67  Aligned_cols=112  Identities=12%  Similarity=0.042  Sum_probs=92.5

Q ss_pred             cchhhhH-HHHHHHhCCCCCCccceEEEEecceEEEEEEecCCC-------CcchHHHHHHHhhCceecccCCCceeEEE
Q 047219          110 KKERQRI-EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPAC-------EIPQLIANLVSHLGLKVEEHGGGSDMGLR  181 (567)
Q Consensus       110 ~~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~v~v~  181 (567)
                      .++++|| +++|++||+.+||+    |+|+|++++++++|++..       ++++|++.+|+|+|+++||     +|+|+
T Consensus        23 ~~~~vrL~~~~~~~L~~~~gd~----VeI~g~~~t~~~~w~~~~~~~d~~~~~I~Id~~~r~n~gv~~Gd-----~V~V~   93 (179)
T 1wlf_A           23 RDCFLHLPRRLVAQLHLLQNQA----IEVASDHQPTYLSWVEGRHFNDQSENVAEINRQVGQKLGLSSGD-----QVFLR   93 (179)
T ss_dssp             SSSCEEECHHHHHHTTCCTTCC----EEEESSSCCEEECEEECSSCC---CCEEEEEHHHHHHTTCCTTC-----EEEEE
T ss_pred             CCcEEECCHHHHHHcCCCCCcE----EEEEeCCeeEEEEEECCCCcccCCCCEEEECHHHHhHCCCCCCC-----EEEEE
Confidence            7889999 59999999999999    999999999999998732       4789999999999999999     99999


Q ss_pred             e-ecccccceeEecCCCCc-cccCCCccccCcccccccchheeee--ceeecCCCCceeee
Q 047219          182 A-WDSAVAWQLTLKPPEKQ-NESGGDRAQSGDMNAREGDLCILIF--RSLITSDKPEIEFI  238 (567)
Q Consensus       182 ~-~~~~~a~~v~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~--~~~~~~~~~~~~~~  238 (567)
                      + ++++.|++|+|+|.+.. ..+.+..  +      ++....+++  +|+..||.+.+...
T Consensus        94 ~~~~~~~A~~V~laP~~~dD~ei~e~~--a------~~le~~Ll~QiR~v~~G~~i~v~~~  146 (179)
T 1wlf_A           94 PCSHVVSCQQVEVEPLSADDWEILELH--A------ISLEQHLLDQIRIVFPKAVVPIWVD  146 (179)
T ss_dssp             ECSCCEECSEEEEEESSHHHHHHHHHS--C------SSHHHHHHHHCCEECTTCEEEEESS
T ss_pred             ECCCCccceEEEEEcCCcCCeEEehhH--H------HHHHHHHhcCceeccCCCEEEEEec
Confidence            9 89999999999998420 2232221  2      344577888  99999998876554

>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=99.08  E-value=2.8e-10  Score=106.89  Aligned_cols=106  Identities=15%  Similarity=0.158  Sum_probs=63.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC-CCCCCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG-AMPWQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~-~~~~~~  353 (567)
                      ...+|+++++.+...+.+.+.+......-              ....+.+++|+||||||||++++++++.+. ..   +
T Consensus         5 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~---g   67 (180)
T 3ec2_A            5 WNANLDTYHPKNVSQNRALLTIRVFVHNF--------------NPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKK---G   67 (180)
T ss_dssp             TTCCSSSCCCCSHHHHHHHHHHHHHHHSC--------------CGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHS---C
T ss_pred             hhCccccccCCCHHHHHHHHHHHHHHHhc--------------cccCCCEEEEECCCCCCHHHHHHHHHHHHHHHc---C
Confidence            44688888875443333333333221111              134468899999999999999999999873 21   4


Q ss_pred             cCeEEechhhHHhhhhchhHH-HHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          354 VPLMYVPLEVVMSKYYGESER-LLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~~-~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ..+.+++..++...+...... .....+....   .+.+|+|||++..
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~llilDE~~~~  112 (180)
T 3ec2_A           68 IRGYFFDTKDLIFRLKHLMDEGKDTKFLKTVL---NSPVLVLDDLGSE  112 (180)
T ss_dssp             CCCCEEEHHHHHHHHHHHHHHTCCSHHHHHHH---TCSEEEEETCSSS
T ss_pred             CeEEEEEHHHHHHHHHHHhcCchHHHHHHHhc---CCCEEEEeCCCCC
Confidence            456677777766554322111 0011222222   2579999999854

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.99  E-value=1e-09  Score=138.83  Aligned_cols=142  Identities=14%  Similarity=0.241  Sum_probs=92.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhc--------------C
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANE--------------L  386 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~--------------~  386 (567)
                      ..+++||+||||||||++|+.+.....     +..+..++++...+.      ..+...++....              .
T Consensus      1266 ~~~~vLL~GPpGtGKT~la~~~l~~~~-----~~~~~~infsa~ts~------~~~~~~i~~~~~~~~~~~g~~~~P~~~ 1334 (2695)
T 4akg_A         1266 SKRGIILCGPPGSGKTMIMNNALRNSS-----LYDVVGINFSKDTTT------EHILSALHRHTNYVTTSKGLTLLPKSD 1334 (2695)
T ss_dssp             HTCEEEEECSTTSSHHHHHHHHHHSCS-----SCEEEEEECCTTCCH------HHHHHHHHHHBCCEEETTTEEEEEBSS
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHhcCC-----CCceEEEEeecCCCH------HHHHHHHHHHhhhccccCCccccCCCC
Confidence            458999999999999999966555442     445666665543321      122223332110              1


Q ss_pred             CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc-------cCCcEEEEEeeCCCC-----CCChHHHhccce
Q 047219          387 PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE-------QDKKVVVIAATNRKQ-----DLDPALISRFDS  454 (567)
Q Consensus       387 a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~-------~~~~viVIaaTN~~~-----~Ld~aL~sRf~~  454 (567)
                      ...+|||||||+.-...+.+.  ....+.+.+++....-..       .-.++.+|||||+++     .++++|+||| .
T Consensus      1335 gk~~VlFiDEinmp~~d~yg~--q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllRrf-~ 1411 (2695)
T 4akg_A         1335 IKNLVLFCDEINLPKLDKYGS--QNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTRHA-A 1411 (2695)
T ss_dssp             SSCEEEEEETTTCSCCCSSSC--CHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHTTE-E
T ss_pred             CceEEEEecccccccccccCc--hhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhhee-e
Confidence            123699999998644332111  112334455553211111       114689999999984     7999999999 9


Q ss_pred             EEEecCCCHHHHHHHHHHHHHh
Q 047219          455 MITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       455 ~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                      ++.++.|+.+++..|+..+++.
T Consensus      1412 vi~i~~P~~~~l~~I~~~il~~ 1433 (2695)
T 4akg_A         1412 ILYLGYPSGKSLSQIYEIYYKA 1433 (2695)
T ss_dssp             EEECCCCTTTHHHHHHHHHHHH
T ss_pred             EEEeCCCCHHHHHHHHHHHHHH
Confidence            9999999999999999988754

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.95  E-value=1.7e-09  Score=103.11  Aligned_cols=109  Identities=14%  Similarity=0.168  Sum_probs=65.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      ...+|+++++.+...+.+.+.+..++...      .       ....+.+++|+||||||||++|+++++.+...   +.
T Consensus        20 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~------~-------~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~---~~   83 (202)
T 2w58_A           20 LRASLSDVDLNDDGRIKAIRFAERFVAEY------E-------PGKKMKGLYLHGSFGVGKTYLLAAIANELAKR---NV   83 (202)
T ss_dssp             GCCCTTSSCCSSHHHHHHHHHHHHHHHHC------C-------SSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT---TC
T ss_pred             HcCCHhhccCCChhHHHHHHHHHHHHHHh------h-------hccCCCeEEEECCCCCCHHHHHHHHHHHHHHc---CC
Confidence            34689999887644443333333221110      0       01234899999999999999999999998544   55


Q ss_pred             CeEEechhhHHhhhhchh-HHHHHHHHHHHhcCCCCcEEEEcCcchhhh
Q 047219          355 PLMYVPLEVVMSKYYGES-ERLLGKVFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~-~~~l~~~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                      ++.+++++.+...+.... ...+...+.....   ..+|||||++....
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~lilDei~~~~~  129 (202)
T 2w58_A           84 SSLIVYVPELFRELKHSLQDQTMNEKLDYIKK---VPVLMLDDLGAEAM  129 (202)
T ss_dssp             CEEEEEHHHHHHHHHHC---CCCHHHHHHHHH---SSEEEEEEECCC--
T ss_pred             eEEEEEhHHHHHHHHHHhccchHHHHHHHhcC---CCEEEEcCCCCCcC
Confidence            788888887765543211 0111223333332   36999999977543

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.89  E-value=1.7e-09  Score=99.28  Aligned_cols=110  Identities=16%  Similarity=0.252  Sum_probs=69.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ....++|+||+|+|||+|++++++.....   +..+++++..++...          .+   . .  .+.+|+|||++.+
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~---g~~~~~~~~~~~~~~----------~~---~-~--~~~lLilDE~~~~   95 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEA---GKNAAYIDAASMPLT----------DA---A-F--EAEYLAVDQVEKL   95 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTT---TCCEEEEETTTSCCC----------GG---G-G--GCSEEEEESTTCC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhc---CCcEEEEcHHHhhHH----------HH---H-h--CCCEEEEeCcccc
Confidence            45789999999999999999999988532   556778877665442          00   1 1  2479999999987


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeC-CCCCCC--hHHHhccceEEEecC
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATN-RKQDLD--PALISRFDSMITFGL  460 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN-~~~~Ld--~aL~sRf~~~I~i~~  460 (567)
                      ....+.           .+...++.....+..++|.||| .+..+.  ++|++||.....+.+
T Consensus        96 ~~~~~~-----------~l~~li~~~~~~g~~~iiits~~~p~~l~~~~~L~SRl~~g~~~~l  147 (149)
T 2kjq_A           96 GNEEQA-----------LLFSIFNRFRNSGKGFLLLGSEYTPQQLVIREDLRTRMAYCLVYEV  147 (149)
T ss_dssp             CSHHHH-----------HHHHHHHHHHHHTCCEEEEEESSCTTTSSCCHHHHHHGGGSEECCC
T ss_pred             ChHHHH-----------HHHHHHHHHHHcCCcEEEEECCCCHHHccccHHHHHHHhcCeeEEe
Confidence            654321           1222222222223332444555 444332  999999966555543

>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=98.88  E-value=1e-07  Score=97.72  Aligned_cols=187  Identities=13%  Similarity=0.150  Sum_probs=110.9

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      ....+.++|.++.++.|.+ +.                      .  ..++|+||+|+|||++++.+++...      ..
T Consensus         9 ~~~~~~~~gR~~el~~L~~-l~----------------------~--~~v~i~G~~G~GKT~L~~~~~~~~~------~~   57 (357)
T 2fna_A            9 KDNRKDFFDREKEIEKLKG-LR----------------------A--PITLVLGLRRTGKSSIIKIGINELN------LP   57 (357)
T ss_dssp             CCSGGGSCCCHHHHHHHHH-TC----------------------S--SEEEEEESTTSSHHHHHHHHHHHHT------CC
T ss_pred             CCCHHHhcChHHHHHHHHH-hc----------------------C--CcEEEECCCCCCHHHHHHHHHHhcC------CC
Confidence            3456789999999888876 52                      2  4899999999999999999999873      23


Q ss_pred             eEEechhhH-----------Hhhh---h--------------ch------------------hHHHHHHHHHHHhcCC-C
Q 047219          356 LMYVPLEVV-----------MSKY---Y--------------GE------------------SERLLGKVFSLANELP-N  388 (567)
Q Consensus       356 ~~~i~~~~l-----------~s~~---~--------------G~------------------~~~~l~~~f~~A~~~a-~  388 (567)
                      ++++++...           ...+   .              +.                  ....+..+++...... .
T Consensus        58 ~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~  137 (357)
T 2fna_A           58 YIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKD  137 (357)
T ss_dssp             EEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSS
T ss_pred             EEEEEchhhccccCCCHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCC
Confidence            555554432           0000   0              00                  0112334444444332 2


Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC---------CCChHHHhccceEEEec
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ---------DLDPALISRFDSMITFG  459 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~---------~Ld~aL~sRf~~~I~i~  459 (567)
                      +.+|+|||++.+............    ..+...      ..++.+|.+++...         .....+..|+...+.+.
T Consensus       138 ~~vlvlDe~~~~~~~~~~~~~~~l----~~~~~~------~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~  207 (357)
T 2fna_A          138 NVIIVLDEAQELVKLRGVNLLPAL----AYAYDN------LKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELK  207 (357)
T ss_dssp             CEEEEEETGGGGGGCTTCCCHHHH----HHHHHH------CTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEEC
T ss_pred             CeEEEEECHHHhhccCchhHHHHH----HHHHHc------CCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecC
Confidence            589999999998642111111222    222211      13566776665432         11223455665789999


Q ss_pred             CCCHHHHHHHHHHHHHh--hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          460 LPDHENRQEIAAQYAKH--LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       460 ~P~~~eR~eIL~~~~~~--~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      ..+.++..+++...+..  ........+...+.|+ +..+..++...
T Consensus       208 ~l~~~e~~~~l~~~~~~~~~~~~~~~~i~~~t~G~-P~~l~~~~~~~  253 (357)
T 2fna_A          208 PFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGI-PGWLTYFGFIY  253 (357)
T ss_dssp             CCCHHHHHHHHHHHHHHHTCCCCCHHHHHHHHCSC-HHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCcHHHHHHHhCCC-HHHHHHHHHHH
Confidence            99999999999876642  2222236666776664 55666665543

>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family; helicase, MCM homolog, DNA replication, ATP-binding, DNA-binding; 1.90A {Methanopyrus kandleri AV19}

Probab=98.88  E-value=3.2e-10  Score=121.70  Aligned_cols=154  Identities=17%  Similarity=0.206  Sum_probs=89.7

Q ss_pred             ccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHH-HHHhCCCCCCCcCeEEec
Q 047219          282 IAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVI-ANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       282 IiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraI-A~~l~~~~~~~~~~~~i~  360 (567)
                      |.|++.+|+.|.-.+...  ++.              .+...+|||.|+||| ||++|+++ ++.+++..     +....
T Consensus       215 I~G~e~vK~aLll~L~GG--~~k--------------~rgdihVLL~G~PGt-KS~Lar~i~~~i~pR~~-----ft~g~  272 (506)
T 3f8t_A          215 LPGAEEVGKMLALQLFSC--VGK--------------NSERLHVLLAGYPVV-CSEILHHVLDHLAPRGV-----YVDLR  272 (506)
T ss_dssp             STTCHHHHHHHHHHHTTC--CSS--------------GGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEE-----EEEGG
T ss_pred             cCCCHHHHHHHHHHHcCC--ccc--------------cCCceeEEEECCCCh-HHHHHHHHHHHhCCCeE-----EecCC
Confidence            899999877665433110  000              123448999999999 99999999 88764421     11111


Q ss_pred             hh---hHHhhhhch--hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEE
Q 047219          361 LE---VVMSKYYGE--SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVI  435 (567)
Q Consensus       361 ~~---~l~s~~~G~--~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVI  435 (567)
                      ++   .+.....+.  ..-.-+ .+.    .+.++++|||||+.+.++.|..+++++++-.-.+    .+...+.++.||
T Consensus       273 ~ss~~gLt~s~r~~tG~~~~~G-~l~----LAdgGvl~lDEIn~~~~~~qsaLlEaMEe~~VtI----~G~~lparf~VI  343 (506)
T 3f8t_A          273 RTELTDLTAVLKEDRGWALRAG-AAV----LADGGILAVDHLEGAPEPHRWALMEAMDKGTVTV----DGIALNARCAVL  343 (506)
T ss_dssp             GCCHHHHSEEEEESSSEEEEEC-HHH----HTTTSEEEEECCTTCCHHHHHHHHHHHHHSEEEE----TTEEEECCCEEE
T ss_pred             CCCccCceEEEEcCCCcccCCC-eeE----EcCCCeeehHhhhhCCHHHHHHHHHHHhCCcEEE----CCEEcCCCeEEE
Confidence            10   111111000  000001 112    2347999999999999888888877765521111    122456789999


Q ss_pred             EeeCCCC-----------CCChHHHhccceEEEe-cCCCHHHH
Q 047219          436 AATNRKQ-----------DLDPALISRFDSMITF-GLPDHENR  466 (567)
Q Consensus       436 aaTN~~~-----------~Ld~aL~sRf~~~I~i-~~P~~~eR  466 (567)
                      ||+|+..           .|++++++|||..+.+ +.|+.+.-
T Consensus       344 AA~NP~~~yd~~~s~~~~~Lp~alLDRFDLi~i~~d~pd~e~d  386 (506)
T 3f8t_A          344 AAINPGEQWPSDPPIARIDLDQDFLSHFDLIAFLGVDPRPGEP  386 (506)
T ss_dssp             EEECCCC--CCSCGGGGCCSCHHHHTTCSEEEETTC-------
T ss_pred             EEeCcccccCCCCCccccCCChHHhhheeeEEEecCCCChhHh
Confidence            9999864           7899999999775544 66665543

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.86  E-value=2e-07  Score=95.37  Aligned_cols=191  Identities=15%  Similarity=0.169  Sum_probs=114.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      +...-+.++|.++.++.|.+.+..                       ...++|+||+|+|||++++.+++..      + 
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~-----------------------~~~v~i~G~~G~GKT~Ll~~~~~~~------~-   56 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLEN-----------------------YPLTLLLGIRRVGKSSLLRAFLNER------P-   56 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHH-----------------------CSEEEEECCTTSSHHHHHHHHHHHS------S-
T ss_pred             CCCChHhcCChHHHHHHHHHHHhc-----------------------CCeEEEECCCcCCHHHHHHHHHHHc------C-
Confidence            334557799999999999887641                       1689999999999999999999886      2 


Q ss_pred             CeEEechhhHH------------hhh---hch---------------------hHHHHHHHHHH----HhcCCCCcEEEE
Q 047219          355 PLMYVPLEVVM------------SKY---YGE---------------------SERLLGKVFSL----ANELPNGAIIFL  394 (567)
Q Consensus       355 ~~~~i~~~~l~------------s~~---~G~---------------------~~~~l~~~f~~----A~~~a~~~ILfI  394 (567)
                       ++++++....            ..+   .+.                     ....+..+++.    +.... +.+|+|
T Consensus        57 -~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~-~~vlvl  134 (350)
T 2qen_A           57 -GILIDCRELYAERGHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELG-EFIVAF  134 (350)
T ss_dssp             -EEEEEHHHHHHTTTCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHS-CEEEEE
T ss_pred             -cEEEEeecccccccCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccC-CEEEEE
Confidence             5566554321            000   000                     00112222222    22222 589999


Q ss_pred             cCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC---------CCChHHHhccceEEEecCCCHHH
Q 047219          395 DEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ---------DLDPALISRFDSMITFGLPDHEN  465 (567)
Q Consensus       395 DEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~---------~Ld~aL~sRf~~~I~i~~P~~~e  465 (567)
                      ||++.+........    ......+....+.   ..++.+|.++....         .....+..|+...+++.+.+.++
T Consensus       135 De~~~~~~~~~~~~----~~~~~~L~~~~~~---~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e  207 (350)
T 2qen_A          135 DEAQYLRFYGSRGG----KELLALFAYAYDS---LPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDT  207 (350)
T ss_dssp             ETGGGGGGBTTTTT----HHHHHHHHHHHHH---CTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHH
T ss_pred             eCHHHHhccCccch----hhHHHHHHHHHHh---cCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHH
Confidence            99999864100000    0111222222221   13566666664321         12233455665689999999999


Q ss_pred             HHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          466 RQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       466 R~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      -.+++...+..    +..+.+..+...+.|+ +.-+..++...|
T Consensus       208 ~~~~l~~~~~~~~~~~~~~~~~~i~~~tgG~-P~~l~~~~~~~~  250 (350)
T 2qen_A          208 SVEFLKRGFREVNLDVPENEIEEAVELLDGI-PGWLVVFGVEYL  250 (350)
T ss_dssp             HHHHHHHHHHTTTCCCCHHHHHHHHHHHTTC-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHHHhCCC-HHHHHHHHHHHh
Confidence            99999876643    4566778888887764 666777665433

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.79  E-value=2.2e-09  Score=110.27  Aligned_cols=75  Identities=12%  Similarity=0.197  Sum_probs=50.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC-CCCCCCcCeEEechhhHHhhhhchh-HHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG-AMPWQGVPLMYVPLEVVMSKYYGES-ERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~-~~~~~~~~~~~i~~~~l~s~~~G~~-~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      .+.+++|+||||||||+||+++++++. ..   +.++.+++++.+...+.... .......+.....   ..+|||||++
T Consensus       151 ~~~~lll~G~~GtGKT~La~aia~~~~~~~---g~~v~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~---~~lLiiDdig  224 (308)
T 2qgz_A          151 EQKGLYLYGDMGIGKSYLLAAMAHELSEKK---GVSTTLLHFPSFAIDVKNAISNGSVKEEIDAVKN---VPVLILDDIG  224 (308)
T ss_dssp             SCCEEEEECSTTSSHHHHHHHHHHHHHHHS---CCCEEEEEHHHHHHHHHCCCC----CCTTHHHHT---SSEEEEETCC
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHHHhc---CCcEEEEEHHHHHHHHHHHhccchHHHHHHHhcC---CCEEEEcCCC
Confidence            368999999999999999999999885 43   56788888887776554321 1111122222221   4699999997


Q ss_pred             hhh
Q 047219          399 SFA  401 (567)
Q Consensus       399 ~L~  401 (567)
                      ...
T Consensus       225 ~~~  227 (308)
T 2qgz_A          225 AEQ  227 (308)
T ss_dssp             C--
T ss_pred             CCC
Confidence            654

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.75  E-value=1.1e-07  Score=120.79  Aligned_cols=137  Identities=18%  Similarity=0.233  Sum_probs=101.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ...++++.||+|||||.+++++|+.+      +.+|+.++|++-+..      ..++.+|..+...  ++++++|||+.+
T Consensus       644 ~~~~~~l~GpaGtGKTe~vk~LA~~l------g~~~v~~nc~e~ld~------~~lg~~~~g~~~~--Gaw~~~DE~nr~  709 (2695)
T 4akg_A          644 QKYGGCFFGPAGTGKTETVKAFGQNL------GRVVVVFNCDDSFDY------QVLSRLLVGITQI--GAWGCFDEFNRL  709 (2695)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHTT------TCCCEEEETTSSCCH------HHHHHHHHHHHHH--TCEEEEETTTSS
T ss_pred             hCCCCcccCCCCCCcHHHHHHHHHHh------CCcEEEEECCCCCCh------hHhhHHHHHHHhc--CCEeeehhhhhc
Confidence            45788999999999999999999999      778999999865541      3456677766654  689999999999


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhh-------cCcccCCcEEEEEeeCC----CCCCChHHHhccceEEEecCCCHHHHHHH
Q 047219          401 AVARDSEMHEATRRILSVLLRQI-------DGFEQDKKVVVIAATNR----KQDLDPALISRFDSMITFGLPDHENRQEI  469 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~l-------d~~~~~~~viVIaaTN~----~~~Ld~aL~sRf~~~I~i~~P~~~eR~eI  469 (567)
                      .....+.+......+...+....       ..+..+.++.|++|.|+    ...|+++|++|| +.+.+..|+.+...+|
T Consensus       710 ~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~~F-r~v~m~~Pd~~~i~ei  788 (2695)
T 4akg_A          710 DEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKKSF-REFSMKSPQSGTIAEM  788 (2695)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHTTE-EEEECCCCCHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHhhe-EEEEeeCCCHHHHHHH
Confidence            87654444333333333322111       11234567889999995    457999999999 8999999999999888


Q ss_pred             HHH
Q 047219          470 AAQ  472 (567)
Q Consensus       470 L~~  472 (567)
                      +-.
T Consensus       789 ~l~  791 (2695)
T 4akg_A          789 ILQ  791 (2695)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            653

>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=98.60  E-value=1.8e-08  Score=103.65  Aligned_cols=118  Identities=19%  Similarity=0.217  Sum_probs=65.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech--hhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCc
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL--EVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEV  397 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~--~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEI  397 (567)
                      .+...++|+||||||||+||.+++...      +..+.+++.  ++..+.+....+..+..+++...+.  . +||||++
T Consensus       121 ~~gsviLI~GpPGsGKTtLAlqlA~~~------G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~--~-LLVIDsI  191 (331)
T 2vhj_A          121 YASGMVIVTGKGNSGKTPLVHALGEAL------GGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQH--R-VIVIDSL  191 (331)
T ss_dssp             EESEEEEEECSCSSSHHHHHHHHHHHH------HTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHC--S-EEEEECC
T ss_pred             CCCcEEEEEcCCCCCHHHHHHHHHHhC------CCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhC--C-EEEEecc
Confidence            345668999999999999999999873      223333333  2222222233445555555555543  2 9999999


Q ss_pred             chhhhhhhhh-hHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChH
Q 047219          398 DSFAVARDSE-MHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPA  447 (567)
Q Consensus       398 D~L~~~~q~~-l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~a  447 (567)
                      +.+....... ......+.+.+++..+.++....++.+|+++|+ ...+++
T Consensus       192 ~aL~~~~~~~s~~G~v~~~lrqlL~~L~~~~k~~gvtVIlttnp-~s~dea  241 (331)
T 2vhj_A          192 KNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNP-TSNDDK  241 (331)
T ss_dssp             TTTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECCC-SSCSSS
T ss_pred             cccccccccccccchHHHHHHHHHHHHHHHHhhCCCEEEEEeCC-cccchh
Confidence            9986543321 000011223444444444333456788888884 444444

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.48  E-value=2.7e-07  Score=88.96  Aligned_cols=109  Identities=19%  Similarity=0.276  Sum_probs=62.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      ..+++||+||||||||++|.++++.+....   ..+  ++...   .+ .         +.   ......+++|||+|.-
T Consensus        57 kkn~ili~GPPGtGKTt~a~ala~~l~g~i---~~f--ans~s---~f-~---------l~---~l~~~kIiiLDEad~~  115 (212)
T 1tue_A           57 KKNCLVFCGPANTGKSYFGMSFIHFIQGAV---ISF--VNSTS---HF-W---------LE---PLTDTKVAMLDDATTT  115 (212)
T ss_dssp             TCSEEEEESCGGGCHHHHHHHHHHHHTCEE---CCC--CCSSS---CG-G---------GG---GGTTCSSEEEEEECHH
T ss_pred             cccEEEEECCCCCCHHHHHHHHHHHhCCCe---eeE--Eeccc---hh-h---------hc---ccCCCCEEEEECCCch
Confidence            346799999999999999999999984220   011  11100   00 0         01   1112469999999842


Q ss_pred             hhhhhhhhHHHHHHHHHHHHHhhcCcc------cC-----CcEEEEEeeCC---CCCCChHHHhccceEEEecCC
Q 047219          401 AVARDSEMHEATRRILSVLLRQIDGFE------QD-----KKVVVIAATNR---KQDLDPALISRFDSMITFGLP  461 (567)
Q Consensus       401 ~~~~q~~l~~~~~~vl~~LL~~ld~~~------~~-----~~viVIaaTN~---~~~Ld~aL~sRf~~~I~i~~P  461 (567)
                      .       .+.+++   .+...+++..      ..     ....+|.|||.   .+.--+.|.+|+ .++.|+.|
T Consensus       116 ~-------~~~~d~---~lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~SRi-~~f~F~~~  179 (212)
T 1tue_A          116 C-------WTYFDT---YMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLESRI-TVFEFPNA  179 (212)
T ss_dssp             H-------HHHHHH---HCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHTSC-EEEECCSC
T ss_pred             h-------HHHHHH---HHHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhhhE-EEEEcCCC
Confidence            1       112222   2333444421      01     13477888986   333447899999 78888644

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.41  E-value=1.1e-06  Score=112.29  Aligned_cols=135  Identities=18%  Similarity=0.200  Sum_probs=101.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~  401 (567)
                      ..+..+.||+|||||.+++.+|+.+      +.+|+.++|++-+.-      ..++.+|..+...  |+..++|||+.+.
T Consensus       604 ~~gg~~~GPaGtGKTet~k~La~~l------gr~~~vfnC~~~~d~------~~~g~i~~G~~~~--GaW~cfDEfNrl~  669 (3245)
T 3vkg_A          604 RMGGNPFGPAGTGKTETVKALGSQL------GRFVLVFCCDEGFDL------QAMSRIFVGLCQC--GAWGCFDEFNRLE  669 (3245)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHT------TCCEEEEECSSCCCH------HHHHHHHHHHHHH--TCEEEEETTTSSC
T ss_pred             cCCCCCCCCCCCCHHHHHHHHHHHh------CCeEEEEeCCCCCCH------HHHHHHHhhHhhc--CcEEEehhhhcCC
Confidence            4566799999999999999999999      778999998764431      3455666666554  6899999999997


Q ss_pred             hhhhhhhHHHHHHHHHHHHHh--------hcCcccCCcEEEEEeeCC----CCCCChHHHhccceEEEecCCCHHHHHHH
Q 047219          402 VARDSEMHEATRRILSVLLRQ--------IDGFEQDKKVVVIAATNR----KQDLDPALISRFDSMITFGLPDHENRQEI  469 (567)
Q Consensus       402 ~~~q~~l~~~~~~vl~~LL~~--------ld~~~~~~~viVIaaTN~----~~~Ld~aL~sRf~~~I~i~~P~~~eR~eI  469 (567)
                      ...-+.....++.+...+...        ...+..+..+.+++|.|+    ...|++.|+.|| +.+.+..||.+...+|
T Consensus       670 ~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNpgY~gr~eLP~nLk~lF-r~v~m~~Pd~~~i~ei  748 (3245)
T 3vkg_A          670 ERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNPGYAGRSNLPDNLKKLF-RSMAMIKPDREMIAQV  748 (3245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCCCGGGCCCSCHHHHTTE-EEEECCSCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCCCccCcccChHHHHhhc-EEEEEeCCCHHHHHHH
Confidence            665554444444444444332        222344567899999996    457999999999 8899999999999888


Q ss_pred             HH
Q 047219          470 AA  471 (567)
Q Consensus       470 L~  471 (567)
                      +-
T Consensus       749 ~L  750 (3245)
T 3vkg_A          749 ML  750 (3245)
T ss_dssp             HH
T ss_pred             HH
Confidence            64

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.41  E-value=2e-07  Score=89.74  Aligned_cols=134  Identities=16%  Similarity=0.175  Sum_probs=76.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC-CC-CCC-cCeEEechhhHHhhhh-------------ch--hHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA-MP-WQG-VPLMYVPLEVVMSKYY-------------GE--SERLLGKVFSLA  383 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~-~~-~~~-~~~~~i~~~~l~s~~~-------------G~--~~~~l~~~f~~A  383 (567)
                      +.-.|++|+||||||++|.+.+..... .+ ..+ .+++..+...+.....             ++  ....+..++..+
T Consensus         5 ~mi~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~   84 (199)
T 2r2a_A            5 AEICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKP   84 (199)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSG
T ss_pred             eeEEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhcc
Confidence            446889999999999999887555310 00 013 3444444443322111             10  011122221111


Q ss_pred             hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCH
Q 047219          384 NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDH  463 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~  463 (567)
                      .  ..+++|+|||++.+.+.+.... +.     ..++..++.. .....-+|.+|+++..++.+++.|+...+++..|..
T Consensus        85 ~--~~~~vliIDEAq~l~~~~~~~~-e~-----~rll~~l~~~-r~~~~~iil~tq~~~~l~~~lr~ri~~~~~l~~~~~  155 (199)
T 2r2a_A           85 E--NIGSIVIVDEAQDVWPARSAGS-KI-----PENVQWLNTH-RHQGIDIFVLTQGPKLLDQNLRTLVRKHYHIASNKM  155 (199)
T ss_dssp             G--GTTCEEEETTGGGTSBCCCTTC-CC-----CHHHHGGGGT-TTTTCEEEEEESCGGGBCHHHHTTEEEEEEEEECSS
T ss_pred             c--cCceEEEEEChhhhccCccccc-hh-----HHHHHHHHhc-CcCCeEEEEECCCHHHHhHHHHHHhheEEEEcCccc
Confidence            2  1268999999999965442211 11     1234444432 334567788888899999999999988888877654


Q ss_pred             H
Q 047219          464 E  464 (567)
Q Consensus       464 ~  464 (567)
                      .
T Consensus       156 ~  156 (199)
T 2r2a_A          156 G  156 (199)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1jr3_D DNA polymerase III, delta subunit; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*

Probab=98.34  E-value=3.7e-06  Score=86.87  Aligned_cols=147  Identities=18%  Similarity=0.123  Sum_probs=94.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDE  396 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDE  396 (567)
                      +.+..+||+||+|+||++.++.+++.+....+.....+.++..           ..++.+++.+.   -.++..+++|||
T Consensus        16 ~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-----------~~~~~l~~~~~~~plf~~~kvvii~~   84 (343)
T 1jr3_D           16 GLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPN-----------TDWNAIFSLCQAMSLFASRQTLLLLL   84 (343)
T ss_dssp             CCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCTT-----------CCHHHHHHHHHHHHHCCSCEEEEEEC
T ss_pred             CCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecCC-----------CCHHHHHHHhcCcCCccCCeEEEEEC
Confidence            4567899999999999999999998763221111122233321           11233333332   234468999999


Q ss_pred             cch-hhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCC------CCCChHHHhccceEEEecCCCHHHHHHH
Q 047219          397 VDS-FAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRK------QDLDPALISRFDSMITFGLPDHENRQEI  469 (567)
Q Consensus       397 ID~-L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~------~~Ld~aL~sRf~~~I~i~~P~~~eR~eI  469 (567)
                      +|. +...           ..+.|+..++.  .+.++++|.+++..      ..+.+++.+|+ ..+++..++.++....
T Consensus        85 ~~~kl~~~-----------~~~aLl~~le~--p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~-~~~~~~~l~~~~l~~~  150 (343)
T 1jr3_D           85 PENGPNAA-----------INEQLLTLTGL--LHDDLLLIVRGNKLSKAQENAAWFTALANRS-VQVTCQTPEQAQLPRW  150 (343)
T ss_dssp             CSSCCCTT-----------HHHHHHHHHTT--CBTTEEEEEEESCCCTTTTTSHHHHHHTTTC-EEEEECCCCTTHHHHH
T ss_pred             CCCCCChH-----------HHHHHHHHHhc--CCCCeEEEEEcCCCChhhHhhHHHHHHHhCc-eEEEeeCCCHHHHHHH
Confidence            998 7533           23456666664  34456666555442      34678889999 8999999999998888


Q ss_pred             HHHHHHh----hCHHHHHHHHHhccC
Q 047219          470 AAQYAKH----LTKAELAELATATEE  491 (567)
Q Consensus       470 L~~~~~~----~~~~~l~~la~~t~g  491 (567)
                      +...++.    +..+.+..++..+.|
T Consensus       151 l~~~~~~~g~~i~~~a~~~l~~~~~g  176 (343)
T 1jr3_D          151 VAARAKQLNLELDDAANQVLCYCYEG  176 (343)
T ss_dssp             HHHHHHHTTCEECHHHHHHHHHSSTT
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHHhch
Confidence            8887764    456666666665543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.31  E-value=3.5e-06  Score=107.87  Aligned_cols=142  Identities=15%  Similarity=0.266  Sum_probs=87.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHH----hc----------
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLA----NE----------  385 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A----~~----------  385 (567)
                      ...++|||+||||||||.+++.....+.     +.+++.++++...+.      ..+...++..    ..          
T Consensus      1302 ~~~~pvLL~GptGtGKT~li~~~L~~l~-----~~~~~~infS~~Tta------~~l~~~~e~~~e~~~~~~~G~~~~p~ 1370 (3245)
T 3vkg_A         1302 SEHRPLILCGPPGSGKTMTLTSTLRAFP-----DFEVVSLNFSSATTP------ELLLKTFDHHCEYKRTPSGETVLRPT 1370 (3245)
T ss_dssp             HTTCCCEEESSTTSSHHHHHHHHGGGCT-----TEEEEEECCCTTCCH------HHHHHHHHHHEEEEECTTSCEEEEES
T ss_pred             HCCCcEEEECCCCCCHHHHHHHHHHhCC-----CCceEEEEeeCCCCH------HHHHHHHhhcceEEeccCCCcccCCC
Confidence            3468999999999999987765544442     344566666543321      1122222210    00          


Q ss_pred             -CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc-------ccCCcEEEEEeeCCCC-----CCChHHHhcc
Q 047219          386 -LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF-------EQDKKVVVIAATNRKQ-----DLDPALISRF  452 (567)
Q Consensus       386 -~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~-------~~~~~viVIaaTN~~~-----~Ld~aL~sRf  452 (567)
                       .....|+||||++.-....-+..  ..-+.+.+++....-+       ..-.++.+|||+|++.     .++++|.+||
T Consensus      1371 ~~Gk~~VlFiDDiNmp~~D~yGtQ--~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r~F 1448 (3245)
T 3vkg_A         1371 QLGKWLVVFCDEINLPSTDKYGTQ--RVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLRHA 1448 (3245)
T ss_dssp             STTCEEEEEETTTTCCCCCTTSCC--HHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHTTC
T ss_pred             cCCceEEEEecccCCCCccccccc--cHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHhhc
Confidence             11235999999985332211111  1123344444332111       1225789999999874     5999999999


Q ss_pred             ceEEEecCCCHHHHHHHHHHHHH
Q 047219          453 DSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       453 ~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                       .++.++.|+.+....|+..++.
T Consensus      1449 -~vi~i~~ps~esL~~If~til~ 1470 (3245)
T 3vkg_A         1449 -PILLVDFPSTSSLTQIYGTFNR 1470 (3245)
T ss_dssp             -CEEECCCCCHHHHHHHHHHHHH
T ss_pred             -eEEEeCCCCHHHHHHHHHHHHH
Confidence             8899999999999999876654

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.26  E-value=1.8e-06  Score=106.75  Aligned_cols=116  Identities=20%  Similarity=0.250  Sum_probs=78.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH----Hhhhhc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV----MSKYYG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l----~s~~~G------------~~~~~l~~~f~~  382 (567)
                      ..++.+++|+||||||||+||.+++.+....   +..+.+++.+..    ..+..|            ..+..+..++..
T Consensus      1424 i~~g~~vll~GppGtGKT~LA~ala~ea~~~---G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~l 1500 (2050)
T 3cmu_A         1424 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDAL 1500 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHc---CCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHH
Confidence            5678999999999999999999999887543   456777776532    222233            234555666666


Q ss_pred             HhcCCCCcEEEEcCcchhhhhhhh------hhHHHHHHHHHHHHHhhcCcccCCcEEEEEee
Q 047219          383 ANELPNGAIIFLDEVDSFAVARDS------EMHEATRRILSVLLRQIDGFEQDKKVVVIAAT  438 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~q~------~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaT  438 (567)
                      ++..+ +++|||||++.+.+..+.      .......+++.+++..+.+.....++.+|++-
T Consensus      1501 vr~~~-~~lVVIDsi~al~p~~~~~g~~~~~~~~~~~R~lsqlL~~L~~~~~~~~v~VI~tN 1561 (2050)
T 3cmu_A         1501 ARSGA-VDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLKQSNTLLIFIN 1561 (2050)
T ss_dssp             HHHTC-CSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHHTTTCEEEEEE
T ss_pred             HhcCC-CCEEEEcChhHhcccccccccccccccchHHHHHHHHHHHHHHHHHhCCcEEEEEc
Confidence            66565 599999999987764321      01111345667777777776666777776664

>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=98.10  E-value=1.1e-05  Score=80.81  Aligned_cols=25  Identities=36%  Similarity=0.522  Sum_probs=23.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++++|+||||||||++|++||+.+
T Consensus       104 ~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A          104 RNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHhhh
Confidence            4679999999999999999999976

>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=97.95  E-value=2.7e-05  Score=73.29  Aligned_cols=24  Identities=33%  Similarity=0.722  Sum_probs=21.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.|.||+|+|||||++.|+..+.
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~   25 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhC
Confidence            478999999999999999999873

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=97.74  E-value=2.5e-05  Score=63.29  Aligned_cols=53  Identities=21%  Similarity=0.340  Sum_probs=47.4

Q ss_pred             cCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          459 GLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       459 ~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      ++|+.++|.+||+.+++++.   ..++..++..+.||||+||.++|++|.+.++++
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~a~~~   56 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRE   56 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHHHHHT
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh
Confidence            57999999999999998864   347999999999999999999999999887765

>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=97.69  E-value=0.00019  Score=77.19  Aligned_cols=103  Identities=20%  Similarity=0.279  Sum_probs=75.7

Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-------------CCCCChHHHhccceE
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-------------KQDLDPALISRFDSM  455 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-------------~~~Ld~aL~sRf~~~  455 (567)
                      ++|+||||+|.|..           ..++.|++.++..  +.++ +|.+||+             +..+++.+++|| ..
T Consensus       296 ~~VliIDEa~~l~~-----------~a~~aLlk~lEe~--~~~~-~il~tn~~~~~i~~~~~~~~~~~l~~~i~sR~-~~  360 (456)
T 2c9o_A          296 PGVLFVDEVHMLDI-----------ECFTYLHRALESS--IAPI-VIFASNRGNCVIRGTEDITSPHGIPLDLLDRV-MI  360 (456)
T ss_dssp             ECEEEEESGGGCBH-----------HHHHHHHHHTTST--TCCE-EEEEECCSEEECBTTSSCEEETTCCHHHHTTE-EE
T ss_pred             ceEEEEechhhcCH-----------HHHHHHHHHhhcc--CCCE-EEEecCCccccccccccccccccCChhHHhhc-ce
Confidence            37999999999963           3557778888853  3345 4444433             668999999999 55


Q ss_pred             EEecCCCHHHHHHHHHHHHH----hhCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          456 ITFGLPDHENRQEIAAQYAK----HLTKAELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       456 I~i~~P~~~eR~eIL~~~~~----~~~~~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      +.|+.|+.++..++++..+.    .+..+.+..++......+++....++..+..
T Consensus       361 ~~~~~~~~~e~~~iL~~~~~~~~~~~~~~~~~~i~~~a~~g~~r~a~~ll~~a~~  415 (456)
T 2c9o_A          361 IRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANL  415 (456)
T ss_dssp             EECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHHHSCHHHHHHTHHHHHH
T ss_pred             eeCCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHccCCCHHHHHHHHHHHHH
Confidence            79999999999999998775    2567777778777622367776677766543

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.68  E-value=0.00094  Score=73.65  Aligned_cols=180  Identities=14%  Similarity=0.101  Sum_probs=97.9

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC--CCCCC-Cc
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG--AMPWQ-GV  354 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~--~~~~~-~~  354 (567)
                      ....++|.+..++.|.+.+...                   ....+.++|+|++|+|||+||+.+++...  ...|. ++
T Consensus       122 ~~~~~vGR~~~l~~L~~~L~~~-------------------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v  182 (591)
T 1z6t_A          122 RPVVFVTRKKLVNAIQQKLSKL-------------------KGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGV  182 (591)
T ss_dssp             CCSSCCCCHHHHHHHHHHHTTS-------------------TTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCE
T ss_pred             CCCeecccHHHHHHHHHHHhcc-------------------cCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCce
Confidence            3456899999999998876421                   23456799999999999999999875321  01111 12


Q ss_pred             CeEEechh---hHHhhh------hc-----------hhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          355 PLMYVPLE---VVMSKY------YG-----------ESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       355 ~~~~i~~~---~l~s~~------~G-----------~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      -++.+...   .+...+      .+           ..+.....+.........+.+|+||+++...             
T Consensus       183 ~wv~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~~-------------  249 (591)
T 1z6t_A          183 HWVSVGKQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDSW-------------  249 (591)
T ss_dssp             EEEEEESCCHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCHH-------------
T ss_pred             EEEECCCCchHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCHH-------------
Confidence            22223221   111111      11           0111122222222222235899999998531             


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEe---cCCCHHHHHHHHHHHHHh---hCHHHHHHHHHh
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITF---GLPDHENRQEIAAQYAKH---LTKAELAELATA  488 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i---~~P~~~eR~eIL~~~~~~---~~~~~l~~la~~  488 (567)
                          .+..+     ..++.||.||........ +  + ...+.+   +..+.++-.+++...+..   -..+....+.+.
T Consensus       250 ----~l~~l-----~~~~~ilvTsR~~~~~~~-~--~-~~~~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~  316 (591)
T 1z6t_A          250 ----VLKAF-----DSQCQILLTTRDKSVTDS-V--M-GPKYVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKE  316 (591)
T ss_dssp             ----HHHTT-----CSSCEEEEEESCGGGGTT-C--C-SCEEEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHH
T ss_pred             ----HHHHh-----cCCCeEEEECCCcHHHHh-c--C-CCceEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHH
Confidence                11111     245677777764331110 0  0 233444   367888888888877643   113466778888


Q ss_pred             ccCCCHHHHHHHHHH
Q 047219          489 TEEMSGRDIRDVCQQ  503 (567)
Q Consensus       489 t~g~s~~dL~~L~~~  503 (567)
                      +.|. +-.|+.+...
T Consensus       317 ~~G~-PLal~~~a~~  330 (591)
T 1z6t_A          317 CKGS-PLVVSLIGAL  330 (591)
T ss_dssp             HTTC-HHHHHHHHHH
T ss_pred             hCCC-cHHHHHHHHH
Confidence            7764 5566655544

>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=97.67  E-value=1.2e-05  Score=84.75  Aligned_cols=107  Identities=21%  Similarity=0.265  Sum_probs=59.6

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCc
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEV  397 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEI  397 (567)
                      +..++..++|+||||+||||++++++....      ..++.+....-...      ..++.+|       ...++++||+
T Consensus       165 ~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~------g~~~~~~~~~~~~~------~~lg~~~-------q~~~~l~dd~  225 (377)
T 1svm_A          165 NIPKKRYWLFKGPIDSGKTTLAAALLELCG------GKALNVNLPLDRLN------FELGVAI-------DQFLVVFEDV  225 (377)
T ss_dssp             CCTTCCEEEEECSTTSSHHHHHHHHHHHHC------CEEECCSSCTTTHH------HHHGGGT-------TCSCEEETTC
T ss_pred             ccCCCCEEEEECCCCCCHHHHHHHHHhhcC------CcEEEEeccchhHH------HHHHHhc-------chhHHHHHHH
Confidence            367778999999999999999999999873      23333222211000      0111111       2367899999


Q ss_pred             chhhhh-hhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHh
Q 047219          398 DSFAVA-RDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALIS  450 (567)
Q Consensus       398 D~L~~~-~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~s  450 (567)
                      +.+... +......... ....+...+++     .+.+++++|+++.+ +++++
T Consensus       226 ~~~~~~~r~l~~~~~~~-~~~~l~~~ldG-----~v~v~~~tn~~~~l-~alf~  272 (377)
T 1svm_A          226 KGTGGESRDLPSGQGIN-NLDNLRDYLDG-----SVKVNLEKKHLNKR-TQIFP  272 (377)
T ss_dssp             CCSTTTTTTCCCCSHHH-HHHTTHHHHHC-----SSCEEECCSSSCCE-EECCC
T ss_pred             HHHHHHHhhccccCcch-HHHHHHHHhcC-----CCeEeeccCchhhH-HHhhc
Confidence            988641 1100000000 11233333432     35667788888777 45554

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=97.64  E-value=2.5e-05  Score=64.72  Aligned_cols=55  Identities=20%  Similarity=0.328  Sum_probs=48.0

Q ss_pred             ecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHH
Q 047219          458 FGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAERSWASKI  512 (567)
Q Consensus       458 i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~  512 (567)
                      -.+|+.++|.+||+.+++++.   ..+++.+++.|.||||+||.++|++|.+.++++.
T Consensus         8 ~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~~alr~~   65 (86)
T 2krk_A            8 HSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMYALRER   65 (86)
T ss_dssp             CCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHc
Confidence            358999999999999998764   3478999999999999999999999998877653

>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=97.56  E-value=0.0011  Score=72.87  Aligned_cols=172  Identities=8%  Similarity=0.051  Sum_probs=93.5

Q ss_pred             cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHH---hCCCCCCCcCeEEe
Q 047219          283 AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQ---AGAMPWQGVPLMYV  359 (567)
Q Consensus       283 iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~---l~~~~~~~~~~~~i  359 (567)
                      +|.+..+++|.+.+...                  .......|.|+|+.|+|||+||+.+++.   --...|...-++.+
T Consensus       131 ~GR~~~~~~l~~~L~~~------------------~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~v  192 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM------------------CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKD  192 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH------------------TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEEC
T ss_pred             CCchHHHHHHHHHHhcc------------------cCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEE
Confidence            59999999999887421                  0224577889999999999999999972   22233433334444


Q ss_pred             chh------hHHhhhh---chh-------------HHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHH
Q 047219          360 PLE------VVMSKYY---GES-------------ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILS  417 (567)
Q Consensus       360 ~~~------~l~s~~~---G~~-------------~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~  417 (567)
                      +..      .+.....   +..             ...+...+.......+..+|+||+++....            .  
T Consensus       193 s~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~~~------------~--  258 (549)
T 2a5y_B          193 SGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEET------------I--  258 (549)
T ss_dssp             CCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHHH------------H--
T ss_pred             CCCCCCCHHHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCchh------------h--
Confidence            332      1111110   100             111222222222222258999999987420            0  


Q ss_pred             HHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhcc---ceEEEecCCCHHHHHHHHHHHHHhhC-----HHHHHHHHHhc
Q 047219          418 VLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRF---DSMITFGLPDHENRQEIAAQYAKHLT-----KAELAELATAT  489 (567)
Q Consensus       418 ~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf---~~~I~i~~P~~~eR~eIL~~~~~~~~-----~~~l~~la~~t  489 (567)
                      .+..       ..+..||.||....     +...+   ...+.++..+.++-.+++..++..-.     .+...++++.+
T Consensus       259 ~~~~-------~~gs~ilvTTR~~~-----v~~~~~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c  326 (549)
T 2a5y_B          259 RWAQ-------ELRLRCLVTTRDVE-----ISNAASQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELS  326 (549)
T ss_dssp             HHHH-------HTTCEEEEEESBGG-----GGGGCCSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHH
T ss_pred             cccc-------cCCCEEEEEcCCHH-----HHHHcCCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHh
Confidence            1111       13456777776422     22222   24688888898888888877642211     12345566665


Q ss_pred             cCCCHHHHHH
Q 047219          490 EEMSGRDIRD  499 (567)
Q Consensus       490 ~g~s~~dL~~  499 (567)
                      .|. |-.|+.
T Consensus       327 ~Gl-PLAl~~  335 (549)
T 2a5y_B          327 SGN-PATLMM  335 (549)
T ss_dssp             TTC-HHHHHH
T ss_pred             CCC-hHHHHH
Confidence            553 434443

>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=97.50  E-value=0.00029  Score=66.98  Aligned_cols=38  Identities=26%  Similarity=0.227  Sum_probs=28.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ..++.-++|+||||+|||++++.++...      +..+++++.+
T Consensus        17 i~~G~~~~i~G~~GsGKTtl~~~l~~~~------~~~v~~i~~~   54 (220)
T 2cvh_A           17 FAPGVLTQVYGPYASGKTTLALQTGLLS------GKKVAYVDTE   54 (220)
T ss_dssp             BCTTSEEEEECSTTSSHHHHHHHHHHHH------CSEEEEEESS
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHHHc------CCcEEEEECC
Confidence            4566779999999999999999999832      3345555543

>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=97.50  E-value=0.00014  Score=75.94  Aligned_cols=81  Identities=17%  Similarity=0.203  Sum_probs=49.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh----HHhhhhch-----------hHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV----VMSKYYGE-----------SERLLGKVFSLA  383 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~----l~s~~~G~-----------~~~~l~~~f~~A  383 (567)
                      ..+...++|+|+||+|||++|..++......   +..+++++.+.    .....+|.           ....+..++...
T Consensus        60 l~~G~ii~I~G~pGsGKTtLal~la~~~~~~---g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l  136 (356)
T 1u94_A           60 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDAL  136 (356)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHH
Confidence            4566779999999999999999998876322   44577776632    11111111           112223333322


Q ss_pred             hcCCCCcEEEEcCcchhhh
Q 047219          384 NELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~~  402 (567)
                      .......+|+||.+..+..
T Consensus       137 ~~~~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          137 ARSGAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HHHTCCSEEEEECGGGCCC
T ss_pred             HhccCCCEEEEcCHHHhcc
Confidence            2222358999999999874

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.49  E-value=0.00016  Score=89.64  Aligned_cols=83  Identities=18%  Similarity=0.215  Sum_probs=55.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhh----ch-----------hHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY----GE-----------SERLLGKVFSLA  383 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~----G~-----------~~~~l~~~f~~A  383 (567)
                      ...+..++|+||||||||+||.+++.+....   +.++.+++.++....++    |.           .......+.+..
T Consensus      1078 i~~g~~vll~G~~GtGKT~la~~~~~ea~k~---Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l 1154 (2050)
T 3cmu_A         1078 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDAL 1154 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHH
T ss_pred             cCCCcEEEEECCCCCCHHHHHHHHHHHHHHc---CCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHH
Confidence            5677889999999999999999999877544   66788888775433332    10           011122222222


Q ss_pred             hcCCCCcEEEEcCcchhhhhh
Q 047219          384 NELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~~~~  404 (567)
                      .+...+.+|+||++..|.+..
T Consensus      1155 ~~~~~~dlvVIDsl~~L~~~~ 1175 (2050)
T 3cmu_A         1155 ARSGAVDVIVVDSVAALTPKA 1175 (2050)
T ss_dssp             HHHTCCSEEEESCGGGCCCHH
T ss_pred             HHhCCCCEEEECCcccccccc
Confidence            222335899999999996543

>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=97.46  E-value=0.00011  Score=76.65  Aligned_cols=80  Identities=25%  Similarity=0.303  Sum_probs=48.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH----hhhhc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM----SKYYG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~----s~~~G------------~~~~~l~~~f~~  382 (567)
                      ..+..-++|+||||+|||+||..++......   +..+.+++.+.-.    ...+|            ..+..+. +...
T Consensus        58 l~~G~iv~I~G~pGsGKTtLal~la~~~~~~---g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~-~~~~  133 (349)
T 2zr9_A           58 LPRGRVIEIYGPESSGKTTVALHAVANAQAA---GGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALE-IADM  133 (349)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHH-HHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHhC---CCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHH-HHHH
Confidence            4456779999999999999999998765322   3456666554311    11112            1122222 2222


Q ss_pred             HhcCCCCcEEEEcCcchhhh
Q 047219          383 ANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~  402 (567)
                      ......+.+|+||++..+..
T Consensus       134 l~~~~~~~lIVIDsl~~l~~  153 (349)
T 2zr9_A          134 LVRSGALDIIVIDSVAALVP  153 (349)
T ss_dssp             HHTTTCCSEEEEECGGGCCC
T ss_pred             HHhcCCCCEEEEcChHhhcc
Confidence            22222358999999999874

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.43  E-value=6.6e-05  Score=70.94  Aligned_cols=24  Identities=21%  Similarity=0.249  Sum_probs=19.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .-++++||+|+|||+++..++..+
T Consensus         4 ~i~vi~G~~gsGKTT~ll~~~~~~   27 (184)
T 2orw_A            4 KLTVITGPMYSGKTTELLSFVEIY   27 (184)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            457899999999999985555443

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.43  E-value=0.00021  Score=68.35  Aligned_cols=28  Identities=25%  Similarity=0.320  Sum_probs=23.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++..++|.||+|+|||++++.++...
T Consensus        20 i~~G~~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           20 IPQGFFIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcCCCEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3456779999999999999999999654

>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=97.42  E-value=0.00026  Score=74.13  Aligned_cols=81  Identities=21%  Similarity=0.233  Sum_probs=49.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh----hhch-----------hHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK----YYGE-----------SERLLGKVFSLA  383 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~----~~G~-----------~~~~l~~~f~~A  383 (567)
                      ..+..-++|+|+||+|||+||..++......   +.++++++.+.-...    .+|.           ....+...++..
T Consensus        71 l~~G~li~I~G~pGsGKTtlal~la~~~~~~---g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l  147 (366)
T 1xp8_A           71 IPRGRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELL  147 (366)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             ccCCcEEEEEcCCCCChHHHHHHHHHHHHHC---CCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHH
Confidence            3556779999999999999999998776322   345666665432111    1111           112222233333


Q ss_pred             hcCCCCcEEEEcCcchhhh
Q 047219          384 NELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~~  402 (567)
                      .......+|+||.+..+..
T Consensus       148 ~~~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          148 VRSGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             HTTTCCSEEEEECTTTCCC
T ss_pred             HhcCCCCEEEEeChHHhcc
Confidence            3333358999999999874

>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=97.39  E-value=0.00051  Score=66.30  Aligned_cols=28  Identities=21%  Similarity=0.133  Sum_probs=24.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....-++|+||||+|||++++.++...
T Consensus        21 i~~G~~~~i~G~~GsGKTtl~~~l~~~~   48 (243)
T 1n0w_A           21 IETGSITEMFGEFRTGKTQICHTLAVTC   48 (243)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcCCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4566779999999999999999999863

>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=97.39  E-value=0.00013  Score=78.46  Aligned_cols=26  Identities=31%  Similarity=0.498  Sum_probs=23.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..++|.|+||||||+++.+++..+..
T Consensus        46 ~~~li~G~aGTGKT~ll~~~~~~l~~   71 (459)
T 3upu_A           46 HHVTINGPAGTGATTLTKFIIEALIS   71 (459)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            38999999999999999999988743

>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=97.35  E-value=0.0002  Score=74.67  Aligned_cols=80  Identities=26%  Similarity=0.260  Sum_probs=48.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh----hhhc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS----KYYG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s----~~~G------------~~~~~l~~~f~~  382 (567)
                      ..+..-++|+||||+|||+|+..++..+...   +..+++++.+....    +-+|            ..+..+..+...
T Consensus        58 i~~G~i~~I~GppGsGKSTLal~la~~~~~~---gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l  134 (356)
T 3hr8_A           58 YPRGRIVEIFGQESSGKTTLALHAIAEAQKM---GGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDEL  134 (356)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHHHhc---CCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHH
Confidence            4556779999999999999999999876322   34566666543211    1111            112222222222


Q ss_pred             HhcCCCCcEEEEcCcchhhh
Q 047219          383 ANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~  402 (567)
                      .... ...+++||.+..+.+
T Consensus       135 ~~~~-~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          135 VRSG-VVDLIVVDSVAALVP  153 (356)
T ss_dssp             HHTS-CCSEEEEECTTTCCC
T ss_pred             hhhc-CCCeEEehHhhhhcC
Confidence            2223 358999999998865

>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=97.30  E-value=0.0034  Score=74.61  Aligned_cols=182  Identities=14%  Similarity=0.099  Sum_probs=99.7

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhC--CCCCC-Cc
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAG--AMPWQ-GV  354 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~--~~~~~-~~  354 (567)
                      ....++|.++.+++|.+.+...                   ....+-+.|+|+.|+|||+||+.+++...  ...|. ++
T Consensus       122 ~~~~~vgR~~~~~~l~~~l~~~-------------------~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~  182 (1249)
T 3sfz_A          122 RPVIFVTRKKLVHAIQQKLWKL-------------------NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGV  182 (1249)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHTT-------------------TTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCE
T ss_pred             CCceeccHHHHHHHHHHHHhhc-------------------cCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeE
Confidence            4467899999999999877421                   23456788999999999999999886531  11111 22


Q ss_pred             CeEEechh---hHH-------hhhhc---------hhHHHHHHHHHH-HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          355 PLMYVPLE---VVM-------SKYYG---------ESERLLGKVFSL-ANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       355 ~~~~i~~~---~l~-------s~~~G---------~~~~~l~~~f~~-A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      -++.+...   .+.       ..+..         .....+...+.. .....+..+|+||+++...             
T Consensus       183 ~~v~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~~-------------  249 (1249)
T 3sfz_A          183 HWVSIGKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDPW-------------  249 (1249)
T ss_dssp             EEEECCSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCHH-------------
T ss_pred             EEEEECCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCHH-------------
Confidence            23333221   011       00000         011112222221 1112235899999998641             


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecC-CCHHHHHHHHHHHHHhhC---HHHHHHHHHhcc
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGL-PDHENRQEIAAQYAKHLT---KAELAELATATE  490 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~-P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~  490 (567)
                         .+    ..+  .....||.||....... .+ ......+.++. ++.++-.+++...+....   .+...++++.+.
T Consensus       250 ---~~----~~~--~~~~~ilvTtR~~~~~~-~~-~~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~  318 (1249)
T 3sfz_A          250 ---VL----KAF--DNQCQILLTTRDKSVTD-SV-MGPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECK  318 (1249)
T ss_dssp             ---HH----TTT--CSSCEEEEEESSTTTTT-TC-CSCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTT
T ss_pred             ---HH----Hhh--cCCCEEEEEcCCHHHHH-hh-cCCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhC
Confidence               11    111  23457777886443221 11 11224677775 788888888887664322   235667777776


Q ss_pred             CCCHHHHHHHHHH
Q 047219          491 EMSGRDIRDVCQQ  503 (567)
Q Consensus       491 g~s~~dL~~L~~~  503 (567)
                      |+ |-.|+.+...
T Consensus       319 gl-PLal~~~~~~  330 (1249)
T 3sfz_A          319 GS-PLVVSLIGAL  330 (1249)
T ss_dssp             TC-HHHHHHHHHH
T ss_pred             CC-HHHHHHHHHH
Confidence            64 5455544443

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=97.23  E-value=0.00018  Score=59.73  Aligned_cols=50  Identities=20%  Similarity=0.268  Sum_probs=44.2

Q ss_pred             CHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          462 DHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       462 ~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      +.++|.+||+.++++++.   .+++.++..|+||||+||.++|++|.+.++++
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~eAa~~a~r~   54 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGMFAIRA   54 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHHHHHHHHHHh
Confidence            567899999999988653   37899999999999999999999999888776

>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=97.23  E-value=0.00032  Score=64.68  Aligned_cols=38  Identities=16%  Similarity=0.403  Sum_probs=30.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      +..++|.|+||+||||+++++++.+      +.+++.++...+.
T Consensus         3 ~~~i~l~G~~GsGKST~a~~La~~l------~~~~~~~~~D~~~   40 (178)
T 1qhx_A            3 TRMIILNGGSSAGKSGIVRCLQSVL------PEPWLAFGVDSLI   40 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS------SSCEEEEEHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc------CCCeEEeccchHh
Confidence            3568999999999999999999998      5556766655443

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.21  E-value=0.00085  Score=65.50  Aligned_cols=165  Identities=17%  Similarity=0.198  Sum_probs=88.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC--eEEech------hhHHhhhh----------ch--hHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP--LMYVPL------EVVMSKYY----------GE--SERLLGKVFS  381 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~--~~~i~~------~~l~s~~~----------G~--~~~~l~~~f~  381 (567)
                      ...+++.|+||||||+++-.+|..+...   +..  ++.++.      ..+....-          |.  .+..+..++.
T Consensus         6 ~l~I~~~~kgGvGKTt~a~~la~~l~~~---G~~V~v~d~D~q~~~~~~al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~   82 (228)
T 2r8r_A            6 RLKVFLGAAPGVGKTYAMLQAAHAQLRQ---GVRVMAGVVETHGRAETEALLNGLPQQPLLRTEYRGMTLEEMDLDALLK   82 (228)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHHHHHT---TCCEEEEECCCTTCHHHHHHHTTSCBCCCEEEEETTEEEEECCHHHHHH
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHHC---CCCEEEEEeCCCCChhHHHHhcCccccCcceeecCCcccccccHHHHHh
Confidence            3579999999999999999999887433   333  334432      11111110          00  1122223222


Q ss_pred             HHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC------------------CCC
Q 047219          382 LANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR------------------KQD  443 (567)
Q Consensus       382 ~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~------------------~~~  443 (567)
                         .  .+.++++||+............ ..+.+ ..++        +..+-+++|+|.                  .+.
T Consensus        83 ---~--~pdlvIVDElG~~~~~~~r~~~-~~qDV-~~~l--------~sgidVitT~Nlqh~esl~d~v~~itg~~v~e~  147 (228)
T 2r8r_A           83 ---A--APSLVLVDELAHTNAPGSRHTK-RWQDI-QELL--------AAGIDVYTTVNVQHLESLNDQVRGITGVQVRET  147 (228)
T ss_dssp             ---H--CCSEEEESCTTCBCCTTCSSSB-HHHHH-HHHH--------HTTCEEEEEEEGGGBGGGHHHHHHHHSCCCCSC
T ss_pred             ---c--CCCEEEEeCCCCCCcccchhHH-HHHHH-HHHH--------cCCCCEEEEccccccccHHHHHHHHcCCCcCCc
Confidence               1  2579999999875322111111 11111 1111        234567777773                  245


Q ss_pred             CChHHHhccceEEEecCCCHHHHHHHHHHHHHh--hCHH-HHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          444 LDPALISRFDSMITFGLPDHENRQEIAAQYAKH--LTKA-ELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       444 Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--~~~~-~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      +++.++.+.+.+.-++.|+.+-+..    +...  +..+ .-..+.   .-|+...|.+|-.-|.+..+.+
T Consensus       148 vpd~~~~~a~~v~lvD~~p~~l~~r----l~~g~vy~~~~~~~a~~---~~f~~~nl~~lrelal~~~a~~  211 (228)
T 2r8r_A          148 LPDWVLQEAFDLVLIDLPPRELLER----LRDGKVYVPEQARAAID---AFFTQTNLTALREMAMQTAAAQ  211 (228)
T ss_dssp             BCHHHHHTCSEEEEBCCCHHHHHHH----HHTTCCCCTTCCHHHHH---HHCCHHHHHHHHHHHHHHHHTC
T ss_pred             CccHHHhhCCeEEEecCCHHHHHHH----HHCCCccChhHHHHHHH---hhhchhhHHHHHHHHHHHHHHH
Confidence            7888888887888888887663322    2221  1111 111122   2377888887777666655544

>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=97.18  E-value=0.0011  Score=68.54  Aligned_cols=45  Identities=18%  Similarity=0.146  Sum_probs=31.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC---CCCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP---WQGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~---~~~~~~~~i~~~~  363 (567)
                      ..+..-++|+||||+|||++|..++.......   ..+..+++++.+.
T Consensus       119 l~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          119 IESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             BCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            45566789999999999999999998742210   0134566666543

>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=97.14  E-value=0.00094  Score=63.79  Aligned_cols=28  Identities=25%  Similarity=0.207  Sum_probs=24.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..-+.|.||+|+|||||++.++...
T Consensus        22 i~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           22 IETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4566779999999999999999999865

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=97.11  E-value=0.00089  Score=65.28  Aligned_cols=77  Identities=18%  Similarity=0.156  Sum_probs=43.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh-------HHhhhhchh-----HHHHHHHHHHHhcC--
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV-------VMSKYYGES-----ERLLGKVFSLANEL--  386 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~-------l~s~~~G~~-----~~~l~~~f~~A~~~--  386 (567)
                      +..-++++|++|+||||++..++..+...   +..+..+....       +.+. .|-.     -.....+++.+...  
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~~~r~~~~---g~kVli~~~~~d~r~~~~i~sr-lG~~~~~~~~~~~~~i~~~i~~~~~   86 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRRLHRLEYA---DVKYLVFKPKIDTRSIRNIQSR-TGTSLPSVEVESAPEILNYIMSNSF   86 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHHHHHHHHT---TCCEEEEEECCCGGGCSSCCCC-CCCSSCCEEESSTHHHHHHHHSTTS
T ss_pred             CcEEEEEECCCCCcHHHHHHHHHHHHHhc---CCEEEEEEeccCchHHHHHHHh-cCCCccccccCCHHHHHHHHHHHhh
Confidence            45568889999999999888887776322   22333332111       1111 1110     00112344444432  


Q ss_pred             -CCCcEEEEcCcchhh
Q 047219          387 -PNGAIIFLDEVDSFA  401 (567)
Q Consensus       387 -a~~~ILfIDEID~L~  401 (567)
                       .+..+|+|||+..|.
T Consensus        87 ~~~~dvViIDEaQ~l~  102 (223)
T 2b8t_A           87 NDETKVIGIDEVQFFD  102 (223)
T ss_dssp             CTTCCEEEECSGGGSC
T ss_pred             CCCCCEEEEecCccCc
Confidence             235799999999874

>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=97.10  E-value=0.0013  Score=67.53  Aligned_cols=45  Identities=20%  Similarity=0.186  Sum_probs=31.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC-C--CCcCeEEechhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMP-W--QGVPLMYVPLEV  363 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~-~--~~~~~~~i~~~~  363 (567)
                      ..+..-++|+||||+|||++|..++....... +  .+..+++++.+.
T Consensus       104 l~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          104 IETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            45567799999999999999999998753210 0  023566666543

>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=97.06  E-value=0.0097  Score=65.54  Aligned_cols=75  Identities=12%  Similarity=0.247  Sum_probs=54.3

Q ss_pred             CcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC--CCChHHHhccceEEEecCCCHHHH
Q 047219          389 GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ--DLDPALISRFDSMITFGLPDHENR  466 (567)
Q Consensus       389 ~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~--~Ld~aL~sRf~~~I~i~~P~~~eR  466 (567)
                      .-+|+|||++.|......    .....+..+.+..    ....+.+|.+|.++.  .++..++.-|...|.+...+..+.
T Consensus       344 ~ivvVIDE~~~L~~~~~~----~~~~~L~~Iar~G----Ra~GIhLIlaTQRPs~d~I~~~Iran~~~RI~lrv~s~~Ds  415 (574)
T 2iut_A          344 TIVVVVDEFADMMMIVGK----KVEELIARIAQKA----RAAGIHLILATQRPSVDVITGLIKANIPTRIAFQVSSKIDS  415 (574)
T ss_dssp             EEEEEESCCTTHHHHTCH----HHHHHHHHHHHHC----TTTTEEEEEEESCCCTTTSCHHHHHTCCEEEEECCSCHHHH
T ss_pred             cEEEEEeCHHHHhhhhhH----HHHHHHHHHHHHH----hhCCeEEEEEecCcccccccHHHHhhhccEEEEEcCCHHHH
Confidence            468999999988643211    1223334444432    356789999998877  799999999989999999998888


Q ss_pred             HHHHH
Q 047219          467 QEIAA  471 (567)
Q Consensus       467 ~eIL~  471 (567)
                      ..++.
T Consensus       416 r~ILd  420 (574)
T 2iut_A          416 RTILD  420 (574)
T ss_dssp             HHHHS
T ss_pred             HHhcC
Confidence            77764

>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=97.04  E-value=0.00059  Score=83.67  Aligned_cols=83  Identities=17%  Similarity=0.202  Sum_probs=54.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh----hc-----------hhHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY----YG-----------ESERLLGKVFSLA  383 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~----~G-----------~~~~~l~~~f~~A  383 (567)
                      ...+..++|+||||||||+||..++......   +..+++++.+......    +|           .....+..+++..
T Consensus        31 i~~G~i~lI~G~pGsGKT~LAlqla~~~~~~---G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L  107 (1706)
T 3cmw_A           31 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDAL  107 (1706)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHHHhhC---CCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHH
Confidence            5667889999999999999999998765322   4567777765432211    11           0122334444444


Q ss_pred             hcCCCCcEEEEcCcchhhhhh
Q 047219          384 NELPNGAIIFLDEVDSFAVAR  404 (567)
Q Consensus       384 ~~~a~~~ILfIDEID~L~~~~  404 (567)
                      .+.....+|+||++..+....
T Consensus       108 ~~~~~~~LVVIDSLt~L~~~~  128 (1706)
T 3cmw_A          108 ARSGAVDVIVVDSVAALTPKA  128 (1706)
T ss_dssp             HHHTCCSEEEESCSTTCCCHH
T ss_pred             HhccCCCEEEEcchhhhcccc
Confidence            332345899999999987653

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=96.99  E-value=0.00029  Score=57.52  Aligned_cols=50  Identities=18%  Similarity=0.418  Sum_probs=43.2

Q ss_pred             CHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          462 DHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       462 ~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      +.++|.+||+.++++++   ..+++.++..+.||||+||.++|++|.+.+.++
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~   54 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRE   54 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTS
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh
Confidence            67899999999998865   337899999999999999999999998766543

>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=96.97  E-value=0.01  Score=64.63  Aligned_cols=75  Identities=13%  Similarity=0.286  Sum_probs=51.7

Q ss_pred             cEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCC--CCChHHHhccceEEEecCCCHHHHH
Q 047219          390 AIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQ--DLDPALISRFDSMITFGLPDHENRQ  467 (567)
Q Consensus       390 ~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~--~Ld~aL~sRf~~~I~i~~P~~~eR~  467 (567)
                      -+|+|||...+.....    ....+.+..+.+..    ....+.+|.+|.++.  .++..++.-|...|.|...+..+..
T Consensus       299 ivlvIDE~~~ll~~~~----~~~~~~l~~Lar~g----Ra~GI~LIlaTQrp~~dvl~~~i~~n~~~RI~lrv~s~~dsr  370 (512)
T 2ius_A          299 IVVLVDEFADLMMTVG----KKVEELIARLAQKA----RAAGIHLVLATQRPSVDVITGLIKANIPTRIAFTVSSKIDSR  370 (512)
T ss_dssp             EEEEEETHHHHHHHHH----HHHHHHHHHHHHHC----GGGTEEEEEEESCCCTTTSCHHHHHHCCEEEEECCSSHHHHH
T ss_pred             EEEEEeCHHHHHhhhh----HHHHHHHHHHHHHh----hhCCcEEEEEecCCccccccHHHHhhcCCeEEEEcCCHHHHH
Confidence            4899999988754211    11223333333322    234678888888876  6889999999889999999998888


Q ss_pred             HHHHH
Q 047219          468 EIAAQ  472 (567)
Q Consensus       468 eIL~~  472 (567)
                      .++..
T Consensus       371 ~ilg~  375 (512)
T 2ius_A          371 TILDQ  375 (512)
T ss_dssp             HHHSS
T ss_pred             HhcCC
Confidence            87753

>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=96.93  E-value=0.00089  Score=60.90  Aligned_cols=23  Identities=22%  Similarity=0.401  Sum_probs=21.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.|+||+||||+++.+++.+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l   25 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKEL   25 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999998

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=96.92  E-value=0.0026  Score=58.16  Aligned_cols=23  Identities=35%  Similarity=0.574  Sum_probs=21.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      |.-++|.|+||+||||+|+.+++
T Consensus         2 ~~~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            2 KKIILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHH
T ss_pred             CeEEEEecCCCCCHHHHHHHHHh
Confidence            35689999999999999999998

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.91  E-value=0.0035  Score=60.42  Aligned_cols=28  Identities=32%  Similarity=0.438  Sum_probs=23.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++..++|.||||+|||+++..++...
T Consensus        20 l~~G~~~~i~G~~GsGKTtl~~~~~~~~   47 (247)
T 2dr3_A           20 IPERNVVLLSGGPGTGKTIFSQQFLWNG   47 (247)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4556779999999999999988887654

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.90  E-value=0.00058  Score=63.38  Aligned_cols=25  Identities=28%  Similarity=0.361  Sum_probs=23.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..++|.|+||+||||+++.+++.+
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l   29 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLT   29 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            5679999999999999999999998

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.89  E-value=0.00063  Score=64.38  Aligned_cols=28  Identities=29%  Similarity=0.421  Sum_probs=24.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+...++|.|+||+||||+++.+++.+
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            3456789999999999999999999998

>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=96.85  E-value=0.0019  Score=58.39  Aligned_cols=22  Identities=32%  Similarity=0.762  Sum_probs=20.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -++|.|+||+||||+|+.+ +.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~   24 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KER   24 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHT
T ss_pred             EEEEECCCCCCHHHHHHHH-HHC
Confidence            5789999999999999999 766

>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=96.82  E-value=0.00095  Score=74.02  Aligned_cols=27  Identities=37%  Similarity=0.688  Sum_probs=23.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ...++|.|+||||||+++.+++..+..
T Consensus       204 ~~~~~I~G~pGTGKTt~i~~l~~~l~~  230 (574)
T 3e1s_A          204 HRLVVLTGGPGTGKSTTTKAVADLAES  230 (574)
T ss_dssp             CSEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            467899999999999999999987643

>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=96.81  E-value=0.0022  Score=65.39  Aligned_cols=28  Identities=21%  Similarity=0.209  Sum_probs=24.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..-++|+|+||+|||++|..++...
T Consensus        95 l~~g~i~~i~G~~gsGKT~la~~la~~~  122 (322)
T 2i1q_A           95 LESQSVTEFAGVFGSGKTQIMHQSCVNL  122 (322)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4556779999999999999999999764

>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=96.79  E-value=0.0019  Score=68.37  Aligned_cols=28  Identities=18%  Similarity=0.131  Sum_probs=23.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..-++|+||||+|||+|++.++-..
T Consensus       175 I~~Gei~~I~G~sGsGKTTLl~~la~~~  202 (400)
T 3lda_A          175 VETGSITELFGEFRTGKSQLCHTLAVTC  202 (400)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             cCCCcEEEEEcCCCCChHHHHHHHHHHh
Confidence            4566779999999999999999876443

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.79  E-value=0.0043  Score=61.07  Aligned_cols=40  Identities=25%  Similarity=0.420  Sum_probs=31.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ...+..++|.|+||+||||+++.++..+.      ..++.++...+
T Consensus        29 ~~~~~~i~l~G~~GsGKSTla~~L~~~l~------~~~~~~~~D~~   68 (253)
T 2p5t_B           29 SKQPIAILLGGQSGAGKTTIHRIKQKEFQ------GNIVIIDGDSF   68 (253)
T ss_dssp             CSSCEEEEEESCGGGTTHHHHHHHHHHTT------TCCEEECGGGG
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHhcC------CCcEEEecHHH
Confidence            45677899999999999999999999883      33555666554

>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=96.78  E-value=0.0029  Score=65.63  Aligned_cols=28  Identities=25%  Similarity=0.207  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..-+.|+||||+|||+|++.++...
T Consensus       128 i~~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          128 IETQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            5567779999999999999999999886

>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=96.76  E-value=0.0016  Score=66.81  Aligned_cols=78  Identities=14%  Similarity=0.232  Sum_probs=44.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh----hhhch------------hHHHHHHHHHHH--hc
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS----KYYGE------------SERLLGKVFSLA--NE  385 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s----~~~G~------------~~~~l~~~f~~A--~~  385 (567)
                      -++|+||||+|||+|+-.++...... ..+..+++++.+.-..    +-+|-            .+...-.+.+.+  .+
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~-g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l~~i~  108 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQ-YPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQLDAIE  108 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHH-CTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHHHTCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc-CCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHHHHhh
Confidence            58999999999999988777665321 0133577777653211    11111            122101222222  12


Q ss_pred             CCCCcEEEEcCcchhhh
Q 047219          386 LPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       386 ~a~~~ILfIDEID~L~~  402 (567)
                      ...+.+|+||-|..|.+
T Consensus       109 ~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          109 RGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             TTCCEEEEEECSTTCBC
T ss_pred             ccCceEEEEeccccccc
Confidence            23458999999999964

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.73  E-value=0.0023  Score=64.56  Aligned_cols=42  Identities=26%  Similarity=0.422  Sum_probs=32.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      ...+..++|.||||+||||+++.+++.+.      ..+..+++..+..
T Consensus        30 ~~~~~livl~G~sGsGKSTla~~L~~~~~------~~~~~Is~D~~R~   71 (287)
T 1gvn_B           30 VESPTAFLLGGQPGSGKTSLRSAIFEETQ------GNVIVIDNDTFKQ   71 (287)
T ss_dssp             CSSCEEEEEECCTTSCTHHHHHHHHHHTT------TCCEEECTHHHHT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhC------CCeEEEechHhHH
Confidence            34567899999999999999999999873      2356677655543

>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=96.70  E-value=0.016  Score=55.11  Aligned_cols=64  Identities=16%  Similarity=0.162  Sum_probs=36.8

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH-HHHHHHHh
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC-ARVIANQA  346 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L-AraIA~~l  346 (567)
                      +..+|+++.-.+...+.+.+.   .+..+..++.-.  +..   ....+.+++.+|+|+|||.. +-.+...+
T Consensus        12 ~~~~f~~l~l~~~l~~~l~~~---g~~~~~~~Q~~~--i~~---~~~~~~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           12 VVYKFDDMELDENLLRGVFGY---GFEEPSAIQQRA--IMP---IIEGHDVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             CCCCGGGGTCCHHHHHHHHHH---TCCSCCHHHHHH--HHH---HHTTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             ccCChhhcCCCHHHHHHHHHC---CCCCCcHHHHHH--HHH---HhcCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            345799986666666655442   233444443321  111   11236799999999999987 34444444

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.69  E-value=0.0026  Score=58.09  Aligned_cols=25  Identities=36%  Similarity=0.678  Sum_probs=22.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..+.|.|++|+||||+++.++..+
T Consensus         4 ~~~i~l~G~~GsGKSTl~~~La~~l   28 (173)
T 1kag_A            4 KRNIFLVGPMGAGKSTIGRQLAQQL   28 (173)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999999999988

>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=96.66  E-value=0.0012  Score=61.40  Aligned_cols=27  Identities=30%  Similarity=0.578  Sum_probs=24.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.-++|.|+||+||||+++.+++.+
T Consensus         3 ~~~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            3 QTPALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             SCCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            346779999999999999999999988

>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=96.65  E-value=0.0011  Score=61.86  Aligned_cols=27  Identities=44%  Similarity=0.672  Sum_probs=24.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH-h
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ-A  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~-l  346 (567)
                      ..+..++|+|+|||||||+++.+++. +
T Consensus         8 ~~~~~I~l~G~~GsGKSTv~~~La~~l~   35 (184)
T 1y63_A            8 PKGINILITGTPGTGKTSMAEMIAAELD   35 (184)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhcC
Confidence            34567999999999999999999998 5

>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=96.64  E-value=0.0012  Score=61.17  Aligned_cols=26  Identities=31%  Similarity=0.597  Sum_probs=23.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..|+|+|+||+||||+++.+++.+
T Consensus        10 ~~~~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           10 LLPNILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCeEEEEeCCCCCHHHHHHHHHHHh
Confidence            45679999999999999999999998

>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=96.62  E-value=0.0013  Score=61.24  Aligned_cols=40  Identities=30%  Similarity=0.495  Sum_probs=30.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ...+..+.|.||||+||||+++.++...      +...+.++...+
T Consensus         6 i~~g~~i~l~G~~GsGKSTl~~~La~~~------~~g~i~i~~d~~   45 (191)
T 1zp6_A            6 DLGGNILLLSGHPGSGKSTIAEALANLP------GVPKVHFHSDDL   45 (191)
T ss_dssp             CCTTEEEEEEECTTSCHHHHHHHHHTCS------SSCEEEECTTHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHhcc------CCCeEEEcccch
Confidence            4566789999999999999999999874      444566665443

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.61  E-value=0.0017  Score=59.73  Aligned_cols=23  Identities=35%  Similarity=0.603  Sum_probs=22.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.|+||+||||+++.|++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHc
Confidence            58999999999999999999998

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.60  E-value=0.0029  Score=67.98  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=30.2

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      +..++.-++|.|+||+|||+++..++......  .+.++.+++.
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~--~g~~Vl~~s~  240 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATK--TNENVAIFSL  240 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHH--SSCCEEEEES
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHh--CCCcEEEEEC
Confidence            35667789999999999999999998876321  0334555543

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.57  E-value=0.0017  Score=60.03  Aligned_cols=37  Identities=16%  Similarity=0.251  Sum_probs=28.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV  363 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~  363 (567)
                      .|+|.|+||+||||+++.+++.++..   +..+..++..+
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~---g~~~~~~~~~~   39 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQ---GINNKIINYGD   39 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTT---TCCEEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc---CceEEEEECCh
Confidence            58899999999999999999988532   34456665443

>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=96.52  E-value=0.0019  Score=60.94  Aligned_cols=28  Identities=36%  Similarity=0.538  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..|+|.|+||+||||+|+.+++.+
T Consensus        17 ~~~~~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           17 RGSHMRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CCSCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3455679999999999999999999998

>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=96.50  E-value=0.0016  Score=60.38  Aligned_cols=24  Identities=29%  Similarity=0.559  Sum_probs=22.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|+|.|+||+||||+|+.+++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (184)
T 2iyv_A            3 PKAVLVGLPGSGKSTIGRRLAKAL   26 (184)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHc
Confidence            358999999999999999999998

>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=96.49  E-value=0.0024  Score=59.09  Aligned_cols=25  Identities=24%  Similarity=0.553  Sum_probs=23.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .-++|.|+||+||||+++.+++.++
T Consensus         4 ~~I~i~G~~GsGKsT~~~~L~~~l~   28 (192)
T 1kht_A            4 KVVVVTGVPGVGSTTSSQLAMDNLR   28 (192)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            5689999999999999999999884

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=96.49  E-value=0.008  Score=64.34  Aligned_cols=77  Identities=18%  Similarity=0.214  Sum_probs=47.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh----------h-----hh-----chhHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS----------K-----YY-----GESERLLGKVF  380 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s----------~-----~~-----G~~~~~l~~~f  380 (567)
                      +|..+++.|++|+||||++..+|..+...   +..+..+.+.....          .     .+     ......+...+
T Consensus        99 ~p~vIlivG~~G~GKTTt~~kLA~~l~~~---G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~~al  175 (443)
T 3dm5_A           99 KPTILLMVGIQGSGKTTTVAKLARYFQKR---GYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAKEGV  175 (443)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTT---TCCEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHHHHH
T ss_pred             CCeEEEEECcCCCCHHHHHHHHHHHHHHC---CCeEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHHHHH
Confidence            57789999999999999999999887543   33343333321100          0     01     11223344555


Q ss_pred             HHHhcCCCCcEEEEcCcchhh
Q 047219          381 SLANELPNGAIIFLDEVDSFA  401 (567)
Q Consensus       381 ~~A~~~a~~~ILfIDEID~L~  401 (567)
                      ..+.... ..+++||....+.
T Consensus       176 ~~a~~~~-~DvVIIDTaGrl~  195 (443)
T 3dm5_A          176 DYFKSKG-VDIIIVDTAGRHK  195 (443)
T ss_dssp             HHHHHTT-CSEEEEECCCCSS
T ss_pred             HHHHhCC-CCEEEEECCCccc
Confidence            6665543 4799999987654

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.48  E-value=0.0017  Score=59.32  Aligned_cols=31  Identities=19%  Similarity=0.266  Sum_probs=26.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      -.+++|.|+||+||||+++.+++.+      +.+++.
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~l------g~~~id   37 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLAL------KLEVLD   37 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHHH------TCCEEE
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHh------CCCEEE
Confidence            3579999999999999999999998      555654

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.44  E-value=0.0035  Score=64.39  Aligned_cols=34  Identities=32%  Similarity=0.499  Sum_probs=27.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      +..++|.||+|+|||++++.+|+.+      +..++..+.
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l------~~~iis~Ds   38 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADAL------PCELISVDS   38 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHS------CEEEEEECT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc------CCcEEeccc
Confidence            4579999999999999999999998      444555543

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=96.40  E-value=0.0019  Score=59.89  Aligned_cols=25  Identities=32%  Similarity=0.507  Sum_probs=23.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.-|+|.|+||+||||+|+.+++.+
T Consensus         3 ~~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            3 PLVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            4678999999999999999999988

>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=96.39  E-value=0.0088  Score=59.52  Aligned_cols=29  Identities=24%  Similarity=0.205  Sum_probs=24.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .....-++|+||+|+|||+|+..++..+.
T Consensus        27 l~~G~i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           27 MVAGTVGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             ccCCCEEEEEcCCCCCHHHHHHHHHHHHh
Confidence            34567799999999999999999997653

>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=96.38  E-value=0.0031  Score=65.69  Aligned_cols=28  Identities=25%  Similarity=0.420  Sum_probs=23.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+...++|.||+|+||||+.++++..+.
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~~l~g~~~  148 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLAAMLDYLN  148 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhccc
Confidence            3445799999999999999999998763

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.36  E-value=0.0034  Score=60.81  Aligned_cols=40  Identities=13%  Similarity=0.279  Sum_probs=31.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      ...++-|+|.||||+||+|.|+.|++.+      +  +..++..++..
T Consensus        26 ~~k~kiI~llGpPGsGKgTqa~~L~~~~------g--~~hIstGdllR   65 (217)
T 3umf_A           26 LAKAKVIFVLGGPGSGKGTQCEKLVQKF------H--FNHLSSGDLLR   65 (217)
T ss_dssp             TTSCEEEEEECCTTCCHHHHHHHHHHHH------C--CEEECHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHH------C--CceEcHHHHHH
Confidence            3556788999999999999999999988      3  55566555443

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=96.34  E-value=0.031  Score=53.24  Aligned_cols=121  Identities=16%  Similarity=0.138  Sum_probs=70.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe---ch------hhHHhhhhc------------------hhHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV---PL------EVVMSKYYG------------------ESER  374 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i---~~------~~l~s~~~G------------------~~~~  374 (567)
                      ...+++|+++|.||||+|-+++-..-..   +..+..+   .+      ..+...+ +                  +...
T Consensus        28 ~g~i~v~tG~GkGKTTaA~GlalRA~g~---G~rV~~vQF~Kg~~~~gE~~~l~~L-~v~~~~~g~gf~~~~~~~~~~~~  103 (196)
T 1g5t_A           28 RGIIIVFTGNGKGKTTAAFGTAARAVGH---GKNVGVVQFIKGTWPNGERNLLEPH-GVEFQVMATGFTWETQNREADTA  103 (196)
T ss_dssp             CCCEEEEESSSSCHHHHHHHHHHHHHHT---TCCEEEEESSCCSSCCHHHHHHGGG-TCEEEECCTTCCCCGGGHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHC---CCeEEEEEeeCCCCCccHHHHHHhC-CcEEEEcccccccCCCCcHHHHH
Confidence            3568999999999999999998876333   3333333   21      1233333 1                  0122


Q ss_pred             HHHHHHHHHhc---CCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhc
Q 047219          375 LLGKVFSLANE---LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISR  451 (567)
Q Consensus       375 ~l~~~f~~A~~---~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sR  451 (567)
                      .....+..+.+   .....+|+|||+.....-.--   +     ...++..+..  .+...-||.|+|..   +++|...
T Consensus       104 ~a~~~l~~a~~~l~~~~yDlvILDEi~~al~~g~l---~-----~~ev~~~l~~--Rp~~~~vIlTGr~a---p~~l~e~  170 (196)
T 1g5t_A          104 ACMAVWQHGKRMLADPLLDMVVLDELTYMVAYDYL---P-----LEEVISALNA--RPGHQTVIITGRGC---HRDILDL  170 (196)
T ss_dssp             HHHHHHHHHHHHTTCTTCSEEEEETHHHHHHTTSS---C-----HHHHHHHHHT--SCTTCEEEEECSSC---CHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCEEEEeCCCccccCCCC---C-----HHHHHHHHHh--CcCCCEEEEECCCC---cHHHHHh
Confidence            33444444443   234689999999653211000   0     1234444442  45667888888863   7788888


Q ss_pred             cceEEEec
Q 047219          452 FDSMITFG  459 (567)
Q Consensus       452 f~~~I~i~  459 (567)
                      -|.+-++.
T Consensus       171 AD~VTem~  178 (196)
T 1g5t_A          171 ADTVSELR  178 (196)
T ss_dssp             CSEEEECC
T ss_pred             Ccceeeec
Confidence            77777664

>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=96.34  E-value=0.0022  Score=61.40  Aligned_cols=26  Identities=27%  Similarity=0.505  Sum_probs=23.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.|+||+||||+++.+++.+
T Consensus         3 ~~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            3 ESIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            35679999999999999999999998

>2fz4_A DNA repair protein RAD25; RECA-like domain, DNA damage recognition domain, DNA binding; HET: DNA; 2.40A {Archaeoglobus fulgidus} SCOP: c.37.1.19

Probab=96.34  E-value=0.0093  Score=58.17  Aligned_cols=23  Identities=30%  Similarity=0.302  Sum_probs=21.1

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++++||+|+|||.++.+++...
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHc
Confidence            49999999999999999998876

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.33  E-value=0.0029  Score=59.59  Aligned_cols=26  Identities=31%  Similarity=0.551  Sum_probs=23.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.-++|.|++|+||||+++.+++.+
T Consensus        17 ~~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           17 FPGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             CSSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35679999999999999999999998

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.32  E-value=0.0022  Score=59.71  Aligned_cols=26  Identities=23%  Similarity=0.480  Sum_probs=23.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.|+||+||||+++.+++.+
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A            8 KTNIIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHh
Confidence            45679999999999999999999988

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.31  E-value=0.0033  Score=58.39  Aligned_cols=43  Identities=23%  Similarity=0.287  Sum_probs=31.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ...+..++|.|+||+||||+++.++..+...   +..+..++...+
T Consensus        10 ~~~~~~i~l~G~~GsGKsT~~~~L~~~l~~~---~~~~~~~~~d~~   52 (186)
T 2yvu_A           10 IEKGIVVWLTGLPGSGKTTIATRLADLLQKE---GYRVEVLDGDWA   52 (186)
T ss_dssp             CSCCEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEEHHHH
T ss_pred             cCCCcEEEEEcCCCCCHHHHHHHHHHHHHhc---CCeEEEeeHHHH
Confidence            3456779999999999999999999988432   334555554443

>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=96.30  E-value=0.031  Score=52.16  Aligned_cols=25  Identities=28%  Similarity=0.304  Sum_probs=18.7

Q ss_pred             CceEEeeCCCCCcHHHHH-HHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCA-RVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LA-raIA~~l  346 (567)
                      .+.+++.+|+|+|||..+ -.+...+
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~l   63 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAERL   63 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHH
Confidence            367999999999999874 3444444

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.29  E-value=0.0028  Score=59.66  Aligned_cols=28  Identities=18%  Similarity=0.404  Sum_probs=24.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..|+|.|+||+||||+++.+++.+
T Consensus        12 ~~~~~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           12 PDQVSVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             TTTCEEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3455679999999999999999999987

>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=96.28  E-value=0.0026  Score=58.78  Aligned_cols=26  Identities=31%  Similarity=0.547  Sum_probs=23.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.|+||+||||+++.+++.+
T Consensus         5 ~~~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            5 KPNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45679999999999999999999988

>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=96.28  E-value=0.0053  Score=60.09  Aligned_cols=27  Identities=22%  Similarity=0.411  Sum_probs=24.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..++|.||||+||||+|+.+++.+
T Consensus        27 ~~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           27 KPDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             SCCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            467789999999999999999999988

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.27  E-value=0.0028  Score=62.64  Aligned_cols=32  Identities=34%  Similarity=0.463  Sum_probs=26.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      .++|.||||+||||+|+.+|+.+      +..++..+.
T Consensus         3 li~I~G~~GSGKSTla~~La~~~------~~~~i~~D~   34 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQET------GWPVVALDR   34 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH------CCCEEECCS
T ss_pred             EEEEECCCCcCHHHHHHHHHhcC------CCeEEeccH
Confidence            47899999999999999999998      455555543

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.27  E-value=0.094  Score=61.69  Aligned_cols=43  Identities=23%  Similarity=0.247  Sum_probs=35.5

Q ss_pred             cCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          283 AGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       283 iG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      +|.+..+++|.+.+..                    ....+-+.|+|+.|+|||+||+.+++.
T Consensus       131 VGRe~eLeeL~elL~~--------------------~d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLE--------------------LRPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCHHHHHHHHHHHHH--------------------CCSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHhc--------------------cCCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            8999999999887742                    123567899999999999999999863

>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=96.27  E-value=0.004  Score=61.61  Aligned_cols=42  Identities=14%  Similarity=0.361  Sum_probs=31.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      +.-|+|.|+||+||||+|+.++..+...   +..++.++...+..
T Consensus         4 ~~lIvl~G~pGSGKSTla~~La~~L~~~---g~~~i~~~~D~~~~   45 (260)
T 3a4m_A            4 IMLIILTGLPGVGKSTFSKNLAKILSKN---NIDVIVLGSDLIRE   45 (260)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEECTHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHHHhC---CCEEEEECchHHHH
Confidence            4578999999999999999999984211   45566556655543

>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=96.26  E-value=0.0023  Score=58.36  Aligned_cols=24  Identities=25%  Similarity=0.476  Sum_probs=22.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++|.|+||+||||+++.+++.+
T Consensus         3 ~~I~l~G~~GsGKsT~a~~La~~l   26 (173)
T 1e6c_A            3 EPIFMVGARGCGMTTVGRELARAL   26 (173)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            358999999999999999999998

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.25  E-value=0.0046  Score=66.17  Aligned_cols=42  Identities=26%  Similarity=0.279  Sum_probs=30.2

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      |..++.-++|.|+||+|||++|..++......  .+.++.+++.
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~--~g~~vl~~sl  237 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALK--EGVGVGIYSL  237 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHT--TCCCEEEEES
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHh--CCCeEEEEEC
Confidence            35666779999999999999999998865321  0345555554

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.24  E-value=0.014  Score=55.57  Aligned_cols=37  Identities=19%  Similarity=0.189  Sum_probs=27.7

Q ss_pred             CCCceEEeeCCCCCcHH-HHHHHHHHHhCCCCCCCcCeEEec
Q 047219          320 NRPRAVLFEGPPGTGKT-SCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT-~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      ....-.+++||.|+||| .|.+++.+...+    +..++.+.
T Consensus        18 ~~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~----~~kvl~~k   55 (195)
T 1w4r_A           18 TRGQIQVILGPMFSGKSTELMRRVRRFQIA----QYKCLVIK   55 (195)
T ss_dssp             -CCEEEEEEECTTSCHHHHHHHHHHHHHHT----TCCEEEEE
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHHc----CCeEEEEc
Confidence            34566889999999999 999999998644    34455554

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.24  E-value=0.0094  Score=54.93  Aligned_cols=23  Identities=26%  Similarity=0.427  Sum_probs=19.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARV  341 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAra  341 (567)
                      ...+.-+.|.||+|+||||++++
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            45567789999999999999993

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=96.23  E-value=0.0026  Score=58.81  Aligned_cols=25  Identities=44%  Similarity=0.748  Sum_probs=22.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..++|.|+||+||||+++.+++.+
T Consensus         4 g~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            4 GQAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999999999988

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=96.23  E-value=0.0022  Score=59.08  Aligned_cols=25  Identities=28%  Similarity=0.505  Sum_probs=19.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..++|.|+||+||||+|+.+++.+
T Consensus         5 ~~~I~l~G~~GsGKST~a~~La~~l   29 (183)
T 2vli_A            5 SPIIWINGPFGVGKTHTAHTLHERL   29 (183)
T ss_dssp             CCEEEEECCC----CHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhc
Confidence            4679999999999999999999998

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.19  E-value=0.0036  Score=59.09  Aligned_cols=28  Identities=32%  Similarity=0.518  Sum_probs=24.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..+.|.||+|+||||+++.++..+
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            3456789999999999999999999988

>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=96.18  E-value=0.0083  Score=56.68  Aligned_cols=25  Identities=28%  Similarity=0.587  Sum_probs=22.2

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +.|+|.||+|+|||+|++.+.+..+
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~   26 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCC
Confidence            4689999999999999999988753

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=96.16  E-value=0.0024  Score=61.18  Aligned_cols=25  Identities=24%  Similarity=0.519  Sum_probs=23.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..++|.|+||+||||+++.+++.+
T Consensus         5 ~~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            5 KHNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3568999999999999999999998

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=96.16  E-value=0.009  Score=60.90  Aligned_cols=40  Identities=25%  Similarity=0.200  Sum_probs=29.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..++.-++|.|+||+|||+++..++......   +.++.+++.
T Consensus        65 l~~G~l~li~G~pG~GKTtl~l~ia~~~a~~---g~~vl~~sl  104 (315)
T 3bh0_A           65 YKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSL  104 (315)
T ss_dssp             BCTTCEEEEECCTTSSHHHHHHHHHHHHHTT---TCEEEEEES
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEEC
Confidence            5667789999999999999999998765322   345555553

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=96.15  E-value=0.0027  Score=61.14  Aligned_cols=27  Identities=26%  Similarity=0.444  Sum_probs=23.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..++|.|+||+||||+++.+++.+
T Consensus         5 ~~~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            5 ARLLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             --CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             ccCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            345679999999999999999999988

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.14  E-value=0.0029  Score=59.05  Aligned_cols=25  Identities=20%  Similarity=0.441  Sum_probs=23.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.-|+|.|+||+||||+++.+++.+
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHh
Confidence            4579999999999999999999998

>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=96.13  E-value=0.0034  Score=60.79  Aligned_cols=27  Identities=30%  Similarity=0.491  Sum_probs=24.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..++|.|+||+||||+++.|++.+
T Consensus        14 ~~~~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           14 PKGVRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            345679999999999999999999998

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=96.12  E-value=0.0033  Score=57.06  Aligned_cols=23  Identities=13%  Similarity=0.288  Sum_probs=21.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l   24 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSL   24 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999988

>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=96.12  E-value=0.009  Score=57.01  Aligned_cols=28  Identities=14%  Similarity=0.379  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.+.|.||+|+|||+|+++|.....
T Consensus        17 ~~g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           17 QGRKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CSCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            4567789999999999999999998764

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=96.11  E-value=0.0044  Score=59.33  Aligned_cols=26  Identities=27%  Similarity=0.546  Sum_probs=24.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.|+||+||||+++.+++.+
T Consensus         4 ~~~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            4 DPLKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             CSCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            45679999999999999999999998

>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=96.11  E-value=0.0031  Score=60.03  Aligned_cols=23  Identities=26%  Similarity=0.485  Sum_probs=21.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.|+||+||||+|+.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3dl0_A            2 NLVLMGLPGAGKGTQGERIVEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999988

>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=96.10  E-value=0.004  Score=57.47  Aligned_cols=42  Identities=21%  Similarity=0.317  Sum_probs=31.1

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ..+..+.|.|++|+||||+++.++..+...   +.+++.++...+
T Consensus         3 ~~g~~i~l~G~~GsGKST~~~~L~~~l~~~---g~~~i~~d~~~~   44 (179)
T 2pez_A            3 MRGCTVWLTGLSGAGKTTVSMALEEYLVCH---GIPCYTLDGDNI   44 (179)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEEHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHhhC---CCcEEEECChHH
Confidence            345678999999999999999999986321   456776665433

>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=96.08  E-value=0.0044  Score=56.84  Aligned_cols=26  Identities=27%  Similarity=0.428  Sum_probs=23.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.|++|+||||+++.++..+
T Consensus         7 ~g~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            7 DHHIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             TSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHhh
Confidence            45678999999999999999999987

>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=96.08  E-value=0.029  Score=56.79  Aligned_cols=62  Identities=13%  Similarity=0.146  Sum_probs=35.9

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .+|+++.-.+..++.+.+   .-+..+..++...-  ...  ......+++.+|+|+|||+.+-..+..
T Consensus         6 ~~f~~~~l~~~~~~~l~~---~g~~~~~~~Q~~~i--~~~--~~~~~~~l~~~~TGsGKT~~~~~~~~~   67 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRN---KGFEKPTDIQMKVI--PLF--LNDEYNIVAQARTGSGKTASFAIPLIE   67 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHH---HTCCSCCHHHHHHH--HHH--HHTCSEEEEECCSSSSHHHHHHHHHHH
T ss_pred             CchhhcCCCHHHHHHHHH---cCCCCCCHHHHHHH--HHH--hCCCCCEEEECCCCChHHHHHHHHHHH
Confidence            568888666666666554   22333333333211  111  112368999999999999886654444

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=96.08  E-value=0.0033  Score=59.72  Aligned_cols=23  Identities=30%  Similarity=0.525  Sum_probs=21.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.|+||+||||+|+.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (216)
T 3fb4_A            2 NIVLMGLPGAGKGTQAEQIIEKY   24 (216)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999988

>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=96.05  E-value=0.055  Score=51.22  Aligned_cols=63  Identities=17%  Similarity=0.134  Sum_probs=36.3

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+|+++.-.+...+.+.+   .-+..|..++.-.-  ..   ....+.+++.+|+|+|||..+-..+-..
T Consensus        13 ~~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~i--~~---~~~~~~~li~~~TGsGKT~~~~~~~~~~   75 (220)
T 1t6n_A           13 SSGFRDFLLKPELLRAIVD---CGFEHPSEVQHECI--PQ---AILGMDVLCQAKSGMGKTAVFVLATLQQ   75 (220)
T ss_dssp             -CCSTTSCCCHHHHHHHHH---TTCCCCCHHHHHHH--HH---HHTTCCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCHhhcCCCHHHHHHHHH---CCCCCCCHHHHHHH--HH---HhCCCCEEEECCCCCchhhhhhHHHHHh
Confidence            3568888666666666654   22333444443211  10   1123579999999999998766555443

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=96.03  E-value=0.019  Score=55.41  Aligned_cols=58  Identities=17%  Similarity=0.177  Sum_probs=33.5

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr  340 (567)
                      +..+|+++.=.+...+.+.+   .-+..+..++...  +..   ....+.+++.+|+|+|||..+-
T Consensus        28 ~~~~f~~l~l~~~l~~~l~~---~g~~~~~~~Q~~a--i~~---i~~~~~~li~apTGsGKT~~~~   85 (237)
T 3bor_A           28 IVDNFDDMNLKESLLRGIYA---YGFEKPSAIQQRA--IIP---CIKGYDVIAQAQSGTGKTATFA   85 (237)
T ss_dssp             CCCSGGGSCCCHHHHHHHHH---HTCCSCCHHHHHH--HHH---HHTTCCEEECCCSSHHHHHHHH
T ss_pred             ccCChhhcCCCHHHHHHHHH---CCCCCCCHHHHHH--HHH---HhCCCCEEEECCCCCcHHHHHH
Confidence            34678998655555555543   2334344444321  111   1123679999999999997643

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=96.00  E-value=0.00073  Score=55.14  Aligned_cols=48  Identities=25%  Similarity=0.302  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          464 ENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       464 ~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      ++|.+||+.+++.++   ..+++.++..+.||||+||.++|++|.+.+.++
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~eAa~~ai~~   51 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGLRAVRK   51 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh
Confidence            468899999988754   336889999999999999999999999887765

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=96.00  E-value=0.041  Score=56.30  Aligned_cols=60  Identities=22%  Similarity=0.318  Sum_probs=33.7

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHH
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVI  342 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraI  342 (567)
                      .+|+++.=.+...+.+.+   .-...|..++.-.-  ...+ ...++++++.+|+|+|||+.+-..
T Consensus         5 ~~f~~~~l~~~l~~~l~~---~~~~~~~~~Q~~~i--~~~~-~~~~~~~lv~a~TGsGKT~~~~~~   64 (395)
T 3pey_A            5 KSFDELGLAPELLKGIYA---MKFQKPSKIQERAL--PLLL-HNPPRNMIAQSQSGTGKTAAFSLT   64 (395)
T ss_dssp             CSSTTSCCCHHHHHHHHH---TTCCSCCHHHHHHH--HHHH-CSSCCCEEEECCTTSCHHHHHHHH
T ss_pred             cCHhhCCCCHHHHHHHHH---CCCCCCCHHHHHHH--HHHH-cCCCCeEEEECCCCCcHHHHHHHH
Confidence            457777655555555544   22333333333211  1111 234588999999999999865543

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.96  E-value=0.0065  Score=58.50  Aligned_cols=27  Identities=33%  Similarity=0.404  Sum_probs=22.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..++.-++|+|+||+|||++|..++..
T Consensus        27 l~~G~l~~i~G~pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           27 FPEGTTVLLTGGTGTGKTTFAAQFIYK   53 (251)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            455667999999999999999887643

>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=95.95  E-value=0.0054  Score=58.86  Aligned_cols=34  Identities=29%  Similarity=0.653  Sum_probs=27.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      .++|.||||+||+|.|+.|++.+      +  +..++..++.
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~------g--~~~istGdll   35 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK------G--FVHISTGDIL   35 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH------C--CEEEEHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH------C--CeEEcHHHHH
Confidence            37889999999999999999998      3  4556655544

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.94  E-value=0.0033  Score=65.36  Aligned_cols=25  Identities=28%  Similarity=0.541  Sum_probs=23.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+++|.|+||+|||++++++++.+
T Consensus        24 ~~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A           24 RVCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eeEEEEECCCCCcHHHHHHHHHHHh
Confidence            3569999999999999999999988

>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=95.93  E-value=0.032  Score=60.98  Aligned_cols=44  Identities=23%  Similarity=0.369  Sum_probs=31.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      ..+.-|+|.|.||+||||+|+.+++.++..   ++.+..++..++..
T Consensus        33 ~~~~lIvlvGlpGSGKSTia~~La~~L~~~---~~d~~v~s~D~~r~   76 (520)
T 2axn_A           33 NSPTVIVMVGLPARGKTYISKKLTRYLNWI---GVPTKVFNVGEYRR   76 (520)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEEHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhhc---CCCeEEecccHHHH
Confidence            345678999999999999999999987322   44455556555443

>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=95.93  E-value=0.038  Score=51.63  Aligned_cols=19  Identities=32%  Similarity=0.420  Sum_probs=16.1

Q ss_pred             CceEEeeCCCCCcHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAr  340 (567)
                      .+++++.+|+|+|||..+-
T Consensus        40 ~~~~lv~apTGsGKT~~~~   58 (206)
T 1vec_A           40 GRDILARAKNGTGKSGAYL   58 (206)
T ss_dssp             TCCEEEECCSSSTTHHHHH
T ss_pred             CCCEEEECCCCCchHHHHH
Confidence            3689999999999997554

>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=95.92  E-value=0.0047  Score=58.28  Aligned_cols=29  Identities=17%  Similarity=0.277  Sum_probs=25.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+||||++++++..+.
T Consensus        22 ~~~g~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           22 DQKGCVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             TSCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45677899999999999999999999884

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=95.91  E-value=0.06  Score=54.24  Aligned_cols=66  Identities=20%  Similarity=0.268  Sum_probs=38.2

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH-HHHHHh
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR-VIANQA  346 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr-aIA~~l  346 (567)
                      +..+|+++.-.+...+.|..   .-+..|..++...  +...+ ..+++.+++++|+|+|||...- .+...+
T Consensus        90 ~~~~f~~l~l~~~l~~~l~~---~g~~~pt~iQ~~a--i~~il-~~~~~~~l~~a~TGsGKT~a~~lp~l~~l  156 (300)
T 3fmo_B           90 SVKSFEELRLKPQLLQGVYA---MGFNRPSKIQENA--LPLML-AEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (300)
T ss_dssp             CCCCSGGGTCCHHHHHHHHH---TTCCSCCHHHHHH--HHHHT-SSSCCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CcCCHhhcCCCHHHHHHHHH---cCCCCCCHHHHHH--HHHHH-cCCCCeEEEECCCCCCccHHHHHHHHHhh
Confidence            34678888666666666554   2334444444321  11111 2345889999999999997643 334443

>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=95.89  E-value=0.019  Score=63.89  Aligned_cols=25  Identities=32%  Similarity=0.504  Sum_probs=21.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...++++|+||||||+++.++...+
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l  188 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAAL  188 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHH
Confidence            3679999999999999998887765

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=95.85  E-value=0.023  Score=54.54  Aligned_cols=64  Identities=13%  Similarity=0.121  Sum_probs=34.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHH-HHHHHHh
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA-RVIANQA  346 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LA-raIA~~l  346 (567)
                      +..+|+++.-.+..++.+.+   .-+..+..++.-.-.  .   ....+++++.+|+|+|||..+ -.+...+
T Consensus        22 ~~~~f~~l~l~~~l~~~l~~---~g~~~~~~~Q~~~i~--~---~~~~~~~l~~a~TGsGKT~~~~l~~l~~l   86 (230)
T 2oxc_A           22 EPADFESLLLSRPVLEGLRA---AGFERPSPVQLKAIP--L---GRCGLDLIVQAKSGTGKTCVFSTIALDSL   86 (230)
T ss_dssp             --CCGGGGTCCHHHHHHHHH---TTCCSCCHHHHHHHH--H---HHTTCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCCCHhhcCCCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HhCCCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            34578888655555555543   223334444332111  1   122467999999999999864 3333443

>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=95.84  E-value=0.016  Score=55.41  Aligned_cols=59  Identities=15%  Similarity=0.104  Sum_probs=32.0

Q ss_pred             CCCCCcccccCcHH-HHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH
Q 047219          274 KSEISWENIAGYDQ-QKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       274 ~~~~~~~dIiG~~~-~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr  340 (567)
                      .+..+|++..+... ..+.+.+   .-+..|..++.-.-  ..   ....+.+++.+|+|+|||..+-
T Consensus        16 ~p~~~f~~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~i--~~---~~~~~~~l~~apTGsGKT~~~~   75 (228)
T 3iuy_A           16 KPTCRFKDAFQQYPDLLKSIIR---VGILKPTPIQSQAW--PI---ILQGIDLIVVAQTGTGKTLSYL   75 (228)
T ss_dssp             CCCCSHHHHHTTCHHHHHHHHH---HTCCSCCHHHHHHH--HH---HHTTCCEEEECCTTSCHHHHHH
T ss_pred             CChhhHhhhhccCHHHHHHHHH---CCCCCCCHHHHHHH--HH---HhCCCCEEEECCCCChHHHHHH
Confidence            34567887544443 3333332   22334444443211  11   1134689999999999998644

>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=95.83  E-value=0.017  Score=61.68  Aligned_cols=28  Identities=29%  Similarity=0.366  Sum_probs=24.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ++.-+++.|++|+||||++..+|..+..
T Consensus        96 ~~~vI~lvG~~GsGKTTt~~kLA~~l~~  123 (433)
T 3kl4_A           96 LPFIIMLVGVQGSGKTTTAGKLAYFYKK  123 (433)
T ss_dssp             SSEEEEECCCTTSCHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            5678999999999999999999988743

>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=95.76  E-value=0.0072  Score=58.94  Aligned_cols=26  Identities=31%  Similarity=0.556  Sum_probs=23.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.-+.|.||+|+||||+++.|++.+
T Consensus        26 ~~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           26 KLLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            45789999999999999999999988

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=95.74  E-value=0.0059  Score=57.35  Aligned_cols=27  Identities=30%  Similarity=0.412  Sum_probs=24.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      +.-|+|.|+||+||||+++.+++.++.
T Consensus         4 ~~~I~i~G~~GsGKsT~~~~L~~~l~~   30 (213)
T 2plr_A            4 GVLIAFEGIDGSGKSSQATLLKDWIEL   30 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHTT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            456899999999999999999999854

>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=95.67  E-value=0.0057  Score=58.26  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.|+||+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~~   24 (214)
T 1e4v_A            2 RIILLGAPVAGKGTQAQFIMEKY   24 (214)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47899999999999999999988

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.67  E-value=0.0061  Score=57.69  Aligned_cols=28  Identities=21%  Similarity=0.389  Sum_probs=24.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..++|.||||+||||+++.+++.+.
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            4567799999999999999999999873

>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=95.64  E-value=0.0079  Score=57.39  Aligned_cols=24  Identities=25%  Similarity=0.596  Sum_probs=22.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.|.||+|+||||+++.++..+
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~   29 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEAL   29 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999988

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=95.62  E-value=0.0073  Score=56.06  Aligned_cols=27  Identities=11%  Similarity=0.313  Sum_probs=23.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.-+.|.||+|+|||||++.++....
T Consensus         4 ~g~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            346789999999999999999998763

>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=95.62  E-value=0.038  Score=53.39  Aligned_cols=22  Identities=27%  Similarity=0.441  Sum_probs=17.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA  343 (567)
                      +..+++.||+|+|||++...+.
T Consensus        76 g~~~~i~g~TGsGKTt~~~~~~   97 (235)
T 3llm_A           76 NSVVIIRGATGCGKTTQVPQFI   97 (235)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHH
T ss_pred             CCEEEEEeCCCCCcHHhHHHHH
Confidence            4689999999999998665554

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=95.60  E-value=0.0073  Score=56.33  Aligned_cols=24  Identities=25%  Similarity=0.470  Sum_probs=22.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.|.|++|+||||+++.+++.++
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~   25 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLG   25 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcC
Confidence            478999999999999999999983

>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=95.59  E-value=0.013  Score=55.07  Aligned_cols=22  Identities=23%  Similarity=0.419  Sum_probs=20.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.|.|++|+||||+++.++. +
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~   24 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-L   24 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-T
T ss_pred             EEEEECCCCcCHHHHHHHHHH-C
Confidence            578999999999999999999 6

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=95.55  E-value=0.0068  Score=56.83  Aligned_cols=27  Identities=22%  Similarity=0.507  Sum_probs=24.1

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.-+.|.||+|+||||+++.++..+
T Consensus         4 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            4 EKGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            456678999999999999999999876

>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=95.53  E-value=0.0079  Score=57.22  Aligned_cols=43  Identities=16%  Similarity=0.176  Sum_probs=32.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC-CCCCCCcCeEEechhhH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG-AMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~-~~~~~~~~~~~i~~~~l  364 (567)
                      ...+..++|.|++|+||||+++.++..+. ..   +.+++.++...+
T Consensus        22 ~~~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~---g~~~~~~~~d~~   65 (211)
T 1m7g_A           22 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDR---RVHAYRLDGDNI   65 (211)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHH---CCCEEEECHHHH
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHhcccc---CCcEEEECChHH
Confidence            45567899999999999999999999873 11   344666765544

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=95.52  E-value=0.062  Score=52.45  Aligned_cols=57  Identities=16%  Similarity=0.153  Sum_probs=31.7

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr  340 (567)
                      ..+|+++.-.+...+.+.+   .-+..+..++.-..  ..   ....+.+++.+|+|+|||..+-
T Consensus        42 ~~~f~~l~l~~~l~~~l~~---~g~~~~~~~Q~~~i--~~---i~~~~~~lv~a~TGsGKT~~~~   98 (249)
T 3ber_A           42 TKTFKDLGVTDVLCEACDQ---LGWTKPTKIQIEAI--PL---ALQGRDIIGLAETGSGKTGAFA   98 (249)
T ss_dssp             HCCTGGGTCCHHHHHHHHH---TTCCSCCHHHHHHH--HH---HHTTCCEEEECCTTSCHHHHHH
T ss_pred             cCCHHHcCCCHHHHHHHHH---cCCCCCCHHHHHHH--HH---HhCCCCEEEEcCCCCCchhHhH
Confidence            3568887555555544433   22333333333211  11   1123679999999999998643

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=95.49  E-value=0.045  Score=51.92  Aligned_cols=18  Identities=28%  Similarity=0.353  Sum_probs=15.6

Q ss_pred             ceEEeeCCCCCcHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAr  340 (567)
                      +.+++.+|+|+|||..+-
T Consensus        42 ~~~lv~a~TGsGKT~~~~   59 (219)
T 1q0u_A           42 ESMVGQSQTGTGKTHAYL   59 (219)
T ss_dssp             CCEEEECCSSHHHHHHHH
T ss_pred             CCEEEECCCCChHHHHHH
Confidence            679999999999998643

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.46  E-value=0.0091  Score=57.45  Aligned_cols=23  Identities=26%  Similarity=0.579  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.|+||+||||+++.+++.+
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            47899999999999999999988

>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=95.45  E-value=0.0083  Score=56.58  Aligned_cols=27  Identities=22%  Similarity=0.377  Sum_probs=24.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.-|+|.|+||+||||+++.+++.++
T Consensus         8 ~~~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A            8 RGALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CCCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            456799999999999999999999874

>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=95.45  E-value=0.019  Score=54.38  Aligned_cols=41  Identities=20%  Similarity=0.306  Sum_probs=30.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      ...+.|+|++|+||||+++.+++.+      +  +..+++..+....++
T Consensus        12 ~~iIgltG~~GSGKSTva~~L~~~l------g--~~vid~D~~~~~~~~   52 (192)
T 2grj_A           12 HMVIGVTGKIGTGKSTVCEILKNKY------G--AHVVNVDRIGHEVLE   52 (192)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHHH------C--CEEEEHHHHHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc------C--CEEEECcHHHHHHHH
Confidence            3458899999999999999999987      4  444566666554443

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=95.44  E-value=0.073  Score=55.00  Aligned_cols=62  Identities=21%  Similarity=0.218  Sum_probs=34.1

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH-HHHHHh
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR-VIANQA  346 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr-aIA~~l  346 (567)
                      .+|+++.-.+...+.+.+   .-+..+..++.-.  +..   ....+.+++.+|+|+|||+.+- .+.+.+
T Consensus        40 ~~f~~~~l~~~~~~~l~~---~~~~~~~~~Q~~~--i~~---~~~~~~~lv~a~TGsGKT~~~~~~~~~~~  102 (414)
T 3eiq_A           40 DSFDDMNLSESLLRGIYA---YGFEKPSAIQQRA--ILP---CIKGYDVIAQAQSGTGKTATFAISILQQI  102 (414)
T ss_dssp             CCGGGGCCCHHHHHHHHH---TTCCSCCHHHHHH--HHH---HHTTCCEEECCCSCSSSHHHHHHHHHHHC
T ss_pred             cCHhhCCCCHHHHHHHHH---cCCCCCCHHHHHH--hHH---HhCCCCEEEECCCCCcccHHHHHHHHHHH
Confidence            467777655555555543   2233333333321  101   1124569999999999998743 344443

>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=95.44  E-value=0.04  Score=51.57  Aligned_cols=24  Identities=33%  Similarity=0.506  Sum_probs=20.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+++.+|+|+|||+++-.++...
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHHH
Confidence            579999999999999888777643

>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=95.44  E-value=0.023  Score=57.86  Aligned_cols=29  Identities=28%  Similarity=0.382  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-++|.|++|+||||++..+|..+.
T Consensus       101 ~~~~~vi~ivG~~GsGKTTl~~~LA~~l~  129 (306)
T 1vma_A          101 PEPPFVIMVVGVNGTGKTTSCGKLAKMFV  129 (306)
T ss_dssp             SSSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEcCCCChHHHHHHHHHHHHH
Confidence            35667899999999999999999998874

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.43  E-value=0.008  Score=56.64  Aligned_cols=27  Identities=19%  Similarity=0.457  Sum_probs=24.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.-|+|.|+||+||||+++.+++.++
T Consensus         9 ~~~~I~l~G~~GsGKST~~~~L~~~l~   35 (212)
T 2wwf_A            9 KGKFIVFEGLDRSGKSTQSKLLVEYLK   35 (212)
T ss_dssp             CSCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             cCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            356799999999999999999999874

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.41  E-value=0.016  Score=54.97  Aligned_cols=28  Identities=25%  Similarity=0.469  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-+.|.||+|+|||||++.|+..+.
T Consensus        20 ~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           20 PGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             CSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4566788999999999999999999873

>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=95.36  E-value=0.011  Score=57.75  Aligned_cols=26  Identities=38%  Similarity=0.590  Sum_probs=23.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..+.|.||+|+||||+++.|++.+
T Consensus         8 ~~~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A            8 GSLVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             -CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            35679999999999999999999998

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.33  E-value=0.021  Score=56.39  Aligned_cols=25  Identities=28%  Similarity=0.535  Sum_probs=23.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.|.|++|+||||+++.++..+
T Consensus        48 g~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           48 GRSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             TCCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhc
Confidence            5679999999999999999999998

>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=95.32  E-value=0.0093  Score=56.75  Aligned_cols=28  Identities=21%  Similarity=0.489  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .++.-+.|.||+|+||||+++.++..+.
T Consensus         6 ~~g~~i~l~GpsGsGKsTl~~~L~~~~~   33 (208)
T 3tau_A            6 ERGLLIVLSGPSGVGKGTVREAVFKDPE   33 (208)
T ss_dssp             CCCCEEEEECCTTSCHHHHHHHHHHSTT
T ss_pred             CCCcEEEEECcCCCCHHHHHHHHHhhCC
Confidence            4566789999999999999999998874

>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=95.28  E-value=0.01  Score=55.58  Aligned_cols=25  Identities=28%  Similarity=0.371  Sum_probs=23.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..+.|.|++|+||||+++.+++.+
T Consensus         4 ~~~I~l~G~~GsGKsT~~~~L~~~l   28 (204)
T 2v54_A            4 GALIVFEGLDKSGKTTQCMNIMESI   28 (204)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHTS
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4678999999999999999999987

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=95.27  E-value=0.075  Score=51.31  Aligned_cols=58  Identities=10%  Similarity=0.010  Sum_probs=33.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr  340 (567)
                      +..+|+++.-.+...+.+.+   .-+..|..++.-.  +..   ....+.+++.+|+|+|||..+-
T Consensus        27 ~~~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~--i~~---~~~g~~~l~~apTGsGKT~~~~   84 (242)
T 3fe2_A           27 PVLNFYEANFPANVMDVIAR---QNFTEPTAIQAQG--WPV---ALSGLDMVGVAQTGSGKTLSYL   84 (242)
T ss_dssp             CCSSTTTTTCCHHHHHHHHT---TTCCSCCHHHHHH--HHH---HHHTCCEEEEECTTSCHHHHHH
T ss_pred             ccCCHhhcCCCHHHHHHHHH---CCCCCCCHHHHHH--HHH---HhCCCCEEEECCCcCHHHHHHH
Confidence            45678887655555555543   2233343343321  100   1123689999999999998643

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=95.26  E-value=0.081  Score=54.54  Aligned_cols=66  Identities=20%  Similarity=0.267  Sum_probs=38.1

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHH-HHHHHHh
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA-RVIANQA  346 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LA-raIA~~l  346 (567)
                      +..+|+++.-.+...+.+.+   .-...|..++...  +...+ ...+..+++.+|+|+|||..+ -.+...+
T Consensus        23 ~~~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~--i~~~~-~~~~~~~lv~apTGsGKT~~~~~~~~~~~   89 (412)
T 3fht_A           23 SVKSFEELRLKPQLLQGVYA---MGFNRPSKIQENA--LPLML-AEPPQNLIAQSQSGTGKTAAFVLAMLSQV   89 (412)
T ss_dssp             CSSCTGGGTCCHHHHHHHHH---TTCCSCCHHHHHH--HHHHH-SSSCCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             ccCCHhhCCCCHHHHHHHHH---cCCCCCCHHHHHH--HHHHh-cCCCCeEEEECCCCchHHHHHHHHHHHHh
Confidence            34578888666666666654   2233444443321  11111 224578999999999999875 3344444

>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=95.25  E-value=0.013  Score=54.88  Aligned_cols=23  Identities=39%  Similarity=0.638  Sum_probs=21.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.|.|++|+||||+++.++..+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~l   26 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAAL   26 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            68899999999999999999988

>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=95.23  E-value=0.024  Score=60.10  Aligned_cols=28  Identities=32%  Similarity=0.431  Sum_probs=24.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-|+|.|+||+||||+|+.+++.+
T Consensus       255 ~~~~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          255 SPNPEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             CSSCCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHhc
Confidence            3456779999999999999999999877

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=95.21  E-value=0.13  Score=53.12  Aligned_cols=60  Identities=18%  Similarity=0.238  Sum_probs=34.9

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHH
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA  343 (567)
                      ..+|+++.=.+..++.+.+   .-+..|..++.-.-.  .   ....+.+++.+|+|+|||..+-..+
T Consensus        36 ~~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~ai~--~---i~~~~~~lv~a~TGsGKT~~~~~~~   95 (410)
T 2j0s_A           36 TPTFDTMGLREDLLRGIYA---YGFEKPSAIQQRAIK--Q---IIKGRDVIAQSQSGTGKTATFSISV   95 (410)
T ss_dssp             CCSGGGGCCCHHHHHHHHH---HTCCSCCHHHHHHHH--H---HHTTCCEEEECCTTSSHHHHHHHHH
T ss_pred             CCCHhhcCCCHHHHHHHHH---cCCCCCCHHHHHHHH--H---HhCCCCEEEECCCCCCchHHHHHHH
Confidence            3578887656666665543   233334444432111  0   1123679999999999997665433

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=95.19  E-value=0.017  Score=61.88  Aligned_cols=41  Identities=24%  Similarity=0.189  Sum_probs=30.7

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      |..++.-++|.|+||+|||++|-.++......   +.++.+++.
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~---g~~vl~fSl  233 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDN---DDVVNLHSL  233 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHT---TCEEEEECS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHc---CCEEEEEEC
Confidence            35667779999999999999999998876322   345665554

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=95.19  E-value=0.13  Score=53.06  Aligned_cols=61  Identities=18%  Similarity=0.142  Sum_probs=34.3

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..+|+++.-.+...+.+.+   .-+..+..++.-...  ..   ...+.+++.+|+|+|||+.+-..+-
T Consensus        20 ~~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~i~--~i---~~~~~~li~a~TGsGKT~~~~~~~~   80 (400)
T 1s2m_A           20 GNTFEDFYLKRELLMGIFE---AGFEKPSPIQEEAIP--VA---ITGRDILARAKNGTGKTAAFVIPTL   80 (400)
T ss_dssp             -CCGGGGCCCHHHHHHHHH---TTCCSCCHHHHHHHH--HH---HHTCCEEEECCTTSCHHHHHHHHHH
T ss_pred             cCChhhcCCCHHHHHHHHH---CCCCCCCHHHHHHHH--HH---hcCCCEEEECCCCcHHHHHHHHHHH
Confidence            3578888666666665544   223333333322110  00   1235699999999999986654443

>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=95.18  E-value=0.07  Score=58.18  Aligned_cols=29  Identities=28%  Similarity=0.296  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+...++|.||+|+|||+|++.++....
T Consensus       278 i~~G~i~~i~G~~GsGKSTLl~~l~g~~~  306 (525)
T 1tf7_A          278 FFKDSIILATGATGTGKTLLVSRFVENAC  306 (525)
T ss_dssp             EESSCEEEEEECTTSSHHHHHHHHHHHHH
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            45667899999999999999999998764

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.17  E-value=0.013  Score=54.93  Aligned_cols=26  Identities=27%  Similarity=0.540  Sum_probs=23.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.-+.|.||+|+||||+++.++...
T Consensus         6 ~g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            6 KANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            45668899999999999999999876

>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=95.15  E-value=0.018  Score=56.38  Aligned_cols=28  Identities=25%  Similarity=0.363  Sum_probs=24.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..|.|.|++|+||||+|+.+++.++
T Consensus        20 ~~~~iI~I~G~~GSGKST~a~~L~~~lg   47 (252)
T 1uj2_A           20 GEPFLIGVSGGTASGKSSVCAKIVQLLG   47 (252)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHhh
Confidence            4456799999999999999999999883

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=95.14  E-value=0.0089  Score=61.82  Aligned_cols=40  Identities=23%  Similarity=0.152  Sum_probs=29.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..+..-++|.|+||+|||++|..++......   +.++.+++.
T Consensus        43 l~~G~LiiIaG~pG~GKTt~al~ia~~~a~~---g~~Vl~fSl   82 (338)
T 4a1f_A           43 FNKGSLVIIGARPSMGKTSLMMNMVLSALND---DRGVAVFSL   82 (338)
T ss_dssp             BCTTCEEEEEECTTSCHHHHHHHHHHHHHHT---TCEEEEEES
T ss_pred             CCCCcEEEEEeCCCCCHHHHHHHHHHHHHHc---CCeEEEEeC
Confidence            5667779999999999999999998875322   445555543

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=95.13  E-value=0.049  Score=55.84  Aligned_cols=65  Identities=17%  Similarity=0.178  Sum_probs=36.3

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH-HHHHHh
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR-VIANQA  346 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr-aIA~~l  346 (567)
                      .+..+|+++.=.+...+.+..   ..+..+..++...  +...   ...+.+++.+|+|+|||..+- .+.+.+
T Consensus        18 ~~~~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~--i~~i---~~~~~~lv~~~TGsGKT~~~~~~~~~~l   83 (394)
T 1fuu_A           18 KVVYKFDDMELDENLLRGVFG---YGFEEPSAIQQRA--IMPI---IEGHDVLAQAQSGTGKTGTFSIAALQRI   83 (394)
T ss_dssp             CCCCSSGGGCCCHHHHHHHHH---HTCCSCCHHHHHH--HHHH---HHTCCEEECCCSSHHHHHHHHHHHHHHC
T ss_pred             cccCChhhcCCCHHHHHHHHH---cCCCCCCHHHHHH--HHHH---hCCCCEEEECCCCChHHHHHHHHHHHHh
Confidence            344679998655555555544   2233343343321  1111   113579999999999998743 334433

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=95.11  E-value=0.011  Score=54.58  Aligned_cols=23  Identities=35%  Similarity=0.524  Sum_probs=21.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -+.|.|++|+||||+++.+++.+
T Consensus         2 ~I~l~G~~GsGKsT~~~~L~~~l   24 (195)
T 2pbr_A            2 LIAFEGIDGSGKTTQAKKLYEYL   24 (195)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999987

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=95.09  E-value=0.11  Score=49.59  Aligned_cols=57  Identities=11%  Similarity=0.075  Sum_probs=33.0

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHH
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAr  340 (567)
                      ..+|+++.-.+...+.+.+   .-...+..++.-.-  ..   ....+.+++.+|+|+|||+.+-
T Consensus        24 ~~~f~~~~l~~~l~~~l~~---~~~~~~~~~Q~~~i--~~---~~~~~~~li~a~TGsGKT~~~~   80 (236)
T 2pl3_A           24 ITRFSDFPLSKKTLKGLQE---AQYRLVTEIQKQTI--GL---ALQGKDVLGAAKTGSGKTLAFL   80 (236)
T ss_dssp             CSBGGGSCCCHHHHHHHHH---TTCCBCCHHHHHHH--HH---HHTTCCEEEECCTTSCHHHHHH
T ss_pred             cCCHhhcCCCHHHHHHHHH---CCCCCCCHHHHHHH--HH---HhCCCCEEEEeCCCCcHHHHHH
Confidence            3468888666666665543   22333333333211  00   1224679999999999998543

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=95.05  E-value=0.11  Score=55.40  Aligned_cols=65  Identities=18%  Similarity=0.256  Sum_probs=37.4

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHH-HHHHHHh
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA-RVIANQA  346 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LA-raIA~~l  346 (567)
                      ..+|+++.-.+...+.+.+   .-+..|..++....  ...+ ...+..+++.||+|+|||..+ -.+...+
T Consensus        91 ~~~f~~~~l~~~l~~~l~~---~g~~~p~~~Q~~ai--~~il-~~~~~~~l~~a~TGsGKT~~~~l~il~~l  156 (479)
T 3fmp_B           91 VKSFEELRLKPQLLQGVYA---MGFNRPSKIQENAL--PLML-AEPPQNLIAQSQSGTGKTAAFVLAMLSQV  156 (479)
T ss_dssp             CCCSGGGTCCHHHHHHHHH---TTCCSCCHHHHHHH--HHHT-SBSCCEEEEECCSSSSHHHHHHHHHHTTC
T ss_pred             cCCHHHcCCCHHHHHHHHH---cCCCCCCHHHHHHH--HHHH-cCCCCcEEEEcCCCCchhHHHHHHHHHHH
Confidence            3578887666666666554   23334433333211  1111 234688999999999999874 3444443

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.05  E-value=0.027  Score=53.14  Aligned_cols=27  Identities=19%  Similarity=0.235  Sum_probs=23.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.-+.|.|++|+||||+++.++..+
T Consensus        20 ~~~~~i~i~G~~GsGKstl~~~l~~~~   46 (201)
T 1rz3_A           20 AGRLVLGIDGLSRSGKTTLANQLSQTL   46 (201)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            445678899999999999999999876

>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=95.04  E-value=0.023  Score=56.81  Aligned_cols=25  Identities=32%  Similarity=0.545  Sum_probs=22.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.-++|.|+||+||||+|+.+++.+
T Consensus         2 ~~~I~l~G~~GsGKST~a~~L~~~~   26 (301)
T 1ltq_A            2 KKIILTIGCPGSGKSTWAREFIAKN   26 (301)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHhC
Confidence            3568999999999999999999863

>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=95.01  E-value=0.067  Score=54.02  Aligned_cols=28  Identities=21%  Similarity=0.316  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..++|.|++|+||||++..+|..+.
T Consensus       103 ~~g~vi~lvG~~GsGKTTl~~~LA~~l~  130 (296)
T 2px0_A          103 IHSKYIVLFGSTGAGKTTTLAKLAAISM  130 (296)
T ss_dssp             CCSSEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3567899999999999999999998774

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=94.99  E-value=0.23  Score=50.74  Aligned_cols=60  Identities=17%  Similarity=0.122  Sum_probs=33.9

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      .+|+++.=.....+.|.+   .-+..+..++...-.  .   ....+.+++.+|+|+|||..+-..+-
T Consensus         8 ~~f~~~~l~~~l~~~l~~---~g~~~~~~~Q~~~i~--~---~~~~~~~lv~a~TGsGKT~~~~~~~~   67 (391)
T 1xti_A            8 SGFRDFLLKPELLRAIVD---CGFEHPSEVQHECIP--Q---AILGMDVLCQAKSGMGKTAVFVLATL   67 (391)
T ss_dssp             -CGGGGCCCHHHHHHHHH---HSCCSCCHHHHHHHH--H---HTTTCCEEEECSSCSSHHHHHHHHHH
T ss_pred             CChhhcCCCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HhcCCcEEEECCCCCcHHHHHHHHHH
Confidence            467787655555555544   223334334332111  1   12246799999999999987654443

>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=94.99  E-value=0.012  Score=54.68  Aligned_cols=23  Identities=30%  Similarity=0.615  Sum_probs=20.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.|.||+|+||||+++.++...
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~   26 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQL   26 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHhccc
Confidence            57899999999999999999754

>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=94.98  E-value=0.014  Score=54.99  Aligned_cols=22  Identities=32%  Similarity=0.453  Sum_probs=20.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..+.|.|++|+||||+++.++.
T Consensus         3 ~~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            3 YIVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            3578999999999999999987

>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=94.93  E-value=0.021  Score=53.16  Aligned_cols=26  Identities=23%  Similarity=0.429  Sum_probs=23.1

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..+..|.|.|++|+||||+++.+++.
T Consensus         6 ~~~~~I~i~G~~GsGKST~~~~La~~   31 (203)
T 1uf9_A            6 KHPIIIGITGNIGSGKSTVAALLRSW   31 (203)
T ss_dssp             CCCEEEEEEECTTSCHHHHHHHHHHT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHC
Confidence            44667999999999999999999986

>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=94.93  E-value=0.027  Score=53.29  Aligned_cols=26  Identities=19%  Similarity=0.126  Sum_probs=21.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...-.+++||.|+|||+.+-.+++.+
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~~a~r~   32 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIRRIRRA   32 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCcHHHHHHHHHHHH
Confidence            34568899999999998887777765

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=94.91  E-value=0.034  Score=62.21  Aligned_cols=23  Identities=39%  Similarity=0.752  Sum_probs=16.8

Q ss_pred             eEEeeCCCCCcHHHHHH-HHHHHh
Q 047219          324 AVLFEGPPGTGKTSCAR-VIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAr-aIA~~l  346 (567)
                      -.||+||||||||+++- .|+..+
T Consensus       207 ~~lI~GPPGTGKT~ti~~~I~~l~  230 (646)
T 4b3f_X          207 LAIIHGPPGTGKTTTVVEIILQAV  230 (646)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ceEEECCCCCCHHHHHHHHHHHHH
Confidence            57899999999996544 444443

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=94.91  E-value=0.013  Score=60.41  Aligned_cols=26  Identities=23%  Similarity=0.419  Sum_probs=23.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++.++|.||+|+|||+|+..||+.+
T Consensus        39 ~~~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           39 KEKLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHC
Confidence            44679999999999999999999988

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=94.89  E-value=0.02  Score=56.27  Aligned_cols=26  Identities=23%  Similarity=0.521  Sum_probs=23.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..+.|.||+|+||||+++.|++.+
T Consensus        26 ~g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           26 IAPVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             TSCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHhc
Confidence            34578899999999999999999988

>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=94.80  E-value=0.056  Score=58.08  Aligned_cols=41  Identities=24%  Similarity=0.391  Sum_probs=29.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV  363 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~  363 (567)
                      ..+..|+|.|.||+|||++++.+++.+...   ..++..++...
T Consensus        37 ~~~~~IvlvGlpGsGKSTia~~La~~l~~~---~~~t~~~~~d~   77 (469)
T 1bif_A           37 NCPTLIVMVGLPARGKTYISKKLTRYLNFI---GVPTREFNVGQ   77 (469)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEEHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHHhcc---CCCceEEecch
Confidence            345679999999999999999999987422   33445544433

>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=94.79  E-value=0.021  Score=58.25  Aligned_cols=28  Identities=29%  Similarity=0.490  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-++|.||+|+|||+||..+|+.++
T Consensus         8 ~~~~~i~i~GptgsGKt~la~~La~~~~   35 (316)
T 3foz_A            8 SLPKAIFLMGPTASGKTALAIELRKILP   35 (316)
T ss_dssp             CCCEEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCCcEEEEECCCccCHHHHHHHHHHhCC
Confidence            4456788999999999999999999984

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.77  E-value=0.023  Score=54.97  Aligned_cols=28  Identities=25%  Similarity=0.559  Sum_probs=24.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..+.|.|++|+||||+++.++..+
T Consensus        13 ~~~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           13 KMKTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             -CCCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             ccCCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4556679999999999999999999988

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.76  E-value=0.016  Score=54.72  Aligned_cols=27  Identities=30%  Similarity=0.672  Sum_probs=22.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++..+.|.||+|+|||||++.+.....
T Consensus         3 ~g~~i~lvGpsGaGKSTLl~~L~~~~~   29 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLLKKLFQEHS   29 (198)
T ss_dssp             --CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            346789999999999999999998763

>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=94.75  E-value=0.081  Score=61.56  Aligned_cols=27  Identities=26%  Similarity=0.427  Sum_probs=22.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+.-+.|.||.|+||||+.|.++..
T Consensus       670 ~~~g~i~~ItGPNGaGKSTlLr~i~~i  696 (918)
T 3thx_B          670 EDSERVMIITGPNMGGKSSYIKQVALI  696 (918)
T ss_dssp             TTSCCEEEEESCCCHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCchHHHHHHHHHH
Confidence            345567999999999999999998743

>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=94.64  E-value=0.025  Score=53.75  Aligned_cols=24  Identities=29%  Similarity=0.433  Sum_probs=21.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.-+.|.|++|+||||+++.++. +
T Consensus         4 ~~~I~i~G~~GSGKST~~~~L~~-l   27 (218)
T 1vht_A            4 RYIVALTGGIGSGKSTVANAFAD-L   27 (218)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHH-T
T ss_pred             ceEEEEECCCCCCHHHHHHHHHH-c
Confidence            45789999999999999999997 5

>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=94.64  E-value=0.015  Score=59.84  Aligned_cols=73  Identities=16%  Similarity=0.218  Sum_probs=43.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhh-H-----Hh--hhh-chhHHHHHHHHHHHhcCCCCcE
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV-V-----MS--KYY-GESERLLGKVFSLANELPNGAI  391 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~-l-----~s--~~~-G~~~~~l~~~f~~A~~~a~~~I  391 (567)
                      +...++|.||+|+||||++++++......    ...+.+.... +     ..  .++ | .....+..+..+.... +.+
T Consensus       170 ~g~~v~i~G~~GsGKTTll~~l~g~~~~~----~g~i~i~~~~e~~~~~~~~~i~~~~g-gg~~~r~~la~aL~~~-p~i  243 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTYIKSIMEFIPKE----ERIISIEDTEEIVFKHHKNYTQLFFG-GNITSADCLKSCLRMR-PDR  243 (330)
T ss_dssp             HTCCEEEEESTTSCHHHHHHHGGGGSCTT----SCEEEEESSCCCCCSSCSSEEEEECB-TTBCHHHHHHHHTTSC-CSE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCcCC----CcEEEECCeeccccccchhEEEEEeC-CChhHHHHHHHHhhhC-CCE
Confidence            45689999999999999999999987432    1122222110 0     00  011 1 1122334445555544 589


Q ss_pred             EEEcCcch
Q 047219          392 IFLDEVDS  399 (567)
Q Consensus       392 LfIDEID~  399 (567)
                      |++||...
T Consensus       244 lildE~~~  251 (330)
T 2pt7_A          244 IILGELRS  251 (330)
T ss_dssp             EEECCCCS
T ss_pred             EEEcCCCh
Confidence            99999975

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=94.63  E-value=0.019  Score=55.16  Aligned_cols=28  Identities=25%  Similarity=0.419  Sum_probs=23.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++..+.|.||+|+|||||++.|+...
T Consensus        20 i~~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           20 MNNIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             --CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4566779999999999999999999976

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=94.59  E-value=0.024  Score=53.74  Aligned_cols=25  Identities=24%  Similarity=0.554  Sum_probs=22.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..+.|.|++|+|||++++.+++.+
T Consensus         3 ~~~i~i~G~~gsGkst~~~~l~~~~   27 (219)
T 2h92_A            3 AINIALDGPAAAGKSTIAKRVASEL   27 (219)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhc
Confidence            3468999999999999999999988

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=94.59  E-value=0.019  Score=54.17  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=23.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.-+.|.||+|+||||+++.|+..+
T Consensus         4 ~~~~~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            4 PKPFVIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             -CCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEEECCCCCCHHHHHHHHHHHh
Confidence            455678899999999999999999987

>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=94.58  E-value=0.023  Score=52.11  Aligned_cols=29  Identities=28%  Similarity=0.466  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||.|+|||||+++|+..++
T Consensus        30 i~~Ge~v~L~G~nGaGKTTLlr~l~g~l~   58 (158)
T 1htw_A           30 TEKAIMVYLNGDLGAGKTTLTRGMLQGIG   58 (158)
T ss_dssp             CSSCEEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHHhCC
Confidence            45666789999999999999999999873

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.54  E-value=0.042  Score=56.27  Aligned_cols=28  Identities=21%  Similarity=0.363  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-+.|.||+|+||||+++.|+..+.
T Consensus        90 ~~p~iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           90 KVPYIIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCCEEEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            4556788999999999999999999885

>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=94.43  E-value=0.021  Score=61.49  Aligned_cols=26  Identities=19%  Similarity=0.259  Sum_probs=22.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|+|++|+|||+|++.++...
T Consensus       150 kGq~~~i~G~sGvGKTtL~~~l~~~~  175 (473)
T 1sky_E          150 KGGKIGLFGGAGVGKTVLIQELIHNI  175 (473)
T ss_dssp             TTCEEEEECCSSSCHHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCccHHHHHHHhhh
Confidence            34568999999999999999988765

>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=94.43  E-value=0.018  Score=54.36  Aligned_cols=28  Identities=18%  Similarity=0.304  Sum_probs=23.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+.|.|++|+||||+++.++..+
T Consensus        18 ~~~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           18 GSKTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             SCCCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            3445678899999999999999999865

>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=94.42  E-value=0.085  Score=61.54  Aligned_cols=24  Identities=21%  Similarity=0.297  Sum_probs=20.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      .+.-++|.||.|+||||+.|.++-
T Consensus       661 ~g~i~~ItGpNGsGKSTlLr~ial  684 (934)
T 3thx_A          661 KQMFHIITGPNMGGKSTYIRQTGV  684 (934)
T ss_dssp             TBCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHH
Confidence            345689999999999999999953

>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=94.42  E-value=0.082  Score=56.14  Aligned_cols=28  Identities=21%  Similarity=0.383  Sum_probs=24.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      +...++|.||+|+||||+.+++...+..
T Consensus       166 ~ggii~I~GpnGSGKTTlL~allg~l~~  193 (418)
T 1p9r_A          166 PHGIILVTGPTGSGKSTTLYAGLQELNS  193 (418)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCC
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHhhcCC
Confidence            4456899999999999999999998853

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=94.41  E-value=0.12  Score=49.66  Aligned_cols=18  Identities=39%  Similarity=0.584  Sum_probs=15.4

Q ss_pred             CceEEeeCCCCCcHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCA  339 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LA  339 (567)
                      .+.+++.+|+|+|||..+
T Consensus        66 ~~~~l~~a~TGsGKT~~~   83 (245)
T 3dkp_A           66 GRELLASAPTGSGKTLAF   83 (245)
T ss_dssp             TCCEEEECCTTSCHHHHH
T ss_pred             CCCEEEECCCCCcHHHHH
Confidence            367999999999999864

>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=94.40  E-value=0.054  Score=54.59  Aligned_cols=29  Identities=31%  Similarity=0.510  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.|++|+||||+++.|+..+.
T Consensus        28 ~~~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           28 NKCPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            34566788999999999999999999874

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=94.40  E-value=0.032  Score=55.33  Aligned_cols=27  Identities=22%  Similarity=0.485  Sum_probs=23.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+...++|.||+|+||||++++++...
T Consensus        23 ~~g~~v~i~Gp~GsGKSTll~~l~g~~   49 (261)
T 2eyu_A           23 RKMGLILVTGPTGSGKSTTIASMIDYI   49 (261)
T ss_dssp             CSSEEEEEECSTTCSHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCccHHHHHHHHHHhC
Confidence            456679999999999999999999876

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=94.39  E-value=0.23  Score=55.95  Aligned_cols=21  Identities=33%  Similarity=0.498  Sum_probs=18.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAr  340 (567)
                      ....++++.||+|+|||+.+-
T Consensus        44 ~~~~~~lv~apTGsGKT~~~~   64 (715)
T 2va8_A           44 LEGNRLLLTSPTGSGKTLIAE   64 (715)
T ss_dssp             TTTCCEEEECCTTSCHHHHHH
T ss_pred             cCCCcEEEEcCCCCcHHHHHH
Confidence            346889999999999999884

>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=94.34  E-value=0.18  Score=54.42  Aligned_cols=41  Identities=17%  Similarity=0.134  Sum_probs=30.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..+..-++|.|+||+|||+++..++.......  +.++.+++.
T Consensus       239 l~~G~l~li~G~pG~GKT~lal~~a~~~a~~~--g~~vl~~s~  279 (503)
T 1q57_A          239 ARGGEVIMVTSGSGMVMSTFVRQQALQWGTAM--GKKVGLAML  279 (503)
T ss_dssp             CCTTCEEEEEESSCHHHHHHHHHHHHHHTTTS--CCCEEEEES
T ss_pred             cCCCeEEEEeecCCCCchHHHHHHHHHHHHhc--CCcEEEEec
Confidence            55667799999999999999999998774321  335565554

>2xau_A PRE-mRNA-splicing factor ATP-dependent RNA helica; hydrolase, ribosome biogenesis, ATPase, ATP-binding, OB-fold; HET: ADP; 1.90A {Saccharomyces cerevisiae} PDB: 3kx2_B*

Probab=94.32  E-value=0.13  Score=58.82  Aligned_cols=24  Identities=25%  Similarity=0.367  Sum_probs=19.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+++.||+|+|||+++..+...
T Consensus       109 ~~~vii~gpTGSGKTtllp~ll~~  132 (773)
T 2xau_A          109 NQIMVFVGETGSGKTTQIPQFVLF  132 (773)
T ss_dssp             CSEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHH
Confidence            457999999999999977666543

>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=94.32  E-value=0.038  Score=61.63  Aligned_cols=41  Identities=22%  Similarity=0.343  Sum_probs=31.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      .+..|+|.|.||+||||+|+++++.+...   +.+++.++...+
T Consensus        51 ~g~lIvLtGlsGSGKSTlAr~La~~L~~~---G~~~v~lDgD~i   91 (630)
T 1x6v_B           51 RGCTVWLTGLSGAGKTTVSMALEEYLVCH---GIPCYTLDGDNI   91 (630)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEESHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHHHhc---CCeEEEechHHh
Confidence            46679999999999999999999987322   445777765544

>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=94.24  E-value=0.025  Score=56.60  Aligned_cols=25  Identities=24%  Similarity=0.323  Sum_probs=22.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.-|.|.|++|+||||+|+.++ .+
T Consensus        74 ~~~iI~I~G~~GSGKSTva~~La-~l   98 (281)
T 2f6r_A           74 GLYVLGLTGISGSGKSSVAQRLK-NL   98 (281)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHH-HH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHH-HC
Confidence            45679999999999999999999 45

>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=94.21  E-value=0.052  Score=60.00  Aligned_cols=42  Identities=17%  Similarity=0.238  Sum_probs=31.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC-cCeEEechhhH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG-VPLMYVPLEVV  364 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~-~~~~~i~~~~l  364 (567)
                      ..+..|+|.|.||+||||+|+++++.+...   + .+++.++...+
T Consensus       394 q~~~~I~l~GlsGSGKSTiA~~La~~L~~~---G~~~~~~lD~D~i  436 (573)
T 1m8p_A          394 TQGFTIFLTGYMNSGKDAIARALQVTLNQQ---GGRSVSLLLGDTV  436 (573)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHHHH---CSSCEEEEEHHHH
T ss_pred             ccceEEEeecCCCCCHHHHHHHHHHHhccc---CCceEEEECcHHH
Confidence            445678999999999999999999998321   1 55677765544

>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=94.20  E-value=0.028  Score=53.18  Aligned_cols=29  Identities=24%  Similarity=0.510  Sum_probs=24.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+||||++++|+....
T Consensus        17 i~~Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           17 AAVGRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             --CCCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            45566788999999999999999999873

>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=94.11  E-value=0.033  Score=56.96  Aligned_cols=25  Identities=28%  Similarity=0.493  Sum_probs=22.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +-++|.||+|+|||+|+..+++.++
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~   28 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLN   28 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTT
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCc
Confidence            4678999999999999999999874

>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=94.07  E-value=0.087  Score=56.18  Aligned_cols=28  Identities=29%  Similarity=0.456  Sum_probs=24.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..++|.|++|+||||++..++..+.
T Consensus        97 ~~~~vI~ivG~~GvGKTTla~~La~~l~  124 (432)
T 2v3c_C           97 KKQNVILLVGIQGSGKTTTAAKLARYIQ  124 (432)
T ss_dssp             SSCCCEEEECCSSSSTTHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3467899999999999999999998763

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.00  E-value=0.031  Score=57.70  Aligned_cols=25  Identities=24%  Similarity=0.396  Sum_probs=22.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .-++|.||+|+|||++|+.|+..++
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~   32 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFN   32 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTT
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcC
Confidence            4688999999999999999999984

>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=93.98  E-value=0.032  Score=56.74  Aligned_cols=28  Identities=25%  Similarity=0.446  Sum_probs=25.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+++..+.|+||+|+|||||++.|+..+
T Consensus       123 i~~Ge~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          123 IPKKNCLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             CTTCSEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             ecCCCEEEEECCCCCcHHHHHHHHhhhc
Confidence            6777889999999999999999999987

>1g41_A Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dependent proteolysis, chaperone; HET: ADP; 2.30A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1g3i_A* 1im2_A* 1kyi_A* 1g4a_E* 1g4b_E 1yyf_A* 1do0_A* 1do2_A* 1e94_E* 1hqy_E* 1ht1_E* 1ht2_E*

Probab=93.89  E-value=0.0092  Score=63.89  Aligned_cols=58  Identities=21%  Similarity=0.148  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHhhcCcccCCcEEEEEe-eCCCCCCChHHHh--ccceEEEecCCCHH-HHHHHH
Q 047219          411 ATRRILSVLLRQIDGFEQDKKVVVIAA-TNRKQDLDPALIS--RFDSMITFGLPDHE-NRQEIA  470 (567)
Q Consensus       411 ~~~~vl~~LL~~ld~~~~~~~viVIaa-TN~~~~Ld~aL~s--Rf~~~I~i~~P~~~-eR~eIL  470 (567)
                      ...+++++|+..||++.....+  +++ ||+++.|+++|++  |||..|++++|+.. .|.+|+
T Consensus       127 ~e~rvl~~LL~~~dg~~~~~~v--~a~~TN~~~~ld~aL~rggr~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          127 AEERILDALLPPAKNQWGEVEN--HDSHSSTRQAFRKKLREGQLDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             ----------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHhhcccccccc--ccccccCHHHHHHHHHcCCCcceEEEEcCCCCccchhhhh
Confidence            4567888999999988665554  455 9999999999998  99999999999987 677775

>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=93.89  E-value=0.035  Score=55.52  Aligned_cols=28  Identities=21%  Similarity=0.267  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++.-++|.||||+|||+|++.++...
T Consensus        32 l~~G~~~~i~G~~G~GKTTl~~~ia~~~   59 (296)
T 1cr0_A           32 ARGGEVIMVTSGSGMGKSTFVRQQALQW   59 (296)
T ss_dssp             BCTTCEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            5667789999999999999999999876

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=93.87  E-value=0.036  Score=53.95  Aligned_cols=29  Identities=28%  Similarity=0.392  Sum_probs=24.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+-|.||+|+||||+++.|+..++
T Consensus        22 i~~g~iigI~G~~GsGKSTl~k~L~~~lG   50 (245)
T 2jeo_A           22 SMRPFLIGVSGGTASGKSTVCEKIMELLG   50 (245)
T ss_dssp             -CCSEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHhc
Confidence            45556688999999999999999999873

>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=93.84  E-value=0.037  Score=53.44  Aligned_cols=28  Identities=18%  Similarity=0.350  Sum_probs=24.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-+.|.||+|+|||||.++++....
T Consensus        14 ~~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           14 AQGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            4566788999999999999999998874

>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=93.84  E-value=0.016  Score=54.69  Aligned_cols=24  Identities=21%  Similarity=0.360  Sum_probs=21.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      -+.|.|++|+||||+++.++..+.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHH
Confidence            378999999999999999999884

>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=93.84  E-value=0.19  Score=57.74  Aligned_cols=25  Identities=28%  Similarity=0.408  Sum_probs=21.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .+.-+.|.||.|+||||+.|.++..
T Consensus       606 ~g~i~~ItGpNGsGKSTlLr~iagl  630 (800)
T 1wb9_A          606 QRRMLIITGPNMGGKSTYMRQTALI  630 (800)
T ss_dssp             SSCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHH
Confidence            4456889999999999999999875

>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=93.76  E-value=0.027  Score=53.82  Aligned_cols=26  Identities=27%  Similarity=0.399  Sum_probs=23.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..++|.||+|+|||++|..+++..
T Consensus        33 ~g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           33 YGLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TTEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHhC
Confidence            46789999999999999999999876

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=93.74  E-value=0.021  Score=54.96  Aligned_cols=28  Identities=25%  Similarity=0.411  Sum_probs=18.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHH-HHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIA-NQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA-~~l  346 (567)
                      ..++.-+.|.||+|+||||+++.++ ...
T Consensus        24 v~~G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           24 KSVGVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             EECCCEEEEECSCC----CHHHHHHC---
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3456678899999999999999999 765

>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=93.70  E-value=0.16  Score=48.86  Aligned_cols=25  Identities=12%  Similarity=-0.027  Sum_probs=19.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..-.+++|+.|+|||+.+-.++...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~   52 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRT   52 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHH
Confidence            3456689999999998877776655

>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=93.65  E-value=0.044  Score=53.13  Aligned_cols=28  Identities=29%  Similarity=0.478  Sum_probs=24.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      .+.-+.|.|+||+||||+++.+++.+..
T Consensus        25 ~g~~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           25 MSAFITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            4567889999999999999999999853

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=93.58  E-value=0.11  Score=56.93  Aligned_cols=45  Identities=24%  Similarity=0.334  Sum_probs=34.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      .+..++|.|++|+||||+|+.+++.+...   +.++..++...+....
T Consensus       371 ~~~~I~l~G~~GsGKSTia~~La~~L~~~---G~~~~~ld~D~ir~~l  415 (546)
T 2gks_A          371 QGFCVWLTGLPCAGKSTIAEILATMLQAR---GRKVTLLDGDVVRTHL  415 (546)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEECHHHHHHHT
T ss_pred             cceEEEccCCCCCCHHHHHHHHHHHhhhc---CCeEEEECchHhhhhh
Confidence            35678999999999999999999987432   4456777776654443

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=93.55  E-value=0.1  Score=51.99  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=19.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+++++.+|+|+|||..+-..+-..
T Consensus        31 ~~~~lv~~~TGsGKT~~~~~~~~~~   55 (337)
T 2z0m_A           31 GKNVVVRAKTGSGKTAAYAIPILEL   55 (337)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCcHHHHHHHHHHhh
Confidence            3579999999999998776655544

>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=93.53  E-value=0.046  Score=57.06  Aligned_cols=28  Identities=21%  Similarity=0.472  Sum_probs=24.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+...++|.||+|+||||++++++..+.
T Consensus       134 ~~g~~i~ivG~~GsGKTTll~~l~~~~~  161 (372)
T 2ewv_A          134 RKMGLILVTGPTGSGKSTTIASMIDYIN  161 (372)
T ss_dssp             SSSEEEEEECSSSSSHHHHHHHHHHHHH
T ss_pred             cCCCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            4566799999999999999999998763

>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=93.49  E-value=0.094  Score=59.08  Aligned_cols=19  Identities=32%  Similarity=0.447  Sum_probs=17.1

Q ss_pred             CceEEeeCCCCCcHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAr  340 (567)
                      ..++++.||+|+|||+.+-
T Consensus        40 ~~~~lv~apTGsGKT~~~~   58 (702)
T 2p6r_A           40 GKNLLLAMPTAAGKTLLAE   58 (702)
T ss_dssp             CSCEEEECSSHHHHHHHHH
T ss_pred             CCcEEEEcCCccHHHHHHH
Confidence            5789999999999999874

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=93.41  E-value=0.18  Score=48.71  Aligned_cols=18  Identities=28%  Similarity=0.425  Sum_probs=15.3

Q ss_pred             ceEEeeCCCCCcHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAr  340 (567)
                      +.+++.+|+|+|||..+-
T Consensus        61 ~~~l~~a~TGsGKT~~~~   78 (253)
T 1wrb_A           61 RDIMACAQTGSGKTAAFL   78 (253)
T ss_dssp             CCEEEECCTTSSHHHHHH
T ss_pred             CCEEEECCCCChHHHHHH
Confidence            579999999999998543

>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=93.39  E-value=0.048  Score=57.56  Aligned_cols=26  Identities=19%  Similarity=0.439  Sum_probs=23.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +.-++|.||+|+|||+|+..++..++
T Consensus         2 ~~~i~i~GptgsGKttla~~La~~~~   27 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQKFN   27 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHHHHT
T ss_pred             CcEEEEECcchhhHHHHHHHHHHHCC
Confidence            34678999999999999999999874

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=93.39  E-value=0.05  Score=51.64  Aligned_cols=29  Identities=21%  Similarity=0.326  Sum_probs=25.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeE
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLM  357 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~  357 (567)
                      .-|.|.|++|||||++++.+|+.+      +++|+
T Consensus         7 ~iI~i~g~~GsGk~ti~~~la~~l------g~~~~   35 (201)
T 3fdi_A            7 IIIAIGREFGSGGHLVAKKLAEHY------NIPLY   35 (201)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHT------TCCEE
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHh------CcCEE
Confidence            468899999999999999999999      66666

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=93.28  E-value=0.056  Score=54.82  Aligned_cols=29  Identities=24%  Similarity=0.430  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+||||+++.++..+.
T Consensus        97 ~~~g~vi~lvG~nGsGKTTll~~Lag~l~  125 (302)
T 3b9q_A           97 FRKPAVIMIVGVNGGGKTTSLGKLAHRLK  125 (302)
T ss_dssp             SSSCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             cCCCcEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            45677899999999999999999999873

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=93.24  E-value=0.085  Score=48.38  Aligned_cols=27  Identities=22%  Similarity=0.509  Sum_probs=23.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....+++.|++|+|||+|..++....
T Consensus        46 ~~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           46 SYQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            445679999999999999999998754

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.21  E-value=0.052  Score=51.12  Aligned_cols=23  Identities=35%  Similarity=0.635  Sum_probs=21.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.|.||+|+||||+++.++..+
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhc
Confidence            47899999999999999999886

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=93.19  E-value=0.24  Score=54.38  Aligned_cols=25  Identities=32%  Similarity=0.298  Sum_probs=20.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+++++|+|+|||..+-.++..+
T Consensus       198 ~~~~ll~~~TGsGKT~~~~~~~~~l  222 (590)
T 3h1t_A          198 KKRSLITMATGTGKTVVAFQISWKL  222 (590)
T ss_dssp             CSEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CCceEEEecCCCChHHHHHHHHHHH
Confidence            4678999999999999987777665

>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=93.18  E-value=0.059  Score=54.89  Aligned_cols=29  Identities=24%  Similarity=0.321  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||++.|+..+.
T Consensus        87 ~~~g~ivgI~G~sGsGKSTL~~~L~gll~  115 (312)
T 3aez_A           87 RPVPFIIGVAGSVAVGKSTTARVLQALLA  115 (312)
T ss_dssp             SCCCEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCchHHHHHHHHHhhcc
Confidence            35566788999999999999999999874

>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=93.06  E-value=0.061  Score=54.61  Aligned_cols=27  Identities=30%  Similarity=0.383  Sum_probs=24.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+..+.|.||+|+||||+++.++..+.
T Consensus       101 ~g~vi~lvG~nGsGKTTll~~Lagll~  127 (304)
T 1rj9_A          101 KGRVVLVVGVNGVGKTTTIAKLGRYYQ  127 (304)
T ss_dssp             SSSEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHHH
Confidence            466789999999999999999998874

>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=93.05  E-value=0.11  Score=52.52  Aligned_cols=28  Identities=25%  Similarity=0.398  Sum_probs=24.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-+.|.||+|+||||+++.|+..+.
T Consensus        78 ~~g~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           78 RIPYIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             CCCEEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4556788999999999999999999874

>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=93.01  E-value=0.18  Score=49.45  Aligned_cols=18  Identities=33%  Similarity=0.412  Sum_probs=15.6

Q ss_pred             ceEEeeCCCCCcHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAr  340 (567)
                      +.+++.+|+|+|||..+-
T Consensus        92 ~~~lv~a~TGsGKT~~~~  109 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAFL  109 (262)
T ss_dssp             CCCEECCCTTSCHHHHHH
T ss_pred             CcEEEEccCCCCchHHHH
Confidence            579999999999998654

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=93.00  E-value=0.063  Score=52.36  Aligned_cols=24  Identities=29%  Similarity=0.522  Sum_probs=21.6

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+-|.|+||+||||+|+.|++.+
T Consensus         9 ~~~~~~G~pGsGKsT~a~~L~~~~   32 (230)
T 3gmt_A            9 MRLILLGAPGAGKGTQANFIKEKF   32 (230)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceeeECCCCCCHHHHHHHHHHHh
Confidence            346689999999999999999988

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=92.94  E-value=0.69  Score=47.97  Aligned_cols=22  Identities=27%  Similarity=0.466  Sum_probs=17.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA  343 (567)
                      .+.+++.+|+|+|||+.+-..+
T Consensus        36 ~~~~lv~apTGsGKT~~~l~~~   57 (414)
T 3oiy_A           36 GKSFTMVAPTGVGKTTFGMMTA   57 (414)
T ss_dssp             TCCEECCSCSSSSHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHH
Confidence            4689999999999999554443

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=92.88  E-value=0.36  Score=49.82  Aligned_cols=56  Identities=18%  Similarity=0.142  Sum_probs=32.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC  338 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L  338 (567)
                      +..+|+++.=.+...+.+..   .-+..|..++...-.  .   ....+.+++.+|+|+|||+.
T Consensus        13 ~~~~f~~~~l~~~l~~~l~~---~~~~~~~~~Q~~~i~--~---i~~~~~~lv~a~TGsGKT~~   68 (417)
T 2i4i_A           13 HIESFSDVEMGEIIMGNIEL---TRYTRPTPVQKHAIP--I---IKEKRDLMACAQTGSGKTAA   68 (417)
T ss_dssp             CCSSGGGSCCCHHHHHHHHH---HTCCSCCHHHHHHHH--H---HHTTCCEEEECCTTSCHHHH
T ss_pred             ccCCHhhCCCCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HccCCCEEEEcCCCCHHHHH
Confidence            34568888555555555543   233344444432111  0   12346899999999999974

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=92.88  E-value=0.33  Score=51.33  Aligned_cols=22  Identities=23%  Similarity=0.374  Sum_probs=17.6

Q ss_pred             CceEEeeCCCCCcHHHHH-HHHH
Q 047219          322 PRAVLFEGPPGTGKTSCA-RVIA  343 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LA-raIA  343 (567)
                      .+.+|+.||+|+|||+.+ -++.
T Consensus         2 g~~~lv~a~TGsGKT~~~l~~~l   24 (431)
T 2v6i_A            2 RELTVLDLHPGAGKTRRVLPQLV   24 (431)
T ss_dssp             CCEEEEECCTTSCTTTTHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHH
Confidence            468999999999999875 4444

>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=92.84  E-value=0.73  Score=49.96  Aligned_cols=19  Identities=32%  Similarity=0.371  Sum_probs=16.4

Q ss_pred             CCceEEeeCCCCCcHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCA  339 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LA  339 (567)
                      ..+.+++.+|+|+|||+.+
T Consensus       110 ~~~~~lv~apTGsGKTl~~  128 (563)
T 3i5x_A          110 EDHDVIARAKTGTGKTFAF  128 (563)
T ss_dssp             SSEEEEEECCTTSCHHHHH
T ss_pred             CCCeEEEECCCCCCccHHH
Confidence            4678999999999999853

>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=92.84  E-value=0.044  Score=53.37  Aligned_cols=28  Identities=25%  Similarity=0.404  Sum_probs=24.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++.-+.|.||+|+|||||.+.|+...
T Consensus        28 i~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   55 (235)
T 3tif_A           28 IKEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (235)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            5667789999999999999999999765

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=92.78  E-value=0.051  Score=54.70  Aligned_cols=40  Identities=13%  Similarity=0.213  Sum_probs=25.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      +.-|.|.|++|+||||+|+.+++.++..   +..+..++...+
T Consensus         5 ~~iIgItG~sGSGKSTva~~L~~~lg~~---~~~~~vI~~D~~   44 (290)
T 1a7j_A            5 HPIISVTGSSGAGTSTVKHTFDQIFRRE---GVKAVSIEGDAF   44 (290)
T ss_dssp             SCEEEEESCC---CCTHHHHHHHHHHHH---TCCEEEEEGGGG
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHhhc---CCCeeEeecchh
Confidence            3468899999999999999999977311   233455554443

>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=92.72  E-value=0.085  Score=50.61  Aligned_cols=29  Identities=28%  Similarity=0.403  Sum_probs=24.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      .+.-|.|.|++|+||||+++.+++.+...
T Consensus         5 ~g~~i~~eG~~gsGKsT~~~~l~~~l~~~   33 (213)
T 4edh_A            5 TGLFVTLEGPEGAGKSTNRDYLAERLRER   33 (213)
T ss_dssp             CCEEEEEECSTTSSHHHHHHHHHHHHHTT
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            35568899999999999999999988544

>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=92.70  E-value=0.047  Score=53.23  Aligned_cols=28  Identities=21%  Similarity=0.221  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++.-+.|.||+|+|||||++.|+...
T Consensus        28 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           28 IPEGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            5667789999999999999999999875

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=92.68  E-value=0.059  Score=50.36  Aligned_cols=25  Identities=20%  Similarity=0.363  Sum_probs=22.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...++||.|++|+|||++|.++...
T Consensus        15 ~G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           15 DKMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            4679999999999999999999874

>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=92.65  E-value=0.32  Score=54.85  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=18.3

Q ss_pred             CceEEeeCCCCCcHHHHH-HHHH
Q 047219          322 PRAVLFEGPPGTGKTSCA-RVIA  343 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LA-raIA  343 (567)
                      ..++++.||+|+|||+.+ -++.
T Consensus        39 ~~~~lv~apTGsGKT~~~~l~il   61 (720)
T 2zj8_A           39 GKNALISIPTASGKTLIAEIAMV   61 (720)
T ss_dssp             TCEEEEECCGGGCHHHHHHHHHH
T ss_pred             CCcEEEEcCCccHHHHHHHHHHH
Confidence            678999999999999987 3443

>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=92.62  E-value=0.28  Score=57.84  Aligned_cols=23  Identities=30%  Similarity=0.372  Sum_probs=20.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      +..++|.||.|+||||+.|.++-
T Consensus       789 g~i~~ItGpNgsGKSTlLr~iGl  811 (1022)
T 2o8b_B          789 AYCVLVTGPNMGGKSTLMRQAGL  811 (1022)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHH
Confidence            46789999999999999999943

>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=92.61  E-value=0.078  Score=49.18  Aligned_cols=26  Identities=19%  Similarity=0.031  Sum_probs=22.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..-+.|.|++|+||||++..++..+.
T Consensus         4 ~~~i~i~G~sGsGKTTl~~~L~~~l~   29 (169)
T 1xjc_A            4 MNVWQVVGYKHSGKTTLMEKWVAAAV   29 (169)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhhH
Confidence            34688999999999999999998874

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=92.61  E-value=0.076  Score=55.22  Aligned_cols=29  Identities=24%  Similarity=0.430  Sum_probs=25.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+||||+++.|+..+.
T Consensus       154 ~~~g~vi~lvG~nGsGKTTll~~Lag~l~  182 (359)
T 2og2_A          154 FRKPAVIMIVGVNGGGKTTSLGKLAHRLK  182 (359)
T ss_dssp             SSSSEEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             cCCCeEEEEEcCCCChHHHHHHHHHhhcc
Confidence            45677899999999999999999999873

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=92.51  E-value=0.041  Score=53.16  Aligned_cols=28  Identities=18%  Similarity=0.285  Sum_probs=24.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++.-+.|.||+|+|||||.++|+...
T Consensus        27 i~~Ge~~~iiG~nGsGKSTLl~~l~Gl~   54 (224)
T 2pcj_A           27 VKKGEFVSIIGASGSGKSTLLYILGLLD   54 (224)
T ss_dssp             EETTCEEEEEECTTSCHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4566778899999999999999999765

>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=92.47  E-value=0.082  Score=54.27  Aligned_cols=29  Identities=31%  Similarity=0.527  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+||||+++.++..+.
T Consensus       126 ~~~g~vi~lvG~nGaGKTTll~~Lag~l~  154 (328)
T 3e70_C          126 AEKPYVIMFVGFNGSGKTTTIAKLANWLK  154 (328)
T ss_dssp             SCSSEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            35677899999999999999999998874

>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=92.39  E-value=0.074  Score=48.74  Aligned_cols=24  Identities=25%  Similarity=0.345  Sum_probs=21.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      -.+|+||.|+|||+++++|+-.+.
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHc
Confidence            678999999999999999998874

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=92.37  E-value=0.072  Score=51.51  Aligned_cols=26  Identities=23%  Similarity=0.470  Sum_probs=23.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +.-+.|.|++|+||||+++.+++.+.
T Consensus         2 ~~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            2 PRRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            45688999999999999999999984

>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=92.33  E-value=0.056  Score=52.84  Aligned_cols=28  Identities=21%  Similarity=0.445  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++..+.|.||+|+|||||.+.|+...
T Consensus        25 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   52 (243)
T 1mv5_A           25 AQPNSIIAFAGPSGGGKSTIFSLLERFY   52 (243)
T ss_dssp             ECTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            5677789999999999999999999865

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=92.31  E-value=0.057  Score=53.50  Aligned_cols=29  Identities=21%  Similarity=0.314  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.++|+....
T Consensus        29 i~~Ge~~~liG~nGsGKSTLlk~l~Gl~~   57 (262)
T 1b0u_A           29 ARAGDVISIIGSSGSGKSTFLRCINFLEK   57 (262)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56677789999999999999999998763

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.23  E-value=0.068  Score=52.32  Aligned_cols=27  Identities=30%  Similarity=0.485  Sum_probs=23.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ... .-+.|.||+|+|||||.++|+...
T Consensus        22 i~~-e~~~liG~nGsGKSTLl~~l~Gl~   48 (240)
T 2onk_A           22 MGR-DYCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             ECS-SEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             ECC-EEEEEECCCCCCHHHHHHHHhCCC
Confidence            456 778899999999999999999875

>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=92.21  E-value=0.2  Score=60.71  Aligned_cols=30  Identities=20%  Similarity=0.329  Sum_probs=26.5

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+++..+.|.||+|+||||+++.|...+.
T Consensus       440 ~i~~G~~vaivG~sGsGKSTll~ll~~~~~  469 (1321)
T 4f4c_A          440 RVNAGQTVALVGSSGCGKSTIISLLLRYYD  469 (1321)
T ss_dssp             EECTTCEEEEEECSSSCHHHHHHHHTTSSC
T ss_pred             eecCCcEEEEEecCCCcHHHHHHHhccccc
Confidence            357778899999999999999999998774

>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=92.20  E-value=0.071  Score=52.98  Aligned_cols=27  Identities=22%  Similarity=0.425  Sum_probs=24.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..++.-+.|.||+|+|||||++.|+..
T Consensus        43 i~~Ge~~~l~G~NGsGKSTLlk~l~Gl   69 (267)
T 2zu0_C           43 VHPGEVHAIMGPNGSGKSTLSATLAGR   69 (267)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            566778999999999999999999986

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=92.15  E-value=0.32  Score=58.13  Aligned_cols=24  Identities=33%  Similarity=0.219  Sum_probs=19.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA  343 (567)
                      ..|..+|++||+|+|||.++-..+
T Consensus       622 g~p~d~ll~~~TGsGKT~val~aa  645 (1151)
T 2eyq_A          622 PLAMDRLVCGDVGFGKTEVAMRAA  645 (1151)
T ss_dssp             SSCCEEEEECCCCTTTHHHHHHHH
T ss_pred             CCcCcEEEECCCCCCHHHHHHHHH
Confidence            456789999999999998876443

>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=92.15  E-value=0.46  Score=54.37  Aligned_cols=25  Identities=36%  Similarity=0.597  Sum_probs=20.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA  343 (567)
                      ...+.++|+.||+|+|||..+-..+
T Consensus       386 ~~~~~~~Ll~a~TGSGKTlvall~i  410 (780)
T 1gm5_A          386 SEKPMNRLLQGDVGSGKTVVAQLAI  410 (780)
T ss_dssp             SSSCCCCEEECCSSSSHHHHHHHHH
T ss_pred             ccCCCcEEEEcCCCCCHHHHHHHHH
Confidence            4556789999999999998775544

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=92.13  E-value=0.93  Score=49.60  Aligned_cols=19  Identities=32%  Similarity=0.371  Sum_probs=16.3

Q ss_pred             CCceEEeeCCCCCcHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCA  339 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LA  339 (567)
                      ..+.+++.+|+|+|||..+
T Consensus        59 ~~~dvlv~apTGsGKTl~~   77 (579)
T 3sqw_A           59 EDHDVIARAKTGTGKTFAF   77 (579)
T ss_dssp             SSEEEEEECCTTSCHHHHH
T ss_pred             CCCeEEEEcCCCcHHHHHH
Confidence            4678999999999999853

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=92.07  E-value=0.093  Score=50.68  Aligned_cols=26  Identities=15%  Similarity=0.089  Sum_probs=19.9

Q ss_pred             CCceEEeeCCCCCcHHH-HHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTS-CARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~-LAraIA~~l  346 (567)
                      .+.-.+++||-|+|||+ |.+.+.+..
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~~~r~~   53 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRRLRRGI   53 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CceEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34557889999999999 667766554

>3ch4_B Pmkase, phosphomevalonate kinase; parallel beta-sheet with the strand order 23145, walker A motif, cholesterol biosynthesis, lipid synthesis; 1.76A {Homo sapiens}

Probab=92.05  E-value=0.64  Score=44.26  Aligned_cols=28  Identities=18%  Similarity=0.318  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+..-++|+|.||+||+++|+.+.+.+
T Consensus         8 ~~~~~II~itGk~~SGKd~va~~l~~~~   35 (202)
T 3ch4_B            8 GAPRLVLLFSGKRKSGKDFVTEALQSRL   35 (202)
T ss_dssp             CCCSEEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             cCCCEEEEEECCCCCChHHHHHHHHHHc
Confidence            4577789999999999999999998866

>1g8f_A Sulfate adenylyltransferase; alpha-beta protein, beta-barrel, rossmann-fold, kinase fold; 1.95A {Saccharomyces cerevisiae} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1g8g_A* 1g8h_A* 1j70_A 1jec_A 1jed_A* 1jee_A*

Probab=91.99  E-value=0.11  Score=56.42  Aligned_cols=28  Identities=0%  Similarity=-0.028  Sum_probs=24.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      .+..++|.|.+|+||||+++++++.+..
T Consensus       394 ~~~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          394 QGFSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cceEEEecccCCCCHHHHHHHHHHHHHH
Confidence            4467999999999999999999999953

>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=91.99  E-value=0.058  Score=53.25  Aligned_cols=29  Identities=31%  Similarity=0.480  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.++|+....
T Consensus        30 i~~Ge~~~liG~nGsGKSTLlk~l~Gl~~   58 (257)
T 1g6h_A           30 VNKGDVTLIIGPNGSGKSTLINVITGFLK   58 (257)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EeCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45667788999999999999999998763

>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=91.94  E-value=0.067  Score=52.57  Aligned_cols=27  Identities=22%  Similarity=0.508  Sum_probs=24.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..++.-+.|.||+|+|||||++.|+..
T Consensus        26 i~~Ge~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           26 VPKGEVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            456677899999999999999999985

>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=91.94  E-value=0.056  Score=52.01  Aligned_cols=28  Identities=32%  Similarity=0.527  Sum_probs=24.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+.|.||+|+|||||.++++...
T Consensus        32 i~~Ge~~~iiG~NGsGKSTLlk~l~Gl~   59 (214)
T 1sgw_A           32 IEKGNVVNFHGPNGIGKTTLLKTISTYL   59 (214)
T ss_dssp             EETTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            4566778899999999999999999865

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=91.94  E-value=0.066  Score=52.97  Aligned_cols=28  Identities=18%  Similarity=0.278  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++..+.|.||+|+|||||++.|+...
T Consensus        43 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~   70 (260)
T 2ghi_A           43 IPSGTTCALVGHTGSGKSTIAKLLYRFY   70 (260)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhccC
Confidence            5677789999999999999999999765

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=91.92  E-value=0.1  Score=49.24  Aligned_cols=27  Identities=30%  Similarity=0.303  Sum_probs=23.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ....++|.|.+|+|||+++..++..+.
T Consensus        29 ~~~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           29 GTVAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             TCEEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CceEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            346789999999999999999998863

>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=91.91  E-value=0.068  Score=53.07  Aligned_cols=29  Identities=24%  Similarity=0.422  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||++.|+....
T Consensus        47 i~~Gei~~liG~NGsGKSTLlk~l~Gl~~   75 (263)
T 2olj_A           47 IREGEVVVVIGPSGSGKSTFLRCLNLLED   75 (263)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEEcCCCCcHHHHHHHHHcCCC
Confidence            56677889999999999999999998763

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=91.91  E-value=0.062  Score=59.12  Aligned_cols=43  Identities=28%  Similarity=0.414  Sum_probs=30.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ..+..+.|.|++|+||||++++|+..+....  +..+..++...+
T Consensus       367 ~~G~iI~LiG~sGSGKSTLar~La~~L~~~~--G~~i~~lDgD~~  409 (552)
T 3cr8_A          367 RQGFTVFFTGLSGAGKSTLARALAARLMEMG--GRCVTLLDGDIV  409 (552)
T ss_dssp             GSCEEEEEEESSCHHHHHHHHHHHHHHHTTC--SSCEEEESSHHH
T ss_pred             ccceEEEEECCCCChHHHHHHHHHHhhcccC--CceEEEECCcHH
Confidence            4567799999999999999999999884210  123444555544

>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=91.90  E-value=0.07  Score=55.49  Aligned_cols=28  Identities=25%  Similarity=0.376  Sum_probs=24.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....-+.|.||+|||||||.++|+...
T Consensus        27 i~~Ge~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           27 LDPGEILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             EcCCCEEEEECCCCchHHHHHHHHhcCC
Confidence            4566778899999999999999999865

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=91.85  E-value=0.068  Score=53.24  Aligned_cols=29  Identities=24%  Similarity=0.405  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||++.|+....
T Consensus        42 i~~Ge~~~i~G~nGsGKSTLlk~l~Gl~~   70 (271)
T 2ixe_A           42 LYPGKVTALVGPNGSGKSTVAALLQNLYQ   70 (271)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56677899999999999999999998763

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=91.85  E-value=0.11  Score=50.18  Aligned_cols=31  Identities=16%  Similarity=0.273  Sum_probs=26.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      ..-|.|.|++|||||++++.+|+.+      +++|+.
T Consensus        14 ~~iI~i~g~~gsGk~~i~~~la~~l------g~~~~d   44 (223)
T 3hdt_A           14 NLIITIEREYGSGGRIVGKKLAEEL------GIHFYD   44 (223)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHHH------TCEEEC
T ss_pred             CeEEEEeCCCCCCHHHHHHHHHHHc------CCcEEc
Confidence            4568899999999999999999999      655543

>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=91.83  E-value=0.11  Score=56.35  Aligned_cols=29  Identities=31%  Similarity=0.430  Sum_probs=25.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.|++|+||||+++.|+..+.
T Consensus       290 i~~GeVI~LVGpNGSGKTTLl~~LAgll~  318 (503)
T 2yhs_A          290 GKAPFVILMVGVNGVGKTTTIGKLARQFE  318 (503)
T ss_dssp             SCTTEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccCCeEEEEECCCcccHHHHHHHHHHHhh
Confidence            45677899999999999999999998773

>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=91.81  E-value=0.11  Score=48.19  Aligned_cols=26  Identities=23%  Similarity=0.229  Sum_probs=22.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..-+.|.|++|+||||+++.+...+.
T Consensus         6 ~~~i~i~G~sGsGKTTl~~~l~~~l~   31 (174)
T 1np6_A            6 IPLLAFAAWSGTGKTTLLKKLIPALC   31 (174)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             ceEEEEEeCCCCCHHHHHHHHHHhcc
Confidence            45688999999999999999998763

>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=91.77  E-value=0.062  Score=52.06  Aligned_cols=29  Identities=28%  Similarity=0.376  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||.+.|+....
T Consensus        31 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           31 IERGQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            45677889999999999999999998763

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=91.76  E-value=0.92  Score=47.73  Aligned_cols=56  Identities=13%  Similarity=0.124  Sum_probs=32.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC  338 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L  338 (567)
                      +-.+|+++.-.+...+.|.+   .-+..|..++...-..     ....+.+++.+|+|+|||+.
T Consensus        54 ~~~~f~~~~l~~~l~~~l~~---~g~~~pt~iQ~~ai~~-----i~~g~d~i~~a~TGsGKT~a  109 (434)
T 2db3_A           54 PIQHFTSADLRDIIIDNVNK---SGYKIPTPIQKCSIPV-----ISSGRDLMACAQTGSGKTAA  109 (434)
T ss_dssp             CCCCGGGSCCCHHHHHHHHH---TTCCSCCHHHHHHHHH-----HHTTCCEEEECCTTSSHHHH
T ss_pred             CcCChhhcCCCHHHHHHHHH---cCCCCCCHHHHHHHHH-----HhcCCCEEEECCCCCCchHH
Confidence            44578887555555554433   2344444444322111     12347899999999999984

>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=91.73  E-value=0.062  Score=52.78  Aligned_cols=29  Identities=17%  Similarity=0.261  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||++.|+....
T Consensus        32 i~~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   60 (247)
T 2ff7_A           32 IKQGEVIGIVGRSGSGKSTLTKLIQRFYI   60 (247)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            45667789999999999999999998763

>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=91.72  E-value=0.062  Score=52.45  Aligned_cols=28  Identities=32%  Similarity=0.404  Sum_probs=24.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+.|.||+|+|||||.+.|+...
T Consensus        29 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~   56 (240)
T 1ji0_A           29 VPRGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            4566778899999999999999999875

>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=91.69  E-value=0.075  Score=52.54  Aligned_cols=29  Identities=28%  Similarity=0.403  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||.++|+....
T Consensus        38 i~~Gei~~l~G~NGsGKSTLlk~l~Gl~~   66 (256)
T 1vpl_A           38 IEEGEIFGLIGPNGAGKTTTLRIISTLIK   66 (256)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCcEEEEECCCCCCHHHHHHHHhcCCC
Confidence            56677899999999999999999998753

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=91.65  E-value=0.086  Score=54.90  Aligned_cols=29  Identities=24%  Similarity=0.316  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.++|+....
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           26 IKDGEFMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCchHHHHHHHHhcCCC
Confidence            45667788999999999999999998753

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=91.65  E-value=0.11  Score=52.98  Aligned_cols=29  Identities=34%  Similarity=0.433  Sum_probs=25.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..++|.|++|+||||++..+|..+.
T Consensus       102 ~~~~~vI~ivG~~G~GKTT~~~~LA~~l~  130 (320)
T 1zu4_A          102 ENRLNIFMLVGVNGTGKTTSLAKMANYYA  130 (320)
T ss_dssp             TTSCEEEEEESSTTSSHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45677899999999999999999998874

>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=91.61  E-value=0.087  Score=55.22  Aligned_cols=29  Identities=34%  Similarity=0.550  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|||||||.++|+....
T Consensus        26 i~~Ge~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           26 IHEGEFVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEEcCCCchHHHHHHHHHcCCC
Confidence            45667788999999999999999998763

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.61  E-value=0.076  Score=52.71  Aligned_cols=29  Identities=24%  Similarity=0.448  Sum_probs=25.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||.+.|+....
T Consensus        30 i~~Ge~~~liG~nGsGKSTLl~~i~Gl~~   58 (266)
T 2yz2_A           30 INEGECLLVAGNTGSGKSTLLQIVAGLIE   58 (266)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            56677889999999999999999998653

>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=91.61  E-value=0.086  Score=54.82  Aligned_cols=28  Identities=29%  Similarity=0.372  Sum_probs=24.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+.|.||+|+|||||.++|+...
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr~iaGl~   53 (359)
T 2yyz_A           26 VKDGEFVALLGPSGCGKTTTLLMLAGIY   53 (359)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             EcCCCEEEEEcCCCchHHHHHHHHHCCC
Confidence            4566778899999999999999999865

>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=91.53  E-value=0.09  Score=54.96  Aligned_cols=29  Identities=31%  Similarity=0.478  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.++|+....
T Consensus        34 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   62 (372)
T 1v43_A           34 IKDGEFLVLLGPSGCGKTTTLRMIAGLEE   62 (372)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            55667788999999999999999998753

>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=91.53  E-value=0.068  Score=52.62  Aligned_cols=28  Identities=21%  Similarity=0.354  Sum_probs=24.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++..+.|.||+|+|||||.+.|+...
T Consensus        23 i~~Ge~~~liG~NGsGKSTLlk~l~Gl~   50 (249)
T 2qi9_C           23 VRAGEILHLVGPNGAGKSTLLARMAGMT   50 (249)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            4566778999999999999999999765

>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=91.51  E-value=0.068  Score=53.47  Aligned_cols=29  Identities=17%  Similarity=0.180  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||+++|+....
T Consensus        31 i~~Ge~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           31 IKRGEVTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCCHHHHHHHHHcCCC
Confidence            45667789999999999999999998663

>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=91.43  E-value=0.07  Score=53.02  Aligned_cols=28  Identities=25%  Similarity=0.409  Sum_probs=24.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++.-+.|.||+|+|||||+++|+...
T Consensus        34 i~~Ge~~~liG~nGsGKSTLl~~l~Gl~   61 (266)
T 4g1u_C           34 IASGEMVAIIGPNGAGKSTLLRLLTGYL   61 (266)
T ss_dssp             EETTCEEEEECCTTSCHHHHHHHHTSSS
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCC
Confidence            4567778999999999999999999865

>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=91.43  E-value=0.075  Score=55.02  Aligned_cols=29  Identities=28%  Similarity=0.328  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.+.|+....
T Consensus        23 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           23 VESGEYFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             ECTTCEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEECCCCccHHHHHHHHHcCCC
Confidence            55667788999999999999999998653

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=91.40  E-value=0.082  Score=50.54  Aligned_cols=24  Identities=42%  Similarity=0.398  Sum_probs=21.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      +.-+.|.||+|+|||||+++++..
T Consensus        22 Ge~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           22 NTIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             CSEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcC
Confidence            456889999999999999999976

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.36  E-value=0.081  Score=54.93  Aligned_cols=29  Identities=34%  Similarity=0.462  Sum_probs=24.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .....-+.|.||+|+|||||.++|+....
T Consensus        38 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           38 IREGEMVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            45667788999999999999999998753

>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=91.33  E-value=0.11  Score=58.00  Aligned_cols=24  Identities=42%  Similarity=0.674  Sum_probs=20.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..++++||||||||+++..+...+
T Consensus       196 ~~~li~GppGTGKT~~~~~~i~~l  219 (624)
T 2gk6_A          196 PLSLIQGPPGTGKTVTSATIVYHL  219 (624)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCeEEECCCCCCHHHHHHHHHHHH
Confidence            357899999999999888777665

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.31  E-value=0.13  Score=48.30  Aligned_cols=27  Identities=22%  Similarity=0.509  Sum_probs=23.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....++|.|++|+|||+|+.++....
T Consensus        10 ~~~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           10 SYQPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCCCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            445679999999999999999999865

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=91.31  E-value=0.073  Score=53.31  Aligned_cols=29  Identities=17%  Similarity=0.252  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.+.|+....
T Consensus        44 i~~Ge~~~liG~NGsGKSTLlk~l~Gl~~   72 (279)
T 2ihy_A           44 IAKGDKWILYGLNGAGKTTLLNILNAYEP   72 (279)
T ss_dssp             EETTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            45667789999999999999999998763

>1p5z_B DCK, deoxycytidine kinase; nucleoside kinase, P-loop, ARAC, cytarabine, transferase; HET: AR3 ADP; 1.60A {Homo sapiens} SCOP: c.37.1.1 PDB: 1p60_A* 1p61_B* 1p62_B* 2a7q_A* 2qrn_A* 2qro_A* 3exk_A* 3hp1_A* 2no7_A* 2no1_A* 2no6_A* 2no0_A* 2no9_A* 2noa_A* 2zi5_A* 2zi4_A* 2zi6_A* 2zi7_B* 2zia_A* 3kfx_A* ...

Probab=91.30  E-value=0.053  Score=53.25  Aligned_cols=28  Identities=18%  Similarity=0.375  Sum_probs=23.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.-|.|.|++|+||||+++.|++.+.
T Consensus        22 ~~~~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           22 TRIKKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             -CCEEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             cCceEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4456789999999999999999999873

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=91.26  E-value=0.2  Score=47.22  Aligned_cols=27  Identities=26%  Similarity=0.252  Sum_probs=23.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ....++|.|.+|+|||+|+..++....
T Consensus        37 ~~~~i~ivG~~gvGKTtl~~~l~~~~~   63 (226)
T 2hf9_A           37 GVVAFDFMGAIGSGKTLLIEKLIDNLK   63 (226)
T ss_dssp             TCEEEEEEESTTSSHHHHHHHHHHHHT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            456788899999999999999998863

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=91.25  E-value=0.55  Score=50.35  Aligned_cols=23  Identities=30%  Similarity=0.543  Sum_probs=18.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..+++.+|+|+|||..+-..+..
T Consensus        23 ~~~l~~~~tGsGKT~~~~~~~~~   45 (556)
T 4a2p_A           23 KNALICAPTGSGKTFVSILICEH   45 (556)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEcCCCChHHHHHHHHHHH
Confidence            57999999999999886655533

>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=91.16  E-value=0.11  Score=48.19  Aligned_cols=24  Identities=21%  Similarity=0.331  Sum_probs=21.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.|.|++|+|||+|.+.+....
T Consensus         6 ~kv~lvG~~g~GKSTLl~~l~~~~   29 (199)
T 2f9l_A            6 FKVVLIGDSGVGKSNLLSRFTRNE   29 (199)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECcCCCCHHHHHHHHhcCC
Confidence            468899999999999999999864

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=91.14  E-value=0.077  Score=52.30  Aligned_cols=29  Identities=17%  Similarity=0.244  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+.|.||+|+|||||.+.|+....
T Consensus        28 i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           28 LNKGDILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             EETTCEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHhCCCC
Confidence            45667788999999999999999998763

>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=91.09  E-value=0.55  Score=49.88  Aligned_cols=16  Identities=38%  Similarity=0.661  Sum_probs=13.9

Q ss_pred             CceEEeeCCCCCcHHH
Q 047219          322 PRAVLFEGPPGTGKTS  337 (567)
Q Consensus       322 p~~VLL~GppGTGKT~  337 (567)
                      ...+++.+|+|+|||+
T Consensus        19 ~~~~lv~a~TGsGKT~   34 (451)
T 2jlq_A           19 KRLTIMDLHPGAGKTK   34 (451)
T ss_dssp             TCEEEECCCTTSSCCT
T ss_pred             CCeEEEECCCCCCHhh
Confidence            4556999999999998

>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=91.09  E-value=0.12  Score=45.86  Aligned_cols=25  Identities=16%  Similarity=0.186  Sum_probs=21.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+++.|++|+|||+|++.+....
T Consensus         5 ~~~i~v~G~~~~GKssl~~~l~~~~   29 (168)
T 1z2a_A            5 AIKMVVVGNGAVGKSSMIQRYCKGI   29 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             eEEEEEECcCCCCHHHHHHHHHcCC
Confidence            4578999999999999999998754

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=91.05  E-value=0.13  Score=45.28  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+++.|++|+|||+|++.+....
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~~   25 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKKR   25 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            58999999999999999998753

>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=91.03  E-value=0.11  Score=48.16  Aligned_cols=24  Identities=21%  Similarity=0.331  Sum_probs=21.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+.|.|++|+|||+|.+.++...
T Consensus        30 ~kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           30 FKVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECcCCCCHHHHHHHHhcCC
Confidence            458899999999999999999865

>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=91.02  E-value=0.091  Score=54.89  Aligned_cols=29  Identities=31%  Similarity=0.496  Sum_probs=24.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||+|+|||||.++|+....
T Consensus        26 i~~Ge~~~llGpnGsGKSTLLr~iaGl~~   54 (372)
T 1g29_1           26 VKDGEFMILLGPSGCGKTTTLRMIAGLEE   54 (372)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EcCCCEEEEECCCCcHHHHHHHHHHcCCC
Confidence            45667788999999999999999998753

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=90.97  E-value=0.087  Score=54.68  Aligned_cols=29  Identities=21%  Similarity=0.433  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+...++|.||+|+||||++++++....
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            34567899999999999999999998874

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=90.96  E-value=0.11  Score=51.59  Aligned_cols=23  Identities=17%  Similarity=0.420  Sum_probs=21.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.|.||+|+|||||.+.|+...
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            57899999999999999999876

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=90.95  E-value=0.078  Score=49.13  Aligned_cols=25  Identities=16%  Similarity=0.143  Sum_probs=22.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+.|.|++|+|||||++.|+..+.
T Consensus         3 ~~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            3 LILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             CEEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhh
Confidence            3578999999999999999999874

>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=90.90  E-value=0.12  Score=53.33  Aligned_cols=26  Identities=19%  Similarity=0.250  Sum_probs=23.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.|.||+|+|||||++.|+..+.
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~  195 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFN  195 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTT
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            56789999999999999999999874

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=90.85  E-value=0.27  Score=58.45  Aligned_cols=23  Identities=26%  Similarity=0.280  Sum_probs=18.5

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ...+|++||+|+|||+.+-..+.
T Consensus       199 g~dvLV~ApTGSGKTlva~l~i~  221 (1108)
T 3l9o_A          199 GESVLVSAHTSAGKTVVAEYAIA  221 (1108)
T ss_dssp             TCCEEEECCSSSHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCChHHHHHHHHH
Confidence            46899999999999988754443

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=90.84  E-value=0.086  Score=57.44  Aligned_cols=27  Identities=19%  Similarity=0.197  Sum_probs=24.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+..++|.||+|+||||+++++...+.
T Consensus       259 ~g~~i~I~GptGSGKTTlL~aL~~~i~  285 (511)
T 2oap_1          259 HKFSAIVVGETASGKTTTLNAIMMFIP  285 (511)
T ss_dssp             TTCCEEEEESTTSSHHHHHHHHGGGSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            456799999999999999999998874

>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=90.80  E-value=0.59  Score=45.51  Aligned_cols=27  Identities=22%  Similarity=0.214  Sum_probs=18.9

Q ss_pred             CCceEEeeCCCCCcHHHHH-HHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCA-RVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LA-raIA~~l~  347 (567)
                      ...-.+++|+.|+|||+.+ +.+.+...
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~   45 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQI   45 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHH
Confidence            3456778999999999655 55555543

>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=90.80  E-value=0.28  Score=50.54  Aligned_cols=27  Identities=22%  Similarity=0.421  Sum_probs=23.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....|.|.|+||+|||+++..++..+
T Consensus        77 ~~~~~I~i~G~~G~GKSTl~~~L~~~l  103 (355)
T 3p32_A           77 GNAHRVGITGVPGVGKSTAIEALGMHL  103 (355)
T ss_dssp             CCSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHHHH
Confidence            445678999999999999999999876

>2fwr_A DNA repair protein RAD25; DNA unwinding, XPB, DNA binding protein; HET: DNA; 2.60A {Archaeoglobus fulgidus} SCOP: c.37.1.19 c.37.1.19 PDB: 2fzl_A*

Probab=90.76  E-value=0.45  Score=50.38  Aligned_cols=24  Identities=29%  Similarity=0.326  Sum_probs=21.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+++.+|+|+|||..+-.++...
T Consensus       109 ~~~ll~~~TGsGKT~~~l~~i~~~  132 (472)
T 2fwr_A          109 KRGCIVLPTGSGKTHVAMAAINEL  132 (472)
T ss_dssp             TEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHc
Confidence            359999999999999998888776

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=90.68  E-value=0.24  Score=52.83  Aligned_cols=25  Identities=36%  Similarity=0.526  Sum_probs=20.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ...+-.++.|+||||||++...+++
T Consensus       159 ~~~~v~~I~G~aGsGKTt~I~~~~~  183 (446)
T 3vkw_A          159 SSAKVVLVDGVPGCGKTKEILSRVN  183 (446)
T ss_dssp             CCSEEEEEEECTTSCHHHHHHHHCC
T ss_pred             ccccEEEEEcCCCCCHHHHHHHHhc
Confidence            3455678999999999999988764

>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=90.64  E-value=0.079  Score=54.97  Aligned_cols=28  Identities=32%  Similarity=0.457  Sum_probs=24.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+.|.||+|+|||||.++|+...
T Consensus        28 i~~Ge~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           28 IENGERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             ECTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            5566778899999999999999999865

>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=90.61  E-value=0.11  Score=54.58  Aligned_cols=28  Identities=18%  Similarity=0.203  Sum_probs=24.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....-+.|.||+|||||||.++|+...
T Consensus        44 i~~Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           44 ISPGQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            5667789999999999999999999754

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=90.50  E-value=0.14  Score=49.63  Aligned_cols=27  Identities=30%  Similarity=0.490  Sum_probs=20.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.-|.|.|++|+||||+++.+++.+.
T Consensus        24 ~g~~I~~eG~~GsGKsT~~~~l~~~l~   50 (227)
T 3v9p_A           24 RGKFITFEGIDGAGKTTHLQWFCDRLQ   50 (227)
T ss_dssp             CCCEEEEECCC---CHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            345688899999999999999999884

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=90.45  E-value=0.18  Score=48.84  Aligned_cols=29  Identities=28%  Similarity=0.424  Sum_probs=24.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..+.-+.|.|++|+||||+++.+++.+..
T Consensus        19 ~~~~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           19 PGSMFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            44667888999999999999999998743

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=90.41  E-value=0.11  Score=51.51  Aligned_cols=27  Identities=37%  Similarity=0.564  Sum_probs=23.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .. +..+.|.||+|+|||||.+.|+...
T Consensus        28 i~-Ge~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           28 VN-GEKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             EC-SSEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EC-CEEEEEECCCCCCHHHHHHHHhCCC
Confidence            55 6778999999999999999999865

>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=90.38  E-value=0.76  Score=47.64  Aligned_cols=23  Identities=39%  Similarity=0.404  Sum_probs=19.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++++.+|+|+|||..+-.++...
T Consensus        25 ~~ll~~~tG~GKT~~~~~~~~~~   47 (494)
T 1wp9_A           25 NCLIVLPTGLGKTLIAMMIAEYR   47 (494)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHH
Confidence            89999999999999888776554

>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=90.35  E-value=0.16  Score=44.64  Aligned_cols=24  Identities=21%  Similarity=0.300  Sum_probs=21.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|++.|++|+|||+|..++....
T Consensus         4 ~~i~v~G~~~~GKSsli~~l~~~~   27 (167)
T 1kao_A            4 YKVVVLGSGGVGKSALTVQFVTGT   27 (167)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999988653

>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=90.34  E-value=0.11  Score=52.43  Aligned_cols=29  Identities=28%  Similarity=0.376  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+.-+.|.||.|+|||||.+.|+....
T Consensus        61 i~~Ge~~~i~G~NGsGKSTLlk~l~Gl~~   89 (290)
T 2bbs_A           61 IERGQLLAVAGSTGAGKTSLLMMIMGELE   89 (290)
T ss_dssp             ECTTCEEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhcCCC
Confidence            56777899999999999999999998763

>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=90.20  E-value=0.17  Score=44.55  Aligned_cols=25  Identities=20%  Similarity=0.314  Sum_probs=21.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|.+.+...-
T Consensus         4 ~~~i~v~G~~~~GKssl~~~l~~~~   28 (168)
T 1u8z_A            4 LHKVIMVGSGGVGKSALTLQFMYDE   28 (168)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHHhCc
Confidence            3579999999999999999998753

>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=90.19  E-value=0.13  Score=47.18  Aligned_cols=21  Identities=24%  Similarity=0.496  Sum_probs=19.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~  344 (567)
                      .++|.|++|+|||+|++.++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~   24 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMK   24 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            588999999999999999986

>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=90.17  E-value=0.17  Score=49.38  Aligned_cols=29  Identities=21%  Similarity=0.442  Sum_probs=24.5

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      .+.-+.|.|++|+||||+++.+++.+...
T Consensus        26 ~~~~i~~eG~~GsGKsT~~~~l~~~l~~~   54 (236)
T 3lv8_A           26 NAKFIVIEGLEGAGKSTAIQVVVETLQQN   54 (236)
T ss_dssp             CCCEEEEEESTTSCHHHHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            35668899999999999999999988543

>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=90.16  E-value=0.16  Score=45.39  Aligned_cols=24  Identities=42%  Similarity=0.585  Sum_probs=20.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...|+|.|++|+|||+|.+.+...
T Consensus         4 ~~ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            4 LYRVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEEEECCCCccHHHHHHHHhcC
Confidence            356999999999999999998754

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=90.15  E-value=0.57  Score=55.20  Aligned_cols=21  Identities=29%  Similarity=0.336  Sum_probs=17.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIA  343 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA  343 (567)
                      .++++.+|+|+|||.++-...
T Consensus       102 ~~vLV~apTGSGKTlva~lai  122 (1010)
T 2xgj_A          102 ESVLVSAHTSAGKTVVAEYAI  122 (1010)
T ss_dssp             CEEEEECCTTSCHHHHHHHHH
T ss_pred             CCEEEECCCCCChHHHHHHHH
Confidence            579999999999999875433

>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=90.11  E-value=0.16  Score=44.61  Aligned_cols=24  Identities=17%  Similarity=0.303  Sum_probs=21.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+++.|++|+|||+|++.+....
T Consensus         4 ~~i~v~G~~~~GKssl~~~l~~~~   27 (166)
T 2ce2_X            4 YKLVVVGAGGVGKSALTIQLIQNH   27 (166)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhCc
Confidence            368999999999999999998754

>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=90.05  E-value=0.17  Score=44.68  Aligned_cols=24  Identities=17%  Similarity=0.246  Sum_probs=21.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|++.|++|+|||+|..++....
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1ek0_A            4 IKLVLLGEAAVGKSSIVLRFVSND   27 (170)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEEECCCCCCHHHHHHHHhcCC
Confidence            468999999999999999998654

>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=90.00  E-value=0.16  Score=45.62  Aligned_cols=23  Identities=17%  Similarity=0.413  Sum_probs=20.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..+.|.|++|+|||+|.+.+...
T Consensus         4 ~~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            4 YEIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhCC
Confidence            45889999999999999999864

>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=89.98  E-value=0.59  Score=49.54  Aligned_cols=25  Identities=24%  Similarity=0.315  Sum_probs=19.3

Q ss_pred             CCCceEEeeCCCCCcHHHHH-HHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCA-RVIAN  344 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LA-raIA~  344 (567)
                      ...+.+++.||+|+|||+.+ -++.+
T Consensus         6 ~~g~~vlv~a~TGSGKT~~~l~~~l~   31 (440)
T 1yks_A            6 KKGMTTVLDFHPGAGKTRRFLPQILA   31 (440)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHH
T ss_pred             hCCCCEEEEcCCCCCHHHHHHHHHHH
Confidence            45678999999999999874 44443

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=89.96  E-value=0.19  Score=48.32  Aligned_cols=27  Identities=26%  Similarity=0.409  Sum_probs=24.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      +.-+.|.|++|+||||+++.+++.+..
T Consensus         5 g~~i~~eG~~g~GKst~~~~l~~~l~~   31 (216)
T 3tmk_A            5 GKLILIEGLDRTGKTTQCNILYKKLQP   31 (216)
T ss_dssp             CCEEEEEECSSSSHHHHHHHHHHHHCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            567889999999999999999999954

>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=89.93  E-value=0.18  Score=44.61  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=22.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|.+.+....
T Consensus         6 ~~~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            6 ELKVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3579999999999999999998764

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=89.88  E-value=0.22  Score=45.28  Aligned_cols=27  Identities=15%  Similarity=0.257  Sum_probs=23.2

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....|++.|++|+|||+|+.++...-
T Consensus         5 ~~~~ki~v~G~~~~GKSsli~~l~~~~   31 (208)
T 3clv_A            5 KSSYKTVLLGESSVGKSSIVLRLTKDT   31 (208)
T ss_dssp             CSSEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHhCc
Confidence            345679999999999999999998763

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=89.84  E-value=0.21  Score=44.71  Aligned_cols=26  Identities=31%  Similarity=0.420  Sum_probs=22.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .....|++.|++|+|||+|...+...
T Consensus         6 ~~~~~i~v~G~~~~GKssl~~~l~~~   31 (178)
T 2lkc_A            6 ERPPVVTIMGHVDHGKTTLLDAIRHS   31 (178)
T ss_dssp             CCCCEEEEESCTTTTHHHHHHHHHTT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            45667999999999999999999764

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=89.79  E-value=0.18  Score=45.30  Aligned_cols=27  Identities=30%  Similarity=0.345  Sum_probs=22.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....|++.|++|+|||+|.+.+....
T Consensus         6 ~~~~~i~v~G~~~~GKSsli~~l~~~~   32 (182)
T 1ky3_A            6 KNILKVIILGDSGVGKTSLMHRYVNDK   32 (182)
T ss_dssp             -CEEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEEECCCCCCHHHHHHHHHhCc
Confidence            345679999999999999999988754

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=89.78  E-value=0.21  Score=44.33  Aligned_cols=27  Identities=26%  Similarity=0.318  Sum_probs=22.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....|++.|++|+|||+|...+...-
T Consensus         5 ~~~~~i~v~G~~~~GKssl~~~l~~~~   31 (171)
T 1upt_A            5 TREMRILILGLDGAGKTTILYRLQVGE   31 (171)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCccEEEEECCCCCCHHHHHHHHhcCC
Confidence            345679999999999999999997643

>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=89.77  E-value=0.19  Score=45.01  Aligned_cols=25  Identities=24%  Similarity=0.271  Sum_probs=21.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|...+...-
T Consensus         7 ~~~i~v~G~~~~GKSsli~~l~~~~   31 (177)
T 1wms_A            7 LFKVILLGDGGVGKSSLMNRYVTNK   31 (177)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcCC
Confidence            4579999999999999999998653

>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=89.76  E-value=0.23  Score=52.54  Aligned_cols=26  Identities=23%  Similarity=0.327  Sum_probs=22.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....+.|.||+|+|||||.++|+...
T Consensus        68 ~~~~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           68 SVLNVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHTCC
T ss_pred             CCeEEEEECCCCCcHHHHHHHHhCCC
Confidence            34568899999999999999999854

>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=89.75  E-value=0.18  Score=44.69  Aligned_cols=25  Identities=24%  Similarity=0.183  Sum_probs=21.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|.+.+....
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~~   30 (170)
T 1z08_A            6 SFKVVLLGEGCVGKTSLVLRYCENK   30 (170)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            4579999999999999999998653

>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=89.68  E-value=0.11  Score=48.28  Aligned_cols=27  Identities=33%  Similarity=0.489  Sum_probs=23.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ......+.|.|++|+|||+|.+++...
T Consensus        23 ~~~~~~v~lvG~~g~GKSTLl~~l~g~   49 (210)
T 1pui_A           23 SDTGIEVAFAGRSNAGKSSALNTLTNQ   49 (210)
T ss_dssp             CSCSEEEEEEECTTSSHHHHHTTTCCC
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHhCC
Confidence            556677999999999999999988754

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=89.66  E-value=0.23  Score=51.02  Aligned_cols=28  Identities=25%  Similarity=0.424  Sum_probs=24.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....-+.|.|+||+|||||.++++..+
T Consensus        52 ~~~g~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           52 TGRAIRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             CCCSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCCeEEEEECCCCCCHHHHHHHHHHhh
Confidence            4556778899999999999999999765

>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=89.62  E-value=0.11  Score=52.66  Aligned_cols=29  Identities=21%  Similarity=0.369  Sum_probs=25.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++..+.|.||+|+|||||++.|+..+.
T Consensus        77 i~~Ge~vaivG~sGsGKSTLl~ll~gl~~  105 (306)
T 3nh6_A           77 VMPGQTLALVGPSGAGKSTILRLLFRFYD  105 (306)
T ss_dssp             ECTTCEEEEESSSCHHHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCchHHHHHHHHHcCCC
Confidence            57778899999999999999999998763

>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=89.52  E-value=0.17  Score=52.64  Aligned_cols=28  Identities=18%  Similarity=0.197  Sum_probs=24.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+-|.||+|+|||||.++|+...
T Consensus        51 i~~Gei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           51 VPAGQIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             ECTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EcCCCEEEEEcCCCchHHHHHHHHhcCC
Confidence            5667778999999999999999999865

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=89.48  E-value=0.15  Score=54.72  Aligned_cols=28  Identities=32%  Similarity=0.358  Sum_probs=24.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+.|.||+|+|||||+|.|+...
T Consensus       135 i~~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          135 NFEGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SSSCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            4566779999999999999999999865

>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=89.43  E-value=0.2  Score=44.25  Aligned_cols=24  Identities=17%  Similarity=0.261  Sum_probs=21.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+++.|++|+|||+|.+++....
T Consensus         4 ~ki~v~G~~~~GKssli~~l~~~~   27 (167)
T 1c1y_A            4 YKLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            468999999999999999998743

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=89.42  E-value=0.2  Score=44.29  Aligned_cols=24  Identities=17%  Similarity=0.207  Sum_probs=21.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...|++.|++|+|||+|..++...
T Consensus         6 ~~~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1r2q_A            6 QFKLVLLGESAVGKSSLVLRFVKG   29 (170)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEEECCCCCCHHHHHHHHHcC
Confidence            356899999999999999999864

>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=89.37  E-value=0.19  Score=57.69  Aligned_cols=24  Identities=42%  Similarity=0.674  Sum_probs=20.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+++||||||||+++..+...+
T Consensus       372 ~~~lI~GppGTGKT~ti~~~i~~l  395 (800)
T 2wjy_A          372 PLSLIQGPPGTGKTVTSATIVYHL  395 (800)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHH
Confidence            357899999999999888777665

>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=89.35  E-value=0.18  Score=44.68  Aligned_cols=24  Identities=21%  Similarity=0.340  Sum_probs=20.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|++.|++|+|||+|...+...-
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~~   27 (170)
T 1g16_A            4 MKILLIGDSGVGKSCLLVRFVEDK   27 (170)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHCC
T ss_pred             eEEEEECcCCCCHHHHHHHHHhCC
Confidence            468999999999999999998643

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=89.32  E-value=0.4  Score=49.35  Aligned_cols=25  Identities=28%  Similarity=0.498  Sum_probs=22.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.|.|+||+|||||..++....
T Consensus        74 ~~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           74 AFRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            4568899999999999999999864

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=89.27  E-value=0.84  Score=54.29  Aligned_cols=21  Identities=24%  Similarity=0.450  Sum_probs=17.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVI  342 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraI  342 (567)
                      .+.+++++|+|+|||+++-..
T Consensus        93 g~dvlv~ApTGSGKTl~~l~~  113 (1104)
T 4ddu_A           93 GKSFTMVAPTGVGKTTFGMMT  113 (1104)
T ss_dssp             TCCEEECCSTTCCHHHHHHHH
T ss_pred             CCCEEEEeCCCCcHHHHHHHH
Confidence            468999999999999965444

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=89.27  E-value=0.21  Score=45.21  Aligned_cols=25  Identities=28%  Similarity=0.235  Sum_probs=21.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|++++...-
T Consensus        11 ~~ki~v~G~~~~GKSsli~~l~~~~   35 (195)
T 3bc1_A           11 LIKFLALGDSGVGKTSVLYQYTDGK   35 (195)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEECCCCCCHHHHHHHHhcCC
Confidence            4579999999999999999998743

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=89.26  E-value=0.21  Score=44.13  Aligned_cols=23  Identities=22%  Similarity=0.252  Sum_probs=20.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+++.|++|+|||+|...+...-
T Consensus         2 ki~~~G~~~~GKssl~~~l~~~~   24 (164)
T 1r8s_A            2 RILMVGLDAAGKTTILYKLKLGE   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999997654

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=89.25  E-value=0.48  Score=54.10  Aligned_cols=25  Identities=36%  Similarity=0.403  Sum_probs=21.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +..+.|.||.|+||||+.|.++...
T Consensus       576 g~i~~I~GpNGsGKSTlLr~iagl~  600 (765)
T 1ewq_A          576 HELVLITGPNMAGKSTFLRQTALIA  600 (765)
T ss_dssp             SCEEEEESCSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHhhh
Confidence            4568899999999999999998753

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=89.22  E-value=0.2  Score=44.36  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=20.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..|++.|++|+|||+|.+++...
T Consensus         4 ~~i~v~G~~~~GKssli~~l~~~   26 (172)
T 2erx_A            4 YRVAVFGAGGVGKSSLVLRFVKG   26 (172)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            46899999999999999999864

>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=89.21  E-value=0.2  Score=52.75  Aligned_cols=28  Identities=32%  Similarity=0.377  Sum_probs=24.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..++|.||+|+|||+|++.|++..
T Consensus       171 i~rGQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          171 IGRGQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             CBTTCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             ecCCcEEEEecCCCCChhHHHHHHHHHH
Confidence            5567789999999999999999999876

>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=89.16  E-value=0.2  Score=44.49  Aligned_cols=21  Identities=29%  Similarity=0.534  Sum_probs=18.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~  344 (567)
                      .++|.|++|+|||+|.+.+..
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            588999999999999999863

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=89.14  E-value=1.2  Score=47.56  Aligned_cols=23  Identities=26%  Similarity=0.498  Sum_probs=18.6

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      +.+++.+|+|+|||..+-..+..
T Consensus        20 ~~~l~~~~tGsGKT~~~~~~~~~   42 (555)
T 3tbk_A           20 KNTIICAPTGCGKTFVSLLICEH   42 (555)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHH
T ss_pred             CCEEEEeCCCChHHHHHHHHHHH
Confidence            57999999999999876655543

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=89.10  E-value=0.36  Score=46.26  Aligned_cols=39  Identities=26%  Similarity=0.384  Sum_probs=29.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY  369 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~  369 (567)
                      -..|-|+|..||||||+++.+++ +      +++  .+++..+....+
T Consensus         9 ~~~iglTGgigsGKStv~~~l~~-~------g~~--vidaD~ia~~l~   47 (210)
T 4i1u_A            9 MYAIGLTGGIGSGKTTVADLFAA-R------GAS--LVDTDLIAHRIT   47 (210)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHH-T------TCE--EEEHHHHHHHHT
T ss_pred             eeEEEEECCCCCCHHHHHHHHHH-C------CCc--EEECcHHHHHHh
Confidence            34688999999999999999987 5      444  455665555444

>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=89.07  E-value=0.2  Score=45.41  Aligned_cols=24  Identities=29%  Similarity=0.488  Sum_probs=21.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+.|.|++|+|||+|.+++...
T Consensus         4 ~~ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            4 GMKVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            456899999999999999999865

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=89.06  E-value=0.2  Score=45.50  Aligned_cols=24  Identities=17%  Similarity=0.401  Sum_probs=21.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+.|.|++|+|||+|.+.+...
T Consensus         7 ~~~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            7 SYEIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHTT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            356999999999999999999863

>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=89.04  E-value=0.26  Score=44.24  Aligned_cols=24  Identities=29%  Similarity=0.292  Sum_probs=21.2

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .-.+|+||.|+|||++..||+-.+
T Consensus        24 g~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHH
Confidence            456899999999999999998766

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=88.98  E-value=0.22  Score=44.49  Aligned_cols=25  Identities=16%  Similarity=0.206  Sum_probs=22.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|.+.+....
T Consensus        15 ~~~i~v~G~~~~GKSsli~~l~~~~   39 (179)
T 1z0f_A           15 IFKYIIIGDMGVGKSCLLHQFTEKK   39 (179)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCC
Confidence            4579999999999999999998754

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=88.98  E-value=0.22  Score=45.35  Aligned_cols=25  Identities=24%  Similarity=0.371  Sum_probs=21.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|++.+....
T Consensus        14 ~~ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           14 NFKIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHTS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHhhc
Confidence            3569999999999999999888765

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=88.98  E-value=0.18  Score=44.65  Aligned_cols=22  Identities=41%  Similarity=0.735  Sum_probs=19.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~  344 (567)
                      -.++|.|++|+|||+|.+.+..
T Consensus         3 ~ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            3 YKVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             CEEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEEECCCCCCHHHHHHHHcC
Confidence            3589999999999999999864

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=88.95  E-value=0.25  Score=47.37  Aligned_cols=28  Identities=25%  Similarity=0.519  Sum_probs=23.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      +.-|.|.|++|+||||.++.+++.+...
T Consensus         3 g~~i~~eG~~gsGKsT~~~~l~~~l~~~   30 (213)
T 4tmk_A            3 SKYIVIEGLEGAGKTTARNVVVETLEQL   30 (213)
T ss_dssp             CCEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            3457889999999999999999988543

>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=88.85  E-value=0.36  Score=58.53  Aligned_cols=30  Identities=17%  Similarity=0.375  Sum_probs=25.8

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+++..+-|+|++|+||||+++.+.+...
T Consensus      1101 ~I~~Ge~vaIVG~SGsGKSTL~~lL~rl~~ 1130 (1321)
T 4f4c_A         1101 SVEPGQTLALVGPSGCGKSTVVALLERFYD 1130 (1321)
T ss_dssp             EECTTCEEEEECSTTSSTTSHHHHHTTSSC
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHhcCcc
Confidence            356677899999999999999999998764

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=88.84  E-value=0.23  Score=44.89  Aligned_cols=24  Identities=17%  Similarity=0.315  Sum_probs=21.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -.|+|.|++|+|||+|..++....
T Consensus         5 ~ki~v~G~~~~GKSsli~~l~~~~   28 (189)
T 4dsu_A            5 YKLVVVGADGVGKSALTIQLIQNH   28 (189)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            468999999999999999998754

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=88.80  E-value=0.24  Score=52.89  Aligned_cols=30  Identities=20%  Similarity=0.205  Sum_probs=26.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ...+.-+.|.||+|||||||++.|+.....
T Consensus       154 i~~Gq~~~IvG~sGsGKSTLl~~Iag~~~~  183 (438)
T 2dpy_A          154 VGRGQRMGLFAGSGVGKSVLLGMMARYTRA  183 (438)
T ss_dssp             CBTTCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHhcccCC
Confidence            556677899999999999999999998743

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=88.78  E-value=0.21  Score=44.83  Aligned_cols=25  Identities=28%  Similarity=0.396  Sum_probs=21.6

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ....|++.|++|+|||+|.+.+...
T Consensus         5 ~~~ki~v~G~~~~GKssl~~~l~~~   29 (178)
T 2hxs_A            5 RQLKIVVLGDGASGKTSLTTCFAQE   29 (178)
T ss_dssp             CEEEEEEECCTTSSHHHHHHHHHGG
T ss_pred             ceEEEEEECcCCCCHHHHHHHHHhC
Confidence            3457999999999999999999864

>1svi_A GTP-binding protein YSXC; ENGB, GTPase, GDP, hydrolase; HET: GDP; 1.95A {Bacillus subtilis} SCOP: c.37.1.8 PDB: 1sul_A* 1svw_A*

Probab=88.76  E-value=0.25  Score=45.17  Aligned_cols=26  Identities=19%  Similarity=0.323  Sum_probs=22.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .....|++.|++|+|||+|...+...
T Consensus        21 ~~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           21 GGLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             SCCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34567999999999999999999754

>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=88.76  E-value=0.16  Score=48.85  Aligned_cols=26  Identities=35%  Similarity=0.523  Sum_probs=22.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..+.-+.|.|+.|+||||+++.|+..
T Consensus        18 ~~g~~i~i~G~~GsGKSTl~~~L~~~   43 (230)
T 2vp4_A           18 TQPFTVLIEGNIGSGKTTYLNHFEKY   43 (230)
T ss_dssp             CCCEEEEEECSTTSCHHHHHHTTGGG
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhc
Confidence            44566889999999999999999886

>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=88.74  E-value=0.42  Score=46.18  Aligned_cols=28  Identities=25%  Similarity=0.342  Sum_probs=24.0

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .....+++.|.+|+||||++..++..+.
T Consensus        12 ~~~~i~~~~GkgGvGKTTl~~~La~~l~   39 (262)
T 1yrb_A           12 MASMIVVFVGTAGSGKTTLTGEFGRYLE   39 (262)
T ss_dssp             CCCEEEEEECSTTSSHHHHHHHHHHHHT
T ss_pred             cceEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence            3456688999999999999999998875

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=88.74  E-value=0.25  Score=45.83  Aligned_cols=27  Identities=19%  Similarity=0.295  Sum_probs=21.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....|+|.|++|+|||+|..++...-
T Consensus        18 ~~~~~i~v~G~~~~GKSsli~~l~~~~   44 (213)
T 3cph_A           18 DSIMKILLIGDSGVGKSCLLVRFVEDK   44 (213)
T ss_dssp             --CEEEEEECSTTSSHHHHHHHHHHCC
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHhCC
Confidence            345679999999999999999998643

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=88.73  E-value=0.21  Score=44.59  Aligned_cols=24  Identities=25%  Similarity=0.299  Sum_probs=21.0

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|++.|++|+|||+|...+...-
T Consensus        15 ~~i~v~G~~~~GKssli~~l~~~~   38 (179)
T 2y8e_A           15 FKLVFLGEQSVGKTSLITRFMYDS   38 (179)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHcCC
Confidence            469999999999999999998643

>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=88.68  E-value=0.33  Score=50.49  Aligned_cols=27  Identities=19%  Similarity=0.226  Sum_probs=23.7

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...++++.|++|+|||++++.++..+.
T Consensus        34 ~~~~~~i~G~~G~GKs~~~~~~~~~~~   60 (392)
T 4ag6_A           34 TNSNWTILAKPGAGKSFTAKMLLLREY   60 (392)
T ss_dssp             CCCCEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ccCceEEEcCCCCCHHHHHHHHHHHHH
Confidence            467899999999999999999987763

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=88.67  E-value=0.24  Score=44.63  Aligned_cols=25  Identities=20%  Similarity=0.314  Sum_probs=21.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|++.+...-
T Consensus        18 ~~ki~v~G~~~~GKSsli~~l~~~~   42 (187)
T 2a9k_A           18 LHKVIMVGSGGVGKSALTLQFMYDE   42 (187)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECCCCCCHHHHHHHHhhCC
Confidence            4579999999999999999998753

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=88.64  E-value=0.24  Score=45.18  Aligned_cols=24  Identities=17%  Similarity=0.303  Sum_probs=21.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|++.|.+|+|||+|+..+....
T Consensus        22 ~ki~vvG~~~~GKSsli~~l~~~~   45 (190)
T 3con_A           22 YKLVVVGAGGVGKSALTIQLIQNH   45 (190)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcCC
Confidence            469999999999999999998754

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=88.63  E-value=0.24  Score=45.36  Aligned_cols=25  Identities=24%  Similarity=0.309  Sum_probs=21.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|.+.+...-
T Consensus        25 ~~ki~v~G~~~~GKSsLi~~l~~~~   49 (193)
T 2oil_A           25 VFKVVLIGESGVGKTNLLSRFTRNE   49 (193)
T ss_dssp             EEEEEEESSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHhcCC
Confidence            3569999999999999999998754

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=88.62  E-value=0.22  Score=44.60  Aligned_cols=25  Identities=28%  Similarity=0.329  Sum_probs=21.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ....|++.|++|+|||+|++++...
T Consensus         8 ~~~~i~v~G~~~~GKssl~~~l~~~   32 (181)
T 3tw8_B            8 HLFKLLIIGDSGVGKSSLLLRFADN   32 (181)
T ss_dssp             EEEEEEEECCTTSCHHHHHHHHCSC
T ss_pred             cceEEEEECCCCCCHHHHHHHHhcC
Confidence            3457999999999999999998753

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=88.62  E-value=0.25  Score=44.43  Aligned_cols=25  Identities=20%  Similarity=0.304  Sum_probs=21.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|.+.+...-
T Consensus        12 ~~ki~v~G~~~~GKSsli~~l~~~~   36 (181)
T 2efe_B           12 NAKLVLLGDVGAGKSSLVLRFVKDQ   36 (181)
T ss_dssp             EEEEEEECCTTSCHHHHHHHHHHCC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3569999999999999999998753

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=88.59  E-value=0.22  Score=44.53  Aligned_cols=25  Identities=16%  Similarity=0.250  Sum_probs=22.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+++.|++|+|||+|.+++....
T Consensus         9 ~~~i~v~G~~~~GKssli~~l~~~~   33 (181)
T 2fn4_A            9 THKLVVVGGGGVGKSALTIQFIQSY   33 (181)
T ss_dssp             EEEEEEEECTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhCc
Confidence            4579999999999999999998763

>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=88.59  E-value=0.21  Score=46.77  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=19.4

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      +|++|++|+|||++|..++..
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~   22 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD   22 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS
T ss_pred             EEEECCCCCcHHHHHHHHHhc
Confidence            689999999999999999865

>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=88.57  E-value=0.44  Score=59.18  Aligned_cols=23  Identities=39%  Similarity=0.687  Sum_probs=19.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVI  342 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraI  342 (567)
                      ....++++..|+|+|||+++...
T Consensus       940 ~~~~nvlv~APTGSGKTliaela  962 (1724)
T 4f92_B          940 NSDDNVFVGAPTGSGKTICAEFA  962 (1724)
T ss_dssp             SCCSCEEEECCTTSCCHHHHHHH
T ss_pred             cCCCcEEEEeCCCCCchHHHHHH
Confidence            45678999999999999988643

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=88.56  E-value=0.22  Score=45.43  Aligned_cols=26  Identities=23%  Similarity=0.296  Sum_probs=22.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....+++.|++|+|||+|++.+...-
T Consensus         6 ~~~ki~v~G~~~vGKSsli~~l~~~~   31 (184)
T 1m7b_A            6 VKCKIVVVGDSQCGKTALLHVFAKDC   31 (184)
T ss_dssp             CEEEEEEEESTTSSHHHHHHHHHHSC
T ss_pred             eEEEEEEECCCCCCHHHHHHHHhcCC
Confidence            44578999999999999999998753

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=88.54  E-value=0.29  Score=43.98  Aligned_cols=26  Identities=19%  Similarity=0.121  Sum_probs=21.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .....+++.|++|+|||+|.+.+...
T Consensus         6 ~~~~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            6 SRFIKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             -CCCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CceEEEEEECCCCCCHHHHHHHHhcC
Confidence            34567999999999999999999864

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=88.49  E-value=0.26  Score=44.78  Aligned_cols=27  Identities=22%  Similarity=0.329  Sum_probs=22.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....+++.|++|+|||+|.+.+...-
T Consensus        16 ~~~~~i~v~G~~~~GKssl~~~l~~~~   42 (186)
T 1ksh_A           16 ERELRLLMLGLDNAGKTTILKKFNGED   42 (186)
T ss_dssp             -CCEEEEEECSTTSSHHHHHHHHTTCC
T ss_pred             CCeeEEEEECCCCCCHHHHHHHHhcCC
Confidence            456789999999999999999987543

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=88.40  E-value=0.22  Score=51.42  Aligned_cols=30  Identities=23%  Similarity=0.249  Sum_probs=26.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ...+.-+.|.||+|+|||||.+.|++....
T Consensus        68 i~~Gq~~gIiG~nGaGKTTLl~~I~g~~~~   97 (347)
T 2obl_A           68 CGIGQRIGIFAGSGVGKSTLLGMICNGASA   97 (347)
T ss_dssp             EETTCEEEEEECTTSSHHHHHHHHHHHSCC
T ss_pred             ecCCCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            455677899999999999999999999743

>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=88.39  E-value=0.21  Score=54.29  Aligned_cols=28  Identities=29%  Similarity=0.291  Sum_probs=22.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHH--HHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVI--ANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraI--A~~l  346 (567)
                      ..++..++|.||+|+|||||++.+  +...
T Consensus        36 i~~Ge~~~l~G~nGsGKSTL~~~~ll~Gl~   65 (525)
T 1tf7_A           36 LPIGRSTLVSGTSGTGKTLFSIQFLYNGII   65 (525)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CCCCeEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence            456778999999999999999994  4443

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=88.38  E-value=0.28  Score=45.26  Aligned_cols=26  Identities=19%  Similarity=0.262  Sum_probs=22.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ......|++.|++|+|||+|+..+..
T Consensus        26 ~~~~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           26 GKKQMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             TTSCEEEEEEESTTSSHHHHHHHHCS
T ss_pred             cCCccEEEEECCCCCCHHHHHHHHHh
Confidence            34567799999999999999999864

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=88.35  E-value=0.24  Score=44.65  Aligned_cols=25  Identities=20%  Similarity=0.163  Sum_probs=21.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|++.|++|+|||+|.+.+....
T Consensus         5 ~~~i~~~G~~~~GKssl~~~l~~~~   29 (186)
T 1mh1_A            5 AIKCVVVGDGAVGKTCLLISYTTNA   29 (186)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEEEECCCCCCHHHHHHHHHcCC
Confidence            3468999999999999999998643

>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=88.32  E-value=1.2  Score=47.55  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=18.4

Q ss_pred             CCCceEEeeCCCCCcHHHH-HHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSC-ARVIA  343 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~L-AraIA  343 (567)
                      .....+++.+|+|+|||+. +-.+.
T Consensus        19 ~~~~~vlv~a~TGsGKT~~~~l~il   43 (459)
T 2z83_A           19 RKRQMTVLDLHPGSGKTRKILPQII   43 (459)
T ss_dssp             STTCEEEECCCTTSCTTTTHHHHHH
T ss_pred             hcCCcEEEECCCCCCHHHHHHHHHH
Confidence            4467899999999999985 34433

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=88.23  E-value=0.24  Score=44.82  Aligned_cols=25  Identities=24%  Similarity=0.278  Sum_probs=21.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|++.+...-
T Consensus        10 ~~ki~v~G~~~~GKSsli~~l~~~~   34 (186)
T 2bme_A           10 LFKFLVIGNAGTGKSCLLHQFIEKK   34 (186)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHHSS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHcCC
Confidence            4579999999999999999998654

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=88.20  E-value=0.26  Score=44.46  Aligned_cols=26  Identities=15%  Similarity=0.225  Sum_probs=22.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +...|+|.|++|+|||+|...+....
T Consensus        17 ~~~ki~v~G~~~~GKSsl~~~l~~~~   42 (183)
T 3kkq_A           17 PTYKLVVVGDGGVGKSALTIQFFQKI   42 (183)
T ss_dssp             CEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CceEEEEECCCCCCHHHHHHHHHhCC
Confidence            34578999999999999999998753

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=88.12  E-value=0.26  Score=56.59  Aligned_cols=24  Identities=42%  Similarity=0.674  Sum_probs=18.7

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..+++.||||||||+++..+...+
T Consensus       376 ~~~lI~GppGTGKT~~i~~~i~~l  399 (802)
T 2xzl_A          376 PLSLIQGPPGTGKTVTSATIVYHL  399 (802)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHH
Confidence            357899999999998876665443

>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=88.09  E-value=0.31  Score=49.05  Aligned_cols=27  Identities=26%  Similarity=0.251  Sum_probs=23.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+..+.+.|++|+||||++..+|..+.
T Consensus        97 ~~~~i~i~g~~G~GKTT~~~~la~~~~  123 (295)
T 1ls1_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYK  123 (295)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            566788899999999999999998874

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=88.08  E-value=0.29  Score=43.92  Aligned_cols=26  Identities=27%  Similarity=0.307  Sum_probs=22.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....|+|.|++|+|||+|...+...-
T Consensus         9 ~~~~i~v~G~~~~GKssli~~l~~~~   34 (180)
T 2g6b_A            9 VAFKVMLVGDSGVGKTCLLVRFKDGA   34 (180)
T ss_dssp             EEEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             cceEEEEECcCCCCHHHHHHHHHhCC
Confidence            34579999999999999999998754

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=88.02  E-value=0.42  Score=56.20  Aligned_cols=22  Identities=23%  Similarity=0.273  Sum_probs=17.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..+++.+|+|+|||+++.....
T Consensus        55 ~~vlv~apTGsGKTlv~~~~i~   76 (997)
T 4a4z_A           55 DSVFVAAHTSAGKTVVAEYAIA   76 (997)
T ss_dssp             CEEEEECCTTSCSHHHHHHHHH
T ss_pred             CCEEEEECCCCcHHHHHHHHHH
Confidence            6899999999999986554433

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=87.97  E-value=0.3  Score=45.07  Aligned_cols=28  Identities=18%  Similarity=0.357  Sum_probs=22.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ......|+|.|++|+|||+|+..+...-
T Consensus        25 ~~~~~ki~v~G~~~~GKSsli~~l~~~~   52 (199)
T 2p5s_A           25 SQKAYKIVLAGDAAVGKSSFLMRLCKNE   52 (199)
T ss_dssp             ---CEEEEEESSTTSSHHHHHHHHHHCC
T ss_pred             cCCCeEEEEECcCCCCHHHHHHHHHhCC
Confidence            3455789999999999999999998653

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=87.93  E-value=0.33  Score=44.67  Aligned_cols=27  Identities=15%  Similarity=0.198  Sum_probs=22.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....|+|.|++|+|||+|++.+...-
T Consensus        26 ~~~~ki~v~G~~~vGKSsli~~l~~~~   52 (196)
T 2atv_A           26 SAEVKLAIFGRAGVGKSALVVRFLTKR   52 (196)
T ss_dssp             -CCEEEEEECCTTSSHHHHHHHHHHSC
T ss_pred             CCceEEEEECCCCCCHHHHHHHHHhCC
Confidence            345679999999999999999998753

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=87.87  E-value=0.28  Score=44.73  Aligned_cols=25  Identities=24%  Similarity=0.317  Sum_probs=21.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|.+++....
T Consensus        16 ~~ki~v~G~~~~GKSsli~~l~~~~   40 (196)
T 3tkl_A           16 LFKLLLIGDSGVGKSCLLLRFADDT   40 (196)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             ceEEEEECcCCCCHHHHHHHHHcCC
Confidence            3579999999999999999998754

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=87.81  E-value=0.28  Score=45.20  Aligned_cols=25  Identities=28%  Similarity=0.470  Sum_probs=21.0

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ....|++.|++|+|||+|.+.+...
T Consensus        22 ~~~ki~~vG~~~vGKSsli~~l~~~   46 (190)
T 1m2o_B           22 KHGKLLFLGLDNAGKTTLLHMLKND   46 (190)
T ss_dssp             --CEEEEEESTTSSHHHHHHHHHHS
T ss_pred             CccEEEEECCCCCCHHHHHHHHhcC
Confidence            3457999999999999999999874

>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=87.80  E-value=0.26  Score=49.72  Aligned_cols=26  Identities=35%  Similarity=0.469  Sum_probs=23.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +..+++.|++|+||||++..+|..+.
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~  123 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYK  123 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            67788999999999999999998774

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=87.77  E-value=0.29  Score=44.68  Aligned_cols=25  Identities=28%  Similarity=0.252  Sum_probs=21.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|+|.|++|+|||+|...+...-
T Consensus        22 ~~ki~vvG~~~~GKSsli~~l~~~~   46 (189)
T 2gf9_A           22 MFKLLLIGNSSVGKTSFLFRYADDS   46 (189)
T ss_dssp             EEEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             eeEEEEECCCCCCHHHHHHHHHcCC
Confidence            3579999999999999999998754

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=87.73  E-value=0.3  Score=53.05  Aligned_cols=28  Identities=25%  Similarity=0.445  Sum_probs=23.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..|+|.|+||+||||++..++..+.
T Consensus        99 ~~~~vI~ivG~~GvGKTTl~~kLA~~l~  126 (504)
T 2j37_W           99 GKQNVIMFVGLQGSGKTTTCSKLAYYYQ  126 (504)
T ss_dssp             S--EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            4567899999999999999999998764

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=87.71  E-value=1.2  Score=49.44  Aligned_cols=24  Identities=25%  Similarity=0.455  Sum_probs=19.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .+++++.+|+|+|||+.+-..+..
T Consensus        28 g~~~iv~~~TGsGKTl~~~~~i~~   51 (696)
T 2ykg_A           28 GKNTIICAPTGCGKTFVSLLICEH   51 (696)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCchHHHHHHHHHHH
Confidence            367999999999999987766653

---

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	567
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	2e-58
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	3e-58
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	7e-44
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	7e-33
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	3e-30
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	2e-20
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	3e-18
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	3e-16
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	5e-16
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	3e-11
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	9e-09
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	3e-08
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	8e-08
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	1e-07
d1ny5a2	247	c.37.1.20 (A:138-384) Transcriptional activator si	3e-06
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	6e-06
d2gnoa2	198	c.37.1.20 (A:11-208) gamma subunit of DNA polymera	6e-05
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	1e-04
d1iqpa2	231	c.37.1.20 (A:2-232) Replication factor C {Archaeon	2e-04
d2fnaa2	283	c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfo	9e-04
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	0.002

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]} Length = 256

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]

 Score =  193 bits (493), Expect = 2e-58
 Identities = 72/243 (29%), Positives = 120/243 (49%), Gaps = 24/243 (9%)

Query: 270 LNTSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEG 329
           L   + + ++ ++AG D+ K E+ + +   L+ P  +         K     P+ VL  G
Sbjct: 2   LTEDQIKTTFADVAGCDEAKEEVAELVEY-LREPSRFQ--------KLGGKIPKGVLMVG 52

Query: 330 PPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNG 389
           PPGTGKT  A+ IA +A       VP   +     +  + G     +  +F  A +    
Sbjct: 53  PPGTGKTLLAKAIAGEAK------VPFFTISGSDFVEMFVGVGASRVRDMFEQAKKA-AP 105

Query: 390 AIIFLDEVDSFAVARDSEM---HEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDP 446
            IIF+DE+D+    R + +   H+   + L+ +L ++DGFE ++ ++VIAATNR   LDP
Sbjct: 106 CIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDP 165

Query: 447 ALI--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVC 501
           AL+   RFD  +  GLPD   R++I   + + +  A     A +A  T   SG D+ ++ 
Sbjct: 166 ALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLV 225

Query: 502 QQA 504
            +A
Sbjct: 226 NEA 228

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]} Length = 247

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]

 Score =  192 bits (490), Expect = 3e-58
 Identities = 78/261 (29%), Positives = 129/261 (49%), Gaps = 24/261 (9%)

Query: 272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPP 331
           T   +++++++AG ++ K E+++ +   L++P  +         +  +  P+ VL  GPP
Sbjct: 1   TEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFH--------EMGARIPKGVLLVGPP 51

Query: 332 GTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAI 391
           G GKT  AR +A +A       VP +       +  + G     +  +F  A       I
Sbjct: 52  GVGKTHLARAVAGEAR------VPFITASGSDFVEMFVGVGAARVRDLFETAKRH-APCI 104

Query: 392 IFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPAL 448
           +F+DE+D+    R S     ++   + L+ LL ++DGFE+D  +VV+AATNR   LDPAL
Sbjct: 105 VFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPDILDPAL 164

Query: 449 I--SRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMSGRDIRDVCQQ 503
           +   RFD  I    PD + R++I   +A+    AE   LA LA  T    G D+ ++  +
Sbjct: 165 LRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNE 224

Query: 504 AERSWASKIIRGQITKDGEQA 524
           A    A +  R    KD E+A
Sbjct: 225 AALLAAREGRRKITMKDLEEA 245

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

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]

 Score =  154 bits (391), Expect = 7e-44
 Identities = 76/260 (29%), Positives = 132/260 (50%), Gaps = 23/260 (8%)

Query: 276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGK 335
           +++WE+I G +  KRE+++ +   ++ P+ +         KF     + VLF GPPG GK
Sbjct: 3   QVTWEDIGGLEDVKRELQELVQYPVEHPDKFL--------KFGMTPSKGVLFYGPPGCGK 54

Query: 336 TSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
           T  A+ IAN+  A        + +    +++ ++GESE  + ++F  A +     ++F D
Sbjct: 55  TLLAKAIANECQA------NFISIKGPELLTMWFGESEANVREIFDKARQ-AAPCVLFFD 107

Query: 396 EVDSFAVAR---DSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--S 450
           E+DS A AR     +   A  R+++ +L ++DG    K V +I ATNR   +DPA++   
Sbjct: 108 ELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPG 167

Query: 451 RFDSMITFGLPDHENRQEIAAQYAKHLTKAEL---AELATATEEMSGRDIRDVCQQAERS 507
           R D +I   LPD ++R  I     +    A+      LA  T   SG D+ ++CQ+A + 
Sbjct: 168 RLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKL 227

Query: 508 WASKIIRGQITKDGEQACLP 527
              + I  +I ++ E+   P
Sbjct: 228 AIRESIESEIRRERERQTNP 247

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

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]

 Score =  124 bits (311), Expect = 7e-33
 Identities = 81/233 (34%), Positives = 119/233 (51%), Gaps = 20/233 (8%)

Query: 277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKT 336
           + ++++ G  +Q  +I++ + L L+ P ++               PR +L  GPPGTGKT
Sbjct: 1   VGYDDVGGCRKQLAQIKEMVELPLRHPALF--------KAIGVKPPRGILLYGPPGTGKT 52

Query: 337 SCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDE 396
             AR +AN+ GA          +    +MSK  GESE  L K F  A +    AIIF+DE
Sbjct: 53  LIARAVANETGAF------FFLINGPEIMSKLAGESESNLRKAFEEAEKNAP-AIIFIDE 105

Query: 397 VDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALI--SRFDS 454
           +D+ A  R+    E  RRI+S LL  +DG +Q   V+V+AATNR   +DPAL    RFD 
Sbjct: 106 LDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDR 165

Query: 455 MITFGLPDHENRQEIAAQY---AKHLTKAELAELATATEEMSGRDIRDVCQQA 504
            +  G+PD   R EI   +    K     +L ++A  T    G D+  +C +A
Sbjct: 166 EVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEA 218

>d1w44a_ c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]} Length = 321

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]

 Score =  118 bits (297), Expect = 3e-30
 Identities = 37/260 (14%), Positives = 72/260 (27%), Gaps = 31/260 (11%)

Query: 260 RRIYGLDEPQLNTSKSEISWENIAGYDQQKR----EIEDTILLSLQSPEVYDDIARGTRC 315
           +RI    E  +      +S   +     ++      ++ T  L   SP V +        
Sbjct: 64  QRIVAYKEKSVKAEDGSVSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAE-------- 115

Query: 316 KFESNRPRAV-LFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESER 374
                    + +  G   +GKT     +    G           V     +S Y  +   
Sbjct: 116 FGGHRYASGMVIVTGKGNSGKTPLVHALGEALGG----KDKYATVRFGEPLSGYNTDFNV 171

Query: 375 LLGKVFSLANELPNGAIIFLDEVDSFAVAR-DSEMHEATRRILSVLLRQIDGFEQDKKVV 433
            +  +     +     +I +D + +   A   +       R    LL  I      +  V
Sbjct: 172 FVDDIARAMLQ---HRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCV 228

Query: 434 VIAATNRKQDLDPAL------ISRFDSMITFGLPDHENRQEIAAQYAK--HLTKAELA-E 484
           VIA+ N     D  +       SR +S       D +   ++  +  +        L   
Sbjct: 229 VIASLNPT-SNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGEGLQRLTHTLQTS 287

Query: 485 LATATEEMSGRDIRDVCQQA 504
               +        +   +QA
Sbjct: 288 YGEHSVLTIHTSKQSGGKQA 307

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]} Length = 246

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]

 Score = 88.8 bits (219), Expect = 2e-20
 Identities = 28/178 (15%), Positives = 65/178 (36%), Gaps = 11/178 (6%)

Query: 316 KFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERL 375
             +     +VL EGPP +GKT+ A  IA ++     +            M  +   ++  
Sbjct: 34  NSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDK------MIGFSETAKCQ 87

Query: 376 LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVI 435
             K           + + +D+++            +   + ++L+       Q +K+++I
Sbjct: 88  AMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKLLII 147

Query: 436 AATNRKQDLDPALI-SRFDSMITFGLPDHENRQEIAA--QYAKHLTKAELAELATATE 490
             T+RK  L    + + F + I    P+    +++    +   +    E   +A   +
Sbjct: 148 GTTSRKDVLQEMEMLNAFSTTIHV--PNIATGEQLLEALELLGNFKDKERTTIAQQVK 203

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

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]

 Score = 84.3 bits (208), Expect = 3e-18
 Identities = 31/221 (14%), Positives = 61/221 (27%), Gaps = 28/221 (12%)

Query: 316 KFESNRP--RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY-GES 372
               N P  R  LF+GP  +GKT+ A  +          G   + V L +    +  G +
Sbjct: 146 CMVYNIPKKRYWLFKGPIDSGKTTLAAALLELC------GGKALNVNLPLDRLNFELGVA 199

Query: 373 ERLLGKVFSLANELPNGA-----IIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE 427
                 VF         +        ++ +D+     D  +     +             
Sbjct: 200 IDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKR------- 252

Query: 428 QDKKVVVIAATNRKQDLDPALI--SRFDSMITFGLPDHENRQ-EIAAQYAKH-LTKAELA 483
                  I   N   +        +RF   I F   D+     E +    +  + ++ +A
Sbjct: 253 TQIFPPGIVTMN---EYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIA 309

Query: 484 ELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQA 524
            L          +     Q     W  ++ +       ++ 
Sbjct: 310 LLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKM 350

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 309

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]

 Score = 77.6 bits (190), Expect = 3e-16
 Identities = 41/230 (17%), Positives = 78/230 (33%), Gaps = 20/230 (8%)

Query: 280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA 339
           ++I G    KR +   +    +  ++ +              P+ +L  GP G GKT  A
Sbjct: 14  QHIIGQADAKRAVAIALRNRWRRMQLQEP-------LRHEVTPKNILMIGPTGVGKTEIA 66

Query: 340 RVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDS 399
           R +A  A A   +     +  +  V  +       L        + +    I+F+DE+D 
Sbjct: 67  RRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDK 126

Query: 400 FAVARDSEMHEATRR-ILSVLLRQIDGFEQDKKVVVIAATN------------RKQDLDP 446
                +    + +R  +   LL  ++G     K  ++   +            R  DL P
Sbjct: 127 ICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPSDLIP 186

Query: 447 ALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRD 496
            L  R    +        + + I  +    LT+   A +AT    ++   
Sbjct: 187 ELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTT 236

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]} Length = 273

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]

 Score = 76.2 bits (186), Expect = 5e-16
 Identities = 26/263 (9%), Positives = 65/263 (24%), Gaps = 18/263 (6%)

Query: 304 EVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEV 363
            + D++    + K     P A L  G PG+GKTS    I  +            +     
Sbjct: 14  RLNDNLEELIQGKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFKQQ-- 71

Query: 364 VMSKYYGESERLLGKVFSLANE-LPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQ 422
               +    +     V               +  +         E    T  +       
Sbjct: 72  -HPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVPIQTATM 130

Query: 423 IDGFEQD---------KKVVVIAATNRKQDLDPAL--ISRFDSMITFGLPDHENRQEIAA 471
           +     +         K    +    R + +       +R        +        +  
Sbjct: 131 LQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNLPTNLET 190

Query: 472 QYAKHLTKAELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACLPPLQE 531
            +   L            +  S  +   +  +       K +  +++    Q  L  +++
Sbjct: 191 LHKTGLFSDIRLYNREGVKLYSSLETPSISPKET---LEKELNRKVSGKEIQPTLERIEQ 247

Query: 532 YIESATNRRRSLLDAAEQSHQNI 554
            +    ++      A +Q  +++
Sbjct: 248 KMVLNKHQETPEFKAIQQKLESL 270

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {Thermus thermophilus [TaxId: 274]} Length = 239

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]

 Score = 61.1 bits (147), Expect = 3e-11
 Identities = 48/250 (19%), Positives = 85/250 (34%), Gaps = 37/250 (14%)

Query: 278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTS 337
           + +   G ++ K+++   +  +    E                    +L  GPPG GKT+
Sbjct: 7   TLDEYIGQERLKQKLRVYLEAAKARKE----------------PLEHLLLFGPPGLGKTT 50

Query: 338 CARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEV 397
            A VIA++ G           V L V       +          LAN L  G I+F+DE+
Sbjct: 51  LAHVIAHELG-----------VNLRVTSGPAIEKPGD---LAAILANSLEEGDILFIDEI 96

Query: 398 DSFAVARDSEMHEATRR-----ILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRF 452
              +   +  ++ A        ++           +  +  +I AT R   +   L+SRF
Sbjct: 97  HRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRF 156

Query: 453 DSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDV--CQQAERSWAS 510
             +        E   +   + A+ L      E A      S   +R      +  R +A 
Sbjct: 157 GIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQ 216

Query: 511 KIIRGQITKD 520
                 IT++
Sbjct: 217 VAGEEVITRE 226

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]} Length = 238

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]

 Score = 53.8 bits (128), Expect = 9e-09
 Identities = 40/217 (18%), Positives = 75/217 (34%), Gaps = 32/217 (14%)

Query: 316 KFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERL 375
           K        VL  GPPG GKT+ A +IA++                       +  S  +
Sbjct: 29  KMRGEVLDHVLLAGPPGLGKTTLAHIIASELQT------------------NIHVTSGPV 70

Query: 376 LGKVFSLANELPN---GAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF-----E 427
           L K   +A  L +   G ++F+DE+     A +  ++ A       ++            
Sbjct: 71  LVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRI 130

Query: 428 QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQE----IAAQYAKHLTKAELA 483
             +   ++ AT R   L   L SRF  ++       +  +E     A+     +  A   
Sbjct: 131 DIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAE 190

Query: 484 ELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKD 520
            +A  +   + R    + ++  R   + +   +I  D
Sbjct: 191 MIAKRS-RGTPRIAIRLTKRV-RDMLTVVKADRINTD 225

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} Length = 276

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]

 Score = 53.3 bits (126), Expect = 3e-08
 Identities = 38/265 (14%), Positives = 78/265 (29%), Gaps = 40/265 (15%)

Query: 280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA 339
           + +   +QQ ++++  +   L++P                +        G PGTGKT   
Sbjct: 16  KRLPHREQQLQQLDILLGNWLRNP---------------GHHYPRATLLGRPGTGKTVTL 60

Query: 340 RVIANQ----AGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLD 395
           R +         A        +Y     ++ +          +     +E     +  L 
Sbjct: 61  RKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLR 120

Query: 396 EVDSFAVARDSEMHEATRRILSV--LLRQIDGFEQDKKVVVIAATNRKQDLD---PALIS 450
           E D +      +       ILS    L Q        ++ ++   +    L+   P+   
Sbjct: 121 ERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRG 180

Query: 451 RF-DSMITFGLPDHENRQEIAAQYAK------HLTKAELAELATATEEMSG--------R 495
                +I F     +   +I    AK        ++  L  +A  T   +         R
Sbjct: 181 IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRGDAR 240

Query: 496 DIRDVCQQAERSWASKIIRGQITKD 520
              D+  ++    A +  R  I  +
Sbjct: 241 LAIDILYRS-AYAAQQNGRKHIAPE 264

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 239

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]

 Score = 51.3 bits (122), Expect = 8e-08
 Identities = 44/226 (19%), Positives = 72/226 (31%), Gaps = 32/226 (14%)

Query: 317 FESNR-PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP--------------L 361
               R   A LF G  G GKTS AR++A               V               +
Sbjct: 28  LSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQGRFVDLI 87

Query: 362 EVVMSKYYGESE-RLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLL 420
           E+  +      + R L      A       +  +DEV              +R   + LL
Sbjct: 88  EIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHML-----------SRHSFNALL 136

Query: 421 RQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKA 480
           + ++  E  + V  + AT   Q L   ++SR        L   + R ++     +     
Sbjct: 137 KTLE--EPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDVEQIRHQLEHILNEEHIAH 194

Query: 481 ELAELATATEEMSGRDIRDVCQQAERSWASKIIRGQITKDGEQACL 526
           E   L       +   +RD     +++ AS    GQ++     A L
Sbjct: 195 EPRALQLLA-RAAEGSLRDALSLTDQAIASG--DGQVSTQAVSAML 237

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]} Length = 287

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]

 Score = 51.3 bits (121), Expect = 1e-07
 Identities = 28/276 (10%), Positives = 69/276 (25%), Gaps = 48/276 (17%)

Query: 280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA 339
             +     +   +    L  L S                S+        G  G GKT+ A
Sbjct: 16  PELRVRRGEAEALARIYLNRLLSGAG------------LSDVNMIYGSIGRVGIGKTTLA 63

Query: 340 RVIANQAGAM--------------------PWQGVPLMYVPLEVVMSKYYGESERLLGKV 379
           +    +                         +  + L+       +      +  +L  +
Sbjct: 64  KFTVKRVSEAAAKEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKAL 123

Query: 380 FSLANELPNGAIIFLDEVDSF-AVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAAT 438
                   +  ++ LDE  S  +  R +     T   +   +   DG  +   ++V +  
Sbjct: 124 VDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDV 183

Query: 439 NRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKA------------ELAELA 486
                +   +      +           +E+     +                  ++++ 
Sbjct: 184 RALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELISDVY 243

Query: 487 TATEEMSG--RDIRDVCQQAERSWASKIIRGQITKD 520
              +   G  R      + A    A  + R  +++D
Sbjct: 244 GEDKGGDGSARRAIVALKMACEM-AEAMGRDSLSED 278

>d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 247

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]

 Score = 46.8 bits (111), Expect = 3e-06
 Identities = 33/127 (25%), Positives = 56/127 (44%), Gaps = 19/127 (14%)

Query: 325 VLFEGPPGTGKTSCARVIANQAGAMPWQGV--PLMYVPLEVVMSKYYG-ESERLLGKVFS 381
           VL  G  G GK   AR+I   +       V   +  +P ++  ++ +G E     G V S
Sbjct: 26  VLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAELFGYEKGAFTGAVSS 85

Query: 382 LAN--ELPNGAIIFLDEVDSFAVARDSEMHEAT-RRILSVL----LRQIDGFEQDK-KVV 433
                EL +G  +FLDE+         E+      ++L V+      ++ G ++ +  V 
Sbjct: 86  KEGFFELADGGTLFLDEIG--------ELSLEAQAKLLRVIESGKFYRLGGRKEIEVNVR 137

Query: 434 VIAATNR 440
           ++AATNR
Sbjct: 138 ILAATNR 144

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 253

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]

 Score = 45.5 bits (106), Expect = 6e-06
 Identities = 28/248 (11%), Positives = 70/248 (28%), Gaps = 24/248 (9%)

Query: 278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTS 337
           + + + G      ++++  L + ++ +       G      S   RA +  GPPG GKT+
Sbjct: 12  NLQQVCGNKGSVMKLKN-WLANWENSKKNSFKHAGKD---GSGVFRAAMLYGPPGIGKTT 67

Query: 338 CARVIANQAGAMPWQGVPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLD 395
            A ++A + G    +          ++ +  K   ++  ++G                  
Sbjct: 68  AAHLVAQELGYDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQN-------- 119

Query: 396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSM 455
                 V    E+   +      + +      +    +++    R              +
Sbjct: 120 LNGKHFVIIMDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDI 179

Query: 456 ITFGLPDHENRQEIAAQYAKH---LTKAELAELATATEEMSGRDIRDVCQQAERSWASKI 512
                  +  +  +     +    L    +  L     + +  DIR V         +  
Sbjct: 180 QFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLI----QTTRGDIRQVINLLSTISTTT- 234

Query: 513 IRGQITKD 520
               I  +
Sbjct: 235 --KTINHE 240

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]} Length = 198

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 42.0 bits (98), Expect = 6e-05
 Identities = 24/175 (13%), Positives = 56/175 (32%), Gaps = 19/175 (10%)

Query: 318 ESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESE-RLL 376
           E +   ++L  G   +     +  +       P +   ++ +  E    +  G  + R +
Sbjct: 11  EKSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE---GENIGIDDIRTI 67

Query: 377 GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIA 436
               + + EL     + +            +    T++  +  L+ +   E  +  V++ 
Sbjct: 68  KDFLNYSPELYTRKYVIVH-----------DCERMTQQAANAFLKAL--EEPPEYAVIVL 114

Query: 437 ATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEE 491
            T R   L P + SR    +   +P    R  +  +      +  L E    T  
Sbjct: 115 NTRRWHYLLPTIKSRV-FRVVVNVPKEF-RDLVKEKIGDLWEELPLLERDFKTAL 167

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]} Length = 207

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]

 Score = 41.6 bits (96), Expect = 1e-04
 Identities = 7/37 (18%), Positives = 15/37 (40%), Gaps = 1/37 (2%)

Query: 317 FESNR-PRAVLFEGPPGTGKTSCARVIANQAGAMPWQ 352
           +++ R   A+L +  PG G  +    ++        Q
Sbjct: 18  YQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQ 54

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 231

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]

 Score = 41.1 bits (95), Expect = 2e-04
 Identities = 39/207 (18%), Positives = 71/207 (34%), Gaps = 25/207 (12%)

Query: 317 FESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLL 376
            ++     +LF GPPG GKT+ A  +A +     W+     +  LE+  S   G      
Sbjct: 40  VKTGSMPHLLFAGPPGVGKTTAALALARELFGENWR-----HNFLELNASDERG------ 88

Query: 377 GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIA 436
             +  +  ++   A        SF +    E    T+     L R ++ F     V  I 
Sbjct: 89  --INVIREKVKEFARTKPIGGASFKIIFLDEADALTQDAQQALRRTMEMF--SSNVRFIL 144

Query: 437 ATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH---LTKAELAELATATEEMS 493
           + N    +   + SR        L D +  + +          LT+  L  +      ++
Sbjct: 145 SCNYSSKIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAIL----YIA 200

Query: 494 GRDIRDVCQQAERSWASKIIRGQITKD 520
             D+R      + + A      +IT +
Sbjct: 201 EGDMRRAINILQAAAALD---KKITDE 224

>d2fnaa2 c.37.1.20 (A:1-283) Archaeal ATPase SSO1545 {Sulfolobus solfataricus [TaxId: 2287]} Length = 283

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]

 Score = 39.3 bits (90), Expect = 9e-04
 Identities = 29/185 (15%), Positives = 56/185 (30%), Gaps = 4/185 (2%)

Query: 316 KFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERL 375
           K +  R    L  G   TGK+S  ++  N+        + L     E      Y +    
Sbjct: 23  KLKGLRAPITLVLGLRRTGKSSIIKIGINELNL---PYIYLDLRKFEERNYISYKDFLLE 79

Query: 376 LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVI 435
           L K  +   +     +  L  +    +  +       R+        ++ FEQ  K  VI
Sbjct: 80  LQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVI 139

Query: 436 AATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGR 495
              +  Q+L           + +   + +  + I +     L   +   +      + GR
Sbjct: 140 IVLDEAQELVKLRGVNLLPALAYAYDNLKRIKFIMSGSEMGLLY-DYLRVEDPESPLFGR 198

Query: 496 DIRDV 500
               V
Sbjct: 199 AFSTV 203

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 227

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]

 Score = 37.4 bits (85), Expect = 0.002
 Identities = 45/216 (20%), Positives = 65/216 (30%), Gaps = 26/216 (12%)

Query: 317 FESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLL 376
            +  +   +LF GPPGTGKTS    +A +     +       + LE+  S   G      
Sbjct: 30  VDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY-----SNMVLELNASDDRGIDVVRN 84

Query: 377 GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIA 436
                 +          L  +D        E    T    + L R I      K      
Sbjct: 85  QIKDFASTRQIFSKGFKLIILD--------EADAMTNAAQNALRRVI--ERYTKNTRFCV 134

Query: 437 ATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAE---LAELATATEEMS 493
             N    L PAL+S+        LP     + IA        K        L     E+S
Sbjct: 135 LANYAHKLTPALLSQCTRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALI----ELS 190

Query: 494 GRDIRDV---CQQAERSWASKIIRGQITKDGEQACL 526
             D+R V    Q   ++        +I+ D    C 
Sbjct: 191 NGDMRRVLNVLQSC-KATLDNPDEDEISDDVIYECC 225

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	567
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.88
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.88
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.86
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.84
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.8
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.76
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.75
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.73
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.72
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.71
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.68
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.67
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.66
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.66
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.61
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.6
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.59
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.59
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.57
d1cz5a1	91	N-terminal domain of VAT-N, VAT-Nn {Archaeon Therm	99.56
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.55
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.54
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.53
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.52
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.5
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.35
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.33
d1e32a1	86	Membrane fusion ATPase p97 N-terminal domain , P97	99.28
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.26
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.86
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.58
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.05
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.03
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.76
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.73
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.5
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.46
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.42
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.41
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.41
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.4
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.36
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.31
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.29
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.26
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.25
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.24
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	97.24
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	97.24
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.22
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.2
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.18
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.17
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.15
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.14
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.09
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.09
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.08
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	96.94
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.92
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.91
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.91
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.9
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.85
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.83
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.78
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	96.77
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.76
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.71
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.65
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.62
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	96.61
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.58
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	96.56
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.53
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.41
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	96.4
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	96.38
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	96.34
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.3
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	96.27
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.24
d1okkd2	207	GTPase domain of the signal recognition particle r	96.22
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.18
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.16
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	96.14
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.14
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.14
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.1
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.0
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	95.95
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	95.9
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	95.79
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	95.74
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	95.73
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.71
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	95.69
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.64
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.63
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.63
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	95.61
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.59
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.59
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	95.36
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	95.26
d2fh5b1	207	Signal recognition particle receptor beta-subunit	95.21
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	95.16
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	95.1
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	95.07
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	95.04
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	95.01
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	94.98
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.94
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	94.84
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	94.78
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.77
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	94.76
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	94.74
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	94.74
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	94.72
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	94.71
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	94.7
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	94.68
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	94.58
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.15
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.13
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.01
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.0
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	93.91
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.58
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.52
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.11
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	92.93
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	92.89
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	92.61
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	92.58
d2awna2	232	Maltose transport protein MalK, N-terminal domain	92.5
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.43
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.32
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	92.32
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	92.2
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	92.09
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	91.97
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.97
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	91.85
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	91.84
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	91.78
d1g2912	240	Maltose transport protein MalK, N-terminal domain	91.76
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	91.76
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	91.62
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	91.55
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	91.46
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	91.44
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	91.37
d1cz5a2	94	C-terminal domain of VAT-N, VAT-Nc {Archaeon Therm	91.34
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	91.18
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	91.17
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	91.04
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	91.01
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	90.88
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	90.87
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	90.85
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	90.73
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	90.5
d1nrjb_	209	Signal recognition particle receptor beta-subunit	90.47
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	90.47
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	90.41
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	90.28
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	90.26
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	90.16
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	90.13
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	90.04
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	90.01
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	89.99
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	89.92
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.84
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	89.82
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	89.79
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	89.77
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	89.7
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	89.65
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	89.54
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	89.45
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	89.38
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	89.37
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	89.34
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	89.25
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	89.17
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	89.02
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	88.91
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	88.83
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	88.74
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	88.71
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	88.64
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	88.53
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	88.43
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	88.42
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	88.42
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	88.33
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	88.33
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	88.31
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	88.3
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	88.27
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	88.06
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	88.01
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	87.87
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	87.7
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	87.69
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	87.59
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	87.59
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	87.48
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	87.32
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	87.22
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.19
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	87.06
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	87.04
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	87.02
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	87.0
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	86.94
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	86.7
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	86.64
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	86.61
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	86.48
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	86.26
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	86.22
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	86.22
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	86.07
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	85.9
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	85.9
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	85.72
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	85.46
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	85.36
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	85.31
d1xpua3	289	Transcription termination factor Rho, ATPase domai	84.23
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	83.97
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	83.96
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	83.78
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	83.57
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	83.28
d1fx0a3	276	Central domain of alpha subunit of F1 ATP synthase	82.6
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	81.87
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	81.72
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	81.64
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	81.24
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	80.58

>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=100.00  E-value=1.4e-36  Score=302.06  Aligned_cols=222  Identities=32%  Similarity=0.540  Sum_probs=196.1

Q ss_pred             CCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC
Q 047219          273 SKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ  352 (567)
Q Consensus       273 ~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~  352 (567)
                      +.|+++|+||+|++++|+.|++.+ .++.+|+.|+++|        ...++++||+||||||||++|+++|+++      
T Consensus         2 ~~p~~~~~di~G~~~~k~~l~~~i-~~l~~~~~~~~~g--------~~~~~giLl~GppGtGKT~la~aia~~~------   66 (247)
T d1ixza_           2 EAPKVTFKDVAGAEEAKEELKEIV-EFLKNPSRFHEMG--------ARIPKGVLLVGPPGVGKTHLARAVAGEA------   66 (247)
T ss_dssp             CCCSCCGGGCCSCHHHHHHHHHHH-HHHHCHHHHHHTT--------CCCCSEEEEECCTTSSHHHHHHHHHHHT------
T ss_pred             CCCCCcHHHHccHHHHHHHHHHHH-HHHHCHHHHHHcC--------CCCCceEEEecCCCCChhHHHHHHHHHc------
Confidence            457899999999999999998876 4689999999886        6788999999999999999999999999      


Q ss_pred             CcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccC
Q 047219          353 GVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQD  429 (567)
Q Consensus       353 ~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~  429 (567)
                      +.++++++++.+.++|+|++++.++.+|+.|+.++| +||||||||.|..++...   ......++++.|+..++++..+
T Consensus        67 ~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~a~~~~p-~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~  145 (247)
T d1ixza_          67 RVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAP-CIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKD  145 (247)
T ss_dssp             TCCEEEEEHHHHHHSCTTHHHHHHHHHHHHHTTSSS-EEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTT
T ss_pred             CCCEEEEEhHHhhhccccHHHHHHHHHHHHHHHcCC-EEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCC
Confidence            788999999999999999999999999999988875 999999999998776433   2345667889999999998888


Q ss_pred             CcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .+++||+|||.++.+|++|++  ||+..|+|+.|+.++|.+|++.++....   ..+++.+++.++||+++||+++|++|
T Consensus       146 ~~vivi~tTn~~~~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~~A  225 (247)
T d1ixza_         146 TAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  225 (247)
T ss_dssp             CCEEEEEEESCGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CCEEEEEeCCCccccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHHHHH
Confidence            899999999999999999996  9999999999999999999999987532   33688999999999999999999999


Q ss_pred             HHHHHH
Q 047219          505 ERSWAS  510 (567)
Q Consensus       505 ~~~a~~  510 (567)
                      +..+++
T Consensus       226 ~l~a~~  231 (247)
T d1ixza_         226 ALLAAR  231 (247)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            876554

>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=100.00  E-value=2.5e-36  Score=301.57  Aligned_cols=223  Identities=31%  Similarity=0.549  Sum_probs=196.2

Q ss_pred             cCCCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          272 TSKSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       272 ~~~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      ++.++++|+||+|+++++++|++.+. ++++++.|+++|        ...++++||+||||||||++|+++|+++     
T Consensus         4 ~~~~~~t~~Di~Gl~~~k~~l~e~v~-~~~~~~~~~~~g--------~~~~~~iLL~GppGtGKT~la~~iA~~~-----   69 (256)
T d1lv7a_           4 EDQIKTTFADVAGCDEAKEEVAELVE-YLREPSRFQKLG--------GKIPKGVLMVGPPGTGKTLLAKAIAGEA-----   69 (256)
T ss_dssp             ECSSCCCGGGSCSCHHHHHHTHHHHH-HHHCGGGC-------------CCCCEEEEECCTTSCHHHHHHHHHHHH-----
T ss_pred             CCCCCCCHHHHhchHHHHHHHHHHHH-HHHCHHHHHHcC--------CCCCCeEEeeCCCCCCccHHHHHHHHHc-----
Confidence            35678999999999999999999875 588999998876        7889999999999999999999999999     


Q ss_pred             CCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCccc
Q 047219          352 QGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~  428 (567)
                       +.+++.++++.+.++|+|+++..++.+|+.|+.++| +||||||+|.+...++..   ......+++++|+..++++..
T Consensus        70 -~~~~~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~P-~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~  147 (256)
T d1lv7a_          70 -KVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAP-CIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG  147 (256)
T ss_dssp             -TCCEEEECSCSSTTSCCCCCHHHHHHHHHHHHTTCS-EEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCS
T ss_pred             -CCCEEEEEhHHhhhcchhHHHHHHHHHHHHHHHcCC-EEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCC
Confidence             889999999999999999999999999999998875 999999999998776533   234556788999999999888


Q ss_pred             CCcEEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          429 DKKVVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       429 ~~~viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      +.+++||+|||.++.+|++|++  ||+..++|+.|+.++|.+|++.+++++.   +.++..++..+.||+++||..+|++
T Consensus       148 ~~~v~vIatTn~~~~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~~  227 (256)
T d1lv7a_         148 NEGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNE  227 (256)
T ss_dssp             SSCEEEEEEESCTTTSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHH
T ss_pred             CCCEEEEEeCCCcccCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHHH
Confidence            8899999999999999999997  9999999999999999999999988753   3478899999999999999999999


Q ss_pred             HHHHHHH
Q 047219          504 AERSWAS  510 (567)
Q Consensus       504 a~~~a~~  510 (567)
                      |...+++
T Consensus       228 A~~~a~~  234 (256)
T d1lv7a_         228 AALFAAR  234 (256)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            8765543

>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=100.00  E-value=3.5e-36  Score=300.94  Aligned_cols=222  Identities=37%  Similarity=0.607  Sum_probs=203.4

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      ++|+||+|++.+|++|++.+..++++|+.|+++|        ..+|+++|||||||||||++|+++|+++      +.++
T Consensus         1 ~~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g--------~~~~~giLL~GppGtGKT~l~~ala~~~------~~~~   66 (258)
T d1e32a2           1 VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIG--------VKPPRGILLYGPPGTGKTLIARAVANET------GAFF   66 (258)
T ss_dssp             CCGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCC--------CCCCCEEEEECCTTSSHHHHHHHHHHHT------TCEE
T ss_pred             CChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCC--------CCCCceeEEecCCCCCchHHHHHHHHHh------CCeE
Confidence            5899999999999999999999999999999886        7889999999999999999999999999      8889


Q ss_pred             EEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEE
Q 047219          357 MYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIA  436 (567)
Q Consensus       357 ~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIa  436 (567)
                      +.++++.+.+.+.|+.+..++.+|..|...+| +||||||+|.+..++.....+...+++..++..++......+++||+
T Consensus        67 ~~i~~~~l~~~~~g~~~~~l~~~f~~A~~~~p-~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~vlvi~  145 (258)
T d1e32a2          67 FLINGPEIMSKLAGESESNLRKAFEEAEKNAP-AIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMA  145 (258)
T ss_dssp             EEECHHHHTTSCTTHHHHHHHHHHHHHHHTCS-EEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCCSSCEEEEE
T ss_pred             EEEEchhhcccccccHHHHHHHHHHHHHhcCC-eEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccccCCccEEE
Confidence            99999999999999999999999999998885 99999999999988776555556677888888888888888999999


Q ss_pred             eeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhC---HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHH
Q 047219          437 ATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLT---KAELAELATATEEMSGRDIRDVCQQAERSWASK  511 (567)
Q Consensus       437 aTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~---~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r  511 (567)
                      |||.++.+|+++++  ||+..|+|+.|+.++|.+|++.+++++.   ..++..+++.|+||+++||+.+|++|...+.++
T Consensus       146 tTn~~~~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~~A~~~a~~~  225 (258)
T d1e32a2         146 ATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRK  225 (258)
T ss_dssp             EESCGGGSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             eCCCccccchhhhhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHHHHHHHHHHh
Confidence            99999999999998  9999999999999999999999887643   236889999999999999999999999888776


Q ss_pred             HH
Q 047219          512 II  513 (567)
Q Consensus       512 ~i  513 (567)
                      ..
T Consensus       226 ~~  227 (258)
T d1e32a2         226 KM  227 (258)
T ss_dssp             HH
T ss_pred             hc
Confidence            54

>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=100.00  E-value=7.9e-35  Score=292.22  Aligned_cols=226  Identities=31%  Similarity=0.570  Sum_probs=196.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      |.++|+||+|+++++++|.+.+..++.+|+.|.++|        ..+++++|||||||||||++|+++|+++      +.
T Consensus         2 p~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g--------~~~~~giLL~Gp~GtGKT~l~~ala~~~------~~   67 (265)
T d1r7ra3           2 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFG--------MTPSKGVLFYGPPGCGKTLLAKAIANEC------QA   67 (265)
T ss_dssp             CCCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCC--------CCCCCEEEEBCCTTSSHHHHHHHHHHHT------TC
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCC--------CCCCCeEEEECCCCCcchhHHHHHHHHh------CC
Confidence            679999999999999999999999999999998876        7889999999999999999999999999      88


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhh---hHHHHHHHHHHHHHhhcCcccCCc
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSE---MHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~---l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      +++.+++..+.+.+.|..+..++.+|..|+.++| |||||||+|.+..++...   .....+++++.|+..++++....+
T Consensus        68 ~~~~~~~~~l~~~~~~~~~~~l~~~f~~A~~~~p-~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~  146 (265)
T d1r7ra3          68 NFISIKGPELLTMWFGESEANVREIFDKARQAAP-CVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKN  146 (265)
T ss_dssp             EEEEECHHHHHTSCTTTHHHHHHHHHHHHHHTCS-EEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------C
T ss_pred             cEEEEEHHHhhhccccchHHHHHHHHHHHHhcCC-cceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCC
Confidence            9999999999999999999999999999998885 999999999998776432   234456788999999998877788


Q ss_pred             EEEEEeeCCCCCCChHHHh--ccceEEEecCCCHHHHHHHHHHHHHhhCH---HHHHHHHHhccCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALIS--RFDSMITFGLPDHENRQEIAAQYAKHLTK---AELAELATATEEMSGRDIRDVCQQAER  506 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~s--Rf~~~I~i~~P~~~eR~eIL~~~~~~~~~---~~l~~la~~t~g~s~~dL~~L~~~a~~  506 (567)
                      ++||+|||.++.+|++|++  ||+.+++|+.|+.++|.+||+.++++...   .+++.++..+.||+++||..+|++|..
T Consensus       147 v~vi~ttn~~~~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~~A~~  226 (265)
T d1r7ra3         147 VFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACK  226 (265)
T ss_dssp             CEEEECCBSCTTTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHHHHHHH
T ss_pred             EEEEEeCCCchhCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            9999999999999999997  99999999999999999999998876432   267899999999999999999999998


Q ss_pred             HHHHHHHhc
Q 047219          507 SWASKIIRG  515 (567)
Q Consensus       507 ~a~~r~i~~  515 (567)
                      .+.++.+..
T Consensus       227 ~A~~~~~~~  235 (265)
T d1r7ra3         227 LAIRESIES  235 (265)
T ss_dssp             HHHHHC---
T ss_pred             HHHHHHHHH
Confidence            887775543

>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=99.88  E-value=8.1e-23  Score=208.50  Aligned_cols=180  Identities=21%  Similarity=0.328  Sum_probs=145.7

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .|+|++++++.|.+++..++++..+......       ..+++++||+||||||||++|+++|+++      +.+|+.++
T Consensus        15 ~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~-------~~~~~~iLl~GPpG~GKT~lAkalA~~~------~~~~~~i~   81 (309)
T d1ofha_          15 HIIGQADAKRAVAIALRNRWRRMQLQEPLRH-------EVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKVE   81 (309)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHH-------HCCCCCEEEECCTTSSHHHHHHHHHHHH------TCCEEEEE
T ss_pred             cccChHHHHHHHHHHHHHHHHHhccCCCCcc-------CCCCceEEEECCCCCCHHHHHHHHhhcc------ccchhccc
Confidence            4899999999999988766555544433221       3478999999999999999999999999      77899999


Q ss_pred             hhhHH--hhhhchhHHHHHHHHHHHhcC----CCCcEEEEcCcchhhhhhhhhhHHHHH-HHHHHHHHhhcCccc-----
Q 047219          361 LEVVM--SKYYGESERLLGKVFSLANEL----PNGAIIFLDEVDSFAVARDSEMHEATR-RILSVLLRQIDGFEQ-----  428 (567)
Q Consensus       361 ~~~l~--s~~~G~~~~~l~~~f~~A~~~----a~~~ILfIDEID~L~~~~q~~l~~~~~-~vl~~LL~~ld~~~~-----  428 (567)
                      ++++.  +.+.|+.+..++.+|..+...    ..+|||||||||++.+.+.....++.. .+++.||..+++...     
T Consensus        82 ~s~~~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~~~~~  161 (309)
T d1ofha_          82 ATKFTEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHG  161 (309)
T ss_dssp             GGGGSSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTE
T ss_pred             ccccccceeEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEecCCe
Confidence            99997  457889999999999987642    125999999999999888776666554 367889999987532     


Q ss_pred             ---CCcEEEEEe----eCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHH
Q 047219          429 ---DKKVVVIAA----TNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQY  473 (567)
Q Consensus       429 ---~~~viVIaa----TN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~  473 (567)
                         ..++.+|++    ++.+..++|+++.||+..+.++.|+..++.+|+..+
T Consensus       162 ~i~~s~ilfi~~ga~~~~~~~~~~p~l~~R~~~~i~~~~~~~~~~~~Il~~~  213 (309)
T d1ofha_         162 MVKTDHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFERILTEP  213 (309)
T ss_dssp             EEECTTCEEEEEECCSSSCGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSS
T ss_pred             EEEccceeEEeccchhhcCcccchhhhhhhhheeeeccCCCHHHHHHHHHHH
Confidence               235667766    467889999999999999999999999999998654

>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=99.88  E-value=4.1e-23  Score=204.14  Aligned_cols=197  Identities=18%  Similarity=0.271  Sum_probs=146.1

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      .+-.+.|+|+.+.++.+.+....+......      .     ...++++|||+||||||||++|++||+++      +.+
T Consensus         5 ~~~~~~~i~~~~~i~~i~~~~~~~~~~~~~------~-----~~~p~~~vLL~GppGtGKT~la~alA~~~------~~~   67 (246)
T d1d2na_           5 SYIMNGIIKWGDPVTRVLDDGELLVQQTKN------S-----DRTPLVSVLLEGPPHSGKTALAAKIAEES------NFP   67 (246)
T ss_dssp             TTCTTCCCCCSHHHHHHHHHHHHHHHHHHH------C-----SSCSEEEEEEECSTTSSHHHHHHHHHHHH------TCS
T ss_pred             HhhccCCcCcCHHHHHHHHHHHHHHHHHhc------c-----CCCCCeEEEEECcCCCCHHHHHHHHhhcc------ccc
Confidence            345567999988888888877755332210      0     14567899999999999999999999999      788


Q ss_pred             eEEechhhHHhhhhchh-HHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccC-CcEE
Q 047219          356 LMYVPLEVVMSKYYGES-ERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQD-KKVV  433 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~-~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~-~~vi  433 (567)
                      |+.+++++....+.+.. .+.++.+|+.|...+ ++||||||||.+...+.... +...+++..++..+++.... .+++
T Consensus        68 ~~~i~~~~~~~g~~~~~~~~~i~~if~~A~~~~-p~il~iDEid~l~~~~~~~~-~~~~~~~~~ll~~l~~~~~~~~~v~  145 (246)
T d1d2na_          68 FIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQ-LSCVVVDDIERLLDYVPIGP-RFSNLVLQALLVLLKKAPPQGRKLL  145 (246)
T ss_dssp             EEEEECGGGCTTCCHHHHHHHHHHHHHHHHTSS-EEEEEECCHHHHTTCBTTTT-BCCHHHHHHHHHHTTCCCSTTCEEE
T ss_pred             ccccccccccccccccchhhhhhhhhhhhhhcc-cceeehhhhhhHhhhccccc-chhHHHHHHHHHHhcCCCcccccee
Confidence            99999887776666654 366899999999887 49999999999976654321 12245667888888876543 4689


Q ss_pred             EEEeeCCCCCCChH-HHhccceEEEecCCCHHHHHHHHHHHHH--hhCHHHHHHHHHhccCCC
Q 047219          434 VIAATNRKQDLDPA-LISRFDSMITFGLPDHENRQEIAAQYAK--HLTKAELAELATATEEMS  493 (567)
Q Consensus       434 VIaaTN~~~~Ld~a-L~sRf~~~I~i~~P~~~eR~eIL~~~~~--~~~~~~l~~la~~t~g~s  493 (567)
                      ||+|||+++.+++. +++||+..|++  |+..+|.++++.+..  .+.......++..+.|..
T Consensus       146 vi~tTn~~~~ld~~~~~~rF~~~i~~--P~~~~r~~il~~l~~~~~~~~~~~~~i~~~~~g~~  206 (246)
T d1d2na_         146 IIGTTSRKDVLQEMEMLNAFSTTIHV--PNIATGEQLLEALELLGNFKDKERTTIAQQVKGKK  206 (246)
T ss_dssp             EEEEESCHHHHHHTTCTTTSSEEEEC--CCEEEHHHHHHHHHHHTCSCHHHHHHHHHHHTTSE
T ss_pred             eeeccCChhhccchhhcCccceEEec--CCchhHHHHHHHHHhccCCChHHHHHHHHHcCCCc
Confidence            99999999988865 66799888877  665566666665433  356667777777776643

>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=99.86  E-value=4.5e-24  Score=217.62  Aligned_cols=162  Identities=17%  Similarity=0.162  Sum_probs=127.7

Q ss_pred             ccChhhHHhhhhcccccccCCCCceEE-eeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHH
Q 047219          300 LQSPEVYDDIARGTRCKFESNRPRAVL-FEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGK  378 (567)
Q Consensus       300 l~~pelf~~l~~~~~~~~~~~~p~~VL-L~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~  378 (567)
                      ...|.+|+.++        ...+++++ |+||||||||++|+++|.++..    +.+|+.++++++.++|.|+++++++.
T Consensus       108 ~~~~~~~~~~~--------~~~~~g~~l~~G~pG~GKT~la~ala~~~~~----~~~~~~~~~~~~~~~~~G~~e~~~~~  175 (321)
T d1w44a_         108 GCSPVVAEFGG--------HRYASGMVIVTGKGNSGKTPLVHALGEALGG----KDKYATVRFGEPLSGYNTDFNVFVDD  175 (321)
T ss_dssp             SBCCEEEEETT--------EEEESEEEEEECSSSSCHHHHHHHHHHHHHT----TSCCEEEEBSCSSTTCBCCHHHHHHH
T ss_pred             ccchHHHHHhh--------cccCCceEEEECCCCccHHHHHHHHHHHhcC----CCCeEEEEhhHhhhcccchHHHHHHH
Confidence            34566666554        45666755 5899999999999999999843    46789999999999999999999999


Q ss_pred             HHHHHhcCCCCcEEEEcCcchhhhhhhhhhHH-HHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCCh----HHHh--c
Q 047219          379 VFSLANELPNGAIIFLDEVDSFAVARDSEMHE-ATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDP----ALIS--R  451 (567)
Q Consensus       379 ~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~-~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~----aL~s--R  451 (567)
                      +|+.|+.   ++||||||||.+.++++..... ..+++++++|..||++....+|+||+|||+ ..+++    ++.+  |
T Consensus       176 ~f~~a~~---~~ilf~DEid~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~~~~v~viaatN~-~~~~~~i~~~~~r~~R  251 (321)
T d1w44a_         176 IARAMLQ---HRVIVIDSLKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAASRGCVVIASLNP-TSNDDKIVELVKEASR  251 (321)
T ss_dssp             HHHHHHH---CSEEEEECCTTTC-----------CCHHHHHHHHHHHHHHHHHTCEEEEECCC-CCCCHHHHHHHHHHHH
T ss_pred             HHHHHhh---ccEEEeehhhhhccccccCCCCCcchhhhhhhhhhccccccCCCeEEEEeCCC-cccccchhhhhhccCc
Confidence            9999985   5899999999999998755443 446899999999999988889999999995 44444    4445  9


Q ss_pred             cceEEEecCCCHHHHHHHHHHHHHhh
Q 047219          452 FDSMITFGLPDHENRQEIAAQYAKHL  477 (567)
Q Consensus       452 f~~~I~i~~P~~~eR~eIL~~~~~~~  477 (567)
                      |+..+.+..|+.++|.+|+..+.+.+
T Consensus       252 f~~~v~v~~pd~~~r~~il~~~~~~~  277 (321)
T d1w44a_         252 SNSTSLVISTDVDGEWQVLTRTGEGL  277 (321)
T ss_dssp             HSCSEEEEECSSTTEEEEEEECBTTC
T ss_pred             ccceeecCCCChHHHHHHHHHhccCc
Confidence            99999999999999999987665543

>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=99.84  E-value=2.8e-20  Score=181.09  Aligned_cols=194  Identities=20%  Similarity=0.282  Sum_probs=137.8

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCe
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPL  356 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~  356 (567)
                      .+|+|++|++++++.|.+++......                .....++|||||||||||++|+++|+++      +.++
T Consensus         6 ~~~~divGqe~~~~~l~~~i~~~~~~----------------~~~~~~~L~~GPpGtGKT~lA~~la~~~------~~~~   63 (238)
T d1in4a2           6 KSLDEFIGQENVKKKLSLALEAAKMR----------------GEVLDHVLLAGPPGLGKTTLAHIIASEL------QTNI   63 (238)
T ss_dssp             SSGGGCCSCHHHHHHHHHHHHHHHHH----------------TCCCCCEEEESSTTSSHHHHHHHHHHHH------TCCE
T ss_pred             CcHHHcCChHHHHHHHHHHHHHHHhc----------------CCCCCeEEEECCCCCcHHHHHHHHHhcc------CCCc
Confidence            48999999999999999988654211                4556789999999999999999999999      6778


Q ss_pred             EEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHH-------HHHHhhcCcccC
Q 047219          357 MYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILS-------VLLRQIDGFEQD  429 (567)
Q Consensus       357 ~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~-------~LL~~ld~~~~~  429 (567)
                      ..++.......      ..+...+..   ...++++|+||+|.+....++.+.........       .....+.  ...
T Consensus        64 ~~~~~~~~~~~------~~~~~~~~~---~~~~~~~~ide~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~--~~~  132 (238)
T d1in4a2          64 HVTSGPVLVKQ------GDMAAILTS---LERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIR--IDI  132 (238)
T ss_dssp             EEEETTTCCSH------HHHHHHHHH---CCTTCEEEEETGGGCCHHHHHHHHHHHHTSCCCC-----------------
T ss_pred             ccccCcccccH------HHHHHHHHh---hccCCchHHHHHHHhhhHHHhhcccceeeeeeeeeecCcccccccc--cCC
Confidence            88776554321      223333333   23468999999999987655544333221000       0000000  123


Q ss_pred             CcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          430 KKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       430 ~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                      .++++|++||.+..+++.+++||+..+.++.|+.+++..+++.....    +..+.++.++..+.| +.+.+.++++.+
T Consensus       133 ~~~~~I~at~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s~g-d~R~ai~~l~~~  210 (238)
T d1in4a2         133 QPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRG-TPRIAIRLTKRV  210 (238)
T ss_dssp             CCCEEEEEESCGGGSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTSTT-CHHHHHHHHHHH
T ss_pred             CCeEEEEecCCCccccccceeeeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhCCC-CHHHHHHHHHHH
Confidence            57899999999999999999999889999999999999999988765    456678888877765 445544555443

>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=99.80  E-value=2e-18  Score=168.04  Aligned_cols=193  Identities=20%  Similarity=0.300  Sum_probs=135.7

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      +.+|+|++|+++++++|+.++......                ...+.++|||||||||||++|+++|+++      +.+
T Consensus         5 P~~~ddivGq~~~~~~L~~~i~~~~~~----------------~~~~~~~Ll~GPpG~GKTtla~~la~~~------~~~   62 (239)
T d1ixsb2           5 PKTLDEYIGQERLKQKLRVYLEAAKAR----------------KEPLEHLLLFGPPGLGKTTLAHVIAHEL------GVN   62 (239)
T ss_dssp             CCSGGGSCSCHHHHHHHHHHHHHHTTS----------------SSCCCCEEEECCTTSCHHHHHHHHHHHH------TCC
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhc----------------CCCCCeEEEECCCCCCHHHHHHHHHHHh------CCC
Confidence            468999999999999999988654221                3567899999999999999999999999      777


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhh--------cCcc
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQI--------DGFE  427 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~l--------d~~~  427 (567)
                      +..++++.....  +.    .......  ....++++||||+|.+....++.+...++..   .....        ....
T Consensus        63 ~~~~~~~~~~~~--~~----~~~~~~~--~~~~~~i~~iDe~~~~~~~~~~~l~~~~e~~---~~~~~~~~~~~~~~~~~  131 (239)
T d1ixsb2          63 LRVTSGPAIEKP--GD----LAAILAN--SLEEGDILFIDEIHRLSRQAEEHLYPAMEDF---VMDIVIGQGPAARTIRL  131 (239)
T ss_dssp             EEEEETTTCCSH--HH----HHHHHHT--TCCTTCEEEEETGGGCCHHHHHHHHHHHHHS---EEEEECSCTTCCCEEEE
T ss_pred             eEeccCCccccc--hh----hHHHHHh--hccCCCeeeeecccccchhHHHhhhhhhhhh---hhhhhhccchhhhhccc
Confidence            888877654321  11    1111111  2233579999999999876555443332210   00000        0012


Q ss_pred             cCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          428 QDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       428 ~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      ...++++|++||.+....+..++|++..+.+..|+.+++..++...+.+    +..+.++.++..+.| ..+...++++
T Consensus       132 ~~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~g-d~R~a~~~l~  209 (239)
T d1ixsb2         132 ELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG-TMRVAKRLFR  209 (239)
T ss_dssp             ECCCCEEEEEESCCSSCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTS-SHHHHHHHHH
T ss_pred             CCCCEEEEeeccCcccccchhhcccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCC-CHHHHHHHHH
Confidence            3457889999988888777777777799999999999999999988775    566788889988877 3333334443

>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=99.76  E-value=6.5e-18  Score=163.53  Aligned_cols=185  Identities=20%  Similarity=0.250  Sum_probs=132.0

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      +.+|+||+|++++++.|+.++..                     ....++||+||||||||++|+++|+++....+ ..+
T Consensus        20 P~~~~diig~~~~~~~l~~~i~~---------------------~~~~~lll~Gp~G~GKTtla~~iak~l~~~~~-~~~   77 (231)
T d1iqpa2          20 PQRLDDIVGQEHIVKRLKHYVKT---------------------GSMPHLLFAGPPGVGKTTAALALARELFGENW-RHN   77 (231)
T ss_dssp             CCSTTTCCSCHHHHHHHHHHHHH---------------------TCCCEEEEESCTTSSHHHHHHHHHHHHHGGGH-HHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHc---------------------CCCCeEEEECCCCCcHHHHHHHHHHHHHhccc-CCC
Confidence            35899999999999999988752                     23457999999999999999999998742211 345


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHHH-HhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEE
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFSL-ANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVV  434 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~~-A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viV  434 (567)
                      +++++++...+.....  ......... ........++++||+|.+....+.           .|+..++  ....++++
T Consensus        78 ~~e~n~s~~~~~~~~~--~~~~~~~~~~~~~~~~~~iilide~d~~~~~~~~-----------~ll~~l~--~~~~~~~~  142 (231)
T d1iqpa2          78 FLELNASDERGINVIR--EKVKEFARTKPIGGASFKIIFLDEADALTQDAQQ-----------ALRRTME--MFSSNVRF  142 (231)
T ss_dssp             EEEEETTCHHHHHTTH--HHHHHHHHSCCGGGCSCEEEEEETGGGSCHHHHH-----------HHHHHHH--HTTTTEEE
T ss_pred             eeEEecCcccchhHHH--HHHHHHHhhhhccCCCceEEeehhhhhcchhHHH-----------HHhhhcc--cCCcceEE
Confidence            7777776544321111  111111110 011223589999999998755333           3344443  23567899


Q ss_pred             EEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHH
Q 047219          435 IAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQ  502 (567)
Q Consensus       435 IaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~  502 (567)
                      |++||....++++|++|| ..+.+..|+..+...+++..+..    +..+.++.+++...|    |++.+++
T Consensus       143 i~~~n~~~~i~~~l~sR~-~~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~~~g----diR~ai~  209 (231)
T d1iqpa2         143 ILSCNYSSKIIEPIQSRC-AIFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIAEG----DMRRAIN  209 (231)
T ss_dssp             EEEESCGGGSCHHHHHTE-EEEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHHTT----CHHHHHH
T ss_pred             EeccCChhhchHhHhCcc-ccccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC----CHHHHHH
Confidence            999999999999999999 78999999999999999988874    567788888887665    5555544

>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=99.75  E-value=3e-19  Score=176.19  Aligned_cols=196  Identities=21%  Similarity=0.277  Sum_probs=139.4

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +.+|.+.+++++.+.+...                   +....+|||+||+|||||++|++||..+...   ..+++.++
T Consensus         1 ~~v~~S~~~~~~~~~~~~~-------------------a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~---~~~~~~~~   58 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKI-------------------SCAECPVLITGESGVGKEVVARLIHKLSDRS---KEPFVALN   58 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHH-------------------TTCCSCEEEECSTTSSHHHHHHHHHHHSTTT---TSCEEEEE
T ss_pred             CeEecCHHHHHHHHHHHHH-------------------hCCCCCEEEECCCCcCHHHHHHHHHHhcCCc---ccccccch
Confidence            4689999999999998865                   5667889999999999999999999987654   44566666


Q ss_pred             hhh-----HHhhhhchhHHH-------HHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCccc
Q 047219          361 LEV-----VMSKYYGESERL-------LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQ  428 (567)
Q Consensus       361 ~~~-----l~s~~~G~~~~~-------l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~  428 (567)
                      +..     ....+||.....       ...+|+.+    .+++|||||||.|+...|..+....+.  ..+....+....
T Consensus        59 ~~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~l~~a----~gGtL~l~~i~~L~~~~Q~~L~~~l~~--~~~~~~~~~~~~  132 (247)
T d1ny5a2          59 VASIPRDIFEAELFGYEKGAFTGAVSSKEGFFELA----DGGTLFLDEIGELSLEAQAKLLRVIES--GKFYRLGGRKEI  132 (247)
T ss_dssp             TTTSCHHHHHHHHHCBCTTSSTTCCSCBCCHHHHT----TTSEEEEESGGGCCHHHHHHHHHHHHH--SEECCBTCCSBE
T ss_pred             hhhhhhcccHHHhcCcccCCcCCcccccCCHHHcc----CCCEEEEeChHhCCHHHHHHHHHHHHh--CCEEECCCCCce
Confidence            643     344445532111       11234443    379999999999987755544333221  001111111122


Q ss_pred             CCcEEEEEeeCC-------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhhCHHHHHHHHHhccCCCHHHHHHHH
Q 047219          429 DKKVVVIAATNR-------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHLTKAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       429 ~~~viVIaaTN~-------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ..++++|++|+.       .+.++++|++|| ..+.+.+|++++|.+++..+++++......++.....+++...+..|.
T Consensus       133 ~~~~RlI~~s~~~l~~l~~~~~f~~~L~~~l-~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~  211 (247)
T d1ny5a2         133 EVNVRILAATNRNIKELVKEGKFREDLYYRL-GVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLL  211 (247)
T ss_dssp             ECCCEEEEEESSCHHHHHHTTSSCHHHHHHH-TTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHH
T ss_pred             ecCeEEEEecCCCHHHHHHcCCCcHHHHhhc-CeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHH
Confidence            347889999875       346999999999 677889999999999999988887777777776666778888888888


Q ss_pred             HHHH
Q 047219          502 QQAE  505 (567)
Q Consensus       502 ~~a~  505 (567)
                      ++.|
T Consensus       212 ~~~W  215 (247)
T d1ny5a2         212 SYPW  215 (247)
T ss_dssp             HSCC
T ss_pred             hCCC
Confidence            8777

>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=99.73  E-value=1.8e-16  Score=154.83  Aligned_cols=182  Identities=20%  Similarity=0.238  Sum_probs=131.9

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc--
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV--  354 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~--  354 (567)
                      .+|+|++|+++.++.|...+..                    ...|+++||+||||||||++|+++++++........  
T Consensus         9 ~~~~dlig~~~~~~~L~~~i~~--------------------~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~   68 (239)
T d1njfa_           9 QTFADVVGQEHVLTALANGLSL--------------------GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATP   68 (239)
T ss_dssp             SSGGGSCSCHHHHHHHHHHHHT--------------------TCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSC
T ss_pred             CCHHHccChHHHHHHHHHHHHc--------------------CCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCc
Confidence            5899999999999999887752                    356778999999999999999999999854311111  


Q ss_pred             ----------------CeEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHH
Q 047219          355 ----------------PLMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLDEVDSFAVARDSEMHEATRRI  415 (567)
Q Consensus       355 ----------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~v  415 (567)
                                      .++.++....      .....++.+++.+...   ....++||||+|.|...           .
T Consensus        69 ~~~~~~~~~i~~~~~~~~~~~~~~~~------~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~~~-----------~  131 (239)
T d1njfa_          69 CGVCDNCREIEQGRFVDLIEIDAASR------TKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLSRH-----------S  131 (239)
T ss_dssp             CSCSHHHHHHHHTCCTTEEEEETTCS------SSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSCHH-----------H
T ss_pred             cccchHHHHHHcCCCCeEEEecchhc------CCHHHHHHHHHHHHhccccCCCEEEEEECcccCCHH-----------H
Confidence                            1222222110      0123345555544322   23469999999999643           3


Q ss_pred             HHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccC
Q 047219          416 LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEE  491 (567)
Q Consensus       416 l~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g  491 (567)
                      ++.|++.++.  .+.++++|++||.+..+.+++++|| ..+.|+.|+.++..+.+...+..    +..+.++.++..+.|
T Consensus       132 q~~Llk~lE~--~~~~~~~il~tn~~~~i~~~i~SRc-~~i~~~~~~~~~i~~~l~~i~~~e~~~~~~~~l~~i~~~s~G  208 (239)
T d1njfa_         132 FNALLKTLEE--PPEHVKFLLATTDPQKLPVTILSRC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG  208 (239)
T ss_dssp             HHHHHHHHHS--CCTTEEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHTTT
T ss_pred             HHHHHHHHhc--CCCCeEEEEEcCCccccChhHhhhh-cccccccCcHHHhhhHHHHHHhhhccCCCHHHHHHHHHHcCC
Confidence            3567777763  4578899999999999999999999 89999999999999888887763    667788888887765


Q ss_pred             CCHHHHHHHHH
Q 047219          492 MSGRDIRDVCQ  502 (567)
Q Consensus       492 ~s~~dL~~L~~  502 (567)
                          |++.+++
T Consensus       209 ----d~R~ain  215 (239)
T d1njfa_         209 ----SLRDALS  215 (239)
T ss_dssp             ----CHHHHHH
T ss_pred             ----CHHHHHH
Confidence                5555444

>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=99.72  E-value=3e-17  Score=158.21  Aligned_cols=186  Identities=21%  Similarity=0.215  Sum_probs=128.0

Q ss_pred             CCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcC
Q 047219          276 EISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVP  355 (567)
Q Consensus       276 ~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~  355 (567)
                      +.+|+|++|++++++.|+.++..                     ....++||+||||||||++|+++++++....+ ...
T Consensus        10 P~~~~divg~~~~~~~L~~~i~~---------------------~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~-~~~   67 (227)
T d1sxjc2          10 PETLDEVYGQNEVITTVRKFVDE---------------------GKLPHLLFYGPPGTGKTSTIVALAREIYGKNY-SNM   67 (227)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHHHT---------------------TCCCCEEEECSSSSSHHHHHHHHHHHHHTTSH-HHH
T ss_pred             CCCHHHccCcHHHHHHHHHHHHc---------------------CCCCeEEEECCCCCChhHHHHHHHHHhhcCCC-cce
Confidence            36899999999999999888752                     23346999999999999999999999743211 122


Q ss_pred             eEEechhhHHhhhhchhHHHHHHHHHHH-hcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEE
Q 047219          356 LMYVPLEVVMSKYYGESERLLGKVFSLA-NELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVV  434 (567)
Q Consensus       356 ~~~i~~~~l~s~~~G~~~~~l~~~f~~A-~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viV  434 (567)
                      +...+.....+......  ......... .......+++|||+|.+....+           +.|+..++.  ....+++
T Consensus        68 ~~e~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~kiiiiDe~d~~~~~~~-----------~~Ll~~le~--~~~~~~~  132 (227)
T d1sxjc2          68 VLELNASDDRGIDVVRN--QIKDFASTRQIFSKGFKLIILDEADAMTNAAQ-----------NALRRVIER--YTKNTRF  132 (227)
T ss_dssp             EEEECTTSCCSHHHHHT--HHHHHHHBCCSSSCSCEEEEETTGGGSCHHHH-----------HHHHHHHHH--TTTTEEE
T ss_pred             eEEecccccCCeeeeec--chhhccccccccCCCeEEEEEeccccchhhHH-----------HHHHHHhhh--cccceee
Confidence            34444443322111111  111110000 0112235999999999975533           344444442  3468899


Q ss_pred             EEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHH
Q 047219          435 IAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQ  503 (567)
Q Consensus       435 IaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~  503 (567)
                      +++||.+..+.+.+++|| ..+.|..|+.++...++...+..    +..+.++.+++...|    |++.+++.
T Consensus       133 ~~~~~~~~~i~~~i~sr~-~~i~~~~~~~~~i~~~l~~I~~~e~i~i~~~~l~~i~~~s~G----d~R~ain~  200 (227)
T d1sxjc2         133 CVLANYAHKLTPALLSQC-TRFRFQPLPQEAIERRIANVLVHEKLKLSPNAEKALIELSNG----DMRRVLNV  200 (227)
T ss_dssp             EEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHTTTCCBCHHHHHHHHHHHTT----CHHHHHHH
T ss_pred             ccccCcHHHhHHHHHHHH-hhhccccccccccccccccccccccccCCHHHHHHHHHHcCC----cHHHHHHH
Confidence            999999999999999999 89999999999999999887754    567788888888765    66666553

>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=99.71  E-value=1.1e-16  Score=154.17  Aligned_cols=188  Identities=15%  Similarity=0.196  Sum_probs=131.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      .+.+|+|++|+++.++.|++++.                     .....++||+||||||||++|+.+++++.... ...
T Consensus        10 rP~~~~d~ig~~~~~~~L~~~~~---------------------~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~-~~~   67 (224)
T d1sxjb2          10 RPQVLSDIVGNKETIDRLQQIAK---------------------DGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-YAD   67 (224)
T ss_dssp             CCSSGGGCCSCTHHHHHHHHHHH---------------------SCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-HHH
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHH---------------------cCCCCeEEEECCCCCCchhhHHHHHHHHhccc-ccc
Confidence            44689999999999999988774                     23345699999999999999999999884210 023


Q ss_pred             CeEEechhhHHhhhhchhHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          355 PLMYVPLEVVMSKYYGESERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       355 ~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ++..+++++..+...  ....... |....   ......++++||+|.+....+..+           +..++  .....
T Consensus        68 ~~~~~n~~~~~~~~~--i~~~~~~-~~~~~~~~~~~~~kviiiDe~d~~~~~~~~~l-----------l~~~e--~~~~~  131 (224)
T d1sxjb2          68 GVLELNASDDRGIDV--VRNQIKH-FAQKKLHLPPGKHKIVILDEADSMTAGAQQAL-----------RRTME--LYSNS  131 (224)
T ss_dssp             HEEEECTTSCCSHHH--HHTHHHH-HHHBCCCCCTTCCEEEEEESGGGSCHHHHHTT-----------HHHHH--HTTTT
T ss_pred             ccccccccccCCcee--hhhHHHH-HHHhhccCCCcceEEEEEecccccchhHHHHH-----------hhhcc--ccccc
Confidence            456666554332110  0011111 11111   112346999999999986644433           33333  24568


Q ss_pred             EEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       432 viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      +++|.+++....+.++|++|| ..+.|+.|+.++...++...++.    +..+.++.++....|    |++.+++...
T Consensus       132 ~~~i~~~~~~~~i~~~l~sr~-~~i~~~~~~~~~i~~~l~~i~~~e~~~i~~~~l~~I~~~s~G----d~R~ai~~Lq  204 (224)
T d1sxjb2         132 TRFAFACNQSNKIIEPLQSQC-AILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTAEG----DMRQAINNLQ  204 (224)
T ss_dssp             EEEEEEESCGGGSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHHTT----CHHHHHHHHH
T ss_pred             eeeeeccCchhhhhhHHHHHH-HHhhhcccchhhhHHHHHHHHHhcccCCCHHHHHHHHHHcCC----cHHHHHHHHH
Confidence            899999999999999999999 88999999999999999988764    567788888887765    5665555443

>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=99.68  E-value=1e-15  Score=147.26  Aligned_cols=193  Identities=17%  Similarity=0.251  Sum_probs=132.0

Q ss_pred             CCCCccccc-C--cHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCC
Q 047219          275 SEISWENIA-G--YDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPW  351 (567)
Q Consensus       275 ~~~~~~dIi-G--~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~  351 (567)
                      |+.+|++.+ |  ...+.+.+++.++.+                   ....++++||||+|||||+|++|+++++...  
T Consensus         5 ~~~tFdnF~vg~~N~~a~~~~~~~~~~~-------------------~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~--   63 (213)
T d1l8qa2           5 PKYTLENFIVGEGNRLAYEVVKEALENL-------------------GSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR--   63 (213)
T ss_dssp             TTCCSSSCCCCTTTHHHHHHHHHHHHTT-------------------TTSCSSEEEECSSSSSHHHHHHHHHHHHHHT--
T ss_pred             CCCChhhccCCCcHHHHHHHHHHHHhCc-------------------CCCCCcEEEECCCCCcHHHHHHHHHHHhccC--
Confidence            678999964 5  444455555554432                   2334569999999999999999999998544  


Q ss_pred             CCcCeEEechhhHHhhhhchhHH-HHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCC
Q 047219          352 QGVPLMYVPLEVVMSKYYGESER-LLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDK  430 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~~G~~~~-~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~  430 (567)
                       +..+++++...+...+...... ....+++... .  ..+|+|||||.+..+.+         ....|...++.....+
T Consensus        64 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~--~dll~iDDi~~i~~~~~---------~~~~lf~lin~~~~~~  130 (213)
T d1l8qa2          64 -GYRVIYSSADDFAQAMVEHLKKGTINEFRNMYK-S--VDLLLLDDVQFLSGKER---------TQIEFFHIFNTLYLLE  130 (213)
T ss_dssp             -TCCEEEEEHHHHHHHHHHHHHHTCHHHHHHHHH-T--CSEEEEECGGGGTTCHH---------HHHHHHHHHHHHHHTT
T ss_pred             -ccceEEechHHHHHHHHHHHHccchhhHHHHHh-h--ccchhhhhhhhhcCchH---------HHHHHHHHHHHHhhcc
Confidence             5578889888777654433211 1222333322 2  46999999999976622         2234444455444556


Q ss_pred             cEEEEEeeCCCCC---CChHHHhccce--EEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHHH
Q 047219          431 KVVVIAATNRKQD---LDPALISRFDS--MITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDVC  501 (567)
Q Consensus       431 ~viVIaaTN~~~~---Ld~aL~sRf~~--~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L~  501 (567)
                      ..+||++...|..   +.++|++||..  ++.++ |+.++|.++++.++..    ++++.++.+++.+.  +.++|..++
T Consensus       131 ~~iiits~~~p~~l~~~~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~--~~R~L~~~l  207 (213)
T d1l8qa2         131 KQIILASDRHPQKLDGVSDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTK--NVREIEGKI  207 (213)
T ss_dssp             CEEEEEESSCGGGCTTSCHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHCS--SHHHHHHHH
T ss_pred             ceEEEecCCcchhccccchHHHHHhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC--cHHHHHHHH
Confidence            6677777777654   56999999844  67776 6788999999998875    57788888888763  578887777


Q ss_pred             HHH
Q 047219          502 QQA  504 (567)
Q Consensus       502 ~~a  504 (567)
                      +..
T Consensus       208 ~~l  210 (213)
T d1l8qa2         208 KLI  210 (213)
T ss_dssp             HHH
T ss_pred             HHh
Confidence            653

>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=99.67  E-value=6.5e-16  Score=150.42  Aligned_cols=188  Identities=13%  Similarity=0.138  Sum_probs=120.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCC--
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQ--  352 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~--  352 (567)
                      .+.+|++++|++++++.|..++..                    ...+.++||+||||||||++|+++++++......  
T Consensus         6 ~P~~~~diig~~~~~~~L~~~~~~--------------------~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~   65 (252)
T d1sxje2           6 RPKSLNALSHNEELTNFLKSLSDQ--------------------PRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRL   65 (252)
T ss_dssp             CCCSGGGCCSCHHHHHHHHTTTTC--------------------TTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC-
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHc--------------------CCCCCeEEEECCCCCCHHHHHHHHHHhhcCcccccc
Confidence            346899999999988888764421                    2345579999999999999999999987322000  


Q ss_pred             Cc---------------------CeEEechhhHHhhhhchhHHHHHHHHHHHh-------------cCCCCcEEEEcCcc
Q 047219          353 GV---------------------PLMYVPLEVVMSKYYGESERLLGKVFSLAN-------------ELPNGAIIFLDEVD  398 (567)
Q Consensus       353 ~~---------------------~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~-------------~~a~~~ILfIDEID  398 (567)
                      ..                     ....+.......    ..............             ......+++|||+|
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d  141 (252)
T d1sxje2          66 KIDVRQFVTASNRKLELNVVSSPYHLEITPSDMGN----NDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEAN  141 (252)
T ss_dssp             -----------------CCEECSSEEEECCC--------CCHHHHHHHHHHHTTTTC------------CCEEEEEECTT
T ss_pred             ccccccccccccchhhhhhccCCccceeeeccccc----CCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEecccc
Confidence            00                     001111111000    00001111111110             11223599999999


Q ss_pred             hhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh--
Q 047219          399 SFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH--  476 (567)
Q Consensus       399 ~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~--  476 (567)
                      .|....+           +.++..++  ....++++|++||..+.+.++|++|| ..|+|+.|+.++..+++...+..  
T Consensus       142 ~l~~~~~-----------~~l~~~~e--~~~~~~~~Il~tn~~~~i~~~l~sR~-~~i~~~~~~~~~~~~~l~~i~~~e~  207 (252)
T d1sxje2         142 SLTKDAQ-----------AALRRTME--KYSKNIRLIMVCDSMSPIIAPIKSQC-LLIRCPAPSDSEISTILSDVVTNER  207 (252)
T ss_dssp             SSCHHHH-----------HHHHHHHH--HSTTTEEEEEEESCSCSSCHHHHTTS-EEEECCCCCHHHHHHHHHHHHHHHT
T ss_pred             ccccccc-----------hhhhcccc--cccccccceeeeccccchhhhhhcch-heeeecccchhhHHHHHHHHHHHcC
Confidence            9864422           33444444  24567899999999999999999999 79999999999999999887764  


Q ss_pred             ---hCHHHHHHHHHhccCCCHHHHHHHHHHH
Q 047219          477 ---LTKAELAELATATEEMSGRDIRDVCQQA  504 (567)
Q Consensus       477 ---~~~~~l~~la~~t~g~s~~dL~~L~~~a  504 (567)
                         ..++.++.++..+.|    |++.+++..
T Consensus       208 ~~~~~~~~l~~i~~~s~G----d~R~ai~~L  234 (252)
T d1sxje2         208 IQLETKDILKRIAQASNG----NLRVSLLML  234 (252)
T ss_dssp             CEECCSHHHHHHHHHHTT----CHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHcCC----cHHHHHHHH
Confidence               235567778777665    666655433

>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=99.66  E-value=7.4e-16  Score=150.28  Aligned_cols=203  Identities=19%  Similarity=0.210  Sum_probs=128.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccCh-hhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSP-EVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~p-elf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .+.+|++|+|+++.+++|++++....... ..+.     .....+....+++||+||||||||++|+++|+++      +
T Consensus         9 ~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~-----~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~------~   77 (253)
T d1sxja2           9 APTNLQQVCGNKGSVMKLKNWLANWENSKKNSFK-----HAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL------G   77 (253)
T ss_dssp             CCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTC-----CCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT------T
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhh-----hhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH------H
Confidence            34589999999999999999886431110 0000     0011124556789999999999999999999999      6


Q ss_pred             cCeEEechhhHHhhhhchhH--HH---------HHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHh
Q 047219          354 VPLMYVPLEVVMSKYYGESE--RL---------LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQ  422 (567)
Q Consensus       354 ~~~~~i~~~~l~s~~~G~~~--~~---------l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~  422 (567)
                      .++..++.+...+.......  ..         ...............++++||+|.+....+....        .+...
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~~~~~~--------~~~~~  149 (253)
T d1sxja2          78 YDILEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGDRGGVG--------QLAQF  149 (253)
T ss_dssp             CEEEEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTSTTHHH--------HHHHH
T ss_pred             hhhhccccccchhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccchhhhhH--------HHhhh
Confidence            67888887765443211100  00         0000001112233579999999999766544322        22222


Q ss_pred             hcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHH
Q 047219          423 IDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIR  498 (567)
Q Consensus       423 ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~  498 (567)
                      ..  .....++++++++....++ .+++|+ ..++|..|+.+++..+++..+..    +..+.++.++..+.|    |++
T Consensus       150 ~~--~~~~~ii~i~~~~~~~~~~-~l~~~~-~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s~G----DiR  221 (253)
T d1sxja2         150 CR--KTSTPLILICNERNLPKMR-PFDRVC-LDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTTRG----DIR  221 (253)
T ss_dssp             HH--HCSSCEEEEESCTTSSTTG-GGTTTS-EEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHTTT----CHH
T ss_pred             hc--ccccccccccccccccccc-ccccee-eeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCC----cHH
Confidence            21  1223455555555444444 577777 89999999999999999988753    456678888887654    887


Q ss_pred             HHHHHH
Q 047219          499 DVCQQA  504 (567)
Q Consensus       499 ~L~~~a  504 (567)
                      .+++..
T Consensus       222 ~ai~~L  227 (253)
T d1sxja2         222 QVINLL  227 (253)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776654

>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=99.66  E-value=3.7e-16  Score=150.77  Aligned_cols=190  Identities=19%  Similarity=0.185  Sum_probs=126.4

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      .+.+|++++|+++.++.|+.++.                     .....++||+||||||||++++++++++........
T Consensus         7 ~P~~~~diig~~~~~~~l~~~i~---------------------~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~   65 (237)
T d1sxjd2           7 RPKNLDEVTAQDHAVTVLKKTLK---------------------SANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKS   65 (237)
T ss_dssp             CCSSTTTCCSCCTTHHHHHHHTT---------------------CTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCHHHccCcHHHHHHHHHHHH---------------------cCCCCeEEEECCCCCChHHHHHHHHHHHcCCccccc
Confidence            45789999999999988877653                     233456999999999999999999998632111122


Q ss_pred             CeEEechhhHHhh-hhchhHHHHH---------HHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhc
Q 047219          355 PLMYVPLEVVMSK-YYGESERLLG---------KVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQID  424 (567)
Q Consensus       355 ~~~~i~~~~l~s~-~~G~~~~~l~---------~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld  424 (567)
                      ....++....... .....-+...         ..... ....+..++||||+|.+....+.           .++..++
T Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~viiiDe~d~l~~~~~~-----------~l~~~~~  133 (237)
T d1sxjd2          66 RILELNASDERGISIVREKVKNFARLTVSKPSKHDLEN-YPCPPYKIIILDEADSMTADAQS-----------ALRRTME  133 (237)
T ss_dssp             SEEEECSSSCCCHHHHTTHHHHHHHSCCCCCCTTHHHH-SCCCSCEEEEETTGGGSCHHHHH-----------HHHHHHH
T ss_pred             chhheeccccccchHHHHHHHHHhhhhhhhhhHHHHhh-ccccCceEEEEecccccCHHHHH-----------HHhhccc
Confidence            3444444322211 1111101000         00011 12223469999999999754322           2333333


Q ss_pred             CcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh----hCHHHHHHHHHhccCCCHHHHHHH
Q 047219          425 GFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH----LTKAELAELATATEEMSGRDIRDV  500 (567)
Q Consensus       425 ~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~----~~~~~l~~la~~t~g~s~~dL~~L  500 (567)
                        .....+++|.+++....+.+++++|| ..+.|+.|+.++..+++...+..    +..+.++.++....|    |++.+
T Consensus       134 --~~~~~~~~i~~~~~~~~~~~~l~sr~-~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~s~g----d~R~a  206 (237)
T d1sxjd2         134 --TYSGVTRFCLICNYVTRIIDPLASQC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAG----DLRRG  206 (237)
T ss_dssp             --HTTTTEEEEEEESCGGGSCHHHHHHS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS----CHHHH
T ss_pred             --cccccccccccccccccccccccchh-hhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHHcCC----CHHHH
Confidence              23467788899999999999999999 89999999999999999988773    677888999888765    56555


Q ss_pred             HHHH
Q 047219          501 CQQA  504 (567)
Q Consensus       501 ~~~a  504 (567)
                      ++..
T Consensus       207 i~~L  210 (237)
T d1sxjd2         207 ITLL  210 (237)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>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=99.61  E-value=3.8e-15  Score=151.47  Aligned_cols=197  Identities=21%  Similarity=0.326  Sum_probs=131.9

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      +.|+|++++++.+.+.+......      +..      ...+...+||+||||||||.||++||+.+      +.+++.+
T Consensus        22 ~~viGQ~~a~~~v~~~v~~~~~~------l~~------~~~p~~~~lf~Gp~GvGKT~lak~la~~l------~~~~i~~   83 (315)
T d1r6bx3          22 MLVFGQDKAIEALTEAIKMARAG------LGH------EHKPVGSFLFAGPTGVGKTEVTVQLSKAL------GIELLRF   83 (315)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTT------CSC------TTSCSEEEEEECSTTSSHHHHHHHHHHHH------TCEEEEE
T ss_pred             CeecChHHHHHHHHHHHHHHHcc------CCC------CCCCceEEEEECCCcchhHHHHHHHHhhc------cCCeeEe
Confidence            46899999999999988643111      100      02334478999999999999999999999      6789999


Q ss_pred             chhhHHhh-----hhch----hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc----
Q 047219          360 PLEVVMSK-----YYGE----SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF----  426 (567)
Q Consensus       360 ~~~~l~s~-----~~G~----~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~----  426 (567)
                      +++++...     +.|.    ........+.......+.+|+++||||+..+.           +.+.|++.++.-    
T Consensus        84 d~s~~~~~~~~~~l~g~~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa~~~-----------V~~~lLqild~G~ltd  152 (315)
T d1r6bx3          84 DMSEYMERHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPD-----------VFNILLQVMDNGTLTD  152 (315)
T ss_dssp             EGGGCSSSSCCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGSCHH-----------HHHHHHHHHHHSEEEE
T ss_pred             ccccccchhhhhhhcccCCCccccccCChhhHHHHhCccchhhhcccccccch-----------HhhhhHHhhccceecC
Confidence            99887543     2222    22222222222233345799999999998754           334444444321    


Q ss_pred             -----ccCCcEEEEEeeCCC-------------------------CCCChHHHhccceEEEecCCCHHHHHHHHHHHHHh
Q 047219          427 -----EQDKKVVVIAATNRK-------------------------QDLDPALISRFDSMITFGLPDHENRQEIAAQYAKH  476 (567)
Q Consensus       427 -----~~~~~viVIaaTN~~-------------------------~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~  476 (567)
                           ..-.++++|+|+|--                         ..|.|+|+.|++.++.|.+.+.++...|+...+..
T Consensus       153 ~~Gr~vdf~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~ii~f~~l~~~~~~~I~~~~l~~  232 (315)
T d1r6bx3         153 NNGRKADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVE  232 (315)
T ss_dssp             TTTEEEECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHH
T ss_pred             CCCCccCccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHhhhhhhhcccchhhhHHHHHHHHHHHH
Confidence                 234689999999941                         14899999999999999999999999998877654


Q ss_pred             h-------------CHHHHHHHHH--hccCCCHHHHHHHHHHHH
Q 047219          477 L-------------TKAELAELAT--ATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       477 ~-------------~~~~l~~la~--~t~g~s~~dL~~L~~~a~  505 (567)
                      +             .++..+.++.  +...+..+.|+.+++.-.
T Consensus       233 ~~~~l~~~~i~l~~~~~a~~~l~~~~yd~~~GaR~L~r~Ie~~i  276 (315)
T d1r6bx3         233 LQVQLDQKGVSLEVSQEARNWLAEKGYDRAMGARPMARVIQDNL  276 (315)
T ss_dssp             HHHHHHHTTEEEEECHHHHHHHHHHHCBTTTBTTTHHHHHHHHH
T ss_pred             HHHHHHhcCcchhhHHHHHHHHHHhCCCCCCChhhHHHHHHHHH
Confidence            2             3444555544  233344566666655444

>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=99.60  E-value=1.5e-15  Score=154.43  Aligned_cols=204  Identities=22%  Similarity=0.313  Sum_probs=131.7

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      +.|+|++++++.+.+.+......      +.      ....+...+||+||+|||||.+|+.+|+.+...   ..+++.+
T Consensus        23 ~~v~GQ~~ai~~v~~~i~~~~~~------l~------~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~---~~~~~~~   87 (315)
T d1qvra3          23 KRVVGQDEAIRAVADAIRRARAG------LK------DPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT---EEAMIRI   87 (315)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGG------CS------CSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS---GGGEEEE
T ss_pred             CeEeCHHHHHHHHHHHHHHHhcC------CC------CCCCCceEEEEECCCcchHHHHHHHHHHHhcCC---CcceEEE
Confidence            46899999999999888654110      00      002333467888999999999999999987432   4578888


Q ss_pred             chhhHHh-----hhhchhHHHH----HHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCc----
Q 047219          360 PLEVVMS-----KYYGESERLL----GKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGF----  426 (567)
Q Consensus       360 ~~~~l~s-----~~~G~~~~~l----~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~----  426 (567)
                      +++++..     +++|......    ...+..+....|.+|++|||||++.+.           +++.|+..++.-    
T Consensus        88 ~~~~~~~~~~~~~L~g~~~gyvG~~~~~~l~~~~~~~p~~Vvl~DEieK~~~~-----------v~~~ll~~l~~g~~~~  156 (315)
T d1qvra3          88 DMTEYMEKHAVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDEIEKAHPD-----------VFNILLQILDDGRLTD  156 (315)
T ss_dssp             CTTTCCSSGGGGGC--------------CHHHHHHHCSSEEEEESSGGGSCHH-----------HHHHHHHHHTTTEECC
T ss_pred             eccccccchhhhhhcCCCCCCcCcccCChHHHHHHhCCCcEEEEehHhhcCHH-----------HHHHHHHHhccCceeC
Confidence            8766543     3333321111    122223233345799999999998755           334444444332    


Q ss_pred             -----ccCCcEEEEEeeCC--------------------------CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          427 -----EQDKKVVVIAATNR--------------------------KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       427 -----~~~~~viVIaaTN~--------------------------~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                           ....++++|+|||-                          .+.+.|+|++||+.++.|.+.+.++..+|+...+.
T Consensus       157 ~~gr~v~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~Ii~F~~L~~~~~~~I~~~~l~  236 (315)
T d1qvra3         157 SHGRTVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLS  236 (315)
T ss_dssp             SSSCCEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             CCCcEecCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHhcCCeeeeccchhhhhhHHHHHHHHH
Confidence                 22368999999995                          34599999999999999999999999999887665


Q ss_pred             hh-------------CHHHHHHHHHh--ccCCCHHHHHHHHHHHHHHHH
Q 047219          476 HL-------------TKAELAELATA--TEEMSGRDIRDVCQQAERSWA  509 (567)
Q Consensus       476 ~~-------------~~~~l~~la~~--t~g~s~~dL~~L~~~a~~~a~  509 (567)
                      .+             ..+..+.+++.  ...+-.+.|+..++.......
T Consensus       237 ~l~~rl~~~~i~l~i~~~~~~~L~~~~y~~~~GAR~L~r~Ie~~i~~~L  285 (315)
T d1qvra3         237 YLRARLAEKRISLELTEAAKDFLAERGYDPVFGARPLRRVIQRELETPL  285 (315)
T ss_dssp             HHHHHHHTTTCEEEECHHHHHHHHHHHCBTTTBTSTHHHHHHHHTHHHH
T ss_pred             HHHHHHHhccccccccHHHHHHHHHhCCCCCCCcchHHHHHHHHHHHHH
Confidence            32             34455555553  334445666666666554433

>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=99.59  E-value=4.8e-14  Score=137.19  Aligned_cols=209  Identities=17%  Similarity=0.151  Sum_probs=136.7

Q ss_pred             CCCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC
Q 047219          274 KSEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG  353 (567)
Q Consensus       274 ~~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~  353 (567)
                      .|.+..+.++|.+.+++.+.+.+...++++               ...+.++||+||||||||++|+++++.+....  .
T Consensus        10 ~~~y~p~~l~~Re~ei~~l~~~l~~~l~~~---------------~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~--~   72 (276)
T d1fnna2          10 SPSYVPKRLPHREQQLQQLDILLGNWLRNP---------------GHHYPRATLLGRPGTGKTVTLRKLWELYKDKT--T   72 (276)
T ss_dssp             STTCCCSCCTTCHHHHHHHHHHHHHHHHST---------------TSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC--C
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHhCC---------------CCCCCceEEECCCCCCHHHHHHHHHHHHhccc--C
Confidence            355667789999999999999887655554               46788999999999999999999999985432  3


Q ss_pred             cCeEEechhhHH------hhh----------hch-hHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHH
Q 047219          354 VPLMYVPLEVVM------SKY----------YGE-SERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRIL  416 (567)
Q Consensus       354 ~~~~~i~~~~l~------s~~----------~G~-~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl  416 (567)
                      ..++.+++....      ...          .+. .......+.+.........++++|++|.+......        ..
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~--------~~  144 (276)
T d1fnna2          73 ARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDILS--------TF  144 (276)
T ss_dssp             CEEEEEETTTCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHHHH--------HH
T ss_pred             CcEEEecchhhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhhhh--------hH
Confidence            345555443211      111          011 12223334444444444578889999988644221        11


Q ss_pred             HHHHHhhcCcccCCcEEEEEeeCCC---CCCChHHHhccc-eEEEecCCCHHHHHHHHHHHHHh------hCHHHHHHHH
Q 047219          417 SVLLRQIDGFEQDKKVVVIAATNRK---QDLDPALISRFD-SMITFGLPDHENRQEIAAQYAKH------LTKAELAELA  486 (567)
Q Consensus       417 ~~LL~~ld~~~~~~~viVIaaTN~~---~~Ld~aL~sRf~-~~I~i~~P~~~eR~eIL~~~~~~------~~~~~l~~la  486 (567)
                      ..++..+.. .....+.+|+++|..   +.+++.+.+|+. ..+.|+.|+.+++.+|++.++..      +.++.++.++
T Consensus       145 ~~~~~~~~~-~~~~~~~~i~~~~~~~~~~~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~~~~~~~~~~~l~~ia  223 (276)
T d1fnna2         145 IRLGQEADK-LGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIA  223 (276)
T ss_dssp             HHHTTCHHH-HSSCCEEEEEEESSTHHHHTSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHH
T ss_pred             HHHHhcccc-ccccceEEeecCCchhhhhhcchhhhhhhcchhccccchhHHHHHHHHHHHHHHhcccccccHHHHHHHH
Confidence            222222211 234567888888863   468899998763 46899999999999999987763      5566777777


Q ss_pred             Hhcc--------CCCHHHHHHHHHHHHHHH
Q 047219          487 TATE--------EMSGRDIRDVCQQAERSW  508 (567)
Q Consensus       487 ~~t~--------g~s~~dL~~L~~~a~~~a  508 (567)
                      ..+.        +-+.+.+..+|+.|+..+
T Consensus       224 ~~~~~~~~~~~~~G~~R~a~~ll~~a~~~A  253 (276)
T d1fnna2         224 DITGAQTPLDTNRGDARLAIDILYRSAYAA  253 (276)
T ss_dssp             HHHSBSSTTCTTSCCHHHHHHHHHHHHHHH
T ss_pred             HHhhhhhhhhhcCCCHHHHHHHHHHHHHHH
Confidence            6542        124556666777666543

>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=99.59  E-value=2e-15  Score=142.51  Aligned_cols=164  Identities=21%  Similarity=0.290  Sum_probs=121.7

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQG  353 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~  353 (567)
                      .++-++|.++.++++.+.+.                     ....++++|.||||+|||++++.+|+.....    .+.+
T Consensus        20 ~ld~~igRd~Ei~~l~~iL~---------------------r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~   78 (195)
T d1jbka_          20 KLDPVIGRDEEIRRTIQVLQ---------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKG   78 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHHT---------------------SSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTT
T ss_pred             CCCCCcCcHHHHHHHHHHHh---------------------ccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcC
Confidence            35678999999998887663                     3445789999999999999999999977322    2446


Q ss_pred             cCeEEechhhHHh--hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          354 VPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~s--~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..++.++...+.+  +|.|+.+.++..+++++.......||||||++.|....+....   ....+.|...+.    ++.
T Consensus        79 ~~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~---~d~~~~Lkp~L~----rg~  151 (195)
T d1jbka_          79 RRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA---MDAGNMLKPALA----RGE  151 (195)
T ss_dssp             CEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------C---CCCHHHHHHHHH----TTS
T ss_pred             ceEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCc---ccHHHHHHHHHh----CCC
Confidence            7899999999885  5778999999999988866554579999999999755332110   011233333333    578


Q ss_pred             EEEEEeeCCC-----CCCChHHHhccceEEEecCCCHHHHHHHH
Q 047219          432 VVVIAATNRK-----QDLDPALISRFDSMITFGLPDHENRQEIA  470 (567)
Q Consensus       432 viVIaaTN~~-----~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL  470 (567)
                      +.+|++|...     -.-+++|.+|| ..|.+..|+.++-..|+
T Consensus       152 l~~IgatT~eey~~~~e~d~aL~rrF-~~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         152 LHCVGATTLDEYRQYIEKDAALERRF-QKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             CCEEEEECHHHHHHHTTTCHHHHTTE-EEEECCCCCHHHHHTTC
T ss_pred             ceEEecCCHHHHHHHHHcCHHHHhcC-CEeecCCCCHHHHHHHh
Confidence            8999999752     24699999999 89999999998877664

>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=99.57  E-value=1.2e-14  Score=144.16  Aligned_cols=169  Identities=19%  Similarity=0.266  Sum_probs=127.2

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQG  353 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~  353 (567)
                      .++.++|.++.++++.+.+.                     .....+++|.||||+|||++++.+|+.+...    ...+
T Consensus        16 ~ld~~igRd~Ei~~l~~iL~---------------------r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~   74 (268)
T d1r6bx2          16 GIDPLIGREKELERAIQVLC---------------------RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMAD   74 (268)
T ss_dssp             CSCCCCSCHHHHHHHHHHHT---------------------SSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTT
T ss_pred             CCCcccChHHHHHHHHHHHh---------------------cCccCCcEEECCCCCcHHHHHHHHHHHHHhCCccccccc
Confidence            35678999999998887663                     3455789999999999999999999876332    2335


Q ss_pred             cCeEEechhhHHh--hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          354 VPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~s--~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..++.++...+.+  ++.|+.+..+..+++.+.... +.||||||++.|....+......  .+.+.|    ...-..+.
T Consensus        75 ~~i~~l~~~~liag~~~~g~~e~r~~~i~~~~~~~~-~iIlfiDeih~l~~~g~~~g~~~--d~a~~L----kp~L~rg~  147 (268)
T d1r6bx2          75 CTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDT-NSILFIDEIHTIIGAGAASGGQV--DAANLI----KPLLSSGK  147 (268)
T ss_dssp             CEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSS-CEEEEETTTTTTTTSCCSSSCHH--HHHHHH----SSCSSSCC
T ss_pred             ceeEEeeechHhccCccchhHHHHHHHHHHHhhccC-CceEEecchHHHhcCCCCCCccc--cHHHHh----hHHHhCCC
Confidence            6789999988886  688999999999999987665 48999999999976533221111  111222    22334789


Q ss_pred             EEEEEeeCC-----CCCCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNR-----KQDLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       432 viVIaaTN~-----~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +.+|++|..     ...-+++|.+|| ..|.+..|+.++-..|+.....
T Consensus       148 i~vIgatT~eey~~~~e~d~al~rrF-~~I~V~Eps~e~t~~IL~~~~~  195 (268)
T d1r6bx2         148 IRVIGSTTYQEFSNIFEKDRALARRF-QKIDITEPSIEETVQIINGLKP  195 (268)
T ss_dssp             CEEEEEECHHHHHCCCCCTTSSGGGE-EEEECCCCCHHHHHHHHHHHHH
T ss_pred             CeEEEeCCHHHHHHHHhhcHHHHhhh-cccccCCCCHHHHHHHHHHhhH
Confidence            999999975     335689999999 8999999999999999987654

>d1cz5a1 b.52.2.3 (A:1-91) N-terminal domain of VAT-N, VAT-Nn {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: All beta proteins
fold: Double psi beta-barrel
superfamily: ADC-like
family: Cdc48 N-terminal domain-like
domain: N-terminal domain of VAT-N, VAT-Nn
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=99.56  E-value=6.1e-16  Score=127.75  Aligned_cols=67  Identities=13%  Similarity=0.153  Sum_probs=62.4

Q ss_pred             hcchhhhH-HHHHHHhCCCCCCccceEEEEecceEEEEEEecCC-C----CcchHHHHHHHhhCceecccCCCceeEEEe
Q 047219          109 AKKERQRI-EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPPA-C----EIPQLIANLVSHLGLKVEEHGGGSDMGLRA  182 (567)
Q Consensus       109 ~~~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~~~~~~~~~~~-~----~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~  182 (567)
                      +|||+||| ++.|++||+.+||+    |+|+|++.|+|++||++ +    +++++++.+|+|+|+++||     +|+|+|
T Consensus        19 ~grgiari~~~~m~~Lgl~~GD~----V~I~Gkr~t~a~v~~~~~~d~~~g~IriDg~~R~Nagv~iGD-----~V~V~k   89 (91)
T d1cz5a1          19 PGMSRVRLDESSRRLLDAEIGDV----VEIEKVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGD-----KVKVRK   89 (91)
T ss_dssp             CCSSEEEECHHHHHTTSCCTTCE----EEEESSSEEEEEEEECSSTTTTTSEEECCHHHHHHHTCCTTC-----CEEEEE
T ss_pred             cCCcEEEECHHHHHHcCCCCCCE----EEEEcCceEEEEEEecCcccCCCCEEEEcHHHHHhCCCCCCC-----EEEEEE
Confidence            89999999 69999999999999    99999999999999973 3    4799999999999999999     999999


Q ss_pred             ec
Q 047219          183 WD  184 (567)
Q Consensus       183 ~~  184 (567)
                      ++
T Consensus        90 ve   91 (91)
T d1cz5a1          90 VR   91 (91)
T ss_dssp             EC
T ss_pred             CC
Confidence            74

>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=99.55  E-value=1.1e-13  Score=144.02  Aligned_cols=169  Identities=22%  Similarity=0.318  Sum_probs=113.4

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC----CCCC
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM----PWQG  353 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~----~~~~  353 (567)
                      .++-++|.++.++++.+.+.                     ....++++|.||||+|||.+++.+|+.+-..    .+.+
T Consensus        20 ~ld~~~gr~~ei~~~~~~L~---------------------r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~   78 (387)
T d1qvra2          20 KLDPVIGRDEEIRRVIQILL---------------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKG   78 (387)
T ss_dssp             CSCCCCSCHHHHHHHHHHHH---------------------CSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTT
T ss_pred             CCCCCcCcHHHHHHHHHHHh---------------------cCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcC
Confidence            35679999999999988775                     3455678999999999999999999876322    3446


Q ss_pred             cCeEEechhhHHh--hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCc
Q 047219          354 VPLMYVPLEVVMS--KYYGESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKK  431 (567)
Q Consensus       354 ~~~~~i~~~~l~s--~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~  431 (567)
                      ..++.++...+.+  +|.|+.+..+..++..+.....+.||||||++.|.+.......   ....+.|...+    ..+.
T Consensus        79 ~~i~~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~---~d~a~~Lkp~L----~rg~  151 (387)
T d1qvra2          79 KRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA---VDAGNMLKPAL----ARGE  151 (387)
T ss_dssp             CEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC----------------------HHHH----HTTC
T ss_pred             ceEEEeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCc---ccHHHHHHHHH----hCCC
Confidence            7799999998886  5789999999999988876654578999999999765332111   12223333333    2578


Q ss_pred             EEEEEeeCCCC----CCChHHHhccceEEEecCCCHHHHHHHHHHHHH
Q 047219          432 VVVIAATNRKQ----DLDPALISRFDSMITFGLPDHENRQEIAAQYAK  475 (567)
Q Consensus       432 viVIaaTN~~~----~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~  475 (567)
                      +.+|++|...+    .=|++|.+|| ..|.+..|+.++-..||+.+..
T Consensus       152 ~~~I~~tT~~ey~~~e~d~al~rrF-~~v~v~ep~~~~~~~il~~~~~  198 (387)
T d1qvra2         152 LRLIGATTLDEYREIEKDPALERRF-QPVYVDEPTVEETISILRGLKE  198 (387)
T ss_dssp             CCEEEEECHHHHHHHTTCTTTCSCC-CCEEECCCCHHHHHHHHHHHHH
T ss_pred             cceeeecCHHHHHHhcccHHHHHhc-ccccCCCCcHHHHHHHHHHHHH
Confidence            89999996511    3489999999 8999999999999999997654

>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=99.54  E-value=6.8e-14  Score=133.57  Aligned_cols=158  Identities=13%  Similarity=0.123  Sum_probs=108.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCC-cCeEE-echhhHHhhhh-------------chhHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQG-VPLMY-VPLEVVMSKYY-------------GESERLLGKVFSLA  383 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~-~~~~~-i~~~~l~s~~~-------------G~~~~~l~~~f~~A  383 (567)
                      ...|+++||+||||+|||++|+.+|+.+....... ..|.. .++..+.....             .-....++.+.+.+
T Consensus        21 ~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~  100 (207)
T d1a5ta2          21 GRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKL  100 (207)
T ss_dssp             TCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHT
T ss_pred             CCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccchhhHHhhhh
Confidence            46678899999999999999999999885321101 00100 01111111100             00123455555554


Q ss_pred             hcC---CCCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecC
Q 047219          384 NEL---PNGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGL  460 (567)
Q Consensus       384 ~~~---a~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~  460 (567)
                      ...   +...|++|||+|.|...           ..+.|++.++.  .+.++++|++||.+..+.+.++||| ..+.|..
T Consensus       101 ~~~~~~~~~kviIide~d~l~~~-----------a~n~Llk~lEe--p~~~~~fIl~t~~~~~ll~tI~SRc-~~i~~~~  166 (207)
T d1a5ta2         101 NEHARLGGAKVVWVTDAALLTDA-----------AANALLKTLEE--PPAETWFFLATREPERLLATLRSRC-RLHYLAP  166 (207)
T ss_dssp             TSCCTTSSCEEEEESCGGGBCHH-----------HHHHHHHHHTS--CCTTEEEEEEESCGGGSCHHHHTTS-EEEECCC
T ss_pred             hhccccCccceEEechhhhhhhh-----------hhHHHHHHHHh--hcccceeeeeecChhhhhhhhccee-EEEecCC
Confidence            422   23469999999999744           44677788874  5678999999999999999999999 9999999


Q ss_pred             CCHHHHHHHHHHHHHhhCHHHHHHHHHhccC
Q 047219          461 PDHENRQEIAAQYAKHLTKAELAELATATEE  491 (567)
Q Consensus       461 P~~~eR~eIL~~~~~~~~~~~l~~la~~t~g  491 (567)
                      |+.++...+++... .+..+.+..++....|
T Consensus       167 ~~~~~~~~~L~~~~-~~~~~~~~~i~~~s~G  196 (207)
T d1a5ta2         167 PPEQYAVTWLSREV-TMSQDALLAALRLSAG  196 (207)
T ss_dssp             CCHHHHHHHHHHHC-CCCHHHHHHHHHHTTT
T ss_pred             CCHHHHHHHHHHcC-CCCHHHHHHHHHHcCC
Confidence            99998888876432 2566777777776655

>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=99.53  E-value=5.8e-14  Score=137.41  Aligned_cols=220  Identities=15%  Similarity=0.035  Sum_probs=135.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CC
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PW  351 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~  351 (567)
                      +.+..+.|.|.+.+++.|.+.+..++.+..            ........++|+||||||||++++++++++...   ..
T Consensus        11 ~~~~P~~~~~Re~e~~~l~~~l~~~~~~~~------------~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~   78 (287)
T d1w5sa2          11 ENYIPPELRVRRGEAEALARIYLNRLLSGA------------GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEG   78 (287)
T ss_dssp             TTCCCSSCSSSCHHHHHHHHHHHHHHHTSS------------CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTT
T ss_pred             CccCCCCCCCHHHHHHHHHHHHHHHHHcCC------------CCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhccccc
Confidence            345567899999999999988765533321            001222356789999999999999999987421   11


Q ss_pred             CCcCeEEechhhHHhhh----------------hchhHHH-HHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHH
Q 047219          352 QGVPLMYVPLEVVMSKY----------------YGESERL-LGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRR  414 (567)
Q Consensus       352 ~~~~~~~i~~~~l~s~~----------------~G~~~~~-l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~  414 (567)
                      ....+.++++.......                .+..... ...+...........++++||+|.+....+... +. ..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~-~~-~~  156 (287)
T d1w5sa2          79 LTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAA-ED-LY  156 (287)
T ss_dssp             CCEEEEEEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCH-HH-HH
T ss_pred             CCceeeeeccccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccch-hH-HH
Confidence            12345555544322111                1122222 233333333344457899999999976544321 11 11


Q ss_pred             HHHHHHHhhcCcccCCcEEEEEeeCCCC------CCChHHHhccceEEEecCCCHHHHHHHHHHHHHh------hCHHHH
Q 047219          415 ILSVLLRQIDGFEQDKKVVVIAATNRKQ------DLDPALISRFDSMITFGLPDHENRQEIAAQYAKH------LTKAEL  482 (567)
Q Consensus       415 vl~~LL~~ld~~~~~~~viVIaaTN~~~------~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~------~~~~~l  482 (567)
                      .+..+...+........+.+|+.+|..+      ...+.+.+||...++|+.|+.++..+|++..++.      +.++.+
T Consensus       157 ~l~~l~~~l~~~~~~~~~~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~~~~~~~~~~al  236 (287)
T d1w5sa2         157 TLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHL  236 (287)
T ss_dssp             HHHTHHHHSCCTTSCCBEEEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHH
T ss_pred             HHHHHHHhcchhhcccceeEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHhhccCCCCHHHH
Confidence            2233344444444556777777776544      3457888899899999999999999999988753      456777


Q ss_pred             HHHHHhccC-----CCHHHHHHHHHHHHHHH
Q 047219          483 AELATATEE-----MSGRDIRDVCQQAERSW  508 (567)
Q Consensus       483 ~~la~~t~g-----~s~~dL~~L~~~a~~~a  508 (567)
                      +.+++.+..     ...+....+|+.|+..+
T Consensus       237 ~~ia~~~~~~~~~~gd~R~ai~~l~~a~~~A  267 (287)
T d1w5sa2         237 ELISDVYGEDKGGDGSARRAIVALKMACEMA  267 (287)
T ss_dssp             HHHHHHHCGGGTSCCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhccccCCCCHHHHHHHHHHHHHHH
Confidence            888776643     23555556666666543

>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=99.52  E-value=1.5e-14  Score=147.54  Aligned_cols=173  Identities=23%  Similarity=0.330  Sum_probs=104.9

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC-----
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM-----  349 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~-----  349 (567)
                      +.+.|.+|+|++.+|+.|.-.+..                     ....++||.||||||||++||+++..++..     
T Consensus         2 ~~~~f~~I~Gq~~~kral~laa~~---------------------~~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~   60 (333)
T d1g8pa_           2 PVFPFSAIVGQEDMKLALLLTAVD---------------------PGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEG   60 (333)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHC---------------------GGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETT
T ss_pred             CCCChhhccCcHHHHHHHHHHHhc---------------------cCCCeEEEECCCCccHHHHHHHHHHhCCCchhhcc
Confidence            457799999999998876544321                     123589999999999999999999876311     


Q ss_pred             -CC---------------------CCcCeEEechhhHHhhhhchhH--HHHH--------HHHHHHhcCCCCcEEEEcCc
Q 047219          350 -PW---------------------QGVPLMYVPLEVVMSKYYGESE--RLLG--------KVFSLANELPNGAIIFLDEV  397 (567)
Q Consensus       350 -~~---------------------~~~~~~~i~~~~l~s~~~G~~~--~~l~--------~~f~~A~~~a~~~ILfIDEI  397 (567)
                       .+                     ...++.......-.+..+|...  ..+.        ..+..|    .++|+||||+
T Consensus        61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A----~~gvl~iDEi  136 (333)
T d1g8pa_          61 CPVSSPNVEMIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARA----NRGYLYIDEC  136 (333)
T ss_dssp             CTTCCSSGGGSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHH----TTEEEEETTG
T ss_pred             CccccCccccccchhhccccCcccccCceeeccCCCCcccccCcchhhhccccCcceeeccccccc----cccEeecccH
Confidence             00                     0112222222222222333210  0000        011122    3689999999


Q ss_pred             chhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC-CCCCChHHHhccceEEEecCC-CHHHHHHHHHH
Q 047219          398 DSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR-KQDLDPALISRFDSMITFGLP-DHENRQEIAAQ  472 (567)
Q Consensus       398 D~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~-~~~Ld~aL~sRf~~~I~i~~P-~~~eR~eIL~~  472 (567)
                      +.+.++.++.+.+.+++-...+-........+.++.+|+|+|+ +..+++++++||+..+.+..| +...+.+++..
T Consensus       137 ~~~~~~~~~aLl~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~~l~~~llDRf~~~i~v~~~~~~~~~~~~~~~  213 (333)
T d1g8pa_         137 NLLEDHIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLDRFGLSVEVLSPRDVETRVEVIRR  213 (333)
T ss_dssp             GGSCHHHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHTTCSEEEECCCCCSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhhhcCCeEEecccCceecCCCCEEEEEecCccccccccchhhhhcceeeccCcchhhHHHHHHHh
Confidence            9998765554444443211111111112234568999999998 456999999999988988766 56777666654

>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=99.50  E-value=6.4e-14  Score=144.93  Aligned_cols=187  Identities=19%  Similarity=0.323  Sum_probs=115.0

Q ss_pred             ccccCcHHHHHHHHHHHHHhccChhhHHhhhhc--------ccc-cccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCC
Q 047219          280 ENIAGYDQQKREIEDTILLSLQSPEVYDDIARG--------TRC-KFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMP  350 (567)
Q Consensus       280 ~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~--------~~~-~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~  350 (567)
                      ..|+||+++++.+-.++....++-..-..+...        ... .....++.++||.||+|||||.+||++|+.+    
T Consensus        17 ~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~----   92 (364)
T d1um8a_          17 NYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL----   92 (364)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT----
T ss_pred             CeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhc----
Confidence            358999999999987775332221111111000        000 0014578899999999999999999999998    


Q ss_pred             CCCcCeEEechhhHHh-hhhch-hHHHHHHHHHHHh---cCCCCcEEEEcCcchhhhhhhhhhH---HHHHHHHHHHHHh
Q 047219          351 WQGVPLMYVPLEVVMS-KYYGE-SERLLGKVFSLAN---ELPNGAIIFLDEVDSFAVARDSEMH---EATRRILSVLLRQ  422 (567)
Q Consensus       351 ~~~~~~~~i~~~~l~s-~~~G~-~~~~l~~~f~~A~---~~a~~~ILfIDEID~L~~~~q~~l~---~~~~~vl~~LL~~  422 (567)
                        +.+|+.++++.+.. .|+|+ .+..++.+...+.   ...+++++++||+|++.+.......   .....+++.||+.
T Consensus        93 --~~~~ir~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~~~lLqi  170 (364)
T d1um8a_          93 --DIPIAISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKI  170 (364)
T ss_dssp             --TCCEEEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHH
T ss_pred             --ccceeehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhccccccccccccccchHHHHhhhhh
Confidence              77899999988776 35554 2334555544332   2235799999999998754322111   1234567778888


Q ss_pred             hcCccc-----------CCcEEEEEeeCC-------------------------------------------------CC
Q 047219          423 IDGFEQ-----------DKKVVVIAATNR-------------------------------------------------KQ  442 (567)
Q Consensus       423 ld~~~~-----------~~~viVIaaTN~-------------------------------------------------~~  442 (567)
                      +++...           ..+.++|.|+|-                                                 ..
T Consensus       171 ld~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  250 (364)
T d1um8a_         171 VEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTY  250 (364)
T ss_dssp             HHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHT
T ss_pred             hcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhhh
Confidence            875211           134556655553                                                 12


Q ss_pred             CCChHHHhccceEEEecCCCHHHHHHHHHH
Q 047219          443 DLDPALISRFDSMITFGLPDHENRQEIAAQ  472 (567)
Q Consensus       443 ~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~  472 (567)
                      .|.|+|+.||+.++.|...+.++..+|+..
T Consensus       251 ~f~PEf~gRi~~iv~f~~L~~~~l~~Il~~  280 (364)
T d1um8a_         251 GLIPELIGRLPVLSTLDSISLEAMVDILQK  280 (364)
T ss_dssp             TCCHHHHTTCCEEEECCCCCHHHHHHHHHS
T ss_pred             hhHHHHHHHhcchhhHhhhhHHHHHHHHHH
Confidence            388999999999999999999999999864

>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=99.35  E-value=7.7e-13  Score=136.54  Aligned_cols=175  Identities=17%  Similarity=0.140  Sum_probs=107.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh-hchhHHHHHHHHHHHhc-----CCCCcEE
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY-YGESERLLGKVFSLANE-----LPNGAII  392 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~-~G~~~~~l~~~f~~A~~-----~a~~~IL  392 (567)
                      .+..+++||+||||||||++|+++|+.+      +.+++.+++++..+.+ .+...+....+|+.+..     ...++++
T Consensus       151 ~~~~~~~~~~g~~~~gk~~~~~~~~~~~------~~~~i~in~s~~rs~~~l~~~~~~~~~l~d~~~~~~~~~~~~~~~~  224 (362)
T d1svma_         151 IPKKRYWLFKGPIDSGKTTLAAALLELC------GGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQ  224 (362)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHHH------CCEEECCSSCTTTHHHHHGGGTTCSCEEETTCCCSTTTTTTCCCCS
T ss_pred             CCCcCeEEEECCCCCCHHHHHHHHHHHc------CCCEEEEECcchhhHHHHHhHHHHHHHHHHHHHHhhhhccCCCCeE
Confidence            4566799999999999999999999999      7789999988876654 23322222222222211     0112566


Q ss_pred             EEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcc----cCCcEEEEEeeCCCCCCChHHHh-ccceEEEecCCCHHHHH
Q 047219          393 FLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFE----QDKKVVVIAATNRKQDLDPALIS-RFDSMITFGLPDHENRQ  467 (567)
Q Consensus       393 fIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~----~~~~viVIaaTN~~~~Ld~aL~s-Rf~~~I~i~~P~~~eR~  467 (567)
                      |+||+|.|....++...           ..++...    ......+|+|||..  ..+.++. ||+..+.+..|+...+.
T Consensus       225 ~~DeiD~l~~~~dg~~~-----------~~~~~~~~~~~~~~~~p~i~ttN~~--~~~~~r~~Rf~~~i~~~~~~~~~~~  291 (362)
T d1svma_         225 GINNLDNLRDYLDGSVK-----------VNLEKKHLNKRTQIFPPGIVTMNEY--SVPKTLQARFVKQIDFRPKDYLKHC  291 (362)
T ss_dssp             HHHHHHTTHHHHHCSSC-----------EEECCSSSCCEEECCCCEEEEECSC--CCCHHHHTTEEEEEECCCCHHHHHH
T ss_pred             EEehHhhcccccCCcch-----------hhhhhhhhchhhhccCCceeecccc--cccccccccCceEEeecCCCcHHHH
Confidence            66666655322211100           0000000    00112478899953  2333333 99999999888876664


Q ss_pred             -HHHHHHHHhhC-HHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHH
Q 047219          468 -EIAAQYAKHLT-KAELAELATATEEMSGRDIRDVCQQAERSWASKI  512 (567)
Q Consensus       468 -eIL~~~~~~~~-~~~l~~la~~t~g~s~~dL~~L~~~a~~~a~~r~  512 (567)
                       +++..++++.. ....+.++..+.+++++|++.+++.+...+.++.
T Consensus       292 ~~~l~~i~~~~~l~~~~~~L~~li~~~s~~D~~~~i~~~~~~~~~~l  338 (362)
T d1svma_         292 LERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERL  338 (362)
T ss_dssp             HHTCTHHHHTTCTTCHHHHHHHHHHHSCGGGSCGGGHHHHHHHHHHH
T ss_pred             HHHHHHHhcccCCCCCHHHHHHHccCCCHHHHHHHHHHHHHHHHHHH
Confidence             45555555432 2355667788889999999999998887666654

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.33  E-value=5.8e-12  Score=119.24  Aligned_cols=125  Identities=12%  Similarity=0.169  Sum_probs=94.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcC---CCCcEEEEc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANEL---PNGAIIFLD  395 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~---a~~~ILfID  395 (567)
                      ...+.++||+||||||||++|..+++...........++.+..+.   +-.  .-+.++.+.+.+...   +...|++||
T Consensus        12 ~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~---~~I--~Id~IR~i~~~~~~~~~~~~~KviIId   86 (198)
T d2gnoa2          12 KSEGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEG---ENI--GIDDIRTIKDFLNYSPELYTRKYVIVH   86 (198)
T ss_dssp             TCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSS---SCB--CHHHHHHHHHHHTSCCSSSSSEEEEET
T ss_pred             cCCCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCc---CCC--CHHHHHHHHHHHhhCcccCCCEEEEEe
Confidence            456789999999999999999999998754433345677776532   111  124556666655533   334699999


Q ss_pred             CcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCC
Q 047219          396 EVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPD  462 (567)
Q Consensus       396 EID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~  462 (567)
                      |+|.|...           ..+.||+.++  +.+.++++|.+|+.++.+.+.++||| ..+.|+.|.
T Consensus        87 ~ad~l~~~-----------aqNaLLK~LE--EPp~~t~fiLit~~~~~ll~TI~SRC-~~i~~~~p~  139 (198)
T d2gnoa2          87 DCERMTQQ-----------AANAFLKALE--EPPEYAVIVLNTRRWHYLLPTIKSRV-FRVVVNVPK  139 (198)
T ss_dssp             TGGGBCHH-----------HHHHTHHHHH--SCCTTEEEEEEESCGGGSCHHHHTTS-EEEECCCCH
T ss_pred             Cccccchh-----------hhhHHHHHHh--CCCCCceeeeccCChhhCHHHHhcce-EEEeCCCch
Confidence            99999744           4467778777  46789999999999999999999999 888887764

>d1e32a1 b.52.2.3 (A:21-106) Membrane fusion ATPase p97 N-terminal domain , P97-Nn {Mouse (Mus musculus) [TaxId: 10090]}

class: All beta proteins
fold: Double psi beta-barrel
superfamily: ADC-like
family: Cdc48 N-terminal domain-like
domain: Membrane fusion ATPase p97 N-terminal domain , P97-Nn
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.28  E-value=4.1e-13  Score=109.75  Aligned_cols=64  Identities=11%  Similarity=0.148  Sum_probs=56.0

Q ss_pred             chhhhH-HHHHHHhCCCCCCccceEEEEecceEEEEEEecC-CC----CcchHHHHHHHhhCceecccCCCceeEEEee
Q 047219          111 KERQRI-EELLKRKGMHYGSCPTFTVAVKGQKVTIKFQVPP-AC----EIPQLIANLVSHLGLKVEEHGGGSDMGLRAW  183 (567)
Q Consensus       111 ~~~~~~-~~~~~~~g~~~g~~~~~~v~~~g~~~~~~~~~~~-~~----~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~  183 (567)
                      +|++|| ++.|++||+.+||+    |+|+|++.|+|++|+. .+    +++++++.+|+|+|+++||     +|+|+++
T Consensus        16 ~~iarl~p~~m~~Lgl~~GD~----V~I~Gkr~t~av~~~~~~~d~~~g~Irid~~~R~Nagv~iGD-----~V~V~p~   85 (86)
T d1e32a1          16 NSVVSLSQPKMDELQLFRGDT----VLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGD-----VISIQPC   85 (86)
T ss_dssp             TTEEEECHHHHHHTTCCTTCE----EEEECSTTCEEEEEEEECTTSCSSEEEECHHHHHHTTCCTTC-----EEEEEEC
T ss_pred             CCEEEECHHHHHHcCCCCCCE----EEEEcCCceeEEEEEeccCCCCCCEEEecHHHHhhcCcCCCC-----EEEEEeC
Confidence            689999 69999999999999    9999998777777663 22    5799999999999999999     9999874

>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=99.26  E-value=3.4e-11  Score=127.18  Aligned_cols=73  Identities=25%  Similarity=0.343  Sum_probs=54.8

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      .|+||+++|+.|--++....      +++...-. .-..-.+++|||.||||||||+|||.||+.+      ++||+.++
T Consensus        15 yVvGQ~~AKk~lsvav~nhy------rR~~~~~~-~~~ei~ksNILliGPTGvGKTlLAr~LAk~l------~VPFv~~d   81 (443)
T d1g41a_          15 HIIGQADAKRAVAIALRNRW------RRMQLQEP-LRHEVTPKNILMIGPTGVGKTEIARRLAKLA------NAPFIKVE   81 (443)
T ss_dssp             TCCSCHHHHHHHHHHHHHHH------HHHHSCTT-TTTTCCCCCEEEECCTTSSHHHHHHHHHHHT------TCCEEEEE
T ss_pred             cccCcHHHHHHHHHHHHHHH------HHhhcccc-cccccccccEEEECCCCCCHHHHHHHHHHHh------CCCEEEee
Confidence            48999999999988876542      22211100 1113457899999999999999999999999      89999999


Q ss_pred             hhhHHh
Q 047219          361 LEVVMS  366 (567)
Q Consensus       361 ~~~l~s  366 (567)
                      ++.+..
T Consensus        82 aT~fTe   87 (443)
T d1g41a_          82 ATKFTE   87 (443)
T ss_dssp             GGGGC-
T ss_pred             cceeee
Confidence            987755

>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=98.86  E-value=9.4e-08  Score=91.67  Aligned_cols=189  Identities=14%  Similarity=0.147  Sum_probs=111.7

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      |...-++++|.++.++++.+                         ...+.++|+||+|+|||+|++.+++...      .
T Consensus         7 p~~~~~~f~GR~~el~~l~~-------------------------~~~~~i~i~G~~G~GKTsLl~~~~~~~~------~   55 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEKLKG-------------------------LRAPITLVLGLRRTGKSSIIKIGINELN------L   55 (283)
T ss_dssp             CCCSGGGSCCCHHHHHHHHH-------------------------TCSSEEEEEESTTSSHHHHHHHHHHHHT------C
T ss_pred             CCCChhhCCChHHHHHHHHh-------------------------ccCCEEEEEcCCCCcHHHHHHHHHHHCC------C
Confidence            44556899999999887754                         1246899999999999999999999883      3


Q ss_pred             CeEEechhhHHhhh----------hch------------------------------------hHHHHHHHHHHHh-cCC
Q 047219          355 PLMYVPLEVVMSKY----------YGE------------------------------------SERLLGKVFSLAN-ELP  387 (567)
Q Consensus       355 ~~~~i~~~~l~s~~----------~G~------------------------------------~~~~l~~~f~~A~-~~a  387 (567)
                      .+.++++.......          +..                                    ....+..+++... ...
T Consensus        56 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~  135 (283)
T d2fnaa2          56 PYIYLDLRKFEERNYISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASK  135 (283)
T ss_dssp             CEEEEEGGGGTTCSCCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCS
T ss_pred             CeEEEEeccccccccccHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcc
Confidence            44444432211110          000                                    0011222333322 223


Q ss_pred             CCcEEEEcCcchhhhhhhhhhHHHHHHHHHHHHHhhcCcccCCcEEEEEeeCC---------CCCCChHHHhccceEEEe
Q 047219          388 NGAIIFLDEVDSFAVARDSEMHEATRRILSVLLRQIDGFEQDKKVVVIAATNR---------KQDLDPALISRFDSMITF  458 (567)
Q Consensus       388 ~~~ILfIDEID~L~~~~q~~l~~~~~~vl~~LL~~ld~~~~~~~viVIaaTN~---------~~~Ld~aL~sRf~~~I~i  458 (567)
                      .+.++++||++.+.......+....       ....+   ....+..+.+...         .......+..|+...+++
T Consensus       136 ~~~~i~id~~~~~~~~~~~~~~~~l-------~~~~~---~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L  205 (283)
T d2fnaa2         136 DNVIIVLDEAQELVKLRGVNLLPAL-------AYAYD---NLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVEL  205 (283)
T ss_dssp             SCEEEEEETGGGGGGCTTCCCHHHH-------HHHHH---HCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEE
T ss_pred             cccccccchhhhhcccchHHHHHHH-------HHHHH---hhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEee
Confidence            4578999999998654333222221       11111   1233444444322         111223344455578999


Q ss_pred             cCCCHHHHHHHHHHHHHh--hCHHHHHHHHHhccCCCHHHHHHHHHHHH
Q 047219          459 GLPDHENRQEIAAQYAKH--LTKAELAELATATEEMSGRDIRDVCQQAE  505 (567)
Q Consensus       459 ~~P~~~eR~eIL~~~~~~--~~~~~l~~la~~t~g~s~~dL~~L~~~a~  505 (567)
                      +..+.++..+++...+..  +..+..+.+.+.+.|. +..|..++...+
T Consensus       206 ~~l~~~e~~~~l~~~~~~~~~~~~~~~~i~~~~~G~-P~~L~~~~~~~~  253 (283)
T d2fnaa2         206 KPFSREEAIEFLRRGFQEADIDFKDYEVVYEKIGGI-PGWLTYFGFIYL  253 (283)
T ss_dssp             CCCCHHHHHHHHHHHHHHHTCCCCCHHHHHHHHCSC-HHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHhhhhhcCCCHHHHHHHHHHhCCC-HHHHHHHHHHHH
Confidence            999999999999887654  3444567788887764 777777766554

>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=98.58  E-value=2.3e-08  Score=96.62  Aligned_cols=44  Identities=25%  Similarity=0.398  Sum_probs=39.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      ...|+++||+||||||||++|++||+++      +.+++.++++++....
T Consensus        29 ~~~P~~ilL~GpPGtGKT~la~~la~~~------~~~~~~i~~d~~~~~~   72 (273)
T d1gvnb_          29 VESPTAFLLGGQPGSGKTSLRSAIFEET------QGNVIVIDNDTFKQQH   72 (273)
T ss_dssp             CSSCEEEEEECCTTSCTHHHHHHHHHHT------TTCCEEECTHHHHTTS
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHh------hcceEEEecHHHHHHh
Confidence            6788999999999999999999999999      6779999998876543

>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=98.05  E-value=8.5e-06  Score=72.98  Aligned_cols=24  Identities=33%  Similarity=0.722  Sum_probs=22.1

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .|+|.||||+|||||+++|+..+.
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~   25 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLG   25 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCC
Confidence            489999999999999999999874

>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=98.03  E-value=3.4e-05  Score=75.17  Aligned_cols=177  Identities=8%  Similarity=0.036  Sum_probs=95.3

Q ss_pred             cccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeE
Q 047219          281 NIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLM  357 (567)
Q Consensus       281 dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~  357 (567)
                      ++.|.+..+++|.+++...                  .......|.|+|..|+|||+||+.+.+.....   .|.++-++
T Consensus        21 ~~~gR~~~~~~i~~~L~~~------------------~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv   82 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEM------------------CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWL   82 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHH------------------TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEE
T ss_pred             ceeCcHHHHHHHHHHHHhc------------------cCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEE
Confidence            4789999999998877532                  02334568899999999999999998875321   22222233


Q ss_pred             Eechh----hHHhhh---h---------------chhHHHHHHHHHHHhcCCCCcEEEEcCcchhhhhhhhhhHHHHHHH
Q 047219          358 YVPLE----VVMSKY---Y---------------GESERLLGKVFSLANELPNGAIIFLDEVDSFAVARDSEMHEATRRI  415 (567)
Q Consensus       358 ~i~~~----~l~s~~---~---------------G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L~~~~q~~l~~~~~~v  415 (567)
                      .+...    .+....   .               ..........+-......+.++++||++....             .
T Consensus        83 ~vs~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~-------------~  149 (277)
T d2a5yb3          83 KDSGTAPKSTFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEE-------------T  149 (277)
T ss_dssp             ECCCCSTTHHHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHH-------------H
T ss_pred             EecCCCCHHHHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHh-------------h
Confidence            33221    111100   0               00111222221111122335899999998531             0


Q ss_pred             HHHHHHhhcCcccCCcEEEEEeeCCCCCCChHHHhccceEEEecCCCHHHHHHHHHHHHHhh-----CHHHHHHHHHhcc
Q 047219          416 LSVLLRQIDGFEQDKKVVVIAATNRKQDLDPALISRFDSMITFGLPDHENRQEIAAQYAKHL-----TKAELAELATATE  490 (567)
Q Consensus       416 l~~LL~~ld~~~~~~~viVIaaTN~~~~Ld~aL~sRf~~~I~i~~P~~~eR~eIL~~~~~~~-----~~~~l~~la~~t~  490 (567)
                      ...+.        .....+|.||.... +-..+.... ..+.++..+.++-.+++..+....     ..+...++.+.+.
T Consensus       150 ~~~~~--------~~~srilvTTR~~~-v~~~~~~~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~  219 (277)
T d2a5yb3         150 IRWAQ--------ELRLRCLVTTRDVE-ISNAASQTC-EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSS  219 (277)
T ss_dssp             HHHHH--------HTTCEEEEEESBGG-GGGGCCSCE-EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHT
T ss_pred             hhhhc--------ccCceEEEEeehHH-HHHhcCCCC-ceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhC
Confidence            11111        12346677776332 111222222 467888999999999887653221     1223466777776


Q ss_pred             CCCHHHHHH
Q 047219          491 EMSGRDIRD  499 (567)
Q Consensus       491 g~s~~dL~~  499 (567)
                      |. |-.|..
T Consensus       220 Gl-PLAl~~  227 (277)
T d2a5yb3         220 GN-PATLMM  227 (277)
T ss_dssp             TC-HHHHHH
T ss_pred             CC-HHHHHH
Confidence            64 444443

>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=97.76  E-value=1.7e-05  Score=68.96  Aligned_cols=24  Identities=38%  Similarity=0.714  Sum_probs=22.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|+|.|||||||||+|+.||+.+
T Consensus         3 k~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           3 RNIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHh
Confidence            579999999999999999999999

>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=97.73  E-value=9.5e-06  Score=72.26  Aligned_cols=40  Identities=13%  Similarity=0.049  Sum_probs=31.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      -.+.|+|.|||||||||+|++|++.+      +.+++......+..
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~~------~~~~i~~~~~~~~~   45 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAVF------NTTSAWEYGREFVF   45 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHHT------TCEEECCTTHHHHH
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHh------CCCeEeeehHHHhh
Confidence            46789999999999999999999998      55666555544433

>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=97.50  E-value=2.8e-05  Score=69.05  Aligned_cols=38  Identities=32%  Similarity=0.543  Sum_probs=32.2

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      ++-|+|.|||||||||+|+++++.+      +.+++.++...+.
T Consensus         4 g~iI~l~G~~GsGKSTia~~La~~l------g~~~~~~~~d~~~   41 (176)
T d1zp6a1           4 GNILLLSGHPGSGKSTIAEALANLP------GVPKVHFHSDDLW   41 (176)
T ss_dssp             TEEEEEEECTTSCHHHHHHHHHTCS------SSCEEEECTTHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh------CCCEEEecHHHHH
Confidence            4568999999999999999999988      7788888765543

>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=97.46  E-value=2.7e-05  Score=68.80  Aligned_cols=30  Identities=30%  Similarity=0.666  Sum_probs=25.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      ..++|.|||||||||+|+.|++.+      +.+++.
T Consensus         5 ~~I~i~G~pGsGKTTia~~La~~l------~~~~i~   34 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLGKELASKS------GLKYIN   34 (173)
T ss_dssp             CCEEEECSTTSSHHHHHHHHHHHH------CCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHH------CCcEEe
Confidence            358899999999999999999999      666654

>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=97.42  E-value=0.00014  Score=64.64  Aligned_cols=32  Identities=25%  Similarity=0.467  Sum_probs=27.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      ++++|.|+||+||||+++.+|+.+      +++|+..+
T Consensus         1 k~I~liG~~GsGKsTi~k~La~~l------~~~~~d~d   32 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLARALAKDL------DLVFLDSD   32 (161)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH------TCEEEEHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh------CCCEEecC
Confidence            468899999999999999999999      66777543

>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=97.41  E-value=3.4e-05  Score=68.48  Aligned_cols=25  Identities=36%  Similarity=0.632  Sum_probs=23.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++|+|+||||||||+++++++..+.
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~   26 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHH
Confidence            6899999999999999999999884

>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=97.41  E-value=0.00024  Score=61.45  Aligned_cols=39  Identities=21%  Similarity=0.301  Sum_probs=29.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      +-|+|+|+||+||||+|+.+....       .++..++..++....
T Consensus         3 klIii~G~pGsGKTTla~~L~~~~-------~~~~~~~~d~~~~~~   41 (152)
T d1ly1a_           3 KIILTIGCPGSGKSTWAREFIAKN-------PGFYNINRDDYRQSI   41 (152)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHS-------TTEEEECHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhC-------CCCEEechHHHHHHH
Confidence            357899999999999999998764       246777776665543

>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=97.40  E-value=7.9e-05  Score=65.74  Aligned_cols=37  Identities=16%  Similarity=0.391  Sum_probs=29.7

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      .+-|+|+|+||+||||+|++|++.+      +.+++.++...+
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l------~~~~~~~~~d~~   39 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVL------PEPWLAFGVDSL   39 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHS------SSCEEEEEHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc------CCCeEEeecchh
Confidence            4578999999999999999999999      555666655443

>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=97.36  E-value=0.00042  Score=64.80  Aligned_cols=40  Identities=23%  Similarity=0.199  Sum_probs=30.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      ..+..-++|+|+||+|||+++..++......   +.++.+++.
T Consensus        23 i~~gsl~li~G~pGsGKT~l~~qia~~~~~~---~~~~~~is~   62 (242)
T d1tf7a2          23 FFKDSIILATGATGTGKTLLVSRFVENACAN---KERAILFAY   62 (242)
T ss_dssp             EESSCEEEEEECTTSSHHHHHHHHHHHHHTT---TCCEEEEES
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHHHHHHh---ccccceeec
Confidence            4566779999999999999999999886433   445556554

>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=97.31  E-value=0.0001  Score=66.90  Aligned_cols=39  Identities=21%  Similarity=0.374  Sum_probs=31.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      |..++|.|||||||||+|+.|++.+        ++..++..++....
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~--------~~~~is~~~~~~~~   41 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY--------QLAHISAGDLLRAE   41 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH--------CCEECCHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH--------CCcEEehhHHHHHh
Confidence            5569999999999999999999998        35566666655543

>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=97.29  E-value=8.2e-05  Score=65.70  Aligned_cols=28  Identities=25%  Similarity=0.423  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+.++-++|.|+|||||||+|+.|++.+
T Consensus         3 ~~~~~iivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           3 NHDHHIYVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             CTTSEEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3456778899999999999999999998

>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=97.26  E-value=6.9e-05  Score=67.07  Aligned_cols=30  Identities=23%  Similarity=0.445  Sum_probs=26.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      ++++|.|+||+||||+++.+|+.+      +++|+.
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~L------g~~~id   32 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARAL------GYEFVD   32 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH------TCEEEE
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHh------CCCEEe
Confidence            568899999999999999999999      666664

>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=97.25  E-value=7.7e-05  Score=65.96  Aligned_cols=27  Identities=44%  Similarity=0.661  Sum_probs=24.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +.+..|+|.||||+||||+|+.|++.+
T Consensus         3 pk~~~I~i~G~~GsGKTT~~~~La~~l   29 (174)
T d1y63a_           3 PKGINILITGTPGTGKTSMAEMIAAEL   29 (174)
T ss_dssp             CSSCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCCEEEEEeCCCCCHHHHHHHHHHHh
Confidence            456679999999999999999999998

>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=97.24  E-value=0.00032  Score=63.15  Aligned_cols=66  Identities=21%  Similarity=0.191  Sum_probs=42.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhchhHHHHHHHHHHHhcCCCCcEEEEcCcc
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYGESERLLGKVFSLANELPNGAIIFLDEVD  398 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID  398 (567)
                      ...|.-++++|+||+||||+|+.++...        .+..++..++...      ..+....+.+...  +..+++|...
T Consensus        11 ~~~p~liil~G~pGsGKST~a~~l~~~~--------~~~~i~~D~~~~~------~~~~~~~~~~l~~--g~~vIiD~t~   74 (172)
T d1yj5a2          11 SPNPEVVVAVGFPGAGKSTFIQEHLVSA--------GYVHVNRDTLGSW------QRCVSSCQAALRQ--GKRVVIDNTN   74 (172)
T ss_dssp             CSSCCEEEEECCTTSSHHHHHHHHTGGG--------TCEEEEHHHHCSH------HHHHHHHHHHHHT--TCCEEEESCC
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHhc--------CCEEEchHHHHHH------HHHHHHHHHHHHC--CCCceeeCcC
Confidence            4567789999999999999999988765        3555666655431      2222333333333  3567788776


Q ss_pred             hh
Q 047219          399 SF  400 (567)
Q Consensus       399 ~L  400 (567)
                      ..
T Consensus        75 ~~   76 (172)
T d1yj5a2          75 PD   76 (172)
T ss_dssp             CS
T ss_pred             CC
Confidence            54

>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=97.24  E-value=0.00035  Score=63.54  Aligned_cols=41  Identities=22%  Similarity=0.356  Sum_probs=31.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      |.-|+++|.||+||||+|++|++.+...   +.++..++.....
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~~---~~~~~~~~~D~~r   42 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNFI---GVPTREFNVGQYR   42 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEEEHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc---CCCCeEEccccee
Confidence            4568999999999999999999988543   4556666665443

>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=97.24  E-value=0.00037  Score=58.78  Aligned_cols=27  Identities=22%  Similarity=0.303  Sum_probs=19.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHH-HHHHHh
Q 047219          320 NRPRAVLFEGPPGTGKTSCAR-VIANQA  346 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAr-aIA~~l  346 (567)
                      +....++|++|||+|||..+- ++....
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~   32 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAEC   32 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHH
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHh
Confidence            456889999999999996663 444433

>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=97.22  E-value=0.00013  Score=66.30  Aligned_cols=39  Identities=23%  Similarity=0.435  Sum_probs=30.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      ...|.-|+|.||||+||||+|+.|++.+      +  +..++..++.
T Consensus         3 ~~kp~iI~i~G~pGSGKsT~a~~La~~~------g--~~~i~~g~~~   41 (194)
T d1qf9a_           3 KSKPNVVFVLGGPGSGKGTQCANIVRDF------G--WVHLSAGDLL   41 (194)
T ss_dssp             CCCCEEEEEEESTTSSHHHHHHHHHHHH------C--CEEEEHHHHH
T ss_pred             CCCCcEEEEECCCCCCHHHHHHHHHHHH------C--CceEchhhHH
Confidence            4567789999999999999999999998      4  4555554444

>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=97.20  E-value=0.0001  Score=65.12  Aligned_cols=28  Identities=18%  Similarity=0.292  Sum_probs=24.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..|+|+|+||+||||+|++|++.+.
T Consensus         4 ~~g~~I~l~G~~GsGKTTia~~La~~L~   31 (183)
T d1m8pa3           4 TQGFTIFLTGYMNSGKDAIARALQVTLN   31 (183)
T ss_dssp             TCCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4556799999999999999999999984

>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=97.18  E-value=0.00021  Score=63.47  Aligned_cols=29  Identities=34%  Similarity=0.620  Sum_probs=24.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      ++|.|+|||||||+++.+|+.+      +.+|+..
T Consensus         4 IvliG~~G~GKSTig~~La~~l------~~~fiD~   32 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKAL------GVGLLDT   32 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH------TCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh------CCCeEee
Confidence            5566999999999999999999      7777643

>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=97.17  E-value=0.00068  Score=62.52  Aligned_cols=29  Identities=21%  Similarity=0.368  Sum_probs=25.6

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.-+.++|+|||+||||++|.+|.+.+.
T Consensus        50 ~PKkn~i~~~GP~~TGKS~f~~sl~~~l~   78 (205)
T d1tuea_          50 TPKKNCLVFCGPANTGKSYFGMSFIHFIQ   78 (205)
T ss_dssp             CTTCSEEEEESCGGGCHHHHHHHHHHHHT
T ss_pred             CCCceEEEEECCCCccHHHHHHHHHHHhC
Confidence            45557899999999999999999999984

>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=97.15  E-value=0.00016  Score=65.83  Aligned_cols=38  Identities=13%  Similarity=0.327  Sum_probs=29.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      +...-++|.||||+||||+|+.|++.+        .+.+++..++.
T Consensus         6 ~~~~iI~i~GppGSGKsT~a~~La~~~--------g~~~is~gdl~   43 (196)
T d1ukza_           6 DQVSVIFVLGGPGAGKGTQCEKLVKDY--------SFVHLSAGDLL   43 (196)
T ss_dssp             TTCEEEEEECSTTSSHHHHHHHHHHHS--------SCEEEEHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHh--------CCeEEehhHHH
Confidence            344568889999999999999999988        35666665554

>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=97.14  E-value=0.00012  Score=64.14  Aligned_cols=25  Identities=28%  Similarity=0.603  Sum_probs=22.6

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +-++|.|||||||||+|+.|++.++
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~   27 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLD   27 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcC
Confidence            4588999999999999999999983

>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=97.09  E-value=0.00099  Score=56.77  Aligned_cols=26  Identities=15%  Similarity=0.259  Sum_probs=20.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....+|.+|+|+|||+++-.+....
T Consensus         7 ~~~~~ll~apTGsGKT~~~~~~~~~~   32 (136)
T d1a1va1           7 SFQVAHLHAPTGSGKSTKVPAAYAAQ   32 (136)
T ss_dssp             SCEEEEEECCTTSCTTTHHHHHHHTT
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHc
Confidence            34678999999999999876555444

>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=97.09  E-value=0.00011  Score=66.08  Aligned_cols=28  Identities=25%  Similarity=0.308  Sum_probs=24.5

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..|+|+|+||+||||+|+.|+..+.
T Consensus        17 ~~g~vI~L~G~pGSGKTTiAk~La~~l~   44 (195)
T d1x6va3          17 FRGCTVWLTGLSGAGKTTVSMALEEYLV   44 (195)
T ss_dssp             CCCEEEEEESSCHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3456788999999999999999999884

>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=97.08  E-value=0.00036  Score=67.62  Aligned_cols=117  Identities=22%  Similarity=0.325  Sum_probs=69.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh-h---hc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK-Y---YG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~-~---~G------------~~~~~l~~~f~~  382 (567)
                      .+.++-+.|+||+|||||++|..++......   +..+++++.+.-... +   +|            ..+..+ ++.+.
T Consensus        54 ip~g~itei~G~~~sGKT~l~l~~~~~aqk~---g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~-~~~~~  129 (268)
T d1xp8a1          54 IPRGRITEIYGPESGGKTTLALAIVAQAQKA---GGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQAL-EIMEL  129 (268)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHH-HHHHH
T ss_pred             ccCceEEEEecCCccchHHHHHHHHHHHHhC---CCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHH-HHHHH
Confidence            3566778999999999999999998877543   556888886532211 1   11            123332 23344


Q ss_pred             HhcCCCCcEEEEcCcchhhhhhhh--hhHH----HHHHHHHHHHHhhcCcccCCcEEEEEeeC
Q 047219          383 ANELPNGAIIFLDEVDSFAVARDS--EMHE----ATRRILSVLLRQIDGFEQDKKVVVIAATN  439 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~q~--~l~~----~~~~vl~~LL~~ld~~~~~~~viVIaaTN  439 (567)
                      ..+..+..+|++|=+..+.+..+-  ...+    ...+.+..+++.+..+-...++.+|.+..
T Consensus       130 l~~~~~~~liIiDSi~al~~r~e~~~~~~~~~~~~~a~~l~~~lr~l~~~~~~~~~~vi~tNQ  192 (268)
T d1xp8a1         130 LVRSGAIDVVVVDSVAALTPRAEIEGDMGDSLPGLQARLMSQALRKLTAILSKTGTAAIFINQ  192 (268)
T ss_dssp             HHTTTCCSEEEEECTTTCCCSTTC--------CCHHHHHHHHHHHHHHHHHTTTCCEEEEEEE
T ss_pred             HHhcCCCcEEEEecccccccHHHHcccccchhHHHHHHHHHHHHHHHHhhhhhcCCeEEEEeE
Confidence            444445689999999998753321  1111    23344455555554444455667776653

>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=96.94  E-value=0.00038  Score=67.19  Aligned_cols=80  Identities=20%  Similarity=0.248  Sum_probs=50.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh----hhc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK----YYG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~----~~G------------~~~~~l~~~f~~  382 (567)
                      .....-+.|+||||+|||++|-.++......   +..+++++.+.-...    -.|            ..+..+. +.+.
T Consensus        51 i~~g~itei~G~~gsGKTtl~l~~~~~~q~~---g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~-~i~~  126 (263)
T d1u94a1          51 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALE-ICDA  126 (263)
T ss_dssp             EETTSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHH-HHHH
T ss_pred             ccCceEEEEecCCCcHHHHHHHHHHHHHHcC---CCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHH-HHHH
Confidence            3566779999999999999999888877543   455777776532111    011            1233332 2233


Q ss_pred             HhcCCCCcEEEEcCcchhhh
Q 047219          383 ANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~  402 (567)
                      ..+..+..++++|-+..+.+
T Consensus       127 l~~~~~~~liViDSi~al~~  146 (263)
T d1u94a1         127 LARSGAVDVIVVDSVAALTP  146 (263)
T ss_dssp             HHHHTCCSEEEEECGGGCCC
T ss_pred             HHhcCCCCEEEEECcccccc
Confidence            23333458999999988864

>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=96.92  E-value=0.00037  Score=63.06  Aligned_cols=36  Identities=22%  Similarity=0.336  Sum_probs=27.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      +..++|.||||+||||+|+.||+.+      +  +..++..++.
T Consensus         3 ~~riil~G~pGSGKsT~a~~La~~~------g--~~~i~~gdll   38 (190)
T d1ak2a1           3 GVRAVLLGPPGAGKGTQAPKLAKNF------C--VCHLATGDML   38 (190)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH------T--CEEEEHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHHHHh------C--CeEEeHHHHH
Confidence            3457788999999999999999998      3  4555555544

>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=96.91  E-value=0.00028  Score=63.00  Aligned_cols=23  Identities=30%  Similarity=0.475  Sum_probs=21.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.||||+||||+|+.||+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1zina1           2 NLVLMGLPGAGKGTQAEKIVAAY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999998

>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=96.91  E-value=0.0011  Score=67.84  Aligned_cols=100  Identities=9%  Similarity=0.154  Sum_probs=63.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCc
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGV  354 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~  354 (567)
                      ...++++++-.+...+.+++++                      ..+..-+|+.||+|+||||+..++.++++..   ..
T Consensus       133 ~~~~l~~LG~~~~~~~~l~~l~----------------------~~~~GliLvtGpTGSGKSTTl~~~l~~~~~~---~~  187 (401)
T d1p9ra_         133 TRLDLHSLGMTAHNHDNFRRLI----------------------KRPHGIILVTGPTGSGKSTTLYAGLQELNSS---ER  187 (401)
T ss_dssp             TCCCGGGSCCCHHHHHHHHHHH----------------------TSSSEEEEEECSTTSCHHHHHHHHHHHHCCT---TS
T ss_pred             cchhhhhhcccHHHHHHHHHHH----------------------hhhhceEEEEcCCCCCccHHHHHHhhhhcCC---Cc
Confidence            3456888888888888877655                      3445668899999999999999999998653   22


Q ss_pred             CeEEechh-hHH-h-----hhhchhHHHHHHHHHHHhcCCCCcEEEEcCcchh
Q 047219          355 PLMYVPLE-VVM-S-----KYYGESERLLGKVFSLANELPNGAIIFLDEVDSF  400 (567)
Q Consensus       355 ~~~~i~~~-~l~-s-----~~~G~~~~~l~~~f~~A~~~a~~~ILfIDEID~L  400 (567)
                      +++.+..+ +.. .     .+.+.........+..+.+.. |.||++.||-..
T Consensus       188 ~i~tiEdPiE~~~~~~~q~~v~~~~~~~~~~~l~~~lR~d-PDvi~igEiRd~  239 (401)
T d1p9ra_         188 NILTVEDPIEFDIDGIGQTQVNPRVDMTFARGLRAILRQD-PDVVMVGEIRDL  239 (401)
T ss_dssp             CEEEEESSCCSCCSSSEEEECBGGGTBCHHHHHHHHGGGC-CSEEEESCCCSH
T ss_pred             eEEEeccCcccccCCCCeeeecCCcCCCHHHHHHHHHhhc-CCEEEecCcCCh
Confidence            33333221 000 0     001111122344555556666 489999999764

>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=96.90  E-value=0.0005  Score=62.49  Aligned_cols=40  Identities=18%  Similarity=0.355  Sum_probs=31.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKY  368 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~  368 (567)
                      .++-|+|.||||+||||+|+.|++.+      +  +..++..++....
T Consensus         7 ~~~iI~l~G~pGSGKsT~a~~La~~~------g--~~~is~g~llr~~   46 (194)
T d3adka_           7 KSKIIFVVGGPGSGKGTQCEKIVQKY------G--YTHLSTGDLLRAE   46 (194)
T ss_dssp             TSCEEEEEECTTSSHHHHHHHHHHHT------C--CEEEEHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh------C--CeeEeccHHHHHH
Confidence            45779999999999999999999988      3  5666766665543

>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=96.85  E-value=0.0004  Score=62.90  Aligned_cols=36  Identities=25%  Similarity=0.415  Sum_probs=28.4

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      |.-|+|.||||+||||.|+.||+.+      +  +..++..++.
T Consensus         1 p~iI~i~GppGSGKsT~a~~La~~~------g--~~~i~~g~ll   36 (194)
T d1teva_           1 PLVVFVLGGPGAGKGTQCARIVEKY------G--YTHLSAGELL   36 (194)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHH------C--CEEEEHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh------C--CceEcHHHHH
Confidence            4568999999999999999999998      3  4555555444

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=96.83  E-value=0.0017  Score=60.36  Aligned_cols=80  Identities=18%  Similarity=0.255  Sum_probs=47.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH-------Hhhh---h----------chhHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV-------MSKY---Y----------GESERLLGK  378 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l-------~s~~---~----------G~~~~~l~~  378 (567)
                      ...|.-++|.||+|+||||.+--+|..+...   +..+.-+.+..+       ...|   .          .+....+..
T Consensus         6 ~~~p~vi~lvGptGvGKTTTiAKLA~~~~~~---g~kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~   82 (211)
T d2qy9a2           6 GKAPFVILMVGVNGVGKTTTIGKLARQFEQQ---GKSVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFD   82 (211)
T ss_dssp             SCTTEEEEEECCTTSCHHHHHHHHHHHHHTT---TCCEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHH
Confidence            5667889999999999999888888776433   333433333221       1111   0          112233444


Q ss_pred             HHHHHhcCCCCcEEEEcCcchhhh
Q 047219          379 VFSLANELPNGAIIFLDEVDSFAV  402 (567)
Q Consensus       379 ~f~~A~~~a~~~ILfIDEID~L~~  402 (567)
                      ..+.++... .-+++||=......
T Consensus        83 ~~~~a~~~~-~d~ilIDTaGr~~~  105 (211)
T d2qy9a2          83 AIQAAKARN-IDVLIADTAGRLQN  105 (211)
T ss_dssp             HHHHHHHTT-CSEEEECCCCCGGG
T ss_pred             HHHHHHHcC-CCEEEeccCCCccc
Confidence            444444333 46999999887643

>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=96.78  E-value=0.00055  Score=60.47  Aligned_cols=35  Identities=26%  Similarity=0.480  Sum_probs=27.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +-|+|.|+||+||||+++.|++.+...   +.++..+.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~~---~~~~~~~~   36 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRKE---GVNYKMVS   36 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHTT---TCCCEEEE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHc---CCCeEEEe
Confidence            468999999999999999999998544   34444443

>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=96.77  E-value=0.00078  Score=65.16  Aligned_cols=116  Identities=23%  Similarity=0.330  Sum_probs=65.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh-hh---hc------------hhHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS-KY---YG------------ESERLLGKVFSL  382 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s-~~---~G------------~~~~~l~~~f~~  382 (567)
                      ...+.-+.|+||||||||++|..++......   +..+++++.+.-.+ .+   +|            ..+..+ ++.+.
T Consensus        57 ~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~---g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~-~~~~~  132 (269)
T d1mo6a1          57 LPRGRVIEIYGPESSGKTTVALHAVANAQAA---GGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQAL-EIADM  132 (269)
T ss_dssp             BCSSSEEEEECSSSSSHHHHHHHHHHHHHHT---TCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHH-HHHHH
T ss_pred             cccceeEEEecCCCcHHHHHHHHHHHHHhcC---CCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHH-HHHHH
Confidence            5667789999999999999997777665433   45577777654211 11   11            122222 23333


Q ss_pred             HhcCCCCcEEEEcCcchhhhhhhh--hhHH----HHHHHHHHHHHhhcCcccCCcEEEEEee
Q 047219          383 ANELPNGAIIFLDEVDSFAVARDS--EMHE----ATRRILSVLLRQIDGFEQDKKVVVIAAT  438 (567)
Q Consensus       383 A~~~a~~~ILfIDEID~L~~~~q~--~l~~----~~~~vl~~LL~~ld~~~~~~~viVIaaT  438 (567)
                      .....+..+|+||-+..+.+..+-  ...+    ...+.+..+++.+.......++.+|.+.
T Consensus       133 l~~~~~~~liIiDSi~al~~~~E~e~~~~~~~~~~~a~~l~~~l~~l~~~~~~~~~~vi~~N  194 (269)
T d1mo6a1         133 LIRSGALDIVVIDSVAALVPRAELEGEMGDSHVGLQARLMSQALRKMTGALNNSGTTAIFIN  194 (269)
T ss_dssp             HHHTTCEEEEEEECSTTCCCHHHHC-------CCHHHHHHHHHHHHHHHHHHHHTCEEEEEE
T ss_pred             HHhcCCCCEEEEecccccccHHHhccccccchHHHHHHHHHHHHHHHHHHHhhcCchhhhhh
Confidence            333445689999999988853221  1111    1234444555544443334566777764

>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=96.76  E-value=0.00038  Score=62.42  Aligned_cols=23  Identities=43%  Similarity=0.694  Sum_probs=21.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.||||+||||+|+.|++.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~   24 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKL   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47899999999999999999998

>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=96.71  E-value=0.0006  Score=61.24  Aligned_cols=35  Identities=20%  Similarity=0.351  Sum_probs=27.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      .++|.||||+||||+|+.||+.+      +  +..++..++..
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~------g--~~~i~~~d~~~   38 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERF------H--AAHLATGDMLR   38 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH------C--CEEEEHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh------C--CceEeccccce
Confidence            47788999999999999999998      3  45566655544

>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=96.65  E-value=0.00065  Score=61.85  Aligned_cols=36  Identities=19%  Similarity=0.293  Sum_probs=28.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      -.++|.||||+||||+|+.||+.+      +  +..++..++..
T Consensus         7 mrIiliG~PGSGKtT~a~~La~~~------g--~~~is~gdllr   42 (189)
T d2ak3a1           7 LRAAIMGAPGSGKGTVSSRITKHF------E--LKHLSSGDLLR   42 (189)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHB------C--CEEEEHHHHHH
T ss_pred             eeEEEECCCCCCHHHHHHHHHHHH------C--CeEEcHHHHHH
Confidence            457788999999999999999988      3  55566655543

>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=96.62  E-value=0.00063  Score=61.07  Aligned_cols=23  Identities=30%  Similarity=0.521  Sum_probs=21.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.||||+||||+|+.||+.+
T Consensus         2 ~I~i~G~pGSGKsT~a~~La~~~   24 (182)
T d1s3ga1           2 NIVLMGLPGAGKGTQADRIVEKY   24 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999998

>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=96.61  E-value=0.00068  Score=62.11  Aligned_cols=35  Identities=17%  Similarity=0.407  Sum_probs=28.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMS  366 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s  366 (567)
                      -|.+.||||+||+|+|+.|++.+        ++.+++..++.-
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~--------gl~~iStGdLlR   39 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEAL--------QWHLLDSGAIYR   39 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH--------TCEEEEHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh--------CCcEECHHHHHH
Confidence            57788999999999999999998        366676655543

>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=96.58  E-value=0.00064  Score=60.79  Aligned_cols=23  Identities=26%  Similarity=0.459  Sum_probs=21.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++|.||||+||||+|+.|++.+
T Consensus         2 ~I~i~G~pGSGKsT~~~~La~~~   24 (179)
T d1e4va1           2 RIILLGAPVAGKGTQAQFIMEKY   24 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            47889999999999999999998

>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=96.56  E-value=0.0038  Score=59.53  Aligned_cols=30  Identities=23%  Similarity=0.383  Sum_probs=26.1

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...+..-+-|.||+|+|||||++.|.....
T Consensus        36 ~i~~Ge~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          36 TLRPGEVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHhcccC
Confidence            367788899999999999999999997663

>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=96.53  E-value=0.0038  Score=62.63  Aligned_cols=23  Identities=35%  Similarity=0.577  Sum_probs=18.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      +-++|+||||||||+++..+...
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~l~~  186 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKLLAA  186 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHHHHH
Confidence            46889999999999987655443

>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=96.41  E-value=0.00079  Score=58.75  Aligned_cols=26  Identities=27%  Similarity=0.282  Sum_probs=22.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      -+.|+|++|+|||||++.+++++...
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~   29 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCAR   29 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHC
Confidence            47899999999999999999987543

>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=96.40  E-value=0.0022  Score=58.43  Aligned_cols=19  Identities=32%  Similarity=0.447  Sum_probs=16.5

Q ss_pred             CceEEeeCCCCCcHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCAR  340 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAr  340 (567)
                      .+++++.+|+|+|||+++-
T Consensus        40 ~~~~il~apTGsGKT~~a~   58 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAE   58 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHHH
Confidence            4679999999999998863

>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=96.38  E-value=0.0043  Score=58.79  Aligned_cols=30  Identities=17%  Similarity=0.255  Sum_probs=26.3

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...++..+-|.||+|+|||||++.|...+.
T Consensus        25 ~i~~Ge~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          25 SIKQGEVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             EEETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            356778899999999999999999998764

>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=96.34  E-value=0.0033  Score=58.68  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=19.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ++++++.+|+|+|||+++-..+..
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~   81 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLF   81 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHH
T ss_pred             CCCEEEEecCCChHHHHHHHHHHH
Confidence            468999999999999876555443

>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=96.30  E-value=0.00089  Score=62.10  Aligned_cols=47  Identities=15%  Similarity=0.104  Sum_probs=35.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSK  367 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~  367 (567)
                      ...+..|+|+|.||+||||+|++|++.+....  +.+++.+++..+...
T Consensus        21 ~~kg~vIwltGlsGsGKTTia~~L~~~l~~~~--~~~~~~ldgD~iR~~   67 (208)
T d1m7ga_          21 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDR--RVHAYRLDGDNIRFG   67 (208)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHH--CCCEEEECHHHHTTT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHhc--CceEEEEcchHHHHh
Confidence            56778899999999999999999997662110  456788888776543

>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=96.27  E-value=0.0012  Score=60.76  Aligned_cols=33  Identities=27%  Similarity=0.658  Sum_probs=25.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVM  365 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~  365 (567)
                      |.+.||||+||||+|+.||+.+      +  +..++...+.
T Consensus         6 IaIdGp~GsGKgT~ak~La~~l------g--~~~istGdl~   38 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDF------G--FTYLDTGAMY   38 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHH------C--CEEEEHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh------C--CcEECHHHHH
Confidence            5577999999999999999999      3  4555555443

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=96.24  E-value=0.0093  Score=55.28  Aligned_cols=30  Identities=27%  Similarity=0.364  Sum_probs=24.6

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ....|.-++|.||+|+||||.+--+|..+.
T Consensus         7 ~~~~p~vi~lvGptGvGKTTTiAKLAa~~~   36 (213)
T d1vmaa2           7 PPEPPFVIMVVGVNGTGKTTSCGKLAKMFV   36 (213)
T ss_dssp             CSSSCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            356788899999999999998777777663

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=96.22  E-value=0.0077  Score=55.62  Aligned_cols=29  Identities=28%  Similarity=0.343  Sum_probs=23.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..++.++|.||+|+||||.+--+|..+..
T Consensus         4 ~~~~vi~lvGptGvGKTTTiaKLA~~~~~   32 (207)
T d1okkd2           4 PKGRVVLVVGVNGVGKTTTIAKLGRYYQN   32 (207)
T ss_dssp             CSSSEEEEECSTTSSHHHHHHHHHHHHHT
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            35678899999999999988778877643

>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=96.18  E-value=0.0065  Score=57.07  Aligned_cols=29  Identities=24%  Similarity=0.400  Sum_probs=25.4

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....+..+-|.||+|||||||.++++...
T Consensus        27 ~i~~Ge~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          27 NIKEGEFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             EECTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCCcchhhHhccCCC
Confidence            45677889999999999999999999765

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.16  E-value=0.008  Score=55.68  Aligned_cols=29  Identities=28%  Similarity=0.386  Sum_probs=19.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...|.-++|.||+|+||||.+--+|..+.
T Consensus         9 ~k~p~vi~lvGptGvGKTTTiAKLA~~~~   37 (211)
T d1j8yf2           9 DKIPYVIMLVGVQGTGKATTAGKLAYFYK   37 (211)
T ss_dssp             SSSSEEEEEECSCCC----HHHHHHHHHH
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            45678899999999999998777777663

>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=96.14  E-value=0.0057  Score=58.29  Aligned_cols=29  Identities=24%  Similarity=0.355  Sum_probs=25.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+...+-|.||+|+|||||++.|+....
T Consensus        38 i~~Ge~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          38 IPAGKTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             ECTTCEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhcccC
Confidence            67778899999999999999999998763

>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=96.14  E-value=0.0019  Score=57.10  Aligned_cols=34  Identities=18%  Similarity=0.309  Sum_probs=26.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      -++|.|+||+||||+++.+++.+...   +..+..+.
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~~---~~~~~~~~   36 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDNQ---GINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTT---TCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc---CCCEEEEE
Confidence            46889999999999999999998544   34444444

>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=96.14  E-value=0.0029  Score=56.37  Aligned_cols=29  Identities=17%  Similarity=0.208  Sum_probs=23.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ..+.-|-|.|++|+||||+|+.|+..+..
T Consensus        20 ~~~~iIgI~G~~GSGKSTla~~L~~~l~~   48 (198)
T d1rz3a_          20 AGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (198)
T ss_dssp             SSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            33445669999999999999999998743

>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=96.10  E-value=0.0043  Score=59.28  Aligned_cols=29  Identities=24%  Similarity=0.359  Sum_probs=25.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..-+.|.||+|+|||||++.|.....
T Consensus        41 i~~Ge~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          41 IEKGETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             ECTTCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHHhcCC
Confidence            57778899999999999999999987653

>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=96.00  E-value=0.0069  Score=55.96  Aligned_cols=27  Identities=26%  Similarity=0.251  Sum_probs=21.8

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .++-++|.||+|+||||.+--+|..+.
T Consensus         9 ~~~vi~lvGp~GvGKTTTiaKLA~~~~   35 (207)
T d1ls1a2           9 DRNLWFLVGLQGSGKTTTAAKLALYYK   35 (207)
T ss_dssp             SSEEEEEECCTTTTHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            345578899999999998888887764

>d1u0ja_ c.37.1.20 (A:) Rep 40 protein helicase domain {Adeno-associated virus 2, AAV2 [TaxId: 10804]}

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: Rep 40 protein helicase domain
species: Adeno-associated virus 2, AAV2 [TaxId: 10804]

Probab=95.95  E-value=0.0065  Score=58.33  Aligned_cols=29  Identities=31%  Similarity=0.436  Sum_probs=25.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+..+.++|+||++||||+++.+|.+.++
T Consensus       101 ~~k~n~~~l~G~~~tGKS~f~~~i~~~lg  129 (267)
T d1u0ja_         101 FGKRNTIWLFGPATTGKTNIAEAIAHTVP  129 (267)
T ss_dssp             STTCCEEEEECSTTSSHHHHHHHHHHHSS
T ss_pred             CCccEEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            35567799999999999999999999884

>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=95.90  E-value=0.014  Score=54.69  Aligned_cols=77  Identities=16%  Similarity=0.147  Sum_probs=42.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh---CCCCCCCc----------CeEEechhhHHh---hhhchhHHHHHHHHHHHhc
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA---GAMPWQGV----------PLMYVPLEVVMS---KYYGESERLLGKVFSLANE  385 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l---~~~~~~~~----------~~~~i~~~~l~s---~~~G~~~~~l~~~f~~A~~  385 (567)
                      .+.++|+||...|||++.|.++-..   ....++..          =+..+...+-..   ..|...-..+..+++.+. 
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~-  119 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNAT-  119 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCC-
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhcc-
Confidence            3678999999999999999998754   11111111          122233222111   122222344555655544 


Q ss_pred             CCCCcEEEEcCcchhh
Q 047219          386 LPNGAIIFLDEVDSFA  401 (567)
Q Consensus       386 ~a~~~ILfIDEID~L~  401 (567)
                        +.++++|||+.+=.
T Consensus       120 --~~sLvliDE~~~gT  133 (234)
T d1wb9a2         120 --EYSLVLMDEIGRGT  133 (234)
T ss_dssp             --TTEEEEEESCCCCS
T ss_pred             --cccEEeecccccCC
Confidence              35899999997643

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.79  E-value=0.022  Score=52.60  Aligned_cols=55  Identities=20%  Similarity=0.218  Sum_probs=36.8

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHH
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA  339 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LA  339 (567)
                      -+|+++.=.+...+.|.+   .-+.+|...+...-..     .-..+.+++..|+|+|||+..
T Consensus        12 ~sF~~l~L~~~l~~~L~~---~g~~~pt~iQ~~aip~-----il~g~dvl~~a~TGsGKTlay   66 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYA---YGFEKPSAIQQRAILP-----CIKGYDVIAQAQSGTGKTATF   66 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHH---HTCCSCCHHHHHHHHH-----HHHTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHCCCCHHHHHHHHH---CCCCCCCHHHHHHHHH-----HHcCCCEEEEcccchhhhhhh
Confidence            489998766666666654   3466666666532111     123578999999999999744

>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=95.74  E-value=0.016  Score=54.88  Aligned_cols=40  Identities=25%  Similarity=0.270  Sum_probs=28.4

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh-CCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA-GAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l-~~~~~~~~~~~~i~~  361 (567)
                      ..+..-++|.|+||+|||+++..++..+ ...   +.++.+++.
T Consensus        32 ~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~---g~~v~~~s~   72 (277)
T d1cr2a_          32 ARGGEVIMVTSGSGMGKSTFVRQQALQWGTAM---GKKVGLAML   72 (277)
T ss_dssp             BCTTCEEEEECSTTSSHHHHHHHHHHHHHHTS---CCCEEEEES
T ss_pred             CCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhc---ccceeEeee
Confidence            5566778999999999999999888643 122   445555543

>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=95.73  E-value=0.055  Score=50.65  Aligned_cols=43  Identities=26%  Similarity=0.320  Sum_probs=30.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHhCCC-------CCCCcCeEEechhh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQAGAM-------PWQGVPLMYVPLEV  363 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l~~~-------~~~~~~~~~i~~~~  363 (567)
                      +..-.+|+|+||+|||+++-.+|..+...       ...+.++++++.+.
T Consensus        28 pg~~~~i~G~~G~GKS~l~l~la~~ia~g~~~~~~~~~~~~~vl~~~~E~   77 (274)
T d1nlfa_          28 AGTVGALVSPGGAGKSMLALQLAAQIAGGPDLLEVGELPTGPVIYLPAED   77 (274)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHTCCCTTCCCCCCCCCEEEEESSS
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHcCCCcccccccCCCceEEEeccc
Confidence            35668899999999999999988765221       11234677777653

>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=95.71  E-value=0.0072  Score=55.04  Aligned_cols=26  Identities=31%  Similarity=0.313  Sum_probs=21.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..++.-++|+|+||+|||++|..++.
T Consensus        23 i~~G~~~~I~G~~G~GKT~la~~~~~   48 (242)
T d1tf7a1          23 LPIGRSTLVSGTSGTGKTLFSIQFLY   48 (242)
T ss_dssp             EETTSEEEEEESTTSSHHHHHHHHHH
T ss_pred             CcCCeEEEEEeCCCCCHHHHHHHHHH
Confidence            45677899999999999999976554

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.69  E-value=0.032  Score=51.18  Aligned_cols=57  Identities=18%  Similarity=0.169  Sum_probs=36.3

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCA  339 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LA  339 (567)
                      +-.+|+++.=.++..+.|.+   .-+..|...+...-.  .   .-.++.+++..|+|||||+..
T Consensus         8 ~~~sF~~l~l~~~l~~~L~~---~g~~~pt~iQ~~aip--~---il~g~dvl~~a~TGsGKT~a~   64 (212)
T d1qdea_           8 VVYKFDDMELDENLLRGVFG---YGFEEPSAIQQRAIM--P---IIEGHDVLAQAQSGTGKTGTF   64 (212)
T ss_dssp             CCCCGGGGTCCHHHHHHHHH---HTCCSCCHHHHHHHH--H---HHTTCCEEEECCTTSSHHHHH
T ss_pred             cccChhhCCCCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HHcCCCEEeecccccchhhhh
Confidence            34789999655555555554   345566555543211  1   123578999999999999743

>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=95.64  E-value=0.0028  Score=57.10  Aligned_cols=25  Identities=28%  Similarity=0.587  Sum_probs=22.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++|+|.||+|+|||+|++.++++.+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~   26 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYP   26 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            5699999999999999999999874

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=95.63  E-value=0.0033  Score=62.20  Aligned_cols=73  Identities=16%  Similarity=0.205  Sum_probs=43.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech-hhHH-------hhhhchhHHHHHHHHHHHhcCCCCcEEE
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL-EVVM-------SKYYGESERLLGKVFSLANELPNGAIIF  393 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~-~~l~-------s~~~G~~~~~l~~~f~~A~~~a~~~ILf  393 (567)
                      ..++|+.|++|+||||+.+++....+..    ...+.+.. .++.       ..+.+..+-....++..+.+.. +..|+
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~~~----~rivtiEd~~El~l~~~~~~~~~~~~~~~~~~~ll~~~lR~~-pd~ii  240 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIPKE----ERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMR-PDRII  240 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTT----CCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSC-CSEEE
T ss_pred             CCCEEEEeeccccchHHHHHHhhhcccc----cceeeccchhhhhcccccccceeccccchhHHHHHHHHhccC-CCccc
Confidence            4679999999999999999999988542    12222211 0000       0001111122345566666665 48999


Q ss_pred             EcCcch
Q 047219          394 LDEVDS  399 (567)
Q Consensus       394 IDEID~  399 (567)
                      +.|+-.
T Consensus       241 vgEiR~  246 (323)
T d1g6oa_         241 LGELRS  246 (323)
T ss_dssp             ESCCCS
T ss_pred             CCccCc
Confidence            999953

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=95.63  E-value=0.031  Score=50.74  Aligned_cols=53  Identities=21%  Similarity=0.245  Sum_probs=32.9

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC  338 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L  338 (567)
                      +|+++.=.++.++.|.+.   -+..|...+...-.  .   .-.++.+++.+|+|+|||+.
T Consensus         2 sF~~l~L~~~l~~~L~~~---g~~~pt~iQ~~aip--~---il~g~dvi~~a~tGsGKTla   54 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEA---GFEKPSPIQEEAIP--V---AITGRDILARAKNGTGKTAA   54 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHT---TCCSCCHHHHHHHH--H---HHHTCCEEEECCTTSCHHHH
T ss_pred             ChHHcCCCHHHHHHHHHC---CCCCCCHHHHHHHH--H---HHcCCCEEEecCCcchhhhh
Confidence            688876666666666552   34555555442211  1   11246799999999999954

>d2j0sa1 c.37.1.19 (A:22-243) Probable ATP-dependent RNA helicase DDX48 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable ATP-dependent RNA helicase DDX48
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.61  E-value=0.052  Score=50.18  Aligned_cols=55  Identities=20%  Similarity=0.263  Sum_probs=36.6

Q ss_pred             CCCCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHH
Q 047219          275 SEISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTS  337 (567)
Q Consensus       275 ~~~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~  337 (567)
                      ...+|+++.=.++.++.|.+   .-+..|...+...-.  .   .-.++.+++..|+|||||+
T Consensus        15 ~~~sF~~l~L~~~l~~~L~~---~g~~~pt~IQ~~aIp--~---il~g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          15 VTPTFDTMGLREDLLRGIYA---YGFEKPSAIQQRAIK--Q---IIKGRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             CCCSGGGGCCCHHHHHHHHH---HTCCSCCHHHHHHHH--H---HHTTCCEEEECCTTSSHHH
T ss_pred             CCCCHHHCCCCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HHCCCCeEEEcCcchhhhh
Confidence            34589999766666776665   235666555543211  1   1235789999999999996

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.59  E-value=0.048  Score=49.68  Aligned_cols=53  Identities=19%  Similarity=0.185  Sum_probs=34.0

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC  338 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L  338 (567)
                      +|+|+.=.++..+.|.+   .-+.+|...+...-.  .   .-.++.+++..|+|||||+.
T Consensus         2 ~F~dl~L~~~l~~~l~~---~g~~~pt~iQ~~aip--~---il~g~dvl~~A~TGsGKTla   54 (207)
T d1t6na_           2 GFRDFLLKPELLRAIVD---CGFEHPSEVQHECIP--Q---AILGMDVLCQAKSGMGKTAV   54 (207)
T ss_dssp             CSTTSCCCHHHHHHHHH---TTCCCCCHHHHHHHH--H---HHTTCCEEEECCTTSCHHHH
T ss_pred             CccccCcCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HHcCCCeEEEeccccccccc
Confidence            57888666666666654   335666665543211  1   12357899999999999864

>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=95.59  E-value=0.003  Score=57.22  Aligned_cols=25  Identities=28%  Similarity=0.638  Sum_probs=22.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++|+|.||+|+|||++++.+++..+
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~   25 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHS   25 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCC
Confidence            3589999999999999999999874

>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=95.36  E-value=0.033  Score=50.78  Aligned_cols=63  Identities=13%  Similarity=0.137  Sum_probs=36.2

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+|+++.=.++..+.+.+   .-+..|...+...-  ...  ......+++..|+|+|||+.+-....+.
T Consensus         4 msf~~l~l~~~l~~~l~~---~g~~~pt~iQ~~~i--p~~--l~g~~d~iv~a~TGsGKT~~~~l~~~~~   66 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRN---KGFEKPTDIQMKVI--PLF--LNDEYNIVAQARTGSGKTASFAIPLIEL   66 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHH---HTCCSCCHHHHHHH--HHH--HHTCSEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             cCHHHcCCCHHHHHHHHH---CCCCCCCHHHHHHH--HHH--HcCCCCeeeechhcccccceeecccccc
Confidence            479998555555555543   23444544443211  000  1123579999999999998776555443

>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=95.26  E-value=0.0044  Score=55.21  Aligned_cols=29  Identities=21%  Similarity=0.117  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..-++|+||||+|||++|..++....
T Consensus        20 i~~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          20 IETGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CcCCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            45677899999999999999999987764

>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=95.21  E-value=0.035  Score=49.95  Aligned_cols=24  Identities=38%  Similarity=0.358  Sum_probs=21.2

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|+|.|+||+|||+|.+++...-
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~~   24 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTGQ   24 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCC
Confidence            479999999999999999998743

>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=95.16  E-value=0.041  Score=52.39  Aligned_cols=27  Identities=33%  Similarity=0.527  Sum_probs=22.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+..-||+|..|+|||.+|-..+..
T Consensus       101 ~~~~m~rLL~GdvGSGKT~Va~~a~~~  127 (264)
T d1gm5a3         101 SEKPMNRLLQGDVGSGKTVVAQLAILD  127 (264)
T ss_dssp             SSSCCCCEEECCSSSSHHHHHHHHHHH
T ss_pred             ccCcceeeeeccccccccHHHHHHHHH
Confidence            567788999999999999988766544

>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=95.10  E-value=0.014  Score=53.47  Aligned_cols=25  Identities=20%  Similarity=0.397  Sum_probs=22.1

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +-++|.||+|+|||+|.+.+.+..+
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4588999999999999999998764

>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=95.07  E-value=0.13  Score=46.31  Aligned_cols=36  Identities=39%  Similarity=0.562  Sum_probs=25.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhh
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYY  369 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~  369 (567)
                      |-|+|++|+||||+|+.+. +.      ++++  +++..+...++
T Consensus         5 IgITG~igSGKStv~~~l~-~~------G~~v--idaD~i~~~l~   40 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT-DL------GVPL--VDADVVAREVV   40 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH-TT------TCCE--EEHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHH-HC------CCeE--EEchHHHHHHH
Confidence            5589999999999999886 34      4444  45665555544

>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=95.04  E-value=0.0068  Score=56.00  Aligned_cols=29  Identities=21%  Similarity=0.061  Sum_probs=24.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..-++|+||||||||++|..++....
T Consensus        34 ip~G~~~~i~G~~GsGKT~lalq~~~~~~   62 (258)
T d1v5wa_          34 IESMAITEAFGEFRTGKTQLSHTLCVTAQ   62 (258)
T ss_dssp             BCSSEEEEEECCTTCTHHHHHHHHHHHTT
T ss_pred             CcCCEEEEEECCCCCCHHHHHHHHHHHHH
Confidence            56667899999999999999999987653

>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=95.01  E-value=0.0076  Score=55.78  Aligned_cols=29  Identities=24%  Similarity=0.188  Sum_probs=24.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+...-++|+||||||||+++-.++....
T Consensus        33 lp~G~~~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          33 IETQAITEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             EESSEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             ccCCEEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            45667799999999999999998887763

>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=94.98  E-value=0.046  Score=50.71  Aligned_cols=74  Identities=19%  Similarity=0.173  Sum_probs=40.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh---CCCCCC----------CcCeEEechhhHHhh---hhchhHHHHHHHHHHHhcCC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA---GAMPWQ----------GVPLMYVPLEVVMSK---YYGESERLLGKVFSLANELP  387 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l---~~~~~~----------~~~~~~i~~~~l~s~---~~G~~~~~l~~~f~~A~~~a  387 (567)
                      -++|+||...|||++.|.++-..   ....++          +.-+..+...+-...   .|...-..+..+++.+.   
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~---  113 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEAT---  113 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCC---
T ss_pred             EEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccCC---
Confidence            58999999999999999988654   111111          111223332222111   12222234455555443   


Q ss_pred             CCcEEEEcCcchh
Q 047219          388 NGAIIFLDEVDSF  400 (567)
Q Consensus       388 ~~~ILfIDEID~L  400 (567)
                      ..++++|||+.+=
T Consensus       114 ~~sLvliDE~~~g  126 (224)
T d1ewqa2         114 ENSLVLLDEVGRG  126 (224)
T ss_dssp             TTEEEEEESTTTT
T ss_pred             CCcEEeecccccC
Confidence            4689999999764

>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=94.94  E-value=0.004  Score=57.23  Aligned_cols=44  Identities=16%  Similarity=0.071  Sum_probs=30.3

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCC---CCCCcCeEEechh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAM---PWQGVPLMYVPLE  362 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~---~~~~~~~~~i~~~  362 (567)
                      .....-++|+||||||||+++-.++......   ...+.++++++..
T Consensus        31 i~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~   77 (251)
T d1szpa2          31 VETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTE   77 (251)
T ss_dssp             EESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESS
T ss_pred             CcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeec
Confidence            4566789999999999999998887654221   1124456666544

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.84  E-value=0.047  Score=49.65  Aligned_cols=54  Identities=17%  Similarity=0.192  Sum_probs=34.1

Q ss_pred             CCcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH
Q 047219          277 ISWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC  338 (567)
Q Consensus       277 ~~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L  338 (567)
                      -+|+++.=.++..+.|.+   .-+..|...+...-.  .   .-.++.+++..|+|||||+.
T Consensus         3 ~~F~~l~L~~~l~~~l~~---~g~~~pt~iQ~~aip--~---il~g~dvl~~a~TGsGKTla   56 (206)
T d1veca_           3 NEFEDYCLKRELLMGIFE---MGWEKPSPIQEESIP--I---ALSGRDILARAKNGTGKSGA   56 (206)
T ss_dssp             SSGGGSCCCHHHHHHHHT---TTCCSCCHHHHHHHH--H---HHTTCCEEEECCSSSTTHHH
T ss_pred             CChhccCcCHHHHHHHHH---CCCCCCCHHHHHHHH--H---HHcCCCEEeeccCccccccc
Confidence            368888656666666654   235556555543211  1   22357899999999999953

>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=94.78  E-value=0.025  Score=50.61  Aligned_cols=22  Identities=41%  Similarity=0.454  Sum_probs=17.6

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~  344 (567)
                      +++|+++|+|+|||.++-.++.
T Consensus        24 ~n~lv~~pTGsGKT~i~~~~~~   45 (200)
T d1wp9a1          24 TNCLIVLPTGLGKTLIAMMIAE   45 (200)
T ss_dssp             SCEEEECCTTSCHHHHHHHHHH
T ss_pred             CCeEEEeCCCCcHHHHHHHHHH
Confidence            3588999999999987665554

>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=94.77  E-value=0.008  Score=53.56  Aligned_cols=26  Identities=27%  Similarity=0.584  Sum_probs=22.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ++-++|.||+|+||||+++.+.+..+
T Consensus         2 G~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           2 GRVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CeEEEEECCCCCCHHHHHHHHHhhCC
Confidence            35688999999999999999998874

>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=94.76  E-value=0.013  Score=51.77  Aligned_cols=29  Identities=28%  Similarity=0.440  Sum_probs=25.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      .++.-|+|.|+=|+|||+++|.+++.+..
T Consensus        31 ~~g~ii~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          31 EKAIMVYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             CCCeEEEEecCCCccHHHHHHHHHhhccc
Confidence            45556899999999999999999999954

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=94.74  E-value=0.04  Score=49.79  Aligned_cols=53  Identities=17%  Similarity=0.174  Sum_probs=31.9

Q ss_pred             CcccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHH
Q 047219          278 SWENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSC  338 (567)
Q Consensus       278 ~~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~L  338 (567)
                      +|+++.=.+...+.|.+   .-+.+|...++..  +..   .-.++.+++..|+|||||+.
T Consensus         2 ~F~~l~L~~~l~~~l~~---~g~~~pt~iQ~~a--ip~---~l~G~dvii~a~TGSGKTla   54 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKT---LRFYKPTEIQERI--IPG---ALRGESMVGQSQTGTGKTHA   54 (209)
T ss_dssp             CGGGSCCCHHHHHHHHH---TTCCSCCHHHHHH--HHH---HHHTCCEEEECCSSHHHHHH
T ss_pred             ccccCCcCHHHHHHHHH---CCCCCCCHHHHHH--HHH---HHCCCCeEeeccccccccee
Confidence            47777656665555543   2344555554332  111   11246899999999999974

>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=94.74  E-value=0.032  Score=54.44  Aligned_cols=45  Identities=18%  Similarity=0.284  Sum_probs=31.8

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      ...|--|-|.|++|+||||+|+.|...+.+.. .+..+..++...+
T Consensus        77 ~k~P~iIGIaG~sgSGKSTla~~L~~lL~~~~-~~~~v~~Is~D~F  121 (308)
T d1sq5a_          77 QRIPYIISIAGSVAVGKSTTARVLQALLSRWP-EHRRVELITTDGF  121 (308)
T ss_dssp             CCCCEEEEEEECTTSSHHHHHHHHHHHHTTST-TCCCEEEEEGGGG
T ss_pred             CCCCEEEEEeCCCCCCCcHHHHHHHHHHhhhc-CCCceEEEeeeee
Confidence            45667788999999999999999999985321 1234555555443

>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=94.72  E-value=0.036  Score=52.57  Aligned_cols=19  Identities=32%  Similarity=0.560  Sum_probs=16.3

Q ss_pred             CCCCceEEeeCCCCCcHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTS  337 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~  337 (567)
                      ....+.+++.+|+|+|||+
T Consensus         6 ~~~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTT
T ss_pred             hhcCCcEEEEECCCCCHHH
Confidence            3466789999999999995

>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=94.71  E-value=0.036  Score=49.26  Aligned_cols=23  Identities=26%  Similarity=0.504  Sum_probs=19.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      |--+-|+|++|+||||+|+.+.+
T Consensus         3 p~IIgitG~~gSGKstva~~l~~   25 (191)
T d1uf9a_           3 PIIIGITGNIGSGKSTVAALLRS   25 (191)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            34466899999999999999954

>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=94.70  E-value=0.0091  Score=52.21  Aligned_cols=33  Identities=21%  Similarity=0.049  Sum_probs=25.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      -+-+.|.+|+|||||+..++.++...   +..+..+
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~---g~~v~vi   35 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVRE---GWRVGTV   35 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT---TCCEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhC---CCeEEEE
Confidence            35699999999999999999988544   3444444

>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=94.68  E-value=0.03  Score=50.93  Aligned_cols=24  Identities=29%  Similarity=0.295  Sum_probs=20.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+|..|+|+|||.++-+++.++.
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~~  110 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINELS  110 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSC
T ss_pred             CcEEEeCCCCCceehHHhHHHHhc
Confidence            457889999999999999888874

>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=94.58  E-value=0.013  Score=50.74  Aligned_cols=23  Identities=22%  Similarity=0.343  Sum_probs=20.1

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.|++|+|||+|.+.+....
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~~   26 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGED   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCC
Confidence            58999999999999999987643

>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=94.15  E-value=0.013  Score=53.27  Aligned_cols=27  Identities=26%  Similarity=0.364  Sum_probs=23.0

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      |--|-|.|++|+||||+|+.|++.+..
T Consensus         2 P~iIgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           2 PFLIGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhch
Confidence            344668999999999999999999853

>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=94.13  E-value=0.074  Score=44.81  Aligned_cols=23  Identities=22%  Similarity=0.252  Sum_probs=20.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|+|.|+||+|||+|.+.+...-
T Consensus         2 kivlvG~~~vGKSsLi~~l~~~~   24 (160)
T d1r8sa_           2 RILMVGLDAAGKTTILYKLKLGE   24 (160)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhcCC
Confidence            37899999999999999987654

>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=94.01  E-value=0.017  Score=51.64  Aligned_cols=26  Identities=12%  Similarity=0.346  Sum_probs=22.8

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+.++|.||+|+||++|++.+.+..+
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCC
Confidence            36799999999999999999998753

>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=94.00  E-value=0.023  Score=54.82  Aligned_cols=28  Identities=32%  Similarity=0.570  Sum_probs=22.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...|--|-|.|++|+||||++..|...+
T Consensus        24 ~~~P~iIGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_          24 NKCPLFIFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             CCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCCCEEEEeECCCCCCHHHHHHHHHHHH
Confidence            3445556689999999999999988765

>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=93.91  E-value=0.28  Score=45.49  Aligned_cols=27  Identities=30%  Similarity=0.139  Sum_probs=22.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+...||+|.+|+|||.++-..+..
T Consensus        73 ~~~~~~~LL~GdvGsGKT~V~~~a~~~   99 (233)
T d2eyqa3          73 QPLAMDRLVCGDVGFGKTEVAMRAAFL   99 (233)
T ss_dssp             SSSCCEEEEECCCCTTTHHHHHHHHHH
T ss_pred             ccCccCeEEEcCCCCCcHHHHHHHHHH
Confidence            567788999999999999887655544

>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=93.58  E-value=0.015  Score=52.97  Aligned_cols=29  Identities=21%  Similarity=0.190  Sum_probs=24.7

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..+..-++|.|+||+|||+++..+|....
T Consensus        31 l~~G~l~~i~G~~G~GKT~~~l~~a~~~~   59 (258)
T d2i1qa2          31 LESQSVTEFAGVFGSGKTQIMHQSCVNLQ   59 (258)
T ss_dssp             EETTEEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             ccCCeEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            45567799999999999999999997663

>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=93.52  E-value=0.023  Score=49.71  Aligned_cols=26  Identities=23%  Similarity=0.267  Sum_probs=21.8

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .....|+|.|+||+|||+|.+.+...
T Consensus        10 ~k~~kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          10 NKEMRILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHTTCC
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHhcC
Confidence            44567999999999999999988653

>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=93.11  E-value=0.041  Score=52.72  Aligned_cols=26  Identities=27%  Similarity=0.318  Sum_probs=19.2

Q ss_pred             CCceEEeeCCCCCcHHHH-HHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSC-ARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~L-AraIA~~l  346 (567)
                      ...++++.|+||||||++ ++.++..+
T Consensus        23 ~~g~~lV~g~aGSGKTt~l~~ri~~ll   49 (318)
T d1pjra1          23 TEGPLLIMAGAGSGKTRVLTHRIAYLM   49 (318)
T ss_dssp             CSSCEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCCCEEEEecCCccHHHHHHHHHHHHH
Confidence            345699999999999964 44555554

>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=92.93  E-value=0.032  Score=52.91  Aligned_cols=24  Identities=29%  Similarity=0.353  Sum_probs=17.9

Q ss_pred             CceEEeeCCCCCcHHHH-HHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSC-ARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~L-AraIA~~  345 (567)
                      ..++|+.|+||||||++ +..++..
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~rv~~l   38 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNKIAHL   38 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEeeCCccHHHHHHHHHHHH
Confidence            46689999999999975 4444444

>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=92.89  E-value=0.043  Score=47.76  Aligned_cols=24  Identities=25%  Similarity=0.386  Sum_probs=20.3

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ...-|++.|+||+|||+|.+.+..
T Consensus        15 ~~~kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          15 QEVRILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             SCEEEEEEESTTSSHHHHHHHHCC
T ss_pred             CEEEEEEECCCCCCHHHHHHHHhc
Confidence            345699999999999999998854

>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=92.61  E-value=0.033  Score=49.90  Aligned_cols=25  Identities=28%  Similarity=0.408  Sum_probs=22.2

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+|||.|++|+|||++|-.+...
T Consensus        13 ~g~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          13 YGLGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHHT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHc
Confidence            4689999999999999999888764

>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=92.58  E-value=0.047  Score=49.86  Aligned_cols=23  Identities=30%  Similarity=0.486  Sum_probs=20.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhC
Q 047219          325 VLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +++.|++|+|||||.+++.+.+.
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~   25 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLE   25 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHT
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHh
Confidence            68999999999999999998764

>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=92.50  E-value=0.03  Score=52.40  Aligned_cols=29  Identities=34%  Similarity=0.594  Sum_probs=25.4

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....+.-+-|.||+|+|||||.+.|+...
T Consensus        22 ~i~~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          22 DIHEGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhcCC
Confidence            45677789999999999999999999765

>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=92.43  E-value=0.1  Score=44.93  Aligned_cols=23  Identities=30%  Similarity=0.365  Sum_probs=19.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .|+|.|++|+|||+|.+.+...-
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~~~   26 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIASGQ   26 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            47899999999999999987643

>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=92.32  E-value=0.034  Score=46.94  Aligned_cols=22  Identities=32%  Similarity=0.522  Sum_probs=19.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ++|.|+||+|||+|...+.+.-
T Consensus         3 I~liG~~nvGKSSLln~l~~~~   24 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKNDR   24 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEECCCCCCHHHHHHHHhCCC
Confidence            7899999999999999998753

>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=92.32  E-value=0.034  Score=47.39  Aligned_cols=24  Identities=25%  Similarity=0.292  Sum_probs=20.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|+|.|.||+|||+|.+++...-
T Consensus         6 ~kI~ivG~~~vGKSSLi~~~~~~~   29 (169)
T d1upta_           6 MRILILGLDGAGKTTILYRLQVGE   29 (169)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             eEEEEECCCCCCHHHHHHHHhCCC
Confidence            358999999999999999997753

>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=92.20  E-value=0.024  Score=51.79  Aligned_cols=29  Identities=31%  Similarity=0.496  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      .+++.-+.|.||.|+|||||.++|+..+.
T Consensus        24 i~~Gei~~l~G~NGsGKSTLl~~i~gl~~   52 (200)
T d1sgwa_          24 IEKGNVVNFHGPNGIGKTTLLKTISTYLK   52 (200)
T ss_dssp             EETTCCEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EcCCCEEEEECCCCChHHHHHHHHhcccc
Confidence            56677788999999999999999998763

>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=92.09  E-value=0.042  Score=50.21  Aligned_cols=33  Identities=21%  Similarity=0.324  Sum_probs=25.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      =|.|.|+.|+||||+++.+++.+...   +.++..+
T Consensus         5 lI~ieG~dGsGKsT~~~~L~~~L~~~---g~~v~~~   37 (209)
T d1nn5a_           5 LIVLEGVDRAGKSTQSRKLVEALCAA---GHRAELL   37 (209)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHT---TCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEE
Confidence            45667999999999999999988544   4445544

>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=91.97  E-value=0.027  Score=50.15  Aligned_cols=29  Identities=31%  Similarity=0.473  Sum_probs=25.0

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...|.-|.|.|+.|+||||+++.|++.+.
T Consensus         6 ~~kp~~I~ieG~~GsGKTTl~~~L~~~l~   34 (197)
T d2vp4a1           6 GTQPFTVLIEGNIGSGKTTYLNHFEKYKN   34 (197)
T ss_dssp             TCCCEEEEEECSTTSCHHHHHHTTGGGTT
T ss_pred             CCCceEEEEECCCCCCHHHHHHHHHHHhC
Confidence            45566788999999999999999999884

>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=91.97  E-value=0.039  Score=49.43  Aligned_cols=32  Identities=22%  Similarity=0.363  Sum_probs=24.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEe
Q 047219          325 VLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYV  359 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i  359 (567)
                      |.|.|..|+||||+++.|++.+...   +.+++.+
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~---g~~v~~~   34 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAA---GRSVATL   34 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC---CCCEEEE
Confidence            5678999999999999999987543   4445444

>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=91.85  E-value=0.078  Score=48.04  Aligned_cols=38  Identities=21%  Similarity=0.407  Sum_probs=27.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhHHhhhhc
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVVMSKYYG  370 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l~s~~~G  370 (567)
                      -|-|+|++|+||||+|+.+. ..      +  +..+++..+..+++.
T Consensus         5 iIgitG~igSGKStv~~~l~-~~------G--~~vidaD~i~~~l~~   42 (208)
T d1vhta_           5 IVALTGGIGSGKSTVANAFA-DL------G--INVIDADIIARQVVE   42 (208)
T ss_dssp             EEEEECCTTSCHHHHHHHHH-HT------T--CEEEEHHHHHHHTTS
T ss_pred             EEEEECCCcCCHHHHHHHHH-HC------C--CcEEEchHHHHHHHh
Confidence            35689999999999999886 44      3  445566666665553

>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=91.84  E-value=0.034  Score=49.85  Aligned_cols=25  Identities=36%  Similarity=0.570  Sum_probs=21.9

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+|||.|++|+|||++|-.+...
T Consensus        14 ~g~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          14 FGVGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             TTEEEEEEESSSSSHHHHHHHHHTT
T ss_pred             CCEEEEEEcCCCCCHHHHHHHHHHc
Confidence            4689999999999999999888753

>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=91.78  E-value=0.041  Score=51.67  Aligned_cols=30  Identities=30%  Similarity=0.461  Sum_probs=25.9

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ......-+-|.||+|+|||||.+.|+....
T Consensus        28 ~v~~Ge~~~liGpsGaGKSTLl~~i~Gl~~   57 (239)
T d1v43a3          28 TIKDGEFLVLLGPSGCGKTTTLRMIAGLEE   57 (239)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EECCCCEEEEECCCCChHHHHHHHHHcCCC
Confidence            356677889999999999999999998763

>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=91.76  E-value=0.034  Score=52.25  Aligned_cols=30  Identities=33%  Similarity=0.520  Sum_probs=25.4

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ......-+-|.||+|+||||++++|+....
T Consensus        25 ~i~~Ge~~~liG~sGaGKSTll~~i~gl~~   54 (240)
T d1g2912          25 EVKDGEFMILLGPSGCGKTTTLRMIAGLEE   54 (240)
T ss_dssp             EEETTCEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhcCCC
Confidence            356677788999999999999999997653

>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=91.76  E-value=0.031  Score=52.59  Aligned_cols=29  Identities=17%  Similarity=0.195  Sum_probs=25.0

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....+.-+-|.||+|+|||||+++|+...
T Consensus        27 ~i~~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          27 HVPAGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             EECSSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            35667789999999999999999998765

>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=91.62  E-value=0.034  Score=51.85  Aligned_cols=29  Identities=28%  Similarity=0.379  Sum_probs=25.4

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ......-+-|.||+|+||||+.++|+...
T Consensus        22 ~i~~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          22 KVESGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             EECTTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             EECCCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            35667779999999999999999999876

>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=91.55  E-value=0.046  Score=48.55  Aligned_cols=25  Identities=28%  Similarity=0.392  Sum_probs=22.1

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ...+|||.|++|+|||++|-++.+.
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            4689999999999999999887765

>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=91.46  E-value=0.048  Score=47.64  Aligned_cols=21  Identities=19%  Similarity=0.365  Sum_probs=18.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      +++.|++|||||+|++.+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999987754

>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=91.44  E-value=0.039  Score=51.91  Aligned_cols=29  Identities=24%  Similarity=0.471  Sum_probs=25.7

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+..-+-|.||+|+|||||++.++...
T Consensus        24 ~i~~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          24 EAQPNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             EECTTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            36777889999999999999999999876

>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=91.37  E-value=0.14  Score=49.99  Aligned_cols=42  Identities=24%  Similarity=0.302  Sum_probs=28.9

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ....-|=|.|+||+|||||..++...+..... .+.++.++.+
T Consensus        49 ~~~~~igitG~pGaGKSTli~~l~~~~~~~g~-~vaViavDps   90 (323)
T d2qm8a1          49 GRAIRVGITGVPGVGKSTTIDALGSLLTAAGH-KVAVLAVDPS   90 (323)
T ss_dssp             CCSEEEEEECCTTSCHHHHHHHHHHHHHHTTC-CEEEEEECGG
T ss_pred             CCceEEeeeCCCCCCHHHHHHHHHHHHhhcCC-ceeeeecccc
Confidence            34455889999999999999999987532111 3445555544

>d1cz5a2 d.31.1.1 (A:92-185) C-terminal domain of VAT-N, VAT-Nc {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Cdc48 domain 2-like
superfamily: Cdc48 domain 2-like
family: Cdc48 domain 2-like
domain: C-terminal domain of VAT-N, VAT-Nc
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=91.34  E-value=0.0028  Score=51.17  Aligned_cols=64  Identities=19%  Similarity=0.075  Sum_probs=41.4

Q ss_pred             cccceeEecCCCC---ccccCCCccccCcccccccchheeeeceeecCCCCceeeeccCcCCHHHHHHHHHHHhhhc
Q 047219          186 AVAWQLTLKPPEK---QNESGGDRAQSGDMNAREGDLCILIFRSLITSDKPEIEFIKKGSLTSEELDALVSVLQLAG  259 (567)
Q Consensus       186 ~~a~~v~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  259 (567)
                      .+|++|+|||+.+   .+++++++.        ++.++.|.++|+..||.+.+..+.  .+....+.+.+..+++.+
T Consensus         2 ~~A~kVvLAP~~~~~~~i~~~~~~~--------~ylk~~L~grPV~~GD~i~v~~~~--~~g~~~i~F~Vv~t~P~g   68 (94)
T d1cz5a2           2 EIAKKVTLAPIIRKDQRLKFGEGIE--------EYVQRALIRRPMLEQDNISVPGLT--LAGQTGLLFKVVKTLPSK   68 (94)
T ss_dssp             CBCSEEEEEECSCTTTTCCCCSSHH--------HHHHHHHSSCEECTTCEECCSSCC--CSSCCCCSEEEEEESSSS
T ss_pred             ccccEEEECcCCCccceEEEcCCHH--------HHHHHHHcCCCCcCCCEEEEeecc--ccCCceEeEEEEEEeCCC
Confidence            3799999999743   344555543        567799999999999999886542  111122344444455554

>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=91.18  E-value=0.12  Score=50.44  Aligned_cols=28  Identities=18%  Similarity=0.242  Sum_probs=23.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ....-|-|+||||+|||||..+++..+.
T Consensus        52 ~~~~~IgitG~pGaGKSTLi~~l~~~~~   79 (327)
T d2p67a1          52 GNTLRLGVTGTPGAGKSTFLEAFGMLLI   79 (327)
T ss_dssp             SCSEEEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             CCceEEEeeCCCCCCHHHHHHHHHHHHH
Confidence            4456688999999999999999998763

>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=91.17  E-value=0.032  Score=52.53  Aligned_cols=29  Identities=31%  Similarity=0.452  Sum_probs=25.6

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ....+.-+-|.||+|+||||++++|+...
T Consensus        27 ~i~~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          27 NIENGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             EECTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             EECCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            45677789999999999999999999865

>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=91.04  E-value=0.047  Score=52.45  Aligned_cols=30  Identities=23%  Similarity=0.360  Sum_probs=26.4

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...++.-+-|.||+|+|||||++.|+..+.
T Consensus        58 ~i~~Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          58 NIEKGEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             EECTTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             EEcCCCEEEEECCCCChHHHHHHHHhCCCc
Confidence            367778899999999999999999998764

>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=91.01  E-value=0.052  Score=50.95  Aligned_cols=24  Identities=29%  Similarity=0.483  Sum_probs=20.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      -+.|.||+|+||||+.+.|+....
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl~~   49 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGIVK   49 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCChHHHHHHHHHcCCC
Confidence            455789999999999999998763

>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=90.88  E-value=0.037  Score=53.39  Aligned_cols=38  Identities=13%  Similarity=0.241  Sum_probs=26.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechhhH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLEVV  364 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~~l  364 (567)
                      -|-+.|++|+||||+++++.+.+...   +++...+....+
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~---~v~~~iI~~Dsf   43 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRRE---GVKAVSIEGDAF   43 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHH---TCCEEEEEGGGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhc---CCCeEEEeCCCC
Confidence            57899999999999999999987543   455666666554

>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=90.87  E-value=0.049  Score=47.09  Aligned_cols=26  Identities=19%  Similarity=0.429  Sum_probs=21.4

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ....-|+|.|+||+|||+|..++...
T Consensus        11 ~k~~kI~lvG~~~vGKTsLl~~l~~~   36 (186)
T d1f6ba_          11 KKTGKLVFLGLDNAGKTTLLHMLKDD   36 (186)
T ss_dssp             TCCEEEEEEEETTSSHHHHHHHHSCC
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHhCC
Confidence            34456999999999999999988543

>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=90.85  E-value=0.06  Score=46.47  Aligned_cols=22  Identities=18%  Similarity=0.255  Sum_probs=19.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|+||+|||+|+..+.+.
T Consensus         4 Kv~liG~~~vGKSsLi~rl~~~   25 (164)
T d1z2aa1           4 KMVVVGNGAVGKSSMIQRYCKG   25 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999887753

>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=90.73  E-value=0.062  Score=46.46  Aligned_cols=21  Identities=19%  Similarity=0.349  Sum_probs=19.1

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |+|.|.+|+|||+|++.+.+.
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988764

>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=90.50  E-value=0.068  Score=46.16  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=19.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4889999999999999998864

>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=90.47  E-value=0.069  Score=47.55  Aligned_cols=24  Identities=25%  Similarity=0.588  Sum_probs=21.3

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ..|+|.|+||+|||+|..++.+.-
T Consensus         4 p~V~lvG~~n~GKTSLln~l~~~~   27 (209)
T d1nrjb_           4 PSIIIAGPQNSGKTSLLTLLTTDS   27 (209)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCC
Confidence            378999999999999999998763

>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=90.47  E-value=0.055  Score=51.34  Aligned_cols=29  Identities=21%  Similarity=0.346  Sum_probs=25.1

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ......-+-|.||+|+|||||+++|+...
T Consensus        24 ~i~~GEi~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          24 QARAGDVISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEcCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            35677789999999999999999998755

>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=90.41  E-value=0.059  Score=46.66  Aligned_cols=26  Identities=19%  Similarity=0.272  Sum_probs=22.1

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      +.-..|+|.|.||+|||+|...+...
T Consensus        13 ~k~~kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          13 HQEHKVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             TSCEEEEEEESTTSSHHHHHHHHHTT
T ss_pred             CCeEEEEEECCCCCCHHHHHHHHhcC
Confidence            44467999999999999999998764

>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=90.28  E-value=0.068  Score=47.04  Aligned_cols=21  Identities=29%  Similarity=0.371  Sum_probs=18.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~  344 (567)
                      -|+|.|++|+|||+|++.+.+
T Consensus         7 Ki~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           7 KLLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEEESCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHhc
Confidence            388999999999999998875

>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=90.26  E-value=0.072  Score=46.23  Aligned_cols=21  Identities=33%  Similarity=0.382  Sum_probs=19.2

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |++.|++|+|||+|.+.+...
T Consensus         8 i~vvG~~~vGKTsLi~~l~~~   28 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYADD   28 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            889999999999999988764

>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=90.16  E-value=0.084  Score=47.58  Aligned_cols=27  Identities=26%  Similarity=0.533  Sum_probs=22.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCCC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGAM  349 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~~  349 (567)
                      +=|.|.|+.|+||||+++.+++.+...
T Consensus         3 kfIviEG~dGsGKsT~~~~L~~~L~~~   29 (210)
T d4tmka_           3 KYIVIEGLEGAGKTTARNVVVETLEQL   29 (210)
T ss_dssp             CEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhC
Confidence            347788999999999999999987543

>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=90.13  E-value=0.068  Score=46.43  Aligned_cols=22  Identities=27%  Similarity=0.477  Sum_probs=19.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -++|.|.+|+|||+|++.+.+.
T Consensus         7 Ki~lvG~~~vGKTsLi~~l~~~   28 (171)
T d2ew1a1           7 KIVLIGNAGVGKTCLVRRFTQG   28 (171)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999998874

>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=90.04  E-value=0.079  Score=45.80  Aligned_cols=22  Identities=27%  Similarity=0.256  Sum_probs=19.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|||||+|++.+...
T Consensus         5 KivlvG~~~vGKTsLi~r~~~~   26 (167)
T d1z08a1           5 KVVLLGEGCVGKTSLVLRYCEN   26 (167)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999988763

>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=90.01  E-value=0.095  Score=49.31  Aligned_cols=40  Identities=30%  Similarity=0.419  Sum_probs=30.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      .+.|+-++++|.-|+||||+|-++|..+...   +..+.-+++
T Consensus         5 ~~~p~~i~~sGKGGVGKTTvaa~lA~~lA~~---G~rVLlvD~   44 (296)
T d1ihua1           5 QNIPPYLFFTGKGGVGKTSISCATAIRLAEQ---GKRVLLVST   44 (296)
T ss_dssp             SSCCSEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEEC
T ss_pred             CCCCeEEEEECCCcChHHHHHHHHHHHHHHC---CCCEEEEeC
Confidence            4668889999999999999999999887443   344444443

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=89.99  E-value=0.4  Score=44.18  Aligned_cols=24  Identities=25%  Similarity=0.404  Sum_probs=18.3

Q ss_pred             CceEEeeCCCCCcHHH--HHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTS--CARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~--LAraIA~~  345 (567)
                      ++.+++..|+|||||+  +.-.+.+.
T Consensus        58 g~dvvi~a~TGsGKTlayllp~l~~l   83 (238)
T d1wrba1          58 HRDIMACAQTGSGKTAAFLIPIINHL   83 (238)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEECCCCCCcceeeHHHHHHHH
Confidence            4789999999999997  44444443

>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=89.92  E-value=0.08  Score=45.91  Aligned_cols=23  Identities=17%  Similarity=0.263  Sum_probs=19.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|++.|.+|+|||+|++.+.+.-
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~   30 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQ   30 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999999988643

>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=89.84  E-value=0.075  Score=46.12  Aligned_cols=22  Identities=18%  Similarity=0.303  Sum_probs=19.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|.+.+...
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~~   28 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQS   28 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999988764

>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=89.82  E-value=0.079  Score=45.93  Aligned_cols=22  Identities=27%  Similarity=0.510  Sum_probs=19.1

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|.|.|+||+|||+|.+++...
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~~   23 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVKK   23 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC-
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4789999999999999999753

>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=89.79  E-value=0.083  Score=46.09  Aligned_cols=22  Identities=23%  Similarity=0.409  Sum_probs=19.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -+++.|++|+|||+|++.+.+.
T Consensus         6 Ki~vvG~~~vGKTsLi~~~~~~   27 (175)
T d2f9la1           6 KVVLIGDSGVGKSNLLSRFTRN   27 (175)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999988764

>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=89.77  E-value=0.085  Score=45.76  Aligned_cols=23  Identities=17%  Similarity=0.264  Sum_probs=19.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|+|.|++|||||+|.+.+.+.-
T Consensus         4 Ki~lvG~~~vGKTsli~r~~~~~   26 (168)
T d2atva1           4 KLAIFGRAGVGKSALVVRFLTKR   26 (168)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhCC
Confidence            37899999999999999888743

>d2ocpa1 c.37.1.1 (A:37-277) Deoxyguanosine 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: Deoxyguanosine kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.70  E-value=0.089  Score=48.19  Aligned_cols=27  Identities=22%  Similarity=0.453  Sum_probs=24.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      |+=+.|.|+-|+||||+++.|++.+..
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhh
Confidence            667889999999999999999999853

>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=89.65  E-value=0.086  Score=46.31  Aligned_cols=21  Identities=38%  Similarity=0.526  Sum_probs=19.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |++.|.+|||||+|++.+.+.
T Consensus         5 v~vvG~~~vGKSSLi~~l~~~   25 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVNK   25 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988763

>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=89.54  E-value=0.15  Score=44.82  Aligned_cols=38  Identities=18%  Similarity=0.304  Sum_probs=25.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      -|+|.|.+|+|||+|.+.+.-.-...+-.++....++.
T Consensus         4 KivllG~~~vGKTsll~r~~f~~~~~pTiG~~~~~~~~   41 (200)
T d1zcba2           4 KILLLGAGESGKSTFLKQMRIIHGQDPTKGIHEYDFEI   41 (200)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHSCCCCSSEEEEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCeeeeEEEEEee
Confidence            48899999999999999984322223333544444443

>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=89.45  E-value=0.093  Score=45.00  Aligned_cols=22  Identities=18%  Similarity=0.267  Sum_probs=19.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|++.+.+.
T Consensus         4 Kv~liG~~~vGKTsLl~~~~~~   25 (165)
T d1z06a1           4 KIIVIGDSNVGKTCLTYRFCAG   25 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999988764

>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=89.38  E-value=0.085  Score=45.54  Aligned_cols=22  Identities=18%  Similarity=0.369  Sum_probs=19.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|++.|++|+|||+|+..+.+.
T Consensus         5 Ki~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            3889999999999999988764

>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=89.37  E-value=0.085  Score=45.47  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=19.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHHh
Q 047219          325 VLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~l  346 (567)
                      +++.|.+|+|||+|++.+.+.-
T Consensus         5 i~vvG~~~vGKTSli~~l~~~~   26 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVEDK   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCC
Confidence            7899999999999999988753

>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=89.34  E-value=0.095  Score=45.42  Aligned_cols=21  Identities=38%  Similarity=0.514  Sum_probs=18.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      ++|.|++|+|||+|++.+.+.
T Consensus         5 i~~vG~~~vGKSsLi~~~~~~   25 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVND   25 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHcC
Confidence            789999999999999988753

>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=89.25  E-value=0.08  Score=46.13  Aligned_cols=22  Identities=18%  Similarity=0.486  Sum_probs=19.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|+|.|+||+|||+|..+|.++
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999754

>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=89.17  E-value=0.084  Score=45.67  Aligned_cols=21  Identities=29%  Similarity=0.305  Sum_probs=18.4

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |++.|.+|+|||+|.+.+...
T Consensus         5 i~viG~~~vGKTsLi~r~~~~   25 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVKG   25 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            789999999999999887753

>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=89.02  E-value=0.094  Score=45.68  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=19.6

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|++.+.+.
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~~   29 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQS   29 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            5999999999999999987764

>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=88.91  E-value=0.096  Score=44.94  Aligned_cols=21  Identities=29%  Similarity=0.381  Sum_probs=18.8

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |+|.|.+|+|||+|++.+.+.
T Consensus         3 v~vvG~~~vGKTsLi~r~~~~   23 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMYD   23 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998753

>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=88.83  E-value=0.11  Score=44.83  Aligned_cols=22  Identities=27%  Similarity=0.370  Sum_probs=19.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|.+.+.+.
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~~   27 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVED   27 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3889999999999999998764

>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=88.74  E-value=0.1  Score=45.04  Aligned_cols=23  Identities=22%  Similarity=0.250  Sum_probs=19.8

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHH
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .-|+|.|++|+|||+|++.+.+.
T Consensus         5 ~Kv~liG~~~vGKTsLl~~~~~~   27 (167)
T d1xtqa1           5 RKIAILGYRSVGKSSLTIQFVEG   27 (167)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCcCHHHHHHHHHhC
Confidence            35889999999999999998754

>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=88.71  E-value=0.094  Score=45.43  Aligned_cols=21  Identities=43%  Similarity=0.781  Sum_probs=18.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |+|.|.+|+|||+|++.+.+.
T Consensus         4 i~lvG~~~vGKTsLi~~~~~~   24 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGGV   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHTC
T ss_pred             EEEECCCCcCHHHHHHHHhCC
Confidence            789999999999999988754

>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=88.64  E-value=0.11  Score=44.89  Aligned_cols=21  Identities=29%  Similarity=0.425  Sum_probs=19.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      +++.|++|+|||+|++.+.+.
T Consensus         9 i~vvG~~~vGKTsli~~~~~~   29 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDG   29 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988764

>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=88.53  E-value=0.11  Score=45.21  Aligned_cols=22  Identities=27%  Similarity=0.446  Sum_probs=19.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|++.|.+|+|||+|.+.+.+.
T Consensus         9 Ki~vvG~~~vGKTsli~~l~~~   30 (177)
T d1x3sa1           9 KILIIGESGVGKSSLLLRFTDD   30 (177)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999998764

>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=88.43  E-value=0.12  Score=44.58  Aligned_cols=23  Identities=17%  Similarity=0.299  Sum_probs=20.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|+|.|.+|+|||+|++.+...-
T Consensus         5 KivvvG~~~vGKTsli~r~~~~~   27 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQGI   27 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHcCC
Confidence            38899999999999999987653

>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=88.42  E-value=0.12  Score=44.87  Aligned_cols=22  Identities=27%  Similarity=0.397  Sum_probs=19.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|++|+|||+|+..+.+.
T Consensus         8 KI~vvG~~~vGKSSli~~~~~~   29 (174)
T d1wmsa_           8 KVILLGDGGVGKSSLMNRYVTN   29 (174)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999887764

>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=88.33  E-value=0.11  Score=45.09  Aligned_cols=21  Identities=29%  Similarity=0.430  Sum_probs=18.9

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |+|.|.+|+|||+|++.+...
T Consensus         8 I~lvG~~~vGKTsll~~~~~~   28 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIEK   28 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999988753

>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=88.33  E-value=0.1  Score=44.32  Aligned_cols=22  Identities=32%  Similarity=0.582  Sum_probs=19.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|+|.|+||+|||+|..++...
T Consensus         3 kI~lvG~~nvGKSsLin~l~~~   24 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAGR   24 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5889999999999999999754

>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=88.31  E-value=0.12  Score=44.73  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=19.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|++.+...
T Consensus         6 KivlvG~~~vGKTsli~~~~~~   27 (168)
T d1u8za_           6 KVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4899999999999999998753

>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=88.30  E-value=0.2  Score=45.84  Aligned_cols=23  Identities=22%  Similarity=0.385  Sum_probs=20.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|-|+|+.||||||+|+.+++..
T Consensus         3 iIgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           3 LIFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            36799999999999999999876

>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=88.27  E-value=0.083  Score=49.42  Aligned_cols=30  Identities=30%  Similarity=0.379  Sum_probs=25.6

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ......-+-|.||.|+||||+.++|+....
T Consensus        28 ~i~~Gei~~liGpnGaGKSTl~~~i~Gl~~   57 (240)
T d1ji0a_          28 KVPRGQIVTLIGANGAGKTTTLSAIAGLVR   57 (240)
T ss_dssp             EEETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             EECCCCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            356677788999999999999999998763

>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=88.06  E-value=0.12  Score=45.11  Aligned_cols=23  Identities=22%  Similarity=0.250  Sum_probs=19.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|++.|.+|+|||+|+..+.+.-
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~~   26 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKDQ   26 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47889999999999998887653

>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=88.01  E-value=0.11  Score=48.61  Aligned_cols=30  Identities=30%  Similarity=0.430  Sum_probs=25.5

Q ss_pred             cCCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          318 ESNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       318 ~~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ...++.-+-|.||.|+|||||.++|+....
T Consensus        24 ~v~~Gei~glvG~nGaGKSTLl~~l~G~~~   53 (238)
T d1vpla_          24 EIEEGEIFGLIGPNGAGKTTTLRIISTLIK   53 (238)
T ss_dssp             EECTTCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEcCCCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            356667788999999999999999998764

>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=87.87  E-value=0.1  Score=45.60  Aligned_cols=26  Identities=31%  Similarity=0.373  Sum_probs=22.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ....-.|+|.|++|+|||+|.+.+..
T Consensus        14 ~~k~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          14 SNKELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             CSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCceEEEEEECCCCCCHHHHHHHHhc
Confidence            55667899999999999999998753

>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=87.70  E-value=0.13  Score=45.12  Aligned_cols=24  Identities=21%  Similarity=0.166  Sum_probs=20.4

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      --++|.|.+|+|||+|.+.+...-
T Consensus         6 iKivviG~~~vGKTsli~~~~~~~   29 (183)
T d1mh1a_           6 IKCVVVGDGAVGKTCLLISYTTNA   29 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhCC
Confidence            458999999999999998887643

>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=87.69  E-value=0.14  Score=44.17  Aligned_cols=22  Identities=18%  Similarity=0.309  Sum_probs=19.0

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|++.+...
T Consensus         5 Ki~vvG~~~vGKTsLi~~~~~~   26 (170)
T d1ek0a_           5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999987654

>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=87.59  E-value=0.058  Score=46.88  Aligned_cols=24  Identities=17%  Similarity=0.267  Sum_probs=21.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          324 AVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      -.+|+||.|+|||++..||.-.+.
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhc
Confidence            467899999999999999998774

>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=87.59  E-value=0.15  Score=44.25  Aligned_cols=22  Identities=18%  Similarity=0.317  Sum_probs=19.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -++|.|.+|||||+|++.+.+.
T Consensus         6 Ki~lvG~~~vGKTsll~~~~~~   27 (169)
T d1x1ra1           6 KLVVVGDGGVGKSALTIQFFQK   27 (169)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999988764

>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=87.48  E-value=0.14  Score=44.50  Aligned_cols=21  Identities=33%  Similarity=0.578  Sum_probs=18.7

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |+|.|.+|+|||+|++.+...
T Consensus         6 v~lvG~~~vGKTsLi~~~~~~   26 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAGV   26 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            889999999999999988753

>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=87.32  E-value=0.066  Score=48.85  Aligned_cols=25  Identities=16%  Similarity=0.385  Sum_probs=22.5

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      +-|.|.|+-|+||||+++.|++.+.
T Consensus         3 k~I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           3 KKISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4578999999999999999999874

>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=87.22  E-value=0.11  Score=48.20  Aligned_cols=28  Identities=21%  Similarity=0.354  Sum_probs=24.2

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-+-|.||.|+|||||.++++...
T Consensus        22 I~~Gei~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          22 VRAGEILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             EETTCEEECBCCTTSSHHHHHHHHHTSC
T ss_pred             EcCCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            5667788999999999999999998743

>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=87.06  E-value=0.14  Score=44.85  Aligned_cols=22  Identities=27%  Similarity=0.415  Sum_probs=19.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|+|.|.+|+|||+|++.+.+.
T Consensus         4 KivliG~~~vGKTsli~r~~~~   25 (179)
T d1m7ba_           4 KIVVVGDSQCGKTALLHVFAKD   25 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999888764

>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=87.04  E-value=0.17  Score=44.99  Aligned_cols=35  Identities=20%  Similarity=0.209  Sum_probs=27.6

Q ss_pred             ceEEeeCC-CCCcHHHHHHHHHHHhCCCCCCCcCeEEec
Q 047219          323 RAVLFEGP-PGTGKTSCARVIANQAGAMPWQGVPLMYVP  360 (567)
Q Consensus       323 ~~VLL~Gp-pGTGKT~LAraIA~~l~~~~~~~~~~~~i~  360 (567)
                      +.++++|- +|+|||+++-.+|..+.+.   +..+..++
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~---G~rVl~id   37 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAA---GYRTAGYK   37 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHT---TCCEEEEC
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHC---CCeEEEEC
Confidence            56899999 5999999999999988554   45566655

>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=87.02  E-value=0.25  Score=44.74  Aligned_cols=27  Identities=26%  Similarity=0.409  Sum_probs=23.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      ++=|.|.|+-|+||||+++.+++.+..
T Consensus         3 Gk~I~iEG~DGsGKST~~~~L~~~L~~   29 (214)
T d1tmka_           3 GKLILIEGLDRTGKTTQCNILYKKLQP   29 (214)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHTTT
T ss_pred             eEEEEEECCCCCcHHHHHHHHHHHHHh
Confidence            345778999999999999999999853

>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=87.00  E-value=0.14  Score=45.36  Aligned_cols=21  Identities=24%  Similarity=0.438  Sum_probs=19.0

Q ss_pred             EEeeCCCCCcHHHHHHHHHHH
Q 047219          325 VLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       325 VLL~GppGTGKT~LAraIA~~  345 (567)
                      |+|.|++|+|||+|++.+...
T Consensus         9 ivvvG~~~vGKTsli~~l~~~   29 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSDD   29 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhhC
Confidence            889999999999999988764

>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=86.94  E-value=0.12  Score=48.79  Aligned_cols=29  Identities=31%  Similarity=0.480  Sum_probs=25.1

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHhC
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQAG  347 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l~  347 (567)
                      ..++.-+-|.||.|+|||||+++|+....
T Consensus        27 v~~Gei~~liG~nGaGKSTLl~~i~Gl~~   55 (254)
T d1g6ha_          27 VNKGDVTLIIGPNGSGKSTLINVITGFLK   55 (254)
T ss_dssp             EETTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             ECCCCEEEEECCCCCcHHHHHHHHHCCCc
Confidence            55667788999999999999999998763

>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=86.70  E-value=0.1  Score=45.39  Aligned_cols=21  Identities=29%  Similarity=0.423  Sum_probs=8.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~  344 (567)
                      -|+|.|.+|||||+|++.+..
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           8 KLLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEEECCCCC-----------
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            388999999999999987765

>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=86.64  E-value=0.17  Score=44.60  Aligned_cols=21  Identities=24%  Similarity=0.436  Sum_probs=19.4

Q ss_pred             eEEeeCCCCCcHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~  344 (567)
                      .|.|.|+||+|||+|.+++.+
T Consensus        25 ~I~lvG~~n~GKSTLin~L~g   45 (195)
T d1svia_          25 EIALAGRSNVGKSSFINSLIN   45 (195)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHhcC
Confidence            599999999999999999974

>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=86.61  E-value=0.16  Score=44.68  Aligned_cols=23  Identities=30%  Similarity=0.294  Sum_probs=19.9

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|+|.|.+|+|||+|.+.+.+..
T Consensus        11 Ki~lvG~~~vGKTsLi~r~~~~~   33 (185)
T d2atxa1          11 KCVVVGDGAVGKTCLLMSYANDA   33 (185)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSS
T ss_pred             EEEEECCCCCCHHHHHHHHhhCC
Confidence            48899999999999999887643

>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=86.48  E-value=0.17  Score=44.04  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=20.1

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|.|.|.||+|||+|.+++...
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5999999999999999999864

>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=86.26  E-value=0.15  Score=50.90  Aligned_cols=37  Identities=32%  Similarity=0.440  Sum_probs=26.6

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEech
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPL  361 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~  361 (567)
                      .+|+++.|++|+|||++++.+...+-..   +.+++.++.
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~---g~~~iiiD~   86 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLR---GDRMVIVDP   86 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHT---TCEEEEEEE
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhC---CCCEEEEeC
Confidence            4789999999999999988766554222   445555554

>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=86.22  E-value=0.13  Score=44.46  Aligned_cols=26  Identities=31%  Similarity=0.473  Sum_probs=21.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ......|.|.|.|++|||+|.+++..
T Consensus        13 ~~~~~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          13 SDTGIEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             CSCSEEEEEEECTTSSHHHHHTTTCC
T ss_pred             CccCCEEEEECCCCCCHHHHHHHHhC
Confidence            34456699999999999999998843

>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=86.22  E-value=0.18  Score=46.52  Aligned_cols=25  Identities=24%  Similarity=0.304  Sum_probs=21.1

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .+..+|.|++|+|||+|..++....
T Consensus        95 ~kt~~~~G~SGVGKSTLiN~L~~~~  119 (225)
T d1u0la2          95 GKISTMAGLSGVGKSSLLNAINPGL  119 (225)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHSTTC
T ss_pred             CCeEEEECCCCCCHHHHHHhhcchh
Confidence            3567899999999999999987554

>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=86.07  E-value=0.34  Score=45.27  Aligned_cols=26  Identities=27%  Similarity=0.396  Sum_probs=22.6

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      ..+..|+|.|.||+|||++..+|..+
T Consensus        30 ~~~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          30 VNSLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             CCEEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CCCcEEEEECCCCCcHHHHHHHHhCC
Confidence            44568999999999999999999864

>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=85.90  E-value=0.31  Score=43.41  Aligned_cols=24  Identities=33%  Similarity=0.459  Sum_probs=18.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .+++++.-|+|+|||..+......
T Consensus        40 g~~vlv~apTGsGKT~~~~~~~~~   63 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIPALL   63 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCcchhhhhhhh
Confidence            368999999999999887554443

>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=85.90  E-value=0.17  Score=43.58  Aligned_cols=22  Identities=23%  Similarity=0.392  Sum_probs=19.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|.|.|.||+|||+|..++.+.
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~~   28 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLGQ   28 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHTC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999864

>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=85.72  E-value=0.18  Score=44.43  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=19.3

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHHh
Q 047219          324 AVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      -|+|.|.+|+|||+|++.+...-
T Consensus         5 KvvllG~~~vGKTSli~r~~~~~   27 (191)
T d2ngra_           5 KCVVVGDGAVGKTCLLISYTTNK   27 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHSC
T ss_pred             EEEEECCCCcCHHHHHHHHHhCC
Confidence            47899999999999998877643

>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=85.46  E-value=0.1  Score=45.33  Aligned_cols=22  Identities=27%  Similarity=0.404  Sum_probs=17.7

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      -|++.|++|+|||+|++.+.+.
T Consensus         5 Ki~vvG~~~vGKTsli~~~~~~   26 (170)
T d1i2ma_           5 KLVLVGDGGTGKTTFVKRHLTG   26 (170)
T ss_dssp             EEEEEECTTSSHHHHHHTTC--
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3789999999999999877654

>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=85.31  E-value=1.3  Score=37.19  Aligned_cols=22  Identities=27%  Similarity=0.345  Sum_probs=17.7

Q ss_pred             EEeeCCCCCcHHH-HHHHHHHHh
Q 047219          325 VLFEGPPGTGKTS-CARVIANQA  346 (567)
Q Consensus       325 VLL~GppGTGKT~-LAraIA~~l  346 (567)
                      -+++||-.+|||+ |.+.+.+..
T Consensus         5 ~~i~GpMfsGKTteLi~~~~~~~   27 (139)
T d2b8ta1           5 EFITGPMFAGKTAELIRRLHRLE   27 (139)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHH
T ss_pred             EEEEccccCHHHHHHHHHHHHHH
Confidence            3688999999998 777776654

>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=84.23  E-value=0.24  Score=47.49  Aligned_cols=28  Identities=32%  Similarity=0.377  Sum_probs=24.5

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      ...+.-++|.|++|||||+|+..+++..
T Consensus        40 igrGQr~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          40 IGRGQRGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             CBTTCEEEEEECSSSSHHHHHHHHHHHH
T ss_pred             ccCCCeeeEeCCCCCCHHHHHHHHHHHH
Confidence            4556779999999999999999999866

>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=83.97  E-value=0.099  Score=44.43  Aligned_cols=22  Identities=23%  Similarity=0.477  Sum_probs=19.8

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|.|.|.||+|||+|..++..+
T Consensus         2 kI~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           2 RMVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999875

>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=83.96  E-value=0.2  Score=43.77  Aligned_cols=21  Identities=29%  Similarity=0.445  Sum_probs=18.5

Q ss_pred             eEEeeCCCCCcHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~  344 (567)
                      .|-|.|+||+|||+|..++.+
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            477999999999999999854

>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=83.78  E-value=0.24  Score=43.09  Aligned_cols=24  Identities=29%  Similarity=0.418  Sum_probs=20.9

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHH
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .-.|.|.|.+|+|||+|..++.+.
T Consensus         8 ~~kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2           8 AIKVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCC
Confidence            456899999999999999999764

>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=83.57  E-value=0.2  Score=43.61  Aligned_cols=22  Identities=27%  Similarity=0.371  Sum_probs=19.2

Q ss_pred             eEEeeCCCCCcHHHHHHHHHHH
Q 047219          324 AVLFEGPPGTGKTSCARVIANQ  345 (567)
Q Consensus       324 ~VLL~GppGTGKT~LAraIA~~  345 (567)
                      .|.|.|.||+|||+|..++.+.
T Consensus         3 ~VaivG~~nvGKSTLin~L~~~   24 (180)
T d1udxa2           3 DVGLVGYPNAGKSSLLAAMTRA   24 (180)
T ss_dssp             SEEEECCGGGCHHHHHHHHCSS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3789999999999999999653

>d1tq4a_ c.37.1.8 (A:) Interferon-inducible GTPase {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: Interferon-inducible GTPase
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.28  E-value=0.38  Score=48.05  Aligned_cols=25  Identities=24%  Similarity=0.371  Sum_probs=22.3

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHH
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIAN  344 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~  344 (567)
                      ..+-.|.+.|.||+|||+|..++..
T Consensus        54 ~~~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          54 SSVLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             HCCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHhC
Confidence            4577899999999999999999974

>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=82.60  E-value=1.3  Score=41.80  Aligned_cols=28  Identities=29%  Similarity=0.229  Sum_probs=21.9

Q ss_pred             CCCCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          319 SNRPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       319 ~~~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .....-++|.|++|+|||+++..+....
T Consensus        64 ig~GQr~~Ifg~~g~GKt~l~~~~~~~~   91 (276)
T d1fx0a3          64 VGRGQRELIIGDRQTGKTAVATDTILNQ   91 (276)
T ss_dssp             CBTTCBCBEEESSSSSHHHHHHHHHHTC
T ss_pred             ccCCceEeeccCCCCChHHHHHHHHhhh
Confidence            4455668999999999999998765544

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=81.87  E-value=4.2  Score=40.31  Aligned_cols=59  Identities=19%  Similarity=0.238  Sum_probs=43.5

Q ss_pred             cccccCcHHHHHHHHHHHHHhccChhhHHhhhhcccccccCCCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEE
Q 047219          279 WENIAGYDQQKREIEDTILLSLQSPEVYDDIARGTRCKFESNRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMY  358 (567)
Q Consensus       279 ~~dIiG~~~~k~~L~e~i~~~l~~pelf~~l~~~~~~~~~~~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~  358 (567)
                      |.--+-+..++++|.+.+.                      ...+..+|.|-+|+|||.++.++++..      +.+++.
T Consensus        10 ~~p~gDQP~aI~~l~~~l~----------------------~g~~~q~l~GltGS~ka~~iA~l~~~~------~rp~LV   61 (413)
T d1t5la1          10 YEPQGDQPQAIAKLVDGLR----------------------RGVKHQTLLGATGTGKTFTISNVIAQV------NKPTLV   61 (413)
T ss_dssp             SCCCTTHHHHHHHHHHHHH----------------------HTCSEEEEEECTTSCHHHHHHHHHHHH------TCCEEE
T ss_pred             CCCCCCCHHHHHHHHHHHh----------------------cCCCcEEEeCCCCcHHHHHHHHHHHHh------CCCEEE
Confidence            4444566777888877664                      234678899999999999999999998      556776


Q ss_pred             echhhHH
Q 047219          359 VPLEVVM  365 (567)
Q Consensus       359 i~~~~l~  365 (567)
                      +..+...
T Consensus        62 Vt~n~~~   68 (413)
T d1t5la1          62 IAHNKTL   68 (413)
T ss_dssp             ECSSHHH
T ss_pred             EeCCHHH
Confidence            6655433

>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=81.72  E-value=0.39  Score=41.85  Aligned_cols=25  Identities=16%  Similarity=0.113  Sum_probs=21.3

Q ss_pred             CceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          322 PRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       322 p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      --.|++.|.+|+|||+|.+.+...-
T Consensus         5 ~~ki~vlG~~~vGKTsLi~~~~~~~   29 (175)
T d2bmja1           5 ELRLGVLGDARSGKSSLIHRFLTGS   29 (175)
T ss_dssp             EEEEEEECCTTTTHHHHHHHHHHSC
T ss_pred             cEEEEEECCCCCCHHHHHHHHHhCC
Confidence            3568999999999999999887754

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

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: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=81.64  E-value=0.41  Score=46.73  Aligned_cols=26  Identities=31%  Similarity=0.548  Sum_probs=22.9

Q ss_pred             ceEEeeCCCCCcHHHHHHHHHHHhCC
Q 047219          323 RAVLFEGPPGTGKTSCARVIANQAGA  348 (567)
Q Consensus       323 ~~VLL~GppGTGKT~LAraIA~~l~~  348 (567)
                      .-|.|-|+-|+||||+++.+++.+..
T Consensus         7 ~rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           7 VRIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEEEECCccCCHHHHHHHHHHHhcc
Confidence            35788999999999999999999854

>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=81.24  E-value=0.18  Score=46.74  Aligned_cols=26  Identities=27%  Similarity=0.542  Sum_probs=20.4

Q ss_pred             CCceEEeeCCCCCcHHHHHHHHHHHh
Q 047219          321 RPRAVLFEGPPGTGKTSCARVIANQA  346 (567)
Q Consensus       321 ~p~~VLL~GppGTGKT~LAraIA~~l  346 (567)
                      .++..+|.|++|+|||+|..++....
T Consensus        96 ~~~~~vl~G~SGVGKSSLiN~L~~~~  121 (231)
T d1t9ha2          96 QDKTTVFAGQSGVGKSSLLNAISPEL  121 (231)
T ss_dssp             TTSEEEEEESHHHHHHHHHHHHCC--
T ss_pred             ccceEEEECCCCccHHHHHHhhccHh
Confidence            34567788999999999999987654

>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=80.58  E-value=0.5  Score=43.83  Aligned_cols=40  Identities=28%  Similarity=0.408  Sum_probs=28.7

Q ss_pred             CCCceEEeeCCCCCcHHHHHHHHHHHhCCCCCCCcCeEEechh
Q 047219          320 NRPRAVLFEGPPGTGKTSCARVIANQAGAMPWQGVPLMYVPLE  362 (567)
Q Consensus       320 ~~p~~VLL~GppGTGKT~LAraIA~~l~~~~~~~~~~~~i~~~  362 (567)
                      ...+-++++|.=|+||||++-.+|..+...   +..+..+++.
T Consensus        18 ~~~~iii~sGKGGVGKTT~a~nLA~~lA~~---G~rVllvD~D   57 (279)
T d1ihua2          18 NEHGLIMLMGKGGVGKTTMAAAIAVRLADM---GFDVHLTTSD   57 (279)
T ss_dssp             TSCEEEEEECSTTSSHHHHHHHHHHHHHHT---TCCEEEEESC
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC---CCcEEEEeCC
Confidence            445667788999999999988888877433   4445555554