Citrus Sinensis ID: 005179

---

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-------570-------580-------590-------600-------610-------620-------630-------640-------650-------660-------670-------680-------690-------700-------710
Protein Sequence
MEVSTCSPLSVNSRCLFANQPPPPRHRLPPLQYVNPMSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccccccccHHHHHHcHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHccccHHHHHHccccHHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHcccccHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHcccccccccccEEEEEccccccccccccHHHHHHHHHHHHHHHcccEEEEEcccHHHHccccccccccccHHHHHcccccccccccHHHHccccHHHHHHHHccccHHHHcccccccccccHHHHHHHHHHcHHHHHHcccccccHHHHHHHHHHcccccccccccccHHHHHHHHHHHHHcccccccHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHcccHHHHHcccccHHHHHHccccccccccccccccHHHHHHHHHHHcccHHHcccHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHcccccccccccEEEEccccccccHHHHHHHHHHHHHcccccccccccccccccHHHHccccc
Secondary Structure Prediction (SSPRO)
ccEcccccccccccEEEccccccccccccccccccccHHHccccEEEcccccccEEEEEccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHccccHHHHHHHHHccccHHHHHHHHHHcccccEEEEEEEcccccccccccccccHHHHHHHHHHHHHHHHcccccccHHHHHHHHHHcccHHHHHHHHHccccHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccccEccHHHHHHHHHHHHHHcccccEEEccccccHHHHHHHHHHHHHcccccHHHcccEEEEEEHHHHHHcccccccHHHHHHHHHHHHHHcccEEEEEEcHHHHHcccccccccccHHHHHHHHHHHHHHHccHHHHcHccHHHHHHHHHHHHHHHHcccccEcccccHHHHHHHHHHHHHHHHHHcccEEcHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccEEcHHHHHHHHHHHccccHHHccHHHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHccccccccccEEEEEEccccccHHHHHHHHHHHHccccccEEEEEccHcccccccEEEEcc
Coil and Loop (DISEMBL)
mevstcsplsvnsrclfanqpppprhrlpplqyvnpmssffNISMISHKVQFFHSnytsnnnncnpicarkrrkiipissVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIaedrhpngflesgiTIDKAREAVVSIWHstnnqdtddaaaqgkpfssaakmpfsiSTKRVFEAAVEYSRsrgynfiapehialglftvddgsagRVLKRLGVDVNHLAAVAVSRLQGElakegrepslakgvrensisgktaalkspgrtrASALEQFCVDLTARAseelidpvigrETEIQRIIQILCRrtknnpillgesgvgKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLigsgtvgrgnkgtgldisnllkpslgrgelqciASTTQDEHRTQFEKDKALARrfqpvlisepsqEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARyisdrylpdkAIDLVDEAGSRAHIELFKRKKEqqtcilskppddywQEIRTVQAMHEVVQGSRLKYDDVVAsmgdtseivvesslpsasdddepavvgpddIAAVASLwsgipvqqiTADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRsrvglkdpnrptaamlfcgptgvgkTELAKSLAACYFGSvrihylffpspfnsVKVALSRQIC
Flexible Loop (DISEMBL)
mevstcsplsvnsrcLFANQPPPPRHRLPPLQYVNPMSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHstnnqdtddaaaqgkpfssaakmpfsiSTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRlqgelakegrepslakgvrensisgktaalkspgrtrASALEQFCVDLTARASeelidpvigretEIQRIIQILCrrtknnpillgesgVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIgsgtvgrgnkgtglDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRfqpvlisepsqedAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIElfkrkkeqqtcilskppddYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVesslpsasdddEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAIsravkrsrvglkdpnrptaAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Low Complexity Region (SEG)
MEVSTCSPLSVNSRCLFANQpppprhrlpplQYVNPMSSFFNISMISHKVQFFHSNYTSnnnncnPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Disordered region (IsUnstruct)
******************************LQYVNPMSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWH**************************ISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL***************************************LEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIA********************FQPVLI******DAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASM***********************VGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKR*RVG******PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVA******
Disordered Region (DISOPRED)
********************************************************************************VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWH**************************ISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSR******************************************QFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHI*********************************V**GS***********************************GPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Disordered Region (DISEMBL)
*********SVNSRCLFANQPPPPRHRLPPLQYVNPMSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAST*********EKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIV*************PAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Disordered Region (DISPRO)
*****CSPLSVNSRCLFANQPPPPRHRLPPLQYVNPMSSFFNISMISHKVQFFHSNYTSNN************KIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQG**********************************ASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEVSTCSPLSVNSRCLFANQPPPPRHRLPPLQYVNPMSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQIC
Positional Conservation
no confident homologs detected

---

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	710	2.2.26 [Sep-21-2011]
P42762	945	Chaperone protein ClpD, c	yes	no	0.904	0.679	0.736	0.0
Q7XL03	937	Chaperone protein ClpD2,	yes	no	0.840	0.637	0.646	0.0
Q6H795	938	Chaperone protein ClpD1,	yes	no	0.839	0.635	0.647	0.0
Q9TM05	854	ATP-dependent Clp proteas	N/A	no	0.809	0.673	0.413	1e-132
P35100	922	Chaperone protein ClpC, c	N/A	no	0.852	0.656	0.435	1e-132
P31541	926	ATP-dependent Clp proteas	N/A	no	0.8	0.613	0.451	1e-131
O78410	819	ATP-dependent Clp proteas	yes	no	0.788	0.683	0.439	1e-130
Q1XDF4	821	ATP-dependent Clp proteas	N/A	no	0.791	0.684	0.435	1e-130
Q9FI56	929	Chaperone protein ClpC1,	no	no	0.825	0.630	0.435	1e-130
P51332	821	ATP-dependent Clp proteas	N/A	no	0.791	0.684	0.435	1e-129

>sp|P42762|CLPD_ARATH Chaperone protein ClpD, chloroplastic OS=Arabidopsis thaliana GN=CLPD PE=1 SV=1

 Score =  957 bits (2474), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 477/648 (73%), Positives = 545/648 (84%), Gaps = 6/648 (0%)

Query: 40  FFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQRE 99
           +  IS+ +  +  F +  T    N      RKR+K  PIS+VFERFTERA++A+IFSQ+E
Sbjct: 42  YLGISLSNRTIHRFSTTPT----NLRRFPQRKRKKFTPISAVFERFTERAIRAIIFSQKE 97

Query: 100 AKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ 159
           AKSLGKDMV+TQHLLLGLIAEDR P GFL SGITIDKAREAV SIW   N+ D+    A 
Sbjct: 98  AKSLGKDMVYTQHLLLGLIAEDRDPQGFLGSGITIDKAREAVWSIWDEANS-DSKQEEAS 156

Query: 160 GKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLG 219
              +S +  MPFSISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG
Sbjct: 157 STSYSKSTDMPFSISTKRVFEAAVEYSRTMDCQYIAPEHIAVGLFTVDDGSAGRVLKRLG 216

Query: 220 VDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSI-SGKTAALKSPGRTRASALEQFCV 278
            ++N L A A++RL+GE+AK+GREPS +      S  SG+ A     G+   + LEQFCV
Sbjct: 217 ANMNLLTAAALTRLKGEIAKDGREPSSSSKGSFESPPSGRIAGSGPGGKKAKNVLEQFCV 276

Query: 279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQA 338
           DLTARASE LIDPVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +A
Sbjct: 277 DLTARASEGLIDPVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAEA 336

Query: 339 EVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSG 398
             P FLL+KRIMSLD+GLLMAGAKERGELEARVT LISE++KSG VILFIDEVHTLIGSG
Sbjct: 337 SAPGFLLTKRIMSLDIGLLMAGAKERGELEARVTALISEVKKSGKVILFIDEVHTLIGSG 396

Query: 399 TVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPS 458
           TVGRGNKG+GLDI+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI+EPS
Sbjct: 397 TVGRGNKGSGLDIANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLINEPS 456

Query: 459 QEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAH 518
           +EDAV+ILLGLREKYEAHHNCK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA 
Sbjct: 457 EEDAVKILLGLREKYEAHHNCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRAR 516

Query: 519 IELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVES 578
           IE F++KKE   CILSKPP+DYWQEI+TVQAMHEVV  SR K DD  A   ++ E+V ES
Sbjct: 517 IEAFRKKKEDAICILSKPPNDYWQEIKTVQAMHEVVLSSRQKQDDGDAISDESGELVEES 576

Query: 579 SLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAV 638
           SLP A+ DDEP +VGPDDIAAVAS+WSGIPVQQITADERMLL+ LE+QL+ RV+GQDEAV
Sbjct: 577 SLPPAAGDDEPILVGPDDIAAVASVWSGIPVQQITADERMLLMSLEDQLRGRVVGQDEAV 636

Query: 639 AAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           AAISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 637 AAISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALAANYFGS 684

Molecular chaperone that may interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.
Arabidopsis thaliana (taxid: 3702)

>sp|Q7XL03|CLPD2_ORYSJ Chaperone protein ClpD2, chloroplastic OS=Oryza sativa subsp. japonica GN=CLPD2 PE=2 SV=2

 Score =  792 bits (2045), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 406/628 (64%), Positives = 491/628 (78%), Gaps = 31/628 (4%)

Query: 76  IPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITID 135
           + + +VFERFTERAVKAV+FSQREA+ +G + V   HLLLGL+AEDR P GFL SG+ ++
Sbjct: 65  VVVRAVFERFTERAVKAVVFSQREARGMGDETVAPHHLLLGLVAEDRSPLGFLASGVRVE 124

Query: 136 KAREAVVSIWHSTNNQDTDDAAAQGK------PFSSAAKMPFSISTKRVFEAAVEYSRSR 189
           +AREA                AA GK      P   A  +PFS ++KRVFEAAVE+SR+ 
Sbjct: 125 RAREAC--------------RAAVGKEGLAQAPVGLATDVPFSGASKRVFEAAVEFSRNM 170

Query: 190 GYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREP-SLAK 248
           G NFI+PEHIALGLF ++D +   VLK LGVD + LA  A++R+QGELAK+GREP  L+ 
Sbjct: 171 GCNFISPEHIALGLFNLNDPTTNNVLKSLGVDSSQLAKQALTRVQGELAKDGREPVGLSS 230

Query: 249 -GVRENSI--SGKTAALKSPGRTR-ASALEQFCVDLTARASEELIDPVIGRETEIQRIIQ 304
             VRE      GK+A +K   + +  SAL  FC+DLT RAS  LIDPVIGR+ EI+R++Q
Sbjct: 231 FKVREKFTPGGGKSAIVKYSNKNKEKSALALFCLDLTMRASGGLIDPVIGRKDEIERVVQ 290

Query: 305 ILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKER 364
           I+CRRTKNNPILLGE+GVGKTAIAEGLA +I   +VP+FL+ KRI+SLD+ LLMAGAKER
Sbjct: 291 IICRRTKNNPILLGEAGVGKTAIAEGLAHKIANGDVPIFLVGKRILSLDVALLMAGAKER 350

Query: 365 GELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGEL 424
           GELEARVT+LI E++K+GDVILFIDEVHTLIGSG  GRG+KG GLDI+NLLKP+L RGEL
Sbjct: 351 GELEARVTSLIREVRKAGDVILFIDEVHTLIGSGIAGRGSKGAGLDIANLLKPALARGEL 410

Query: 425 QCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE 484
           QCIASTT DEHR  F+KDKALARRFQPVL++EPSQEDAV+ILLGLREKYE +H CK+TLE
Sbjct: 411 QCIASTTLDEHRLHFDKDKALARRFQPVLVNEPSQEDAVKILLGLREKYETYHKCKYTLE 470

Query: 485 AINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEI 544
           +INAAV+LSARYI+DR+LPDKAIDL+DEAGSRA +E FKRKKE+Q  ILSK PD+YWQEI
Sbjct: 471 SINAAVYLSARYIADRHLPDKAIDLIDEAGSRARMESFKRKKEEQCSILSKSPDEYWQEI 530

Query: 545 RTVQAMHEVVQGSRLKYDDVVASMGDTS--EIVVESSLPSAS----DDDEPAVVGPDDIA 598
           R VQ MHEV   +++KY        D    E+V E     AS      D+P++VG ++IA
Sbjct: 531 RAVQNMHEVALTNKVKYSLNQNDQEDAVDIELVGEDKTSPASMLSTSTDKPSLVGSEEIA 590

Query: 599 AVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRP 658
            V SLWSGIPVQQ+TADER LLVGL+++L+KRVIGQD+AV AIS+AVKRSRVGL DP+RP
Sbjct: 591 RVTSLWSGIPVQQLTADERKLLVGLDDELRKRVIGQDDAVLAISKAVKRSRVGLNDPDRP 650

Query: 659 TAAMLFCGPTGVGKTELAKSLAACYFGS 686
            A ++FCGPTGVGKTEL K+LAA YFGS
Sbjct: 651 IATLIFCGPTGVGKTELTKALAASYFGS 678

Molecular chaperone that may interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q6H795|CLPD1_ORYSJ Chaperone protein ClpD1, chloroplastic OS=Oryza sativa subsp. japonica GN=CLPD1 PE=2 SV=1

 Score =  768 bits (1982), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 399/616 (64%), Positives = 478/616 (77%), Gaps = 20/616 (3%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAV 141
           FERFTERAVKAV+ SQREAK LG+  V  +HLLLGLIAEDR   GFL SGI I++ARE  
Sbjct: 74  FERFTERAVKAVVLSQREAKGLGEGAVAPRHLLLGLIAEDRSAGGFLSSGINIERAREEC 133

Query: 142 VSIWHSTNNQDTDDAAAQGKPFSSAAKM--PFSISTKRVFEAAVEYSRSRGYNFIAPEHI 199
             I         D       P  S  +M  PFS S KRVFE AVE+SR+ G +FI+PEH+
Sbjct: 134 RGIGAR------DLTPGAPSPSGSGLEMDIPFSGSCKRVFEVAVEFSRNMGCSFISPEHL 187

Query: 200 ALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSIS--- 256
           AL LFT+DD +   +L+ LG D + LA+VA++RLQ ELAK+ REP+ A   +    S   
Sbjct: 188 ALALFTLDDPTTNSLLRSLGADPSQLASVALTRLQAELAKDCREPAGASSFKVPKKSPAG 247

Query: 257 -GKTAALKS-PGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP 314
            G++A  KS   +    AL+QFC+DLT +AS   IDP+IGRE EI+R++QI+CRRTKNNP
Sbjct: 248 AGRSAFSKSLNSKKEKGALDQFCLDLTTQASGGFIDPIIGREEEIERVVQIICRRTKNNP 307

Query: 315 ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTL 374
           ILLGE+GVGKTAIAEGLA+RI   +VP++L++KRIMSLD+GLL+AGAKERGELE+RVT+L
Sbjct: 308 ILLGEAGVGKTAIAEGLALRIANGDVPIYLVAKRIMSLDVGLLIAGAKERGELESRVTSL 367

Query: 375 ISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDE 434
           I E++++GDVILFIDEVH LIGSGTVG+G KG GLDI NLLKP L RGELQCIA+TT DE
Sbjct: 368 IREVREAGDVILFIDEVHNLIGSGTVGKG-KGAGLDIGNLLKPPLARGELQCIAATTLDE 426

Query: 435 HRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSA 494
           HR  FEKDKALARRFQPVL+ EPSQ+DAV+ILLGLREKYE +H CKFTLEAINAAV+LSA
Sbjct: 427 HRMHFEKDKALARRFQPVLVEEPSQDDAVKILLGLREKYETYHKCKFTLEAINAAVYLSA 486

Query: 495 RYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVV 554
           RYI DR LPDKAIDL+DEAGSRA +E F RKKE Q+ IL K PD+YWQEIR  Q MHEVV
Sbjct: 487 RYIPDRQLPDKAIDLIDEAGSRARMESFNRKKEGQSSILLKSPDEYWQEIRAAQNMHEVV 546

Query: 555 QGSRLKY----DDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQ 610
             +++KY    ++  A++   SE + E  L S    +EP VVG ++IA VASLWSGIPVQ
Sbjct: 547 SSNQMKYSPRQENGSAAIKAPSEDMNE--LTSELQVEEPIVVGTEEIARVASLWSGIPVQ 604

Query: 611 QITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGV 670
           Q+TAD+R LLVGL+ +L+KRVIGQD+AV AISRAVKRSRVGL DP+RP A +LFCGPTGV
Sbjct: 605 QLTADDRKLLVGLDGELRKRVIGQDDAVMAISRAVKRSRVGLNDPDRPIATLLFCGPTGV 664

Query: 671 GKTELAKSLAACYFGS 686
           GKTEL K+LAA YFGS
Sbjct: 665 GKTELTKALAASYFGS 680

Molecular chaperone that may function in heat stress response. May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Oryza sativa subsp. japonica (taxid: 39947)

>sp|Q9TM05|CLPC_CYACA ATP-dependent Clp protease ATP-binding subunit clpA homolog OS=Cyanidium caldarium GN=clpC PE=3 SV=1

 Score =  474 bits (1220), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 269/651 (41%), Positives = 392/651 (60%), Gaps = 76/651 (11%)

Query: 52  FFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQ 111
           F  +  T  N   N +C   ++      ++FERFTE+AVK ++ +Q EA+ LG + V T+
Sbjct: 9   FLKAMLTLLNIKGNNMCWAHKK------NMFERFTEKAVKVIMLAQEEARRLGHNFVGTE 62

Query: 112 HLLLGLIAEDR--HPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKM 169
            +LLG++ E            GIT+  AR  V  I              +G  F  A ++
Sbjct: 63  QILLGILGEGTGLAAKALKSMGITLKDARIEVEKII------------GRGSGFV-AIEI 109

Query: 170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVA 229
           PF+   K++ E A+E SR   +N++  EH+ LGL    +G A RVL+ LGVD+  L +  
Sbjct: 110 PFTPRAKKILELAIEESRILTHNYVGTEHLLLGLIKEGEGVAARVLENLGVDLPKLRS-N 168

Query: 230 VSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELI 289
           + R+ GE                   + + +   + GR++   LE+F  +LT  A E  +
Sbjct: 169 IIRMIGE-------------------TSEVSVGATSGRSKVPTLEEFGTNLTQMAVEGKL 209

Query: 290 DPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRI 349
           DPV+GR  EI+R++QIL RRTKNNP+L+GE GVGKTAIAEGLA RI+  EVP  L  K++
Sbjct: 210 DPVVGRAKEIERVVQILGRRTKNNPVLIGEPGVGKTAIAEGLAQRIINNEVPDTLEDKKV 269

Query: 350 MSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGL 409
           ++LD+ LL+AG K RGE E R+  ++ EI+ + +VIL IDEVHTLIG+G          +
Sbjct: 270 ITLDVSLLVAGTKYRGEFEERLKKIMDEIRMADNVILVIDEVHTLIGAGAA-----EGAI 324

Query: 410 DISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGL 469
           D +N+LKP+L RGELQCI +TT +E+R   EKD AL RRFQPV++ EP+ E+ + IL GL
Sbjct: 325 DAANILKPALARGELQCIGATTLEEYRKHIEKDAALERRFQPVMVEEPTVEETIEILRGL 384

Query: 470 REKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQ 529
           R++YEAHH  K +  AI AA  LS +YI+DR+LPDKAIDLVDEA SR  +  +K      
Sbjct: 385 RDRYEAHHRLKISDSAIVAAAKLSDQYIADRFLPDKAIDLVDEASSRVRLMNYKL----- 439

Query: 530 TCILSKPPDDYW--QEIRTVQAM-HEVV------QGSRLKYDDV-----VASMGDTSEIV 575
                 PP   +  +E+R +Q + +E++      + S+ +  ++     +A++    +  
Sbjct: 440 ------PPSAEYLDEELRHIQKIKNELIRSGDFEEASQFREREIEVKVQMAALMKAKKEA 493

Query: 576 VESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQD 635
           +E  L        P +V  DDIA + S W+GIPV ++T  E   L+ +EE L  R++GQ+
Sbjct: 494 IEEELAL-----NPPIVNEDDIANIVSSWTGIPVSKLTKSESEKLLHMEETLHSRIVGQN 548

Query: 636 EAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           EAV A+S+A++R+RVGLK+PNRP A+ +F GPTGVGKTEL K++A+ +FGS
Sbjct: 549 EAVIAVSKAIRRARVGLKNPNRPIASFIFSGPTGVGKTELTKAMASYFFGS 599

May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Cyanidium caldarium (taxid: 2771)

>sp|P35100|CLPC_PEA Chaperone protein ClpC, chloroplastic OS=Pisum sativum PE=2 SV=1

 Score =  472 bits (1215), Expect = e-132,   Method: Compositional matrix adjust.
 Identities = 289/663 (43%), Positives = 397/663 (59%), Gaps = 58/663 (8%)

Query: 37  MSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRR--KIIPISSVFERFTERAVKAVI 94
           MS F  +   +H           ++     + +R+ R  + IP  ++FERFTE+A+K ++
Sbjct: 46  MSGFSGLRTFNHLNTMMRPGLDFHSKVSKAVSSRRARAKRFIP-RAMFERFTEKAIKVIM 104

Query: 95  FSQREAKSLGKDMVFTQHLLLGLIAEDRH-PNGFLES-GITIDKAREAVVSIWHSTNNQD 152
            +Q EA+ LG + V T+ +LLGLI E        L+S GI +  AR  V  I        
Sbjct: 105 LAQEEARRLGHNFVGTEQILLGLIGEGTGIAAKVLKSMGINLKDARVEVEKII------- 157

Query: 153 TDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAG 212
                 +G  F  A ++PF+   KRV E + E +R  G+N+I  EH+ LGL    +G A 
Sbjct: 158 -----GRGSGFV-AVEIPFTPRAKRVLELSQEEARQLGHNYIGSEHLLLGLLREGEGVAA 211

Query: 213 RVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASA 272
           RVL+ LG D  ++    V R+ GE A              +S++    +  S  +T    
Sbjct: 212 RVLENLGADPTNIR-TQVIRMVGESA--------------DSVTATVGSGSSNNKT--PT 254

Query: 273 LEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLA 332
           LE++  +LT  A E  +DPV+GR+ +I+R+ QIL RRTKNNP L+GE GVGKTAIAEGLA
Sbjct: 255 LEEYGTNLTKLAEEGKLDPVVGRQPQIERVTQILGRRTKNNPCLIGEPGVGKTAIAEGLA 314

Query: 333 IRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVH 392
            RI   +VP  +  K++++LDMGLL+AG K RGE E R+  L+ EI++S D+ILFIDEVH
Sbjct: 315 QRIANGDVPETIEGKKVITLDMGLLVAGTKYRGEFEERLKKLMEEIKQSDDIILFIDEVH 374

Query: 393 TLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPV 452
           TLIG+G          +D +N+LKP+L RGELQCI +TT DE+R   EKD  L RRFQPV
Sbjct: 375 TLIGAGAA-----EGAIDAANILKPALARGELQCIGATTLDEYRKHIEKDPDLERRFQPV 429

Query: 453 LISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDE 512
            + EP+ ++ ++IL GLRE+YE HH  ++T EA+ AA  LS +YISDR+LPDKAIDLVDE
Sbjct: 430 KVPEPTVDETIQILKGLRERYEIHHKLRYTDEALIAAAQLSYQYISDRFLPDKAIDLVDE 489

Query: 513 AGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRT-VQAMHEVVQGS--------RLKYDD 563
           AGSR  +         Q   L +   +  +E+R  V+   E V+          R K  D
Sbjct: 490 AGSRVRL---------QHAQLPEEAKELDKEVRKIVKEKEEYVRNQDFEKAGELRDKEMD 540

Query: 564 VVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGL 623
           + A +    E   E S       DE  +V   DI  + S W+GIPV +++ADE   L+ +
Sbjct: 541 LKAQISALIEKGKEMSKAETETADEGPIVTEVDIQHIVSSWTGIPVDKVSADESDRLLKM 600

Query: 624 EEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY 683
           E+ L KR+IGQDEAV AISRA++R+RVGLK+PNRP A+ +F GPTGVGK+ELAK+LAA Y
Sbjct: 601 EDTLHKRIIGQDEAVQAISRAIRRARVGLKNPNRPIASFIFSGPTGVGKSELAKALAAYY 660

Query: 684 FGS 686
           FGS
Sbjct: 661 FGS 663

Molecular chaperone tha may interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Pisum sativum (taxid: 3888)

>sp|P31541|CLPAA_SOLLC ATP-dependent Clp protease ATP-binding subunit clpA homolog CD4A, chloroplastic OS=Solanum lycopersicum GN=CD4A PE=3 SV=1

 Score =  468 bits (1204), Expect = e-131,   Method: Compositional matrix adjust.
 Identities = 282/625 (45%), Positives = 388/625 (62%), Gaps = 57/625 (9%)

Query: 74  KIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH-PNGFLES-G 131
           + +P  ++FERFTE+A+K ++ +Q EA+ LG + V T+ +LLGLI E        L+S G
Sbjct: 87  RFVP-KAMFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLGLIGEGTGIAAKVLKSMG 145

Query: 132 ITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGY 191
           I +  AR  V  I              +G  F  A ++PF+   KRV E ++E +R  G+
Sbjct: 146 INLKDARVEVEKII------------GRGSGFI-AVEIPFTPRAKRVLELSLEEARQLGH 192

Query: 192 NFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVR 251
           N+I  EH+ LGL    +G A RVL+ LG D  ++    V R+ GE        S A G  
Sbjct: 193 NYIGSEHLLLGLLREGEGVAARVLENLGADPTNIR-TQVIRMVGE-------SSEAVGA- 243

Query: 252 ENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTK 311
             S+ G T+ LK P       LE++  +LT  A E  +DPV+GR+ +I+R+ QIL RRTK
Sbjct: 244 --SVGGGTSGLKMP------TLEEYGTNLTKLAEEGKLDPVVGRQAQIERVTQILGRRTK 295

Query: 312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARV 371
           NNP L+GE GVGKTAIAEGLA RI   +VP  +  K++++LDMGLL+AG K RGE E R+
Sbjct: 296 NNPCLIGEPGVGKTAIAEGLAQRIANGDVPETIEGKKVITLDMGLLVAGTKYRGEFEERL 355

Query: 372 TTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT 431
             L+ EI++S ++ILFIDEVHTLIG+G          +D +N+LKP+L RGELQCI +TT
Sbjct: 356 KKLMEEIKQSDEIILFIDEVHTLIGAGAA-----EGAIDAANILKPALARGELQCIGATT 410

Query: 432 QDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH 491
            DE+R   EKD AL RRFQPV + EPS ++ ++IL GLRE+YE HH   +T EAI AA  
Sbjct: 411 LDEYRKHIEKDPALERRFQPVKVPEPSVDETIQILKGLRERYEIHHKLHYTDEAIEAAAK 470

Query: 492 LSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTV-QAM 550
           LS +YISDR+LPDKAIDL+DEAGSR  +         +   L +   +  +E+R + +  
Sbjct: 471 LSHQYISDRFLPDKAIDLIDEAGSRVRL---------RHAQLPEEARELEKELRQITKEK 521

Query: 551 HEVVQGSRLKY-----DDVVASMGDTSEIVVESSLPSASDDDEPAVVGP----DDIAAVA 601
           +E V+G   +      D  +      S ++ ++   S ++ +     GP     DI  + 
Sbjct: 522 NEAVRGQDFEKAGELRDREMDLKAQISALIDKNKEKSKAESEAGDAAGPIVTEADIQHIV 581

Query: 602 SLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAA 661
           S W+GIPV++++ DE   L+ +EE L  RVIGQDEAV AISRA++R+RVGLK+PNRP A+
Sbjct: 582 SSWTGIPVEKVSTDESDRLLKMEETLHTRVIGQDEAVKAISRAIRRARVGLKNPNRPIAS 641

Query: 662 MLFCGPTGVGKTELAKSLAACYFGS 686
            +F GPTGVGK+ELAKSLA  YFGS
Sbjct: 642 FIFSGPTGVGKSELAKSLATYYFGS 666

May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Solanum lycopersicum (taxid: 4081)

>sp|O78410|CLPC_GUITH ATP-dependent Clp protease ATP-binding subunit clpA homolog OS=Guillardia theta GN=clpC PE=3 SV=1

 Score =  467 bits (1201), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 269/612 (43%), Positives = 378/612 (61%), Gaps = 52/612 (8%)

Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH-PNGFLES-GITIDKAR 138
           +FERFTE+A+K ++ +Q EA+ LG + V T+ +LLGLI E        L+S G+ +  AR
Sbjct: 1   MFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLGLIGEGTGIAAKVLKSMGVNLKDAR 60

Query: 139 EAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEH 198
             V  I              +G  F  A ++PF+   KRV E ++E +R  G+N+I  EH
Sbjct: 61  VEVEKII------------GRGSGFV-AVEIPFTPRAKRVLELSLEEARQLGHNYIGTEH 107

Query: 199 IALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGK 258
           + LGL    +G A RVL+ L +D+  +    V RL G+ A+             ++ +G+
Sbjct: 108 LLLGLIREGEGVAARVLENLALDLTKVRT-QVIRLLGDTAEV------------SATNGQ 154

Query: 259 TAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLG 318
           T   K+P       LE+F  +LT +A+E  +DPVIGR+ EI+R+IQIL RRTKNNPIL+G
Sbjct: 155 TKG-KTP------TLEEFGSNLTQKAAEGKLDPVIGRQKEIERVIQILGRRTKNNPILIG 207

Query: 319 ESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEI 378
           E GVGKTAIAEGLA RI   +VP  L  KR+++LD+GLL+AG K RGE E R+  +I EI
Sbjct: 208 EPGVGKTAIAEGLAQRINNRDVPDILEDKRVVTLDIGLLVAGTKYRGEFEERLKKIIDEI 267

Query: 379 QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQ 438
           + + +VIL IDEVHTLIG+G          +D +N+LKP+L RGE+QCI +TT +E+R  
Sbjct: 268 RVANNVILVIDEVHTLIGAGAA-----EGAIDAANILKPALARGEMQCIGATTLEEYRKH 322

Query: 439 FEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS 498
            EKD AL RRFQPV++ EPS E+ + IL GLR++YE HH    + EA++AA   + +YI+
Sbjct: 323 IEKDSALERRFQPVMVGEPSVEETIEILYGLRDRYEKHHKLVISDEALSAAAKFADQYIA 382

Query: 499 DRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSR 558
           DR+LPDKAIDL+DEAGSR       R    Q    ++  D   +EI  ++   E V+   
Sbjct: 383 DRFLPDKAIDLIDEAGSRV------RLMNSQLPPAARELDKELREI--LKQKDEAVRSQD 434

Query: 559 L----KYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITA 614
                +  D    +      +  S      +  E +VV  +DIA + + W+GIPV ++T 
Sbjct: 435 FETAGQLRDREMEIKAQIAAIAHSKKGDEENTKEVSVVTEEDIAQIVAAWTGIPVNKMTR 494

Query: 615 DERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTE 674
            E   L+ +EE L  R+IGQDEAV A+S+A++R+RVGLK+PNRP A+ +F GPTGVGKTE
Sbjct: 495 SESEKLLQMEETLHGRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFIFSGPTGVGKTE 554

Query: 675 LAKSLAACYFGS 686
           L K+LA+ +FGS
Sbjct: 555 LTKALASYFFGS 566

May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Guillardia theta (taxid: 55529)

>sp|Q1XDF4|CLPC_PORYE ATP-dependent Clp protease ATP-binding subunit clpA homolog OS=Porphyra yezoensis GN=clpC PE=3 SV=1

 Score =  465 bits (1197), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 267/613 (43%), Positives = 376/613 (61%), Gaps = 51/613 (8%)

Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +FERFTE+A+K ++ +Q EA+ LG + V T+ +LLGL+ E         +GI     +  
Sbjct: 1   MFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLGLVGEG--------TGIAAQVLKSM 52

Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
            V++  +    + +    +G  F  A ++PF+   KRV E ++E +R  G+N+I  EH+ 
Sbjct: 53  NVNLKDA--RVEVEKIIGRGSGFV-AVEIPFTPRAKRVLELSLEEARQLGHNYIGTEHLL 109

Query: 201 LGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTA 260
           +GL    +G A RVL+ L VDV+ + A  +  L GE A             E ++SG   
Sbjct: 110 MGLVREGEGVAARVLENLAVDVSSIRAEVIQML-GENA-------------EANVSGSNT 155

Query: 261 ALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGES 320
              +  R++   LE+F  +LT  A E  +DPV+GR+ EI+R+IQIL RRTKNNP+L+GE 
Sbjct: 156 ---TQARSKTPTLEEFGSNLTQMAMEGGLDPVVGRQKEIERVIQILGRRTKNNPVLIGEP 212

Query: 321 GVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK 380
           GVGKTAIAEGLA RI   +VP  L  K +++LD+GLL+AG K RGE E R+  ++ EI+ 
Sbjct: 213 GVGKTAIAEGLAQRIANRDVPSILEDKLVITLDVGLLVAGTKYRGEFEERLKRIMDEIKS 272

Query: 381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFE 440
           + +VIL IDEVHTLIG+G          +D +NLLKP+L RGELQCI +TT +E+R   E
Sbjct: 273 ADNVILVIDEVHTLIGAGAA-----EGAIDAANLLKPALARGELQCIGATTLEEYRKHIE 327

Query: 441 KDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDR 500
           KD AL RRFQPV++ EPS E+ + IL GLR++YE HH    +  A+ AA   + +YISDR
Sbjct: 328 KDPALERRFQPVVVGEPSVEETIEILFGLRDRYEKHHQLTMSDGALAAAAKYANQYISDR 387

Query: 501 YLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTV-QAMHEVVQGSRL 559
           +LPDKAIDL+DEAGSR  +             L     +  +E+R V +   E ++    
Sbjct: 388 FLPDKAIDLIDEAGSRVRL---------LNSQLPPAARELDKELRAVLKTKDEAIRAQ-- 436

Query: 560 KYDDVVASMGDTSEIVVESSLPSASDDDEP------AVVGPDDIAAVASLWSGIPVQQIT 613
           KY+          EI  + +  + S  +EP       VV  DDIA + + W+GIPV ++T
Sbjct: 437 KYETAEQYRAREMEIKAQIAAIAQSKKNEPDLNLEDPVVTEDDIAEIVAAWTGIPVTKLT 496

Query: 614 ADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKT 673
             E   L+ +EE L  R+IGQDEAV A+SRA++R+RVGLK+PNRP A+ +F GPTGVGKT
Sbjct: 497 KSESEKLMHMEETLHGRIIGQDEAVVAVSRAIRRARVGLKNPNRPIASFIFSGPTGVGKT 556

Query: 674 ELAKSLAACYFGS 686
           EL K+LA+ +FGS
Sbjct: 557 ELTKALASYFFGS 569

May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Porphyra yezoensis (taxid: 2788)

>sp|Q9FI56|CLPC1_ARATH Chaperone protein ClpC1, chloroplastic OS=Arabidopsis thaliana GN=CLPC1 PE=1 SV=1

 Score =  465 bits (1196), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 282/647 (43%), Positives = 396/647 (61%), Gaps = 61/647 (9%)

Query: 51  QFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFT 110
           Q FHS      N      +R       + ++FERFTE+A+K ++ +Q EA+ LG + V T
Sbjct: 69  QDFHSKVRQAMNVPKGKASR-----FTVKAMFERFTEKAIKVIMLAQEEARRLGHNFVGT 123

Query: 111 QHLLLGLIAEDRH-PNGFLES-GITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAK 168
           + +LLGLI E        L+S GI +  AR  V  I              +G  F  A +
Sbjct: 124 EQILLGLIGEGTGIAAKVLKSMGINLKDARVEVEKII------------GRGSGFV-AVE 170

Query: 169 MPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAV 228
           +PF+   KRV E ++E +R  G+N+I  EH+ LGL    +G A RVL+ LG D +++   
Sbjct: 171 IPFTPRAKRVLELSLEEARQLGHNYIGSEHLLLGLLREGEGVAARVLENLGADPSNIR-T 229

Query: 229 AVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEEL 288
            V R+ GE             V  N + G +++ K P       LE++  +LT  A E  
Sbjct: 230 QVIRMVGE----------NNEVTAN-VGGGSSSNKMP------TLEEYGTNLTKLAEEGK 272

Query: 289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKR 348
           +DPV+GR+ +I+R++QIL RRTKNNP L+GE GVGKTAIAEGLA RI   +VP  +  K+
Sbjct: 273 LDPVVGRQPQIERVVQILGRRTKNNPCLIGEPGVGKTAIAEGLAQRIASGDVPETIEGKK 332

Query: 349 IMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTG 408
           +++LDMGLL+AG K RGE E R+  L+ EI++S ++ILFIDEVHTLIG+G          
Sbjct: 333 VITLDMGLLVAGTKYRGEFEERLKKLMEEIRQSDEIILFIDEVHTLIGAGAA-----EGA 387

Query: 409 LDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLG 468
           +D +N+LKP+L RGELQCI +TT DE+R   EKD AL RRFQPV + EP+ ++ ++IL G
Sbjct: 388 IDAANILKPALARGELQCIGATTLDEYRKHIEKDPALERRFQPVKVPEPTVDETIQILKG 447

Query: 469 LREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQ 528
           LRE+YE HH  ++T E++ AA  LS +YISDR+LPDKAIDL+DEAGSR  +   +  +E 
Sbjct: 448 LRERYEIHHKLRYTDESLVAAAQLSYQYISDRFLPDKAIDLIDEAGSRVRLRHAQVPEEA 507

Query: 529 QTCILSKPPDDYWQEIRTV-QAMHEVVQGSRLKY-----DDVVASMGDTSEIVV---ESS 579
           +         +  +E+R + +  +E V+G   +      D  +    + S I     E S
Sbjct: 508 R---------ELEKELRQITKEKNEAVRGQDFEKAGTLRDREIELRAEVSAIQAKGKEMS 558

Query: 580 LPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVA 639
              +   +E  +V   DI  + S W+GIPV++++ DE   L+ +EE L KR+IGQDEAV 
Sbjct: 559 KAESETGEEGPMVTESDIQHIVSSWTGIPVEKVSTDESDRLLKMEETLHKRIIGQDEAVK 618

Query: 640 AISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           AISRA++R+RVGLK+PNRP A+ +F GPTGVGK+ELAK+LAA YFGS
Sbjct: 619 AISRAIRRARVGLKNPNRPIASFIFSGPTGVGKSELAKALAAYYFGS 665

Molecular chaperone that hydrolyzes ATP and is associated with the chloroplast protein import apparatus. May function as the motor for chloroplast protein translocation, as translocation requires ATP hydrolysis in the stroma. May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast. Involved in the regulation of chlorophyll b biosynthesis through the destabilization of chlorophyllide a oxygenase (CAO) protein in response to the accumulation of chlorophyll b. Involved in leaf iron homeostasis.

Arabidopsis thaliana (taxid: 3702)

>sp|P51332|CLPC_PORPU ATP-dependent Clp protease ATP-binding subunit clpA homolog OS=Porphyra purpurea GN=clpC PE=3 SV=1

 Score =  464 bits (1194), Expect = e-129,   Method: Compositional matrix adjust.
 Identities = 267/613 (43%), Positives = 376/613 (61%), Gaps = 51/613 (8%)

Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +FERFTE+A+K ++ +Q EA+ LG + V T+ +LLGL+ E         +GI     +  
Sbjct: 1   MFERFTEKAIKVIMLAQEEARRLGHNFVGTEQILLGLVGEG--------TGIAAQVLKSM 52

Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
            V++  +    + +    +G  F  A ++PF+   KRV E ++E +R  G+N+I  EH+ 
Sbjct: 53  NVNLKDA--RVEVEKIIGRGSGFV-AVEIPFTPRAKRVLELSLEEARQLGHNYIGTEHLL 109

Query: 201 LGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTA 260
           +GL    +G A RVL+ L VDV+ + A  +  L GE A             E ++SG  A
Sbjct: 110 MGLVREGEGVAARVLENLAVDVSSIRAEVIQML-GENA-------------EANVSGSNA 155

Query: 261 ALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGES 320
              +  R++   LE+F  +LT  A E  +DPV+GR+ EI+R+IQIL RRTKNNP+L+GE 
Sbjct: 156 ---TQARSKTPTLEEFGSNLTQMAIEGGLDPVVGRQKEIERVIQILGRRTKNNPVLIGEP 212

Query: 321 GVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK 380
           GVGKTAIAEGLA RI   +VP  L  K +++LD+GLL+AG K RGE E R+  ++ EI+ 
Sbjct: 213 GVGKTAIAEGLAQRIANRDVPSILEDKLVITLDVGLLVAGTKYRGEFEERLKRIMDEIKS 272

Query: 381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFE 440
           + +VIL IDEVHTLIG+G          +D +NLLKP+L RGELQCI +TT +E+R   E
Sbjct: 273 ADNVILVIDEVHTLIGAGAA-----EGAIDAANLLKPALARGELQCIGATTLEEYRKHIE 327

Query: 441 KDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDR 500
           KD AL RRF PV++ EPS E+ + IL GLR++YE HH    +  A+ AA   + +YISDR
Sbjct: 328 KDPALERRFHPVVVGEPSVEETIEILFGLRDRYEKHHQLTMSDGALAAAAKYANQYISDR 387

Query: 501 YLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTV-QAMHEVVQGSRL 559
           +LPDKAIDL+DEAGSR  +             L     +  +E+R V +   E ++    
Sbjct: 388 FLPDKAIDLIDEAGSRVRL---------LNSQLPPAARELDKELRAVLKTKDEAIRAQ-- 436

Query: 560 KYDDVVASMGDTSEIVVESSLPSASDDDEP------AVVGPDDIAAVASLWSGIPVQQIT 613
           KY+          EI  + +  + S  +EP       VV  DDIA + + W+GIPV ++T
Sbjct: 437 KYETAEQYRAREMEIKAQIAAIAQSKKNEPDLNLEDPVVTEDDIAEIVAAWTGIPVTKLT 496

Query: 614 ADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKT 673
             E   L+ +EE L  R+IGQDEAV A+SRA++R+RVGLK+PNRP A+ +F GPTGVGKT
Sbjct: 497 KSESEKLMQMEETLHGRIIGQDEAVIAVSRAIRRARVGLKNPNRPIASFIFSGPTGVGKT 556

Query: 674 ELAKSLAACYFGS 686
           EL K+LA+ +FGS
Sbjct: 557 ELTKALASYFFGS 569

May interact with a clpP-like protease involved in degradation of denatured proteins in the chloroplast.

Porphyra purpurea (taxid: 2787)

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	710
224119914	948	predicted protein [Populus trichocarpa]	0.908	0.680	0.745	0.0
387169509	946	hypothetical protein 11M19.14 [Arabidops	0.904	0.678	0.741	0.0
297792419	946	hypothetical protein ARALYDRAFT_495173 [	0.904	0.678	0.734	0.0
387169538	943	hypothetical protein 7G9.17 [Boechera st	0.904	0.680	0.738	0.0
312282443	950	unnamed protein product [Thellungiella h	0.956	0.714	0.699	0.0
255539981	946	ERD1 protein, chloroplast precursor, put	0.898	0.674	0.731	0.0
18423233	945	ERD1 protein [Arabidopsis thaliana] gi|1	0.904	0.679	0.736	0.0
387169561	945	hypothetical protein 34G24.25 [Capsella	0.904	0.679	0.730	0.0
359493969	946	PREDICTED: chaperone protein ClpD, chlor	0.887	0.665	0.735	0.0
224134250	939	predicted protein [Populus trichocarpa]	0.890	0.673	0.724	0.0

>gi|224119914|ref|XP_002318194.1| predicted protein [Populus trichocarpa] gi|222858867|gb|EEE96414.1| predicted protein [Populus trichocarpa]

 Score =  978 bits (2527), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 488/655 (74%), Positives = 562/655 (85%), Gaps = 10/655 (1%)

Query: 35  NPMSSFFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVI 94
           +P SS F IS IS K Q   +      N+       K+R+I+ +S+VFERFTERA+KAV+
Sbjct: 42  SPFSSCFGIS-ISQKHQNRKTLLLKRFNSS------KKRRILQVSAVFERFTERAIKAVV 94

Query: 95  FSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWH-STNNQDT 153
           FSQREA++LGKDMVFTQHLLLGLI EDR PNGFL SGI IDKARE V SIW   +++ + 
Sbjct: 95  FSQREARALGKDMVFTQHLLLGLIIEDRDPNGFLGSGIKIDKAREVVKSIWQRESDSAEA 154

Query: 154 DDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGR 213
            +  ++G+   S + +PFS STKRVFEAA+EYSR+ G+NFIAPEHIA+GLFTVDDGSAGR
Sbjct: 155 SELVSKGERGVSHSDVPFSASTKRVFEAAIEYSRTMGHNFIAPEHIAIGLFTVDDGSAGR 214

Query: 214 VLKRLGVDVNHLAAVAVSRLQGELAKEGREPSL-AKGVRENSISGKTAALKSPGRTR-AS 271
           VL RLGVD + LAA+A+++LQGEL K+GREPS+ +KG    S+S + AAL+S  +T+  S
Sbjct: 215 VLNRLGVDGDALAAIAITKLQGELVKDGREPSVESKGKHGKSVSKRAAALRSYEKTKEKS 274

Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           AL QFCVDLTARASE  IDPVIGR +EI+RI+QILCRRTKNNPILLGESGVGKTAIAEGL
Sbjct: 275 ALAQFCVDLTARASEGRIDPVIGRHSEIERIVQILCRRTKNNPILLGESGVGKTAIAEGL 334

Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEV 391
           AI+I QA++PVFLL KR+MSLD+GLL+AGAKERGELEARVT+LI EIQK GDVILFIDEV
Sbjct: 335 AIKIAQADIPVFLLEKRVMSLDVGLLIAGAKERGELEARVTSLIREIQKEGDVILFIDEV 394

Query: 392 HTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQP 451
           HTL+G+GTVGRGNKG+GLDI+N+LKPSLGRGELQCIASTT DE+RT FE DKALARRFQP
Sbjct: 395 HTLVGTGTVGRGNKGSGLDIANILKPSLGRGELQCIASTTLDEYRTHFEIDKALARRFQP 454

Query: 452 VLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVD 511
           VLI+EPSQEDA+RILLGLR++YEAHHNC+FT EAINAAVHLSARYI+DRYLPDKAIDL+D
Sbjct: 455 VLINEPSQEDAIRILLGLRQRYEAHHNCRFTPEAINAAVHLSARYIADRYLPDKAIDLID 514

Query: 512 EAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDT 571
           EAGSRA IE ++RKKEQQT ILSK PDDYWQEIRTVQAMHEVV  SRL  D  ++SM  +
Sbjct: 515 EAGSRARIEAYRRKKEQQTFILSKTPDDYWQEIRTVQAMHEVVLASRLANDCSLSSMDGS 574

Query: 572 SEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRV 631
            EI +ESSLP AS+ DEPAVVGPDDIAAVASLWSGIPVQQ+TADER  LVGLEE+L+KRV
Sbjct: 575 GEITIESSLPPASNADEPAVVGPDDIAAVASLWSGIPVQQLTADERKFLVGLEEELRKRV 634

Query: 632 IGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           IGQDEAVAAISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LA  YFGS
Sbjct: 635 IGQDEAVAAISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALARNYFGS 689

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|387169509|gb|AFJ66170.1| hypothetical protein 11M19.14 [Arabidopsis halleri]

 Score =  968 bits (2503), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 481/649 (74%), Positives = 549/649 (84%), Gaps = 7/649 (1%)

Query: 40  FFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQRE 99
           +  IS+ +  +  F S  T    N      RKR+K  PIS+VFERFTERA++A+IFSQ+E
Sbjct: 42  YLGISLSNRTIHRFSSTPT----NFRRFPQRKRKKFTPISAVFERFTERAIRAIIFSQKE 97

Query: 100 AKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ 159
           AKSLGKDMV+TQHLLLGLIAEDR P GFL SGITIDKAREAV SIW   N+ D+      
Sbjct: 98  AKSLGKDMVYTQHLLLGLIAEDRDPQGFLGSGITIDKAREAVWSIWDEANS-DSKQEEVS 156

Query: 160 GKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLG 219
              +S +  MPFSISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG
Sbjct: 157 STSYSKSTDMPFSISTKRVFEAAVEYSRTMDCQYIAPEHIAVGLFTVDDGSAGRVLKRLG 216

Query: 220 VDVNHLAAVAVSRLQGELAKEGREPSLA-KGVRENSISGKTAALKSPGRTRA-SALEQFC 277
            ++N L A A++RL+GE+AK+GREPS + KG  E   SG+     + G+ +A + LEQFC
Sbjct: 217 ANMNLLTAAALTRLKGEIAKDGREPSSSSKGSYEAPPSGRIVGSGTGGKAKAKTVLEQFC 276

Query: 278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ 337
           VDLTARASE LIDPVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +
Sbjct: 277 VDLTARASEGLIDPVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAE 336

Query: 338 AEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGS 397
           A+ P FLL+KRIMSLD+GLLMAGAKERGELEARVT LISE++KSG VILFIDEVHTLIGS
Sbjct: 337 AKAPGFLLTKRIMSLDIGLLMAGAKERGELEARVTALISEVKKSGKVILFIDEVHTLIGS 396

Query: 398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEP 457
           GTVGRGNKG+GLDI+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI+EP
Sbjct: 397 GTVGRGNKGSGLDIANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLINEP 456

Query: 458 SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA 517
           S+EDAV+ILLGLREKYEAHHNCK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA
Sbjct: 457 SEEDAVKILLGLREKYEAHHNCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRA 516

Query: 518 HIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE 577
            IE F++KKE   CILSKPP+DYWQEI+TVQAMHEVV  SR K DD  A   ++ E+V E
Sbjct: 517 RIEAFRKKKEDAICILSKPPNDYWQEIKTVQAMHEVVLSSRQKQDDGDAIADESGELVEE 576

Query: 578 SSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA 637
           SSLP AS DDEP +VGPDDIAAVAS WSGIPVQQITADERMLL+GLE+QL+ RV+GQDEA
Sbjct: 577 SSLPPASGDDEPILVGPDDIAAVASAWSGIPVQQITADERMLLMGLEDQLRSRVVGQDEA 636

Query: 638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           VAAISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 637 VAAISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALAANYFGS 685

Source: Arabidopsis halleri

Species: Arabidopsis halleri

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297792419|ref|XP_002864094.1| hypothetical protein ARALYDRAFT_495173 [Arabidopsis lyrata subsp. lyrata] gi|297309929|gb|EFH40353.1| hypothetical protein ARALYDRAFT_495173 [Arabidopsis lyrata subsp. lyrata]

 Score =  961 bits (2485), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 477/649 (73%), Positives = 548/649 (84%), Gaps = 7/649 (1%)

Query: 40  FFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQRE 99
           +  IS+ +  +  F +  T           RKR+K  PIS+VFERFTERA++A+IFSQ+E
Sbjct: 42  YLGISLSNRTIHRFSTTPTKFRR----FPQRKRKKFTPISAVFERFTERAIRAIIFSQKE 97

Query: 100 AKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ 159
           AKSLGKDMV+TQHLLLGLIAEDR P GFL SGITIDKAREAV SIW   N+ D+      
Sbjct: 98  AKSLGKDMVYTQHLLLGLIAEDRDPQGFLGSGITIDKAREAVWSIWDEANS-DSKQEEVS 156

Query: 160 GKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLG 219
              +S +  MPFSISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG
Sbjct: 157 STSYSKSTDMPFSISTKRVFEAAVEYSRTMDCQYIAPEHIAVGLFTVDDGSAGRVLKRLG 216

Query: 220 VDVNHLAAVAVSRLQGELAKEGREPSLA-KGVRENSISGKTAALKSPGRTRA-SALEQFC 277
            ++N L A A++RL+GE+AK+GREPS + KG  +   +G+ A   + G+ +A + LEQFC
Sbjct: 217 ANMNLLTAAALTRLKGEIAKDGREPSSSSKGSFQAPPAGRIAGSGTGGKAKAKNVLEQFC 276

Query: 278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ 337
           VDLTARASE LIDPVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +
Sbjct: 277 VDLTARASEGLIDPVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAE 336

Query: 338 AEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGS 397
           A  P FLL+KRIMSLD+GLLMAGAKERGELEARVT LISE++KSG VILFIDEVHTLIGS
Sbjct: 337 ANAPGFLLTKRIMSLDIGLLMAGAKERGELEARVTALISEVKKSGKVILFIDEVHTLIGS 396

Query: 398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEP 457
           GTVGRGNKG+GLDI+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI+EP
Sbjct: 397 GTVGRGNKGSGLDIANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLINEP 456

Query: 458 SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA 517
           S+EDAV+ILLGLREKYEAHHNCK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA
Sbjct: 457 SEEDAVKILLGLREKYEAHHNCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRA 516

Query: 518 HIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE 577
            IE F++KKE   CILSKPP+DYWQEI+TVQAMHEVV  SR K DD  A   ++ E+V E
Sbjct: 517 RIEAFRKKKEDAICILSKPPNDYWQEIKTVQAMHEVVLSSRQKQDDGDAIADESGELVEE 576

Query: 578 SSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA 637
           SSLP A+ DDEP +VGPDDIAAVAS WSGIPVQQITADERMLL+GLE+QL+ RV+GQDEA
Sbjct: 577 SSLPPAAGDDEPILVGPDDIAAVASAWSGIPVQQITADERMLLMGLEDQLRSRVVGQDEA 636

Query: 638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           VAAISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 637 VAAISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALAANYFGS 685

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|387169538|gb|AFJ66198.1| hypothetical protein 7G9.17 [Boechera stricta]

 Score =  961 bits (2483), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 479/649 (73%), Positives = 546/649 (84%), Gaps = 7/649 (1%)

Query: 40  FFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQRE 99
           +  IS+ +  +  F    ++   N      RKR+K  PIS+VFERFTERA++A+IFSQ+E
Sbjct: 43  YLGISLSNRTIHRF----STTPANFRRFPGRKRKKFTPISAVFERFTERAIRAIIFSQKE 98

Query: 100 AKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ 159
           AKSLGKDMV+TQHLLLGLIAEDR P GFL SGITIDKAREAV SIW   N  D+      
Sbjct: 99  AKSLGKDMVYTQHLLLGLIAEDRDPQGFLGSGITIDKAREAVWSIWDEAN-PDSKQEEVS 157

Query: 160 GKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLG 219
              +S +  MPFSISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG
Sbjct: 158 STSYSKSTDMPFSISTKRVFEAAVEYSRTMECQYIAPEHIAVGLFTVDDGSAGRVLKRLG 217

Query: 220 VDVNHLAAVAVSRLQGELAKEGREPSLA-KGVRENSISGKTAALKSPGRTRA-SALEQFC 277
            ++N L A A++RL+GE+AK+GREPS + K   + S +G+ A   + G+T+A S LEQFC
Sbjct: 218 ANMNLLTAAALTRLKGEMAKDGREPSSSSKRSFDASPNGRIAGSGTGGKTKAKSVLEQFC 277

Query: 278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ 337
           VDLTARASE LIDPVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +
Sbjct: 278 VDLTARASEGLIDPVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAE 337

Query: 338 AEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGS 397
           A  P FLL+KRIMSLD+GLLMAGAKERGELEARVT LISE++KSG VILFIDEVHTLIGS
Sbjct: 338 AYAPGFLLTKRIMSLDIGLLMAGAKERGELEARVTALISEVKKSGKVILFIDEVHTLIGS 397

Query: 398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEP 457
           GTVGRGNKG+GLDI+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI EP
Sbjct: 398 GTVGRGNKGSGLDIANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLIDEP 457

Query: 458 SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA 517
           S+EDAV+ILLGLREKYE HHNCK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA
Sbjct: 458 SEEDAVKILLGLREKYEVHHNCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRA 517

Query: 518 HIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE 577
            IE F++KKE   CILSKPPDDYWQEIRTVQAMHEVV  SR K DD  A   ++ E+V E
Sbjct: 518 RIEAFRKKKEDAVCILSKPPDDYWQEIRTVQAMHEVVLSSRQKQDDGDAIADESGELVEE 577

Query: 578 SSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA 637
           SSLP  + DDEP +VGPDDIAAVAS WSGIPVQQITADERMLL+GLEEQL+ RV+GQDEA
Sbjct: 578 SSLPPIAGDDEPILVGPDDIAAVASAWSGIPVQQITADERMLLMGLEEQLRSRVVGQDEA 637

Query: 638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           VAAISRAVKRSRVGLKDP+RP +AMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 638 VAAISRAVKRSRVGLKDPDRPISAMLFCGPTGVGKTELTKALAANYFGS 686

Source: Boechera stricta

Species: Boechera stricta

Genus: Boechera

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|312282443|dbj|BAJ34087.1| unnamed protein product [Thellungiella halophila]

 Score =  959 bits (2479), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 487/696 (69%), Positives = 573/696 (82%), Gaps = 17/696 (2%)

Query: 1   MEV-STCSPLSVNSRCLFAN-----QPPPPRHRLPPLQYVNPMSSFFNISMISHKVQFFH 54
           MEV +T SPL+++SR L ++         P          +  SS+  IS+ +  +  F 
Sbjct: 1   MEVLTTSSPLTLHSRRLASSSAHRFDSSSPVASFAASSLSSFASSYLGISLSNRTIHRF- 59

Query: 55  SNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLL 114
           S   SN     P   ++R+K  PIS+VFERFTERA++A+IFSQ+EAKSLGKDMV+TQHLL
Sbjct: 60  STSPSNFRRFPP---KRRKKFTPISAVFERFTERAIRAIIFSQKEAKSLGKDMVYTQHLL 116

Query: 115 LGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ---GKPFSSAAKMPF 171
           LGLIAEDR P GFL SGITIDKAREAV SIW   N+ D++ +  Q      +S +  MPF
Sbjct: 117 LGLIAEDRDPQGFLGSGITIDKAREAVWSIWEEANS-DSNSSKQQEESSTSYSKSTDMPF 175

Query: 172 SISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVS 231
           SISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG ++N L A A++
Sbjct: 176 SISTKRVFEAAVEYSRTLDCQYIAPEHIAVGLFTVDDGSAGRVLKRLGANLNLLTAAALT 235

Query: 232 RLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRA-SALEQFCVDLTARASEELID 290
           R++GE+AK+GRE  L++  ++ S +G+ A   S GRT+A S LEQFCVDLTARASE LID
Sbjct: 236 RIKGEMAKDGRE--LSQSSKDASTNGRIAGPGSAGRTKAKSVLEQFCVDLTARASEGLID 293

Query: 291 PVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM 350
           PVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +A+ P FLL+KRIM
Sbjct: 294 PVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAEAKAPGFLLTKRIM 353

Query: 351 SLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLD 410
           SLD+GLLMAGAKERGELE+RVT LISE++KSG VILFIDEVHTLIGSGTVGRGNKG+GLD
Sbjct: 354 SLDIGLLMAGAKERGELESRVTALISEVKKSGKVILFIDEVHTLIGSGTVGRGNKGSGLD 413

Query: 411 ISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLR 470
           I+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI EPS+EDAV+ILLGLR
Sbjct: 414 IANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLIDEPSEEDAVKILLGLR 473

Query: 471 EKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQT 530
           EKYEAHH+CK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA IE F++KKE  T
Sbjct: 474 EKYEAHHHCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRARIEAFRKKKEDAT 533

Query: 531 CILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPA 590
           CILSKPP+DYWQEI+TVQAMHEVV  SR K DD  A   ++ E+  ESSLP  ++D+EP 
Sbjct: 534 CILSKPPNDYWQEIKTVQAMHEVVLSSRQKQDDGDAVADESGELAEESSLPPVAEDEEPI 593

Query: 591 VVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRV 650
           +VGPDDIAAVAS WSGIPVQQ+TADERMLL+GLEEQL+ RV+GQD+AV AISRAVKRSRV
Sbjct: 594 LVGPDDIAAVASAWSGIPVQQVTADERMLLMGLEEQLRSRVVGQDDAVVAISRAVKRSRV 653

Query: 651 GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           GLKDP+RP AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 654 GLKDPDRPIAAMLFCGPTGVGKTELTKALAANYFGS 689

Source: Thellungiella halophila

Species: Eutrema halophilum

Genus: Eutrema

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255539981|ref|XP_002511055.1| ERD1 protein, chloroplast precursor, putative [Ricinus communis] gi|223550170|gb|EEF51657.1| ERD1 protein, chloroplast precursor, putative [Ricinus communis]

 Score =  958 bits (2476), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 484/662 (73%), Positives = 551/662 (83%), Gaps = 24/662 (3%)

Query: 48  HKVQFFHSNYT--SNNNNC---------NPI------CARKRRK--IIPISSVFERFTER 88
           H +  FH N T  S  ++C         NP+      C++ RRK  I+PISSVFERFTER
Sbjct: 27  HPLLTFHCNNTVASAYSSCFGISISYRRNPLNSLSFKCSKSRRKRRILPISSVFERFTER 86

Query: 89  AVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHST 148
           A+K VIFSQREA++LGKDMVFTQHLLLGLI EDR P+GFL SGI IDKARE V +IW S 
Sbjct: 87  AIKVVIFSQREARALGKDMVFTQHLLLGLIGEDRDPDGFLGSGIKIDKAREIVQNIWSSD 146

Query: 149 NN--QDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTV 206
            +    +  +  +     SA  +PF+ISTKRVFEAAVEYSR+ GYNFIAPEHIA+GL TV
Sbjct: 147 GDGTNASGSSTGKSGGGGSATDVPFAISTKRVFEAAVEYSRTMGYNFIAPEHIAIGLLTV 206

Query: 207 DDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSL-AKGVRENSISGKTAALKSP 265
           DDGSA RVLKRLG +++ LA  AV+RLQGELAKEGREPS+ AKG RE S   K  AL S 
Sbjct: 207 DDGSASRVLKRLGANLDDLATAAVARLQGELAKEGREPSVEAKGAREKSFLKKAGALSSS 266

Query: 266 GRTRA-SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGK 324
            +TR  SAL QFCVDLTARASE LIDPVIGRETEI+RI+QILCRRTKNNPILLGESGVGK
Sbjct: 267 EQTREESALAQFCVDLTARASEGLIDPVIGRETEIERIVQILCRRTKNNPILLGESGVGK 326

Query: 325 TAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDV 384
           TAIAEGLA RI Q +VP+FL++KR+MSLDMGLL+AGAKERGELEARVT LI EI K G++
Sbjct: 327 TAIAEGLATRIAQTDVPLFLIAKRVMSLDMGLLIAGAKERGELEARVTALIKEILKEGNI 386

Query: 385 ILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKA 444
           ILFIDEVHT++G+GTVGRGNKG+GLDI+NLLKP LGRGELQCIASTT DE+R  FE DKA
Sbjct: 387 ILFIDEVHTIVGTGTVGRGNKGSGLDIANLLKPPLGRGELQCIASTTIDEYRAHFEIDKA 446

Query: 445 LARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD 504
           LARRFQPV I EPSQEDAV+ILLGLR+KYEAHHNC+FTLEAINAAV+LSARY++DRYLPD
Sbjct: 447 LARRFQPVTIDEPSQEDAVKILLGLRQKYEAHHNCRFTLEAINAAVYLSARYVADRYLPD 506

Query: 505 KAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDV 564
           KAIDL+DEAGSRA IE  K+KKEQQTCILSK PDDYWQEIRTVQAMHEVV  SR+ +D  
Sbjct: 507 KAIDLIDEAGSRARIESHKKKKEQQTCILSKSPDDYWQEIRTVQAMHEVVLASRMTHDGS 566

Query: 565 VASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLE 624
            +S  D+ EI+++S+      DDEP VVGPDDIAAVASLWSGIPVQQ+TADERM LVGL+
Sbjct: 567 ASSTDDSGEIILKST-EHVMLDDEPTVVGPDDIAAVASLWSGIPVQQLTADERMFLVGLD 625

Query: 625 EQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF 684
           ++L+KRVIGQDEAV+AIS AVKRSRVGLKDP+RP AAM+FCGPTGVGKTELAK+LAACYF
Sbjct: 626 DELRKRVIGQDEAVSAISCAVKRSRVGLKDPDRPIAAMMFCGPTGVGKTELAKALAACYF 685

Query: 685 GS 686
           GS
Sbjct: 686 GS 687

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18423233|ref|NP_568750.1| ERD1 protein [Arabidopsis thaliana] gi|1169544|sp|P42762.1|CLPD_ARATH RecName: Full=Chaperone protein ClpD, chloroplastic; AltName: Full=ATP-dependent Clp protease ATP-binding subunit ClpD homolog; AltName: Full=Casein lytic proteinase D; AltName: Full=ERD1 protein; AltName: Full=Protein EARLY RESPONSIVE TO DEHYDRATION 1; AltName: Full=Protein SENESCENCE ASSOCIATED GENE 15; Flags: Precursor gi|497629|dbj|BAA04506.1| ERD1 protein [Arabidopsis thaliana] gi|10177198|dbj|BAB10330.1| Erd1 protein precursor [Arabidopsis thaliana] gi|14334878|gb|AAK59617.1| putative ATP-dependent Clp protease ATP-binding subunit ClpD, ERD1 protein precursor [Arabidopsis thaliana] gi|22136916|gb|AAM91802.1| putative ATP-dependent Clp protease ATP-binding subunit ClpD, ERD1 protein precursor [Arabidopsis thaliana] gi|332008646|gb|AED96029.1| ERD1 protein [Arabidopsis thaliana]

 Score =  957 bits (2474), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 477/648 (73%), Positives = 545/648 (84%), Gaps = 6/648 (0%)

Query: 40  FFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQRE 99
           +  IS+ +  +  F +  T    N      RKR+K  PIS+VFERFTERA++A+IFSQ+E
Sbjct: 42  YLGISLSNRTIHRFSTTPT----NLRRFPQRKRKKFTPISAVFERFTERAIRAIIFSQKE 97

Query: 100 AKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ 159
           AKSLGKDMV+TQHLLLGLIAEDR P GFL SGITIDKAREAV SIW   N+ D+    A 
Sbjct: 98  AKSLGKDMVYTQHLLLGLIAEDRDPQGFLGSGITIDKAREAVWSIWDEANS-DSKQEEAS 156

Query: 160 GKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLG 219
              +S +  MPFSISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG
Sbjct: 157 STSYSKSTDMPFSISTKRVFEAAVEYSRTMDCQYIAPEHIAVGLFTVDDGSAGRVLKRLG 216

Query: 220 VDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSI-SGKTAALKSPGRTRASALEQFCV 278
            ++N L A A++RL+GE+AK+GREPS +      S  SG+ A     G+   + LEQFCV
Sbjct: 217 ANMNLLTAAALTRLKGEIAKDGREPSSSSKGSFESPPSGRIAGSGPGGKKAKNVLEQFCV 276

Query: 279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQA 338
           DLTARASE LIDPVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +A
Sbjct: 277 DLTARASEGLIDPVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAEA 336

Query: 339 EVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSG 398
             P FLL+KRIMSLD+GLLMAGAKERGELEARVT LISE++KSG VILFIDEVHTLIGSG
Sbjct: 337 SAPGFLLTKRIMSLDIGLLMAGAKERGELEARVTALISEVKKSGKVILFIDEVHTLIGSG 396

Query: 399 TVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPS 458
           TVGRGNKG+GLDI+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI+EPS
Sbjct: 397 TVGRGNKGSGLDIANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLINEPS 456

Query: 459 QEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAH 518
           +EDAV+ILLGLREKYEAHHNCK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA 
Sbjct: 457 EEDAVKILLGLREKYEAHHNCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRAR 516

Query: 519 IELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVES 578
           IE F++KKE   CILSKPP+DYWQEI+TVQAMHEVV  SR K DD  A   ++ E+V ES
Sbjct: 517 IEAFRKKKEDAICILSKPPNDYWQEIKTVQAMHEVVLSSRQKQDDGDAISDESGELVEES 576

Query: 579 SLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAV 638
           SLP A+ DDEP +VGPDDIAAVAS+WSGIPVQQITADERMLL+ LE+QL+ RV+GQDEAV
Sbjct: 577 SLPPAAGDDEPILVGPDDIAAVASVWSGIPVQQITADERMLLMSLEDQLRGRVVGQDEAV 636

Query: 639 AAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           AAISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 637 AAISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALAANYFGS 684

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|387169561|gb|AFJ66220.1| hypothetical protein 34G24.25 [Capsella rubella]

 Score =  945 bits (2443), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 474/649 (73%), Positives = 541/649 (83%), Gaps = 7/649 (1%)

Query: 40  FFNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQRE 99
           +  IS+ +  +  F    ++   N      RKR+K  PIS+VFERFTERA++A+IFSQ+E
Sbjct: 41  YLGISLSNRTIHRF----STTPANFRRFPGRKRKKFTPISAVFERFTERAIRAIIFSQKE 96

Query: 100 AKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQ 159
           AKSLGKDMV+TQHLLLGLIAEDR P GFL SGITIDKAREAV SIW   N  D+      
Sbjct: 97  AKSLGKDMVYTQHLLLGLIAEDRDPQGFLGSGITIDKAREAVWSIWDEAN-PDSKQEEVS 155

Query: 160 GKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLG 219
              +S +  MPFSISTKRVFEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG
Sbjct: 156 STSYSKSTDMPFSISTKRVFEAAVEYSRNMDCQYIAPEHIAIGLFTVDDGSAGRVLKRLG 215

Query: 220 VDVNHLAAVAVSRLQGELAKEGREPSLA-KGVRENSISGKTAALKSPGRTRA-SALEQFC 277
            ++N L A A++RL+ E+AK+GREPS + KG  + S +   A   + G+T+A + LEQFC
Sbjct: 216 ANMNLLTAAALTRLKSEMAKDGREPSSSSKGSFDASSNSGIAGSGAGGKTKAKNVLEQFC 275

Query: 278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ 337
           VDLTARASE LIDPVIGRE E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +
Sbjct: 276 VDLTARASEGLIDPVIGREKEVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAE 335

Query: 338 AEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGS 397
           A  P FLL+KRIMSLD+GLLMAGAKERGELEARVT LISE++ SG VILFIDEVHTLIGS
Sbjct: 336 ANAPGFLLTKRIMSLDIGLLMAGAKERGELEARVTALISEVKNSGKVILFIDEVHTLIGS 395

Query: 398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEP 457
           GTVGRGNKG+GLDI+NLLKPSLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI EP
Sbjct: 396 GTVGRGNKGSGLDIANLLKPSLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLIDEP 455

Query: 458 SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA 517
           S+EDAV+ILLGL+EKYEAHHNCK+T EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA
Sbjct: 456 SEEDAVKILLGLQEKYEAHHNCKYTAEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRA 515

Query: 518 HIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE 577
            IE F++KKE   CILSKPPDDYWQEIRTVQAMHEVV  SRLK D   +   ++ E+  E
Sbjct: 516 RIEAFRKKKEDAICILSKPPDDYWQEIRTVQAMHEVVLSSRLKQDGGDSIADESGELDEE 575

Query: 578 SSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA 637
           SSLP  + DDEP +VGPDDIAAVAS WSGIPVQQITADERMLL+ LEEQL+ RV+GQDEA
Sbjct: 576 SSLPPVAGDDEPILVGPDDIAAVASAWSGIPVQQITADERMLLMSLEEQLRNRVVGQDEA 635

Query: 638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           VAAISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct: 636 VAAISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALAANYFGS 684

Source: Capsella rubella

Species: Capsella rubella

Genus: Capsella

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493969|ref|XP_002283802.2| PREDICTED: chaperone protein ClpD, chloroplastic-like [Vitis vinifera] gi|147770910|emb|CAN67541.1| hypothetical protein VITISV_012383 [Vitis vinifera] gi|302142786|emb|CBI20081.3| unnamed protein product [Vitis vinifera]

 Score =  938 bits (2424), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 472/642 (73%), Positives = 543/642 (84%), Gaps = 12/642 (1%)

Query: 57  YTSNNNNCNPICARKR--------RKIIP-ISSVFERFTERAVKAVIFSQREAKSLGKDM 107
           ++S+  +C  I   +R        RK  P IS+VFERFTERA+KAVIFSQREAK+LG++M
Sbjct: 44  FSSSTCSCFGISISQRPHSHSFVFRKSSPRISAVFERFTERAIKAVIFSQREAKALGRNM 103

Query: 108 VFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGK-PFSSA 166
           VFTQHLLLGL+AEDR  +GFL SGITID AR+AV SIWH  N+          +   +S+
Sbjct: 104 VFTQHLLLGLVAEDRSLDGFLGSGITIDDARDAVRSIWHDYNDSSIISGIPSSQTSVASS 163

Query: 167 AKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLA 226
             +PFSISTKRVFEAA+EYSR+ GYNFIAPEHIA+GLFTVDDGSAGRVLKRLG +VNHLA
Sbjct: 164 TDVPFSISTKRVFEAAIEYSRTMGYNFIAPEHIAIGLFTVDDGSAGRVLKRLGANVNHLA 223

Query: 227 AVAVSRLQGELAKEGREPSLA-KGVRENSISGKTAALKSPGRTRAS-ALEQFCVDLTARA 284
           AVAVSRLQGELAK+G EPS   KG++  S SGK A +KS G+ +   AL QFCVDLTARA
Sbjct: 224 AVAVSRLQGELAKDGSEPSATFKGMQGKSFSGKAAIVKSSGKKKEKSALAQFCVDLTARA 283

Query: 285 SEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL 344
           ++ LIDPVIGR+ E+QR++QILCRRTKNNPILLGESGVGKTAIAEGLAI I +A+VP FL
Sbjct: 284 TDGLIDPVIGRDMEVQRVVQILCRRTKNNPILLGESGVGKTAIAEGLAISIAEADVPSFL 343

Query: 345 LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN 404
           L+KRIMSLD+GLLMAG KERGELEARVTTLIS+I KSG++ILFIDEVH L+GSG  GRGN
Sbjct: 344 LTKRIMSLDIGLLMAGTKERGELEARVTTLISDILKSGNIILFIDEVHMLVGSGIAGRGN 403

Query: 405 KGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVR 464
           KG+GLDI++LLKPSLGRG+LQC ASTT DE+   FEKDKALARRFQPVLI+EPSQE+AVR
Sbjct: 404 KGSGLDIASLLKPSLGRGQLQCFASTTIDEYVKLFEKDKALARRFQPVLINEPSQEEAVR 463

Query: 465 ILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKR 524
           ILLGLREKYEAHH C+FTLEAINAAVHLSARYI DR LPDKAIDL+DEAGS+A +E +KR
Sbjct: 464 ILLGLREKYEAHHKCRFTLEAINAAVHLSARYIPDRRLPDKAIDLIDEAGSKARMEAYKR 523

Query: 525 KKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSAS 584
           KKE+QT +L K PDDYWQEIR V+AMHE+V  S+LK  +  + M D S ++ ES LPS S
Sbjct: 524 KKEKQTSVLLKSPDDYWQEIRAVKAMHEMVMASKLKNCNGASCMEDGSTVLFESPLPSMS 583

Query: 585 DDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRA 644
           DD+EP VVGP++IA VASLWSGIPVQQITADERMLLVGL EQL+KRV+GQD A+A+ISRA
Sbjct: 584 DDNEPIVVGPNEIAVVASLWSGIPVQQITADERMLLVGLHEQLRKRVVGQDNAIASISRA 643

Query: 645 VKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           VKRSRVGLKDPNRP AAMLFCGPTGVGKTELAK+LAACYFGS
Sbjct: 644 VKRSRVGLKDPNRPIAAMLFCGPTGVGKTELAKALAACYFGS 685

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224134250|ref|XP_002321773.1| predicted protein [Populus trichocarpa] gi|222868769|gb|EEF05900.1| predicted protein [Populus trichocarpa]

 Score =  936 bits (2418), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 469/647 (72%), Positives = 539/647 (83%), Gaps = 15/647 (2%)

Query: 41  FNISMISHKVQFFHSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREA 100
           F IS IS ++Q   + +    N+       K+R+I+ +S+VFERF ERA+KAVIFSQREA
Sbjct: 48  FGIS-ISQRLQSKKTLFLKRFNSS------KKRRILQVSAVFERFAERAIKAVIFSQREA 100

Query: 101 KSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQG 160
            +LGKD VFTQHLLLGLI ED  P GFL SGI ID+ARE V S W S ++      +   
Sbjct: 101 IALGKDTVFTQHLLLGLIGEDCDPKGFLGSGIKIDEAREVVKSTWDSESDSVDASESVSK 160

Query: 161 KPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGV 220
           +   S + +PFSI+TKRVFE AVEYSR+ G+NFIAPEHIA+GLFTV+DG+A RVLKR GV
Sbjct: 161 ESGVSPSNVPFSINTKRVFEVAVEYSRAMGHNFIAPEHIAIGLFTVEDGNADRVLKRFGV 220

Query: 221 DVNHLAAVAVSRLQGELAKEGREPSL-AKGVRENSISGKTAALKSPGRTRASALEQFCVD 279
           D +HLAA+AV++LQGEL K+GREPS+ +KG RE S S K        +T  SAL QFCVD
Sbjct: 221 DGDHLAAIAVTKLQGELVKDGREPSVESKGKREKSFSKK-------AQTNKSALAQFCVD 273

Query: 280 LTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAE 339
           LTA+ASE LIDPVIGR +EI+RI+QILCRR KNNPILLGESGVGKTAIAEGLA  I QA+
Sbjct: 274 LTAQASEGLIDPVIGRHSEIERIVQILCRRAKNNPILLGESGVGKTAIAEGLATSIAQAD 333

Query: 340 VPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGT 399
           VPVFLL KR+MSLD+GLL+AGAKERGELEARVTTLI EI K G++ILFIDEVHTL+GSGT
Sbjct: 334 VPVFLLEKRVMSLDVGLLIAGAKERGELEARVTTLIREILKEGNIILFIDEVHTLVGSGT 393

Query: 400 VGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQ 459
           VG+GNKG+GLDI+NLLKPSLGRGE QCIASTT DE+RT FE DKALARRFQPVLI+EPSQ
Sbjct: 394 VGKGNKGSGLDIANLLKPSLGRGEFQCIASTTVDEYRTHFENDKALARRFQPVLINEPSQ 453

Query: 460 EDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHI 519
           EDAVRILLGL++KYEAHHNC+FTLEAINAAV+LSARYI+DRYLPDKAIDL+DEAGSRA I
Sbjct: 454 EDAVRILLGLQQKYEAHHNCRFTLEAINAAVNLSARYIADRYLPDKAIDLIDEAGSRARI 513

Query: 520 ELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESS 579
           E ++RKKEQ++ ILSK PDDYWQEIRTVQAMHE+V  SRL  DD  +SM  T EI +ES 
Sbjct: 514 EAYRRKKEQKSFILSKSPDDYWQEIRTVQAMHEMVLASRLTNDDSASSMDGTGEITLESR 573

Query: 580 LPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVA 639
           LP A +DDEP VVG DDIAAVASLWSGIPVQQ+TA+ERM LV LEE+L+KRVIGQDEA+A
Sbjct: 574 LPPALNDDEPPVVGRDDIAAVASLWSGIPVQQLTAEERMFLVDLEEELRKRVIGQDEAIA 633

Query: 640 AISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           AISRAVKRSRVGLKDP+RP AAMLFCGPTGVGKTEL K+LA  YFGS
Sbjct: 634 AISRAVKRSRVGLKDPDRPIAAMLFCGPTGVGKTELTKALARSYFGS 680

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	710
TAIR|locus:2157363	945	ERD1 "EARLY RESPONSIVE TO DEHY	0.959	0.720	0.715	7.1e-251
UNIPROTKB|Q6H795	938	CLPD1 "Chaperone protein ClpD1	0.856	0.648	0.642	2e-200
TAIR|locus:2099433	952	HSP93-III [Arabidopsis thalian	0.6	0.447	0.492	1.5e-125
TAIR|locus:2157383	929	CLPC1 "CLPC homologue 1" [Arab	0.571	0.437	0.505	1e-124
UNIPROTKB|Q81VV9	811	BAS0081 "Negative regulator of	0.619	0.542	0.470	6.9e-115
TIGR_CMR|BA_0080	811	BA_0080 "negative regulator of	0.619	0.542	0.470	6.9e-115
UNIPROTKB|Q3A9N1	811	CHY_2348 "Negative regulator o	0.695	0.609	0.456	3.8e-110
TIGR_CMR|CHY_2348	811	CHY_2348 "negative regulator o	0.695	0.609	0.456	3.8e-110
UNIPROTKB|P63288	848	clpB "Chaperone protein ClpB"	0.4	0.334	0.496	1.7e-103
UNIPROTKB|P0A522	848	clpC "Probable ATP-dependent C	0.709	0.594	0.437	2.9e-103

TAIR|locus:2157363 ERD1 "EARLY RESPONSIVE TO DEHYDRATION 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 2416 (855.5 bits), Expect = 7.1e-251, P = 7.1e-251
 Identities = 493/689 (71%), Positives = 568/689 (82%)

Query:     1 MEV-STCSPLSVNS-RCLFANQXXXXXXXXXXXQYVNPMSSFFNISMISHKVQFFHSNYT 58
             MEV ST SPL+++S R L A+               +  SS+  IS+ +  +  F +  T
Sbjct:     1 MEVLSTSSPLTLHSHRLLSASSSSSHVTSIAASSLSSFASSYLGISLSNRTIHRFSTTPT 60

Query:    59 SXXXXXXPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLI 118
             +      P   RKR+K  PIS+VFERFTERA++A+IFSQ+EAKSLGKDMV+TQHLLLGLI
Sbjct:    61 NLRRF--P--QRKRKKFTPISAVFERFTERAIRAIIFSQKEAKSLGKDMVYTQHLLLGLI 116

Query:   119 AEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRV 178
             AEDR P GFL SGITIDKAREAV SIW   N+ D+    A    +S +  MPFSISTKRV
Sbjct:   117 AEDRDPQGFLGSGITIDKAREAVWSIWDEANS-DSKQEEASSTSYSKSTDMPFSISTKRV 175

Query:   179 FEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELA 238
             FEAAVEYSR+    +IAPEHIA+GLFTVDDGSAGRVLKRLG ++N L A A++RL+GE+A
Sbjct:   176 FEAAVEYSRTMDCQYIAPEHIAVGLFTVDDGSAGRVLKRLGANMNLLTAAALTRLKGEIA 235

Query:   239 KEGREPSLA-KGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRET 297
             K+GREPS + KG  E+  SG+ A     G+   + LEQFCVDLTARASE LIDPVIGRE 
Sbjct:   236 KDGREPSSSSKGSFESPPSGRIAGSGPGGKKAKNVLEQFCVDLTARASEGLIDPVIGREK 295

Query:   298 EIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL 357
             E+QR+IQILCRRTKNNPILLGE+GVGKTAIAEGLAI I +A  P FLL+KRIMSLD+GLL
Sbjct:   296 EVQRVIQILCRRTKNNPILLGEAGVGKTAIAEGLAISIAEASAPGFLLTKRIMSLDIGLL 355

Query:   358 MAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP 417
             MAGAKERGELEARVT LISE++KSG VILFIDEVHTLIGSGTVGRGNKG+GLDI+NLLKP
Sbjct:   356 MAGAKERGELEARVTALISEVKKSGKVILFIDEVHTLIGSGTVGRGNKGSGLDIANLLKP 415

Query:   418 SLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHH 477
             SLGRGELQCIASTT DE R+QFEKDKALARRFQPVLI+EPS+EDAV+ILLGLREKYEAHH
Sbjct:   416 SLGRGELQCIASTTLDEFRSQFEKDKALARRFQPVLINEPSEEDAVKILLGLREKYEAHH 475

Query:   478 NCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPP 537
             NCK+T+EAI+AAV+LS+RYI+DR+LPDKAIDL+DEAGSRA IE F++KKE   CILSKPP
Sbjct:   476 NCKYTMEAIDAAVYLSSRYIADRFLPDKAIDLIDEAGSRARIEAFRKKKEDAICILSKPP 535

Query:   538 DDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDI 597
             +DYWQEI+TVQAMHEVV  SR K DD  A   ++ E+V ESSLP A+ DDEP +VGPDDI
Sbjct:   536 NDYWQEIKTVQAMHEVVLSSRQKQDDGDAISDESGELVEESSLPPAAGDDEPILVGPDDI 595

Query:   598 AAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNR 657
             AAVAS+WSGIPVQQITADERMLL+ LE+QL+ RV+GQDEAVAAISRAVKRSRVGLKDP+R
Sbjct:   596 AAVASVWSGIPVQQITADERMLLMSLEDQLRGRVVGQDEAVAAISRAVKRSRVGLKDPDR 655

Query:   658 PTAAMLFCGPTGVGKTELAKSLAACYFGS 686
             P AAMLFCGPTGVGKTEL K+LAA YFGS
Sbjct:   656 PIAAMLFCGPTGVGKTELTKALAANYFGS 684

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

GO:0019538 "protein metabolic process" evidence=IEA

GO:0009570 "chloroplast stroma" evidence=IDA;TAS

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0034214 "protein hexamerization" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0009646 "response to absence of light" evidence=RCA

UNIPROTKB|Q6H795 CLPD1 "Chaperone protein ClpD1, chloroplastic" [Oryza sativa Japonica Group (taxid:39947)]

 Score = 1940 (688.0 bits), Expect = 2.0e-200, P = 2.0e-200
 Identities = 404/629 (64%), Positives = 489/629 (77%)

Query:    69 ARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFL 128
             AR+ R+ + + +VFERFTERAVKAV+ SQREAK LG+  V  +HLLLGLIAEDR   GFL
Sbjct:    62 ARRARRAV-VRAVFERFTERAVKAVVLSQREAKGLGEGAVAPRHLLLGLIAEDRSAGGFL 120

Query:   129 ESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKM--PFSISTKRVFEAAVEYS 186
              SGI I++ARE    I      +D    A    P  S  +M  PFS S KRVFE AVE+S
Sbjct:   121 SSGINIERAREECRGI----GARDLTPGAPS--PSGSGLEMDIPFSGSCKRVFEVAVEFS 174

Query:   187 RSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSL 246
             R+ G +FI+PEH+AL LFT+DD +   +L+ LG D + LA+VA++RLQ ELAK+ REP+ 
Sbjct:   175 RNMGCSFISPEHLALALFTLDDPTTNSLLRSLGADPSQLASVALTRLQAELAKDCREPAG 234

Query:   247 AKGVRENSIS----GKTAALKS-PGRTRASALEQFCVDLTARASEELIDPVIGRETEIQR 301
             A   +    S    G++A  KS   +    AL+QFC+DLT +AS   IDP+IGRE EI+R
Sbjct:   235 ASSFKVPKKSPAGAGRSAFSKSLNSKKEKGALDQFCLDLTTQASGGFIDPIIGREEEIER 294

Query:   302 IIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA 361
             ++QI+CRRTKNNPILLGE+GVGKTAIAEGLA+RI   +VP++L++KRIMSLD+GLL+AGA
Sbjct:   295 VVQIICRRTKNNPILLGEAGVGKTAIAEGLALRIANGDVPIYLVAKRIMSLDVGLLIAGA 354

Query:   362 KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR 421
             KERGELE+RVT+LI E++++GDVILFIDEVH LIGSGTVG+G KG GLDI NLLKP L R
Sbjct:   355 KERGELESRVTSLIREVREAGDVILFIDEVHNLIGSGTVGKG-KGAGLDIGNLLKPPLAR 413

Query:   422 GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKF 481
             GELQCIA+TT DEHR  FEKDKALARRFQPVL+ EPSQ+DAV+ILLGLREKYE +H CKF
Sbjct:   414 GELQCIAATTLDEHRMHFEKDKALARRFQPVLVEEPSQDDAVKILLGLREKYETYHKCKF 473

Query:   482 TLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYW 541
             TLEAINAAV+LSARYI DR LPDKAIDL+DEAGSRA +E F RKKE Q+ IL K PD+YW
Sbjct:   474 TLEAINAAVYLSARYIPDRQLPDKAIDLIDEAGSRARMESFNRKKEGQSSILLKSPDEYW 533

Query:   542 QEIRTVQAMHEVVQGSRLKY----DDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDI 597
             QEIR  Q MHEVV  +++KY    ++  A++   SE + E  L S    +EP VVG ++I
Sbjct:   534 QEIRAAQNMHEVVSSNQMKYSPRQENGSAAIKAPSEDMNE--LTSELQVEEPIVVGTEEI 591

Query:   598 AAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNR 657
             A VASLWSGIPVQQ+TAD+R LLVGL+ +L+KRVIGQD+AV AISRAVKRSRVGL DP+R
Sbjct:   592 ARVASLWSGIPVQQLTADDRKLLVGLDGELRKRVIGQDDAVMAISRAVKRSRVGLNDPDR 651

Query:   658 PTAAMLFCGPTGVGKTELAKSLAACYFGS 686
             P A +LFCGPTGVGKTEL K+LAA YFGS
Sbjct:   652 PIATLLFCGPTGVGKTELTKALAASYFGS 680

GO:0034605 "cellular response to heat" evidence=IGI

TAIR|locus:2099433 HSP93-III [Arabidopsis thaliana (taxid:3702)]

 Score = 1018 (363.4 bits), Expect = 1.5e-125, Sum P(2) = 1.5e-125
 Identities = 218/443 (49%), Positives = 305/443 (68%)

Query:   250 VRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRR 309
             V EN+    +    S G ++   LE++  +LT  A E  +DPV+GR+ +I+R++QIL RR
Sbjct:   255 VGENNEVTASVGGGSSGNSKMPTLEEYGTNLTKLAEEGKLDPVVGRQPQIERVVQILARR 314

Query:   310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEA 369
             TKNNP L+GE GVGKTAIAEGLA RI   +VP  +  K +++LDMGLL+AG K RGE E 
Sbjct:   315 TKNNPCLIGEPGVGKTAIAEGLAQRIASGDVPETIEGKTVITLDMGLLVAGTKYRGEFEE 374

Query:   370 RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAS 429
             R+  L+ EI++S ++ILFIDEVHTLIG+G      +G  +D +N+LKP+L RGELQCI +
Sbjct:   375 RLKKLMEEIRQSDEIILFIDEVHTLIGAGAA----EGA-IDAANILKPALARGELQCIGA 429

Query:   430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAA 489
             TT DE+R   EKD AL RRFQPV + EP+ E+A++IL GLRE+YE HH  ++T EA+ AA
Sbjct:   430 TTIDEYRKHIEKDPALERRFQPVKVPEPTVEEAIQILQGLRERYEIHHKLRYTDEALVAA 489

Query:   490 VHLSARYISDRYLPDKAIDLVDEAGSRA---HIELFK--RKKEQQTCILSKPPDDYWQEI 544
               LS +YISDR+LPDKAIDL+DEAGSR    H +L +  R+ E+Q   ++K  ++    +
Sbjct:   490 AQLSHQYISDRFLPDKAIDLIDEAGSRVRLRHAQLPEEARELEKQLRQITKEKNE---AV 546

Query:   545 RTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE-SSLPSASDDDEPAVVGPDDIAAVASL 603
             R+     E+    R +  ++ A + +      E +   + +++  P V    DI  + + 
Sbjct:   547 RSQD--FEMAGSHRDREIELKAEIANVLSRGKEVAKAENEAEEGGPTVT-ESDIQHIVAT 603

Query:   604 WSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAML 663
             W+GIPV+++++DE   L+ +E+ L  RVIGQDEAV AISRA++R+RVGLK+PNRP A+ +
Sbjct:   604 WTGIPVEKVSSDESSRLLQMEQTLHTRVIGQDEAVKAISRAIRRARVGLKNPNRPIASFI 663

Query:   664 FCGPTGVGKTELAKSLAACYFGS 686
             F GPTGVGK+ELAK+LAA YFGS
Sbjct:   664 FSGPTGVGKSELAKALAAYYFGS 686

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

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

GO:0009507 "chloroplast" evidence=ISM;IDA

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

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

GO:0019538 "protein metabolic process" evidence=IEA

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009532 "plastid stroma" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0009658 "chloroplast organization" evidence=ISS

GO:0045037 "protein import into chloroplast stroma" evidence=ISS

GO:0016020 "membrane" evidence=IDA

GO:0034214 "protein hexamerization" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

GO:0009536 "plastid" evidence=IDA

TAIR|locus:2157383 CLPC1 "CLPC homologue 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1010 (360.6 bits), Expect = 1.0e-124, Sum P(2) = 1.0e-124
 Identities = 211/417 (50%), Positives = 287/417 (68%)

Query:   273 LEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLA 332
             LE++  +LT  A E  +DPV+GR+ +I+R++QIL RRTKNNP L+GE GVGKTAIAEGLA
Sbjct:   257 LEEYGTNLTKLAEEGKLDPVVGRQPQIERVVQILGRRTKNNPCLIGEPGVGKTAIAEGLA 316

Query:   333 IRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVH 392
              RI   +VP  +  K++++LDMGLL+AG K RGE E R+  L+ EI++S ++ILFIDEVH
Sbjct:   317 QRIASGDVPETIEGKKVITLDMGLLVAGTKYRGEFEERLKKLMEEIRQSDEIILFIDEVH 376

Query:   393 TLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPV 452
             TLIG+G      +G  +D +N+LKP+L RGELQCI +TT DE+R   EKD AL RRFQPV
Sbjct:   377 TLIGAGAA----EGA-IDAANILKPALARGELQCIGATTLDEYRKHIEKDPALERRFQPV 431

Query:   453 LISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDE 512
              + EP+ ++ ++IL GLRE+YE HH  ++T E++ AA  LS +YISDR+LPDKAIDL+DE
Sbjct:   432 KVPEPTVDETIQILKGLRERYEIHHKLRYTDESLVAAAQLSYQYISDRFLPDKAIDLIDE 491

Query:   513 AGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTS 572
             AGSR  +   +  +E +   L K      +E        +  +   L+ D  +    + S
Sbjct:   492 AGSRVRLRHAQVPEEARE--LEKELRQITKEKNEAVRGQDFEKAGTLR-DREIELRAEVS 548

Query:   573 EIVV---ESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKK 629
              I     E S   +   +E  +V   DI  + S W+GIPV++++ DE   L+ +EE L K
Sbjct:   549 AIQAKGKEMSKAESETGEEGPMVTESDIQHIVSSWTGIPVEKVSTDESDRLLKMEETLHK 608

Query:   630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
             R+IGQDEAV AISRA++R+RVGLK+PNRP A+ +F GPTGVGK+ELAK+LAA YFGS
Sbjct:   609 RIIGQDEAVKAISRAIRRARVGLKNPNRPIASFIFSGPTGVGKSELAKALAAYYFGS 665

GO:0000166 "nucleotide binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0004518 "nuclease activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA;ISS

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

GO:0009507 "chloroplast" evidence=ISM;IDA

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0019538 "protein metabolic process" evidence=IEA

GO:0009941 "chloroplast envelope" evidence=IDA

GO:0009532 "plastid stroma" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

GO:0009535 "chloroplast thylakoid membrane" evidence=IDA

GO:0009658 "chloroplast organization" evidence=IMP

GO:0031897 "Tic complex" evidence=TAS

GO:0045037 "protein import into chloroplast stroma" evidence=IMP

GO:0009570 "chloroplast stroma" evidence=IDA

GO:0005618 "cell wall" evidence=IDA

GO:0010380 "regulation of chlorophyll biosynthetic process" evidence=IMP

GO:0045036 "protein targeting to chloroplast" evidence=IMP

GO:0005829 "cytosol" evidence=RCA

GO:0009706 "chloroplast inner membrane" evidence=IDA

GO:0009902 "chloroplast relocation" evidence=RCA

GO:0010027 "thylakoid membrane organization" evidence=RCA

GO:0010304 "PSII associated light-harvesting complex II catabolic process" evidence=RCA

GO:0034660 "ncRNA metabolic process" evidence=RCA

GO:0042744 "hydrogen peroxide catabolic process" evidence=RCA

GO:0042793 "transcription from plastid promoter" evidence=RCA

GO:0009536 "plastid" evidence=IDA

GO:0004176 "ATP-dependent peptidase activity" evidence=IDA

UNIPROTKB|Q81VV9 BAS0081 "Negative regulator of genetic competence ClpC/MecB" [Bacillus anthracis (taxid:1392)]

 Score = 962 (343.7 bits), Expect = 6.9e-115, Sum P(2) = 6.9e-115
 Identities = 220/468 (47%), Positives = 294/468 (62%)

Query:   225 LAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARA 284
             +AA  ++ L   L K  ++     G  E S SG      +   T    L+    DLT  A
Sbjct:   119 VAARVLNNLGVSLNKARQQVLQLLGSNEAS-SGHQGGSSTNANT--PTLDSLARDLTVVA 175

Query:   285 SEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL 344
              E  +DPVIGR  EIQR+I++L RRTKNNP+L+GE GVGKTAIAEGLA +IV  EVP  L
Sbjct:   176 RENRLDPVIGRGKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIVNNEVPETL 235

Query:   345 LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN 404
               KR+M+LDMG ++AG K RGE E R+  ++ EI+++G++ILFIDE+HTLIG+G    G 
Sbjct:   236 RDKRVMTLDMGTVVAGTKYRGEFEDRLKKVMDEIRQAGNIILFIDELHTLIGAG----GA 291

Query:   405 KGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVR 464
             +G  +D SN+LKPSL RGELQCI +TT DE+R   EKD AL RRFQP+ + EPS +++ +
Sbjct:   292 EGA-IDASNILKPSLARGELQCIGATTLDEYRKYIEKDAALERRFQPIHVDEPSLDESTQ 350

Query:   465 ILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKR 524
             IL GLR++YEAHH    T +AI+AAV LS RYI+DR+LPDKAIDL+DEA S+  +  +  
Sbjct:   351 ILKGLRDRYEAHHRVSITDDAIDAAVKLSDRYITDRFLPDKAIDLIDEAASKVRLRSYTT 410

Query:   525 K---KEQQTCI--LSKPPDD--YWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE 577
                 KE +  +  + K  D     QE     ++ ++ Q  R K +D      +       
Sbjct:   411 PPNLKELEVKLEEIRKEKDAAVQSQEFEKAASLRDMEQRLREKLEDTKRQWKEQQ----- 465

Query:   578 SSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA 637
                    ++ E  V   +DIA V S W+ IPV ++   E   L+ LE  L  RVIGQDEA
Sbjct:   466 -----GKENSEVTV---EDIANVVSTWTRIPVSKLAQTETDKLLNLESILHDRVIGQDEA 517

Query:   638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG 685
             V A+++AV+R+R GLKDP RP  + +F GPTGVGKTELA++LA   FG
Sbjct:   518 VVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFG 565

GO:0003674 "molecular_function" evidence=ND

TIGR_CMR|BA_0080 BA_0080 "negative regulator of genetic competence ClpC/MecB" [Bacillus anthracis str. Ames (taxid:198094)]

 Score = 962 (343.7 bits), Expect = 6.9e-115, Sum P(2) = 6.9e-115
 Identities = 220/468 (47%), Positives = 294/468 (62%)

Query:   225 LAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARA 284
             +AA  ++ L   L K  ++     G  E S SG      +   T    L+    DLT  A
Sbjct:   119 VAARVLNNLGVSLNKARQQVLQLLGSNEAS-SGHQGGSSTNANT--PTLDSLARDLTVVA 175

Query:   285 SEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL 344
              E  +DPVIGR  EIQR+I++L RRTKNNP+L+GE GVGKTAIAEGLA +IV  EVP  L
Sbjct:   176 RENRLDPVIGRGKEIQRVIEVLSRRTKNNPVLIGEPGVGKTAIAEGLAQQIVNNEVPETL 235

Query:   345 LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN 404
               KR+M+LDMG ++AG K RGE E R+  ++ EI+++G++ILFIDE+HTLIG+G    G 
Sbjct:   236 RDKRVMTLDMGTVVAGTKYRGEFEDRLKKVMDEIRQAGNIILFIDELHTLIGAG----GA 291

Query:   405 KGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVR 464
             +G  +D SN+LKPSL RGELQCI +TT DE+R   EKD AL RRFQP+ + EPS +++ +
Sbjct:   292 EGA-IDASNILKPSLARGELQCIGATTLDEYRKYIEKDAALERRFQPIHVDEPSLDESTQ 350

Query:   465 ILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKR 524
             IL GLR++YEAHH    T +AI+AAV LS RYI+DR+LPDKAIDL+DEA S+  +  +  
Sbjct:   351 ILKGLRDRYEAHHRVSITDDAIDAAVKLSDRYITDRFLPDKAIDLIDEAASKVRLRSYTT 410

Query:   525 K---KEQQTCI--LSKPPDD--YWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVE 577
                 KE +  +  + K  D     QE     ++ ++ Q  R K +D      +       
Sbjct:   411 PPNLKELEVKLEEIRKEKDAAVQSQEFEKAASLRDMEQRLREKLEDTKRQWKEQQ----- 465

Query:   578 SSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA 637
                    ++ E  V   +DIA V S W+ IPV ++   E   L+ LE  L  RVIGQDEA
Sbjct:   466 -----GKENSEVTV---EDIANVVSTWTRIPVSKLAQTETDKLLNLESILHDRVIGQDEA 517

Query:   638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG 685
             V A+++AV+R+R GLKDP RP  + +F GPTGVGKTELA++LA   FG
Sbjct:   518 VVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESMFG 565

GO:0003674 "molecular_function" evidence=ND

GO:0009294 "DNA mediated transformation" evidence=ISS

UNIPROTKB|Q3A9N1 CHY_2348 "Negative regulator of genetic competence clpC/mecB" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 1088 (388.1 bits), Expect = 3.8e-110, P = 3.8e-110
 Identities = 237/519 (45%), Positives = 325/519 (62%)

Query:   167 AKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLA 226
             A++ F+   KRV E +V+ +   G+N++  EH+ LGL    +G A RVL  LG D+  + 
Sbjct:    76 AEIAFTPRAKRVLELSVDEAARFGHNYVGTEHLLLGLIREGEGVAARVLVSLGADLERVR 135

Query:   227 AVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASE 286
             A     L G     G  P           SG+          R   L++   DLTA A E
Sbjct:   136 AEITQVLSG-----GPIPGT---------SGQAGGQAKKKAVRTPTLDEHGRDLTALARE 181

Query:   287 ELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS 346
               +DPV+GRE EI+R+IQ+L RRTKNNP+L+GE GVGKTAI EGLA RIVQ +VP  L+ 
Sbjct:   182 NKLDPVVGREKEIERVIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVQKKVPEILID 241

Query:   347 KRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKG 406
             KR+++LD+  ++AG K RGE E R+  ++ EI+ +G+VI+FIDE+HTLIG+G      +G
Sbjct:   242 KRVVTLDLASMVAGTKYRGEFEERLKKVLEEIKNAGNVIVFIDEIHTLIGAGAA----EG 297

Query:   407 TGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRIL 466
               +D +N+LKPSL RGE+QC+ +TT DE+R   EKD AL RRFQP+++ EP+ E+ V IL
Sbjct:   298 A-IDAANILKPSLARGEIQCVGATTLDEYRKYIEKDPALERRFQPIMVDEPTVEETVEIL 356

Query:   467 LGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKK 526
              GLR++YEAHH  K T EAI AA  LS RYI+DR+LPDKAIDL+DEA SR  +  F    
Sbjct:   357 KGLRDRYEAHHRVKITDEAIIAAAKLSDRYITDRFLPDKAIDLIDEAASRVRLNAFTAPP 416

Query:   527 EQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDD 586
               +   L +  ++  +E     A  E  + ++L+  D    +   +E+  +         
Sbjct:   417 NLKE--LEEKINEIRKEKEAAVAAQEFEKAAKLR--DQEQKL--KAELEEKKKEWEKEQS 470

Query:   587 DEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVK 646
             D    V  DDIA + S W+GIPV+++  +E   L+ LEE L +RVIGQDEAV A++RAV+
Sbjct:   471 DHLLSVTEDDIAQIVSQWTGIPVKKLAEEESERLLKLEEILHQRVIGQDEAVKAVARAVR 530

Query:   647 RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG 685
             R+R GLKDP RP  + +F GPTGVGKTELA++LA   FG
Sbjct:   531 RARAGLKDPKRPIGSFIFLGPTGVGKTELARALAEALFG 569

GO:0003674 "molecular_function" evidence=ND

GO:0009294 "DNA mediated transformation" evidence=ISS

TIGR_CMR|CHY_2348 CHY_2348 "negative regulator of genetic competence clpC/mecB" [Carboxydothermus hydrogenoformans Z-2901 (taxid:246194)]

 Score = 1088 (388.1 bits), Expect = 3.8e-110, P = 3.8e-110
 Identities = 237/519 (45%), Positives = 325/519 (62%)

Query:   167 AKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLA 226
             A++ F+   KRV E +V+ +   G+N++  EH+ LGL    +G A RVL  LG D+  + 
Sbjct:    76 AEIAFTPRAKRVLELSVDEAARFGHNYVGTEHLLLGLIREGEGVAARVLVSLGADLERVR 135

Query:   227 AVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASE 286
             A     L G     G  P           SG+          R   L++   DLTA A E
Sbjct:   136 AEITQVLSG-----GPIPGT---------SGQAGGQAKKKAVRTPTLDEHGRDLTALARE 181

Query:   287 ELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS 346
               +DPV+GRE EI+R+IQ+L RRTKNNP+L+GE GVGKTAI EGLA RIVQ +VP  L+ 
Sbjct:   182 NKLDPVVGREKEIERVIQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVQKKVPEILID 241

Query:   347 KRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKG 406
             KR+++LD+  ++AG K RGE E R+  ++ EI+ +G+VI+FIDE+HTLIG+G      +G
Sbjct:   242 KRVVTLDLASMVAGTKYRGEFEERLKKVLEEIKNAGNVIVFIDEIHTLIGAGAA----EG 297

Query:   407 TGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRIL 466
               +D +N+LKPSL RGE+QC+ +TT DE+R   EKD AL RRFQP+++ EP+ E+ V IL
Sbjct:   298 A-IDAANILKPSLARGEIQCVGATTLDEYRKYIEKDPALERRFQPIMVDEPTVEETVEIL 356

Query:   467 LGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKK 526
              GLR++YEAHH  K T EAI AA  LS RYI+DR+LPDKAIDL+DEA SR  +  F    
Sbjct:   357 KGLRDRYEAHHRVKITDEAIIAAAKLSDRYITDRFLPDKAIDLIDEAASRVRLNAFTAPP 416

Query:   527 EQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDD 586
               +   L +  ++  +E     A  E  + ++L+  D    +   +E+  +         
Sbjct:   417 NLKE--LEEKINEIRKEKEAAVAAQEFEKAAKLR--DQEQKL--KAELEEKKKEWEKEQS 470

Query:   587 DEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVK 646
             D    V  DDIA + S W+GIPV+++  +E   L+ LEE L +RVIGQDEAV A++RAV+
Sbjct:   471 DHLLSVTEDDIAQIVSQWTGIPVKKLAEEESERLLKLEEILHQRVIGQDEAVKAVARAVR 530

Query:   647 RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG 685
             R+R GLKDP RP  + +F GPTGVGKTELA++LA   FG
Sbjct:   531 RARAGLKDPKRPIGSFIFLGPTGVGKTELARALAEALFG 569

GO:0003674 "molecular_function" evidence=ND

GO:0009294 "DNA mediated transformation" evidence=ISS

UNIPROTKB|P63288 clpB "Chaperone protein ClpB" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 702 (252.2 bits), Expect = 1.7e-103, Sum P(3) = 1.7e-103
 Identities = 146/294 (49%), Positives = 198/294 (67%)

Query:   237 LAKEGREPSLAKGVRENSISGK-TAALKSPG-RTRASALEQFCVDLTARASEELIDPVIG 294
             L   G  P   + +RE  +  + +A + SP       AL+++  DLTARA E  +DPVIG
Sbjct:   126 LTGHGASP---QALREAFVKVRGSARVTSPEPEATYQALQKYSTDLTARAREGKLDPVIG 182

Query:   295 RETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM 354
             R+ EI+R++Q+L RRTKNNP+L+GE GVGKTAI EGLA RIV  +VP  L  K I++LD+
Sbjct:   183 RDNEIRRVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVAGDVPESLRDKTIVALDL 242

Query:   355 GLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISN 413
             G ++AG+K RGE E R+  ++ +I+ S G +I FIDE+HT++G+G  G G     +D  N
Sbjct:   243 GSMVAGSKYRGEFEERLKAVLDDIKNSAGQIITFIDELHTIVGAGATGEG----AMDAGN 298

Query:   414 LLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKY 473
             ++KP L RGEL+ + +TT DE+R   EKD AL RRFQ V + EPS ED + IL GL+++Y
Sbjct:   299 MIKPMLARGELRLVGATTLDEYRKHIEKDAALERRFQQVYVGEPSVEDTIGILRGLKDRY 358

Query:   474 EAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKE 527
             E HH  + T  A+ AA  LS RYI+ R+LPDKAIDLVDEA SR  +E+  R  E
Sbjct:   359 EVHHGVRITDSALVAAATLSDRYITARFLPDKAIDLVDEAASRLRMEIDSRPVE 412

GO:0005618 "cell wall" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0040007 "growth" evidence=IMP

UNIPROTKB|P0A522 clpC "Probable ATP-dependent Clp protease ATP-binding subunit" [Mycobacterium tuberculosis (taxid:1773)]

 Score = 1023 (365.2 bits), Expect = 2.9e-103, P = 2.9e-103
 Identities = 235/537 (43%), Positives = 330/537 (61%)

Query:   154 DDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGR 213
             ++   QG+   S   +PF+   K+V E ++  +   G+N+I  EHI LGL    +G A +
Sbjct:    64 EEIIGQGQQAPSG-HIPFTPRAKKVLELSLREALQLGHNYIGTEHILLGLIREGEGVAAQ 122

Query:   214 VLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASAL 273
             VL +LG ++  +    +  L G   KE  E     G R    SG      SP  + +  L
Sbjct:   123 VLVKLGAELTRVRQQVIQLLSGYQGKEAAEAGT--GGRGGE-SG------SP--STSLVL 171

Query:   274 EQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAI 333
             +QF  +LTA A E  +DPVIGRE EI+R++Q+L RRTKNNP+L+GE GVGKTA+ EGLA 
Sbjct:   172 DQFGRNLTAAAMEGKLDPVIGREKEIERVMQVLSRRTKNNPVLIGEPGVGKTAVVEGLAQ 231

Query:   334 RIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHT 393
              IV  EVP  L  K++ +LD+G L+AG++ RG+ E R+  ++ EI   GD+ILFIDE+HT
Sbjct:   232 AIVHGEVPETLKDKQLYTLDLGSLVAGSRYRGDFEERLKKVLKEINTRGDIILFIDELHT 291

Query:   394 LIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVL 453
             L+G+G      +G  +D +++LKP L RGELQ I +TT DE+R   EKD AL RRFQPV 
Sbjct:   292 LVGAGAA----EGA-IDAASILKPKLARGELQTIGATTLDEYRKYIEKDAALERRFQPVQ 346

Query:   454 ISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEA 513
             + EP+ E  + IL GLR++YEAHH    T  A+ AA  L+ RYI+DR+LPDKAIDL+DEA
Sbjct:   347 VGEPTVEHTIEILKGLRDRYEAHHRVSITDAAMVAAATLADRYINDRFLPDKAIDLIDEA 406

Query:   514 GSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSE 573
             G+R  I    R+       ++ PPD    + +  +A  E       +  +  AS+ D  +
Sbjct:   407 GARMRI----RR-------MTAPPDLREFDEKIAEARREKESAIDAQDFEKAASLRDREK 455

Query:   574 IVV----ESSLPSASDD-DEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLK 628
              +V    E      S D D  A V  + IA V   W+GIPV ++T  E   L+ +EE+L 
Sbjct:   456 TLVAQRAEREKQWRSGDLDVVAEVDDEQIAEVLGNWTGIPVFKLTEAETTRLLRMEEELH 515

Query:   629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG 685
             KR+IGQ++AV A+S+A++R+R GLKDP RP+ + +F GP+GVGKTEL+K+LA   FG
Sbjct:   516 KRIIGQEDAVKAVSKAIRRTRAGLKDPKRPSGSFIFAGPSGVGKTELSKALANFLFG 572

GO:0005515 "protein binding" evidence=IPI

GO:0005618 "cell wall" evidence=IDA

GO:0005829 "cytosol" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0006457 "protein folding" evidence=IMP

GO:0016887 "ATPase activity" evidence=IDA

GO:0040007 "growth" evidence=IMP

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0044183 "protein binding involved in protein folding" evidence=IMP

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q6H795	CLPD1_ORYSJ	No assigned EC number	0.6477	0.8394	0.6353	yes	no
P42762	CLPD_ARATH	No assigned EC number	0.7361	0.9042	0.6793	yes	no
Q7XL03	CLPD2_ORYSJ	No assigned EC number	0.6464	0.8408	0.6371	yes	no

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: fgenesh4_pg.C_LG_XII001082 hypothetical protein (948 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	710
COG0542	786	COG0542, clpA, ATP-binding subunits of Clp proteas	0.0
CHL00095	821	CHL00095, clpC, Clp protease ATP binding subunit	0.0
TIGR02639	730	TIGR02639, ClpA, ATP-dependent Clp protease ATP-bi	1e-157
TIGR03345	852	TIGR03345, VI_ClpV1, type VI secretion ATPase, Clp	1e-137
PRK10865	857	PRK10865, PRK10865, protein disaggregation chapero	1e-128
TIGR03346	852	TIGR03346, chaperone_ClpB, ATP-dependent chaperone	1e-123
PRK11034	758	PRK11034, clpA, ATP-dependent Clp protease ATP-bin	1e-111
TIGR03346	852	TIGR03346, chaperone_ClpB, ATP-dependent chaperone	9e-35
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	5e-19
smart00382	148	smart00382, AAA, ATPases associated with a variety	3e-10
pfam02861	53	pfam02861, Clp_N, Clp amino terminal domain	7e-09
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	3e-07
TIGR02397	355	TIGR02397, dnaX_nterm, DNA polymerase III, subunit	2e-06
pfam07724	168	pfam07724, AAA_2, AAA domain (Cdc48 subfamily)	7e-06
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	4e-05
pfam13191	154	pfam13191, AAA_16, AAA ATPase domain	1e-04
COG3899	849	COG3899, COG3899, Predicted ATPase [General functi	1e-04
pfam02861	53	pfam02861, Clp_N, Clp amino terminal domain	5e-04
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	7e-04
COG1220	444	COG1220, HslU, ATP-dependent protease HslVU (ClpYQ	7e-04
PRK05342	412	PRK05342, clpX, ATP-dependent protease ATP-binding	7e-04
TIGR00390	441	TIGR00390, hslU, ATP-dependent protease HslVU, ATP	0.001
PRK09183	259	PRK09183, PRK09183, transposase/IS protein; Provis	0.001
COG0714	329	COG0714, COG0714, MoxR-like ATPases [General funct	0.002
PRK13341	725	PRK13341, PRK13341, recombination factor protein R	0.002
pfam13401	124	pfam13401, AAA_22, AAA domain	0.003
PRK14956	484	PRK14956, PRK14956, DNA polymerase III subunits ga	0.003
COG1219	408	COG1219, ClpX, ATP-dependent protease Clp, ATPase	0.004
PRK07399	314	PRK07399, PRK07399, DNA polymerase III subunit del	0.004
PRK14953	486	PRK14953, PRK14953, DNA polymerase III subunits ga	0.004

>gnl|CDD|223616 COG0542, clpA, ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

 Score =  585 bits (1511), Expect = 0.0
 Identities = 260/627 (41%), Positives = 351/627 (55%), Gaps = 58/627 (9%)

Query: 84  RFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVS 143
           + TERA KA+  +Q  A+    + V  +HLLL L+ + +        GI +DK R+ +  
Sbjct: 1   KLTERAQKALELAQELARMRRHEYVTPEHLLLALLDQPKGDELLNLCGIDLDKLRQEL-- 58

Query: 144 IWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGL 203
                     ++   +      +  +   +  KRV E A   ++S G  +++ EH+ L L
Sbjct: 59  ----------EEFIDKLPKVLGSPYLSPRL--KRVLERAWLLAQSLGDEYVSTEHLLLAL 106

Query: 204 FTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALK 263
               +  A  +LK+LGV    +  +                          + G      
Sbjct: 107 LNEPESVAAYILKKLGVTRKDVEELI-----------------------EELRGGNEVDS 143

Query: 264 SPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVG 323
                   ALE++  DLT  A E  +DPVIGR+ EI+R IQIL RRTKNNP+L+GE GVG
Sbjct: 144 KNAEEDQDALEKYTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVG 203

Query: 324 KTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGD 383
           KTAI EGLA RIV  +VP  L  KRI SLD+G L+AGAK RGE E R+  ++ E++KS +
Sbjct: 204 KTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKN 263

Query: 384 VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDK 443
           VILFIDE+HT++G+G      +G  +D +NLLKP+L RGEL+CI +TT DE+R   EKD 
Sbjct: 264 VILFIDEIHTIVGAG----ATEGGAMDAANLLKPALARGELRCIGATTLDEYRKYIEKDA 319

Query: 444 ALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP 503
           AL RRFQ VL+ EPS ED + IL GL+E+YEAHH  + T EA+ AAV LS RYI DR+LP
Sbjct: 320 ALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRITDEALVAAVTLSDRYIPDRFLP 379

Query: 504 DKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDD 563
           DKAIDL+DEAG+R  +E            + KP +    E    Q   E     R +  D
Sbjct: 380 DKAIDLLDEAGARVRLE------------IDKPEELDELERELAQLEIEKEALEREQ--D 425

Query: 564 VVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGL 623
                     I ++       + +  A V  DDIA V + W+GIPV ++  DE+  L+ L
Sbjct: 426 EKEKKLIDEIIKLKEGRIPELEKELEAEVDEDDIAEVVARWTGIPVAKLLEDEKEKLLNL 485

Query: 624 EEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY 683
           E +LKKRVIGQDEAV A+S A++R+R GL DPNRP  + LF GPTGVGKTELAK+LA   
Sbjct: 486 ERRLKKRVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEAL 545

Query: 684 FGSVRIHYLFF-PSPFNSVKVALSRQI 709
           FG      +    S +   K ++SR I
Sbjct: 546 FGD-EQALIRIDMSEYME-KHSVSRLI 570

Length = 786

>gnl|CDD|214361 CHL00095, clpC, Clp protease ATP binding subunit

 Score =  542 bits (1398), Expect = 0.0
 Identities = 272/609 (44%), Positives = 372/609 (61%), Gaps = 48/609 (7%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNG--FLESGITIDKARE 139
           FERFTE+A+K ++ SQ EA+ LG + V T+ +LLGLI E            G+T+  AR 
Sbjct: 2   FERFTEKAIKVIMLSQEEARRLGHNFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARI 61

Query: 140 AVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHI 199
            V  I              +G  F  A ++PF+   KRV E ++E +R  G+N+I  EH+
Sbjct: 62  EVEKI------------IGRGTGFV-AVEIPFTPRAKRVLEMSLEEARDLGHNYIGTEHL 108

Query: 200 ALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKT 259
            L L    +G A RVL+ LGVD++ + ++ +  L GE+              E  +  + 
Sbjct: 109 LLALLEEGEGVAARVLENLGVDLSKIRSL-ILNLIGEII-------------EAILGAEQ 154

Query: 260 AALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGE 319
           +  K+P       LE+F  +LT  A +  +DPVIGRE EI+R+IQIL RRTKNNPIL+GE
Sbjct: 155 SRSKTP------TLEEFGTNLTKEAIDGNLDPVIGREKEIERVIQILGRRTKNNPILIGE 208

Query: 320 SGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ 379
            GVGKTAIAEGLA RIV  +VP  L  K +++LD+GLL+AG K RGE E R+  +  EIQ
Sbjct: 209 PGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQ 268

Query: 380 KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQF 439
           ++ ++IL IDEVHTLIG+     G     +D +N+LKP+L RGELQCI +TT DE+R   
Sbjct: 269 ENNNIILVIDEVHTLIGA-----GAAEGAIDAANILKPALARGELQCIGATTLDEYRKHI 323

Query: 440 EKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD 499
           EKD AL RRFQPV + EPS E+ + IL GLR +YE HHN   + +A+ AA  LS +YI+D
Sbjct: 324 EKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHNLSISDKALEAAAKLSDQYIAD 383

Query: 500 RYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMH--EVVQGS 557
           R+LPDKAIDL+DEAGSR  + L   +       L K   +  ++          E  +  
Sbjct: 384 RFLPDKAIDLLDEAGSR--VRLINSRLPPAARELDKELREILKDKDEAIREQDFETAKQL 441

Query: 558 RLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADER 617
           R +  +V A +      +++S         E  VV  +DIA + S W+GIPV ++T  E 
Sbjct: 442 RDREMEVRAQIA----AIIQSKKTEEEKRLEVPVVTEEDIAEIVSAWTGIPVNKLTKSES 497

Query: 618 MLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAK 677
             L+ +EE L KR+IGQDEAV A+S+A++R+RVGLK+PNRP A+ LF GPTGVGKTEL K
Sbjct: 498 EKLLHMEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTK 557

Query: 678 SLAACYFGS 686
           +LA+ +FGS
Sbjct: 558 ALASYFFGS 566

Length = 821

>gnl|CDD|233959 TIGR02639, ClpA, ATP-dependent Clp protease ATP-binding subunit clpA

 Score =  471 bits (1213), Expect = e-157
 Identities = 215/598 (35%), Positives = 319/598 (53%), Gaps = 94/598 (15%)

Query: 85  FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSI 144
            +E   + +  +  EAK    + V  +HLLL L+ ++       E G  ++  R+ +   
Sbjct: 1   ISEELERILSDALEEAKERRHEFVTLEHLLLALLDDNEAIEILEECGGDVELLRKRLEDY 60

Query: 145 WHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLF 204
                    ++     +P         ++  +RV + A+ + +S G   I    + + LF
Sbjct: 61  LEENLPVIEEEI--DEEPE-------QTVGVQRVIQRALLHVKSAGKKEIDIGDLLVALF 111

Query: 205 TVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKS 264
             +D  A   LK  G+         +                  G+ ++    +      
Sbjct: 112 DEEDSHASYFLKSQGITRL-----DILNYISH------------GISKDDGKDQLGEEAG 154

Query: 265 P-GRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVG 323
              +    ALE++ VDLT +A    IDP+IGRE E++R IQ+LCRR KNNP+L+GE GVG
Sbjct: 155 KEEKKGQDALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVG 214

Query: 324 KTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGD 383
           KTAI EGLA+RI + +VP  L + +I SLDMG L+AG K RG+ E R+  ++SEI+K  +
Sbjct: 215 KTAIVEGLALRIAEGKVPERLKNAKIYSLDMGTLLAGTKYRGDFEERLKAVVSEIEKEPN 274

Query: 384 VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDK 443
            ILFIDE+HT++G+G    G+    +D SNLLKP+L  G+++CI STT +E++  FEKD+
Sbjct: 275 AILFIDEIHTIVGAGATSGGS----MDASNLLKPALSSGKIRCIGSTTYEEYKNHFEKDR 330

Query: 444 ALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP 503
           AL+RRFQ + + EPS E+ V+IL GL+E+YE  H+ K++ EA+ AAV LSARYI+DR+LP
Sbjct: 331 ALSRRFQKIDVGEPSIEETVKILKGLKEQYEEFHHVKYSDEALEAAVELSARYINDRFLP 390

Query: 504 DKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDD 563
           DKAID++DEAG+   +    +KK               ++I                 ++
Sbjct: 391 DKAIDVIDEAGAAFRLRPKAKKKANVNV----------KDI-----------------EN 423

Query: 564 VVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGL 623
           VVA M                                    + IPV+ +++D+R  L  L
Sbjct: 424 VVAKM------------------------------------AKIPVKTVSSDDREQLKNL 447

Query: 624 EEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAA 681
           E+ LK ++ GQDEA+  +  A+KRSR GL DPN+P  + LF GPTGVGKTELAK LA 
Sbjct: 448 EKNLKAKIFGQDEAIDQLVSAIKRSRAGLGDPNKPVGSFLFVGPTGVGKTELAKQLAE 505

[Protein fate, Degradation of proteins, peptides, and glycopeptides]. Length = 730

>gnl|CDD|234172 TIGR03345, VI_ClpV1, type VI secretion ATPase, ClpV1 family

 Score =  424 bits (1093), Expect = e-137
 Identities = 208/574 (36%), Positives = 299/574 (52%), Gaps = 69/574 (12%)

Query: 164 SSAAKMP-FSISTKRVFEAAVEYSRSR-GYNFIAPEHIALGLFTVDDGSAGRVLKRLGVD 221
               + P FS     + + A   +    G   I   H+ L L T  +      L+RL   
Sbjct: 68  RGNTRTPVFSPHLVELLQEAWLLASLELGDGRIRSGHLLLALLTDPE------LRRLLGS 121

Query: 222 VNHLAAVAVSRLQGELAKEGREPSLAKGVRENSI----SGKTAALKSPGRTRASALEQFC 277
           +    +  ++++  E  +E   P+L +G  E S     +G  AA      T  SAL+Q+ 
Sbjct: 122 I----SPELAKIDREALREAL-PALVEGSAEASAAAADAGPAAAAAGAAGT--SALDQYT 174

Query: 278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ 337
            DLTA+A E  IDPV+GR+ EI+++I IL RR +NNPIL GE+GVGKTA+ EGLA+RI  
Sbjct: 175 TDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVVEGLALRIAA 234

Query: 338 AEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGD-VILFIDEVHTLIG 396
            +VP  L + R++SLD+GLL AGA  +GE E R+ ++I E++ S   +ILFIDE HTLIG
Sbjct: 235 GDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIG 294

Query: 397 SGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISE 456
           +G    G  G G D +NLLKP+L RGEL+ IA+TT  E++  FEKD AL RRFQ V + E
Sbjct: 295 AG----GQAGQG-DAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEE 349

Query: 457 PSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSR 516
           P +E A+R+L GL    E HH      EA+ AAV LS RYI  R LPDKA+ L+D A +R
Sbjct: 350 PDEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACAR 409

Query: 517 ---------AHIELFKRKKEQ---QTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDV 564
                    A +E  +R+      +   L +           +  +   +     +   +
Sbjct: 410 VALSQNATPAALEDLRRRIAALELELDALEREAALGADHDERLAELRAELAALEAELAAL 469

Query: 565 VASMGDTSEIV-----VESSLPSASDDDE---------------------------PAVV 592
            A      E+V     + + L + +D                                 V
Sbjct: 470 EARWQQEKELVEAILALRAELEADADAPADDDAALRAQLAELEAALASAQGEEPLVFPEV 529

Query: 593 GPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGL 652
               +A V + W+GIPV ++  DE   ++ L ++L +RVIGQD A+ AI+  ++ +R GL
Sbjct: 530 DAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGL 589

Query: 653 KDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           +DP +P    L  GP+GVGKTE A +LA   +G 
Sbjct: 590 EDPRKPLGVFLLVGPSGVGKTETALALAELLYGG 623

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 [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]. Length = 852

>gnl|CDD|182791 PRK10865, PRK10865, protein disaggregation chaperone; Provisional

 Score =  401 bits (1032), Expect = e-128
 Identities = 240/617 (38%), Positives = 330/617 (53%), Gaps = 124/617 (20%)

Query: 189 RGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAV---AVSRL-QGELAKEGREP 244
               FI P H+   L   + GS   +L   G++   L      A+SRL Q E      +P
Sbjct: 24  HDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQALSRLPQVEGTGGDVQP 83

Query: 245 S------------LAKGVRENSISGK-------------TAALKSPGRTRAS-------- 271
           S            LA+   +N IS +                LK+ G T A+        
Sbjct: 84  SQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGTLADILKAAGATTANITQAIEQM 143

Query: 272 ----------------ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPI 315
                           AL+++ +DLT RA +  +DPVIGR+ EI+R IQ+L RRTKNNP+
Sbjct: 144 RGGESVNDQGAEDQRQALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPV 203

Query: 316 LLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLI 375
           L+GE GVGKTAI EGLA RI+  EVP  L  +R+++LDMG L+AGAK RGE E R+  ++
Sbjct: 204 LIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVL 263

Query: 376 SEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQD 433
           +++ K  G+VILFIDE+HT++G+G      K  G +D  N+LKP+L RGEL C+ +TT D
Sbjct: 264 NDLAKQEGNVILFIDELHTMVGAG------KADGAMDAGNMLKPALARGELHCVGATTLD 317

Query: 434 EHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLS 493
           E+R   EKD AL RRFQ V ++EPS ED + IL GL+E+YE HH+ + T  AI AA  LS
Sbjct: 318 EYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELHHHVQITDPAIVAAATLS 377

Query: 494 ARYISDRYLPDKAIDLVDEAGS--RAHIE------------LFKRKKEQQTCILSKPPDD 539
            RYI+DR LPDKAIDL+DEA S  R  I+            + + K EQQ   L K  D+
Sbjct: 378 HRYIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQA--LMKESDE 435

Query: 540 Y-------------------------WQ----EIRTVQAMHEVVQGSRLKYDDV--VASM 568
                                     W+     +   Q +   ++ +++  +    V  +
Sbjct: 436 ASKKRLDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDL 495

Query: 569 GDTSEI------VVESSLPSASDDDEPAV------VGPDDIAAVASLWSGIPVQQITADE 616
              SE+       +E  L +A+  +   +      V   +IA V + W+GIPV ++   E
Sbjct: 496 ARMSELQYGKIPELEKQLAAATQLEGKTMRLLRNKVTDAEIAEVLARWTGIPVSRMLESE 555

Query: 617 RMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELA 676
           R  L+ +E++L  RVIGQ+EAV A+S A++RSR GL DPNRP  + LF GPTGVGKTEL 
Sbjct: 556 REKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELC 615

Query: 677 KSLAACYFGS----VRI 689
           K+LA   F S    VRI
Sbjct: 616 KALANFMFDSDDAMVRI 632

Length = 857

>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB

 Score =  388 bits (999), Expect = e-123
 Identities = 184/442 (41%), Positives = 260/442 (58%), Gaps = 47/442 (10%)

Query: 85  FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFL--ESGITIDKAREAVV 142
           FTE+  +A+  +Q  A       +  +HLL  L+ ++      L  ++G+ +   R+A+ 
Sbjct: 1   FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQAL- 59

Query: 143 SIWHSTNNQDTDD-AAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIAL 201
                   ++ +      G       ++  S    R+   A + ++ RG  FI+ EH+ L
Sbjct: 60  -------EKELEKLPKVSGPG----GQVYLSPELNRLLNLAEKLAQKRGDEFISSEHLLL 108

Query: 202 GLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAA 261
            L   D G+ G++LK  G   + L A A++ ++G                     G+   
Sbjct: 109 ALLD-DKGTLGKLLKEAGATADALEA-AINAVRG---------------------GQKVT 145

Query: 262 LKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESG 321
             +       ALE++  DLT RA E  +DPVIGR+ EI+R IQ+L RRTKNNP+L+GE G
Sbjct: 146 SANAEDQYE-ALEKYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPG 204

Query: 322 VGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS 381
           VGKTAI EGLA RIV  +VP  L +KR+++LDMG L+AGAK RGE E R+  +++E+ KS
Sbjct: 205 VGKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKS 264

Query: 382 -GDVILFIDEVHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQDEHRTQF 439
            G +ILFIDE+HTL+G+G      K  G +D  N+LKP+L RGEL CI +TT DE+R   
Sbjct: 265 EGQIILFIDELHTLVGAG------KAEGAMDAGNMLKPALARGELHCIGATTLDEYRKYI 318

Query: 440 EKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD 499
           EKD AL RRFQPV + EP+ ED + IL GL+E+YE HH  + T  AI AA  LS RYI+D
Sbjct: 319 EKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRITDPAIVAAATLSHRYITD 378

Query: 500 RYLPDKAIDLVDEAGSRAHIEL 521
           R+LPDKAIDL+DEA +R  +E+
Sbjct: 379 RFLPDKAIDLIDEAAARIRMEI 400

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 [Protein fate, Protein folding and stabilization]. Length = 852

>gnl|CDD|236828 PRK11034, clpA, ATP-dependent Clp protease ATP-binding subunit; Provisional

 Score =  352 bits (906), Expect = e-111
 Identities = 200/575 (34%), Positives = 301/575 (52%), Gaps = 98/575 (17%)

Query: 111 QHLLLGLIAEDRHPNGFLESGITIDKAREAVVS-IWHSTNNQDTDDAAAQGKPFSSAAKM 169
           +HLLL L++            + +   R+ + + I  +T      +     +P       
Sbjct: 28  EHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVLPASEEERDTQP------- 80

Query: 170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVA 229
             ++S +RV + AV + +S G + +   ++ + +F+  +  A  +L++   +V+ L  V 
Sbjct: 81  --TLSFQRVLQRAVFHVQSSGRSEVTGANVLVAIFSEQESQAAYLLRK--HEVSRLDVVN 136

Query: 230 VSRLQGELAKEGREPSLAKGVRENSISGKTAALKSP-GRTRASA---LEQFCVDLTARAS 285
                           ++ G R++  S  +     P    +A     +E F  +L   A 
Sbjct: 137 F---------------ISHGTRKDEPSQSSDPGSQPNSEEQAGGEERMENFTTNLNQLAR 181

Query: 286 EELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL 345
              IDP+IGRE E++R IQ+LCRR KNNP+L+GESGVGKTAIAEGLA RIVQ +VP  + 
Sbjct: 182 VGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMA 241

Query: 346 SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNK 405
              I SLD+G L+AG K RG+ E R   L+ ++++  + ILFIDE+HT+IG+G    G  
Sbjct: 242 DCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQ- 300

Query: 406 GTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRI 465
              +D +NL+KP L  G+++ I STT  E    FEKD+ALARRFQ + I+EPS E+ V+I
Sbjct: 301 ---VDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQI 357

Query: 466 LLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRK 525
           + GL+ KYEAHH+ ++T +A+ AAV L+ +YI+DR+LPDKAID++DEAG+RA +    ++
Sbjct: 358 INGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKR 417

Query: 526 KEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASD 585
           K                  +TV              + VVA +    E  V     S SD
Sbjct: 418 K------------------KTVNVA---------DIESVVARIARIPEKSV-----SQSD 445

Query: 586 DDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAV 645
            D                                L  L ++LK  V GQD+A+ A++ A+
Sbjct: 446 RD-------------------------------TLKNLGDRLKMLVFGQDKAIEALTEAI 474

Query: 646 KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA 680
           K SR GL   ++P  + LF GPTGVGKTE+   L+
Sbjct: 475 KMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLS 509

Length = 758

>gnl|CDD|234173 TIGR03346, chaperone_ClpB, ATP-dependent chaperone ClpB

 Score =  141 bits (358), Expect = 9e-35
 Identities = 57/102 (55%), Positives = 71/102 (69%), Gaps = 4/102 (3%)

Query: 592 VGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVG 651
           V  ++IA V S W+GIPV ++   ER  L+ +EE L +RV+GQDEAV A+S A++RSR G
Sbjct: 528 VTAEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAG 587

Query: 652 LKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS----VRI 689
           L DPNRP  + LF GPTGVGKTELAK+LA   F      VRI
Sbjct: 588 LSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRI 629

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 [Protein fate, Protein folding and stabilization]. Length = 852

>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 = 84.1 bits (208), Expect = 5e-19
 Identities = 36/160 (22%), Positives = 63/160 (39%), Gaps = 18/160 (11%)

Query: 293 IGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL 352
           +G+E  I+ + + L      N +L G  G GKT +A  +A  + +   P          L
Sbjct: 1   VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFL-------YL 53

Query: 353 DMGLLMAGAKERGELEARVTTLISEIQKSGDV-ILFIDEVHTLIGSGTVGRGNKGTGLDI 411
           +   L+ G          +  L+ E+ +     +LFIDE+ +L       RG +   L +
Sbjct: 54  NASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSL------SRGAQNALLRV 107

Query: 412 SNLLKPSL-GRGELQCIASTTQDEHRTQFEKDKALARRFQ 450
              L      R  ++ I +T +       + D+AL  R  
Sbjct: 108 LETLNDLRIDRENVRVIGATNRPL---LGDLDRALYDRLD 144

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

 Score = 58.5 bits (141), Expect = 3e-10
 Identities = 29/150 (19%), Positives = 58/150 (38%), Gaps = 12/150 (8%)

Query: 310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS-----KRIMSLDMGLLMAGAKER 364
                +++G  G GKT +A  LA  +      V  +      + ++   + +++ G K  
Sbjct: 1   PGEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKAS 60

Query: 365 GELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGEL 424
           G  E R+   ++  +K    +L +DE+ +L+ +           L+   LL        L
Sbjct: 61  GSGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLL---LEELRLLLLLKSEKNL 117

Query: 425 QCIASTTQDEHRTQFEKDKALARRFQPVLI 454
             I +T    +  +      L RRF   ++
Sbjct: 118 TVILTT----NDEKDLGPALLRRRFDRRIV 143

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|217254 pfam02861, Clp_N, Clp amino terminal domain

 Score = 51.8 bits (125), Expect = 7e-09
 Identities = 18/42 (42%), Positives = 27/42 (64%)

Query: 182 AVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVN 223
           A E ++  G+ +I  EH+ L L   DDG A R+LK+ GVD++
Sbjct: 1   AQELAKELGHQYIGTEHLLLALLEEDDGIAARLLKKAGVDLD 42

This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site. Length = 53

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

 Score = 49.5 bits (119), Expect = 3e-07
 Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 14/105 (13%)

Query: 315 ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTL 374
           +L G  G GKT +A+ +A      E     L    + +    L++  K  GE E R+  L
Sbjct: 2   LLYGPPGTGKTTLAKAVA-----KE-----LGAPFIEISGSELVS--KYVGESEKRLREL 49

Query: 375 ISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL 419
               +K    ++FIDE+  L GS   G G       + N L   L
Sbjct: 50  FEAAKKLAPCVIFIDEIDALAGSR--GSGGDSESRRVVNQLLTEL 92

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

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

 Score = 50.3 bits (121), Expect = 2e-06
 Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 8/52 (15%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC 682
           VIGQ+  V  +  A+K  R+          A LF GP G GKT +A+  A  
Sbjct: 16  VIGQEHIVQTLKNAIKNGRIAH--------AYLFSGPRGTGKTSIARIFAKA 59

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

>gnl|CDD|219536 pfam07724, AAA_2, AAA domain (Cdc48 subfamily)

 Score = 46.4 bits (111), Expect = 7e-06
 Identities = 21/32 (65%), Positives = 23/32 (71%)

Query: 657 RPTAAMLFCGPTGVGKTELAKSLAACYFGSVR 688
           RP  + LF GPTGVGKTELAK+LA   FG  R
Sbjct: 1   RPIGSFLFLGPTGVGKTELAKALAELLFGDER 32

This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. Length = 168

>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 = 44.1 bits (104), Expect = 4e-05
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 9/49 (18%)

Query: 632 IGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA 680
           +GQ+EA+ A+  A++           P   +L  GP G GKT LA+++A
Sbjct: 1   VGQEEAIEALREALEL---------PPPKNLLLYGPPGTGKTTLARAIA 40

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|221970 pfam13191, AAA_16, AAA ATPase domain

 Score = 42.6 bits (100), Expect = 1e-04
 Identities = 31/129 (24%), Positives = 52/129 (40%), Gaps = 27/129 (20%)

Query: 291 PVIGRETEIQRIIQILCRRTKNNP---ILLGESGVGKTAIAE-------GLAIRIVQAEV 340
            ++GRE E++R++  L R     P   +L G SG GKT++           A +  QAE 
Sbjct: 1   RLVGREEELERLLDALRRARSGGPPSVLLTGPSGTGKTSLLRELLEGLLVAAGKCDQAER 60

Query: 341 -PVFLLSKRIMSLDMGLLMAGAKERGELEAR----------------VTTLISEIQKSGD 383
            P +  S+ +  L   LL   A E   L                   V  L   + ++  
Sbjct: 61  NPPYAFSQALRELLRQLLRELAAELLLLREALLAALGAELIEGLQDLVELLERLLARARP 120

Query: 384 VILFIDEVH 392
           ++L +D++ 
Sbjct: 121 LVLVLDDLQ 129

This family of domains contain a P-loop motif that is characteristic of the AAA superfamily. Length = 154

>gnl|CDD|226415 COG3899, COG3899, Predicted ATPase [General function prediction only]

 Score = 44.7 bits (106), Expect = 1e-04
 Identities = 18/50 (36%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 291 PVIGRETEIQRIIQILCRRTKNNP--ILL-GESGVGKTAIAEGLAIRIVQ 337
           P+ GRETE+ +++    R +K     +L+ GESG+GK+A+   +   I Q
Sbjct: 1   PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQ 50

Length = 849

>gnl|CDD|217254 pfam02861, Clp_N, Clp amino terminal domain

 Score = 38.3 bits (90), Expect = 5e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 96  SQREAKSLGKDMVFTQHLLLGLIAEDRHP--NGFLESGITIDKAREAVVSI 144
           +Q  AK LG   + T+HLLL L+ ED         ++G+ +D  REA+  +
Sbjct: 1   AQELAKELGHQYIGTEHLLLALLEEDDGIAARLLKKAGVDLDALREAIEKL 51

This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site. Length = 53

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

 Score = 42.5 bits (100), Expect = 7e-04
 Identities = 54/298 (18%), Positives = 89/298 (29%), Gaps = 56/298 (18%)

Query: 133 TIDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYN 192
            +D  +   V +  +TN  D             A + P      R  E  +     R   
Sbjct: 110 LMDGLKRGQVIVIGATNRPDG---------LDPAKRRP--GRFDREIEVNLPDEAGRLEI 158

Query: 193 FIAPEH-----IALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLA 247
                            T+   + G+    LG      A   + R    + +     +  
Sbjct: 159 LQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEAALRELRRAIDLVGEY-IGVTED 217

Query: 248 KGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILC 307
                        ALK    +R    E   V L      E          E++  I+   
Sbjct: 218 D---------FEEALKKVLPSRGVLFEDEDVTLDDIGGLEEAKE------ELKEAIETPL 262

Query: 308 RR-----TKNNP-----ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL 357
           +R               +L G  G GKT +A+ +A+              R +S+    L
Sbjct: 263 KRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVAL----------ESRSRFISVKGSEL 312

Query: 358 MAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLL 415
           ++  K  GE E  +  L  + +K    I+FIDE+ +L      G    G+G  +   L
Sbjct: 313 LS--KWVGESEKNIRELFEKARKLAPSIIFIDEIDSLA--SGRGPSEDGSGRRVVGQL 366

Length = 494

>gnl|CDD|224141 COG1220, HslU, ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

 Score = 42.3 bits (100), Expect = 7e-04
 Identities = 26/62 (41%), Positives = 39/62 (62%), Gaps = 7/62 (11%)

Query: 625 EQLKKRVIGQDEAVAAISRAVK----RSRV--GLKDPNRPTAAMLFCGPTGVGKTELAKS 678
            +L + +IGQDEA  A++ A++    R ++   L+D   P   +L  GPTGVGKTE+A+ 
Sbjct: 11  SELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKN-ILMIGPTGVGKTEIARR 69

Query: 679 LA 680
           LA
Sbjct: 70  LA 71

Length = 444

>gnl|CDD|235422 PRK05342, clpX, ATP-dependent protease ATP-binding subunit ClpX; Provisional

 Score = 42.1 bits (100), Expect = 7e-04
 Identities = 25/57 (43%), Positives = 31/57 (54%), Gaps = 7/57 (12%)

Query: 631 VIGQDEAVAAISRAV----KRSRVGLKDPNRPTAA---MLFCGPTGVGKTELAKSLA 680
           VIGQ+ A   +S AV    KR R G K  +        +L  GPTG GKT LA++LA
Sbjct: 73  VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLA 129

Length = 412

>gnl|CDD|213527 TIGR00390, hslU, ATP-dependent protease HslVU, ATPase subunit

 Score = 41.7 bits (98), Expect = 0.001
 Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 7/61 (11%)

Query: 626 QLKKRVIGQDEAVAAISRAVK----RSRV--GLKDPNRPTAAMLFCGPTGVGKTELAKSL 679
           +L K +IGQDEA  +++ A++    RS++   LKD   P   +L  GPTGVGKTE+A+ L
Sbjct: 9   ELDKYIIGQDEAKKSVAIALRNRYRRSQLPEELKDEVTPKN-ILMIGPTGVGKTEIARRL 67

Query: 680 A 680
           A
Sbjct: 68  A 68

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 MEDLINE:98389714, is Ser in other members of the seed alignment [Protein fate, Protein folding and stabilization]. Length = 441

>gnl|CDD|181681 PRK09183, PRK09183, transposase/IS protein; Provisional

 Score = 40.8 bits (96), Expect = 0.001
 Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 9/79 (11%)

Query: 313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVT 372
           N +LLG SGVGKT +A  L    V+A + V    +   + D+ L ++ A+ +G  +  + 
Sbjct: 104 NIVLLGPSGVGKTHLAIALGYEAVRAGIKV----RFTTAADLLLQLSTAQRQGRYKTTLQ 159

Query: 373 TLISEIQKSGDVILFIDEV 391
             +         +L IDE+
Sbjct: 160 RGV-----MAPRLLIIDEI 173

Length = 259

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

 Score = 40.9 bits (96), Expect = 0.002
 Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 12/72 (16%)

Query: 620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSL 679
           L  +  +L+K V+G +E +     A+                 L  GP GVGKT LA++L
Sbjct: 15  LGKIRSELEKVVVGDEEVIELALLALLA--------GGHV---LLEGPPGVGKTLLARAL 63

Query: 680 AACYFGS-VRIH 690
           A       VRI 
Sbjct: 64  ARALGLPFVRIQ 75

Length = 329

>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown domain fusion protein; Reviewed

 Score = 41.2 bits (97), Expect = 0.002
 Identities = 52/187 (27%), Positives = 81/187 (43%), Gaps = 44/187 (23%)

Query: 313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE-RGELEARV 371
           + IL G  GVGKT +A  +A    +A               +  ++AG K+ R E++   
Sbjct: 54  SLILYGPPGVGKTTLARIIA-NHTRAHF-----------SSLNAVLAGVKDLRAEVDRAK 101

Query: 372 TTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT 431
             L    +++   ILFIDEVH         R NK       + L P +  G +  I +TT
Sbjct: 102 ERLERHGKRT---ILFIDEVH---------RFNKAQ----QDALLPWVENGTITLIGATT 145

Query: 432 QDEHRTQFEKDKALARR-----FQPVLISEPSQEDAVRILL-GLREKYEAHHNCKFTLEA 485
           ++ +   FE +KAL  R      + +     S ED  ++L   L++K   + + K  LE 
Sbjct: 146 ENPY---FEVNKALVSRSRLFRLKSL-----SDEDLHQLLKRALQDKERGYGDRKVDLEP 197

Query: 486 INAAVHL 492
             A  HL
Sbjct: 198 -EAEKHL 203

Length = 725

>gnl|CDD|222104 pfam13401, AAA_22, AAA domain

 Score = 38.0 bits (89), Expect = 0.003
 Identities = 25/92 (27%), Positives = 38/92 (41%), Gaps = 6/92 (6%)

Query: 308 RRTKNNPILLGESGVGKTAIAEGLA-----IRIVQAEVPVFLLSKRIMSLDMGLLMAGAK 362
           RR     +L GESG GKT +   LA      R+V  E P     K ++   +  L     
Sbjct: 1   RRGAGIGVLTGESGSGKTTLLRRLARQLPNRRVVYVEAPSLGTPKDLLRKILRALGLPLS 60

Query: 363 ERGELEARVTTLISEIQKSGDVILFIDEVHTL 394
             G     +  ++  +++ G  +L IDE   L
Sbjct: 61  -GGTTAELLEAILDALKRRGRPLLIIDEAQHL 91

Length = 124

>gnl|CDD|184920 PRK14956, PRK14956, DNA polymerase III subunits gamma and tau; Provisional

 Score = 40.3 bits (94), Expect = 0.003
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 8/55 (14%)

Query: 626 QLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA 680
           Q  + VI QD A+ A+  A+K  ++G         A +F GP GVGKT +A+ LA
Sbjct: 15  QFFRDVIHQDLAIGALQNALKSGKIG--------HAYIFFGPRGVGKTTIARILA 61

Length = 484

>gnl|CDD|224140 COG1219, ClpX, ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

 Score = 39.9 bits (94), Expect = 0.004
 Identities = 25/61 (40%), Positives = 31/61 (50%), Gaps = 16/61 (26%)

Query: 631 VIGQDEAVAAISRAV----KRSR-------VGLKDPNRPTAAMLFCGPTGVGKTELAKSL 679
           VIGQ++A   +S AV    KR         V L   N     +L  GPTG GKT LA++L
Sbjct: 63  VIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSN-----ILLIGPTGSGKTLLAQTL 117

Query: 680 A 680
           A
Sbjct: 118 A 118

Length = 408

>gnl|CDD|236011 PRK07399, PRK07399, DNA polymerase III subunit delta'; Validated

 Score = 39.5 bits (93), Expect = 0.004
 Identities = 17/51 (33%), Positives = 26/51 (50%), Gaps = 8/51 (15%)

Query: 627 LKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAK 677
           L   +IGQ  A+  ++ A+K++R+          A LF GP GVG+   A 
Sbjct: 2   LFANLIGQPLAIELLTAAIKQNRI--------APAYLFAGPEGVGRKLAAL 44

Length = 314

>gnl|CDD|237867 PRK14953, PRK14953, DNA polymerase III subunits gamma and tau; Provisional

 Score = 39.8 bits (93), Expect = 0.004
 Identities = 22/52 (42%), Positives = 28/52 (53%), Gaps = 8/52 (15%)

Query: 629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA 680
           K VIGQ+  V  +  AVK  RV        + A +F GP G GKT +A+ LA
Sbjct: 16  KEVIGQEIVVRILKNAVKLQRV--------SHAYIFAGPRGTGKTTIARILA 59

Length = 486

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	710
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	100.0
CHL00095	821	clpC Clp protease ATP binding subunit	100.0
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	100.0
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	100.0
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	100.0
PRK10865	857	protein disaggregation chaperone; Provisional	100.0
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	100.0
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.95
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.93
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.93
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.89
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.87
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.86
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	99.85
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.84
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	99.83
CHL00195	489	ycf46 Ycf46; Provisional	99.81
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.81
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.81
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	99.81
PRK03992	389	proteasome-activating nucleotidase; Provisional	99.78
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	99.77
KOG2028	554	consensus ATPase related to the helicase subunit o	99.77
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	99.76
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.76
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	99.76
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.76
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	99.75
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	99.75
PRK13342	413	recombination factor protein RarA; Reviewed	99.75
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.74
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.74
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.74
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.74
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.74
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.73
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.73
CHL00176	638	ftsH cell division protein; Validated	99.73
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.73
CHL00181	287	cbbX CbbX; Provisional	99.72
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.71
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.71
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	99.71
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	99.71
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	99.71
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.71
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.7
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.7
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.7
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.7
PRK13341	725	recombination factor protein RarA/unknown domain f	99.7
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.69
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.69
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.69
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.68
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.68
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	99.68
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.67
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.67
CHL00095	821	clpC Clp protease ATP binding subunit	99.67
PLN03025	319	replication factor C subunit; Provisional	99.66
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	99.66
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	99.66
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.65
CHL00206	2281	ycf2 Ycf2; Provisional	99.65
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.65
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.65
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	99.63
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.63
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.63
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	99.63
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.63
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.62
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.6
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	99.6
PRK12402	337	replication factor C small subunit 2; Reviewed	99.6
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.6
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK08084	235	DNA replication initiation factor; Provisional	99.59
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.59
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.59
PHA02544	316	44 clamp loader, small subunit; Provisional	99.59
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK04195	482	replication factor C large subunit; Provisional	99.58
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.58
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	99.58
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.57
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	99.57
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.57
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.56
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.56
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.55
PF00004	132	AAA: ATPase family associated with various cellula	99.55
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.55
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.54
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK05642	234	DNA replication initiation factor; Validated	99.53
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.53
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.53
PRK12422	445	chromosomal replication initiation protein; Provis	99.52
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.52
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.51
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.51
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.51
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.5
PRK06893	229	DNA replication initiation factor; Validated	99.5
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.5
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.5
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.49
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.49
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.49
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.48
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.48
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.48
PRK08727	233	hypothetical protein; Validated	99.48
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.48
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.48
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.47
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.46
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.44
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.41
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.41
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.41
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.41
CHL00195	489	ycf46 Ycf46; Provisional	99.4
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.38
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.37
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.37
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.37
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.36
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.36
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.36
PRK09087	226	hypothetical protein; Validated	99.35
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.34
PRK06620	214	hypothetical protein; Validated	99.33
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.32
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.32
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.31
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.31
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.29
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.28
PRK13531	498	regulatory ATPase RavA; Provisional	99.27
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.27
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	99.27
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.27
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	99.25
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.25
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.24
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.24
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	99.21
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	99.2
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.2
PRK10865	857	protein disaggregation chaperone; Provisional	99.2
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.17
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	99.16
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.16
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	99.16
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.15
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	99.15
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	99.14
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.13
COG2204	464	AtoC Response regulator containing CheY-like recei	99.12
COG0714	329	MoxR-like ATPases [General function prediction onl	99.12
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.09
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.08
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	99.08
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.08
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	99.08
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.07
COG1221	403	PspF Transcriptional regulators containing an AAA-	99.06
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.05
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.05
PRK05022	509	anaerobic nitric oxide reductase transcription reg	99.04
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	99.03
PHA02244	383	ATPase-like protein	99.03
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.03
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	99.03
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.02
PRK15424	538	propionate catabolism operon regulatory protein Pr	99.02
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.02
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	99.02
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.01
PRK04132	846	replication factor C small subunit; Provisional	99.0
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	98.99
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	98.98
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	98.98
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.98
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	98.98
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.97
PRK05707	328	DNA polymerase III subunit delta'; Validated	98.95
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	98.95
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	98.94
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.94
PRK08769	319	DNA polymerase III subunit delta'; Validated	98.94
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	98.94
) 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	98.94
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	98.93
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	98.93
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.92
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.9
smart00350	509	MCM minichromosome maintenance proteins.	98.9
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.87
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.85
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	98.85
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.84
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.83
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.83
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	98.82
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	98.81
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	98.81
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	98.8
PRK06871	325	DNA polymerase III subunit delta'; Validated	98.79
PRK08116	268	hypothetical protein; Validated	98.79
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.79
PRK12377	248	putative replication protein; Provisional	98.77
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.77
PRK08181	269	transposase; Validated	98.77
PF07726	131	AAA_3: ATPase family associated with various cellu	98.77
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.77
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	98.77
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	98.76
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.76
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.75
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	98.75
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	98.75
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	98.73
PRK06526	254	transposase; Provisional	98.72
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.72
PRK06090	319	DNA polymerase III subunit delta'; Validated	98.72
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.7
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.7
PF02861	53	Clp_N: Clp amino terminal domain; InterPro: IPR004	98.7
smart00382	148	AAA ATPases associated with a variety of cellular	98.69
CHL00181	287	cbbX CbbX; Provisional	98.69
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.68
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.67
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	98.67
PF13173	128	AAA_14: AAA domain	98.62
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	98.62
PRK07952	244	DNA replication protein DnaC; Validated	98.62
PRK09862	506	putative ATP-dependent protease; Provisional	98.62
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.61
PRK13765	637	ATP-dependent protease Lon; Provisional	98.6
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	98.59
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	98.59
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.59
PF02861	53	Clp_N: Clp amino terminal domain; InterPro: IPR004	98.59
PRK09183	259	transposase/IS protein; Provisional	98.57
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.57
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	98.54
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.53
PRK06835	329	DNA replication protein DnaC; Validated	98.51
PRK15115	444	response regulator GlrR; Provisional	98.5
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	98.5
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	98.5
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.5
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	98.48
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	98.48
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.48
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.48
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.46
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	98.46
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	98.45
PRK06921	266	hypothetical protein; Provisional	98.44
PRK03992	389	proteasome-activating nucleotidase; Provisional	98.42
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.42
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	98.42
PLN03025	319	replication factor C subunit; Provisional	98.41
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	98.39
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.38
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	98.38
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	98.37
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.35
PHA00729	226	NTP-binding motif containing protein	98.33
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.32
PF05729	166	NACHT: NACHT domain	98.31
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.29
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	98.29
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	98.29
COG2256	436	MGS1 ATPase related to the helicase subunit of the	98.28
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.27
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.27
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	98.26
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	98.26
PRK08939	306	primosomal protein DnaI; Reviewed	98.25
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	98.22
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	98.22
PRK07940	394	DNA polymerase III subunit delta'; Validated	98.22
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	98.22
PRK12402	337	replication factor C small subunit 2; Reviewed	98.21
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	98.2
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	98.18
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.18
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	98.18
PRK04195	482	replication factor C large subunit; Provisional	98.16
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.12
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	98.12
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	98.11
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	98.11
PRK15455	644	PrkA family serine protein kinase; Provisional	98.1
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	98.1
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.1
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.09
COG1241	682	MCM2 Predicted ATPase involved in replication cont	98.09
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.09
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	98.09
CHL00176	638	ftsH cell division protein; Validated	98.08
PRK13531	498	regulatory ATPase RavA; Provisional	98.08
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	98.08
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	98.07
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	98.07
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	98.06
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	98.06
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	98.06
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.03
PF14516	331	AAA_35: AAA-like domain	98.03
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	98.03
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	98.02
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	98.01
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.0
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	97.99
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	97.99
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	97.99
PRK00440	319	rfc replication factor C small subunit; Reviewed	97.98
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	97.98
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	97.97
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	97.96
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.96
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	97.95
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	97.94
PF00004	132	AAA: ATPase family associated with various cellula	97.94
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	97.93
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	97.92
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	97.91
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.91
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	97.9
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	97.9
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	97.89
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	97.89
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	97.88
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	97.88
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	97.88
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	97.87
CHL00206	2281	ycf2 Ycf2; Provisional	97.87
PRK13342	413	recombination factor protein RarA; Reviewed	97.87
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	97.86
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	97.86
PHA02544	316	44 clamp loader, small subunit; Provisional	97.86
PRK05818	261	DNA polymerase III subunit delta'; Validated	97.85
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	97.84
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	97.84
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.84
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	97.83
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	97.83
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	97.82
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	97.82
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	97.81
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	97.8
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	97.79
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	97.78
COG0606	490	Predicted ATPase with chaperone activity [Posttran	97.78
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	97.77
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.76
PRK07471	365	DNA polymerase III subunit delta'; Validated	97.76
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	97.75
COG0714	329	MoxR-like ATPases [General function prediction onl	97.74
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.72
smart00382	148	AAA ATPases associated with a variety of cellular	97.71
PRK06893	229	DNA replication initiation factor; Validated	97.7
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	97.69
PRK07399	314	DNA polymerase III subunit delta'; Validated	97.69
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	97.68
KOG2028	554	consensus ATPase related to the helicase subunit o	97.68
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.68
PRK08903	227	DnaA regulatory inactivator Hda; Validated	97.66
PRK13341	725	recombination factor protein RarA/unknown domain f	97.66
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	97.66
PRK12377	248	putative replication protein; Provisional	97.65
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	97.64
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	97.64
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	97.63
PRK14700	300	recombination factor protein RarA; Provisional	97.6
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	97.59
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	97.58
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	97.58
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	97.57
PRK13765	637	ATP-dependent protease Lon; Provisional	97.57
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	97.55
PRK05564	313	DNA polymerase III subunit delta'; Validated	97.55
PRK07952	244	DNA replication protein DnaC; Validated	97.54
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.53
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	97.53
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	97.52
PLN03210	1153	Resistant to P. syringae 6; Provisional	97.51
PRK09112	351	DNA polymerase III subunit delta'; Validated	97.5
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	97.5
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	97.49
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	97.48
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	97.48
PTZ00202	550	tuzin; Provisional	97.48
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	97.44
PF10923	416	DUF2791: P-loop Domain of unknown function (DUF279	97.43
PRK08058	329	DNA polymerase III subunit delta'; Validated	97.43
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.43
PRK08116	268	hypothetical protein; Validated	97.42
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	97.41
PRK06835	329	DNA replication protein DnaC; Validated	97.4
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.39
PRK08939	306	primosomal protein DnaI; Reviewed	97.38
PRK00411	394	cdc6 cell division control protein 6; Reviewed	97.36
PRK06581	263	DNA polymerase III subunit delta'; Validated	97.35
PRK10536	262	hypothetical protein; Provisional	97.3
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	97.3
COG4088	261	Predicted nucleotide kinase [Nucleotide transport	97.3
PHA02774	613	E1; Provisional	97.29
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	97.29
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.28
COG1484	254	DnaC DNA replication protein [DNA replication, rec	97.27
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.27
PF07726	131	AAA_3: ATPase family associated with various cellu	97.27
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.27
) 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	97.27
KOG1808	1856	consensus AAA ATPase containing von Willebrand fac	97.27
PRK15455	644	PrkA family serine protein kinase; Provisional	97.27
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	97.26
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	97.26
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	97.24
cd01128	249	rho_factor Transcription termination factor rho is	97.24
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	97.24
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.23
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	97.23
PRK08181	269	transposase; Validated	97.23
PRK04296	190	thymidine kinase; Provisional	97.23
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	97.21
PHA02244	383	ATPase-like protein	97.21
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	97.2
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	97.19
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	97.19
PRK06526	254	transposase; Provisional	97.17
PRK13695	174	putative NTPase; Provisional	97.16
PRK04841	903	transcriptional regulator MalT; Provisional	97.16
PRK08118	167	topology modulation protein; Reviewed	97.15
PRK05642	234	DNA replication initiation factor; Validated	97.11
PRK09376	416	rho transcription termination factor Rho; Provisio	97.11
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.09
TIGR02237	209	recomb_radB DNA repair and recombination protein R	97.09
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	97.08
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	97.07
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	97.06
PRK08727	233	hypothetical protein; Validated	97.06
PRK08084	235	DNA replication initiation factor; Provisional	97.06
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	97.05
PHA00729	226	NTP-binding motif containing protein	97.05
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.04
PRK06921	266	hypothetical protein; Provisional	97.03
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.02
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	97.0
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.0
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	96.98
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	96.96
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	96.96
PRK00771	437	signal recognition particle protein Srp54; Provisi	96.95
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	96.95
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	96.93
COG4650	531	RtcR Sigma54-dependent transcription regulator con	96.93
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	96.92
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	96.92
COG3899	849	Predicted ATPase [General function prediction only	96.91
PRK09183	259	transposase/IS protein; Provisional	96.91
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	96.9
PRK05022	509	anaerobic nitric oxide reductase transcription reg	96.89
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	96.88
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.88
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.87
PRK04220	301	2-phosphoglycerate kinase; Provisional	96.84
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.83
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.83
PRK06067	234	flagellar accessory protein FlaH; Validated	96.83
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.82
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	96.81
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.8
PRK06620	214	hypothetical protein; Validated	96.79
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.79
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.77
PHA02624	647	large T antigen; Provisional	96.77
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	96.76
PRK12422	445	chromosomal replication initiation protein; Provis	96.74
PRK11608	326	pspF phage shock protein operon transcriptional ac	96.74
PRK06696	223	uridine kinase; Validated	96.74
PRK13947	171	shikimate kinase; Provisional	96.74
PRK11823	446	DNA repair protein RadA; Provisional	96.74
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	96.73
PHA02624	647	large T antigen; Provisional	96.73
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.72

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.1e-98  Score=842.71  Aligned_cols=569  Identities=45%  Similarity=0.670  Sum_probs=491.2

Q ss_pred             HhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCcHHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcCCCC
Q 005179           84 RFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPF  163 (710)
Q Consensus        84 ~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (710)
                      +||++++++|..|+.+|++++|++|++||||++|+.++.+..+|..+|++++.++..+...+++.+...           
T Consensus         1 ~~~~~~~~~l~~a~~~a~~~~h~~~~~eHll~~ll~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~-----------   69 (786)
T COG0542           1 KLTERAQKALELAQELARMRRHEYVTPEHLLLALLDQPKGDELLNLCGIDLDKLRQELEEFIDKLPKVL-----------   69 (786)
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHcCCchHHHHHHcCCCHHHHHHHHHHHHhccCCCC-----------
Confidence            589999999999999999999999999999999999998889999999999999999999999887531           


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhhcccCCC
Q 005179          164 SSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGRE  243 (710)
Q Consensus       164 ~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~~~~~~~  243 (710)
                      +  . +.+|+.++++++.|+.+|+..++.||+++|||+|++.++++.+..+|..+|++...+.. +...+.+......  
T Consensus        70 ~--~-~~~s~~~~~~~~~a~~~a~~~~~~~v~~~~llla~~~~~~~~~~~~l~~~~~~~~~~~~-~~~~~~~~~~~~~--  143 (786)
T COG0542          70 G--S-PYLSPRLKRVLERAWLLAQSLGDEYVSTEHLLLALLNEPESVAAYILKKLGVTRKDVEE-LIEELRGGNEVDS--  143 (786)
T ss_pred             C--C-CCCCHHHHHHHHHHHHHHHhccCccccHHHHHHHHhcccchHHHHHHHhccCCHHHHHH-HHHHHhcccccCC--
Confidence            1  2 77899999999999999999999999999999999999999999999999999998844 4444432210000  


Q ss_pred             CccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCCh
Q 005179          244 PSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVG  323 (710)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~G  323 (710)
                                          .........|++|+.|+++.++.|++||+|||++|+++++++|+|+.+||++|+|+||||
T Consensus       144 --------------------~~~~~~~~~L~~y~~dlt~~Ar~gklDPvIGRd~EI~r~iqIL~RR~KNNPvLiGEpGVG  203 (786)
T COG0542         144 --------------------KNAEEDQDALEKYTRDLTELAREGKLDPVIGRDEEIRRTIQILSRRTKNNPVLVGEPGVG  203 (786)
T ss_pred             --------------------cccccchhhHHHHhhhhHHHHhcCCCCCCcChHHHHHHHHHHHhccCCCCCeEecCCCCC
Confidence                                000113478999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC
Q 005179          324 KTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG  403 (710)
Q Consensus       324 KT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~  403 (710)
                      ||+++++||+++.++++|..+.++.++.+|++.+++|++++|+||++++.+++++.+.+++||||||+|.++++|..   
T Consensus       204 KTAIvEGLA~rIv~g~VP~~L~~~~i~sLD~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~---  280 (786)
T COG0542         204 KTAIVEGLAQRIVNGDVPESLKDKRIYSLDLGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGAT---  280 (786)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHcCCEEEEecHHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcc---
Confidence            99999999999999999999999999999999999999999999999999999999988999999999999999765   


Q ss_pred             CCCC-hHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCC
Q 005179          404 NKGT-GLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFT  482 (710)
Q Consensus       404 ~~~~-~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~  482 (710)
                        ++ .+|+.|+|+|.|++|.+.|||+||..+|+++++.|++|.|||+.|.|.+|+.++...||+++..+|+.+|++.|+
T Consensus       281 --~G~a~DAaNiLKPaLARGeL~~IGATT~~EYRk~iEKD~AL~RRFQ~V~V~EPs~e~ti~ILrGlk~~yE~hH~V~i~  358 (786)
T COG0542         281 --EGGAMDAANLLKPALARGELRCIGATTLDEYRKYIEKDAALERRFQKVLVDEPSVEDTIAILRGLKERYEAHHGVRIT  358 (786)
T ss_pred             --cccccchhhhhHHHHhcCCeEEEEeccHHHHHHHhhhchHHHhcCceeeCCCCCHHHHHHHHHHHHHHHHHccCceec
Confidence              22 589999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccch
Q 005179          483 LEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYD  562 (710)
Q Consensus       483 ~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  562 (710)
                      ++++.+++.++.||+++|++||||||++|+||+++++... .|.+  +..+..+......++..+...++ +...++.+.
T Consensus       359 D~Al~aAv~LS~RYI~dR~LPDKAIDLiDeA~a~~~l~~~-~p~~--l~~~~~~~~~l~~e~~~~~~e~~-~~~k~~~~~  434 (786)
T COG0542         359 DEALVAAVTLSDRYIPDRFLPDKAIDLLDEAGARVRLEID-KPEE--LDELERELAQLEIEKEALEREQD-EKEKKLIDE  434 (786)
T ss_pred             HHHHHHHHHHHHhhcccCCCCchHHHHHHHHHHHHHhccc-CCcc--hhHHHHHHHHHHHHHHHHhhhhh-HHHHHHHHH
Confidence            9999999999999999999999999999999999999877 6553  11111111111111111111111 000011100


Q ss_pred             hhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHH
Q 005179          563 DVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAIS  642 (710)
Q Consensus       563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~  642 (710)
                      ...+..  .........+    .   . .|+.++|+++++.|||||+.++..++...+.++++.|+++|+||++|++.|+
T Consensus       435 ~~~~~~--~~~~~~~~~~----~---~-~v~~~~Ia~vv~~~TgIPv~~l~~~e~~kll~le~~L~~rViGQd~AV~avs  504 (786)
T COG0542         435 IIKLKE--GRIPELEKEL----E---A-EVDEDDIAEVVARWTGIPVAKLLEDEKEKLLNLERRLKKRVIGQDEAVEAVS  504 (786)
T ss_pred             HHHHhh--hhhhhHHHHH----h---h-ccCHHHHHHHHHHHHCCChhhhchhhHHHHHHHHHHHhcceeChHHHHHHHH
Confidence            000000  0000011111    0   1 2999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          643 RAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       643 ~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      ++|+++|+|+++|+||+|+|||.||||||||+|||+||..|||++.+||||||||| .++||+||||
T Consensus       505 ~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy-~EkHsVSrLI  570 (786)
T COG0542         505 DAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEY-MEKHSVSRLI  570 (786)
T ss_pred             HHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHH-HHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999 6899999998

>CHL00095 clpC Clp protease ATP binding subunit

Probab=100.00  E-value=9.1e-83  Score=752.25  Aligned_cols=586  Identities=45%  Similarity=0.708  Sum_probs=486.9

Q ss_pred             hHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhh
Q 005179           81 VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAA  158 (710)
Q Consensus        81 ~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~  158 (710)
                      ||++||++++++|..|+.+|++++|++|+|||||+|||.++++  .++|..+|++++.++..+...+++.+.        
T Consensus         1 m~~rfT~~a~~vL~~A~~~A~~~~h~~V~~EHLLLaLL~~~~~~a~~iL~~~gid~~~l~~~l~~~l~~~~~--------   72 (821)
T CHL00095          1 MFERFTEKAIKVIMLSQEEARRLGHNFVGTEQILLGLIGEGTGIAARALKSMGVTLKDARIEVEKIIGRGTG--------   72 (821)
T ss_pred             ChhhHhHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHHhcCCC--------
Confidence            7999999999999999999999999999999999999999876  789999999999999999988876432        


Q ss_pred             cCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhhc
Q 005179          159 QGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELA  238 (710)
Q Consensus       159 ~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~~  238 (710)
                           .....++||+.++++|+.|..+|..+++.+|+++|||+||++++++.+.++|..+|++.+.++..+...+.....
T Consensus        73 -----~~~~~~~~S~~~~~vL~~A~~~A~~~~~~~I~~eHLLlALL~~~ds~a~~iL~~~gvd~~~L~~~l~~~l~~~~e  147 (821)
T CHL00095         73 -----FVAVEIPFTPRAKRVLEMSLEEARDLGHNYIGTEHLLLALLEEGEGVAARVLENLGVDLSKIRSLILNLIGEIIE  147 (821)
T ss_pred             -----CCccccccCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhCCCchHHHHHHHcCCCHHHHHHHHHHHhccccc
Confidence                 122468999999999999999999999999999999999999988889999999999999988776654421100


Q ss_pred             ccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEc
Q 005179          239 KEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLG  318 (710)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~G  318 (710)
                      .  ..+   .        +.       .....+.|++|++||++.+++|++++++||++++++++++|+++.++|++|+|
T Consensus       148 ~--~~~---~--------~~-------~~~~~~~l~~~~~~l~~~a~~~~~~~~igr~~ei~~~~~~L~r~~~~n~lL~G  207 (821)
T CHL00095        148 A--ILG---A--------EQ-------SRSKTPTLEEFGTNLTKEAIDGNLDPVIGREKEIERVIQILGRRTKNNPILIG  207 (821)
T ss_pred             c--ccc---c--------cc-------ccccchHHHHHHHHHHHHHHcCCCCCCCCcHHHHHHHHHHHcccccCCeEEEC
Confidence            0  000   0        00       00134689999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCC
Q 005179          319 ESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSG  398 (710)
Q Consensus       319 ppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~  398 (710)
                      |||||||++|+++|+.+..+++|..+.+++++.+|++.+++|.+++|+|+++++.+++++...+++||||||+|.+++.+
T Consensus       208 ~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g  287 (821)
T CHL00095        208 EPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLDIGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAG  287 (821)
T ss_pred             CCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeHHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCC
Confidence            99999999999999999999999999999999999999999999999999999999999988788999999999999876


Q ss_pred             CCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcC
Q 005179          399 TVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHN  478 (710)
Q Consensus       399 ~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~  478 (710)
                      ..     .+..++.++|++.+++|++++|++||.++|+++++.|++|.+||+.|.+++|+.++...|++.+...|+.+++
T Consensus       288 ~~-----~g~~~~a~lLkp~l~rg~l~~IgaTt~~ey~~~ie~D~aL~rRf~~I~v~ep~~~e~~aILr~l~~~~e~~~~  362 (821)
T CHL00095        288 AA-----EGAIDAANILKPALARGELQCIGATTLDEYRKHIEKDPALERRFQPVYVGEPSVEETIEILFGLRSRYEKHHN  362 (821)
T ss_pred             CC-----CCcccHHHHhHHHHhCCCcEEEEeCCHHHHHHHHhcCHHHHhcceEEecCCCCHHHHHHHHHHHHHHHHHHcC
Confidence            43     3356889999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhcc
Q 005179          479 CKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSR  558 (710)
Q Consensus       479 ~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  558 (710)
                      +.++++++..++.++.+|+++|++|+||++++|+||+++++.....|.+.  ..+.+....+..+........++..+..
T Consensus       363 v~i~deal~~i~~ls~~yi~~r~lPdkaidlld~a~a~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~  440 (821)
T CHL00095        363 LSISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGSRVRLINSRLPPAA--RELDKELREILKDKDEAIREQDFETAKQ  440 (821)
T ss_pred             CCCCHHHHHHHHHHhhccCccccCchHHHHHHHHHHHHHHhhccCCchhH--HHHHHHHHHHHHHHHHHHhCcchHHHHH
Confidence            99999999999999999999999999999999999999988765544321  1111111111111111111111111111


Q ss_pred             ccchhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHH
Q 005179          559 LKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAV  638 (710)
Q Consensus       559 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~  638 (710)
                      +.+....+..............  .........|+.+||.++++.|||||+.++..++..++.++++.|.++|+||++|+
T Consensus       441 ~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~v~~~~i~~~~~~~tgip~~~~~~~~~~~l~~l~~~L~~~v~GQ~~ai  518 (821)
T CHL00095        441 LRDREMEVRAQIAAIIQSKKTE--EEKRLEVPVVTEEDIAEIVSAWTGIPVNKLTKSESEKLLHMEETLHKRIIGQDEAV  518 (821)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhh--hcccccCCccCHHHHHHHHHHHHCCCchhhchhHHHHHHHHHHHhcCcCcChHHHH
Confidence            1110000000000000000000  00011235799999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          639 AAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       639 ~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      +.|..++++.+.|+.+|+||+++|||+||||||||+||++||+.|||++..++++|||+|+. +++++++|
T Consensus       519 ~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~-~~~~~~l~  588 (821)
T CHL00095        519 VAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYME-KHTVSKLI  588 (821)
T ss_pred             HHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccc-cccHHHhc
Confidence            99999999999999999999999999999999999999999999999999999999999954 67777765

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=100.00  E-value=1.2e-80  Score=729.38  Aligned_cols=593  Identities=35%  Similarity=0.517  Sum_probs=475.2

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKP  162 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  162 (710)
                      +|++++++|..|+++|++++|++|+|||||+|||.++++  ..+|..+|++++.+++++...+...+..           
T Consensus         1 Lt~~a~~~L~~A~~~A~~~~h~~I~~eHLLlaLL~~~~~~~~~iL~~~Gvd~~~Lr~~le~~l~~~p~~-----------   69 (852)
T TIGR03345         1 LNPTSRRALEQAAALCVARGHPEVELEHWLLALLDQPDSDLAAILRHFGVDLGRLKADLARALDKLPRG-----------   69 (852)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhccCCCC-----------
Confidence            589999999999999999999999999999999998776  6789999999999999999888765421           


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHH-HHHHcCCCccCHHHHHHHhhhcCCc--hHHHHHHHh-cCCHHHHHHHHHHhhhhhhc
Q 005179          163 FSSAAKMPFSISTKRVFEAAVE-YSRSRGYNFIAPEHIALGLFTVDDG--SAGRVLKRL-GVDVNHLAAVAVSRLQGELA  238 (710)
Q Consensus       163 ~~~~~~~~~s~~~~~vl~~A~~-~a~~~g~~~I~~ehlLlall~~~~~--~a~~iL~~~-gv~~~~l~~~~~~~l~~~~~  238 (710)
                        .+..+++|+.++++|+.|.. .+..+|+.+|+++|||+||++++++  .+..++..+ |++.+.+.+.+.....+.  
T Consensus        70 --~~~~~~~S~~l~~vL~~A~~~~a~~~g~~~I~teHLLlALl~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  145 (852)
T TIGR03345        70 --NTRTPVFSPHLVELLQEAWLLASLELGDGRIRSGHLLLALLTDPELRRLLGSISPELAKIDREALREALPALVEGS--  145 (852)
T ss_pred             --CCCCCCcCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHccccchhHHHHHHHHHhCCCHHHHHHHHHHHhcCC--
Confidence              11357899999999999997 4667899999999999999998765  566788887 999988877665422211  


Q ss_pred             ccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEc
Q 005179          239 KEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLG  318 (710)
Q Consensus       239 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~G  318 (710)
                      ............     ....     ......+.|++|+.||++.+|+|+++++|||++++++++++|+++.++|++|+|
T Consensus       146 ~~~~~~~~~~~~-----~~~~-----~~~~~~~~l~~~~~~L~~~~r~~~ld~~iGr~~ei~~~i~~l~r~~~~n~lLvG  215 (852)
T TIGR03345       146 AEASAAAADAGP-----AAAA-----AGAAGTSALDQYTTDLTAQAREGKIDPVLGRDDEIRQMIDILLRRRQNNPILTG  215 (852)
T ss_pred             cccccccccccc-----cccc-----ccccchhhHHHHhhhHHHHhcCCCCCcccCCHHHHHHHHHHHhcCCcCceeEEC
Confidence            000000000000     0000     000134689999999999999999999999999999999999999999999999


Q ss_pred             CCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh-cCCeEEEEccchhhhhC
Q 005179          319 ESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK-SGDVILFIDEVHTLIGS  397 (710)
Q Consensus       319 ppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~  397 (710)
                      |||||||++++++|+.+..+.+|..+.+.+++.++++.+.+|.+++|+|+.+++.+++++.. ..++||||||+|.+++.
T Consensus       216 ~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~  295 (852)
T TIGR03345       216 EAGVGKTAVVEGLALRIAAGDVPPALRNVRLLSLDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGA  295 (852)
T ss_pred             CCCCCHHHHHHHHHHHHhhCCCCccccCCeEEEeehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccC
Confidence            99999999999999999999999999999999999999999999999999999999999975 45799999999999887


Q ss_pred             CCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhc
Q 005179          398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHH  477 (710)
Q Consensus       398 ~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~  477 (710)
                      |..     .+..++.++|++.+++|.++|||+||.++|.+++++|++|.|||+.|.|++|+.+++..||+++...|+.+|
T Consensus       296 g~~-----~~~~d~~n~Lkp~l~~G~l~~IgaTT~~e~~~~~~~d~AL~rRf~~i~v~eps~~~~~~iL~~~~~~~e~~~  370 (852)
T TIGR03345       296 GGQ-----AGQGDAANLLKPALARGELRTIAATTWAEYKKYFEKDPALTRRFQVVKVEEPDEETAIRMLRGLAPVLEKHH  370 (852)
T ss_pred             CCc-----cccccHHHHhhHHhhCCCeEEEEecCHHHHhhhhhccHHHHHhCeEEEeCCCCHHHHHHHHHHHHHhhhhcC
Confidence            643     235678899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhH-----Hh-------hhhCCCC----hH--
Q 005179          478 NCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQ-----QT-------CILSKPP----DD--  539 (710)
Q Consensus       478 ~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~-----~~-------~~l~~~~----~~--  539 (710)
                      ++.++++++..++.++.||++++++|||||||+|+||+++++.....+.+.     ++       ..+.++.    +.  
T Consensus       371 ~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdlldea~a~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  450 (852)
T TIGR03345       371 GVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACARVALSQNATPAALEDLRRRIAALELELDALEREAALGADHDE  450 (852)
T ss_pred             CCeeCHHHHHHHHHHcccccccccCccHHHHHHHHHHHHHHHhccCCchhHHHHHHHHHHHHHHHHHHhhhhccccchHH
Confidence            999999999999999999999999999999999999999998755444321     00       0111110    00  


Q ss_pred             ----HH-------HHHHHHHHhhHHHh--hccc-------cchhhhhccCCc----chh-hhhccC--CCCCCCCCCCcC
Q 005179          540 ----YW-------QEIRTVQAMHEVVQ--GSRL-------KYDDVVASMGDT----SEI-VVESSL--PSASDDDEPAVV  592 (710)
Q Consensus       540 ----~~-------~~~~~~~~~~~~~~--~~~~-------~~~~~~~~~~~~----~~~-~~~~~~--~~~~~~~~~~~v  592 (710)
                          +.       +++......++.+.  ..+.       ...... .....    ..+ .....+  ...........|
T Consensus       451 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  529 (852)
T TIGR03345       451 RLAELRAELAALEAELAALEARWQQEKELVEAILALRAELEADADA-PADDDAALRAQLAELEAALASAQGEEPLVFPEV  529 (852)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc-hhhhhHHHHHHHHHHHHHHHHHhhcccccccee
Confidence                00       00000000000000  0000       000000 00000    000 000000  000111234569


Q ss_pred             CHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcH
Q 005179          593 GPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGK  672 (710)
Q Consensus       593 ~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGK  672 (710)
                      +.++|+++++.|||||+.++..++..++.++++.|.++|+||++|++.|..++++++.|+.+|.||++.|||+|||||||
T Consensus       530 ~~~~i~~vv~~~tgip~~~~~~~e~~~l~~l~~~L~~~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGK  609 (852)
T TIGR03345       530 DAQAVAEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGK  609 (852)
T ss_pred             cHHHHHHHHHHHHCCCchhhchhHHHHHHHHHHHhcCeEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          673 TELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       673 T~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      |++|++||+.|||++..++++|||+|+ .+++++++|
T Consensus       610 T~lA~~La~~l~~~~~~~~~~dmse~~-~~~~~~~l~  645 (852)
T TIGR03345       610 TETALALAELLYGGEQNLITINMSEFQ-EAHTVSRLK  645 (852)
T ss_pred             HHHHHHHHHHHhCCCcceEEEeHHHhh-hhhhhcccc
Confidence            999999999999999999999999995 688888886

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.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=100.00  E-value=5.5e-79  Score=712.78  Aligned_cols=529  Identities=42%  Similarity=0.656  Sum_probs=466.2

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCcHHHHHHCCCCHHHHHHHHHHHhhc-CCCCCCchhhhcCCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHS-TNNQDTDDAAAQGKPF  163 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~l~~~gv~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~  163 (710)
                      ||++++++|..|+++|++++|.+|++||||+|||.++++.++|..+|++++.+++++...++. .+...          .
T Consensus         1 ~~~~a~~~L~~A~~~A~~~~h~~V~~EHLLlaLL~~~~~~~iL~~~gid~~~l~~~l~~~l~~~~p~~~----------~   70 (731)
T TIGR02639         1 ISEELERILDAALEEAKKRRHEFVTLEHILLALLFDSDAIEILEECGGDVEALRKDLEDYLENNLPSIT----------E   70 (731)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCcCcHHHHHHHHHcCchHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCC----------C
Confidence            689999999999999999999999999999999999877889999999999999999988873 32210          1


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhhcccCCC
Q 005179          164 SSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGRE  243 (710)
Q Consensus       164 ~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~~~~~~~  243 (710)
                      ..+..+++|+.++++|+.|+.+|..+|+.+|+++|||+||++++++.+..+|..+|++.+.+...+.......   ....
T Consensus        71 ~~~~~~~~S~~lk~vL~~A~~~A~~~g~~~I~teHLLLALl~~~~~~a~~lL~~~gi~~~~l~~~l~~~~~~~---~~~~  147 (731)
T TIGR02639        71 ENEADPEQTVGVQRVLQRALLHVKSAGKKEIGIGDILVALFDEEDSHASYFLKSQGITRLDILEYISHGIPKD---DGKN  147 (731)
T ss_pred             CCCCCCCcCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHhcCcccHHHHHHHHcCCCHHHHHHHHHhhcccc---cccc
Confidence            1124688999999999999999999999999999999999999889899999999999988876654211100   0000


Q ss_pred             CccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCCh
Q 005179          244 PSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVG  323 (710)
Q Consensus       244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~G  323 (710)
                      .... .      ....     ......+.|++|+.||++.+++|++++++||++++++++++|+++.++|+||+||||||
T Consensus       148 ~~~~-~------~~~~-----~~~~~~~~l~~~~~~l~~~~r~~~l~~~igr~~ei~~~~~~L~~~~~~n~lL~G~pG~G  215 (731)
T TIGR02639       148 RDAE-E------AGKE-----EAKKQEDALEKYTVDLTEKAKNGKIDPLIGREDELERTIQVLCRRKKNNPLLVGEPGVG  215 (731)
T ss_pred             cccc-c------cccc-----ccccchhHHHHHhhhHHHHHhcCCCCcccCcHHHHHHHHHHHhcCCCCceEEECCCCCC
Confidence            0000 0      0000     00013468999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC
Q 005179          324 KTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG  403 (710)
Q Consensus       324 KT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~  403 (710)
                      ||++++++|+.+..+++|..+.+++++.++++.+.+|.++.|+++++++.+++++....++||||||+|.+++++..   
T Consensus       216 KT~l~~~la~~~~~~~~p~~l~~~~~~~~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~---  292 (731)
T TIGR02639       216 KTAIAEGLALRIAEGKVPENLKNAKIYSLDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGAT---  292 (731)
T ss_pred             HHHHHHHHHHHHHhCCCchhhcCCeEEEecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCC---
Confidence            99999999999999999999999999999999999999999999999999999998777899999999999987643   


Q ss_pred             CCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH
Q 005179          404 NKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTL  483 (710)
Q Consensus       404 ~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~  483 (710)
                       .++..+++++|++.+++|.+.+||+||..+|.++++.|++|.|||+.|.|++|+.+++.+||+.+..+|+.+|++.+++
T Consensus       293 -~~~~~~~~~~L~~~l~~g~i~~IgaTt~~e~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~e~~~~v~i~~  371 (731)
T TIGR02639       293 -SGGSMDASNLLKPALSSGKLRCIGSTTYEEYKNHFEKDRALSRRFQKIDVGEPSIEETVKILKGLKEKYEEFHHVKYSD  371 (731)
T ss_pred             -CCccHHHHHHHHHHHhCCCeEEEEecCHHHHHHHhhhhHHHHHhCceEEeCCCCHHHHHHHHHHHHHHHHhccCcccCH
Confidence             1335678999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccchh
Q 005179          484 EAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDD  563 (710)
Q Consensus       484 ~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  563 (710)
                      +++..++.++.+|++++++|+||++++|+|++++++.....                                       
T Consensus       372 ~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~---------------------------------------  412 (731)
T TIGR02639       372 EALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAK---------------------------------------  412 (731)
T ss_pred             HHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccc---------------------------------------
Confidence            99999999999999999999999999999998766531100                                       


Q ss_pred             hhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHH
Q 005179          564 VVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISR  643 (710)
Q Consensus       564 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~  643 (710)
                                              ....|+.+||..+++.|+|||+..+++++..++.++++.|.++|+||++|++.|..
T Consensus       413 ------------------------~~~~v~~~~i~~~i~~~tgiP~~~~~~~~~~~l~~l~~~l~~~v~GQ~~ai~~l~~  468 (731)
T TIGR02639       413 ------------------------KKANVSVKDIENVVAKMAHIPVKTVSVDDREKLKNLEKNLKAKIFGQDEAIDSLVS  468 (731)
T ss_pred             ------------------------cccccCHHHHHHHHHHHhCCChhhhhhHHHHHHHHHHHHHhcceeCcHHHHHHHHH
Confidence                                    12468999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          644 AVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       644 ~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      ++++.+.|+.+|+||.++|||+||||||||++|++||+.++   ..++++|||+|++ +++++++|
T Consensus       469 ~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~---~~~~~~d~se~~~-~~~~~~li  530 (731)
T TIGR02639       469 SIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALG---VHLERFDMSEYME-KHTVSRLI  530 (731)
T ss_pred             HHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhc---CCeEEEeCchhhh-cccHHHHh
Confidence            99999999999999999999999999999999999999985   4799999999954 67777765

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=100.00  E-value=2.6e-78  Score=715.94  Aligned_cols=584  Identities=42%  Similarity=0.638  Sum_probs=478.3

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKP  162 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~  162 (710)
                      ||++++++|..|+.+|++++|++|+|||||+||+.++++  .++|..+|++++.+++++...+++.+..           
T Consensus         1 fT~~a~~vL~~A~~~A~~~~h~~V~~EHLLlaLl~~~~g~a~~iL~~~Gvd~~~l~~~l~~~l~~~~~~-----------   69 (852)
T TIGR03346         1 FTEKFQEALQAAQSLALGRDHQQIEPEHLLKALLDQEGGLARRLLQKAGVNVGALRQALEKELEKLPKV-----------   69 (852)
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHhcccccC-----------
Confidence            799999999999999999999999999999999999876  7899999999999999999988875432           


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhhcccCC
Q 005179          163 FSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGR  242 (710)
Q Consensus       163 ~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~~~~~~  242 (710)
                      .+.+..++||+.++++|+.|+.+|..+|+.+|+++|||+||++++++ ++++|..+|++.+.+.+.+.+...+.    ..
T Consensus        70 ~~~~~~~~~S~~~~~vLe~A~~~A~~~g~~~I~teHLLlALl~e~~~-a~~iL~~~gi~~~~l~~~l~~~~~~~----~~  144 (852)
T TIGR03346        70 SGPGGQVYLSPELNRLLNLAEKLAQKRGDEFISSEHLLLALLDDKGT-LGKLLKEAGATADALEAAINAVRGGQ----KV  144 (852)
T ss_pred             CCCCCCCCcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcc-HHHHHHHcCCCHHHHHHHHHhhccCc----cc
Confidence            11124688999999999999999999999999999999999998776 67899999999988877654322100    00


Q ss_pred             CCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCC
Q 005179          243 EPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGV  322 (710)
Q Consensus       243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~  322 (710)
                      + .           ..       .....+.|++|+.||++.+++|++++++||++++++++++|+++.++|++|+|||||
T Consensus       145 ~-~-----------~~-------~~~~~~~l~~~~~~l~~~~~~~~~~~~igr~~ei~~~~~~l~r~~~~n~lL~G~pGv  205 (852)
T TIGR03346       145 T-S-----------AN-------AEDQYEALEKYARDLTERAREGKLDPVIGRDEEIRRTIQVLSRRTKNNPVLIGEPGV  205 (852)
T ss_pred             c-c-----------cc-------cccchhHHHHHhhhHHHHhhCCCCCcCCCcHHHHHHHHHHHhcCCCCceEEEcCCCC
Confidence            0 0           00       001346899999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCC
Q 005179          323 GKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVG  401 (710)
Q Consensus       323 GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~  401 (710)
                      |||++++++++.+..+.+|..+.+.+++.++++.+++|.+++|+++.+++.+++.+... .++||||||+|.|+++|.. 
T Consensus       206 GKT~l~~~la~~i~~~~~p~~l~~~~~~~l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~-  284 (852)
T TIGR03346       206 GKTAIVEGLAQRIVNGDVPESLKNKRLLALDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKA-  284 (852)
T ss_pred             CHHHHHHHHHHHHhccCCchhhcCCeEEEeeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCC-
Confidence            99999999999999999999999999999999999999999999999999999998654 5899999999999876543 


Q ss_pred             CCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCC
Q 005179          402 RGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKF  481 (710)
Q Consensus       402 ~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i  481 (710)
                          .+..++.++|++.+++|.+.|||+||.++|+++++.|+++.+||+.|.+++|+.+++..||+.+..+|+.+|++.+
T Consensus       285 ----~~~~d~~~~Lk~~l~~g~i~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~~p~~~~~~~iL~~~~~~~e~~~~v~~  360 (852)
T TIGR03346       285 ----EGAMDAGNMLKPALARGELHCIGATTLDEYRKYIEKDAALERRFQPVFVDEPTVEDTISILRGLKERYEVHHGVRI  360 (852)
T ss_pred             ----cchhHHHHHhchhhhcCceEEEEeCcHHHHHHHhhcCHHHHhcCCEEEeCCCCHHHHHHHHHHHHHHhccccCCCC
Confidence                3456789999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhh-----HHh-------hhhCCCChH--------HH
Q 005179          482 TLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKE-----QQT-------CILSKPPDD--------YW  541 (710)
Q Consensus       482 ~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~-----~~~-------~~l~~~~~~--------~~  541 (710)
                      +++++..++.++.+|+.+|++||||++|+|+||+++++.....|.+     .++       ..+.++.++        +.
T Consensus       361 ~d~~i~~~~~ls~~yi~~r~lPdkAidlld~a~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  440 (852)
T TIGR03346       361 TDPAIVAAATLSHRYITDRFLPDKAIDLIDEAAARIRMEIDSKPEELDELDRRIIQLEIEREALKKEKDEASKERLEDLE  440 (852)
T ss_pred             CHHHHHHHHHhccccccccCCchHHHHHHHHHHHHHHhhccCCchhHHHHHHHHHHHHHHHHHHHhcchhHHHHHHHHHH
Confidence            9999999999999999999999999999999999998875544432     111       111111110        00


Q ss_pred             HHHHH-------HHHhhHHHh--h---cccc-----------------chhhhhccCCc------chhhh-hccCCC-CC
Q 005179          542 QEIRT-------VQAMHEVVQ--G---SRLK-----------------YDDVVASMGDT------SEIVV-ESSLPS-AS  584 (710)
Q Consensus       542 ~~~~~-------~~~~~~~~~--~---~~~~-----------------~~~~~~~~~~~------~~~~~-~~~~~~-~~  584 (710)
                      .++..       ....+..+.  .   ..+.                 +..........      +.+.. ...... ..
T Consensus       441 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  520 (852)
T TIGR03346       441 KELAELEEEYADLEEQWKAEKAAIQGIQQIKEEIEQVRLELEQAEREGDLAKAAELQYGKLPELEKRLQAAEAKLGEETK  520 (852)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHhhhcchHHHHHHHHHHHHHhhhccc
Confidence            01100       000000000  0   0000                 00000000000      00000 000000 00


Q ss_pred             CCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEE
Q 005179          585 DDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLF  664 (710)
Q Consensus       585 ~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf  664 (710)
                      .......|+.++|..+++.|||||+.++..++..++.++++.|.++|+||++|++.|..++++.+.|+.+|+||.+.|||
T Consensus       521 ~~l~~~~v~~~~i~~v~~~~tgip~~~~~~~e~~~l~~l~~~l~~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf  600 (852)
T TIGR03346       521 PRLLREEVTAEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLF  600 (852)
T ss_pred             cccccCCcCHHHHHHHHHHhcCCCcccccHHHHHHHHHHHHHhhcccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEE
Confidence            11233569999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          665 CGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       665 ~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      +||||||||++|++||+.+|+++..++++|||+|+. +++++++|
T Consensus       601 ~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~-~~~~~~l~  644 (852)
T TIGR03346       601 LGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYME-KHSVARLI  644 (852)
T ss_pred             EcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcc-cchHHHhc
Confidence            999999999999999999999999999999999965 66777664

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=100.00  E-value=7.1e-78  Score=708.58  Aligned_cols=589  Identities=39%  Similarity=0.585  Sum_probs=480.6

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      |||++||+.++.+|..|+.+|++++|.+|++||||+||+.++++  ..+|..+|++.+.+++.+...+++.+..      
T Consensus         1 ~~~~~~~~~~~~~l~~a~~~a~~~~~~~~~~~hll~~l~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~------   74 (857)
T PRK10865          1 MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVRPLLTSAGINAGQLRTDINQALSRLPQV------   74 (857)
T ss_pred             CChHHhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCccHHHHHHHHcCCCHHHHHHHHHHHHhhCCCC------
Confidence            46899999999999999999999999999999999999998876  7789999999999999999988876531      


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGEL  237 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~  237 (710)
                           .+....+++|+.++++|+.|+.++..+|+.+|+++|||+|++.++++ .+.+|..+|++.+.+.+.+.+...+. 
T Consensus        75 -----~~~~~~~~~~~~~~~~l~~a~~~~~~~~~~~i~~~~ll~~~~~~~~~-~~~~l~~~~~~~~~~~~~~~~~~~~~-  147 (857)
T PRK10865         75 -----EGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALESRGT-LADILKAAGATTANITQAIEQMRGGE-  147 (857)
T ss_pred             -----CCCCCCCCcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCcch-HHHHHHHcCCCHHHHHHHHHHhhccc-
Confidence                 11124688999999999999999999999999999999999987654 44689999999998877654321110 


Q ss_pred             cccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEE
Q 005179          238 AKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILL  317 (710)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~  317 (710)
                         ...   .         ..      + ....+.|++|+.||++.+++|+++++|||++++++++++|+++.++|++|+
T Consensus       148 ---~~~---~---------~~------~-~~~~~~l~~~~~~l~~~~r~~~l~~vigr~~ei~~~i~iL~r~~~~n~lL~  205 (857)
T PRK10865        148 ---SVN---D---------QG------A-EDQRQALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLI  205 (857)
T ss_pred             ---ccc---c---------cc------c-ccchhHHHHHhhhHHHHHhcCCCCcCCCCHHHHHHHHHHHhcCCcCceEEE
Confidence               000   0         00      0 013468999999999999999999999999999999999999999999999


Q ss_pred             cCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh-cCCeEEEEccchhhhh
Q 005179          318 GESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK-SGDVILFIDEVHTLIG  396 (710)
Q Consensus       318 GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~  396 (710)
                      ||||||||++++++|+.+..+.+|..+.+.+++.++++.+++|.+++|+|+.+++.+++++.. ..++||||||+|.+++
T Consensus       206 G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~  285 (857)
T PRK10865        206 GEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVG  285 (857)
T ss_pred             CCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEEEehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhcc
Confidence            999999999999999999999999999999999999999999999999999999999998754 4689999999999988


Q ss_pred             CCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhh
Q 005179          397 SGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAH  476 (710)
Q Consensus       397 ~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~  476 (710)
                      ++..     .++.+.+++|++.+++|.+.|||+||.++|+++++.|++|.|||+.|.+.+|+.+++..||+.+..+|+.+
T Consensus       286 ~~~~-----~~~~d~~~~lkp~l~~g~l~~IgaTt~~e~r~~~~~d~al~rRf~~i~v~eP~~~~~~~iL~~l~~~~e~~  360 (857)
T PRK10865        286 AGKA-----DGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILRGLKERYELH  360 (857)
T ss_pred             CCCC-----ccchhHHHHhcchhhcCCCeEEEcCCCHHHHHHhhhcHHHHhhCCEEEeCCCCHHHHHHHHHHHhhhhccC
Confidence            7643     44678999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhH-----H-------hhhhCCCChH-----
Q 005179          477 HNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQ-----Q-------TCILSKPPDD-----  539 (710)
Q Consensus       477 ~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~-----~-------~~~l~~~~~~-----  539 (710)
                      |++.++++++..++.++.||+.++++|++|++++|.+++..++....+|...     .       ...+..+.+.     
T Consensus       361 ~~v~~~d~a~~~a~~ls~ry~~~~~~pdkAi~LiD~aaa~~rl~~~~kp~~L~rLer~l~~L~~E~e~l~~e~~~~~~~~  440 (857)
T PRK10865        361 HHVQITDPAIVAAATLSHRYIADRQLPDKAIDLIDEAASSIRMQIDSKPEELDRLDRRIIQLKLEQQALMKESDEASKKR  440 (857)
T ss_pred             CCCCcCHHHHHHHHHHhhccccCCCCChHHHHHHHHHhcccccccccChHHHHHHHHHHHHHHHHHHHHHhhhhhHHHHH
Confidence            9999999999999999999999999999999999999999988766655431     1       1111111100     


Q ss_pred             ---HHHHHHHHHHhhH-------HH--hhcc---ccch----h---hhh----------ccCCcc------hhhhhccCC
Q 005179          540 ---YWQEIRTVQAMHE-------VV--QGSR---LKYD----D---VVA----------SMGDTS------EIVVESSLP  581 (710)
Q Consensus       540 ---~~~~~~~~~~~~~-------~~--~~~~---~~~~----~---~~~----------~~~~~~------~~~~~~~~~  581 (710)
                         ..+++...+....       ..  ....   ..+.    .   ...          +.....      .+.......
T Consensus       441 ~~~l~~~l~~lq~e~~~L~eq~k~~k~el~~~~~~~~ele~l~~kie~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  520 (857)
T PRK10865        441 LDMLNEELSDKERQYSELEEEWKAEKASLSGTQTIKAELEQAKIAIEQARRVGDLARMSELQYGKIPELEKQLAAATQLE  520 (857)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHhhhhhhHHHHHHHHHHHhhh
Confidence               0001111100000       00  0000   0000    0   000          000000      000000000


Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeE
Q 005179          582 SASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAA  661 (710)
Q Consensus       582 ~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~  661 (710)
                      ..........|+.++|+.+++.|||||+.++..++..++.++++.|.++|+||+.|++.|..+++..++|+.+|++|++.
T Consensus       521 ~~~~~~~~~~v~~~~i~~vv~~~tgip~~~~~~~~~~~l~~l~~~l~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~  600 (857)
T PRK10865        521 GKTMRLLRNKVTDAEIAEVLARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGS  600 (857)
T ss_pred             ccccccccCccCHHHHHHHHHHHHCCCchhhhhhHHHHHHHHHHHhCCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCce
Confidence            00111223569999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          662 MLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      |||+||||||||++|++||+.+|+++..++++|||+|.. .+++++++
T Consensus       601 ~Lf~Gp~G~GKT~lA~aLa~~l~~~~~~~i~id~se~~~-~~~~~~Li  647 (857)
T PRK10865        601 FLFLGPTGVGKTELCKALANFMFDSDDAMVRIDMSEFME-KHSVSRLV  647 (857)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhhcCCCcEEEEEhHHhhh-hhhHHHHh
Confidence            999999999999999999999999999999999999954 56666654

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=100.00  E-value=6.9e-75  Score=667.71  Aligned_cols=533  Identities=36%  Similarity=0.572  Sum_probs=460.5

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCcHHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcCCCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFS  164 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (710)
                      +|+.+..+|..|+.+|+.++|.+|++||||++|+.+++...+|..+|++.+.+++.+...++...+..     +   ...
T Consensus         2 ~~~~~~~~l~~a~~~a~~~~~~~~~~~h~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~---~~~   73 (758)
T PRK11034          2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVL-----P---ASE   73 (758)
T ss_pred             cCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHcChhHHHHHHHcCCCHHHHHHHHHHHHhhcCCcC-----C---CCC
Confidence            68999999999999999999999999999999998776678999999999999999998877422110     0   001


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhhcccCCCC
Q 005179          165 SAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREP  244 (710)
Q Consensus       165 ~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~~~~~~~~  244 (710)
                      ...+++++..++++|+.|+.+|+.+++.+|+++|||+||++++++.+..+|..+|++...+...+.+   +.......+.
T Consensus        74 ~~~~~~~~~~~~~~l~~a~~~~~~~~~~~i~~~~ll~a~~~~~~~~~~~~l~~~~~~~~~~~~~~~~---~~~~~~~~~~  150 (758)
T PRK11034         74 EERDTQPTLSFQRVLQRAVFHVQSSGRSEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISH---GTRKDEPSQS  150 (758)
T ss_pred             CcCCcCCCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcchHHHHHHHcCCCHHHHHHHHHh---CCcccccccc
Confidence            1135778999999999999999999999999999999999998899999999999998876554221   1000000000


Q ss_pred             ccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChH
Q 005179          245 SLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGK  324 (710)
Q Consensus       245 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GK  324 (710)
                         ......+ .++.      .......|++|++||++.++.|++++++||++++++++++|+++.++|+||+|||||||
T Consensus       151 ---~~~~~~~-~~~~------~~~~~~~l~~~~~~l~~~a~~g~~~~liGR~~ei~~~i~iL~r~~~~n~LLvGppGvGK  220 (758)
T PRK11034        151 ---SDPGSQP-NSEE------QAGGEERMENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGK  220 (758)
T ss_pred             ---ccccccc-cccc------cccchhHHHHHHHhHHHHHHcCCCCcCcCCCHHHHHHHHHHhccCCCCeEEECCCCCCH
Confidence               0000000 0000      00123689999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC
Q 005179          325 TAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN  404 (710)
Q Consensus       325 T~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~  404 (710)
                      |++|+++++.+...++|..+.++.++.+++..++.|.++.|+++.+++.+++.+...++.||||||+|.+++.+..    
T Consensus       221 T~lae~la~~i~~~~vP~~l~~~~~~~l~~~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~----  296 (758)
T PRK11034        221 TAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAA----  296 (758)
T ss_pred             HHHHHHHHHHHHhcCCCchhcCCeEEeccHHHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCC----
Confidence            9999999999999999999999999999999999999999999999999999998878899999999999987643    


Q ss_pred             CCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH
Q 005179          405 KGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE  484 (710)
Q Consensus       405 ~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~  484 (710)
                      .++..++.++|++++++|++.||++||.++|.++++.|++|.|||+.|.|++|+.+++..||+.+..+|+.+|++.++++
T Consensus       297 ~~g~~d~~nlLkp~L~~g~i~vIgATt~~E~~~~~~~D~AL~rRFq~I~v~ePs~~~~~~IL~~~~~~ye~~h~v~i~~~  376 (758)
T PRK11034        297 SGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAK  376 (758)
T ss_pred             CCcHHHHHHHHHHHHhCCCeEEEecCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHhhhccCCCcCHH
Confidence            23467889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccchhh
Q 005179          485 AINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDV  564 (710)
Q Consensus       485 ~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  564 (710)
                      ++..++.++.+|++++++|+|+++++|+||++.++.....                                        
T Consensus       377 al~~a~~ls~ryi~~r~lPdKaidlldea~a~~~~~~~~~----------------------------------------  416 (758)
T PRK11034        377 AVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSK----------------------------------------  416 (758)
T ss_pred             HHHHHHHHhhccccCccChHHHHHHHHHHHHhhccCcccc----------------------------------------
Confidence            9999999999999999999999999999998765521000                                        


Q ss_pred             hhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHH
Q 005179          565 VASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRA  644 (710)
Q Consensus       565 ~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~  644 (710)
                                             ....|+.+||.++++.|+|||+..+..++...+.++++.|.++|+||++|++.|..+
T Consensus       417 -----------------------~~~~v~~~~i~~v~~~~tgip~~~~~~~~~~~l~~l~~~L~~~ViGQ~~ai~~l~~~  473 (758)
T PRK11034        417 -----------------------RKKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEA  473 (758)
T ss_pred             -----------------------cccccChhhHHHHHHHHhCCChhhhhhhHHHHHHHHHHHhcceEeCcHHHHHHHHHH
Confidence                                   013578899999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          645 VKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       645 i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      ++..+.|+.+|+||+++|||+||||||||++|++||+.+.   ..++++|||+|+. .++++++|
T Consensus       474 i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~---~~~i~id~se~~~-~~~~~~Li  534 (758)
T PRK11034        474 IKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALG---IELLRFDMSEYME-RHTVSRLI  534 (758)
T ss_pred             HHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHhC---CCcEEeechhhcc-cccHHHHc
Confidence            9999999999999999999999999999999999999983   5899999999954 45566654

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=4.6e-74  Score=651.79  Aligned_cols=587  Identities=37%  Similarity=0.512  Sum_probs=491.3

Q ss_pred             CcchhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCC-CCHHHHHHHHHHHhhcCCCCCC
Q 005179           77 PISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESG-ITIDKAREAVVSIWHSTNNQDT  153 (710)
Q Consensus        77 ~~~~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~g-v~~~~l~~~~~~~~~~~~~~~~  153 (710)
                      +.+.+++.||++|.++|..|+.+|+++||++++|+|++.+||.++++  .+++...+ ++...+...+...+.+.|..  
T Consensus         4 ~~~t~~q~lT~~Aa~~L~~a~~~Arrrgh~qvtplH~~~~LLs~~t~~lr~ac~~~~~l~~ralelc~~v~l~rlpt~--   81 (898)
T KOG1051|consen    4 GVYTVQQTLTEEAATVLKQAVTEARRRGHAQVTPLHVASTLLSSPTGILRRACIKSHPLQCRALELCFNVSLNRLPTS--   81 (898)
T ss_pred             cccchHhhhCHHHHHHHHHHHHHHHHcCCCCcchHHHHHHHHcCCchHHHHHHHhcCcccHHHHHHHHHHHHHhccCC--
Confidence            35678999999999999999999999999999999999999999998  67888888 99999999999999999875  


Q ss_pred             chhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          154 DDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                               .+++...++++.+++++..+.+.+..+++.||..||+.+.++-.+++.+.++++++|++..+++..+.+..
T Consensus        82 ---------~~p~~sn~l~aalkr~qa~qrr~~~~~~~~~vkvE~~~li~silDdp~vsrv~reag~~s~~vK~~ve~~~  152 (898)
T KOG1051|consen   82 ---------YGPPVSNALMAALKRAQAHQRRGCEEQQQQAVKVELEQLILSILDDPSVSRVMREAGFSSSAVKSAVEQPV  152 (898)
T ss_pred             ---------CCCccchHhHHHHHHHHHHHHhcchhhccchhhHhHHhhheeeecCchHHHHHHHhcCChHHHHHHHHhhc
Confidence                     34456678888888888888898999999999999997777777888999999999999999999888766


Q ss_pred             hhhhcccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccC-HHHHHHHHHHHHcCCCC
Q 005179          234 QGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGR-ETEIQRIIQILCRRTKN  312 (710)
Q Consensus       234 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr-~~~i~~l~~~L~~~~~~  312 (710)
                      ...    +.++.                  .| ......|.+|+.++++.++.|.++|++|+ ++++++++++|.++.++
T Consensus       153 g~~----~~~~~------------------~~-~~~~~~L~~~~~dl~p~a~~gkldPvigr~deeirRvi~iL~Rrtk~  209 (898)
T KOG1051|consen  153 GQF----RSPSR------------------GP-LWPLLFLENYGTDLTPRARQGKLDPVIGRHDEEIRRVIEILSRKTKN  209 (898)
T ss_pred             ccc----CCCCc------------------CC-ccchhHHHhcccccChhhhccCCCCccCCchHHHHHHHHHHhccCCC
Confidence            211    11110                  01 11457899999999999999999999999 99999999999999999


Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHH-hcCCeEEEEccc
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ-KSGDVILFIDEV  391 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~-~~~~~IL~IDEi  391 (710)
                      |++|+|+||+|||.++..+++++..+++|..+.+..++.+|+..+++|.+++|+++.+++.+++++. ..+++||||||+
T Consensus       210 NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfigel  289 (898)
T KOG1051|consen  210 NPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFLGEL  289 (898)
T ss_pred             CceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEecce
Confidence            9999999999999999999999999999999999999999999999999999999999999999998 457899999999


Q ss_pred             hhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHH
Q 005179          392 HTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       392 d~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      |++++.+..     .+..++.+.|++.+.++.+++||+||.++|+++++.+|+|.+||+.+.|+.|+.++...||.++..
T Consensus       290 h~lvg~g~~-----~~~~d~~nlLkp~L~rg~l~~IGatT~e~Y~k~iekdPalErrw~l~~v~~pS~~~~~~iL~~l~~  364 (898)
T KOG1051|consen  290 HWLVGSGSN-----YGAIDAANLLKPLLARGGLWCIGATTLETYRKCIEKDPALERRWQLVLVPIPSVENLSLILPGLSE  364 (898)
T ss_pred             eeeecCCCc-----chHHHHHHhhHHHHhcCCeEEEecccHHHHHHHHhhCcchhhCcceeEeccCcccchhhhhhhhhh
Confidence            999988655     447899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhh
Q 005179          472 KYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMH  551 (710)
Q Consensus       472 ~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  551 (710)
                      +|+.+|++.++++++..++.++.+|++.+++|+++++++++||+..+......|...  ..+.........++..++..+
T Consensus       365 ~~e~~hg~~~s~~a~~~a~~~s~~~~t~r~lpd~aidl~dEa~a~~~~~~~~lP~wL--~~~~~~~~~~~~e~~~L~kk~  442 (898)
T KOG1051|consen  365 RYEVHHGVRISDESLFSAAQLSARYITLSFLPDCAIDLEDEAAALVKSQAESLPPWL--QNLERVDIKLQDEISELQKKW  442 (898)
T ss_pred             hhccccCCcccccccccccchhhhhcccCcCchhcccHHHHHHHHHhhhhhhCCHHH--HhhhhhhhhhHHHHHHHHHhh
Confidence            999999999999999999999999999999999999999999999999888888742  232222211222222222222


Q ss_pred             H--------HHhhccccchh-----------hhhc-------cCCcchhhhhccCCCCCC----------------CCCC
Q 005179          552 E--------VVQGSRLKYDD-----------VVAS-------MGDTSEIVVESSLPSASD----------------DDEP  589 (710)
Q Consensus       552 ~--------~~~~~~~~~~~-----------~~~~-------~~~~~~~~~~~~~~~~~~----------------~~~~  589 (710)
                      +        .......+...           +...       ......+...........                ....
T Consensus       443 d~~~h~r~~~~~~~~~~~~~~~l~~~~~~~~s~~~~l~~~~~~~~~~~~~~k~~r~~d~~~~~~l~~~~~p~~~~~~~~~  522 (898)
T KOG1051|consen  443 NQALHKRPSLESLAPSKPTQQPLSASVDSERSVIEELKLKKNSLDRNSLLAKAHRPNDYTRETDLRYGRIPDELSEKSND  522 (898)
T ss_pred             hhhhccccccccccccccccccchhhhccchhHHhhhccccCCcccchhhhcccCCCCcchhhhccccccchhhhhhccc
Confidence            2        00000000000           0000       000000000000000000                0000


Q ss_pred             CcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCC
Q 005179          590 AVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTG  669 (710)
Q Consensus       590 ~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpG  669 (710)
                      ...++.+|..+.+.|+|+|+......+..++..|++.|+++|+||++|+.+|+.+|+++|.|+++| +|++.|||.||+|
T Consensus       523 ~~~~~~~i~~~~s~~tgip~~~~~~~e~~~l~~L~~~L~~~V~gQ~eAv~aIa~AI~~sr~gl~~~-~~~awflflGpdg  601 (898)
T KOG1051|consen  523 NQGGESDISEVVSRWTGIPVDRLAEAEAERLKKLEERLHERVIGQDEAVAAIAAAIRRSRAGLKDP-NPDAWFLFLGPDG  601 (898)
T ss_pred             ccCCccchhhhhhhhcCCchhhhhhhHHHHHHHHHHHHHhhccchHHHHHHHHHHHHhhhcccCCC-CCCeEEEEECCCc
Confidence            111677999999999999999999999999999999999999999999999999999999999999 9999999999999


Q ss_pred             CcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          670 VGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       670 tGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      ||||+|||+||++|||++++|||+|||||+.    +|++|
T Consensus       602 vGKt~lAkaLA~~~Fgse~~~IriDmse~~e----vskli  637 (898)
T KOG1051|consen  602 VGKTELAKALAEYVFGSEENFIRLDMSEFQE----VSKLI  637 (898)
T ss_pred             hhHHHHHHHHHHHHcCCccceEEechhhhhh----hhhcc
Confidence            9999999999999999999999999999987    77765

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

Probab=100.00  E-value=1.5e-37  Score=331.09  Aligned_cols=358  Identities=19%  Similarity=0.267  Sum_probs=245.6

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|.++-|.+..+..|++++..            ..++++||+||||||||.||+++|.++          +.+++.+..
T Consensus       187 v~f~diGG~d~~~~el~~li~~i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel----------~vPf~~isA  256 (802)
T KOG0733|consen  187 VSFSDIGGLDKTLAELCELIIHIKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGEL----------GVPFLSISA  256 (802)
T ss_pred             cchhhccChHHHHHHHHHHHHHhcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhc----------CCceEeecc
Confidence            3588899999999888876432            456789999999999999999999999          888999999


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--------CCCeEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--------RGELQC  426 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--------~~~v~v  426 (710)
                      ..++.|  +.|+.|++++++|+++....|+|+||||||.+.+++...  +++....+...|...|.        ...++|
T Consensus       257 peivSG--vSGESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~a--qreMErRiVaQLlt~mD~l~~~~~~g~~VlV  332 (802)
T KOG0733|consen  257 PEIVSG--VSGESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEA--QREMERRIVAQLLTSMDELSNEKTKGDPVLV  332 (802)
T ss_pred             hhhhcc--cCcccHHHHHHHHHHHhccCCeEEEeecccccccchhhH--HHHHHHHHHHHHHHhhhcccccccCCCCeEE
Confidence            999966  579999999999999999999999999999997765431  12334445555555443        246899


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH-HHHHHHHHHhhhhhcCCCC
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTL-EAINAAVHLSARYISDRYL  502 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~-~~l~~l~~ls~~~i~~r~~  502 (710)
                      ||+||.++     .+||+|+|  ||+ .|.+..|+..+|.+||+.+++.+      .++. -....++.++.+|++    
T Consensus       333 IgATnRPD-----slDpaLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~l------rl~g~~d~~qlA~lTPGfVG----  397 (802)
T KOG0733|consen  333 IGATNRPD-----SLDPALRRAGRFDREICLGVPSETAREEILRIICRGL------RLSGDFDFKQLAKLTPGFVG----  397 (802)
T ss_pred             EecCCCCc-----ccCHHHhccccccceeeecCCchHHHHHHHHHHHhhC------CCCCCcCHHHHHhcCCCccc----
Confidence            99999998     89999999  997 89999999999999999999854      2222 235788999999988    


Q ss_pred             cchHHHHHHHHHhhhhhhhhhchhh--HHhhhhCCCC-hHHHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhcc
Q 005179          503 PDKAIDLVDEAGSRAHIELFKRKKE--QQTCILSKPP-DDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESS  579 (710)
Q Consensus       503 p~~ai~ll~~a~~~~~~~~~~~~~~--~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  579 (710)
                       .+...|+.+|+..+--+.......  .+...-.... .+...+...+.....           ...+...+.-+.....
T Consensus       398 -ADL~AL~~~Aa~vAikR~ld~~~~p~~~~~~~ed~~~~~~~~d~S~i~~~~~-----------~~~~~~ld~v~~~~i~  465 (802)
T KOG0733|consen  398 -ADLMALCREAAFVAIKRILDQSSSPLTKVPISEDSSNKDAEEDQSSIKITSN-----------AERPLELDRVVQDAIL  465 (802)
T ss_pred             -hhHHHHHHHHHHHHHHHHhhcccCccccCCccccccCCCccchhhhhhcCCc-----------ccccccHHHHHHHHHH
Confidence             445666766664443332221110  0000000000 000001101100000           0000000000000000


Q ss_pred             ---CCCCCCCCCCCcCCHHHHHHHHHhhh-------CCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhh
Q 005179          580 ---LPSASDDDEPAVVGPDDIAAVASLWS-------GIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSR  649 (710)
Q Consensus       580 ---~~~~~~~~~~~~v~~~di~~~~s~~~-------gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r  649 (710)
                         .+..........|..+|+..+++..-       -+.+..++|++++.+.+++.+|...|.+.      |.++-.+.+
T Consensus       466 ~~~d~~S~E~~~~L~i~~eDF~~Al~~iQPSakREGF~tVPdVtW~dIGaL~~vR~eL~~aI~~P------iK~pd~~k~  539 (802)
T KOG0733|consen  466 NNPDPLSKELLEGLSIKFEDFEEALSKIQPSAKREGFATVPDVTWDDIGALEEVRLELNMAILAP------IKRPDLFKA  539 (802)
T ss_pred             hCCCCcChHHhccceecHHHHHHHHHhcCcchhcccceecCCCChhhcccHHHHHHHHHHHHhhh------ccCHHHHHH
Confidence               00001112346789999999886532       12344899999999999999888555433      555557778


Q ss_pred             cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          650 VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       650 ~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .|+..|    +|+|||||||||||+||||+|++   ++-++|.+-..|+
T Consensus       540 lGi~~P----sGvLL~GPPGCGKTLlAKAVANE---ag~NFisVKGPEL  581 (802)
T KOG0733|consen  540 LGIDAP----SGVLLCGPPGCGKTLLAKAVANE---AGANFISVKGPEL  581 (802)
T ss_pred             hCCCCC----CceEEeCCCCccHHHHHHHHhhh---ccCceEeecCHHH
Confidence            899887    89999999999999999999999   8888888876554

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

Probab=99.97  E-value=6.7e-31  Score=285.13  Aligned_cols=280  Identities=23%  Similarity=0.286  Sum_probs=210.3

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcC-CeEE
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSG-DVIL  386 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~-~~IL  386 (710)
                      .+.+.++|+|||||+|||.+++++|++.          +..++.++...++  .++.|+.+..++..|+++.+.. |+++
T Consensus       215 ~~~prg~Ll~gppg~Gkt~l~~aVa~e~----------~a~~~~i~~peli--~k~~gEte~~LR~~f~~a~k~~~psii  282 (693)
T KOG0730|consen  215 IKPPRGLLLYGPPGTGKTFLVRAVANEY----------GAFLFLINGPELI--SKFPGETESNLRKAFAEALKFQVPSII  282 (693)
T ss_pred             CCCCCCccccCCCCCChHHHHHHHHHHh----------CceeEecccHHHH--HhcccchHHHHHHHHHHHhccCCCeeE
Confidence            3566889999999999999999999998          7889999999888  5678999999999999999888 9999


Q ss_pred             EEccchhhhhCCCCCCCCCCChHhHHHhhcccc----cCCCeEEEEccChHHHHhhhhccHHHHc-ccc-ceEecCCCHH
Q 005179          387 FIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL----GRGELQCIASTTQDEHRTQFEKDKALAR-RFQ-PVLISEPSQE  460 (710)
Q Consensus       387 ~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l----~~~~v~vI~att~~~~~~~~~~d~aL~~-Rf~-~I~v~~Ps~~  460 (710)
                      ||||+|.+++......   .....+...|..++    ..++++||++|+.+.     .+|++++| ||+ .+.+..|+..
T Consensus       283 ~IdEld~l~p~r~~~~---~~e~Rv~sqlltL~dg~~~~~~vivl~atnrp~-----sld~alRRgRfd~ev~IgiP~~~  354 (693)
T KOG0730|consen  283 FIDELDALCPKREGAD---DVESRVVSQLLTLLDGLKPDAKVIVLAATNRPD-----SLDPALRRGRFDREVEIGIPGSD  354 (693)
T ss_pred             eHHhHhhhCCcccccc---hHHHHHHHHHHHHHhhCcCcCcEEEEEecCCcc-----ccChhhhcCCCcceeeecCCCch
Confidence            9999999987643311   11333444443333    357899999999987     89999998 997 8999999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHH
Q 005179          461 DAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDY  540 (710)
Q Consensus       461 ~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~  540 (710)
                      +|.+|++.+..++    +.. ++..+..++..+++|++     .+...++.+|...+..+                    
T Consensus       355 ~RldIl~~l~k~~----~~~-~~~~l~~iA~~thGyvG-----aDL~~l~~ea~~~~~r~--------------------  404 (693)
T KOG0730|consen  355 GRLDILRVLTKKM----NLL-SDVDLEDIAVSTHGYVG-----ADLAALCREASLQATRR--------------------  404 (693)
T ss_pred             hHHHHHHHHHHhc----CCc-chhhHHHHHHHccchhH-----HHHHHHHHHHHHHHhhh--------------------
Confidence            9999999888754    333 56778899999999987     44555666554222111                    


Q ss_pred             HHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHH
Q 005179          541 WQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLL  620 (710)
Q Consensus       541 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l  620 (710)
                              .++++..+                                ...+.+..+++.+     ++..+++|++++++
T Consensus       405 --------~~~~~~~A--------------------------------~~~i~psa~Re~~-----ve~p~v~W~dIGGl  439 (693)
T KOG0730|consen  405 --------TLEIFQEA--------------------------------LMGIRPSALREIL-----VEMPNVSWDDIGGL  439 (693)
T ss_pred             --------hHHHHHHH--------------------------------HhcCCchhhhhee-----ccCCCCChhhccCH
Confidence                    00000000                                0223344444433     56669999999999


Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .++++.|.+.|.|.      +....++.+.|+++|    .|+|||||||||||++|||||++   +.-+++.+-.
T Consensus       440 E~lK~elq~~V~~p------~~~pe~F~r~Gi~pp----kGVLlyGPPGC~KT~lAkalAne---~~~nFlsvkg  501 (693)
T KOG0730|consen  440 EELKRELQQAVEWP------LKHPEKFARFGISPP----KGVLLYGPPGCGKTLLAKALANE---AGMNFLSVKG  501 (693)
T ss_pred             HHHHHHHHHHHhhh------hhchHHHHHhcCCCC----ceEEEECCCCcchHHHHHHHhhh---hcCCeeeccC
Confidence            99988777555444      444456788898776    79999999999999999999999   6667777643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.95  E-value=1.6e-26  Score=271.98  Aligned_cols=320  Identities=21%  Similarity=0.304  Sum_probs=207.8

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|++++|.+++++++.+.+..             ..+.++||+||||||||++++++|..+          +..++.++
T Consensus       175 ~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~----------~~~~i~i~  244 (733)
T TIGR01243       175 VTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEA----------GAYFISIN  244 (733)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHh----------CCeEEEEe
Confidence            4678899999999888776532             345689999999999999999999988          66778888


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc----cCCCeEEEEc
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL----GRGELQCIAS  429 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l----~~~~v~vI~a  429 (710)
                      ...+.  .++.|+.+..++.+|+.+....+.||||||+|.+........+  .....+.+.|..++    .++.+++|++
T Consensus       245 ~~~i~--~~~~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~--~~~~~~~~~Ll~~ld~l~~~~~vivI~a  320 (733)
T TIGR01243       245 GPEIM--SKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTG--EVEKRVVAQLLTLMDGLKGRGRVIVIGA  320 (733)
T ss_pred             cHHHh--cccccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcc--hHHHHHHHHHHHHhhccccCCCEEEEee
Confidence            77776  4567888889999999998888999999999999865432111  11233444444444    4578899999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCC-HHHHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFT-LEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~-~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ||..+     .+|+++.+  ||+ .|.++.|+.++|.+||+....      ++.+. +..++.++..+.+|..     .+
T Consensus       321 tn~~~-----~ld~al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~------~~~l~~d~~l~~la~~t~G~~g-----ad  384 (733)
T TIGR01243       321 TNRPD-----ALDPALRRPGRFDREIVIRVPDKRARKEILKVHTR------NMPLAEDVDLDKLAEVTHGFVG-----AD  384 (733)
T ss_pred             cCChh-----hcCHHHhCchhccEEEEeCCcCHHHHHHHHHHHhc------CCCCccccCHHHHHHhCCCCCH-----HH
Confidence            99876     68999988  897 799999999999999995543      23332 3346778888877754     23


Q ss_pred             HHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCC
Q 005179          506 AIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASD  585 (710)
Q Consensus       506 ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  585 (710)
                      ...+...++..+..+.....                                +..-....++                ..
T Consensus       385 l~~l~~~a~~~al~r~~~~~--------------------------------~~~~~~~~i~----------------~~  416 (733)
T TIGR01243       385 LAALAKEAAMAALRRFIREG--------------------------------KINFEAEEIP----------------AE  416 (733)
T ss_pred             HHHHHHHHHHHHHHHHhhcc--------------------------------cccccccccc----------------ch
Confidence            33444444422211100000                                0000000000                00


Q ss_pred             CCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHH--------hhcCCCCCCC
Q 005179          586 DDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKR--------SRVGLKDPNR  657 (710)
Q Consensus       586 ~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~--------~r~gl~~p~r  657 (710)
                      ......++.+|+..++.....-...       ..+.+....-+..|+|++++++.+...+.+        .+.|+..|  
T Consensus       417 ~~~~~~v~~~df~~Al~~v~ps~~~-------~~~~~~~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~--  487 (733)
T TIGR01243       417 VLKELKVTMKDFMEALKMVEPSAIR-------EVLVEVPNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPP--  487 (733)
T ss_pred             hcccccccHHHHHHHHhhccccccc-------hhhccccccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCC--
Confidence            0012346667776666433211100       000111112223377777777776665532        33455443  


Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                        .++|||||||||||++|+++|+++   ..+++.++.+++
T Consensus       488 --~giLL~GppGtGKT~lakalA~e~---~~~fi~v~~~~l  523 (733)
T TIGR01243       488 --KGVLLFGPPGTGKTLLAKAVATES---GANFIAVRGPEI  523 (733)
T ss_pred             --ceEEEECCCCCCHHHHHHHHHHhc---CCCEEEEehHHH
Confidence              689999999999999999999994   467888888765

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.

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

Probab=99.93  E-value=1.4e-25  Score=243.31  Aligned_cols=295  Identities=18%  Similarity=0.223  Sum_probs=202.0

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEE
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFI  388 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~I  388 (710)
                      ....|+||+||+|+|||.|++++++++....      .+++..++++.+-. .+ ...+...+..+|.++....|+|+++
T Consensus       429 ~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~------~~hv~~v~Cs~l~~-~~-~e~iQk~l~~vfse~~~~~PSiIvL  500 (952)
T KOG0735|consen  429 FRHGNILLNGPKGSGKTNLVKALFDYYSKDL------IAHVEIVSCSTLDG-SS-LEKIQKFLNNVFSEALWYAPSIIVL  500 (952)
T ss_pred             cccccEEEeCCCCCCHhHHHHHHHHHhcccc------ceEEEEEechhccc-hh-HHHHHHHHHHHHHHHHhhCCcEEEE
Confidence            3567899999999999999999999985322      56777888877652 22 4456677888888888899999999


Q ss_pred             ccchhhhhCCCCCCCCCC-ChHhHH----HhhcccccCCC-eEEEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCH
Q 005179          389 DEVHTLIGSGTVGRGNKG-TGLDIS----NLLKPSLGRGE-LQCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQ  459 (710)
Q Consensus       389 DEid~l~~~~~~~~~~~~-~~~~~~----~~L~~~l~~~~-v~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~  459 (710)
                      ||+|.|++......+..+ ......    +.++.++.++. +.+|++....+     .+++.|.+  +|+ ++.++.|..
T Consensus       501 Ddld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~~~~~~ia~Iat~qe~q-----tl~~~L~s~~~Fq~~~~L~ap~~  575 (952)
T KOG0735|consen  501 DDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYLKRNRKIAVIATGQELQ-----TLNPLLVSPLLFQIVIALPAPAV  575 (952)
T ss_pred             cchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHHccCcEEEEEEechhhh-----hcChhhcCccceEEEEecCCcch
Confidence            999999883222111111 111122    23344555554 57888776644     67777776  777 899999999


Q ss_pred             HHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChH
Q 005179          460 EDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDD  539 (710)
Q Consensus       460 ~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~  539 (710)
                      .+|.+||..++.+-    ...+..+.++.+...+.+|..     .+..-++++|...+.+....                
T Consensus       576 ~~R~~IL~~~~s~~----~~~~~~~dLd~ls~~TEGy~~-----~DL~ifVeRai~~a~leris----------------  630 (952)
T KOG0735|consen  576 TRRKEILTTIFSKN----LSDITMDDLDFLSVKTEGYLA-----TDLVIFVERAIHEAFLERIS----------------  630 (952)
T ss_pred             hHHHHHHHHHHHhh----hhhhhhHHHHHHHHhcCCccc-----hhHHHHHHHHHHHHHHHHhc----------------
Confidence            99999999988743    234566667778888888865     45566777776443321110                


Q ss_pred             HHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHH
Q 005179          540 YWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERML  619 (710)
Q Consensus       540 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~  619 (710)
                                                                     ..+..++.+++...++.++......++.....+
T Consensus       631 -----------------------------------------------~~~klltke~f~ksL~~F~P~aLR~ik~~k~tg  663 (952)
T KOG0735|consen  631 -----------------------------------------------NGPKLLTKELFEKSLKDFVPLALRGIKLVKSTG  663 (952)
T ss_pred             -----------------------------------------------cCcccchHHHHHHHHHhcChHHhhhccccccCC
Confidence                                                           112367888888888877655444443322211


Q ss_pred             HHHHHHHhhCcccChHHHHHHHHH----HHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISR----AVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~----~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                       ..+     +.|+|..++++.+.+    +.+|.....+.|-|...|+|||||||||||.||.|+|..   ..-++|.+..
T Consensus       664 -i~w-----~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~---~~~~fisvKG  734 (952)
T KOG0735|consen  664 -IRW-----EDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASN---SNLRFISVKG  734 (952)
T ss_pred             -CCc-----eecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhh---CCeeEEEecC
Confidence             112     225666666555544    447788888889888899999999999999999999988   5556666665


Q ss_pred             CC
Q 005179          696 SP  697 (710)
Q Consensus       696 se  697 (710)
                      .|
T Consensus       735 PE  736 (952)
T KOG0735|consen  735 PE  736 (952)
T ss_pred             HH
Confidence            44

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

Probab=99.93  E-value=1.6e-24  Score=237.48  Aligned_cols=298  Identities=18%  Similarity=0.273  Sum_probs=192.5

Q ss_pred             CcccCHHHHHHHHHHHHcCCC---------CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc
Q 005179          291 PVIGRETEIQRIIQILCRRTK---------NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA  361 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~---------~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~  361 (710)
                      ...+++..+..++.++..+..         ..+||+|+||||||++++++|.++          +.+++++|+.++.+. 
T Consensus       402 ~~~~~~~~~~~l~~vl~p~~~~s~~~~~~~~~vLLhG~~g~GK~t~V~~vas~l----------g~h~~evdc~el~~~-  470 (953)
T KOG0736|consen  402 SPPGLEAKVLELVAVLSPQKQPSGALLTLNPSVLLHGPPGSGKTTVVRAVASEL----------GLHLLEVDCYELVAE-  470 (953)
T ss_pred             CCccchHHHHHHHHHhCcccCcchhccccceEEEEeCCCCCChHHHHHHHHHHh----------CCceEeccHHHHhhc-
Confidence            345667677778887765322         347999999999999999999999          999999999999854 


Q ss_pred             ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------CCCeEEEEccChHH
Q 005179          362 KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------RGELQCIASTTQDE  434 (710)
Q Consensus       362 ~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------~~~v~vI~att~~~  434 (710)
                       ..+..+..+..++..++...|.|||+-++|.+......     +....++..+...++       .+.+++|++++..+
T Consensus       471 -s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~dg-----ged~rl~~~i~~~ls~e~~~~~~~~~ivv~t~~s~~  544 (953)
T KOG0736|consen  471 -SASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQDG-----GEDARLLKVIRHLLSNEDFKFSCPPVIVVATTSSIE  544 (953)
T ss_pred             -ccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCCC-----chhHHHHHHHHHHHhcccccCCCCceEEEEeccccc
Confidence             35677888999999999999999999999998532111     223334444444333       45788999988876


Q ss_pred             HHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH-HHHHHHHHHhhhhhcCCCCcchHHHHHHH
Q 005179          435 HRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTL-EAINAAVHLSARYISDRYLPDKAIDLVDE  512 (710)
Q Consensus       435 ~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~-~~l~~l~~ls~~~i~~r~~p~~ai~ll~~  512 (710)
                           .+.+.+.+-|- .|.++.|+.+||.+||+.+....      .+.. ..+..++..+.+|..     .+.-.++..
T Consensus       545 -----~lp~~i~~~f~~ei~~~~lse~qRl~iLq~y~~~~------~~n~~v~~k~~a~~t~gfs~-----~~L~~l~~~  608 (953)
T KOG0736|consen  545 -----DLPADIQSLFLHEIEVPALSEEQRLEILQWYLNHL------PLNQDVNLKQLARKTSGFSF-----GDLEALVAH  608 (953)
T ss_pred             -----cCCHHHHHhhhhhccCCCCCHHHHHHHHHHHHhcc------ccchHHHHHHHHHhcCCCCH-----HHHHHHhcC
Confidence                 78899999774 89999999999999999877633      2333 335566666665533     222223222


Q ss_pred             HHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCCCCCCCcC
Q 005179          513 AGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVV  592 (710)
Q Consensus       513 a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  592 (710)
                      ....+...                             ..+...++.+...       ..           .........+
T Consensus       609 ~s~~~~~~-----------------------------i~~~~l~g~~~~~-------~~-----------~~~~~~~~~l  641 (953)
T KOG0736|consen  609 SSLAAKTR-----------------------------IKNKGLAGGLQEE-------DE-----------GELCAAGFLL  641 (953)
T ss_pred             chHHHHHH-----------------------------HHhhcccccchhc-------cc-----------ccccccccee
Confidence            20000000                             0000000000000       00           0001112567


Q ss_pred             CHHHHHHHHHh-------hhCCC-hhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHh---hcCCCCCCCCCeE
Q 005179          593 GPDDIAAVASL-------WSGIP-VQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRS---RVGLKDPNRPTAA  661 (710)
Q Consensus       593 ~~~di~~~~s~-------~~gip-~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~---r~gl~~p~rp~~~  661 (710)
                      +.+|+..++++       -.|.| +.+++|+|++++.+++.          ++.++|..+++..   -.|++    +.+|
T Consensus       642 ~~edf~kals~~~~~fs~aiGAPKIPnV~WdDVGGLeevK~----------eIldTIqlPL~hpeLfssglr----kRSG  707 (953)
T KOG0736|consen  642 TEEDFDKALSRLQKEFSDAIGAPKIPNVSWDDVGGLEEVKT----------EILDTIQLPLKHPELFSSGLR----KRSG  707 (953)
T ss_pred             cHHHHHHHHHHHHHhhhhhcCCCCCCccchhcccCHHHHHH----------HHHHHhcCcccChhhhhcccc----ccce
Confidence            78888877763       33544 45889998555554444          2223333333332   33554    3489


Q ss_pred             EEEEcCCCCcHHHHHHHHHHH
Q 005179          662 MLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      +|||||||||||++|||+|.+
T Consensus       708 ILLYGPPGTGKTLlAKAVATE  728 (953)
T KOG0736|consen  708 ILLYGPPGTGKTLLAKAVATE  728 (953)
T ss_pred             eEEECCCCCchHHHHHHHHhh
Confidence            999999999999999999998

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

Probab=99.89  E-value=1.7e-22  Score=205.70  Aligned_cols=199  Identities=22%  Similarity=0.296  Sum_probs=161.2

Q ss_pred             cCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+++++-|-+++++.+.+.+.             -..+.++|||||||||||.||+++|+..          ++.++.+.
T Consensus       148 vtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T----------~AtFIrvv  217 (406)
T COG1222         148 VTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQT----------DATFIRVV  217 (406)
T ss_pred             CChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhcc----------CceEEEec
Confidence            357788999999998888643             2456789999999999999999999988          88899998


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------CCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------RGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------~~~v~v  426 (710)
                      .+.++  .+|.|+-...++++|.-++...|+|+||||||.+...+....  .++..+++..+.++|.       ++++.|
T Consensus       218 gSElV--qKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~--t~gDrEVQRTmleLL~qlDGFD~~~nvKV  293 (406)
T COG1222         218 GSELV--QKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSG--TSGDREVQRTMLELLNQLDGFDPRGNVKV  293 (406)
T ss_pred             cHHHH--HHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCC--CCchHHHHHHHHHHHHhccCCCCCCCeEE
Confidence            99998  688999889999999999999999999999999976543322  2557778877777664       589999


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCC
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYL  502 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~  502 (710)
                      |++||..+     -+||+|.|  ||+ .|+|+.|+.+.|.+||+-..++.      ++.+++ ++.++..+.++.+    
T Consensus       294 I~ATNR~D-----~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM------~l~~dvd~e~la~~~~g~sG----  358 (406)
T COG1222         294 IMATNRPD-----ILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKM------NLADDVDLELLARLTEGFSG----  358 (406)
T ss_pred             EEecCCcc-----ccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhc------cCccCcCHHHHHHhcCCCch----
Confidence            99999987     79999999  998 89999999999999999887754      444432 6677777766543    


Q ss_pred             cchHHHHHHHHHh
Q 005179          503 PDKAIDLVDEAGS  515 (710)
Q Consensus       503 p~~ai~ll~~a~~  515 (710)
                       .+...++.+|+.
T Consensus       359 -AdlkaictEAGm  370 (406)
T COG1222         359 -ADLKAICTEAGM  370 (406)
T ss_pred             -HHHHHHHHHHhH
Confidence             344455666653

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

Probab=99.87  E-value=2.2e-21  Score=204.88  Aligned_cols=311  Identities=22%  Similarity=0.233  Sum_probs=194.8

Q ss_pred             HHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh-----
Q 005179          306 LCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK-----  380 (710)
Q Consensus       306 L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-----  380 (710)
                      |....-.++|||||||||||.+|+.|...+. ..-|...        +...+.  .+|.|+.|+.++.+|..+++     
T Consensus       251 lGi~HVKGiLLyGPPGTGKTLiARqIGkMLN-ArePKIV--------NGPeIL--~KYVGeSE~NvR~LFaDAEeE~r~~  319 (744)
T KOG0741|consen  251 LGIKHVKGILLYGPPGTGKTLIARQIGKMLN-AREPKIV--------NGPEIL--NKYVGESEENVRKLFADAEEEQRRL  319 (744)
T ss_pred             cCccceeeEEEECCCCCChhHHHHHHHHHhc-CCCCccc--------CcHHHH--HHhhcccHHHHHHHHHhHHHHHHhh
Confidence            3334456789999999999999999998873 3333332        333444  67899999999999988864     


Q ss_pred             ---cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC----CCeEEEEccChHHHHhhhhccHHHHc--ccc-
Q 005179          381 ---SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR----GELQCIASTTQDEHRTQFEKDKALAR--RFQ-  450 (710)
Q Consensus       381 ---~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~----~~v~vI~att~~~~~~~~~~d~aL~~--Rf~-  450 (710)
                         ++--|+++||||.+|..+.+..++.+-...+.|.|+.-+..    +++.|||.||+.+     -+|.+|.|  ||+ 
T Consensus       320 g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeqLNNILVIGMTNR~D-----lIDEALLRPGRlEV  394 (744)
T KOG0741|consen  320 GANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQLNNILVIGMTNRKD-----LIDEALLRPGRLEV  394 (744)
T ss_pred             CccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHHhcccHHhhhcEEEEeccCchh-----hHHHHhcCCCceEE
Confidence               23468889999999986544344345556677777766652    6899999999987     68999999  997 


Q ss_pred             ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHh
Q 005179          451 PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQT  530 (710)
Q Consensus       451 ~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~  530 (710)
                      .+++..|+..-|.+||+-...+...+ +.--++-.++.++.++..|.+     ...-.++..|.+.+..+.-.....   
T Consensus       395 qmEIsLPDE~gRlQIl~IHT~rMre~-~~l~~dVdl~elA~lTKNfSG-----AEleglVksA~S~A~nR~vk~~~~---  465 (744)
T KOG0741|consen  395 QMEISLPDEKGRLQILKIHTKRMREN-NKLSADVDLKELAALTKNFSG-----AELEGLVKSAQSFAMNRHVKAGGK---  465 (744)
T ss_pred             EEEEeCCCccCceEEEEhhhhhhhhc-CCCCCCcCHHHHHHHhcCCch-----hHHHHHHHHHHHHHHHhhhccCcc---
Confidence            79999999999999999776665433 222233347788888888754     333445555543322211100000   


Q ss_pred             hhhCCCChHHHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChh
Q 005179          531 CILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQ  610 (710)
Q Consensus       531 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~  610 (710)
                                                                       ........+...|+.+|+..+++...  |.-
T Consensus       466 -------------------------------------------------~~~~~~~~e~lkV~r~DFl~aL~dVk--PAF  494 (744)
T KOG0741|consen  466 -------------------------------------------------VEVDPVAIENLKVTRGDFLNALEDVK--PAF  494 (744)
T ss_pred             -------------------------------------------------eecCchhhhheeecHHHHHHHHHhcC--ccc
Confidence                                                             00011122345778888877776432  111


Q ss_pred             hccHHHHHHHHHHHHHhhCc-ccChHHHHHHHHHHHHHhhcCCCCC-CCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          611 QITADERMLLVGLEEQLKKR-VIGQDEAVAAISRAVKRSRVGLKDP-NRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       611 ~~~~~~~~~l~~l~~~L~~~-v~Gq~~a~~~i~~~i~~~r~gl~~p-~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      .++..+      +++.+..- +.|-..+-.-+.+...+.. ..+.+ ..|.-++||.||||+|||.||-.+|..   ++-
T Consensus       495 G~see~------l~~~~~~Gmi~~g~~v~~il~~G~llv~-qvk~s~~s~lvSvLl~Gp~~sGKTaLAA~iA~~---S~F  564 (744)
T KOG0741|consen  495 GISEED------LERFVMNGMINWGPPVTRILDDGKLLVQ-QVKNSERSPLVSVLLEGPPGSGKTALAAKIALS---SDF  564 (744)
T ss_pred             CCCHHH------HHHHHhCCceeecccHHHHHhhHHHHHH-HhhccccCcceEEEEecCCCCChHHHHHHHHhh---cCC
Confidence            222222      22222221 2222222222222222221 22333 335679999999999999999999987   776


Q ss_pred             cceeeC-------CCCCCCcc
Q 005179          689 IHYLFF-------PSPFNSVK  702 (710)
Q Consensus       689 ~li~~d-------~se~~~~~  702 (710)
                      ++|++-       |||+..+.
T Consensus       565 PFvKiiSpe~miG~sEsaKc~  585 (744)
T KOG0741|consen  565 PFVKIISPEDMIGLSESAKCA  585 (744)
T ss_pred             CeEEEeChHHccCccHHHHHH
Confidence            677653       56664443

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

Probab=99.86  E-value=2.8e-21  Score=200.09  Aligned_cols=197  Identities=26%  Similarity=0.348  Sum_probs=154.9

Q ss_pred             hhhHHhhhhcCCCCcccCHHHH---HHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          278 VDLTARASEELIDPVIGRETEI---QRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i---~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .+|...+||.+|+++||+++.+   .-+..++....-.+.+|||||||||||+|+.||+..          +..+..++ 
T Consensus        12 ~PLA~rmRP~~lde~vGQ~HLlg~~~~lrr~v~~~~l~SmIl~GPPG~GKTTlA~liA~~~----------~~~f~~~s-   80 (436)
T COG2256          12 MPLAERLRPKSLDEVVGQEHLLGEGKPLRRAVEAGHLHSMILWGPPGTGKTTLARLIAGTT----------NAAFEALS-   80 (436)
T ss_pred             cChHHHhCCCCHHHhcChHhhhCCCchHHHHHhcCCCceeEEECCCCCCHHHHHHHHHHhh----------CCceEEec-
Confidence            3788999999999999999877   346666777788999999999999999999999988          67777654 


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~at  430 (710)
                       ....|.+       .++.+++++++    ....||||||||++             +..-++.|++.+++|.+++||+|
T Consensus        81 -Av~~gvk-------dlr~i~e~a~~~~~~gr~tiLflDEIHRf-------------nK~QQD~lLp~vE~G~iilIGAT  139 (436)
T COG2256          81 -AVTSGVK-------DLREIIEEARKNRLLGRRTILFLDEIHRF-------------NKAQQDALLPHVENGTIILIGAT  139 (436)
T ss_pred             -cccccHH-------HHHHHHHHHHHHHhcCCceEEEEehhhhc-------------ChhhhhhhhhhhcCCeEEEEecc
Confidence             3333332       37777777743    33689999999999             34457899999999999999999


Q ss_pred             ChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhh---cCCCCCHHHHHHHHHHhhhhhcCCCCcchHH
Q 005179          431 TQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAH---HNCKFTLEAINAAVHLSARYISDRYLPDKAI  507 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~---~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai  507 (710)
                      |.++   +|+++++|++|+..+.+.+.+.++..++|+..+...+..   ..+.+++++++.++..+.+-.      +.++
T Consensus       140 TENP---sF~ln~ALlSR~~vf~lk~L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~------R~aL  210 (436)
T COG2256         140 TENP---SFELNPALLSRARVFELKPLSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDA------RRAL  210 (436)
T ss_pred             CCCC---CeeecHHHhhhhheeeeecCCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchH------HHHH
Confidence            9986   789999999999999999999999999888744333221   124589999999999877642      2345


Q ss_pred             HHHHHHHh
Q 005179          508 DLVDEAGS  515 (710)
Q Consensus       508 ~ll~~a~~  515 (710)
                      .+++.+..
T Consensus       211 N~LE~~~~  218 (436)
T COG2256         211 NLLELAAL  218 (436)
T ss_pred             HHHHHHHH
Confidence            55555443

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

Probab=99.85  E-value=1.1e-20  Score=183.75  Aligned_cols=194  Identities=23%  Similarity=0.308  Sum_probs=149.3

Q ss_pred             HhhhhcCCCCcccCHHHHHHHH---HHHH------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          282 ARASEELIDPVIGRETEIQRII---QILC------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       282 ~~~~~~~l~~liGr~~~i~~l~---~~L~------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      +..+.-+|+++||+++..+.+.   +.|.      ...+.|+|+|||||||||++|+++|.+.          +.+++.+
T Consensus       113 e~~~~it~ddViGqEeAK~kcrli~~yLenPe~Fg~WAPknVLFyGppGTGKTm~Akalane~----------kvp~l~v  182 (368)
T COG1223         113 EIISDITLDDVIGQEEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTMMAKALANEA----------KVPLLLV  182 (368)
T ss_pred             hhhccccHhhhhchHHHHHHHHHHHHHhhChHHhcccCcceeEEECCCCccHHHHHHHHhccc----------CCceEEe
Confidence            3445667999999997765543   3332      2457899999999999999999999988          6677777


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEEEE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQCIA  428 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~vI~  428 (710)
                      ....++  ..+.|+-..+++++++.+++..|||+||||+|.+.-...... -.+...++.|.|+.-|.    +..++.|+
T Consensus       183 kat~li--GehVGdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQe-lRGDVsEiVNALLTelDgi~eneGVvtIa  259 (368)
T COG1223         183 KATELI--GEHVGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQE-LRGDVSEIVNALLTELDGIKENEGVVTIA  259 (368)
T ss_pred             chHHHH--HHHhhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHH-hcccHHHHHHHHHHhccCcccCCceEEEe
Confidence            777777  457788889999999999999999999999999854332211 12234566777765553    45789999


Q ss_pred             ccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          429 STTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      +||.++     -+|+++++||. .|+|..|+.++|..||+...+++    .+.+.-. ++.++..+.++.+
T Consensus       260 aTN~p~-----~LD~aiRsRFEeEIEF~LP~~eEr~~ile~y~k~~----Plpv~~~-~~~~~~~t~g~Sg  320 (368)
T COG1223         260 ATNRPE-----LLDPAIRSRFEEEIEFKLPNDEERLEILEYYAKKF----PLPVDAD-LRYLAAKTKGMSG  320 (368)
T ss_pred             ecCChh-----hcCHHHHhhhhheeeeeCCChHHHHHHHHHHHHhC----CCccccC-HHHHHHHhCCCCc
Confidence            999988     78999999997 89999999999999999877755    3444333 6777777777644

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

Probab=99.84  E-value=8.1e-20  Score=199.26  Aligned_cols=200  Identities=22%  Similarity=0.295  Sum_probs=159.3

Q ss_pred             cCCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -.|+++-|.++..+.+.+.+             .-..+..||||||||||||++|+++|.+.          ++.++++.
T Consensus       431 v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~----------~~nFlsvk  500 (693)
T KOG0730|consen  431 VSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEA----------GMNFLSVK  500 (693)
T ss_pred             CChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhh----------cCCeeecc
Confidence            35667777776555555432             22456789999999999999999999998          88899998


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEEEEc
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQCIAS  429 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~vI~a  429 (710)
                      ...++  ++|.|+.|..++++|+.+++..|+|+|+||||.+.+.+..+.+  +....+.+.|+..|.    ..++.||++
T Consensus       501 gpEL~--sk~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~--~v~~RVlsqLLtEmDG~e~~k~V~ViAA  576 (693)
T KOG0730|consen  501 GPELF--SKYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSS--GVTDRVLSQLLTEMDGLEALKNVLVIAA  576 (693)
T ss_pred             CHHHH--HHhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCcc--chHHHHHHHHHHHcccccccCcEEEEec
Confidence            88888  6899999999999999999999999999999999887652211  223445555555443    458999999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ||.++     .+|++|.|  ||+ .|+|+.|+.+.|.+||+...+      ++.+.++ .++.+++.+.+|.+     .+
T Consensus       577 TNRpd-----~ID~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~k------kmp~~~~vdl~~La~~T~g~SG-----Ae  640 (693)
T KOG0730|consen  577 TNRPD-----MIDPALLRPGRLDRIIYVPLPDLEARLEILKQCAK------KMPFSEDVDLEELAQATEGYSG-----AE  640 (693)
T ss_pred             cCChh-----hcCHHHcCCcccceeEeecCccHHHHHHHHHHHHh------cCCCCccccHHHHHHHhccCCh-----HH
Confidence            99997     89999999  998 899999999999999997766      4566666 57889998888855     56


Q ss_pred             HHHHHHHHHhh
Q 005179          506 AIDLVDEAGSR  516 (710)
Q Consensus       506 ai~ll~~a~~~  516 (710)
                      ...++.+|+..
T Consensus       641 l~~lCq~A~~~  651 (693)
T KOG0730|consen  641 IVAVCQEAALL  651 (693)
T ss_pred             HHHHHHHHHHH
Confidence            67788888743

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

Probab=99.83  E-value=2.5e-19  Score=183.68  Aligned_cols=203  Identities=20%  Similarity=0.263  Sum_probs=149.8

Q ss_pred             hhcCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          285 SEELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       285 ~~~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      ..-+++++.|..+..+-|.+.+-            ++.=..+|++||||||||.||+++|.++          +..++.+
T Consensus       207 p~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc----------~tTFFNV  276 (491)
T KOG0738|consen  207 PNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATEC----------GTTFFNV  276 (491)
T ss_pred             CCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccceeeeeCCCCCcHHHHHHHHHHhh----------cCeEEEe
Confidence            33478899999987777666431            1222579999999999999999999998          7777777


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------CCC-e
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------RGE-L  424 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------~~~-v  424 (710)
                      ..+.+.  ++++|+.|+.++-+|+.++...|++|||||||.|+..+... +..+.+..+.+-|+-.|.       +.+ |
T Consensus       277 Ssstlt--SKwRGeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s-~EHEaSRRvKsELLvQmDG~~~t~e~~k~V  353 (491)
T KOG0738|consen  277 SSSTLT--SKWRGESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGS-SEHEASRRVKSELLVQMDGVQGTLENSKVV  353 (491)
T ss_pred             chhhhh--hhhccchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCc-cchhHHHHHHHHHHHHhhccccccccceeE
Confidence            666666  78999999999999999999999999999999998764331 223344445444433332       223 5


Q ss_pred             EEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          425 QCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      .|+++||.+-     ++|.+|+|||. .|.|+.|+.+.|..+|+..++..+..     ++-.++.+++.+.+|.+     
T Consensus       354 mVLAATN~PW-----diDEAlrRRlEKRIyIPLP~~~~R~~Li~~~l~~~~~~-----~~~~~~~lae~~eGySG-----  418 (491)
T KOG0738|consen  354 MVLAATNFPW-----DIDEALRRRLEKRIYIPLPDAEARSALIKILLRSVELD-----DPVNLEDLAERSEGYSG-----  418 (491)
T ss_pred             EEEeccCCCc-----chHHHHHHHHhhheeeeCCCHHHHHHHHHHhhccccCC-----CCccHHHHHHHhcCCCh-----
Confidence            5666677653     89999999998 89999999999999999877643222     22336778888888865     


Q ss_pred             chHHHHHHHHHh
Q 005179          504 DKAIDLVDEAGS  515 (710)
Q Consensus       504 ~~ai~ll~~a~~  515 (710)
                      ++...++.+|..
T Consensus       419 aDI~nvCreAsm  430 (491)
T KOG0738|consen  419 ADITNVCREASM  430 (491)
T ss_pred             HHHHHHHHHHHH
Confidence            445556666543

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.81  E-value=9.9e-19  Score=193.61  Aligned_cols=202  Identities=21%  Similarity=0.273  Sum_probs=149.3

Q ss_pred             cCCCCcccCHHHHHHHHHHH----------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          287 ELIDPVIGRETEIQRIIQIL----------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L----------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      .+|+++.|.+...+.+.+..          ....+.++||+||||||||.+|+++|..+          +..++.++++.
T Consensus       225 ~~~~dvgGl~~lK~~l~~~~~~~~~~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~----------~~~~~~l~~~~  294 (489)
T CHL00195        225 EKISDIGGLDNLKDWLKKRSTSFSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDW----------QLPLLRLDVGK  294 (489)
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHhhHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEEhHH
Confidence            35677888776665554421          11345789999999999999999999998          78899999988


Q ss_pred             hhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEEccChHH
Q 005179          357 LMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIASTTQDE  434 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~att~~~  434 (710)
                      +.  .++.|+.+.+++.+|..++...|+||||||||.++..... .++.+....+.+.|...+.  +..+.+|+|||..+
T Consensus       295 l~--~~~vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~-~~d~~~~~rvl~~lL~~l~~~~~~V~vIaTTN~~~  371 (489)
T CHL00195        295 LF--GGIVGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSES-KGDSGTTNRVLATFITWLSEKKSPVFVVATANNID  371 (489)
T ss_pred             hc--ccccChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccC-CCCchHHHHHHHHHHHHHhcCCCceEEEEecCChh
Confidence            77  4578889999999999999889999999999998764221 1111223344444544444  45688999999876


Q ss_pred             HHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHH
Q 005179          435 HRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVD  511 (710)
Q Consensus       435 ~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~  511 (710)
                           .+|+++.|  ||+ .|.|+.|+.++|.+||+.++.+..   .....+..++.++..+.+|.+     .+...++.
T Consensus       372 -----~Ld~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~---~~~~~~~dl~~La~~T~GfSG-----AdI~~lv~  438 (489)
T CHL00195        372 -----LLPLEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFR---PKSWKKYDIKKLSKLSNKFSG-----AEIEQSII  438 (489)
T ss_pred             -----hCCHHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcC---CCcccccCHHHHHhhcCCCCH-----HHHHHHHH
Confidence                 79999998  998 899999999999999998887542   112234457788888888755     34444555


Q ss_pred             HHH
Q 005179          512 EAG  514 (710)
Q Consensus       512 ~a~  514 (710)
                      +|+
T Consensus       439 eA~  441 (489)
T CHL00195        439 EAM  441 (489)
T ss_pred             HHH
Confidence            544

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

Probab=99.81  E-value=9.7e-19  Score=192.48  Aligned_cols=202  Identities=23%  Similarity=0.339  Sum_probs=151.3

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+++++-|-++....+.+.+.-            +...++|||||||||||.+|+++|.++          ...++++..
T Consensus       669 V~WdDVGGLeevK~eIldTIqlPL~hpeLfssglrkRSGILLYGPPGTGKTLlAKAVATEc----------sL~FlSVKG  738 (953)
T KOG0736|consen  669 VSWDDVGGLEEVKTEILDTIQLPLKHPELFSSGLRKRSGILLYGPPGTGKTLLAKAVATEC----------SLNFLSVKG  738 (953)
T ss_pred             cchhcccCHHHHHHHHHHHhcCcccChhhhhccccccceeEEECCCCCchHHHHHHHHhhc----------eeeEEeecC
Confidence            3688998988777777765432            235689999999999999999999998          677888888


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHh--HHHhhcc--ccc---CCCeEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLD--ISNLLKP--SLG---RGELQCI  427 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~--~~~~L~~--~l~---~~~v~vI  427 (710)
                      .+++  ..|.|+.|+.++++|+.++.+.|||||+||+|.+.+.+.. .|++++.+|  +..+|.+  -|.   ...+.||
T Consensus       739 PELL--NMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~-sGDSGGVMDRVVSQLLAELDgls~~~s~~VFVi  815 (953)
T KOG0736|consen  739 PELL--NMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGR-SGDSGGVMDRVVSQLLAELDGLSDSSSQDVFVI  815 (953)
T ss_pred             HHHH--HHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCC-CCCccccHHHHHHHHHHHhhcccCCCCCceEEE
Confidence            8888  6799999999999999999999999999999999976432 122344443  3333322  222   3568999


Q ss_pred             EccChHHHHhhhhccHHHHc--ccc-ceEecCC-CHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          428 ASTTQDEHRTQFEKDKALAR--RFQ-PVLISEP-SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~P-s~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      |+||+++     -+||+|.|  ||+ -+++.++ +.+....||+.+.+++....++.     +..+++.+.--++    .
T Consensus       816 GATNRPD-----LLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVd-----L~eiAk~cp~~~T----G  881 (953)
T KOG0736|consen  816 GATNRPD-----LLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVD-----LVEIAKKCPPNMT----G  881 (953)
T ss_pred             ecCCCcc-----ccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcC-----HHHHHhhCCcCCc----h
Confidence            9999998     78999999  998 6788877 47788999999999885444433     4556666654333    2


Q ss_pred             chHHHHHHHHHh
Q 005179          504 DKAIDLVDEAGS  515 (710)
Q Consensus       504 ~~ai~ll~~a~~  515 (710)
                      .+...++..|..
T Consensus       882 ADlYsLCSdA~l  893 (953)
T KOG0736|consen  882 ADLYSLCSDAML  893 (953)
T ss_pred             hHHHHHHHHHHH
Confidence            445666666543

>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=99.81  E-value=6.3e-20  Score=179.02  Aligned_cols=189  Identities=21%  Similarity=0.305  Sum_probs=126.6

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      .++.+.+||.+|+++||+++.+..+.-.+..     ..-.++|||||||+||||||+.||+++          +..+..+
T Consensus        12 ~~l~~~lRP~~L~efiGQ~~l~~~l~i~i~aa~~r~~~l~h~lf~GPPG~GKTTLA~IIA~e~----------~~~~~~~   81 (233)
T PF05496_consen   12 APLAERLRPKSLDEFIGQEHLKGNLKILIRAAKKRGEALDHMLFYGPPGLGKTTLARIIANEL----------GVNFKIT   81 (233)
T ss_dssp             S-HHHHTS-SSCCCS-S-HHHHHHHHHHHHHHHCTTS---EEEEESSTTSSHHHHHHHHHHHC----------T--EEEE
T ss_pred             hhhHHhcCCCCHHHccCcHHHHhhhHHHHHHHHhcCCCcceEEEECCCccchhHHHHHHHhcc----------CCCeEec
Confidence            3566788999999999999988876544332     123579999999999999999999998          5566554


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCC---------
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGE---------  423 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~---------  423 (710)
                      +...+.    ..++    +..++..+.  .+.||||||||++             +...++.|.+.|+++.         
T Consensus        82 sg~~i~----k~~d----l~~il~~l~--~~~ILFIDEIHRl-------------nk~~qe~LlpamEd~~idiiiG~g~  138 (233)
T PF05496_consen   82 SGPAIE----KAGD----LAAILTNLK--EGDILFIDEIHRL-------------NKAQQEILLPAMEDGKIDIIIGKGP  138 (233)
T ss_dssp             ECCC------SCHH----HHHHHHT----TT-EEEECTCCC---------------HHHHHHHHHHHHCSEEEEEBSSSS
T ss_pred             cchhhh----hHHH----HHHHHHhcC--CCcEEEEechhhc-------------cHHHHHHHHHHhccCeEEEEecccc
Confidence            432211    1222    334444443  3569999999999             6667889988888653         


Q ss_pred             -----------eEEEEccChHHHHhhhhccHHHHccccc-eEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          424 -----------LQCIASTTQDEHRTQFEKDKALARRFQP-VLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       424 -----------v~vI~att~~~~~~~~~~d~aL~~Rf~~-I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                                 +.+||+||...     .+.+.|++||.. ..+..++.++..+|++.-..    ..++.+++++...++.
T Consensus       139 ~ar~~~~~l~~FTligATTr~g-----~ls~pLrdRFgi~~~l~~Y~~~el~~Iv~r~a~----~l~i~i~~~~~~~Ia~  209 (233)
T PF05496_consen  139 NARSIRINLPPFTLIGATTRAG-----LLSSPLRDRFGIVLRLEFYSEEELAKIVKRSAR----ILNIEIDEDAAEEIAR  209 (233)
T ss_dssp             S-BEEEEE----EEEEEESSGC-----CTSHCCCTTSSEEEE----THHHHHHHHHHCCH----CTT-EE-HHHHHHHHH
T ss_pred             ccceeeccCCCceEeeeecccc-----ccchhHHhhcceecchhcCCHHHHHHHHHHHHH----HhCCCcCHHHHHHHHH
Confidence                       55788888875     678999999984 57999999998888875444    5689999999999988


Q ss_pred             HhhhhhcCCCCcchHHHHHHHHH
Q 005179          492 LSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       492 ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      .|.+      .|.-|..++..+-
T Consensus       210 rsrG------tPRiAnrll~rvr  226 (233)
T PF05496_consen  210 RSRG------TPRIANRLLRRVR  226 (233)
T ss_dssp             CTTT------SHHHHHHHHHHHC
T ss_pred             hcCC------ChHHHHHHHHHHH
Confidence            7554      4777888887664

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.

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

Probab=99.81  E-value=8.1e-19  Score=188.62  Aligned_cols=199  Identities=21%  Similarity=0.284  Sum_probs=152.5

Q ss_pred             CCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +|+++-+.++.-.+|...+             .-..+.++||+||||||||.||+++|++.          +..++.+..
T Consensus       509 tW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEa----------g~NFisVKG  578 (802)
T KOG0733|consen  509 TWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEA----------GANFISVKG  578 (802)
T ss_pred             ChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhc----------cCceEeecC
Confidence            4566666555444444332             22456789999999999999999999998          788899988


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~vI~at  430 (710)
                      ..|+  .+|.|+.|..++.+|..++.+.|+|+|+||+|.|+..+..+.  .+.+..+.|.|+.-|.    +..+.||++|
T Consensus       579 PELl--NkYVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~--s~~s~RvvNqLLtElDGl~~R~gV~viaAT  654 (802)
T KOG0733|consen  579 PELL--NKYVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEG--SSVSSRVVNQLLTELDGLEERRGVYVIAAT  654 (802)
T ss_pred             HHHH--HHHhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCC--chhHHHHHHHHHHHhcccccccceEEEeec
Confidence            8888  689999999999999999999999999999999998755432  2445566777665443    5679999999


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhh--hhhcCCCCcc
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSA--RYISDRYLPD  504 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~--~~i~~r~~p~  504 (710)
                      |.++     -+||+++|  ||+ .+.|+.|+.++|..||+.+.+.    ++..+++++ ++.++....  +|.+     .
T Consensus       655 NRPD-----iIDpAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn----~k~pl~~dVdl~eia~~~~c~gftG-----A  720 (802)
T KOG0733|consen  655 NRPD-----IIDPAILRPGRLDKLLYVGLPNAEERVAILKTITKN----TKPPLSSDVDLDEIARNTKCEGFTG-----A  720 (802)
T ss_pred             CCCc-----ccchhhcCCCccCceeeecCCCHHHHHHHHHHHhcc----CCCCCCcccCHHHHhhcccccCCch-----h
Confidence            9997     78999999  998 7899999999999999988773    344454443 566665544  5544     3


Q ss_pred             hHHHHHHHHH
Q 005179          505 KAIDLVDEAG  514 (710)
Q Consensus       505 ~ai~ll~~a~  514 (710)
                      +.-.|+.+|.
T Consensus       721 DLaaLvreAs  730 (802)
T KOG0733|consen  721 DLAALVREAS  730 (802)
T ss_pred             hHHHHHHHHH
Confidence            4455666654

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=99.78  E-value=5.4e-18  Score=184.99  Aligned_cols=198  Identities=22%  Similarity=0.284  Sum_probs=146.0

Q ss_pred             CCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .++++.|.+++++.+.+.+..             ..+.++||+||||||||++|+++|..+          +..++.++.
T Consensus       129 ~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~----------~~~~i~v~~  198 (389)
T PRK03992        129 TYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET----------NATFIRVVG  198 (389)
T ss_pred             CHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHh----------CCCEEEeeh
Confidence            467889999999888875421             346789999999999999999999988          667888888


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQCI  427 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~vI  427 (710)
                      +.+.  .++.|+.+..++.+|..+....|+||||||+|.+......+..  .+..++...+..++       ..+++.+|
T Consensus       199 ~~l~--~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~--~~~~~~~~~l~~lL~~ld~~~~~~~v~VI  274 (389)
T PRK03992        199 SELV--QKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGT--SGDREVQRTLMQLLAEMDGFDPRGNVKII  274 (389)
T ss_pred             HHHh--HhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCC--CccHHHHHHHHHHHHhccccCCCCCEEEE
Confidence            7776  4467777888899999888888999999999999765432111  12233333333322       23678999


Q ss_pred             EccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH-HHHHHHHHHhhhhhcCCCCc
Q 005179          428 ASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTL-EAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~-~~l~~l~~ls~~~i~~r~~p  503 (710)
                      ++||..+     .+|+++.|  ||+ .|.|+.|+.++|.+||+......      .+.. ..+..++..+.+|.+     
T Consensus       275 ~aTn~~~-----~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~------~~~~~~~~~~la~~t~g~sg-----  338 (389)
T PRK03992        275 AATNRID-----ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKM------NLADDVDLEELAELTEGASG-----  338 (389)
T ss_pred             EecCChh-----hCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccC------CCCCcCCHHHHHHHcCCCCH-----
Confidence            9999876     78999997  997 89999999999999999766533      2222 235667777766643     


Q ss_pred             chHHHHHHHHHh
Q 005179          504 DKAIDLVDEAGS  515 (710)
Q Consensus       504 ~~ai~ll~~a~~  515 (710)
                      .+...++.+|+.
T Consensus       339 adl~~l~~eA~~  350 (389)
T PRK03992        339 ADLKAICTEAGM  350 (389)
T ss_pred             HHHHHHHHHHHH
Confidence            555667776663

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

Probab=99.77  E-value=2.1e-18  Score=182.61  Aligned_cols=203  Identities=21%  Similarity=0.262  Sum_probs=141.0

Q ss_pred             hcCCCCcccCHHH---HHHHHHHHHc---------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          286 EELIDPVIGRETE---IQRIIQILCR---------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       286 ~~~l~~liGr~~~---i~~l~~~L~~---------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      .-+|+++-|.|+.   ++.+++.|..         +-+.+|||+||||||||.||+++|-+.          +.+++...
T Consensus       300 nv~F~dVkG~DEAK~ELeEiVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA----------~VPFF~~s  369 (752)
T KOG0734|consen  300 NVTFEDVKGVDEAKQELEEIVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEA----------GVPFFYAS  369 (752)
T ss_pred             ccccccccChHHHHHHHHHHHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhccc----------CCCeEecc
Confidence            3468899999864   4555555543         445789999999999999999999877          44455544


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~v  426 (710)
                      .+.+-  ..+.|.-..+++++|..++...|||+||||||.+-+++...    . ..-....|.++|       .+..++|
T Consensus       370 GSEFd--Em~VGvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~----~-~~y~kqTlNQLLvEmDGF~qNeGiIv  442 (752)
T KOG0734|consen  370 GSEFD--EMFVGVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPS----D-QHYAKQTLNQLLVEMDGFKQNEGIIV  442 (752)
T ss_pred             ccchh--hhhhcccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCcc----H-HHHHHHHHHHHHHHhcCcCcCCceEE
Confidence            43332  23455567889999999999999999999999995544321    1 111222333332       2457999


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      |++||.++     .+|++|.|  ||+ .|.|+.|+..-|.+||+....+..  +.-.+++.+   +++-+.+|.+     
T Consensus       443 igATNfpe-----~LD~AL~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~--~~~~VD~~i---iARGT~GFsG-----  507 (752)
T KOG0734|consen  443 IGATNFPE-----ALDKALTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIP--LDEDVDPKI---IARGTPGFSG-----  507 (752)
T ss_pred             EeccCChh-----hhhHHhcCCCccceeEecCCCCcccHHHHHHHHHhcCC--cccCCCHhH---hccCCCCCch-----
Confidence            99999998     89999999  998 899999999999999998877542  222344443   3333333322     


Q ss_pred             chHHHHHHHHHhhhhhh
Q 005179          504 DKAIDLVDEAGSRAHIE  520 (710)
Q Consensus       504 ~~ai~ll~~a~~~~~~~  520 (710)
                      .+.-.++..|+-++.+.
T Consensus       508 AdLaNlVNqAAlkAa~d  524 (752)
T KOG0734|consen  508 ADLANLVNQAALKAAVD  524 (752)
T ss_pred             HHHHHHHHHHHHHHHhc
Confidence            45566777776665554

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=99.77  E-value=4.9e-18  Score=172.49  Aligned_cols=187  Identities=22%  Similarity=0.311  Sum_probs=141.2

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHH---HHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          278 VDLTARASEELIDPVIGRETEIQR---IIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~---l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .+|.+.+||.++++++|+++.+-+   |...+...+-++++|+||||||||+||+.|+......       .++++++  
T Consensus       126 ~PLaermRPktL~dyvGQ~hlv~q~gllrs~ieq~~ipSmIlWGppG~GKTtlArlia~tsk~~-------Syrfvel--  196 (554)
T KOG2028|consen  126 KPLAERMRPKTLDDYVGQSHLVGQDGLLRSLIEQNRIPSMILWGPPGTGKTTLARLIASTSKKH-------SYRFVEL--  196 (554)
T ss_pred             CChhhhcCcchHHHhcchhhhcCcchHHHHHHHcCCCCceEEecCCCCchHHHHHHHHhhcCCC-------ceEEEEE--
Confidence            378999999999999999987643   4556677778899999999999999999998765211       2334443  


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHh-----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQK-----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~-----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~a  429 (710)
                      +...++.+       .++.+|+..+.     ....||||||||++             +...++.+++.+++|.+.+||+
T Consensus       197 SAt~a~t~-------dvR~ife~aq~~~~l~krkTilFiDEiHRF-------------NksQQD~fLP~VE~G~I~lIGA  256 (554)
T KOG2028|consen  197 SATNAKTN-------DVRDIFEQAQNEKSLTKRKTILFIDEIHRF-------------NKSQQDTFLPHVENGDITLIGA  256 (554)
T ss_pred             eccccchH-------HHHHHHHHHHHHHhhhcceeEEEeHHhhhh-------------hhhhhhcccceeccCceEEEec
Confidence            33333222       26666666643     34789999999999             3345789999999999999999


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHh---------hcCCCCCHHHHHHHHHHhhhh
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEA---------HHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~---------~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      ||.++   .|.++.+|.+||.++.+...+.+....||..-..-+..         +..+.+++.++++++.++.+.
T Consensus       257 TTENP---SFqln~aLlSRC~VfvLekL~~n~v~~iL~raia~l~dser~~~~l~n~s~~ve~siidyla~lsdGD  329 (554)
T KOG2028|consen  257 TTENP---SFQLNAALLSRCRVFVLEKLPVNAVVTILMRAIASLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGD  329 (554)
T ss_pred             ccCCC---ccchhHHHHhccceeEeccCCHHHHHHHHHHHHHhhccccccCCCCCCcchhhhHHHHHHHHHhcCch
Confidence            99876   67899999999999999999999999998874432211         111346778888888877653

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

Probab=99.76  E-value=1.5e-17  Score=180.58  Aligned_cols=200  Identities=20%  Similarity=0.257  Sum_probs=143.5

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+++++.|.+.+++.+.+.+.-             ..+.++||+||||||||++++++|..+          +..++.+.
T Consensus       142 v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l----------~~~fi~i~  211 (398)
T PTZ00454        142 VTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHT----------TATFIRVV  211 (398)
T ss_pred             CCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc----------CCCEEEEe
Confidence            3577899999888877765421             346789999999999999999999987          56677777


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~v  426 (710)
                      .+.+.  .++.|+.+..++.+|..+....|+||||||+|.++........  +........+..++       ...++.+
T Consensus       212 ~s~l~--~k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~--~~d~~~~r~l~~LL~~ld~~~~~~~v~V  287 (398)
T PTZ00454        212 GSEFV--QKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQT--GADREVQRILLELLNQMDGFDQTTNVKV  287 (398)
T ss_pred             hHHHH--HHhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccC--CccHHHHHHHHHHHHHhhccCCCCCEEE
Confidence            66665  3466777788999999998888999999999999765322111  11223333332222       2357889


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      |++|+..+     .+|+++.|  ||+ .|.|+.|+.++|..||+.+..+.    ++. .+-.+..++..+.+|.+     
T Consensus       288 I~aTN~~d-----~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~----~l~-~dvd~~~la~~t~g~sg-----  352 (398)
T PTZ00454        288 IMATNRAD-----TLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKM----NLS-EEVDLEDFVSRPEKISA-----  352 (398)
T ss_pred             EEecCCch-----hCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcC----CCC-cccCHHHHHHHcCCCCH-----
Confidence            99999876     89999998  997 89999999999999999877643    222 11235566666666533     


Q ss_pred             chHHHHHHHHHh
Q 005179          504 DKAIDLVDEAGS  515 (710)
Q Consensus       504 ~~ai~ll~~a~~  515 (710)
                      .+...++.+|+.
T Consensus       353 aDI~~l~~eA~~  364 (398)
T PTZ00454        353 ADIAAICQEAGM  364 (398)
T ss_pred             HHHHHHHHHHHH
Confidence            555666666653

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.76  E-value=1.2e-17  Score=181.76  Aligned_cols=202  Identities=20%  Similarity=0.203  Sum_probs=152.4

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc------------
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL------------  344 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l------------  344 (710)
                      ..|.+++||.+|++++|++..+..|...+..+...+ +||+||+|||||++|+.+|+.+.+...+...            
T Consensus         6 ~~L~~KyRP~~f~dvVGQe~iv~~L~~~i~~~ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~sC~~i~   85 (484)
T PRK14956          6 EVLSRKYRPQFFRDVIHQDLAIGALQNALKSGKIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTSCLEIT   85 (484)
T ss_pred             chhHHHhCCCCHHHHhChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcHHHHHH
Confidence            367889999999999999999999999888766555 7999999999999999999998653211100            


Q ss_pred             --cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          345 --LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       345 --~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                        ....++.+|...      ..|  ...++.+.+.+.    .....|+||||+|.|             ..+.++.|+..
T Consensus        86 ~g~~~dviEIdaas------~~g--Vd~IReL~e~l~~~p~~g~~KV~IIDEah~L-------------s~~A~NALLKt  144 (484)
T PRK14956         86 KGISSDVLEIDAAS------NRG--IENIRELRDNVKFAPMGGKYKVYIIDEVHML-------------TDQSFNALLKT  144 (484)
T ss_pred             ccCCccceeechhh------ccc--HHHHHHHHHHHHhhhhcCCCEEEEEechhhc-------------CHHHHHHHHHH
Confidence              011233333211      111  122444444443    234569999999999             45678888888


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +++  +.+++|++|+...     .+.+++++||+.+.|.+++.++..+.|+.++..    .++.++++++..++..+.+.
T Consensus       145 LEEPp~~viFILaTte~~-----kI~~TI~SRCq~~~f~~ls~~~i~~~L~~i~~~----Egi~~e~eAL~~Ia~~S~Gd  215 (484)
T PRK14956        145 LEEPPAHIVFILATTEFH-----KIPETILSRCQDFIFKKVPLSVLQDYSEKLCKI----ENVQYDQEGLFWIAKKGDGS  215 (484)
T ss_pred             hhcCCCceEEEeecCChh-----hccHHHHhhhheeeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCh
Confidence            886  7888898888754     678999999999999999999988888887764    47899999999999998775


Q ss_pred             hcCCCCcchHHHHHHHHHh
Q 005179          497 ISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~~  515 (710)
                            +++++.+|+.+++
T Consensus       216 ------~RdAL~lLeq~i~  228 (484)
T PRK14956        216 ------VRDMLSFMEQAIV  228 (484)
T ss_pred             ------HHHHHHHHHHHHH
Confidence                  4568888888764

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

Probab=99.76  E-value=3.5e-18  Score=169.37  Aligned_cols=190  Identities=21%  Similarity=0.265  Sum_probs=150.9

Q ss_pred             cCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+++++-|-+...+.|.+.+-            |..-+.+||||||||||+.||+++|.+.          +..++++..
T Consensus       130 VkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEA----------nSTFFSvSS  199 (439)
T KOG0739|consen  130 VKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPWRGILLYGPPGTGKSYLAKAVATEA----------NSTFFSVSS  199 (439)
T ss_pred             CchhhhccchhHHHHHHhheeecccchhhhcCCCCcceeEEEeCCCCCcHHHHHHHHHhhc----------CCceEEeeh
Confidence            368899999988888877431            1223679999999999999999999988          678889988


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----CCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----RGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----~~~v~vI~a  429 (710)
                      ++++  +++-|+.+..++.+|+.++++.|+|+||||||.+++.+..+.+  +....+..-|+-.|.     +..+.|+|+
T Consensus       200 SDLv--SKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEs--easRRIKTEfLVQMqGVG~d~~gvLVLgA  275 (439)
T KOG0739|consen  200 SDLV--SKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENES--EASRRIKTEFLVQMQGVGNDNDGVLVLGA  275 (439)
T ss_pred             HHHH--HHHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCch--HHHHHHHHHHHHhhhccccCCCceEEEec
Confidence            8888  6789999999999999999999999999999999887655332  333334333322222     346888999


Q ss_pred             cChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcC
Q 005179          430 TTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~  499 (710)
                      ||.+-     .+|.+++|||+ .|.|+.|....|..+++-.+.    .....+++..+..+...+.+|.+.
T Consensus       276 TNiPw-----~LDsAIRRRFekRIYIPLPe~~AR~~MF~lhlG----~tp~~LT~~d~~eL~~kTeGySGs  337 (439)
T KOG0739|consen  276 TNIPW-----VLDSAIRRRFEKRIYIPLPEAHARARMFKLHLG----DTPHVLTEQDFKELARKTEGYSGS  337 (439)
T ss_pred             CCCch-----hHHHHHHHHhhcceeccCCcHHHhhhhheeccC----CCccccchhhHHHHHhhcCCCCcC
Confidence            99874     78999999998 899999999999888875443    334678888999999999999764

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.76  E-value=3.4e-17  Score=169.66  Aligned_cols=213  Identities=19%  Similarity=0.212  Sum_probs=148.6

Q ss_pred             CCCCcccCHHHHHHHHHHHHc---------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          288 LIDPVIGRETEIQRIIQILCR---------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~---------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      +++.++|.+....++.++...               +...|++|+||||||||++|+.+++.+.....   .....++.+
T Consensus         4 ~l~~~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~---~~~~~~v~~   80 (261)
T TIGR02881         4 ELSRMVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNV---LSKGHLIEV   80 (261)
T ss_pred             HHHHhcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCc---ccCCceEEe
Confidence            356789988776666543210               13357899999999999999999998754321   223457777


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEcc
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIAST  430 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~at  430 (710)
                      +.+.+.  ..+.|+....+..+++.+.   +.||||||+|.|...+..     ....+..+.|...++.  +.+++|+++
T Consensus        81 ~~~~l~--~~~~g~~~~~~~~~~~~a~---~~VL~IDE~~~L~~~~~~-----~~~~~~i~~Ll~~~e~~~~~~~vila~  150 (261)
T TIGR02881        81 ERADLV--GEYIGHTAQKTREVIKKAL---GGVLFIDEAYSLARGGEK-----DFGKEAIDTLVKGMEDNRNEFVLILAG  150 (261)
T ss_pred             cHHHhh--hhhccchHHHHHHHHHhcc---CCEEEEechhhhccCCcc-----chHHHHHHHHHHHHhccCCCEEEEecC
Confidence            877776  3456777777777776543   579999999999532111     2234566777777764  567778777


Q ss_pred             ChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc--C--CCCcch
Q 005179          431 TQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS--D--RYLPDK  505 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~--~--r~~p~~  505 (710)
                      +..+......++|+|.+||. .|.+++++.+++.+|++.++..    .+..++++++..+.+...++..  .  ..-...
T Consensus       151 ~~~~~~~~~~~~p~L~sRf~~~i~f~~~~~~el~~Il~~~~~~----~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~  226 (261)
T TIGR02881       151 YSDEMDYFLSLNPGLRSRFPISIDFPDYTVEELMEIAERMVKE----REYKLTEEAKWKLREHLYKVDQLSSREFSNARY  226 (261)
T ss_pred             CcchhHHHHhcChHHHhccceEEEECCCCHHHHHHHHHHHHHH----cCCccCHHHHHHHHHHHHHHHhccCCCCchHHH
Confidence            76665566778999999996 7999999999999999987763    4678999999988877665431  1  111234


Q ss_pred             HHHHHHHHHhhh
Q 005179          506 AIDLVDEAGSRA  517 (710)
Q Consensus       506 ai~ll~~a~~~~  517 (710)
                      +..+++.|..+.
T Consensus       227 ~~n~~e~a~~~~  238 (261)
T TIGR02881       227 VRNIIEKAIRRQ  238 (261)
T ss_pred             HHHHHHHHHHHH
Confidence            566676666444

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.

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=99.75  E-value=3.4e-17  Score=184.87  Aligned_cols=202  Identities=21%  Similarity=0.279  Sum_probs=142.5

Q ss_pred             cCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|++++|.++...++.+++.            ...+.++||+||||||||++++++|...          +.+++.++.
T Consensus        52 ~~~~di~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~----------~~~~~~i~~  121 (495)
T TIGR01241        52 VTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA----------GVPFFSISG  121 (495)
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc----------CCCeeeccH
Confidence            356778888876655554432            2345689999999999999999999887          667788877


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC-CCChHhHHHhhcccc----cCCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSL----GRGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l----~~~~v~vI~a  429 (710)
                      +.+..  .+.|..+..++.+|+.+....|+||||||+|.+......+.++ ........+.|...+    .++.++||++
T Consensus       122 ~~~~~--~~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~~~~v~vI~a  199 (495)
T TIGR01241       122 SDFVE--MFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAA  199 (495)
T ss_pred             HHHHH--HHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccCCCCeEEEEe
Confidence            76652  3455566788999999988889999999999997654332110 011122333333222    3567899999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ||.++     .+|+++.|  ||+ .|.|+.|+.++|.+||+......    .+. .+..+..++..+.+|.+     .+.
T Consensus       200 Tn~~~-----~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~----~~~-~~~~l~~la~~t~G~sg-----adl  264 (495)
T TIGR01241       200 TNRPD-----VLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNK----KLA-PDVDLKAVARRTPGFSG-----ADL  264 (495)
T ss_pred             cCChh-----hcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcC----CCC-cchhHHHHHHhCCCCCH-----HHH
Confidence            99986     79999998  897 89999999999999999876532    111 23346677777666543     455


Q ss_pred             HHHHHHHHh
Q 005179          507 IDLVDEAGS  515 (710)
Q Consensus       507 i~ll~~a~~  515 (710)
                      ..++.+|+.
T Consensus       265 ~~l~~eA~~  273 (495)
T TIGR01241       265 ANLLNEAAL  273 (495)
T ss_pred             HHHHHHHHH
Confidence            667776653

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.

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

Probab=99.75  E-value=2.7e-17  Score=179.54  Aligned_cols=201  Identities=23%  Similarity=0.287  Sum_probs=143.8

Q ss_pred             hhcCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEE
Q 005179          285 SEELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMS  351 (710)
Q Consensus       285 ~~~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~  351 (710)
                      ...+++++.|.+.+++.+.+.+..             ..+.++||+||||||||++|+++|..+          +..++.
T Consensus       178 p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el----------~~~fi~  247 (438)
T PTZ00361        178 PLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANET----------SATFLR  247 (438)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhh----------CCCEEE
Confidence            345778899999999888776531             345679999999999999999999987          455666


Q ss_pred             eehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCe
Q 005179          352 LDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGEL  424 (710)
Q Consensus       352 ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v  424 (710)
                      +..+.+.  .++.|+.+..++.+|..+....++||||||+|.+........  ..+..++...+..++       ...++
T Consensus       248 V~~seL~--~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~--sgg~~e~qr~ll~LL~~Ldg~~~~~~V  323 (438)
T PTZ00361        248 VVGSELI--QKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDAT--SGGEKEIQRTMLELLNQLDGFDSRGDV  323 (438)
T ss_pred             Eecchhh--hhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCC--CcccHHHHHHHHHHHHHHhhhcccCCe
Confidence            6666655  356777778889999988888899999999999976543211  122333333332222       34678


Q ss_pred             EEEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCC
Q 005179          425 QCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDR  500 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r  500 (710)
                      .||++||..+     .+|+++.|  ||+ .|.|+.|+.++|.+||+....+.      .+.++ .+..++..+.+|.+  
T Consensus       324 ~VI~ATNr~d-----~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~------~l~~dvdl~~la~~t~g~sg--  390 (438)
T PTZ00361        324 KVIMATNRIE-----SLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKM------TLAEDVDLEEFIMAKDELSG--  390 (438)
T ss_pred             EEEEecCChH-----HhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcC------CCCcCcCHHHHHHhcCCCCH--
Confidence            9999999876     78999987  897 89999999999999999766533      33332 34556666666543  


Q ss_pred             CCcchHHHHHHHHHh
Q 005179          501 YLPDKAIDLVDEAGS  515 (710)
Q Consensus       501 ~~p~~ai~ll~~a~~  515 (710)
                         .+...++.+|+.
T Consensus       391 ---AdI~~i~~eA~~  402 (438)
T PTZ00361        391 ---ADIKAICTEAGL  402 (438)
T ss_pred             ---HHHHHHHHHHHH
Confidence               444556666653

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.75  E-value=2.4e-17  Score=181.86  Aligned_cols=194  Identities=26%  Similarity=0.351  Sum_probs=148.7

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHH---HHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          279 DLTARASEELIDPVIGRETEIQR---IIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~---l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +|.+++||.+|+++||+++.+..   +..++......+++|+||||||||++|+.+++.+          +..++.++..
T Consensus         1 pla~~~RP~~l~d~vGq~~~v~~~~~L~~~i~~~~~~~ilL~GppGtGKTtLA~~ia~~~----------~~~~~~l~a~   70 (413)
T PRK13342          1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGAT----------DAPFEALSAV   70 (413)
T ss_pred             ChhhhhCCCCHHHhcCcHHHhCcchHHHHHHHcCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEecc
Confidence            47889999999999999998766   8888888778899999999999999999999977          4455555432


Q ss_pred             hhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccC
Q 005179          356 LLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT  431 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att  431 (710)
                      ..  +       ...++.+++.+.    ...+.||||||+|.+             ....++.|.+.++++.+++|++|+
T Consensus        71 ~~--~-------~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l-------------~~~~q~~LL~~le~~~iilI~att  128 (413)
T PRK13342         71 TS--G-------VKDLREVIEEARQRRSAGRRTILFIDEIHRF-------------NKAQQDALLPHVEDGTITLIGATT  128 (413)
T ss_pred             cc--c-------HHHHHHHHHHHHHhhhcCCceEEEEechhhh-------------CHHHHHHHHHHhhcCcEEEEEeCC
Confidence            11  1       112344444432    235689999999999             345677888889999999999887


Q ss_pred             hHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCC-CCCHHHHHHHHHHhhhhhcCCCCcchHHHHH
Q 005179          432 QDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNC-KFTLEAINAAVHLSARYISDRYLPDKAIDLV  510 (710)
Q Consensus       432 ~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~-~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll  510 (710)
                      ...   .+.+++++.+||..+.+.+++.++...+++..+.....  ++ .+++++++.++.++.+.      +..++.++
T Consensus       129 ~n~---~~~l~~aL~SR~~~~~~~~ls~e~i~~lL~~~l~~~~~--~~i~i~~~al~~l~~~s~Gd------~R~aln~L  197 (413)
T PRK13342        129 ENP---SFEVNPALLSRAQVFELKPLSEEDIEQLLKRALEDKER--GLVELDDEALDALARLANGD------ARRALNLL  197 (413)
T ss_pred             CCh---hhhccHHHhccceeeEeCCCCHHHHHHHHHHHHHHhhc--CCCCCCHHHHHHHHHhCCCC------HHHHHHHH
Confidence            654   34678999999999999999999999999987765432  44 89999999998876542      45567777


Q ss_pred             HHHHh
Q 005179          511 DEAGS  515 (710)
Q Consensus       511 ~~a~~  515 (710)
                      +.++.
T Consensus       198 e~~~~  202 (413)
T PRK13342        198 ELAAL  202 (413)
T ss_pred             HHHHH
Confidence            76653

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.74  E-value=1.1e-16  Score=188.74  Aligned_cols=199  Identities=20%  Similarity=0.280  Sum_probs=148.7

Q ss_pred             CCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +++++.|.+...+.+.+.+.             ...+.++||+||||||||++|+++|..+          +..++.++.
T Consensus       451 ~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~----------~~~fi~v~~  520 (733)
T TIGR01243       451 RWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATES----------GANFIAVRG  520 (733)
T ss_pred             chhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhc----------CCCEEEEeh
Confidence            57888998887777766543             1345679999999999999999999988          677888888


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc----cCCCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL----GRGELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l----~~~~v~vI~at  430 (710)
                      +.+.  .++.|+.+..++.+|..+....|+||||||+|.++........ ......+.+.|...+    ...+++||++|
T Consensus       521 ~~l~--~~~vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~-~~~~~~~~~~lL~~ldg~~~~~~v~vI~aT  597 (733)
T TIGR01243       521 PEIL--SKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFD-TSVTDRIVNQLLTEMDGIQELSNVVVIAAT  597 (733)
T ss_pred             HHHh--hcccCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCC-ccHHHHHHHHHHHHhhcccCCCCEEEEEeC
Confidence            8877  5678999999999999999999999999999999875432111 111223444443333    35679999999


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCCCcchH
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      |.++     .+|+++.|  ||+ .|.++.|+.++|.+||+....      +..+.++ .++.+++.+.+|.+     .+.
T Consensus       598 n~~~-----~ld~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~------~~~~~~~~~l~~la~~t~g~sg-----adi  661 (733)
T TIGR01243       598 NRPD-----ILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTR------SMPLAEDVDLEELAEMTEGYTG-----ADI  661 (733)
T ss_pred             CChh-----hCCHhhcCCCccceEEEeCCcCHHHHHHHHHHHhc------CCCCCccCCHHHHHHHcCCCCH-----HHH
Confidence            9987     79999998  998 899999999999999985543      2333332 36778888777644     344


Q ss_pred             HHHHHHHHh
Q 005179          507 IDLVDEAGS  515 (710)
Q Consensus       507 i~ll~~a~~  515 (710)
                      ..++.+|+.
T Consensus       662 ~~~~~~A~~  670 (733)
T TIGR01243       662 EAVCREAAM  670 (733)
T ss_pred             HHHHHHHHH
Confidence            445555553

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.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.74  E-value=1.8e-17  Score=166.07  Aligned_cols=205  Identities=19%  Similarity=0.204  Sum_probs=155.0

Q ss_pred             hhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          277 CVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       277 ~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      -..|++++||.+|++++|++..+.-|...+.++...|.|||||||||||+.++++++.+..    +.+..+++.+++.+.
T Consensus        23 ~~swteKYrPkt~de~~gQe~vV~~L~~a~~~~~lp~~LFyGPpGTGKTStalafar~L~~----~~~~~~rvl~lnaSd   98 (346)
T KOG0989|consen   23 HRSWTEKYRPKTFDELAGQEHVVQVLKNALLRRILPHYLFYGPPGTGKTSTALAFARALNC----EQLFPCRVLELNASD   98 (346)
T ss_pred             ccchHHHhCCCcHHhhcchHHHHHHHHHHHhhcCCceEEeeCCCCCcHhHHHHHHHHHhcC----ccccccchhhhcccc
Confidence            3468899999999999999999999999999988899999999999999999999999955    223345555555433


Q ss_pred             hhhccccCccHHHHHHHHHHHHH-----hcC-CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEE
Q 005179          357 LMAGAKERGELEARVTTLISEIQ-----KSG-DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIA  428 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~-----~~~-~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~  428 (710)
                      .. |.....+-...+..+.....     .++ .-|++|||+|.|             ..++++.|+..|++  ...++|.
T Consensus        99 er-Gisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsm-------------tsdaq~aLrr~mE~~s~~trFiL  164 (346)
T KOG0989|consen   99 ER-GISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSM-------------TSDAQAALRRTMEDFSRTTRFIL  164 (346)
T ss_pred             cc-cccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhh-------------hHHHHHHHHHHHhccccceEEEE
Confidence            22 11111110011111111110     012 269999999999             66788999988885  6788899


Q ss_pred             ccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHH
Q 005179          429 STTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID  508 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~  508 (710)
                      .||+.+     .+.+.+.+|++.+.|++...++....|+.++.+    .++.+++++++.++..+.+-+      ++|+.
T Consensus       165 Icnyls-----rii~pi~SRC~KfrFk~L~d~~iv~rL~~Ia~~----E~v~~d~~al~~I~~~S~GdL------R~Ait  229 (346)
T KOG0989|consen  165 ICNYLS-----RIIRPLVSRCQKFRFKKLKDEDIVDRLEKIASK----EGVDIDDDALKLIAKISDGDL------RRAIT  229 (346)
T ss_pred             EcCChh-----hCChHHHhhHHHhcCCCcchHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHcCCcH------HHHHH
Confidence            999977     788999999999999999999999999988884    489999999999999988753      35666


Q ss_pred             HHHHHH
Q 005179          509 LVDEAG  514 (710)
Q Consensus       509 ll~~a~  514 (710)
                      .|+.+.
T Consensus       230 ~Lqsls  235 (346)
T KOG0989|consen  230 TLQSLS  235 (346)
T ss_pred             HHHHhh
Confidence            666554

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=99.74  E-value=4.4e-16  Score=183.22  Aligned_cols=177  Identities=19%  Similarity=0.261  Sum_probs=124.9

Q ss_pred             CcccCHHHHHHHHHHHHcC---------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--
Q 005179          291 PVIGRETEIQRIIQILCRR---------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~---------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--  359 (710)
                      .++|+++.++.+...+.+.         ...+++|+||+|||||++|++||+.+          +..++.+|++.+..  
T Consensus       455 ~v~GQ~~ai~~l~~~i~~~~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l----------~~~~~~~d~se~~~~~  524 (731)
T TIGR02639       455 KIFGQDEAIDSLVSSIKRSRAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEAL----------GVHLERFDMSEYMEKH  524 (731)
T ss_pred             ceeCcHHHHHHHHHHHHHHhcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHh----------cCCeEEEeCchhhhcc
Confidence            4899999999998877642         12357999999999999999999988          55677777666532  


Q ss_pred             ------c--cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------
Q 005179          360 ------G--AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------  422 (710)
Q Consensus       360 ------g--~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------  422 (710)
                            |  ..+.|.-  .-..+.+.++..+..||+|||+|.+             ..++++.|.+++++|         
T Consensus       525 ~~~~lig~~~gyvg~~--~~~~l~~~~~~~p~~VvllDEieka-------------~~~~~~~Ll~~ld~g~~~d~~g~~  589 (731)
T TIGR02639       525 TVSRLIGAPPGYVGFE--QGGLLTEAVRKHPHCVLLLDEIEKA-------------HPDIYNILLQVMDYATLTDNNGRK  589 (731)
T ss_pred             cHHHHhcCCCCCcccc--hhhHHHHHHHhCCCeEEEEechhhc-------------CHHHHHHHHHhhccCeeecCCCcc
Confidence                  1  1122210  1122334445566789999999988             567888888888765         


Q ss_pred             ----CeEEEEccChHH--HH----------------h--hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh--
Q 005179          423 ----ELQCIASTTQDE--HR----------------T--QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA--  475 (710)
Q Consensus       423 ----~v~vI~att~~~--~~----------------~--~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~--  475 (710)
                          +.++|.|+|...  +.                .  .....|.|.+||+ .|.|.+.+.++..+|++..+.++..  
T Consensus       590 vd~~~~iii~Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~~l  669 (731)
T TIGR02639       590 ADFRNVILIMTSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRNRLDAIIHFNPLSEEVLEKIVQKFVDELSKQL  669 (731)
T ss_pred             cCCCCCEEEECCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHhcCCeEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence                345777776421  00                0  0114688999997 8999999999999999987765432  


Q ss_pred             -hc--CCCCCHHHHHHHHHH
Q 005179          476 -HH--NCKFTLEAINAAVHL  492 (710)
Q Consensus       476 -~~--~~~i~~~~l~~l~~l  492 (710)
                       .+  .+.++++++++++..
T Consensus       670 ~~~~~~l~i~~~a~~~La~~  689 (731)
T TIGR02639       670 NEKNIKLELTDDAKKYLAEK  689 (731)
T ss_pred             HhCCCeEEeCHHHHHHHHHh
Confidence             22  367899999999875

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.74  E-value=2.9e-17  Score=184.81  Aligned_cols=201  Identities=17%  Similarity=0.192  Sum_probs=150.4

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      -|.+++|+.+|+++||+++.++.|...+..++..|. ||+||+|||||++++.|++.+.+.......             
T Consensus         5 vLarKYRPqtFdEVIGQe~Vv~~L~~aL~~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~sCr~I~~   84 (830)
T PRK07003          5 VLARKWRPKDFASLVGQEHVVRALTHALDGGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRACREIDE   84 (830)
T ss_pred             hHHHHhCCCcHHHHcCcHHHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHHHHHHhc
Confidence            478899999999999999999999999887665555 899999999999999999998653211100             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++++|...      .++  .+.++.+++.+.    ..+..|+||||+|.|             ....+|.|+..|
T Consensus        85 G~h~DviEIDAas------~rg--VDdIReLIe~a~~~P~~gr~KVIIIDEah~L-------------T~~A~NALLKtL  143 (830)
T PRK07003         85 GRFVDYVEMDAAS------NRG--VDEMAALLERAVYAPVDARFKVYMIDEVHML-------------TNHAFNAMLKTL  143 (830)
T ss_pred             CCCceEEEecccc------ccc--HHHHHHHHHHHHhccccCCceEEEEeChhhC-------------CHHHHHHHHHHH
Confidence             011244443221      111  122445555443    234569999999999             445677777788


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  .++.+|.+||...     .+.+.+++||+.+.|..++.++..+.|+.++..    .++.++++.+..+++.+.+. 
T Consensus       144 EEPP~~v~FILaTtd~~-----KIp~TIrSRCq~f~Fk~Ls~eeIv~~L~~Il~~----EgI~id~eAL~lIA~~A~Gs-  213 (830)
T PRK07003        144 EEPPPHVKFILATTDPQ-----KIPVTVLSRCLQFNLKQMPAGHIVSHLERILGE----ERIAFEPQALRLLARAAQGS-  213 (830)
T ss_pred             HhcCCCeEEEEEECChh-----hccchhhhheEEEecCCcCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC-
Confidence            76  4788888888765     567899999999999999999999998887764    47899999999999987764 


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                           .++++.+++.++.
T Consensus       214 -----mRdALsLLdQAia  226 (830)
T PRK07003        214 -----MRDALSLTDQAIA  226 (830)
T ss_pred             -----HHHHHHHHHHHHH
Confidence                 3568888887764

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

Probab=99.74  E-value=1.8e-16  Score=179.41  Aligned_cols=289  Identities=25%  Similarity=0.266  Sum_probs=182.6

Q ss_pred             HHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcC
Q 005179          303 IQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSG  382 (710)
Q Consensus       303 ~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~  382 (710)
                      .+.+......+++++||||+|||.++++++..   ..       .. ..++.....  .++.|+.+..+..++..+....
T Consensus        10 ~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~---~~-------~~-~~~~~~~~~--~~~~~~~~~~~~~~~~~a~~~~   76 (494)
T COG0464          10 FKKLGIEPPKGVLLHGPPGTGKTLLARALANE---GA-------EF-LSINGPEIL--SKYVGESELRLRELFEEAEKLA   76 (494)
T ss_pred             HHHhCCCCCCCceeeCCCCCchhHHHHHHHhc---cC-------cc-cccCcchhh--hhhhhHHHHHHHHHHHHHHHhC
Confidence            33444566788999999999999999999987   11       11 222222222  4567788888999999999888


Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc---cCCCeEEEEccChHHHHhhhhccHHHHc--ccc-ceEecC
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL---GRGELQCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISE  456 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l---~~~~v~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~  456 (710)
                      +.++++||++.+.+......  ......+...+...+   .++.+.+++.++...     .+++++.+  ||. .+.+..
T Consensus        77 ~~ii~~d~~~~~~~~~~~~~--~~~~~~v~~~l~~~~d~~~~~~v~~~~~~~~~~-----~~~~a~~~~~~~~~~~~~~~  149 (494)
T COG0464          77 PSIIFIDEIDALAPKRSSDQ--GEVERRVVAQLLALMDGLKRGQVIVIGATNRPD-----GLDPAKRRPGRFDREIEVNL  149 (494)
T ss_pred             CCeEeechhhhcccCccccc--cchhhHHHHHHHHhcccccCCceEEEeecCCcc-----ccChhHhCccccceeeecCC
Confidence            89999999999987654311  122223333332222   244467777676654     67888887  886 799999


Q ss_pred             CCHHHHHHHHHHHHHHHHhhcCCCCC-HHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCC
Q 005179          457 PSQEDAVRILLGLREKYEAHHNCKFT-LEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSK  535 (710)
Q Consensus       457 Ps~~~~~~IL~~l~~~~~~~~~~~i~-~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~  535 (710)
                      |+...+.+|+......      +.+. +.....++..+.+|..     .+...+...+......+..             
T Consensus       150 ~~~~~~~ei~~~~~~~------~~~~~~~~~~~~a~~~~~~~~-----~~~~~l~~~~~~~~~~r~~-------------  205 (494)
T COG0464         150 PDEAGRLEILQIHTRL------MFLGPPGTGKTLAARTVGKSG-----ADLGALAKEAALRELRRAI-------------  205 (494)
T ss_pred             CCHHHHHHHHHHHHhc------CCCcccccHHHHHHhcCCccH-----HHHHHHHHHHHHHHHHhhh-------------
Confidence            9999888887765442      2222 3455566666665544     2223333233211111100             


Q ss_pred             CChHHHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhC-----CChh
Q 005179          536 PPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSG-----IPVQ  610 (710)
Q Consensus       536 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~g-----ip~~  610 (710)
                                                                      ........++.+++...+....+     ....
T Consensus       206 ------------------------------------------------~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  237 (494)
T COG0464         206 ------------------------------------------------DLVGEYIGVTEDDFEEALKKVLPSRGVLFEDE  237 (494)
T ss_pred             ------------------------------------------------ccCcccccccHHHHHHHHHhcCcccccccCCC
Confidence                                                            00011234566666666666533     3445


Q ss_pred             hccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhh----cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          611 QITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSR----VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       611 ~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r----~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .+.|.+.+++...++.+.+.          +...+++..    .|+.+|    .++|||||||||||+|||++|.+   .
T Consensus       238 ~v~~~diggl~~~k~~l~e~----------v~~~~~~~e~~~~~~~~~~----~giLl~GpPGtGKT~lAkava~~---~  300 (494)
T COG0464         238 DVTLDDIGGLEEAKEELKEA----------IETPLKRPELFRKLGLRPP----KGVLLYGPPGTGKTLLAKAVALE---S  300 (494)
T ss_pred             CcceehhhcHHHHHHHHHHH----------HHhHhhChHHHHhcCCCCC----CeeEEECCCCCCHHHHHHHHHhh---C
Confidence            67888877776666655422          223333332    355544    69999999999999999999997   6


Q ss_pred             CCcceeeCCCCCCC
Q 005179          687 VRIHYLFFPSPFNS  700 (710)
Q Consensus       687 ~~~li~~d~se~~~  700 (710)
                      +.+++.++++++.+
T Consensus       301 ~~~fi~v~~~~l~s  314 (494)
T COG0464         301 RSRFISVKGSELLS  314 (494)
T ss_pred             CCeEEEeeCHHHhc
Confidence            77899999987754

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

Probab=99.73  E-value=2e-16  Score=157.01  Aligned_cols=191  Identities=20%  Similarity=0.267  Sum_probs=140.9

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcC-----CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRR-----TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~-----~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      +.....||..|+++||+++..+++.-.+...     .--|+||+||||.||||||+-+|+++          +..+....
T Consensus        15 ~~e~~lRP~~l~efiGQ~~vk~~L~ifI~AAk~r~e~lDHvLl~GPPGlGKTTLA~IIA~Em----------gvn~k~ts   84 (332)
T COG2255          15 KIERSLRPKTLDEFIGQEKVKEQLQIFIKAAKKRGEALDHVLLFGPPGLGKTTLAHIIANEL----------GVNLKITS   84 (332)
T ss_pred             hhhcccCcccHHHhcChHHHHHHHHHHHHHHHhcCCCcCeEEeeCCCCCcHHHHHHHHHHHh----------cCCeEecc
Confidence            3445678999999999998887776655432     23579999999999999999999999          44444333


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------  421 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------  421 (710)
                      ...+.    ..|+    +..++..++.  +.||||||||++             +..+.++|.+.|+.            
T Consensus        85 Gp~le----K~gD----laaiLt~Le~--~DVLFIDEIHrl-------------~~~vEE~LYpaMEDf~lDI~IG~gp~  141 (332)
T COG2255          85 GPALE----KPGD----LAAILTNLEE--GDVLFIDEIHRL-------------SPAVEEVLYPAMEDFRLDIIIGKGPA  141 (332)
T ss_pred             ccccc----Chhh----HHHHHhcCCc--CCeEEEehhhhc-------------ChhHHHHhhhhhhheeEEEEEccCCc
Confidence            22222    1222    3444444443  569999999999             44566777777763            


Q ss_pred             --------CCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          422 --------GELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       422 --------~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                              ..+.+||+||...     .+...|+.||. ...+..++.++..+|+..-..    ..++.++++....++..
T Consensus       142 Arsv~ldLppFTLIGATTr~G-----~lt~PLrdRFGi~~rlefY~~~eL~~Iv~r~a~----~l~i~i~~~~a~eIA~r  212 (332)
T COG2255         142 ARSIRLDLPPFTLIGATTRAG-----MLTNPLRDRFGIIQRLEFYTVEELEEIVKRSAK----ILGIEIDEEAALEIARR  212 (332)
T ss_pred             cceEeccCCCeeEeeeccccc-----cccchhHHhcCCeeeeecCCHHHHHHHHHHHHH----HhCCCCChHHHHHHHHh
Confidence                    2577999999976     67789999998 788999999998888876555    45889999998888877


Q ss_pred             hhhhhcCCCCcchHHHHHHHHHhhh
Q 005179          493 SARYISDRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       493 s~~~i~~r~~p~~ai~ll~~a~~~~  517 (710)
                      ++      ..|.-|..||.+.-..+
T Consensus       213 SR------GTPRIAnRLLrRVRDfa  231 (332)
T COG2255         213 SR------GTPRIANRLLRRVRDFA  231 (332)
T ss_pred             cc------CCcHHHHHHHHHHHHHH
Confidence            54      45788888887665433

>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]

Probab=99.73  E-value=4.8e-16  Score=176.60  Aligned_cols=181  Identities=20%  Similarity=0.267  Sum_probs=128.3

Q ss_pred             CcccCHHHHHHHHHHHHcC---------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--
Q 005179          291 PVIGRETEIQRIIQILCRR---------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~---------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--  359 (710)
                      .++|+++.+..+...+.+.         .-.++||.||+|||||.||++||..+...       ...++.+|++.+..  
T Consensus       492 rViGQd~AV~avs~aIrraRaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~-------e~aliR~DMSEy~EkH  564 (786)
T COG0542         492 RVIGQDEAVEAVSDAIRRARAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGD-------EQALIRIDMSEYMEKH  564 (786)
T ss_pred             ceeChHHHHHHHHHHHHHHhcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCC-------CccceeechHHHHHHH
Confidence            4999999999999887652         12357899999999999999999999433       46788889888762  


Q ss_pred             ------c--cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------
Q 005179          360 ------G--AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------  422 (710)
Q Consensus       360 ------g--~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------  422 (710)
                            |  ..|.|--+  =..+-+.++..+.+|+++|||+..             ..++.|+|++.|..|         
T Consensus       565 sVSrLIGaPPGYVGyee--GG~LTEaVRr~PySViLlDEIEKA-------------HpdV~nilLQVlDdGrLTD~~Gr~  629 (786)
T COG0542         565 SVSRLIGAPPGYVGYEE--GGQLTEAVRRKPYSVILLDEIEKA-------------HPDVFNLLLQVLDDGRLTDGQGRT  629 (786)
T ss_pred             HHHHHhCCCCCCceecc--ccchhHhhhcCCCeEEEechhhhc-------------CHHHHHHHHHHhcCCeeecCCCCE
Confidence                  1  12222111  112233445566789999999998             788999999999865         


Q ss_pred             ----CeEEEEccChHHHH-----------------hh------hhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHH
Q 005179          423 ----ELQCIASTTQDEHR-----------------TQ------FEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYE  474 (710)
Q Consensus       423 ----~v~vI~att~~~~~-----------------~~------~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~  474 (710)
                          +.++|.|+|-....                 ..      ....|.|++|++ .|.|.+.+.+...+|+...+.+..
T Consensus       630 VdFrNtiIImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLNRid~II~F~~L~~~~l~~Iv~~~L~~l~  709 (786)
T COG0542         630 VDFRNTIIIMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLNRIDEIIPFNPLSKEVLERIVDLQLNRLA  709 (786)
T ss_pred             EecceeEEEEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHhhcccEEeccCCCHHHHHHHHHHHHHHHH
Confidence                34566666532100                 00      012488899998 899999999999999887665543


Q ss_pred             h-----hcCCCCCHHHHHHHHHHh
Q 005179          475 A-----HHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       475 ~-----~~~~~i~~~~l~~l~~ls  493 (710)
                      .     ...+.+++++.+.+++.+
T Consensus       710 ~~L~~~~i~l~~s~~a~~~l~~~g  733 (786)
T COG0542         710 KRLAERGITLELSDEAKDFLAEKG  733 (786)
T ss_pred             HHHHhCCceEEECHHHHHHHHHhc
Confidence            2     334678999988887663

>CHL00176 ftsH cell division protein; Validated

Probab=99.73  E-value=1.1e-16  Score=182.79  Aligned_cols=202  Identities=21%  Similarity=0.276  Sum_probs=141.4

Q ss_pred             cCCCCcccCHHHHHHHHHHH---Hc---------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQIL---CR---------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L---~~---------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|++++|.++..+.+.+++   ..         ..+.++||+||||||||++|+++|.+.          +.+++.+++
T Consensus       180 ~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~----------~~p~i~is~  249 (638)
T CHL00176        180 ITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEA----------EVPFFSISG  249 (638)
T ss_pred             CCHHhccChHHHHHHHHHHHHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCeeeccH
Confidence            36788999887666655543   21         235689999999999999999999987          667778777


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC-CCChHhHHHhhcccc----cCCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSL----GRGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l----~~~~v~vI~a  429 (710)
                      +.+..  .+.|....+++.+|..+....|+||||||+|.+......+.+. ........+.|...+    .+..+++|++
T Consensus       250 s~f~~--~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~~~~ViVIaa  327 (638)
T CHL00176        250 SEFVE--MFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKGNKGVIVIAA  327 (638)
T ss_pred             HHHHH--HhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccCCCCeeEEEe
Confidence            76652  2344455678889999988889999999999997543221110 011112233333222    3467899999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ||..+     .+|+++.|  ||+ .|.++.|+.++|.+||+..+...     ....+..+..++..+.+|..     .+.
T Consensus       328 TN~~~-----~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~-----~~~~d~~l~~lA~~t~G~sg-----aDL  392 (638)
T CHL00176        328 TNRVD-----ILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNK-----KLSPDVSLELIARRTPGFSG-----ADL  392 (638)
T ss_pred             cCchH-----hhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhc-----ccchhHHHHHHHhcCCCCCH-----HHH
Confidence            99976     68899998  897 89999999999999999877642     12234456677776666533     456


Q ss_pred             HHHHHHHHh
Q 005179          507 IDLVDEAGS  515 (710)
Q Consensus       507 i~ll~~a~~  515 (710)
                      ..++++|+.
T Consensus       393 ~~lvneAal  401 (638)
T CHL00176        393 ANLLNEAAI  401 (638)
T ss_pred             HHHHHHHHH
Confidence            667777653

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.73  E-value=4.3e-17  Score=181.36  Aligned_cols=201  Identities=17%  Similarity=0.202  Sum_probs=150.3

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCC-----Cc--cc------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEV-----PV--FL------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~-----p~--~l------  344 (710)
                      .|.+++|+.+|+++||+++.++.|.+.+...+..|. ||+||+|||||++++.|++.+.+..-     +.  ..      
T Consensus         5 vLarKYRPqtFddVIGQe~vv~~L~~al~~gRLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PCG~C~sC   84 (700)
T PRK12323          5 VLARKWRPRDFTTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPCGQCRAC   84 (700)
T ss_pred             hHHHHhCCCcHHHHcCcHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCCcccHHH
Confidence            577899999999999999999999999988776665 89999999999999999999976210     00  00      


Q ss_pred             ------cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHh
Q 005179          345 ------LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNL  414 (710)
Q Consensus       345 ------~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~  414 (710)
                            ....++++|...      ..+  .+.++++++.+.    ..+..|+||||+|.|             +...+|.
T Consensus        85 ~~I~aG~hpDviEIdAas------~~g--VDdIReLie~~~~~P~~gr~KViIIDEah~L-------------s~~AaNA  143 (700)
T PRK12323         85 TEIDAGRFVDYIEMDAAS------NRG--VDEMAQLLDKAVYAPTAGRFKVYMIDEVHML-------------TNHAFNA  143 (700)
T ss_pred             HHHHcCCCCcceEecccc------cCC--HHHHHHHHHHHHhchhcCCceEEEEEChHhc-------------CHHHHHH
Confidence                  011344444321      111  123445555443    234579999999999             4456788


Q ss_pred             hcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          415 LKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       415 L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      |+..|++  +++.+|.+||...     .+.+++++||+.+.|..++.++..+.|+.++..    .++.+++++++.++..
T Consensus       144 LLKTLEEPP~~v~FILaTtep~-----kLlpTIrSRCq~f~f~~ls~eei~~~L~~Il~~----Egi~~d~eAL~~IA~~  214 (700)
T PRK12323        144 MLKTLEEPPEHVKFILATTDPQ-----KIPVTVLSRCLQFNLKQMPPGHIVSHLDAILGE----EGIAHEVNALRLLAQA  214 (700)
T ss_pred             HHHhhccCCCCceEEEEeCChH-----hhhhHHHHHHHhcccCCCChHHHHHHHHHHHHH----cCCCCCHHHHHHHHHH
Confidence            8888886  6788888888765     677999999999999999999988888877763    4788999999998888


Q ss_pred             hhhhhcCCCCcchHHHHHHHHHh
Q 005179          493 SARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       493 s~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      +++.      +.+++.+++.++.
T Consensus       215 A~Gs------~RdALsLLdQaia  231 (700)
T PRK12323        215 AQGS------MRDALSLTDQAIA  231 (700)
T ss_pred             cCCC------HHHHHHHHHHHHH
Confidence            7664      4567888887654

>CHL00181 cbbX CbbX; Provisional

Probab=99.72  E-value=3.1e-16  Score=163.71  Aligned_cols=210  Identities=18%  Similarity=0.244  Sum_probs=142.8

Q ss_pred             CcccCHHHHHHHHHHHH--------c-------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          291 PVIGRETEIQRIIQILC--------R-------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~--------~-------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +++|.++..+++.++..        .       ..+.|++|+||||||||++|+++++.+....+   ....+++.++..
T Consensus        24 ~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~---~~~~~~~~v~~~  100 (287)
T CHL00181         24 ELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGY---IKKGHLLTVTRD  100 (287)
T ss_pred             hcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCC---CCCCceEEecHH
Confidence            48888776665554321        1       12456899999999999999999998754321   123357777777


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChH
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQD  433 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~  433 (710)
                      .+..  .+.|+.......+++.+   .+.||||||+|.+...+..    ...+.++++.|...|++  +++++|++++..
T Consensus       101 ~l~~--~~~g~~~~~~~~~l~~a---~ggVLfIDE~~~l~~~~~~----~~~~~e~~~~L~~~me~~~~~~~vI~ag~~~  171 (287)
T CHL00181        101 DLVG--QYIGHTAPKTKEVLKKA---MGGVLFIDEAYYLYKPDNE----RDYGSEAIEILLQVMENQRDDLVVIFAGYKD  171 (287)
T ss_pred             HHHH--HHhccchHHHHHHHHHc---cCCEEEEEccchhccCCCc----cchHHHHHHHHHHHHhcCCCCEEEEEeCCcH
Confidence            6653  24455455555565543   4579999999999643211    13356777888887764  568889998877


Q ss_pred             HHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc--chHHHHH
Q 005179          434 EHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP--DKAIDLV  510 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p--~~ai~ll  510 (710)
                      ....++..+|+|.+||. .|.|++++.+++.+|++.++.+.    +..++++....+..+..+......+.  .....++
T Consensus       172 ~~~~~~~~np~L~sR~~~~i~F~~~t~~el~~I~~~~l~~~----~~~l~~~~~~~L~~~i~~~~~~~~~GNaR~vrn~v  247 (287)
T CHL00181        172 RMDKFYESNPGLSSRIANHVDFPDYTPEELLQIAKIMLEEQ----QYQLTPEAEKALLDYIKKRMEQPLFANARSVRNAL  247 (287)
T ss_pred             HHHHHHhcCHHHHHhCCceEEcCCcCHHHHHHHHHHHHHHh----cCCCChhHHHHHHHHHHHhCCCCCCccHHHHHHHH
Confidence            66667778899999997 89999999999999999888754    56788888777666544422222111  2344455


Q ss_pred             HHHHhh
Q 005179          511 DEAGSR  516 (710)
Q Consensus       511 ~~a~~~  516 (710)
                      +.+..+
T Consensus       248 e~~~~~  253 (287)
T CHL00181        248 DRARMR  253 (287)
T ss_pred             HHHHHH
Confidence            555533

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

Probab=99.71  E-value=1.2e-16  Score=165.99  Aligned_cols=158  Identities=16%  Similarity=0.148  Sum_probs=120.5

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh-----cCC
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK-----SGD  383 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-----~~~  383 (710)
                      +.+..++|+||||||||.+|+++|.++          +..++.++.+++.  .++.|+.+..++++|..+..     ..|
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~el----------g~~~i~vsa~eL~--sk~vGEsEk~IR~~F~~A~~~a~~~~aP  213 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKM----------GIEPIVMSAGELE--SENAGEPGKLIRQRYREAADIIKKKGKM  213 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHc----------CCCeEEEEHHHhh--cCcCCcHHHHHHHHHHHHHHHhhccCCC
Confidence            456778999999999999999999999          8889999999988  67899999999999998864     469


Q ss_pred             eEEEEccchhhhhCCCCCCCCCCChHhHH-Hhhcccc----------------cCCCeEEEEccChHHHHhhhhccHHHH
Q 005179          384 VILFIDEVHTLIGSGTVGRGNKGTGLDIS-NLLKPSL----------------GRGELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       384 ~IL~IDEid~l~~~~~~~~~~~~~~~~~~-~~L~~~l----------------~~~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                      +||||||||.+++......  ......+. ..|...+                ....+.||+|||..+     .+|++|+
T Consensus       214 cVLFIDEIDA~~g~r~~~~--~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~V~VIaTTNrpd-----~LDpALl  286 (413)
T PLN00020        214 SCLFINDLDAGAGRFGTTQ--YTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPRVPIIVTGNDFS-----TLYAPLI  286 (413)
T ss_pred             eEEEEehhhhcCCCCCCCC--cchHHHHHHHHHHHHhcCCccccccccccccccCCCceEEEeCCCcc-----cCCHhHc
Confidence            9999999999987643211  11111221 2333221                145688999999987     7999999


Q ss_pred             c--cccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          447 R--RFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       447 ~--Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      |  ||+.. +..|+.++|.+||+.+.++      ..++...+..++..
T Consensus       287 RpGRfDk~-i~lPd~e~R~eIL~~~~r~------~~l~~~dv~~Lv~~  327 (413)
T PLN00020        287 RDGRMEKF-YWAPTREDRIGVVHGIFRD------DGVSREDVVKLVDT  327 (413)
T ss_pred             CCCCCCce-eCCCCHHHHHHHHHHHhcc------CCCCHHHHHHHHHc
Confidence            9  99853 4689999999999988773      35566555555443

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

Probab=99.71  E-value=1.1e-16  Score=174.97  Aligned_cols=198  Identities=22%  Similarity=0.262  Sum_probs=154.0

Q ss_pred             CCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +++++-|..+...-+.+++.-             +...++|||||||||||.||.++|...          +.+++++..
T Consensus       665 ~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~----------~~~fisvKG  734 (952)
T KOG0735|consen  665 RWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNS----------NLRFISVKG  734 (952)
T ss_pred             CceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhC----------CeeEEEecC
Confidence            467777877666666665532             334689999999999999999999987          788999988


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC----CCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR----GELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~----~~v~vI~at  430 (710)
                      ..+.  .+|.|..|+.++.+|..++.+.|||||+||+|.+.+.+.-+  +.+-...+.|.|+.-|..    ..+.++++|
T Consensus       735 PElL--~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhD--sTGVTDRVVNQlLTelDG~Egl~GV~i~aaT  810 (952)
T KOG0735|consen  735 PELL--SKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHD--STGVTDRVVNQLLTELDGAEGLDGVYILAAT  810 (952)
T ss_pred             HHHH--HHHhcccHHHHHHHHHHhhccCCeEEEeccccccCcccCCC--CCCchHHHHHHHHHhhccccccceEEEEEec
Confidence            8888  68999999999999999999999999999999998775432  223445567777666652    357888999


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHH
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAI  507 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai  507 (710)
                      ++++     -+||+|.|  |++ .|..+.|+..+|.+||+.+...+...     ++-.++.++..+.+|.+     .+..
T Consensus       811 sRpd-----liDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~-----~~vdl~~~a~~T~g~tg-----ADlq  875 (952)
T KOG0735|consen  811 SRPD-----LIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKD-----TDVDLECLAQKTDGFTG-----ADLQ  875 (952)
T ss_pred             CCcc-----ccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCc-----cccchHHHhhhcCCCch-----hhHH
Confidence            8887     68999999  998 78999999999999999988754221     23347788888888755     3445


Q ss_pred             HHHHHHH
Q 005179          508 DLVDEAG  514 (710)
Q Consensus       508 ~ll~~a~  514 (710)
                      .++..|-
T Consensus       876 ~ll~~A~  882 (952)
T KOG0735|consen  876 SLLYNAQ  882 (952)
T ss_pred             HHHHHHH
Confidence            5555553

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

Probab=99.71  E-value=1.4e-16  Score=179.37  Aligned_cols=201  Identities=22%  Similarity=0.276  Sum_probs=145.0

Q ss_pred             cCCCCcccCHHHHHHHHHH---HH---------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQI---LC---------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~---L~---------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -.|.++-|.++..+.|.++   |.         .+.+..+||+||||||||.||+++|.+.          +.+++.+..
T Consensus       308 V~FkDVAG~deAK~El~E~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEA----------gVPF~svSG  377 (774)
T KOG0731|consen  308 VKFKDVAGVDEAKEELMEFVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEA----------GVPFFSVSG  377 (774)
T ss_pred             CccccccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhccc----------CCceeeech
Confidence            3689999999766666554   32         2456889999999999999999999988          788889888


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH---HHhhccccc----CCCeEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI---SNLLKPSLG----RGELQCI  427 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~---~~~L~~~l~----~~~v~vI  427 (710)
                      +.++..-  .|.-..+++++|..++...|+|+||||||.+..... |.+...++.+-   .|.|+.-|.    ...++++
T Consensus       378 SEFvE~~--~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~-G~~~~~~~~e~e~tlnQll~emDgf~~~~~vi~~  454 (774)
T KOG0731|consen  378 SEFVEMF--VGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRG-GKGTGGGQDEREQTLNQLLVEMDGFETSKGVIVL  454 (774)
T ss_pred             HHHHHHh--cccchHHHHHHHHHhhccCCeEEEeccccccccccc-ccccCCCChHHHHHHHHHHHHhcCCcCCCcEEEE
Confidence            8887433  333367899999999999999999999999976542 10011122222   333332222    4679999


Q ss_pred             EccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcc
Q 005179          428 ASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD  504 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~  504 (710)
                      ++||.++     .+|++|+|  ||+ .|.++.|+...|.+|++..++..    ++...+..+..++.++.+|.+     .
T Consensus       455 a~tnr~d-----~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~----~~~~e~~dl~~~a~~t~gf~g-----a  520 (774)
T KOG0731|consen  455 AATNRPD-----ILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKK----KLDDEDVDLSKLASLTPGFSG-----A  520 (774)
T ss_pred             eccCCcc-----ccCHHhcCCCccccceeccCCchhhhHHHHHHHhhcc----CCCcchhhHHHHHhcCCCCcH-----H
Confidence            9999987     79999999  998 89999999999999999776633    222233334446666665533     4


Q ss_pred             hHHHHHHHHH
Q 005179          505 KAIDLVDEAG  514 (710)
Q Consensus       505 ~ai~ll~~a~  514 (710)
                      +...++.+|+
T Consensus       521 dl~n~~neaa  530 (774)
T KOG0731|consen  521 DLANLCNEAA  530 (774)
T ss_pred             HHHhhhhHHH
Confidence            5555666654

>TIGR03689 pup_AAA proteasome ATPase

Probab=99.71  E-value=1.1e-16  Score=176.97  Aligned_cols=180  Identities=20%  Similarity=0.284  Sum_probs=127.7

Q ss_pred             hhhcCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          284 ASEELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       284 ~~~~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ...-+|+++.|.+.+++++.+.+.             ...++++|||||||||||++++++|+.+.............++
T Consensus       176 ~p~v~~~dIgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p~GILLyGPPGTGKT~LAKAlA~eL~~~i~~~~~~~~~fl  255 (512)
T TIGR03689       176 VPDVTYADIGGLDSQIEQIRDAVELPFLHPELYREYDLKPPKGVLLYGPPGCGKTLIAKAVANSLAQRIGAETGDKSYFL  255 (512)
T ss_pred             CCCCCHHHcCChHHHHHHHHHHHHHHhhCHHHHHhccCCCCcceEEECCCCCcHHHHHHHHHHhhccccccccCCceeEE
Confidence            345578899999999988877642             1346789999999999999999999988432110000112233


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CC
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RG  422 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~  422 (710)
                      .+....+.  .++.|+.+..++.+|+.+..    ..++||||||+|.++..+..+.. ++....+.+.|...|.    .+
T Consensus       256 ~v~~~eLl--~kyvGete~~ir~iF~~Ar~~a~~g~p~IIfIDEiD~L~~~R~~~~s-~d~e~~il~~LL~~LDgl~~~~  332 (512)
T TIGR03689       256 NIKGPELL--NKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVS-SDVETTVVPQLLSELDGVESLD  332 (512)
T ss_pred             eccchhhc--ccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCcc-chHHHHHHHHHHHHhcccccCC
Confidence            33344444  45788888889988887765    36899999999999876433211 1112233344444433    36


Q ss_pred             CeEEEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHH
Q 005179          423 ELQCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       423 ~v~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      ++.+|++||..+     .+|+++.|  ||+ .|.|+.|+.+++.+||+..+.
T Consensus       333 ~ViVI~ATN~~d-----~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~  379 (512)
T TIGR03689       333 NVIVIGASNRED-----MIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLT  379 (512)
T ss_pred             ceEEEeccCChh-----hCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhh
Confidence            789999999987     78999999  998 799999999999999997654

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.

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

Probab=99.71  E-value=3.4e-16  Score=166.88  Aligned_cols=204  Identities=21%  Similarity=0.254  Sum_probs=157.8

Q ss_pred             hhhhcCCCCcccCHHHHHHHHHHH------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          283 RASEELIDPVIGRETEIQRIIQIL------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       283 ~~~~~~l~~liGr~~~i~~l~~~L------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ..++-.++++-|.+..-..+.+.+            .|.....+||.||||+|||+|++++|.+.          +..++
T Consensus       146 ~~~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr~p~rglLLfGPpgtGKtmL~~aiAsE~----------~atff  215 (428)
T KOG0740|consen  146 TLRNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLREPVRGLLLFGPPGTGKTMLAKAIATES----------GATFF  215 (428)
T ss_pred             cCCcccccCCcchhhHHHHhhhhhhhcccchHhhhccccccchhheecCCCCchHHHHHHHHhhh----------cceEe
Confidence            334556888888665444444321            23445679999999999999999999988          77888


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHh-HHHhhcccc-----cCCCe
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLD-ISNLLKPSL-----GRGEL  424 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~-~~~~L~~~l-----~~~~v  424 (710)
                      .+..+.+.  .++.|+.+..++.+|.-++...|.|+||||+|.++.....+..  +.+.. -..+|.+..     .+.++
T Consensus       216 ~iSassLt--sK~~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~e~--e~srr~ktefLiq~~~~~s~~~drv  291 (428)
T KOG0740|consen  216 NISASSLT--SKYVGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDNEH--ESSRRLKTEFLLQFDGKNSAPDDRV  291 (428)
T ss_pred             eccHHHhh--hhccChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCccc--ccchhhhhHHHhhhccccCCCCCeE
Confidence            88888777  6889999999999999999999999999999999987633211  22222 233333332     24589


Q ss_pred             EEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          425 QCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      .+|||||.+.     ++|.+++|||+ .+.|+.|+.+.|..+|..++.+.    +..+.+..+..+++.+++|...    
T Consensus       292 lvigaTN~P~-----e~Dea~~Rrf~kr~yiplPd~etr~~~~~~ll~~~----~~~l~~~d~~~l~~~Tegysgs----  358 (428)
T KOG0740|consen  292 LVIGATNRPW-----ELDEAARRRFVKRLYIPLPDYETRSLLWKQLLKEQ----PNGLSDLDISLLAKVTEGYSGS----  358 (428)
T ss_pred             EEEecCCCch-----HHHHHHHHHhhceeeecCCCHHHHHHHHHHHHHhC----CCCccHHHHHHHHHHhcCcccc----
Confidence            9999999986     89999999998 79999999999999999988743    6678888899999999999763    


Q ss_pred             chHHHHHHHHH
Q 005179          504 DKAIDLVDEAG  514 (710)
Q Consensus       504 ~~ai~ll~~a~  514 (710)
                       +..+++.+|.
T Consensus       359 -di~~l~kea~  368 (428)
T KOG0740|consen  359 -DITALCKEAA  368 (428)
T ss_pred             -cHHHHHHHhh
Confidence             4556666665

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.71  E-value=7.5e-16  Score=165.08  Aligned_cols=186  Identities=20%  Similarity=0.252  Sum_probs=132.1

Q ss_pred             HHhhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          281 TARASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       281 ~~~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      ..++||..|++++|++++++.+...+..     ...++++|+||||||||++|+.+|+.+          +..+......
T Consensus        16 ~~~~rP~~~~~~vG~~~~~~~l~~~l~~~~~~~~~~~~~ll~GppG~GKT~la~~ia~~l----------~~~~~~~~~~   85 (328)
T PRK00080         16 ERSLRPKSLDEFIGQEKVKENLKIFIEAAKKRGEALDHVLLYGPPGLGKTTLANIIANEM----------GVNIRITSGP   85 (328)
T ss_pred             hhhcCcCCHHHhcCcHHHHHHHHHHHHHHHhcCCCCCcEEEECCCCccHHHHHHHHHHHh----------CCCeEEEecc
Confidence            5678999999999999999888776642     334689999999999999999999988          3444433322


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--------------
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--------------  421 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--------------  421 (710)
                      .+.    ..+    .+..++..+  ..+.||||||+|.+..             ...+.|...++.              
T Consensus        86 ~~~----~~~----~l~~~l~~l--~~~~vl~IDEi~~l~~-------------~~~e~l~~~~e~~~~~~~l~~~~~~~  142 (328)
T PRK00080         86 ALE----KPG----DLAAILTNL--EEGDVLFIDEIHRLSP-------------VVEEILYPAMEDFRLDIMIGKGPAAR  142 (328)
T ss_pred             ccc----ChH----HHHHHHHhc--ccCCEEEEecHhhcch-------------HHHHHHHHHHHhcceeeeeccCcccc
Confidence            111    111    233344333  2467999999999832             122222222221              


Q ss_pred             ------CCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q 005179          422 ------GELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       422 ------~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~  494 (710)
                            ..+.+|++|+...     .+++.|.+||. .+.+++|+.+++.+|++.....    .++.++++++..++..+.
T Consensus       143 ~~~~~l~~~~li~at~~~~-----~l~~~L~sRf~~~~~l~~~~~~e~~~il~~~~~~----~~~~~~~~~~~~ia~~~~  213 (328)
T PRK00080        143 SIRLDLPPFTLIGATTRAG-----LLTSPLRDRFGIVQRLEFYTVEELEKIVKRSARI----LGVEIDEEGALEIARRSR  213 (328)
T ss_pred             ceeecCCCceEEeecCCcc-----cCCHHHHHhcCeeeecCCCCHHHHHHHHHHHHHH----cCCCcCHHHHHHHHHHcC
Confidence                  2367888888764     57789999996 7899999999999999976663    478999999999998877


Q ss_pred             hhhcCCCCcchHHHHHHHHH
Q 005179          495 RYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       495 ~~i~~r~~p~~ai~ll~~a~  514 (710)
                      ++      |..+..+++.+.
T Consensus       214 G~------pR~a~~~l~~~~  227 (328)
T PRK00080        214 GT------PRIANRLLRRVR  227 (328)
T ss_pred             CC------chHHHHHHHHHH
Confidence            64      566677776554

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.70  E-value=1.1e-15  Score=162.39  Aligned_cols=179  Identities=21%  Similarity=0.291  Sum_probs=125.6

Q ss_pred             CCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc
Q 005179          288 LIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK  362 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~  362 (710)
                      +|++++|++++++.+..++..     ...++++|+||||||||++++++++.+          +..+.........    
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~~~~~~~~ll~Gp~G~GKT~la~~ia~~~----------~~~~~~~~~~~~~----   67 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEM----------GVNLKITSGPALE----   67 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh----------CCCEEEeccchhc----
Confidence            578899999999988887752     335679999999999999999999987          3333333222111    


Q ss_pred             cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--------------------C
Q 005179          363 ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--------------------G  422 (710)
Q Consensus       363 ~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--------------------~  422 (710)
                      ..+.    +...+..+  ..+.+|||||+|.+..             +..+.|...+++                    .
T Consensus        68 ~~~~----l~~~l~~~--~~~~vl~iDEi~~l~~-------------~~~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~  128 (305)
T TIGR00635        68 KPGD----LAAILTNL--EEGDVLFIDEIHRLSP-------------AVEELLYPAMEDFRLDIVIGKGPSARSVRLDLP  128 (305)
T ss_pred             Cchh----HHHHHHhc--ccCCEEEEehHhhhCH-------------HHHHHhhHHHhhhheeeeeccCccccceeecCC
Confidence            1122    22233322  2356999999999832             223334333321                    2


Q ss_pred             CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCC
Q 005179          423 ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRY  501 (710)
Q Consensus       423 ~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~  501 (710)
                      .+.+|++|+...     .+++++.+||. .+.+.+|+.++..++++..+..    .++.+++++++.+++.+.++     
T Consensus       129 ~~~li~~t~~~~-----~l~~~l~sR~~~~~~l~~l~~~e~~~il~~~~~~----~~~~~~~~al~~ia~~~~G~-----  194 (305)
T TIGR00635       129 PFTLVGATTRAG-----MLTSPLRDRFGIILRLEFYTVEELAEIVSRSAGL----LNVEIEPEAALEIARRSRGT-----  194 (305)
T ss_pred             CeEEEEecCCcc-----ccCHHHHhhcceEEEeCCCCHHHHHHHHHHHHHH----hCCCcCHHHHHHHHHHhCCC-----
Confidence            367888888764     57889999996 6799999999999999877663    47889999999999887775     


Q ss_pred             CcchHHHHHHHHH
Q 005179          502 LPDKAIDLVDEAG  514 (710)
Q Consensus       502 ~p~~ai~ll~~a~  514 (710)
                       |..+..+++.+.
T Consensus       195 -pR~~~~ll~~~~  206 (305)
T TIGR00635       195 -PRIANRLLRRVR  206 (305)
T ss_pred             -cchHHHHHHHHH
Confidence             455666766554

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.

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.70  E-value=3.5e-16  Score=170.04  Aligned_cols=199  Identities=23%  Similarity=0.290  Sum_probs=138.9

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -.++++.|.+++++++.+.+..             ..+.+++|+||||||||++|++++..+          +..++.+.
T Consensus       119 ~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l----------~~~~~~v~  188 (364)
T TIGR01242       119 VSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHET----------NATFIRVV  188 (364)
T ss_pred             CCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhC----------CCCEEecc
Confidence            3567899999999998876532             234679999999999999999999987          45556665


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~v  426 (710)
                      ...+.  ..+.|+....++.++..+....|+||||||+|.+.........  .+.......+..++       ..+++.+
T Consensus       189 ~~~l~--~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~--~~~~~~~~~l~~ll~~ld~~~~~~~v~v  264 (364)
T TIGR01242       189 GSELV--RKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGT--SGDREVQRTLMQLLAELDGFDPRGNVKV  264 (364)
T ss_pred             hHHHH--HHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCC--CccHHHHHHHHHHHHHhhCCCCCCCEEE
Confidence            55554  3455666677888888888778899999999999754322111  11222222222222       2467899


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH-HHHHHHHHHhhhhhcCCCC
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTL-EAINAAVHLSARYISDRYL  502 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~-~~l~~l~~ls~~~i~~r~~  502 (710)
                      |++||..+     .+|+++.+  ||+ .|.|+.|+.++|.+||+......      .+.+ ..+..++..+.+|.+    
T Consensus       265 I~ttn~~~-----~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~------~l~~~~~~~~la~~t~g~sg----  329 (364)
T TIGR01242       265 IAATNRPD-----ILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKM------KLAEDVDLEAIAKMTEGASG----  329 (364)
T ss_pred             EEecCChh-----hCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcC------CCCccCCHHHHHHHcCCCCH----
Confidence            99999876     68999987  887 79999999999999998765532      2222 235667777666533    


Q ss_pred             cchHHHHHHHHHh
Q 005179          503 PDKAIDLVDEAGS  515 (710)
Q Consensus       503 p~~ai~ll~~a~~  515 (710)
                       .+...++.+|+.
T Consensus       330 -~dl~~l~~~A~~  341 (364)
T TIGR01242       330 -ADLKAICTEAGM  341 (364)
T ss_pred             -HHHHHHHHHHHH
Confidence             455556666653

Many proteins may score above the trusted cutoff because an internal

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.70  E-value=2.7e-16  Score=180.37  Aligned_cols=202  Identities=18%  Similarity=0.221  Sum_probs=151.1

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCc----cc--------
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPV----FL--------  344 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~----~l--------  344 (710)
                      ..|.+++||.+|+++||++..++.|...+...+-.+. ||+||+|||||++|+.+|+.+.+.....    ..        
T Consensus         4 ~~LaeKyRP~tFddIIGQe~Iv~~LknaI~~~rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~sC~~i~   83 (944)
T PRK14949          4 QVLARKWRPATFEQMVGQSHVLHALTNALTQQRLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSSCVEIA   83 (944)
T ss_pred             hhHHHHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchHHHHHh
Confidence            3678899999999999999999999998888776775 8999999999999999999996542110    00        


Q ss_pred             --cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          345 --LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       345 --~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                        ....+++++.      ....+  ...++.+++.+.    .++..|+||||+|.|             ..+.++.|++.
T Consensus        84 ~g~~~DviEidA------as~~k--VDdIReLie~v~~~P~~gk~KViIIDEAh~L-------------T~eAqNALLKt  142 (944)
T PRK14949         84 QGRFVDLIEVDA------ASRTK--VDDTRELLDNVQYRPSRGRFKVYLIDEVHML-------------SRSSFNALLKT  142 (944)
T ss_pred             cCCCceEEEecc------ccccC--HHHHHHHHHHHHhhhhcCCcEEEEEechHhc-------------CHHHHHHHHHH
Confidence              0011222222      11111  122444444443    234579999999999             56688999999


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      |+.  +.+++|++||...     .+.+.+++||..+.|.+++.++....|+.++..    .++.++++++..++..+.+.
T Consensus       143 LEEPP~~vrFILaTTe~~-----kLl~TIlSRCq~f~fkpLs~eEI~~~L~~il~~----EgI~~edeAL~lIA~~S~Gd  213 (944)
T PRK14949        143 LEEPPEHVKFLLATTDPQ-----KLPVTVLSRCLQFNLKSLTQDEIGTQLNHILTQ----EQLPFEAEALTLLAKAANGS  213 (944)
T ss_pred             HhccCCCeEEEEECCCch-----hchHHHHHhheEEeCCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC
Confidence            986  6788888887765     467899999999999999999999888887764    37899999999999887764


Q ss_pred             hcCCCCcchHHHHHHHHHh
Q 005179          497 ISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~~  515 (710)
                            +++++.+++.+++
T Consensus       214 ------~R~ALnLLdQala  226 (944)
T PRK14949        214 ------MRDALSLTDQAIA  226 (944)
T ss_pred             ------HHHHHHHHHHHHH
Confidence                  4567888877663

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.70  E-value=2.6e-16  Score=175.63  Aligned_cols=201  Identities=18%  Similarity=0.180  Sum_probs=149.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--------------  343 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--------------  343 (710)
                      .|.+++||.+|+++||++..++.|...+...+..+ +||+||+|||||++|+.+|+.+.+...+..              
T Consensus         4 ~LarKyRPktFddVIGQe~vv~~L~~aI~~grl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~sC~~I~~   83 (702)
T PRK14960          4 VLARKYRPRNFNELVGQNHVSRALSSALERGRLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCATCKAVNE   83 (702)
T ss_pred             hHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHHHHHHhc
Confidence            57789999999999999999999999888766554 599999999999999999999865321110              


Q ss_pred             ccCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          344 LLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       344 l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                      .....++.+|.++      ..+  ...++.++..+.    ..+..|+||||+|.|             +....+.|+..+
T Consensus        84 g~hpDviEIDAAs------~~~--VddIReli~~~~y~P~~gk~KV~IIDEVh~L-------------S~~A~NALLKtL  142 (702)
T PRK14960         84 GRFIDLIEIDAAS------RTK--VEDTRELLDNVPYAPTQGRFKVYLIDEVHML-------------STHSFNALLKTL  142 (702)
T ss_pred             CCCCceEEecccc------cCC--HHHHHHHHHHHhhhhhcCCcEEEEEechHhc-------------CHHHHHHHHHHH
Confidence            0111344444321      111  223555555443    234579999999999             445678888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+.+|.+|+...     .+.+.+++||..+.|.+++.++....|+.++.+    .++.++++++..++..+.+- 
T Consensus       143 EEPP~~v~FILaTtd~~-----kIp~TIlSRCq~feFkpLs~eEI~k~L~~Il~k----EgI~id~eAL~~IA~~S~Gd-  212 (702)
T PRK14960        143 EEPPEHVKFLFATTDPQ-----KLPITVISRCLQFTLRPLAVDEITKHLGAILEK----EQIAADQDAIWQIAESAQGS-  212 (702)
T ss_pred             hcCCCCcEEEEEECChH-----hhhHHHHHhhheeeccCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC-
Confidence            86  6677888777654     456889999999999999999998888888764    47899999999999887653 


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                           .++++.+++.+++
T Consensus       213 -----LRdALnLLDQaIa  225 (702)
T PRK14960        213 -----LRDALSLTDQAIA  225 (702)
T ss_pred             -----HHHHHHHHHHHHH
Confidence                 3567777777664

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.70  E-value=2.6e-16  Score=181.94  Aligned_cols=200  Identities=25%  Similarity=0.331  Sum_probs=147.3

Q ss_pred             hhHHhhhhcCCCCcccCHHHHH---HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          279 DLTARASEELIDPVIGRETEIQ---RIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~---~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +|.+++||.+|++++|+++.+.   .+...+......+++|+|||||||||+|+++++.+          +..++.++..
T Consensus        17 PLaek~RP~tldd~vGQe~ii~~~~~L~~~i~~~~~~slLL~GPpGtGKTTLA~aIA~~~----------~~~f~~lna~   86 (725)
T PRK13341         17 PLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHT----------RAHFSSLNAV   86 (725)
T ss_pred             ChHHhcCCCcHHHhcCcHHHhhhhHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHh----------cCcceeehhh
Confidence            6888899999999999999884   56677777777899999999999999999999876          3344444432


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHH
Q 005179          356 LLMAGAKERGELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDE  434 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~  434 (710)
                        ..+.   .++...+..+...... ....+|||||+|.+             ....++.|.+.++++.+++|++|+...
T Consensus        87 --~~~i---~dir~~i~~a~~~l~~~~~~~IL~IDEIh~L-------------n~~qQdaLL~~lE~g~IiLI~aTTenp  148 (725)
T PRK13341         87 --LAGV---KDLRAEVDRAKERLERHGKRTILFIDEVHRF-------------NKAQQDALLPWVENGTITLIGATTENP  148 (725)
T ss_pred             --hhhh---HHHHHHHHHHHHHhhhcCCceEEEEeChhhC-------------CHHHHHHHHHHhcCceEEEEEecCCCh
Confidence              1111   1122222222111111 24579999999999             344567788889999999999888765


Q ss_pred             HHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHh---hcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHH
Q 005179          435 HRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEA---HHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVD  511 (710)
Q Consensus       435 ~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~---~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~  511 (710)
                         .+.+++++.+|+..+.+++++.+++..+++..+..+..   ..++.+++++++.++..+.+.      .+.++.+|+
T Consensus       149 ---~~~l~~aL~SR~~v~~l~pLs~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD------~R~lln~Le  219 (725)
T PRK13341        149 ---YFEVNKALVSRSRLFRLKSLSDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGD------ARSLLNALE  219 (725)
T ss_pred             ---HhhhhhHhhccccceecCCCCHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCC------HHHHHHHHH
Confidence               34678999999999999999999999999988775433   235889999999999886542      245667777


Q ss_pred             HHHh
Q 005179          512 EAGS  515 (710)
Q Consensus       512 ~a~~  515 (710)
                      .++.
T Consensus       220 ~a~~  223 (725)
T PRK13341        220 LAVE  223 (725)
T ss_pred             HHHH
Confidence            6653

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.69  E-value=2.1e-15  Score=157.68  Aligned_cols=188  Identities=20%  Similarity=0.245  Sum_probs=134.7

Q ss_pred             CcccCHHHHHHHHHHHH--------c-------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          291 PVIGRETEIQRIIQILC--------R-------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~--------~-------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      .++|.++..+++.++..        .       ..+.+++|+||||||||++|+++++.+.....   .....++.++..
T Consensus        23 ~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~---~~~~~~v~v~~~   99 (284)
T TIGR02880        23 ELIGLKPVKTRIREIAALLLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGY---VRKGHLVSVTRD   99 (284)
T ss_pred             hccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCC---cccceEEEecHH
Confidence            37888876666554321        0       12347999999999999999999998865321   112357777776


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChH
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQD  433 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~  433 (710)
                      .+..  .+.|+.+..+..+++.+   .+.+|||||++.|...+..    ...+.++++.|...|+.  +++++|++++.+
T Consensus       100 ~l~~--~~~g~~~~~~~~~~~~a---~~gvL~iDEi~~L~~~~~~----~~~~~~~~~~Ll~~le~~~~~~~vI~a~~~~  170 (284)
T TIGR02880       100 DLVG--QYIGHTAPKTKEILKRA---MGGVLFIDEAYYLYRPDNE----RDYGQEAIEILLQVMENQRDDLVVILAGYKD  170 (284)
T ss_pred             HHhH--hhcccchHHHHHHHHHc---cCcEEEEechhhhccCCCc----cchHHHHHHHHHHHHhcCCCCEEEEEeCCcH
Confidence            6653  34555555566666654   3579999999998543211    12355677788887764  478899998877


Q ss_pred             HHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q 005179          434 EHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~  494 (710)
                      ....++..+|+|.+||. .|.|++++.+++..|++.++.+.    +..+++++++.+..+..
T Consensus       171 ~~~~~~~~np~L~sR~~~~i~fp~l~~edl~~I~~~~l~~~----~~~l~~~a~~~L~~~l~  228 (284)
T TIGR02880       171 RMDSFFESNPGFSSRVAHHVDFPDYSEAELLVIAGLMLKEQ----QYRFSAEAEEAFADYIA  228 (284)
T ss_pred             HHHHHHhhCHHHHhhCCcEEEeCCcCHHHHHHHHHHHHHHh----ccccCHHHHHHHHHHHH
Confidence            66667778999999997 89999999999999999888754    46788888887766544

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.

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.69  E-value=3.7e-16  Score=177.10  Aligned_cols=200  Identities=19%  Similarity=0.199  Sum_probs=148.5

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCcc--cc----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVF--LL----------  345 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~--l~----------  345 (710)
                      .|.+++||.+|+++||++..++.|...+...+-.+. ||+||+|||||++|+.+|+.+.+......  ..          
T Consensus         5 ~La~KyRP~~f~divGQe~vv~~L~~~l~~~rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~C~~i~~   84 (647)
T PRK07994          5 VLARKWRPQTFAEVVGQEHVLTALANALDLGRLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDNCREIEQ   84 (647)
T ss_pred             hHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHHHHHHHc
Confidence            578899999999999999999999999887666664 89999999999999999999976421100  00          


Q ss_pred             --CceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          346 --SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       346 --~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                        ...++.+|...      .. . .+.++.+++.+.    .++..|+||||+|.|             +...+|.|+..|
T Consensus        85 g~~~D~ieidaas------~~-~-VddiR~li~~~~~~p~~g~~KV~IIDEah~L-------------s~~a~NALLKtL  143 (647)
T PRK07994         85 GRFVDLIEIDAAS------RT-K-VEDTRELLDNVQYAPARGRFKVYLIDEVHML-------------SRHSFNALLKTL  143 (647)
T ss_pred             CCCCCceeecccc------cC-C-HHHHHHHHHHHHhhhhcCCCEEEEEechHhC-------------CHHHHHHHHHHH
Confidence              01233333211      11 1 122455555543    234569999999999             556788888899


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+.+|.+|+...     .+.+.+++||..+.|.+++.++....|+.++..    .++.++++++..++..+.+. 
T Consensus       144 EEPp~~v~FIL~Tt~~~-----kLl~TI~SRC~~~~f~~Ls~~ei~~~L~~il~~----e~i~~e~~aL~~Ia~~s~Gs-  213 (647)
T PRK07994        144 EEPPEHVKFLLATTDPQ-----KLPVTILSRCLQFHLKALDVEQIRQQLEHILQA----EQIPFEPRALQLLARAADGS-  213 (647)
T ss_pred             HcCCCCeEEEEecCCcc-----ccchHHHhhheEeeCCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC-
Confidence            87  6788888887765     577899999999999999999988888877763    37889999999998887764 


Q ss_pred             cCCCCcchHHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~  514 (710)
                           +++++.+++.+.
T Consensus       214 -----~R~Al~lldqai  225 (647)
T PRK07994        214 -----MRDALSLTDQAI  225 (647)
T ss_pred             -----HHHHHHHHHHHH
Confidence                 345666666554

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

Probab=99.69  E-value=6.2e-16  Score=175.08  Aligned_cols=202  Identities=24%  Similarity=0.332  Sum_probs=149.6

Q ss_pred             cCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -.++++.|.+.....+.+.+.             .+....+||+||||||||++|+++|..+          +.+++.++
T Consensus       239 v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~----------~~~fi~v~  308 (494)
T COG0464         239 VTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALES----------RSRFISVK  308 (494)
T ss_pred             cceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhC----------CCeEEEee
Confidence            345666666655554444321             2344579999999999999999999987          88999999


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc---c-CCCeEEEEc
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL---G-RGELQCIAS  429 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l---~-~~~v~vI~a  429 (710)
                      .+.+.  .++.|+.++.++.+|..++...|+||||||+|.++.....+.+  .....+.+.|+..+   + ...+.+|++
T Consensus       309 ~~~l~--sk~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~--~~~~r~~~~lL~~~d~~e~~~~v~vi~a  384 (494)
T COG0464         309 GSELL--SKWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSED--GSGRRVVGQLLTELDGIEKAEGVLVIAA  384 (494)
T ss_pred             CHHHh--ccccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCc--hHHHHHHHHHHHHhcCCCccCceEEEec
Confidence            98777  6789999999999999999999999999999999876543211  11234555554444   2 356889999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCC-CCHHHHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCK-FTLEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~-i~~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ||.+.     .+|+++.|  ||+ .|.|+.|+.++|.+|++....+.    +.. ..+-.++.+++.+.+|..     .+
T Consensus       385 TN~p~-----~ld~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~----~~~~~~~~~~~~l~~~t~~~sg-----ad  450 (494)
T COG0464         385 TNRPD-----DLDPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDK----KPPLAEDVDLEELAEITEGYSG-----AD  450 (494)
T ss_pred             CCCcc-----ccCHhhcccCccceEeecCCCCHHHHHHHHHHHhccc----CCcchhhhhHHHHHHHhcCCCH-----HH
Confidence            99987     89999999  998 89999999999999999877643    221 234456667776666433     55


Q ss_pred             HHHHHHHHHhh
Q 005179          506 AIDLVDEAGSR  516 (710)
Q Consensus       506 ai~ll~~a~~~  516 (710)
                      ...++.+|+..
T Consensus       451 i~~i~~ea~~~  461 (494)
T COG0464         451 IAALVREAALE  461 (494)
T ss_pred             HHHHHHHHHHH
Confidence            56666666543

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=99.68  E-value=5.8e-15  Score=171.59  Aligned_cols=177  Identities=19%  Similarity=0.244  Sum_probs=122.3

Q ss_pred             CcccCHHHHHHHHHHHHcC---------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--
Q 005179          291 PVIGRETEIQRIIQILCRR---------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~---------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--  359 (710)
                      .++|+++.++.+...+.+.         ...++||+||||||||.+|+.+|+.+          +..++.+|++.+..  
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~~~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l----------~~~~i~id~se~~~~~  528 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL----------GIELLRFDMSEYMERH  528 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhccccCCCCCcceEEEECCCCCCHHHHHHHHHHHh----------CCCcEEeechhhcccc
Confidence            4899999999999887631         12468999999999999999999988          44566666655431  


Q ss_pred             ------cc--ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------
Q 005179          360 ------GA--KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------  422 (710)
Q Consensus       360 ------g~--~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------  422 (710)
                            |.  .+.|..+  -..+.+.+...+.+||||||+|.+             ..++++.|.++|++|         
T Consensus       529 ~~~~LiG~~~gyvg~~~--~g~L~~~v~~~p~sVlllDEieka-------------~~~v~~~LLq~ld~G~ltd~~g~~  593 (758)
T PRK11034        529 TVSRLIGAPPGYVGFDQ--GGLLTDAVIKHPHAVLLLDEIEKA-------------HPDVFNLLLQVMDNGTLTDNNGRK  593 (758)
T ss_pred             cHHHHcCCCCCcccccc--cchHHHHHHhCCCcEEEeccHhhh-------------hHHHHHHHHHHHhcCeeecCCCce
Confidence                  11  1222100  011223344566789999999999             567888888887754         


Q ss_pred             ----CeEEEEccChHHH---H-----------------hhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh--
Q 005179          423 ----ELQCIASTTQDEH---R-----------------TQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA--  475 (710)
Q Consensus       423 ----~v~vI~att~~~~---~-----------------~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~--  475 (710)
                          +.++|.|||...-   .                 -.....|.|.+|++ .|.|.+++.++..+|+...+..+..  
T Consensus       594 vd~rn~iiI~TsN~g~~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~Rid~ii~f~~L~~~~l~~I~~~~l~~~~~~l  673 (758)
T PRK11034        594 ADFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQAQL  673 (758)
T ss_pred             ecCCCcEEEEeCCcCHHHHhhcccCcccchhhHHHHHHHHHhcCHHHHccCCEEEEcCCCCHHHHHHHHHHHHHHHHHHH
Confidence                3457888773210   0                 00124589999997 7899999999999999876654432  


Q ss_pred             ---hcCCCCCHHHHHHHHHH
Q 005179          476 ---HHNCKFTLEAINAAVHL  492 (710)
Q Consensus       476 ---~~~~~i~~~~l~~l~~l  492 (710)
                         ...+.+++++++.++..
T Consensus       674 ~~~~i~l~~~~~~~~~l~~~  693 (758)
T PRK11034        674 DQKGVSLEVSQEARDWLAEK  693 (758)
T ss_pred             HHCCCCceECHHHHHHHHHh
Confidence               23467899999988765

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=5.8e-16  Score=171.63  Aligned_cols=201  Identities=20%  Similarity=0.237  Sum_probs=143.3

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.+++||.+|++++|+++....+...+......+ +||+|||||||||+|+.+|+.+.+...+...             
T Consensus         3 ~l~~kyRP~~~~divGq~~i~~~L~~~i~~~~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~c~~i~~   82 (472)
T PRK14962          3 ALYRKYRPKTFSEVVGQDHVKKLIINALKKNSISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRACRSIDE   82 (472)
T ss_pred             hhHHHHCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHHHHHHhc
Confidence            46789999999999999999888888887766555 7999999999999999999998543211100             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++..      ...|  ...++.+.+.+..    ....|+||||+|.+             ..+.++.|+..+
T Consensus        83 g~~~dv~el~aa------~~~g--id~iR~i~~~~~~~p~~~~~kVvIIDE~h~L-------------t~~a~~~LLk~L  141 (472)
T PRK14962         83 GTFMDVIELDAA------SNRG--IDEIRKIRDAVGYRPMEGKYKVYIIDEVHML-------------TKEAFNALLKTL  141 (472)
T ss_pred             CCCCccEEEeCc------ccCC--HHHHHHHHHHHhhChhcCCeEEEEEEChHHh-------------HHHHHHHHHHHH
Confidence             01123333321      1111  1224444444332    23569999999999             334567777777


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+++|++|+...     .+.+++.+||+.+.+.+++.++...+++..+.    ..++.+++++++.++..+.+-+
T Consensus       142 E~p~~~vv~Ilattn~~-----kl~~~L~SR~~vv~f~~l~~~el~~~L~~i~~----~egi~i~~eal~~Ia~~s~Gdl  212 (472)
T PRK14962        142 EEPPSHVVFVLATTNLE-----KVPPTIISRCQVIEFRNISDELIIKRLQEVAE----AEGIEIDREALSFIAKRASGGL  212 (472)
T ss_pred             HhCCCcEEEEEEeCChH-----hhhHHHhcCcEEEEECCccHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHhCCCH
Confidence            76  6788887777543     56899999999999999999998888887766    3478999999999998765432


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                            +.++..|+.++.
T Consensus       213 ------R~aln~Le~l~~  224 (472)
T PRK14962        213 ------RDALTMLEQVWK  224 (472)
T ss_pred             ------HHHHHHHHHHHH
Confidence                  346666766543

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

Probab=99.68  E-value=2.7e-16  Score=152.50  Aligned_cols=177  Identities=20%  Similarity=0.288  Sum_probs=136.5

Q ss_pred             hhcCCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEE
Q 005179          285 SEELIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMS  351 (710)
Q Consensus       285 ~~~~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~  351 (710)
                      ...+.+-+-|-+.+|+.+.+++             ....+.++|||||||+|||.||+++|...          .|.++.
T Consensus       142 PDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht----------~c~fir  211 (404)
T KOG0728|consen  142 PDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHT----------DCTFIR  211 (404)
T ss_pred             CccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhc----------ceEEEE
Confidence            3334444556677776666543             33566789999999999999999999877          888899


Q ss_pred             eehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------CCCe
Q 005179          352 LDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------RGEL  424 (710)
Q Consensus       352 ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------~~~v  424 (710)
                      +..+.++  .++.|+-...++++|--++.+.|+|+|+||||.+-.+...+  ++++..+++..++.+|.       ..++
T Consensus       212 vsgselv--qk~igegsrmvrelfvmarehapsiifmdeidsigs~r~e~--~~ggdsevqrtmlellnqldgfeatkni  287 (404)
T KOG0728|consen  212 VSGSELV--QKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVES--GSGGDSEVQRTMLELLNQLDGFEATKNI  287 (404)
T ss_pred             echHHHH--HHHhhhhHHHHHHHHHHHHhcCCceEeeecccccccccccC--CCCccHHHHHHHHHHHHhccccccccce
Confidence            9888888  67888888889999999999999999999999995543322  22345555555444443       4678


Q ss_pred             EEEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCC
Q 005179          425 QCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCK  480 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~  480 (710)
                      .+|.+||.-+     -+||+|.|  |++ .|+|++|+.+.|.+||+-..++.....+++
T Consensus       288 kvimatnrid-----ild~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~  341 (404)
T KOG0728|consen  288 KVIMATNRID-----ILDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGIN  341 (404)
T ss_pred             EEEEeccccc-----cccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccC
Confidence            9999999876     68999999  887 899999999999999998777665555554

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=9.6e-16  Score=171.66  Aligned_cols=202  Identities=18%  Similarity=0.185  Sum_probs=150.2

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.+++||.+|+++||++..++.|...+...+..+ +||+||+|||||++|+.+|+.+.+...+...             
T Consensus         5 ~l~~kyRP~~f~divGq~~v~~~L~~~~~~~~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~   84 (509)
T PRK14958          5 VLARKWRPRCFQEVIGQAPVVRALSNALDQQYLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCENCREIDE   84 (509)
T ss_pred             hHHHHHCCCCHHHhcCCHHHHHHHHHHHHhCCCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHHHHHHhc
Confidence            47889999999999999999999999998876666 5899999999999999999999764322110             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++++|..+      .. . .+.++.+++.+..    ....|+||||+|.|             ..+.++.|+..|
T Consensus        85 g~~~d~~eidaas------~~-~-v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~l-------------s~~a~naLLk~L  143 (509)
T PRK14958         85 GRFPDLFEVDAAS------RT-K-VEDTRELLDNIPYAPTKGRFKVYLIDEVHML-------------SGHSFNALLKTL  143 (509)
T ss_pred             CCCceEEEEcccc------cC-C-HHHHHHHHHHHhhccccCCcEEEEEEChHhc-------------CHHHHHHHHHHH
Confidence             111245554321      11 1 1224555555432    33469999999999             445678888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+.+|.+|+...     .+.+.+.+||..+.+.+++.++....++.++..    .++.++++++..++..+.+- 
T Consensus       144 Eepp~~~~fIlattd~~-----kl~~tI~SRc~~~~f~~l~~~~i~~~l~~il~~----egi~~~~~al~~ia~~s~Gs-  213 (509)
T PRK14958        144 EEPPSHVKFILATTDHH-----KLPVTVLSRCLQFHLAQLPPLQIAAHCQHLLKE----ENVEFENAALDLLARAANGS-  213 (509)
T ss_pred             hccCCCeEEEEEECChH-----hchHHHHHHhhhhhcCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCc-
Confidence            86  4677887777654     466789999999999999999988888877764    47899999999998887642 


Q ss_pred             cCCCCcchHHHHHHHHHhh
Q 005179          498 SDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~~  516 (710)
                           +.+++.+++.+++.
T Consensus       214 -----lR~al~lLdq~ia~  227 (509)
T PRK14958        214 -----VRDALSLLDQSIAY  227 (509)
T ss_pred             -----HHHHHHHHHHHHhc
Confidence                 45678888877643

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=1.1e-15  Score=168.50  Aligned_cols=202  Identities=18%  Similarity=0.226  Sum_probs=151.9

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCcc--------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEVPVF--------------  343 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~~--------------  343 (710)
                      +|..++||.+|+++||++..++.|...+...+-. ++||+||+|+||||+|+.+|+.+.+...|..              
T Consensus         2 ~la~KyRP~~f~dliGQe~vv~~L~~a~~~~ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~C~~i~~   81 (491)
T PRK14964          2 NLALKYRPSSFKDLVGQDVLVRILRNAFTLNKIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHNCISIKN   81 (491)
T ss_pred             ChhHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHHHHHHhc
Confidence            4678999999999999999999998887765544 6899999999999999999999876443321              


Q ss_pred             ccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          344 LLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       344 l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                      .....++++|.++      ..|  .+.++.+++.+..    ....|+||||+|.|             ....++.|+..+
T Consensus        82 ~~~~Dv~eidaas------~~~--vddIR~Iie~~~~~P~~~~~KVvIIDEah~L-------------s~~A~NaLLK~L  140 (491)
T PRK14964         82 SNHPDVIEIDAAS------NTS--VDDIKVILENSCYLPISSKFKVYIIDEVHML-------------SNSAFNALLKTL  140 (491)
T ss_pred             cCCCCEEEEeccc------CCC--HHHHHHHHHHHHhccccCCceEEEEeChHhC-------------CHHHHHHHHHHH
Confidence            1233456655431      111  2235666665542    34569999999999             445678888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+.+|.+|+...     .+.+.+.+||+.+.+.+++.++....++.++.+    .++.+++++++.+++.+.+. 
T Consensus       141 EePp~~v~fIlatte~~-----Kl~~tI~SRc~~~~f~~l~~~el~~~L~~ia~~----Egi~i~~eAL~lIa~~s~Gs-  210 (491)
T PRK14964        141 EEPAPHVKFILATTEVK-----KIPVTIISRCQRFDLQKIPTDKLVEHLVDIAKK----ENIEHDEESLKLIAENSSGS-  210 (491)
T ss_pred             hCCCCCeEEEEEeCChH-----HHHHHHHHhheeeecccccHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC-
Confidence            86  5677887777654     466899999999999999999988888887774    47899999999999887653 


Q ss_pred             cCCCCcchHHHHHHHHHhh
Q 005179          498 SDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~~  516 (710)
                           ...++.+++.++..
T Consensus       211 -----lR~alslLdqli~y  224 (491)
T PRK14964        211 -----MRNALFLLEQAAIY  224 (491)
T ss_pred             -----HHHHHHHHHHHHHh
Confidence                 34577777777643

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.67  E-value=2.3e-14  Score=170.70  Aligned_cols=181  Identities=19%  Similarity=0.242  Sum_probs=123.2

Q ss_pred             CCcccCHHHHHHHHHHHHcC-------C-C-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-
Q 005179          290 DPVIGRETEIQRIIQILCRR-------T-K-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~-------~-~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-  359 (710)
                      ..++|++..++.+...+.+.       . + .++||+||+|||||++|++||+.+...       ...++.+|++.+.. 
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~-------~~~~~~~d~s~~~~~  581 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFLFSGPTGVGKTELTKALASYFFGS-------EDAMIRLDMSEYMEK  581 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcccCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCC-------ccceEEEEchhcccc
Confidence            35899999999998877531       1 1 246899999999999999999988432       34566666655431 


Q ss_pred             -------c--cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------
Q 005179          360 -------G--AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------  422 (710)
Q Consensus       360 -------g--~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------  422 (710)
                             |  ..+.|.-+  ...+.+.+...+..|++|||+|.+             ..++++.|++.++.|        
T Consensus       582 ~~~~~l~g~~~gyvg~~~--~~~l~~~~~~~p~~VvllDeieka-------------~~~v~~~Llq~le~g~~~d~~g~  646 (821)
T CHL00095        582 HTVSKLIGSPPGYVGYNE--GGQLTEAVRKKPYTVVLFDEIEKA-------------HPDIFNLLLQILDDGRLTDSKGR  646 (821)
T ss_pred             ccHHHhcCCCCcccCcCc--cchHHHHHHhCCCeEEEECChhhC-------------CHHHHHHHHHHhccCceecCCCc
Confidence                   1  11222100  112334455566689999999988             567888888888764        


Q ss_pred             -----CeEEEEccChHH-----------------------HHhh---------hhccHHHHcccc-ceEecCCCHHHHHH
Q 005179          423 -----ELQCIASTTQDE-----------------------HRTQ---------FEKDKALARRFQ-PVLISEPSQEDAVR  464 (710)
Q Consensus       423 -----~v~vI~att~~~-----------------------~~~~---------~~~d~aL~~Rf~-~I~v~~Ps~~~~~~  464 (710)
                           +.++|.|+|...                       |...         ....|.|.+|++ .|.|.+.+.++..+
T Consensus       647 ~v~~~~~i~I~Tsn~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~peflnRid~ii~F~pL~~~~l~~  726 (821)
T CHL00095        647 TIDFKNTLIIMTSNLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLNRLDEIIVFRQLTKNDVWE  726 (821)
T ss_pred             EEecCceEEEEeCCcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhccCCeEEEeCCCCHHHHHH
Confidence                 345777766321                       0000         013478899995 88999999999999


Q ss_pred             HHHHHHHHHH---hhc--CCCCCHHHHHHHHHH
Q 005179          465 ILLGLREKYE---AHH--NCKFTLEAINAAVHL  492 (710)
Q Consensus       465 IL~~l~~~~~---~~~--~~~i~~~~l~~l~~l  492 (710)
                      |+...+.++.   ..+  .+.+++++++.+++.
T Consensus       727 Iv~~~l~~l~~rl~~~~i~l~~~~~~~~~La~~  759 (821)
T CHL00095        727 IAEIMLKNLFKRLNEQGIQLEVTERIKTLLIEE  759 (821)
T ss_pred             HHHHHHHHHHHHHHHCCcEEEECHHHHHHHHHh
Confidence            9987666542   122  367899999988876

>PLN03025 replication factor C subunit; Provisional

Probab=99.66  E-value=4.2e-16  Score=166.33  Aligned_cols=196  Identities=15%  Similarity=0.219  Sum_probs=140.7

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      +|.+++||.+|++++|+++.+..+..++......|+||+||||||||++|+++|+.+.+...     ...+++++.++..
T Consensus         2 ~w~~kyrP~~l~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~G~GKTtla~~la~~l~~~~~-----~~~~~eln~sd~~   76 (319)
T PLN03025          2 PWVEKYRPTKLDDIVGNEDAVSRLQVIARDGNMPNLILSGPPGTGKTTSILALAHELLGPNY-----KEAVLELNASDDR   76 (319)
T ss_pred             ChhhhcCCCCHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccC-----ccceeeecccccc
Confidence            68899999999999999999999998888777788999999999999999999999854321     1234444432211


Q ss_pred             hccccCccHHHHHHHHHHHH---HhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChH
Q 005179          359 AGAKERGELEARVTTLISEI---QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQD  433 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~---~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~  433 (710)
                          ....+...++......   ......|++|||+|.+             ..+.++.|+..++.  ....+|.+|+..
T Consensus        77 ----~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~l-------------t~~aq~aL~~~lE~~~~~t~~il~~n~~  139 (319)
T PLN03025         77 ----GIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSM-------------TSGAQQALRRTMEIYSNTTRFALACNTS  139 (319)
T ss_pred             ----cHHHHHHHHHHHHhccccCCCCCeEEEEEechhhc-------------CHHHHHHHHHHHhcccCCceEEEEeCCc
Confidence                0112222222211110   0123569999999999             33456777777764  445566666654


Q ss_pred             HHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHH
Q 005179          434 EHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVD  511 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~  511 (710)
                      .     .+.+++++|+..+.+.+|+.++....|+.++.    ..++.++++++++++..+.+-+      ..++..|+
T Consensus       140 ~-----~i~~~L~SRc~~i~f~~l~~~~l~~~L~~i~~----~egi~i~~~~l~~i~~~~~gDl------R~aln~Lq  202 (319)
T PLN03025        140 S-----KIIEPIQSRCAIVRFSRLSDQEILGRLMKVVE----AEKVPYVPEGLEAIIFTADGDM------RQALNNLQ  202 (319)
T ss_pred             c-----ccchhHHHhhhcccCCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCCH------HHHHHHHH
Confidence            3     56689999999999999999999999888776    3488999999999998876532      35666665

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

Probab=99.66  E-value=3.7e-16  Score=151.67  Aligned_cols=149  Identities=19%  Similarity=0.297  Sum_probs=121.4

Q ss_pred             HHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeE
Q 005179          306 LCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVI  385 (710)
Q Consensus       306 L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~I  385 (710)
                      +....++++|+|||||||||+|++++|+..          ...++.+..+.++  .+|-|+-...++++|..++++.|.|
T Consensus       184 igidpprgvllygppg~gktml~kava~~t----------~a~firvvgsefv--qkylgegprmvrdvfrlakenapsi  251 (408)
T KOG0727|consen  184 IGIDPPRGVLLYGPPGTGKTMLAKAVANHT----------TAAFIRVVGSEFV--QKYLGEGPRMVRDVFRLAKENAPSI  251 (408)
T ss_pred             hCCCCCcceEEeCCCCCcHHHHHHHHhhcc----------chheeeeccHHHH--HHHhccCcHHHHHHHHHHhccCCcE
Confidence            344678899999999999999999999876          5566777777777  5677777777999999999999999


Q ss_pred             EEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------CCCeEEEEccChHHHHhhhhccHHHHc--ccc-ceEec
Q 005179          386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------RGELQCIASTTQDEHRTQFEKDKALAR--RFQ-PVLIS  455 (710)
Q Consensus       386 L~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------~~~v~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~  455 (710)
                      +||||+|.+..+.-..++  +...+++.+|..+|.       ..++.+|.+||..+     .+||+|.|  |++ .|+|+
T Consensus       252 ifideidaiatkrfdaqt--gadrevqril~ellnqmdgfdq~~nvkvimatnrad-----tldpallrpgrldrkiefp  324 (408)
T KOG0727|consen  252 IFIDEIDAIATKRFDAQT--GADREVQRILIELLNQMDGFDQTTNVKVIMATNRAD-----TLDPALLRPGRLDRKIEFP  324 (408)
T ss_pred             EEeehhhhHhhhhccccc--cccHHHHHHHHHHHHhccCcCcccceEEEEecCccc-----ccCHhhcCCccccccccCC
Confidence            999999999866433222  446677777766654       34788999999987     79999999  887 89999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 005179          456 EPSQEDAVRILLGLREKY  473 (710)
Q Consensus       456 ~Ps~~~~~~IL~~l~~~~  473 (710)
                      .|+..++.-++..+..+.
T Consensus       325 lpdrrqkrlvf~titskm  342 (408)
T KOG0727|consen  325 LPDRRQKRLVFSTITSKM  342 (408)
T ss_pred             CCchhhhhhhHHhhhhcc
Confidence            999999999998887754

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

Probab=99.66  E-value=7.9e-16  Score=158.38  Aligned_cols=183  Identities=21%  Similarity=0.333  Sum_probs=141.9

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          288 LIDPVIGRETEIQRIIQILCR--------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      +|+++-|.+..+..+.+.+.-              +...++||+||||||||.+|+++|++.          +..++.+.
T Consensus        90 ~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akea----------ga~fInv~  159 (386)
T KOG0737|consen   90 SFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEA----------GANFINVS  159 (386)
T ss_pred             ehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHc----------CCCcceee
Confidence            466777888777776664211              245789999999999999999999998          77888888


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcc--------cccCC--C
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP--------SLGRG--E  423 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~--------~l~~~--~  423 (710)
                      ++.+.  .++-|+-++.++.+|..+.+-.|+|+||||++.+.+.+..      ...++...++.        +..+.  .
T Consensus       160 ~s~lt--~KWfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~s------~dHEa~a~mK~eFM~~WDGl~s~~~~r  231 (386)
T KOG0737|consen  160 VSNLT--SKWFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRS------TDHEATAMMKNEFMALWDGLSSKDSER  231 (386)
T ss_pred             ccccc--hhhHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhccc------chHHHHHHHHHHHHHHhccccCCCCce
Confidence            88877  4778999999999999998888999999999999887632      13333333321        22233  4


Q ss_pred             eEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          424 LQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       424 v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      +.|+|+||++.     .+|.++.||+. .+.|+.|+.++|.+||+-++.......+     -.+..++..+.+|.+
T Consensus       232 VlVlgATNRP~-----DlDeAiiRR~p~rf~V~lP~~~qR~kILkviLk~e~~e~~-----vD~~~iA~~t~GySG  297 (386)
T KOG0737|consen  232 VLVLGATNRPF-----DLDEAIIRRLPRRFHVGLPDAEQRRKILKVILKKEKLEDD-----VDLDEIAQMTEGYSG  297 (386)
T ss_pred             EEEEeCCCCCc-----cHHHHHHHhCcceeeeCCCchhhHHHHHHHHhcccccCcc-----cCHHHHHHhcCCCcH
Confidence            88999999985     89999999996 8999999999999999998875532222     236778888888865

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=2.1e-15  Score=163.52  Aligned_cols=202  Identities=21%  Similarity=0.184  Sum_probs=145.8

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc------------
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL------------  344 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l------------  344 (710)
                      ..|.+++||.+|++++|++..++.+...+......| +||+||+|+|||++|+.+|+.+.+...+...            
T Consensus         4 ~~l~~kyrP~~~~~iiGq~~~~~~l~~~~~~~~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~c~~~~   83 (363)
T PRK14961          4 QILARKWRPQYFRDIIGQKHIVTAISNGLSLGRIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCIICKEIE   83 (363)
T ss_pred             HHHHHHhCCCchhhccChHHHHHHHHHHHHcCCCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHh
Confidence            358899999999999999999999999888766555 5899999999999999999998542211100            


Q ss_pred             c--CceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          345 L--SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       345 ~--~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                      .  ...++.++..      . ... ...++.+++.+..    ....|+||||+|.+             ....++.|+..
T Consensus        84 ~~~~~d~~~~~~~------~-~~~-v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l-------------~~~a~naLLk~  142 (363)
T PRK14961         84 KGLCLDLIEIDAA------S-RTK-VEEMREILDNIYYSPSKSRFKVYLIDEVHML-------------SRHSFNALLKT  142 (363)
T ss_pred             cCCCCceEEeccc------c-cCC-HHHHHHHHHHHhcCcccCCceEEEEEChhhc-------------CHHHHHHHHHH
Confidence            0  0122332221      0 011 2235556555432    23469999999999             33456667777


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      ++.  +.+.+|.+|+...     .+.+++.+||..+.+.+|+.++..++|+..+..    .++.+++++++.++..+.+ 
T Consensus       143 lEe~~~~~~fIl~t~~~~-----~l~~tI~SRc~~~~~~~l~~~el~~~L~~~~~~----~g~~i~~~al~~ia~~s~G-  212 (363)
T PRK14961        143 LEEPPQHIKFILATTDVE-----KIPKTILSRCLQFKLKIISEEKIFNFLKYILIK----ESIDTDEYALKLIAYHAHG-  212 (363)
T ss_pred             HhcCCCCeEEEEEcCChH-----hhhHHHHhhceEEeCCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCC-
Confidence            774  5667777776544     477899999999999999999999998887764    3688999999999888654 


Q ss_pred             hcCCCCcchHHHHHHHHHh
Q 005179          497 ISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~~  515 (710)
                           .+++++.+++.++.
T Consensus       213 -----~~R~al~~l~~~~~  226 (363)
T PRK14961        213 -----SMRDALNLLEHAIN  226 (363)
T ss_pred             -----CHHHHHHHHHHHHH
Confidence                 35668888887764

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=2.3e-15  Score=169.88  Aligned_cols=199  Identities=19%  Similarity=0.159  Sum_probs=145.9

Q ss_pred             hHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc---------------
Q 005179          280 LTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF---------------  343 (710)
Q Consensus       280 l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~---------------  343 (710)
                      |.+++||.+|++++|++..++.|...+...+..| +||+||+|||||++|+.+|+.+.+...+..               
T Consensus         3 l~~kyRP~~f~eivGq~~i~~~L~~~i~~~r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~C~~i~~~   82 (584)
T PRK14952          3 LYRKYRPATFAEVVGQEHVTEPLSSALDAGRINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCESCVALAPN   82 (584)
T ss_pred             HHHHhCCCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHHHHHhhcc
Confidence            5678999999999999999999999998877777 589999999999999999999875432210               


Q ss_pred             -ccCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          344 -LLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       344 -l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                       .....++++|...      ..|  ...++.+.+.+.    .....|+||||+|.|             ....+|.|+..
T Consensus        83 ~~~~~dvieidaas------~~g--vd~iRel~~~~~~~P~~~~~KVvIIDEah~L-------------t~~A~NALLK~  141 (584)
T PRK14952         83 GPGSIDVVELDAAS------HGG--VDDTRELRDRAFYAPAQSRYRIFIVDEAHMV-------------TTAGFNALLKI  141 (584)
T ss_pred             cCCCceEEEecccc------ccC--HHHHHHHHHHHHhhhhcCCceEEEEECCCcC-------------CHHHHHHHHHH
Confidence             0112344443211      111  122344444442    234569999999999             45578888888


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      |++  +.+++|.+|+...     .+.+++++|++.+.|..++.++..+.|..++.+    .++.++++++..++..+.+-
T Consensus       142 LEEpp~~~~fIL~tte~~-----kll~TI~SRc~~~~F~~l~~~~i~~~L~~i~~~----egi~i~~~al~~Ia~~s~Gd  212 (584)
T PRK14952        142 VEEPPEHLIFIFATTEPE-----KVLPTIRSRTHHYPFRLLPPRTMRALIARICEQ----EGVVVDDAVYPLVIRAGGGS  212 (584)
T ss_pred             HhcCCCCeEEEEEeCChH-----hhHHHHHHhceEEEeeCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC
Confidence            986  6788888877664     667899999999999999999988888877763    37889999999988876643


Q ss_pred             hcCCCCcchHHHHHHHHH
Q 005179          497 ISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~  514 (710)
                            +.+++.+|+..+
T Consensus       213 ------lR~aln~Ldql~  224 (584)
T PRK14952        213 ------PRDTLSVLDQLL  224 (584)
T ss_pred             ------HHHHHHHHHHHH
Confidence                  234555555543

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=2.5e-15  Score=168.08  Aligned_cols=200  Identities=20%  Similarity=0.214  Sum_probs=145.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--c-----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--L-----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--l-----------  344 (710)
                      .|.+++||.+|+++||++..+..+...+......+ +||+||+|||||++|+.+|+.+.+......  .           
T Consensus         5 ~La~KyRP~~f~diiGq~~~v~~L~~~i~~~rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~sC~~i~~   84 (546)
T PRK14957          5 ALARKYRPQSFAEVAGQQHALNSLVHALETQKVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCENCVAINN   84 (546)
T ss_pred             hHHHHHCcCcHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhc
Confidence            58889999999999999999999999888766655 689999999999999999998865221100  0           


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++...      ..| . ..++.+++.+.    .....|+||||+|.+             ....++.|+..+
T Consensus        85 ~~~~dlieidaas------~~g-v-d~ir~ii~~~~~~p~~g~~kViIIDEa~~l-------------s~~a~naLLK~L  143 (546)
T PRK14957         85 NSFIDLIEIDAAS------RTG-V-EETKEILDNIQYMPSQGRYKVYLIDEVHML-------------SKQSFNALLKTL  143 (546)
T ss_pred             CCCCceEEeeccc------ccC-H-HHHHHHHHHHHhhhhcCCcEEEEEechhhc-------------cHHHHHHHHHHH
Confidence             011333333211      111 1 12444544443    234679999999999             456788888999


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+.+|++|+...     .+.+++++|+..+.+.+++.++....|+.++.+    .++.++++++..++..+.+- 
T Consensus       144 Eepp~~v~fIL~Ttd~~-----kil~tI~SRc~~~~f~~Ls~~eI~~~L~~il~~----egi~~e~~Al~~Ia~~s~Gd-  213 (546)
T PRK14957        144 EEPPEYVKFILATTDYH-----KIPVTILSRCIQLHLKHISQADIKDQLKIILAK----ENINSDEQSLEYIAYHAKGS-  213 (546)
T ss_pred             hcCCCCceEEEEECChh-----hhhhhHHHheeeEEeCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC-
Confidence            87  4677787776543     456789999999999999999988888877764    37899999999999887653 


Q ss_pred             cCCCCcchHHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~  514 (710)
                           .++++.+++.++
T Consensus       214 -----lR~alnlLek~i  225 (546)
T PRK14957        214 -----LRDALSLLDQAI  225 (546)
T ss_pred             -----HHHHHHHHHHHH
Confidence                 234566666544

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.65  E-value=1.5e-15  Score=182.43  Aligned_cols=177  Identities=16%  Similarity=0.150  Sum_probs=125.8

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc-------------c-------------
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA-------------K-------------  362 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~-------------~-------------  362 (710)
                      ..++++||+||||||||.||+++|...          +.+++.+.++.++...             .             
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~es----------~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~ 1697 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATNS----------YVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDL 1697 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHhc----------CCceEEEEHHHHhhccccccccccccccccccccccccccccc
Confidence            345789999999999999999999988          6777788777776321             0             


Q ss_pred             ---------------cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------
Q 005179          363 ---------------ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------  420 (710)
Q Consensus       363 ---------------~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------  420 (710)
                                     ..+.-..+++.+|+.|+...|+||||||||.+.....        .....+.|...|.       
T Consensus      1698 ~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~ds--------~~ltL~qLLneLDg~~~~~s 1769 (2281)
T CHL00206       1698 DTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVNES--------NYLSLGLLVNSLSRDCERCS 1769 (2281)
T ss_pred             chhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCCcc--------ceehHHHHHHHhccccccCC
Confidence                           0011123478899999999999999999999954311        1111233333332       


Q ss_pred             CCCeEEEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH--HHHHHHHHhhh
Q 005179          421 RGELQCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE--AINAAVHLSAR  495 (710)
Q Consensus       421 ~~~v~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~--~l~~l~~ls~~  495 (710)
                      ...++|||||+.++     .+||+|.|  ||+ .|.|+.|+..+|.+++..+..    ..++.+.++  .++.++..+.+
T Consensus      1770 ~~~VIVIAATNRPD-----~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~----tkg~~L~~~~vdl~~LA~~T~G 1840 (2281)
T CHL00206       1770 TRNILVIASTHIPQ-----KVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSY----TRGFHLEKKMFHTNGFGSITMG 1840 (2281)
T ss_pred             CCCEEEEEeCCCcc-----cCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHh----hcCCCCCcccccHHHHHHhCCC
Confidence            34689999999987     89999999  998 899999999999998876542    123333332  25677777777


Q ss_pred             hhcCCCCcchHHHHHHHHHhhh
Q 005179          496 YISDRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       496 ~i~~r~~p~~ai~ll~~a~~~~  517 (710)
                      |.+     .+...++.+|+..+
T Consensus      1841 fSG-----ADLanLvNEAaliA 1857 (2281)
T CHL00206       1841 SNA-----RDLVALTNEALSIS 1857 (2281)
T ss_pred             CCH-----HHHHHHHHHHHHHH
Confidence            755     56677888877443

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=2.2e-15  Score=170.54  Aligned_cols=201  Identities=19%  Similarity=0.204  Sum_probs=145.6

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCc-------cc------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPV-------FL------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~-------~l------  344 (710)
                      -|.+++||.+|+++||++..++.|...+...+..+. ||+||+|||||++++.+|+.+.+.....       ..      
T Consensus         5 vla~KyRP~~f~dviGQe~vv~~L~~~l~~~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pCg~C~~C   84 (618)
T PRK14951          5 VLARKYRPRSFSEMVGQEHVVQALTNALTQQRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPCGVCQAC   84 (618)
T ss_pred             HHHHHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCCCccHHH
Confidence            477899999999999999999999999988776665 8999999999999999999997532100       00      


Q ss_pred             ------cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHh
Q 005179          345 ------LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNL  414 (710)
Q Consensus       345 ------~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~  414 (710)
                            ....++++|..      ...+  .+.++.+++.+..    .+..|+||||+|.|             +.+.+|.
T Consensus        85 ~~i~~g~h~D~~eldaa------s~~~--Vd~iReli~~~~~~p~~g~~KV~IIDEvh~L-------------s~~a~Na  143 (618)
T PRK14951         85 RDIDSGRFVDYTELDAA------SNRG--VDEVQQLLEQAVYKPVQGRFKVFMIDEVHML-------------TNTAFNA  143 (618)
T ss_pred             HHHHcCCCCceeecCcc------cccC--HHHHHHHHHHHHhCcccCCceEEEEEChhhC-------------CHHHHHH
Confidence                  01123333321      1111  2235555555432    23469999999999             4456788


Q ss_pred             hcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          415 LKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       415 L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      |+..+++  +.+.+|.+|+...     .+.+.+++||..+.|.+++.++....|+.++.    ..++.++++++..++..
T Consensus       144 LLKtLEEPP~~~~fIL~Ttd~~-----kil~TIlSRc~~~~f~~Ls~eei~~~L~~i~~----~egi~ie~~AL~~La~~  214 (618)
T PRK14951        144 MLKTLEEPPEYLKFVLATTDPQ-----KVPVTVLSRCLQFNLRPMAPETVLEHLTQVLA----AENVPAEPQALRLLARA  214 (618)
T ss_pred             HHHhcccCCCCeEEEEEECCch-----hhhHHHHHhceeeecCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHH
Confidence            8888886  5677787776654     45678999999999999999998888887766    34889999999999988


Q ss_pred             hhhhhcCCCCcchHHHHHHHHHh
Q 005179          493 SARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       493 s~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      +.+-      ..+++.+++.++.
T Consensus       215 s~Gs------lR~al~lLdq~ia  231 (618)
T PRK14951        215 ARGS------MRDALSLTDQAIA  231 (618)
T ss_pred             cCCC------HHHHHHHHHHHHH
Confidence            7653      3456666665543

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.65  E-value=2.4e-15  Score=175.87  Aligned_cols=200  Identities=19%  Similarity=0.153  Sum_probs=147.1

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.+++|+.+|++|||++..++.|...+...+..| +||+||+|||||++++.|++.+.+.+.+...             
T Consensus         4 ~l~~KyRP~~f~eiiGqe~v~~~L~~~i~~~ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~sC~~~~~   83 (824)
T PRK07764          4 ALYRRYRPATFAEVIGQEHVTEPLSTALDSGRINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECDSCVALAP   83 (824)
T ss_pred             hHHHHhCCCCHHHhcCcHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccHHHHHHHc
Confidence            46789999999999999999999999998877777 6899999999999999999999764322110             


Q ss_pred             ---cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcc
Q 005179          345 ---LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP  417 (710)
Q Consensus       345 ---~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~  417 (710)
                         ....++.+|...      ..+  ...++.+.+.+.    .....|+||||+|.|             ..+.+|.|+.
T Consensus        84 g~~~~~dv~eidaas------~~~--Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~l-------------t~~a~NaLLK  142 (824)
T PRK07764         84 GGPGSLDVTEIDAAS------HGG--VDDARELRERAFFAPAESRYKIFIIDEAHMV-------------TPQGFNALLK  142 (824)
T ss_pred             CCCCCCcEEEecccc------cCC--HHHHHHHHHHHHhchhcCCceEEEEechhhc-------------CHHHHHHHHH
Confidence               112334443211      111  122334433332    234569999999999             4567889999


Q ss_pred             cccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          418 SLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       418 ~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      +|++  ..+++|++|+..+     .+.+.|++|++.+.|..++.++...+|+.++.    ..++.++++++..++.++.+
T Consensus       143 ~LEEpP~~~~fIl~tt~~~-----kLl~TIrSRc~~v~F~~l~~~~l~~~L~~il~----~EGv~id~eal~lLa~~sgG  213 (824)
T PRK07764        143 IVEEPPEHLKFIFATTEPD-----KVIGTIRSRTHHYPFRLVPPEVMRGYLERICA----QEGVPVEPGVLPLVIRAGGG  213 (824)
T ss_pred             HHhCCCCCeEEEEEeCChh-----hhhHHHHhheeEEEeeCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCC
Confidence            9986  6778888776654     46688999999999999999998888887766    34789999999998888765


Q ss_pred             hhcCCCCcchHHHHHHHHH
Q 005179          496 YISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       496 ~i~~r~~p~~ai~ll~~a~  514 (710)
                      .+      ..++.+|+..+
T Consensus       214 dl------R~Al~eLEKLi  226 (824)
T PRK07764        214 SV------RDSLSVLDQLL  226 (824)
T ss_pred             CH------HHHHHHHHHHH
Confidence            32      45666666655

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

Probab=99.63  E-value=1.1e-15  Score=149.13  Aligned_cols=187  Identities=19%  Similarity=0.274  Sum_probs=134.4

Q ss_pred             CCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      ...++-|.+.+|+.|++.+             ..+.+.++|+|||||||||.+|++.|...          +..+..+-.
T Consensus       169 ~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT----------~aTFLKLAg  238 (424)
T KOG0652|consen  169 QYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQT----------NATFLKLAG  238 (424)
T ss_pred             cccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhc----------cchHHHhcc
Confidence            4567889999999998864             22456789999999999999999988765          333333333


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQCI  427 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~vI  427 (710)
                      ..++  ..+.|+-...++..|..++...|.|+||||+|.+-..+..  +...+..+++..++.+|       .+.++.+|
T Consensus       239 PQLV--QMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfD--Sek~GDREVQRTMLELLNQLDGFss~~~vKvi  314 (424)
T KOG0652|consen  239 PQLV--QMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFD--SEKAGDREVQRTMLELLNQLDGFSSDDRVKVI  314 (424)
T ss_pred             hHHH--hhhhcchHHHHHHHHHHhhccCCeEEEEechhhhcccccc--ccccccHHHHHHHHHHHHhhcCCCCccceEEE
Confidence            3333  3356666777899999999899999999999998433221  12344556655554443       34679999


Q ss_pred             EccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          428 ASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      ++||..+     -+||+|.|  |++ .|+|+.|+.+.|..|++-..++.....+++     .+.+++.+..|-+
T Consensus       315 AATNRvD-----iLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvN-----feELaRsTddFNG  378 (424)
T KOG0652|consen  315 AATNRVD-----ILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVN-----FEELARSTDDFNG  378 (424)
T ss_pred             eeccccc-----ccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCC-----HHHHhhcccccCc
Confidence            9999976     68999998  887 899999999999999998777553333333     4456666555543

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=4.9e-15  Score=164.82  Aligned_cols=203  Identities=20%  Similarity=0.224  Sum_probs=149.2

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCC-CCCcEEEcCCCChHHHHHHHHHHHHHhcCCC----c----c-----
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRT-KNNPILLGESGVGKTAIAEGLAIRIVQAEVP----V----F-----  343 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~-~~nvLL~GppG~GKT~la~~la~~l~~~~~p----~----~-----  343 (710)
                      ..|.+++||.+|++++|++..++.|...+...+ ..++||+||+|||||++|+.+|+.+.+....    .    .     
T Consensus         9 ~~la~kyRP~~f~dliGq~~vv~~L~~ai~~~ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C~~C~~C   88 (507)
T PRK06645          9 IPFARKYRPSNFAELQGQEVLVKVLSYTILNDRLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTCEQCTNC   88 (507)
T ss_pred             cchhhhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCCCCChHH
Confidence            467889999999999999999999888666544 4578999999999999999999998653210    0    0     


Q ss_pred             -----ccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHh
Q 005179          344 -----LLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNL  414 (710)
Q Consensus       344 -----l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~  414 (710)
                           .....++++|..      ...  -...++.+++.+..    ....|+||||+|.+             .....+.
T Consensus        89 ~~i~~~~h~Dv~eidaa------s~~--~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~L-------------s~~a~na  147 (507)
T PRK06645         89 ISFNNHNHPDIIEIDAA------SKT--SVDDIRRIIESAEYKPLQGKHKIFIIDEVHML-------------SKGAFNA  147 (507)
T ss_pred             HHHhcCCCCcEEEeecc------CCC--CHHHHHHHHHHHHhccccCCcEEEEEEChhhc-------------CHHHHHH
Confidence                 001233443321      111  12345666666543    34569999999999             3455777


Q ss_pred             hcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          415 LKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       415 L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      |...+++  ..+++|.+|+...     .+.+++.+|+..+.+.+++.++...+++.++.+    .++.+++++++.++..
T Consensus       148 LLk~LEepp~~~vfI~aTte~~-----kI~~tI~SRc~~~ef~~ls~~el~~~L~~i~~~----egi~ie~eAL~~Ia~~  218 (507)
T PRK06645        148 LLKTLEEPPPHIIFIFATTEVQ-----KIPATIISRCQRYDLRRLSFEEIFKLLEYITKQ----ENLKTDIEALRIIAYK  218 (507)
T ss_pred             HHHHHhhcCCCEEEEEEeCChH-----HhhHHHHhcceEEEccCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHH
Confidence            7777775  5677777776654     567899999999999999999999999988773    4789999999999887


Q ss_pred             hhhhhcCCCCcchHHHHHHHHHhh
Q 005179          493 SARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       493 s~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                      +.+.      +.+++.+++.++..
T Consensus       219 s~Gs------lR~al~~Ldkai~~  236 (507)
T PRK06645        219 SEGS------ARDAVSILDQAASM  236 (507)
T ss_pred             cCCC------HHHHHHHHHHHHHh
Confidence            6653      45688888887654

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.63  E-value=3.2e-15  Score=169.06  Aligned_cols=213  Identities=23%  Similarity=0.271  Sum_probs=145.6

Q ss_pred             hhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          277 CVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       277 ~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      ..+|.+++|+..|++++|++..++.+...+......++||+||||||||++|+++++.........+..+..++.+|+..
T Consensus        52 ~~~~~~~~rp~~f~~iiGqs~~i~~l~~al~~~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~  131 (531)
T TIGR02902        52 TEPLSEKTRPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATT  131 (531)
T ss_pred             cchHHHhhCcCCHHHeeCcHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEcccc
Confidence            45899999999999999999999999988877778899999999999999999998765332111111235667777543


Q ss_pred             hhh----------ccc----cCc--cHH--HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          357 LMA----------GAK----ERG--ELE--ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       357 l~~----------g~~----~~g--~~e--~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                      ...          +..    +.+  .+.  .....-...+....+.+|||||++.|             ..+.++.|...
T Consensus       132 ~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L-------------~~~~q~~LL~~  198 (531)
T TIGR02902       132 ARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGEL-------------HPVQMNKLLKV  198 (531)
T ss_pred             ccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhC-------------CHHHHHHHHHH
Confidence            110          000    000  000  00000001122345679999999999             44556665544


Q ss_pred             ccCC------------------------------CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHH
Q 005179          419 LGRG------------------------------ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLG  468 (710)
Q Consensus       419 l~~~------------------------------~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~  468 (710)
                      |+++                              ++++|++|+...    ..+++++++||..|.+++++.+++..|++.
T Consensus       199 Le~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p----~~L~paLrsR~~~I~f~pL~~eei~~Il~~  274 (531)
T TIGR02902       199 LEDRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNP----EEIPPALRSRCVEIFFRPLLDEEIKEIAKN  274 (531)
T ss_pred             HHhCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCc----ccCChHHhhhhheeeCCCCCHHHHHHHHHH
Confidence            4321                              356777766543    268899999999999999999999999998


Q ss_pred             HHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhh
Q 005179          469 LREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       469 l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~  517 (710)
                      .+++    .++.+++++++.+..++..       ...++.+++.|+..+
T Consensus       275 ~a~k----~~i~is~~al~~I~~y~~n-------~Rel~nll~~Aa~~A  312 (531)
T TIGR02902       275 AAEK----IGINLEKHALELIVKYASN-------GREAVNIVQLAAGIA  312 (531)
T ss_pred             HHHH----cCCCcCHHHHHHHHHhhhh-------HHHHHHHHHHHHHHH
Confidence            7774    4688999999877665431       256778888777543

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.

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

Probab=99.63  E-value=2.4e-15  Score=166.99  Aligned_cols=201  Identities=22%  Similarity=0.297  Sum_probs=143.2

Q ss_pred             cCCCCcccCHHHHHHHHHH---HHc---------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQI---LCR---------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~---L~~---------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|.++-|.++..+.+.++   |..         +-+..++|+||||||||.||+++|-+.          +.+++++..
T Consensus       147 v~F~DVAG~dEakeel~EiVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA----------~VPFf~iSG  216 (596)
T COG0465         147 VTFADVAGVDEAKEELSELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEA----------GVPFFSISG  216 (596)
T ss_pred             cChhhhcCcHHHHHHHHHHHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhccc----------CCCceeccc
Confidence            3678899998877666654   332         345789999999999999999999887          666677777


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH---HHhhccccc----CCCeEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI---SNLLKPSLG----RGELQCI  427 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~---~~~L~~~l~----~~~v~vI  427 (710)
                      ++++  .-+.|--..+++++|.++++..|+|+||||+|.+-..+..+.+  ++..+.   .|.|+.-|.    +..+++|
T Consensus       217 S~FV--emfVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~G--ggnderEQTLNQlLvEmDGF~~~~gvivi  292 (596)
T COG0465         217 SDFV--EMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLG--GGNDEREQTLNQLLVEMDGFGGNEGVIVI  292 (596)
T ss_pred             hhhh--hhhcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCC--CCchHHHHHHHHHHhhhccCCCCCceEEE
Confidence            7766  3344555677999999999999999999999999665543322  223333   333333332    3468999


Q ss_pred             EccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCCc
Q 005179          428 ASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYLP  503 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~p  503 (710)
                      ++||.++     -+|++|.|  ||+ .|.++.|+...|.+|++-..+..      .+++++ +..+++.+.+|..     
T Consensus       293 aaTNRpd-----VlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~------~l~~~Vdl~~iAr~tpGfsG-----  356 (596)
T COG0465         293 AATNRPD-----VLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNK------PLAEDVDLKKIARGTPGFSG-----  356 (596)
T ss_pred             ecCCCcc-----cchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcC------CCCCcCCHHHHhhhCCCccc-----
Confidence            9999987     78999999  997 89999999999999999655532      232221 3336666666654     


Q ss_pred             chHHHHHHHHHhhh
Q 005179          504 DKAIDLVDEAGSRA  517 (710)
Q Consensus       504 ~~ai~ll~~a~~~~  517 (710)
                      .+...++.+|+-.+
T Consensus       357 AdL~nl~NEAal~a  370 (596)
T COG0465         357 ADLANLLNEAALLA  370 (596)
T ss_pred             chHhhhHHHHHHHH
Confidence            45566776665443

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=4.3e-15  Score=167.60  Aligned_cols=202  Identities=18%  Similarity=0.212  Sum_probs=148.3

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCccc------------c
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEVPVFL------------L  345 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~~l------------~  345 (710)
                      .|.+++||.+|+++||++..++.|...+..++.. .+||+||+|||||++|+.+++.+.+...+...            .
T Consensus         5 vLarKYRP~tFddIIGQe~vv~~L~~ai~~~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~sCr~i~~   84 (709)
T PRK08691          5 VLARKWRPKTFADLVGQEHVVKALQNALDEGRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQSCTQIDA   84 (709)
T ss_pred             hHHHHhCCCCHHHHcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHHHHHHhc
Confidence            4778999999999999999999999988876544 57999999999999999999998654321100            0


Q ss_pred             --CceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          346 --SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       346 --~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                        ...++.++..      ...+  ...++.+++.+..    ....|+||||+|.|             ....++.|+..|
T Consensus        85 g~~~DvlEidaA------s~~g--Vd~IRelle~a~~~P~~gk~KVIIIDEad~L-------------s~~A~NALLKtL  143 (709)
T PRK08691         85 GRYVDLLEIDAA------SNTG--IDNIREVLENAQYAPTAGKYKVYIIDEVHML-------------SKSAFNAMLKTL  143 (709)
T ss_pred             cCccceEEEecc------ccCC--HHHHHHHHHHHHhhhhhCCcEEEEEECcccc-------------CHHHHHHHHHHH
Confidence              0122333321      1111  2335566654432    34569999999998             345667777778


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+.+|.+|+...     .+.+.+++||..+.|.+++.++....|+.++..    .++.++++++..+++.+.+- 
T Consensus       144 EEPp~~v~fILaTtd~~-----kL~~TIrSRC~~f~f~~Ls~eeI~~~L~~Il~k----Egi~id~eAL~~Ia~~A~Gs-  213 (709)
T PRK08691        144 EEPPEHVKFILATTDPH-----KVPVTVLSRCLQFVLRNMTAQQVADHLAHVLDS----EKIAYEPPALQLLGRAAAGS-  213 (709)
T ss_pred             HhCCCCcEEEEEeCCcc-----ccchHHHHHHhhhhcCCCCHHHHHHHHHHHHHH----cCCCcCHHHHHHHHHHhCCC-
Confidence            74  5677888777654     567889999999999999999999988887773    47899999999999887653 


Q ss_pred             cCCCCcchHHHHHHHHHhh
Q 005179          498 SDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~~  516 (710)
                           .++++.+|+.++..
T Consensus       214 -----lRdAlnLLDqaia~  227 (709)
T PRK08691        214 -----MRDALSLLDQAIAL  227 (709)
T ss_pred             -----HHHHHHHHHHHHHh
Confidence                 45688888887653

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.62  E-value=6.8e-15  Score=165.41  Aligned_cols=199  Identities=20%  Similarity=0.228  Sum_probs=143.2

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCC-CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc--c-----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRT-KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVF--L-----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~-~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~--l-----------  344 (710)
                      .|.+++||.+|+++||++..+..|...+...+ ..++||+||+|||||++|+.+|+.+.+...+..  .           
T Consensus         5 ~la~KyRP~sf~dIiGQe~v~~~L~~ai~~~ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~sC~~i~~   84 (624)
T PRK14959          5 SLTARYRPQTFAEVAGQETVKAILSRAAQENRVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQCRKVTQ   84 (624)
T ss_pred             hHHHHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHHHHHHhc
Confidence            67899999999999999999888888887654 566789999999999999999999865321110  0           


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++..      ...+  ...++.+.+.+.    .....|+||||+|.|             ..+.++.|+..|
T Consensus        85 g~hpDv~eId~a------~~~~--Id~iR~L~~~~~~~p~~g~~kVIIIDEad~L-------------t~~a~naLLk~L  143 (624)
T PRK14959         85 GMHVDVVEIDGA------SNRG--IDDAKRLKEAIGYAPMEGRYKVFIIDEAHML-------------TREAFNALLKTL  143 (624)
T ss_pred             CCCCceEEEecc------cccC--HHHHHHHHHHHHhhhhcCCceEEEEEChHhC-------------CHHHHHHHHHHh
Confidence             01123444321      1111  122333333332    234579999999999             445678888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+++|++|+...     .+.+.+.+||+.|.|.+++.++...+|+.++.    ..++.+++++++.++.++.+. 
T Consensus       144 EEP~~~~ifILaTt~~~-----kll~TI~SRcq~i~F~pLs~~eL~~~L~~il~----~egi~id~eal~lIA~~s~Gd-  213 (624)
T PRK14959        144 EEPPARVTFVLATTEPH-----KFPVTIVSRCQHFTFTRLSEAGLEAHLTKVLG----REGVDYDPAAVRLIARRAAGS-  213 (624)
T ss_pred             hccCCCEEEEEecCChh-----hhhHHHHhhhhccccCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC-
Confidence            75  5777888777654     45578999999999999999999888887665    347889999999999887643 


Q ss_pred             cCCCCcchHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEA  513 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a  513 (710)
                           .++++.+|+.+
T Consensus       214 -----lR~Al~lLeql  224 (624)
T PRK14959        214 -----VRDSMSLLGQV  224 (624)
T ss_pred             -----HHHHHHHHHHH
Confidence                 34567777654

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.60  E-value=1.9e-13  Score=163.33  Aligned_cols=181  Identities=20%  Similarity=0.292  Sum_probs=121.9

Q ss_pred             CCcccCHHHHHHHHHHHHcCC---------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-
Q 005179          290 DPVIGRETEIQRIIQILCRRT---------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~---------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-  359 (710)
                      ..++|++..++.+...+.+..         ...++|+||+|||||++|++|++.+...       +..++.+|++.+.. 
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl~~~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~-------~~~~i~~d~s~~~~~  637 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELAKALAEFLFDD-------EDAMVRIDMSEYMEK  637 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccCCCCCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCC-------CCcEEEEechhhccc
Confidence            359999999999998876521         2347899999999999999999988433       34566666655431 


Q ss_pred             -------cc--ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------
Q 005179          360 -------GA--KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------  422 (710)
Q Consensus       360 -------g~--~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------  422 (710)
                             |.  .+.|--+  -..+...+...+..||+||||+.+             ..++++.|.++++.|        
T Consensus       638 ~~~~~l~g~~~g~~g~~~--~g~l~~~v~~~p~~vlllDeieka-------------~~~v~~~Ll~~l~~g~l~d~~g~  702 (852)
T TIGR03346       638 HSVARLIGAPPGYVGYEE--GGQLTEAVRRKPYSVVLFDEVEKA-------------HPDVFNVLLQVLDDGRLTDGQGR  702 (852)
T ss_pred             chHHHhcCCCCCccCccc--ccHHHHHHHcCCCcEEEEeccccC-------------CHHHHHHHHHHHhcCceecCCCe
Confidence                   11  1111100  112333344556679999999988             667888888887654        


Q ss_pred             -----CeEEEEccChHHH--Hh------------------hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh-
Q 005179          423 -----ELQCIASTTQDEH--RT------------------QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA-  475 (710)
Q Consensus       423 -----~v~vI~att~~~~--~~------------------~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~-  475 (710)
                           +.++|.|||...-  ..                  .-...|.|..|++ .|.+.+++.++...|+......... 
T Consensus       703 ~vd~rn~iiI~TSn~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~Rid~IivF~PL~~e~l~~I~~l~L~~l~~~  782 (852)
T TIGR03346       703 TVDFRNTVIIMTSNLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKR  782 (852)
T ss_pred             EEecCCcEEEEeCCcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhcCcCeEEecCCcCHHHHHHHHHHHHHHHHHH
Confidence                 3447888776210  00                  0113478888996 7888999999999999876654332 


Q ss_pred             --hc--CCCCCHHHHHHHHHH
Q 005179          476 --HH--NCKFTLEAINAAVHL  492 (710)
Q Consensus       476 --~~--~~~i~~~~l~~l~~l  492 (710)
                        ..  .+.+++++++.++..
T Consensus       783 l~~~~~~l~i~~~a~~~L~~~  803 (852)
T TIGR03346       783 LAERKITLELSDAALDFLAEA  803 (852)
T ss_pred             HHHCCCeecCCHHHHHHHHHh
Confidence              22  367899999888765

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.

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

Probab=99.60  E-value=5.7e-16  Score=153.31  Aligned_cols=166  Identities=26%  Similarity=0.333  Sum_probs=128.7

Q ss_pred             cCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      .++.++-|.+.++..+.+.+.             ...+..++|||+||||||.||+++|+..          ...++.+-
T Consensus       182 Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqT----------SATFlRvv  251 (440)
T KOG0726|consen  182 ETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQT----------SATFLRVV  251 (440)
T ss_pred             hhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhccc----------chhhhhhh
Confidence            345677888888888877542             2456789999999999999999999865          34444555


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~v  426 (710)
                      .+.++  .+|.|+-...++++|+-+..+.|+|+||||||.+-..+.  .+++++..+++..++.+|       .++++.|
T Consensus       252 GseLi--QkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRy--ds~SggerEiQrtmLELLNQldGFdsrgDvKv  327 (440)
T KOG0726|consen  252 GSELI--QKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRY--DSNSGGEREIQRTMLELLNQLDGFDSRGDVKV  327 (440)
T ss_pred             hHHHH--HHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccc--cCCCccHHHHHHHHHHHHHhccCccccCCeEE
Confidence            56666  567777778899999999999999999999999843322  123456667766655544       3689999


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHH
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      |.+||.-+     .+||+|.|  |++ .|.|+.|+...+..|+.-...
T Consensus       328 imATnrie-----~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs  370 (440)
T KOG0726|consen  328 IMATNRIE-----TLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTS  370 (440)
T ss_pred             EEeccccc-----ccCHhhcCCCccccccccCCCchhhhceeEEEeec
Confidence            99999977     89999999  887 899999999999999875444

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.60  E-value=2.2e-14  Score=154.68  Aligned_cols=190  Identities=15%  Similarity=0.258  Sum_probs=132.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      -|.++++|..|++++|++..++++...+..+...+++|+||||||||++|+++++.+....     .+..+..+++..+.
T Consensus         4 ~w~~ky~P~~~~~~~g~~~~~~~L~~~~~~~~~~~lll~Gp~GtGKT~la~~~~~~l~~~~-----~~~~~~~i~~~~~~   78 (337)
T PRK12402          4 LWTEKYRPALLEDILGQDEVVERLSRAVDSPNLPHLLVQGPPGSGKTAAVRALARELYGDP-----WENNFTEFNVADFF   78 (337)
T ss_pred             chHHhhCCCcHHHhcCCHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHhcCcc-----cccceEEechhhhh
Confidence            4788999999999999999999999988876666899999999999999999999885321     12234555554432


Q ss_pred             hccc--------c---Cc-------cHHHHHHHHHHHHHh-----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhh
Q 005179          359 AGAK--------E---RG-------ELEARVTTLISEIQK-----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLL  415 (710)
Q Consensus       359 ~g~~--------~---~g-------~~e~~l~~~~~~~~~-----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L  415 (710)
                      ....        .   .+       .....++.++.....     ....+|||||+|.+             ..+..+.|
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l-------------~~~~~~~L  145 (337)
T PRK12402         79 DQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEAL-------------REDAQQAL  145 (337)
T ss_pred             hcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccC-------------CHHHHHHH
Confidence            1100        0   00       012233444433322     23458999999988             22334555


Q ss_pred             cccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHh
Q 005179          416 KPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       416 ~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls  493 (710)
                      ..+++.  ....+|.+++...     .+.+.|.+|+..+.+.+|+.++...+++..+.    ..++.+++++++.++..+
T Consensus       146 ~~~le~~~~~~~~Il~~~~~~-----~~~~~L~sr~~~v~~~~~~~~~~~~~l~~~~~----~~~~~~~~~al~~l~~~~  216 (337)
T PRK12402        146 RRIMEQYSRTCRFIIATRQPS-----KLIPPIRSRCLPLFFRAPTDDELVDVLESIAE----AEGVDYDDDGLELIAYYA  216 (337)
T ss_pred             HHHHHhccCCCeEEEEeCChh-----hCchhhcCCceEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHc
Confidence            555542  3345555555433     45578999999999999999998888887766    447889999999999876


Q ss_pred             hh
Q 005179          494 AR  495 (710)
Q Consensus       494 ~~  495 (710)
                      .+
T Consensus       217 ~g  218 (337)
T PRK12402        217 GG  218 (337)
T ss_pred             CC
Confidence            43

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=1.7e-14  Score=161.32  Aligned_cols=187  Identities=21%  Similarity=0.226  Sum_probs=137.4

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCc--ccc----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEVPV--FLL----------  345 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~--~l~----------  345 (710)
                      .|.+++||..|++++|++..++.+...+...... .+||+||+|+|||++|+.+|+.+.+.....  ...          
T Consensus         5 ~~~~KyRP~~F~dIIGQe~iv~~L~~aI~~~rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~sCr~i~~   84 (605)
T PRK05896          5 TFYRKYRPHNFKQIIGQELIKKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSVCESINT   84 (605)
T ss_pred             hHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHHc
Confidence            6889999999999999999999999988765544 478999999999999999999986533111  000          


Q ss_pred             --CceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          346 --SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       346 --~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                        ...+++++...      ..|  ...++.+++.+..    .+..|++|||+|.|             ....++.|+..|
T Consensus        85 ~~h~DiieIdaas------~ig--Vd~IReIi~~~~~~P~~~~~KVIIIDEad~L-------------t~~A~NaLLKtL  143 (605)
T PRK05896         85 NQSVDIVELDAAS------NNG--VDEIRNIIDNINYLPTTFKYKVYIIDEAHML-------------STSAWNALLKTL  143 (605)
T ss_pred             CCCCceEEecccc------ccC--HHHHHHHHHHHHhchhhCCcEEEEEechHhC-------------CHHHHHHHHHHH
Confidence              11233333211      111  1224555554432    23468999999999             334677888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      ++  +.+++|.+|+...     .+.+++++||+.+.+.+|+.++....|+..+.+    .++.+++++++.++.++.+
T Consensus       144 EEPp~~tvfIL~Tt~~~-----KLl~TI~SRcq~ieF~~Ls~~eL~~~L~~il~k----egi~Is~eal~~La~lS~G  212 (605)
T PRK05896        144 EEPPKHVVFIFATTEFQ-----KIPLTIISRCQRYNFKKLNNSELQELLKSIAKK----EKIKIEDNAIDKIADLADG  212 (605)
T ss_pred             HhCCCcEEEEEECCChH-----hhhHHHHhhhhhcccCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCC
Confidence            85  4577777776543     567899999999999999999988888877763    4788999999999888765

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=9.3e-15  Score=164.82  Aligned_cols=201  Identities=19%  Similarity=0.209  Sum_probs=146.5

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--c-----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--L-----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--l-----------  344 (710)
                      .|.+++||.+|++++|++..++.+...+...+..+ +||+||+|+|||++|+.+|+.+.+......  .           
T Consensus         5 ~l~~k~rP~~f~divGq~~v~~~L~~~i~~~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~C~~i~~   84 (527)
T PRK14969          5 VLARKWRPKSFSELVGQEHVVRALTNALEQQRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSACLEIDS   84 (527)
T ss_pred             HHHHHhCCCcHHHhcCcHHHHHHHHHHHHcCCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhc
Confidence            47789999999999999999999999888766666 489999999999999999999865321110  0           


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++..      ...  ....++.+++.+..    .+..|+||||+|.|             ....+|.|+..+
T Consensus        85 ~~~~d~~ei~~~------~~~--~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~l-------------s~~a~naLLK~L  143 (527)
T PRK14969         85 GRFVDLIEVDAA------SNT--QVDAMRELLDNAQYAPTRGRFKVYIIDEVHML-------------SKSAFNAMLKTL  143 (527)
T ss_pred             CCCCceeEeecc------ccC--CHHHHHHHHHHHhhCcccCCceEEEEcCcccC-------------CHHHHHHHHHHH
Confidence             01123333321      111  12335666665543    23569999999999             445678888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  +.+.+|.+|+...     .+.+.+++||..+.|.+++.++....|..++.    ..++.++++++..++..+.+. 
T Consensus       144 Eepp~~~~fIL~t~d~~-----kil~tI~SRc~~~~f~~l~~~~i~~~L~~il~----~egi~~~~~al~~la~~s~Gs-  213 (527)
T PRK14969        144 EEPPEHVKFILATTDPQ-----KIPVTVLSRCLQFNLKQMPPPLIVSHLQHILE----QENIPFDATALQLLARAAAGS-  213 (527)
T ss_pred             hCCCCCEEEEEEeCChh-----hCchhHHHHHHHHhcCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC-
Confidence            86  5678888877654     45567999999999999999998888877766    347889999999998887643 


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                           +++++.+++.++.
T Consensus       214 -----lr~al~lldqai~  226 (527)
T PRK14969        214 -----MRDALSLLDQAIA  226 (527)
T ss_pred             -----HHHHHHHHHHHHH
Confidence                 4567777776654

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.59  E-value=2.2e-14  Score=146.07  Aligned_cols=177  Identities=13%  Similarity=0.143  Sum_probs=121.5

Q ss_pred             CCCcc-c-CHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCcc
Q 005179          289 IDPVI-G-RETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGE  366 (710)
Q Consensus       289 l~~li-G-r~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~  366 (710)
                      |++++ | ....+..+.++......++++|+||+|||||||++++++.+...       +..+.++.+......      
T Consensus        21 fd~f~~~~n~~a~~~l~~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~-------~~~v~y~~~~~~~~~------   87 (235)
T PRK08084         21 FASFYPGDNDSLLAALQNALRQEHSGYIYLWSREGAGRSHLLHAACAELSQR-------GRAVGYVPLDKRAWF------   87 (235)
T ss_pred             ccccccCccHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEEHHHHhhh------
Confidence            44444 4 34455555555555566789999999999999999999987532       456666665443211      


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHH
Q 005179          367 LEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       367 ~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                          ..++++.+...  .+|+|||+|.+.+..       .....+.+++...+++++..+|.+++.+. ..+-...+.|+
T Consensus        88 ----~~~~~~~~~~~--dlliiDdi~~~~~~~-------~~~~~lf~l~n~~~e~g~~~li~ts~~~p-~~l~~~~~~L~  153 (235)
T PRK08084         88 ----VPEVLEGMEQL--SLVCIDNIECIAGDE-------LWEMAIFDLYNRILESGRTRLLITGDRPP-RQLNLGLPDLA  153 (235)
T ss_pred             ----hHHHHHHhhhC--CEEEEeChhhhcCCH-------HHHHHHHHHHHHHHHcCCCeEEEeCCCCh-HHcCcccHHHH
Confidence                12223333322  489999999984321       22445677777778777766666655433 22223579999


Q ss_pred             ccc---cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          447 RRF---QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       447 ~Rf---~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +||   ..+.+.+|+.+++.++++..+.    .+++.++++++++++..+.+-
T Consensus       154 SRl~~g~~~~l~~~~~~~~~~~l~~~a~----~~~~~l~~~v~~~L~~~~~~d  202 (235)
T PRK08084        154 SRLDWGQIYKLQPLSDEEKLQALQLRAR----LRGFELPEDVGRFLLKRLDRE  202 (235)
T ss_pred             HHHhCCceeeecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhhcCC
Confidence            999   4899999999999999886554    347999999999999887764

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.59  E-value=1.6e-14  Score=161.53  Aligned_cols=199  Identities=21%  Similarity=0.241  Sum_probs=142.9

Q ss_pred             hHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcC-CCcc------------cc
Q 005179          280 LTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAE-VPVF------------LL  345 (710)
Q Consensus       280 l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~-~p~~------------l~  345 (710)
                      |.+++||.+|++++|+++.++.|...+......+. ||+||||||||++|+.+|+.+.+.+ .+..            ..
T Consensus         4 l~~KyRP~~~~dvvGq~~v~~~L~~~i~~~~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc~~i~~~~   83 (504)
T PRK14963          4 LYQRARPITFDEVVGQEHVKEVLLAALRQGRLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESCLAVRRGA   83 (504)
T ss_pred             HHHhhCCCCHHHhcChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhhHHHhcCC
Confidence            55789999999999999999999998888776666 9999999999999999999986522 1100            11


Q ss_pred             CceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC
Q 005179          346 SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR  421 (710)
Q Consensus       346 ~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~  421 (710)
                      ...++.++...      ..+  ...++.+.+.+..    ....|+||||+|.+             ..+.++.|...+++
T Consensus        84 h~dv~el~~~~------~~~--vd~iR~l~~~~~~~p~~~~~kVVIIDEad~l-------------s~~a~naLLk~LEe  142 (504)
T PRK14963         84 HPDVLEIDAAS------NNS--VEDVRDLREKVLLAPLRGGRKVYILDEAHMM-------------SKSAFNALLKTLEE  142 (504)
T ss_pred             CCceEEecccc------cCC--HHHHHHHHHHHhhccccCCCeEEEEECcccc-------------CHHHHHHHHHHHHh
Confidence            22344444321      111  1224444444332    34569999999988             34456677777775


Q ss_pred             --CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcC
Q 005179          422 --GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       422 --~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~  499 (710)
                        ..+++|.+++...     .+.+.+.+|+..+.|.+|+.++....|+.++.    ..++.+++++++.++..+.+.+  
T Consensus       143 p~~~t~~Il~t~~~~-----kl~~~I~SRc~~~~f~~ls~~el~~~L~~i~~----~egi~i~~~Al~~ia~~s~Gdl--  211 (504)
T PRK14963        143 PPEHVIFILATTEPE-----KMPPTILSRTQHFRFRRLTEEEIAGKLRRLLE----AEGREAEPEALQLVARLADGAM--  211 (504)
T ss_pred             CCCCEEEEEEcCChh-----hCChHHhcceEEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCCH--
Confidence              4567777766543     57789999999999999999998888888776    4478999999999998877542  


Q ss_pred             CCCcchHHHHHHHHH
Q 005179          500 RYLPDKAIDLVDEAG  514 (710)
Q Consensus       500 r~~p~~ai~ll~~a~  514 (710)
                          .+++.+|+.++
T Consensus       212 ----R~aln~Lekl~  222 (504)
T PRK14963        212 ----RDAESLLERLL  222 (504)
T ss_pred             ----HHHHHHHHHHH
Confidence                34556666544

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.59  E-value=2.1e-14  Score=159.80  Aligned_cols=202  Identities=22%  Similarity=0.242  Sum_probs=148.2

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCcc--------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVF--------------  343 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~--------------  343 (710)
                      .|.+++||.+|++++|++..+..+...+....-.+. ||+||+|+|||++|+.+++.+.+...+..              
T Consensus         3 ~l~~KyRP~~fdeiiGqe~v~~~L~~~I~~grl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~C~~~~~   82 (535)
T PRK08451          3 ALALKYRPKHFDELIGQESVSKTLSLALDNNRLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQCQSALE   82 (535)
T ss_pred             cHHHHHCCCCHHHccCcHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhh
Confidence            467899999999999999999999998887766665 89999999999999999999865432210              


Q ss_pred             ccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          344 LLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       344 l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                      ..+..++.++..      ..+|  ...++.++..+..    +...|++|||+|.|             ..+.++.|+..+
T Consensus        83 ~~h~dv~eldaa------s~~g--Id~IRelie~~~~~P~~~~~KVvIIDEad~L-------------t~~A~NALLK~L  141 (535)
T PRK08451         83 NRHIDIIEMDAA------SNRG--IDDIRELIEQTKYKPSMARFKIFIIDEVHML-------------TKEAFNALLKTL  141 (535)
T ss_pred             cCCCeEEEeccc------cccC--HHHHHHHHHHHhhCcccCCeEEEEEECcccC-------------CHHHHHHHHHHH
Confidence            012233433321      1111  1234555544321    23469999999999             556788888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      +.  ..+.+|.+|+...     .+.+++++|+..++|.+++.++....++.++..    .++.++++++..++..+.+- 
T Consensus       142 EEpp~~t~FIL~ttd~~-----kL~~tI~SRc~~~~F~~Ls~~ei~~~L~~Il~~----EGi~i~~~Al~~Ia~~s~Gd-  211 (535)
T PRK08451        142 EEPPSYVKFILATTDPL-----KLPATILSRTQHFRFKQIPQNSIISHLKTILEK----EGVSYEPEALEILARSGNGS-  211 (535)
T ss_pred             hhcCCceEEEEEECChh-----hCchHHHhhceeEEcCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCc-
Confidence            86  4567777776543     567899999999999999999988888877763    47899999999999887643 


Q ss_pred             cCCCCcchHHHHHHHHHhh
Q 005179          498 SDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~~  516 (710)
                           +++++.+++.++..
T Consensus       212 -----lR~alnlLdqai~~  225 (535)
T PRK08451        212 -----LRDTLTLLDQAIIY  225 (535)
T ss_pred             -----HHHHHHHHHHHHHh
Confidence                 45677788776654

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.59  E-value=1.4e-14  Score=154.74  Aligned_cols=184  Identities=16%  Similarity=0.211  Sum_probs=131.6

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEE-EcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPIL-LGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL-~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      .|.+++||.+|++++|+++....+...+......+++| +||||+|||++++++++.+          +..++.++... 
T Consensus        10 ~w~~kyrP~~~~~~~~~~~~~~~l~~~~~~~~~~~~lll~G~~G~GKT~la~~l~~~~----------~~~~~~i~~~~-   78 (316)
T PHA02544         10 MWEQKYRPSTIDECILPAADKETFKSIVKKGRIPNMLLHSPSPGTGKTTVAKALCNEV----------GAEVLFVNGSD-   78 (316)
T ss_pred             cceeccCCCcHHHhcCcHHHHHHHHHHHhcCCCCeEEEeeCcCCCCHHHHHHHHHHHh----------CccceEeccCc-
Confidence            57789999999999999999999999888766666666 8999999999999999877          34455555433 


Q ss_pred             hhccccCccHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHH
Q 005179          358 MAGAKERGELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDE  434 (710)
Q Consensus       358 ~~g~~~~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~  434 (710)
                        +.  .......+......... ..+.+|||||+|.+.            ..+..+.|+.+++.  +...+|.+++...
T Consensus        79 --~~--~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~------------~~~~~~~L~~~le~~~~~~~~Ilt~n~~~  142 (316)
T PHA02544         79 --CR--IDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLG------------LADAQRHLRSFMEAYSKNCSFIITANNKN  142 (316)
T ss_pred             --cc--HHHHHHHHHHHHHhhcccCCCeEEEEECccccc------------CHHHHHHHHHHHHhcCCCceEEEEcCChh
Confidence              11  11122223222222211 346799999999881            11244555655653  5667888877654


Q ss_pred             HHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHH---hhcCCCCCHHHHHHHHHHhh
Q 005179          435 HRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYE---AHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       435 ~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~---~~~~~~i~~~~l~~l~~ls~  494 (710)
                           .+.+++++||..+.++.|+.+++..+++.+..+..   ...++.++++++..++..+.
T Consensus       143 -----~l~~~l~sR~~~i~~~~p~~~~~~~il~~~~~~~~~~~~~~~~~i~~~al~~l~~~~~  200 (316)
T PHA02544        143 -----GIIEPLRSRCRVIDFGVPTKEEQIEMMKQMIVRCKGILEAEGVEVDMKVLAALVKKNF  200 (316)
T ss_pred             -----hchHHHHhhceEEEeCCCCHHHHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhcC
Confidence                 57799999999999999999999998887655543   24678999999888876543

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=2.9e-14  Score=161.89  Aligned_cols=201  Identities=19%  Similarity=0.200  Sum_probs=145.6

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.+++||.+|++++|+++.++.+...+......+ +||+||+|+|||++|+.+|+.+.+...+...             
T Consensus         5 al~~k~rP~~f~~viGq~~v~~~L~~~i~~~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~C~~i~~   84 (559)
T PRK05563          5 ALYRKWRPQTFEDVVGQEHITKTLKNAIKQGKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEICKAITN   84 (559)
T ss_pred             HHHHHhCCCcHHhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHHHHHHhc
Confidence            46688999999999999999999999988766556 6789999999999999999998764322110             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.+|..      ...  -...++.+.+.+..    ....|+||||+|.|             .....+.|+..+
T Consensus        85 g~~~dv~eidaa------s~~--~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~L-------------t~~a~naLLKtL  143 (559)
T PRK05563         85 GSLMDVIEIDAA------SNN--GVDEIRDIRDKVKYAPSEAKYKVYIIDEVHML-------------STGAFNALLKTL  143 (559)
T ss_pred             CCCCCeEEeecc------ccC--CHHHHHHHHHHHhhCcccCCeEEEEEECcccC-------------CHHHHHHHHHHh
Confidence             11233444321      111  12335556655542    34579999999999             344677777778


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+++|.+|+...     .+.+.+.+|++.+.|.+|+.++....|+.++.    ..++.++++++..++..+.+- 
T Consensus       144 Eepp~~~ifIlatt~~~-----ki~~tI~SRc~~~~f~~~~~~ei~~~L~~i~~----~egi~i~~~al~~ia~~s~G~-  213 (559)
T PRK05563        144 EEPPAHVIFILATTEPH-----KIPATILSRCQRFDFKRISVEDIVERLKYILD----KEGIEYEDEALRLIARAAEGG-  213 (559)
T ss_pred             cCCCCCeEEEEEeCChh-----hCcHHHHhHheEEecCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC-
Confidence            75  4567777776543     57789999999999999999998888887776    448899999999988876542 


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                           +.+++.+++.++.
T Consensus       214 -----~R~al~~Ldq~~~  226 (559)
T PRK05563        214 -----MRDALSILDQAIS  226 (559)
T ss_pred             -----HHHHHHHHHHHHH
Confidence                 3456666665543

>PRK04195 replication factor C large subunit; Provisional

Probab=99.58  E-value=1.1e-14  Score=163.97  Aligned_cols=182  Identities=15%  Similarity=0.195  Sum_probs=133.5

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCC----CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRT----KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~----~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .|+++++|.++++++|+++.+..+..++....    ..++||+||||||||++|+++|+.+          +..++.++.
T Consensus         3 ~W~eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~g~~~~~lLL~GppG~GKTtla~ala~el----------~~~~ielna   72 (482)
T PRK04195          3 PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKPKKALLLYGPPGVGKTSLAHALANDY----------GWEVIELNA   72 (482)
T ss_pred             CchhhcCCCCHHHhcCCHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEcc
Confidence            68899999999999999999999988876432    5789999999999999999999988          667777765


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHh------cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQK------SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIA  428 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~------~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~  428 (710)
                      ++...        ...+..++..+..      ..+.||+|||+|.+.+..         .....+.|..++......+|.
T Consensus        73 sd~r~--------~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~~---------d~~~~~aL~~~l~~~~~~iIl  135 (482)
T PRK04195         73 SDQRT--------ADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGNE---------DRGGARAILELIKKAKQPIIL  135 (482)
T ss_pred             ccccc--------HHHHHHHHHHhhccCcccCCCCeEEEEecCccccccc---------chhHHHHHHHHHHcCCCCEEE
Confidence            43221        1123333333322      246799999999985421         112234455555555556666


Q ss_pred             ccChHHHHhhhhccH-HHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          429 STTQDEHRTQFEKDK-ALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       429 att~~~~~~~~~~d~-aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      ++|...     ...+ .+++|+..|.|++|+..+...+|+.++.    ..++.+++++++.++..+.+.
T Consensus       136 i~n~~~-----~~~~k~Lrsr~~~I~f~~~~~~~i~~~L~~i~~----~egi~i~~eaL~~Ia~~s~GD  195 (482)
T PRK04195        136 TANDPY-----DPSLRELRNACLMIEFKRLSTRSIVPVLKRICR----KEGIECDDEALKEIAERSGGD  195 (482)
T ss_pred             eccCcc-----ccchhhHhccceEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC
Confidence            666542     3444 7888999999999999999999988776    458899999999999887653

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3e-14  Score=161.78  Aligned_cols=202  Identities=19%  Similarity=0.221  Sum_probs=147.3

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCC-----Ccc--c-----
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEV-----PVF--L-----  344 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~-----p~~--l-----  344 (710)
                      ..|.+++||.+|+++||++..++.|...+...+.. .+||+||+|+|||++|+.+|+.+.+...     |..  .     
T Consensus        12 ~~la~KyRP~~f~dliGq~~~v~~L~~~~~~gri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~cg~c~~   91 (598)
T PRK09111         12 RVLARKYRPQTFDDLIGQEAMVRTLTNAFETGRIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDLCGVGEH   91 (598)
T ss_pred             hhHHhhhCCCCHHHhcCcHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCccccCcccHH
Confidence            45788999999999999999999999988876654 4899999999999999999999865321     100  0     


Q ss_pred             -------cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHH
Q 005179          345 -------LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISN  413 (710)
Q Consensus       345 -------~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~  413 (710)
                             ....+++++..      +..|  ...++.+++.+..    ....|+||||+|.|             +....+
T Consensus        92 C~~i~~g~h~Dv~e~~a~------s~~g--vd~IReIie~~~~~P~~a~~KVvIIDEad~L-------------s~~a~n  150 (598)
T PRK09111         92 CQAIMEGRHVDVLEMDAA------SHTG--VDDIREIIESVRYRPVSARYKVYIIDEVHML-------------STAAFN  150 (598)
T ss_pred             HHHHhcCCCCceEEeccc------ccCC--HHHHHHHHHHHHhchhcCCcEEEEEEChHhC-------------CHHHHH
Confidence                   01123333321      1111  2335666665543    34569999999999             445678


Q ss_pred             hhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          414 LLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       414 ~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                      .|+.+|++  ..+.+|.+|+...     .+.+.+++||+.+.|..|+.++....|+.++.    ..++.+++++++.++.
T Consensus       151 aLLKtLEePp~~~~fIl~tte~~-----kll~tI~SRcq~~~f~~l~~~el~~~L~~i~~----kegi~i~~eAl~lIa~  221 (598)
T PRK09111        151 ALLKTLEEPPPHVKFIFATTEIR-----KVPVTVLSRCQRFDLRRIEADVLAAHLSRIAA----KEGVEVEDEALALIAR  221 (598)
T ss_pred             HHHHHHHhCCCCeEEEEEeCChh-----hhhHHHHhheeEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHH
Confidence            88888886  5677777776544     45678999999999999999998888887776    4488999999999998


Q ss_pred             HhhhhhcCCCCcchHHHHHHHHHh
Q 005179          492 LSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       492 ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      .+.+.      +..++.+++.++.
T Consensus       222 ~a~Gd------lr~al~~Ldkli~  239 (598)
T PRK09111        222 AAEGS------VRDGLSLLDQAIA  239 (598)
T ss_pred             HcCCC------HHHHHHHHHHHHh
Confidence            87754      3456666766543

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3.7e-14  Score=161.71  Aligned_cols=201  Identities=23%  Similarity=0.289  Sum_probs=145.7

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-----------c
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-----------L  345 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-----------~  345 (710)
                      ..|.+++||.+|++++|++..++.|...+......+ .||+||+|+|||++|+.+|+.+.+.......           .
T Consensus         6 ~~l~~KyRP~~f~dIiGQe~~v~~L~~aI~~~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~~~~~~   85 (725)
T PRK07133          6 KALYRKYRPKTFDDIVGQDHIVQTLKNIIKSNKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECIENVNN   85 (725)
T ss_pred             hhHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHHHhhcC
Confidence            367889999999999999999999999888766555 4899999999999999999998664321100           0


Q ss_pred             CceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC
Q 005179          346 SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR  421 (710)
Q Consensus       346 ~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~  421 (710)
                      ...++.++.      ....+  ...++.+++.+..    +...|++|||+|.|             ....++.|+..|+.
T Consensus        86 ~~Dvieida------asn~~--vd~IReLie~~~~~P~~g~~KV~IIDEa~~L-------------T~~A~NALLKtLEE  144 (725)
T PRK07133         86 SLDIIEMDA------ASNNG--VDEIRELIENVKNLPTQSKYKIYIIDEVHML-------------SKSAFNALLKTLEE  144 (725)
T ss_pred             CCcEEEEec------cccCC--HHHHHHHHHHHHhchhcCCCEEEEEEChhhC-------------CHHHHHHHHHHhhc
Confidence            112222221      11111  2235566665543    34569999999999             34567888888886


Q ss_pred             --CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcC
Q 005179          422 --GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       422 --~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~  499 (710)
                        +.+++|.+|+...     .+.+++++||+.+.|.+|+.++...+|+.++.+    .++.+++++++.++.++.+-   
T Consensus       145 PP~~tifILaTte~~-----KLl~TI~SRcq~ieF~~L~~eeI~~~L~~il~k----egI~id~eAl~~LA~lS~Gs---  212 (725)
T PRK07133        145 PPKHVIFILATTEVH-----KIPLTILSRVQRFNFRRISEDEIVSRLEFILEK----ENISYEKNALKLIAKLSSGS---  212 (725)
T ss_pred             CCCceEEEEEcCChh-----hhhHHHHhhceeEEccCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC---
Confidence              4577777776554     667899999999999999999988888877664    37889999999998887643   


Q ss_pred             CCCcchHHHHHHHHH
Q 005179          500 RYLPDKAIDLVDEAG  514 (710)
Q Consensus       500 r~~p~~ai~ll~~a~  514 (710)
                         .+.++.+++.++
T Consensus       213 ---lR~AlslLekl~  224 (725)
T PRK07133        213 ---LRDALSIAEQVS  224 (725)
T ss_pred             ---HHHHHHHHHHHH
Confidence               345666666543

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

Probab=99.58  E-value=4.3e-15  Score=145.35  Aligned_cols=165  Identities=22%  Similarity=0.293  Sum_probs=130.9

Q ss_pred             CCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +..++-|..++|+++.+++.             ...+..+|||||||||||.+|+++|++.          +.-++.+-.
T Consensus       175 ty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrt----------dacfirvig  244 (435)
T KOG0729|consen  175 TYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRT----------DACFIRVIG  244 (435)
T ss_pred             ccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhccc----------CceEEeehh
Confidence            56688899999998888653             2456789999999999999999999887          666777767


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQCI  427 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~vI  427 (710)
                      +.++  .+|.|+-...++++|+-++...-+|+|+||||.+-++.-..  +.++..+++..++.++       .+|++.++
T Consensus       245 selv--qkyvgegarmvrelf~martkkaciiffdeidaiggarfdd--g~ggdnevqrtmleli~qldgfdprgnikvl  320 (435)
T KOG0729|consen  245 SELV--QKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFDD--GAGGDNEVQRTMLELINQLDGFDPRGNIKVL  320 (435)
T ss_pred             HHHH--HHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCccccC--CCCCcHHHHHHHHHHHHhccCCCCCCCeEEE
Confidence            7777  67888888889999999888888999999999996553221  1233445554444333       37899999


Q ss_pred             EccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHH
Q 005179          428 ASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      .+||.+.     .+||+|.|  |++ .|+|..|+.+-|..|++-..+
T Consensus       321 matnrpd-----tldpallrpgrldrkvef~lpdlegrt~i~kihak  362 (435)
T KOG0729|consen  321 MATNRPD-----TLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAK  362 (435)
T ss_pred             eecCCCC-----CcCHhhcCCcccccceeccCCcccccceeEEEecc
Confidence            9999987     79999999  887 899999999999999885544

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.57  E-value=2.7e-14  Score=165.24  Aligned_cols=203  Identities=20%  Similarity=0.273  Sum_probs=137.4

Q ss_pred             CCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          289 IDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      |+++.|.+...+++.+++.            ...+.+++|+||||||||+++++++..+          +.+++.++.+.
T Consensus       151 ~~di~g~~~~~~~l~~i~~~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~----------~~~f~~is~~~  220 (644)
T PRK10733        151 FADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA----------KVPFFTISGSD  220 (644)
T ss_pred             HHHHcCHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEehHH
Confidence            4455666655555544332            1235679999999999999999999988          66778888776


Q ss_pred             hhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC-CCChHhHHHhhcccc----cCCCeEEEEccC
Q 005179          357 LMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSL----GRGELQCIASTT  431 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l----~~~~v~vI~att  431 (710)
                      +..  .+.|.....++.++..+....|+||||||+|.+......+.+. ........+.|+..+    .+..+++|++||
T Consensus       221 ~~~--~~~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~~~~vivIaaTN  298 (644)
T PRK10733        221 FVE--MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAATN  298 (644)
T ss_pred             hHH--hhhcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccCCCCeeEEEecC
Confidence            653  3455566778889998888889999999999997654322110 111122333333222    245689999999


Q ss_pred             hHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHH
Q 005179          432 QDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID  508 (710)
Q Consensus       432 ~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~  508 (710)
                      .++     .+|+++.|  ||+ .|.|+.|+.++|.+||+.+..+.....  .+   .+..+++.+.+|.     +.+...
T Consensus       299 ~p~-----~lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~--~~---d~~~la~~t~G~s-----gadl~~  363 (644)
T PRK10733        299 RPD-----VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAP--DI---DAAIIARGTPGFS-----GADLAN  363 (644)
T ss_pred             Chh-----hcCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCC--cC---CHHHHHhhCCCCC-----HHHHHH
Confidence            987     78999998  997 899999999999999998776432111  11   1334555555543     355666


Q ss_pred             HHHHHHhhhh
Q 005179          509 LVDEAGSRAH  518 (710)
Q Consensus       509 ll~~a~~~~~  518 (710)
                      ++++|+..+.
T Consensus       364 l~~eAa~~a~  373 (644)
T PRK10733        364 LVNEAALFAA  373 (644)
T ss_pred             HHHHHHHHHH
Confidence            7777765443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=99.57  E-value=7.6e-15  Score=141.23  Aligned_cols=196  Identities=16%  Similarity=0.280  Sum_probs=141.4

Q ss_pred             cchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCce
Q 005179          269 RASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKR  348 (710)
Q Consensus       269 ~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~  348 (710)
                      +.+.-..|..+|.+++||..+.+++|.++.++++..+...+.-+|++|.||||+||||-+..||+++....+.     ..
T Consensus         6 ~~~~~~~~~l~wVeKYrP~~l~dIVGNe~tv~rl~via~~gnmP~liisGpPG~GKTTsi~~LAr~LLG~~~k-----e~   80 (333)
T KOG0991|consen    6 EMSKSDKYQLPWVEKYRPSVLQDIVGNEDTVERLSVIAKEGNMPNLIISGPPGTGKTTSILCLARELLGDSYK-----EA   80 (333)
T ss_pred             cCCccccccchHHHhhCchHHHHhhCCHHHHHHHHHHHHcCCCCceEeeCCCCCchhhHHHHHHHHHhChhhh-----hH
Confidence            3444556667799999999999999999999999999888889999999999999999999999998432211     12


Q ss_pred             EEEeehhhhhhccccCc--cHHHHHHHHHHHH-H--hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--C
Q 005179          349 IMSLDMGLLMAGAKERG--ELEARVTTLISEI-Q--KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--R  421 (710)
Q Consensus       349 v~~ld~~~l~~g~~~~g--~~e~~l~~~~~~~-~--~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~  421 (710)
                      +.+++.+      ..+|  -...+++.+-+.- .  .+...|+++||+|.+             ..-++..|+..|+  .
T Consensus        81 vLELNAS------deRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSM-------------T~gAQQAlRRtMEiyS  141 (333)
T KOG0991|consen   81 VLELNAS------DERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSM-------------TAGAQQALRRTMEIYS  141 (333)
T ss_pred             hhhccCc------cccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchh-------------hhHHHHHHHHHHHHHc
Confidence            3333322      2333  2233333332211 1  133568999999999             3335677777666  5


Q ss_pred             CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          422 GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       422 ~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ...+++.+||..+     .+-..+.+||..+++...+..+...-|..+.+    ..+++++++.+++++-.+++.+
T Consensus       142 ~ttRFalaCN~s~-----KIiEPIQSRCAiLRysklsd~qiL~Rl~~v~k----~Ekv~yt~dgLeaiifta~GDM  208 (333)
T KOG0991|consen  142 NTTRFALACNQSE-----KIIEPIQSRCAILRYSKLSDQQILKRLLEVAK----AEKVNYTDDGLEAIIFTAQGDM  208 (333)
T ss_pred             ccchhhhhhcchh-----hhhhhHHhhhHhhhhcccCHHHHHHHHHHHHH----HhCCCCCcchHHHhhhhccchH
Confidence            6677888888765     45578899999899999988886555555544    4589999999999988877643

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=3.3e-14  Score=162.23  Aligned_cols=200  Identities=19%  Similarity=0.188  Sum_probs=144.7

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--c-----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--L-----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--l-----------  344 (710)
                      -|.+++||.+|+++||+++.++.|...+......+ +||+||+|+|||++++.+++.+.+...+..  .           
T Consensus         5 ~l~~k~RP~~f~~iiGq~~v~~~L~~~i~~~~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~c~~i~~   84 (576)
T PRK14965          5 VLARKYRPQTFSDLTGQEHVSRTLQNAIDTGRVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPPCVEITE   84 (576)
T ss_pred             HHHHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHHHHHHhc
Confidence            46789999999999999999999999888766555 589999999999999999999865432110  0           


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.+|.      ....+  ...++.+.+.+..    ....|+||||+|.|             +...+|.|+.+|
T Consensus        85 g~~~d~~eid~------~s~~~--v~~ir~l~~~~~~~p~~~~~KVvIIdev~~L-------------t~~a~naLLk~L  143 (576)
T PRK14965         85 GRSVDVFEIDG------ASNTG--VDDIRELRENVKYLPSRSRYKIFIIDEVHML-------------STNAFNALLKTL  143 (576)
T ss_pred             CCCCCeeeeec------cCccC--HHHHHHHHHHHHhccccCCceEEEEEChhhC-------------CHHHHHHHHHHH
Confidence             0112333322      11111  2235555555542    23468999999999             455788898889


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+++|.+|+...     .+.+++++||..+.|.+++.++....|..++.+    .++.++++++..++..+.+-+
T Consensus       144 Eepp~~~~fIl~t~~~~-----kl~~tI~SRc~~~~f~~l~~~~i~~~L~~i~~~----egi~i~~~al~~la~~a~G~l  214 (576)
T PRK14965        144 EEPPPHVKFIFATTEPH-----KVPITILSRCQRFDFRRIPLQKIVDRLRYIADQ----EGISISDAALALVARKGDGSM  214 (576)
T ss_pred             HcCCCCeEEEEEeCChh-----hhhHHHHHhhhhhhcCCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHcCCCH
Confidence            86  4677887777654     567899999999999999999988888777663    488999999999988877532


Q ss_pred             cCCCCcchHHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~  514 (710)
                            ++++.+++.++
T Consensus       215 ------r~al~~Ldqli  225 (576)
T PRK14965        215 ------RDSLSTLDQVL  225 (576)
T ss_pred             ------HHHHHHHHHHH
Confidence                  34555555443

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.56  E-value=8.4e-14  Score=157.53  Aligned_cols=200  Identities=21%  Similarity=0.188  Sum_probs=143.1

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      -|..++||.+|++++|++..+..+...+..+...+ +||+||+|+|||++|+.+|+.+.+...+...             
T Consensus         5 ~l~~kyRP~~f~diiGqe~iv~~L~~~i~~~~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~C~~i~~   84 (563)
T PRK06647          5 GTATKRRPRDFNSLEGQDFVVETLKHSIESNKIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSSCKSIDN   84 (563)
T ss_pred             HHHHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchHHHHHHc
Confidence            46678999999999999999999999988766555 7899999999999999999998654222110             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++.      ....+  ...++.+.+.+.    ..+..|++|||+|.|             ....++.|+..+
T Consensus        85 ~~~~dv~~idg------as~~~--vddIr~l~e~~~~~p~~~~~KVvIIDEa~~L-------------s~~a~naLLK~L  143 (563)
T PRK06647         85 DNSLDVIEIDG------ASNTS--VQDVRQIKEEIMFPPASSRYRVYIIDEVHML-------------SNSAFNALLKTI  143 (563)
T ss_pred             CCCCCeEEecC------cccCC--HHHHHHHHHHHHhchhcCCCEEEEEEChhhc-------------CHHHHHHHHHhh
Confidence             0112232221      11111  122444444333    244679999999999             445677888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+++|.+|+...     .+.+++.+||+.+.+.+++.++...+|+..+.    ..++.++++++..++..+.+. 
T Consensus       144 Eepp~~~vfI~~tte~~-----kL~~tI~SRc~~~~f~~l~~~el~~~L~~i~~----~egi~id~eAl~lLa~~s~Gd-  213 (563)
T PRK06647        144 EEPPPYIVFIFATTEVH-----KLPATIKSRCQHFNFRLLSLEKIYNMLKKVCL----EDQIKYEDEALKWIAYKSTGS-  213 (563)
T ss_pred             ccCCCCEEEEEecCChH-----HhHHHHHHhceEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC-
Confidence            86  5677777776643     46689999999999999999998888887665    347899999999998886643 


Q ss_pred             cCCCCcchHHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~  514 (710)
                           +..++.+++.++
T Consensus       214 -----lR~alslLdkli  225 (563)
T PRK06647        214 -----VRDAYTLFDQVV  225 (563)
T ss_pred             -----HHHHHHHHHHHH
Confidence                 345666666544

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

Probab=99.56  E-value=7.6e-14  Score=161.49  Aligned_cols=205  Identities=23%  Similarity=0.268  Sum_probs=152.5

Q ss_pred             cCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -.|+.+-|-+..+..|.+++.             -..++.+|++||||||||..|+++|..+..+.-     ...++--+
T Consensus       262 v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~-----kisffmrk  336 (1080)
T KOG0732|consen  262 VGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNR-----KISFFMRK  336 (1080)
T ss_pred             cCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhccccc-----ccchhhhc
Confidence            357888888888877776532             134677999999999999999999998865421     11111112


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEEEEc
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQCIAS  429 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~vI~a  429 (710)
                      ..+..  .++.|+.+..++.+|++++...|+|+|+|||+-|......-.  ......+...|+.+|.    +|.+++||+
T Consensus       337 gaD~l--skwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSskq--Eqih~SIvSTLLaLmdGldsRgqVvvigA  412 (1080)
T KOG0732|consen  337 GADCL--SKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQ--EQIHASIVSTLLALMDGLDSRGQVVVIGA  412 (1080)
T ss_pred             Cchhh--ccccCcHHHHHHHHHHHHhccCceEEeccccccccccccchH--HHhhhhHHHHHHHhccCCCCCCceEEEcc
Confidence            22222  578999999999999999999999999999998876543210  1223345555655554    799999999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ||+++     .+||+|+|  ||+ .+.++.|+.+.|.+|+.-...++    .-.++...+..+++.+.+|.+     .+.
T Consensus       413 TnRpd-----a~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw----~~~i~~~l~~~la~~t~gy~g-----aDl  478 (1080)
T KOG0732|consen  413 TNRPD-----AIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKW----EPPISRELLLWLAEETSGYGG-----ADL  478 (1080)
T ss_pred             cCCcc-----ccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCC----CCCCCHHHHHHHHHhccccch-----HHH
Confidence            99988     78999998  897 89999999999999998666544    356788889999999999876     234


Q ss_pred             HHHHHHHH
Q 005179          507 IDLVDEAG  514 (710)
Q Consensus       507 i~ll~~a~  514 (710)
                      ..++.+|.
T Consensus       479 kaLCTeAa  486 (1080)
T KOG0732|consen  479 KALCTEAA  486 (1080)
T ss_pred             HHHHHHHh
Confidence            44555544

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.55  E-value=1e-13  Score=150.60  Aligned_cols=201  Identities=21%  Similarity=0.220  Sum_probs=141.6

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      +|.+++||..|++++|++..++.+.+.+......+ +||+||||+|||++++.+++.+.+...+...             
T Consensus         3 ~~~~~~rp~~~~~iig~~~~~~~l~~~~~~~~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~   82 (355)
T TIGR02397         3 VLARKYRPQTFEDVIGQEHIVQTLKNAIKNGRIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECESCKEINS   82 (355)
T ss_pred             cHHHHhCCCcHhhccCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHhc
Confidence            57889999999999999999999999887765444 6899999999999999999998654221110             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++..      ...  -...++.+++.+..    .+..|++|||+|.+             .....+.|...+
T Consensus        83 ~~~~~~~~~~~~------~~~--~~~~~~~l~~~~~~~p~~~~~~vviidea~~l-------------~~~~~~~Ll~~l  141 (355)
T TIGR02397        83 GSSLDVIEIDAA------SNN--GVDDIREILDNVKYAPSSGKYKVYIIDEVHML-------------SKSAFNALLKTL  141 (355)
T ss_pred             CCCCCEEEeecc------ccC--CHHHHHHHHHHHhcCcccCCceEEEEeChhhc-------------CHHHHHHHHHHH
Confidence             01223333321      011  11234556655543    33569999999998             233456666666


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+.+|.+++...     .+.+++.+|+..+.+++|+.++...+++..+.    ..++.+++++++.++..+.+  
T Consensus       142 e~~~~~~~lIl~~~~~~-----~l~~~l~sr~~~~~~~~~~~~~l~~~l~~~~~----~~g~~i~~~a~~~l~~~~~g--  210 (355)
T TIGR02397       142 EEPPEHVVFILATTEPH-----KIPATILSRCQRFDFKRIPLEDIVERLKKILD----KEGIKIEDEALELIARAADG--  210 (355)
T ss_pred             hCCccceeEEEEeCCHH-----HHHHHHHhheeEEEcCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCC--
Confidence            64  4566666665543     45688999999999999999998888887776    34788999999999887654  


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                          .+..+...++.++.
T Consensus       211 ----~~~~a~~~lekl~~  224 (355)
T TIGR02397       211 ----SLRDALSLLDQLIS  224 (355)
T ss_pred             ----ChHHHHHHHHHHHh
Confidence                24556666666553

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.

>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=99.55  E-value=2.7e-14  Score=131.69  Aligned_cols=123  Identities=26%  Similarity=0.392  Sum_probs=96.0

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcC-CeEEEEccch
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSG-DVILFIDEVH  392 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~-~~IL~IDEid  392 (710)
                      +||+||||||||++++.+++.+          +.+++.++...+.  ..+.++.+..+..++..+.... ++||||||+|
T Consensus         1 ill~G~~G~GKT~l~~~la~~l----------~~~~~~i~~~~~~--~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d   68 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL----------GFPFIEIDGSELI--SSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEID   68 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT----------TSEEEEEETTHHH--TSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGG
T ss_pred             CEEECcCCCCeeHHHHHHHhhc----------ccccccccccccc--cccccccccccccccccccccccceeeeeccch
Confidence            5899999999999999999998          7889999998887  4467788899999999998876 8999999999


Q ss_pred             hhhhCCCCCCCCCCChHhHHHhhccccc-----CCCeEEEEccChHHHHhhhhccHHHH-cccc-ceEec
Q 005179          393 TLIGSGTVGRGNKGTGLDISNLLKPSLG-----RGELQCIASTTQDEHRTQFEKDKALA-RRFQ-PVLIS  455 (710)
Q Consensus       393 ~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----~~~v~vI~att~~~~~~~~~~d~aL~-~Rf~-~I~v~  455 (710)
                      .+......  ........+.+.|...++     .+++.+|++|+..+     .+++.+. +||+ .|.++
T Consensus        69 ~l~~~~~~--~~~~~~~~~~~~L~~~l~~~~~~~~~~~vI~ttn~~~-----~i~~~l~~~rf~~~i~~~  131 (132)
T PF00004_consen   69 KLFPKSQP--SSSSFEQRLLNQLLSLLDNPSSKNSRVIVIATTNSPD-----KIDPALLRSRFDRRIEFP  131 (132)
T ss_dssp             GTSHHCST--SSSHHHHHHHHHHHHHHHTTTTTSSSEEEEEEESSGG-----GSCHHHHSTTSEEEEEE-
T ss_pred             hccccccc--ccccccccccceeeecccccccccccceeEEeeCChh-----hCCHhHHhCCCcEEEEcC
Confidence            99876511  111223344555544443     24689999999866     7999999 9997 56654

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 ....

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.55  E-value=1e-13  Score=155.19  Aligned_cols=163  Identities=15%  Similarity=0.167  Sum_probs=111.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHH-HHHHHHHHHHhcCCeEEEEcc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEA-RVTTLISEIQKSGDVILFIDE  390 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~-~l~~~~~~~~~~~~~IL~IDE  390 (710)
                      ++++|||++|+|||+|++++++.+....     .+..+++++...+....  ...+.. .+..+.+....  ..+|+|||
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~-----~g~~V~Yitaeef~~el--~~al~~~~~~~f~~~y~~--~DLLlIDD  385 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLY-----PGTRVRYVSSEEFTNEF--INSIRDGKGDSFRRRYRE--MDILLVDD  385 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEeeHHHHHHHH--HHHHHhccHHHHHHHhhc--CCEEEEeh
Confidence            5689999999999999999999885421     25678888776655211  000000 11122222222  45999999


Q ss_pred             chhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHcccc---ceEecCCCHHHHHHHHH
Q 005179          391 VHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ---PVLISEPSQEDAVRILL  467 (710)
Q Consensus       391 id~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~---~I~v~~Ps~~~~~~IL~  467 (710)
                      |+.+.+..       .....+.+++..+.+++..+||.+...+.  .+-.+++.|.+||.   .+.|.+|+.+.|..||+
T Consensus       386 Iq~l~gke-------~tqeeLF~l~N~l~e~gk~IIITSd~~P~--eL~~l~~rL~SRf~~GLvv~I~~PD~EtR~aIL~  456 (617)
T PRK14086        386 IQFLEDKE-------STQEEFFHTFNTLHNANKQIVLSSDRPPK--QLVTLEDRLRNRFEWGLITDVQPPELETRIAILR  456 (617)
T ss_pred             hccccCCH-------HHHHHHHHHHHHHHhcCCCEEEecCCChH--hhhhccHHHHhhhhcCceEEcCCCCHHHHHHHHH
Confidence            99995432       12456777777777766655554443332  22357899999996   78999999999999999


Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          468 GLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       468 ~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      ..+.    ..++.++++++++++....+-
T Consensus       457 kka~----~r~l~l~~eVi~yLa~r~~rn  481 (617)
T PRK14086        457 KKAV----QEQLNAPPEVLEFIASRISRN  481 (617)
T ss_pred             HHHH----hcCCCCCHHHHHHHHHhccCC
Confidence            8766    458999999999998775543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.54  E-value=8.7e-14  Score=152.61  Aligned_cols=201  Identities=19%  Similarity=0.179  Sum_probs=140.7

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCc---cc----c-----
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPV---FL----L-----  345 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~---~l----~-----  345 (710)
                      -|.+++||.+|++++|++..++.|...+....-.+ +||+||||+|||++|+.+|+.+.+.....   ..    .     
T Consensus         5 ~l~~k~RP~~~~eiiGq~~~~~~L~~~~~~~~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~~~c~~c   84 (397)
T PRK14955          5 VIARKYRPKKFADITAQEHITRTIQNSLRMGRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVTEPCGEC   84 (397)
T ss_pred             HHHHhcCCCcHhhccChHHHHHHHHHHHHhCCcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCCCCCCCC
Confidence            46789999999999999999999999888766655 88999999999999999999996532100   00    0     


Q ss_pred             ----------CceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhH
Q 005179          346 ----------SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDI  411 (710)
Q Consensus       346 ----------~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~  411 (710)
                                ...++.++.      ....+  .+.++.+.+.+..    ....|+||||+|.+             ....
T Consensus        85 ~~c~~~~~~~~~n~~~~~~------~~~~~--id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l-------------~~~~  143 (397)
T PRK14955         85 ESCRDFDAGTSLNISEFDA------ASNNS--VDDIRLLRENVRYGPQKGRYRVYIIDEVHML-------------SIAA  143 (397)
T ss_pred             HHHHHHhcCCCCCeEeecc------cccCC--HHHHHHHHHHHhhchhcCCeEEEEEeChhhC-------------CHHH
Confidence                      011222221      11111  2334555555532    34569999999999             3335


Q ss_pred             HHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHH
Q 005179          412 SNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAA  489 (710)
Q Consensus       412 ~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l  489 (710)
                      ++.|..++++  ...++|.+++...     .+.+++.+|+..+++.+++.++....++..+.    ..++.+++++++.+
T Consensus       144 ~~~LLk~LEep~~~t~~Il~t~~~~-----kl~~tl~sR~~~v~f~~l~~~ei~~~l~~~~~----~~g~~i~~~al~~l  214 (397)
T PRK14955        144 FNAFLKTLEEPPPHAIFIFATTELH-----KIPATIASRCQRFNFKRIPLEEIQQQLQGICE----AEGISVDADALQLI  214 (397)
T ss_pred             HHHHHHHHhcCCCCeEEEEEeCChH-----HhHHHHHHHHHHhhcCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHH
Confidence            6667777775  3566666665432     55688999999999999999998888777665    34789999999999


Q ss_pred             HHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          490 VHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       490 ~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      +..+.+.      +..+...++.++.
T Consensus       215 ~~~s~g~------lr~a~~~L~kl~~  234 (397)
T PRK14955        215 GRKAQGS------MRDAQSILDQVIA  234 (397)
T ss_pred             HHHcCCC------HHHHHHHHHHHHH
Confidence            9998754      3456666665543

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=1.9e-13  Score=151.59  Aligned_cols=200  Identities=19%  Similarity=0.196  Sum_probs=141.1

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.+++||.+|+++||++..+..+...+..+.-. .+||+||+|+|||++|+.+|+.+.+.......             
T Consensus         6 ~~~~kyRP~~~~diiGq~~~v~~L~~~i~~~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~~C~~i~   85 (451)
T PRK06305          6 VSSRKYRPQTFSEILGQDAVVAVLKNALRFNRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCASCKEIS   85 (451)
T ss_pred             HHHHHhCCCCHHHhcCcHHHHHHHHHHHHcCCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccHHHHHHh
Confidence            5788999999999999999999999988776544 47899999999999999999998653211000             


Q ss_pred             --cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          345 --LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       345 --~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                        ....++.++      |....|  ...++.+.+.+.    .....|+||||+|.+             ....++.|..+
T Consensus        86 ~~~~~d~~~i~------g~~~~g--id~ir~i~~~l~~~~~~~~~kvvIIdead~l-------------t~~~~n~LLk~  144 (451)
T PRK06305         86 SGTSLDVLEID------GASHRG--IEDIRQINETVLFTPSKSRYKIYIIDEVHML-------------TKEAFNSLLKT  144 (451)
T ss_pred             cCCCCceEEee------ccccCC--HHHHHHHHHHHHhhhhcCCCEEEEEecHHhh-------------CHHHHHHHHHH
Confidence              011222222      111111  112333333222    245679999999999             33457788888


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +++  +.+.+|++|+...     .+.+++.+|+..+.+.+++.++....|...+.+    .++.+++++++.++..+.+-
T Consensus       145 lEep~~~~~~Il~t~~~~-----kl~~tI~sRc~~v~f~~l~~~el~~~L~~~~~~----eg~~i~~~al~~L~~~s~gd  215 (451)
T PRK06305        145 LEEPPQHVKFFLATTEIH-----KIPGTILSRCQKMHLKRIPEETIIDKLALIAKQ----EGIETSREALLPIARAAQGS  215 (451)
T ss_pred             hhcCCCCceEEEEeCChH-----hcchHHHHhceEEeCCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC
Confidence            876  5677777776543     567899999999999999999988888876663    47889999999999887653


Q ss_pred             hcCCCCcchHHHHHHHHH
Q 005179          497 ISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~  514 (710)
                            .+.++.+++..+
T Consensus       216 ------lr~a~~~Lekl~  227 (451)
T PRK06305        216 ------LRDAESLYDYVV  227 (451)
T ss_pred             ------HHHHHHHHHHHH
Confidence                  235666666544

>PRK05642 DNA replication initiation factor; Validated

Probab=99.53  E-value=1.9e-13  Score=138.96  Aligned_cols=154  Identities=17%  Similarity=0.206  Sum_probs=111.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEcc
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDE  390 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDE  390 (710)
                      .++++|+|++|+|||+|++++++.+...       +..+++++...+...          ...+++.+...  .+|+|||
T Consensus        45 ~~~l~l~G~~G~GKTHLl~a~~~~~~~~-------~~~v~y~~~~~~~~~----------~~~~~~~~~~~--d~LiiDD  105 (234)
T PRK05642         45 ESLIYLWGKDGVGRSHLLQAACLRFEQR-------GEPAVYLPLAELLDR----------GPELLDNLEQY--ELVCLDD  105 (234)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhC-------CCcEEEeeHHHHHhh----------hHHHHHhhhhC--CEEEEec
Confidence            3678899999999999999999887432       567778877666531          12333334433  3899999


Q ss_pred             chhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccc---cceEecCCCHHHHHHHHH
Q 005179          391 VHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRF---QPVLISEPSQEDAVRILL  467 (710)
Q Consensus       391 id~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf---~~I~v~~Ps~~~~~~IL~  467 (710)
                      ++.+.+..       .....+.+++....+++..++|++++.+..  +....+.|.+||   ..+.+.+|+.+++..+++
T Consensus       106 i~~~~~~~-------~~~~~Lf~l~n~~~~~g~~ilits~~~p~~--l~~~~~~L~SRl~~gl~~~l~~~~~e~~~~il~  176 (234)
T PRK05642        106 LDVIAGKA-------DWEEALFHLFNRLRDSGRRLLLAASKSPRE--LPIKLPDLKSRLTLALVFQMRGLSDEDKLRALQ  176 (234)
T ss_pred             hhhhcCCh-------HHHHHHHHHHHHHHhcCCEEEEeCCCCHHH--cCccCccHHHHHhcCeeeecCCCCHHHHHHHHH
Confidence            99884331       113456777777777788888888776542  223479999999   478899999999999998


Q ss_pred             HHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          468 GLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       468 ~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      ..+.    ..++.++++++++++....+-
T Consensus       177 ~ka~----~~~~~l~~ev~~~L~~~~~~d  201 (234)
T PRK05642        177 LRAS----RRGLHLTDEVGHFILTRGTRS  201 (234)
T ss_pred             HHHH----HcCCCCCHHHHHHHHHhcCCC
Confidence            6443    347899999999999887664

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.53  E-value=5.4e-14  Score=154.59  Aligned_cols=202  Identities=20%  Similarity=0.254  Sum_probs=152.9

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc--ccC---------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVF--LLS---------  346 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~--l~~---------  346 (710)
                      .|-.++||..|++++|++...+.|...+...+- ...+|.||.|||||++|+.+|+.+.+...+..  ...         
T Consensus         5 ~L~rKyRP~~F~evvGQe~v~~~L~nal~~~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~Ck~I~~   84 (515)
T COG2812           5 VLARKYRPKTFDDVVGQEHVVKTLSNALENGRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCISCKEINE   84 (515)
T ss_pred             HHHHHhCcccHHHhcccHHHHHHHHHHHHhCcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhhhHhhhc
Confidence            466789999999999999999999998876554 44689999999999999999999977542211  111         


Q ss_pred             ---ceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          347 ---KRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       347 ---~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                         ..++++|.      .+..  -.+.++.+.+.+.-    ...-|.+|||+|.|             +..+.|.|+..|
T Consensus        85 g~~~DviEiDa------ASn~--gVddiR~i~e~v~y~P~~~ryKVyiIDEvHML-------------S~~afNALLKTL  143 (515)
T COG2812          85 GSLIDVIEIDA------ASNT--GVDDIREIIEKVNYAPSEGRYKVYIIDEVHML-------------SKQAFNALLKTL  143 (515)
T ss_pred             CCcccchhhhh------hhcc--ChHHHHHHHHHhccCCccccceEEEEecHHhh-------------hHHHHHHHhccc
Confidence               11222221      1111  12335666666542    44679999999999             556788888888


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  .++.+|.+||...     .+.+.+.+||+.+.+...+.++....|..++.    ..++.++++++..+++.+++-+
T Consensus       144 EEPP~hV~FIlATTe~~-----Kip~TIlSRcq~f~fkri~~~~I~~~L~~i~~----~E~I~~e~~aL~~ia~~a~Gs~  214 (515)
T COG2812         144 EEPPSHVKFILATTEPQ-----KIPNTILSRCQRFDFKRLDLEEIAKHLAAILD----KEGINIEEDALSLIARAAEGSL  214 (515)
T ss_pred             ccCccCeEEEEecCCcC-----cCchhhhhccccccccCCCHHHHHHHHHHHHH----hcCCccCHHHHHHHHHHcCCCh
Confidence            86  4688898888876     78999999999999999999998887777776    5589999999999998877643


Q ss_pred             cCCCCcchHHHHHHHHHhh
Q 005179          498 SDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~~  516 (710)
                            +++..++|.+...
T Consensus       215 ------RDalslLDq~i~~  227 (515)
T COG2812         215 ------RDALSLLDQAIAF  227 (515)
T ss_pred             ------hhHHHHHHHHHHc
Confidence                  4577888888754

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.53  E-value=1.7e-13  Score=152.76  Aligned_cols=201  Identities=21%  Similarity=0.254  Sum_probs=142.2

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCcc--c-----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVF--L-----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~--l-----------  344 (710)
                      +|.+++||..|++++|++..+..+...+......|. ||+||+|+|||++|+.+|+.+.+......  .           
T Consensus         5 ~~~~kyRP~~f~diiGq~~i~~~L~~~i~~~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~nc~~i~~   84 (486)
T PRK14953          5 PFARKYRPKFFKEVIGQEIVVRILKNAVKLQRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCENCVEIDK   84 (486)
T ss_pred             HHHHhhCCCcHHHccChHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHHHHHHhc
Confidence            788999999999999999999999999988666664 78999999999999999999864221110  0           


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.+|.      ....|  ...++.+.+.+..    +...|++|||+|.+             .....+.|...+
T Consensus        85 g~~~d~~eida------as~~g--vd~ir~I~~~~~~~P~~~~~KVvIIDEad~L-------------t~~a~naLLk~L  143 (486)
T PRK14953         85 GSFPDLIEIDA------ASNRG--IDDIRALRDAVSYTPIKGKYKVYIIDEAHML-------------TKEAFNALLKTL  143 (486)
T ss_pred             CCCCcEEEEeC------ccCCC--HHHHHHHHHHHHhCcccCCeeEEEEEChhhc-------------CHHHHHHHHHHH
Confidence             0112333322      11111  1223444444432    34569999999998             344567777777


Q ss_pred             cCC--CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GRG--ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~~--~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      +..  .+++|.+|+...     .+.+++.+|++.+.+.+|+.++...+|..++.+    .++.+++++++.++..+.+- 
T Consensus       144 Eepp~~~v~Il~tt~~~-----kl~~tI~SRc~~i~f~~ls~~el~~~L~~i~k~----egi~id~~al~~La~~s~G~-  213 (486)
T PRK14953        144 EEPPPRTIFILCTTEYD-----KIPPTILSRCQRFIFSKPTKEQIKEYLKRICNE----EKIEYEEKALDLLAQASEGG-  213 (486)
T ss_pred             hcCCCCeEEEEEECCHH-----HHHHHHHHhceEEEcCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC-
Confidence            753  556666665433     466789999999999999999998888877774    47899999999998876643 


Q ss_pred             cCCCCcchHHHHHHHHHh
Q 005179          498 SDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~~  515 (710)
                           ...++.+++.++.
T Consensus       214 -----lr~al~~Ldkl~~  226 (486)
T PRK14953        214 -----MRDAASLLDQAST  226 (486)
T ss_pred             -----HHHHHHHHHHHHH
Confidence                 3456777776653

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.52  E-value=1.6e-13  Score=151.48  Aligned_cols=185  Identities=17%  Similarity=0.242  Sum_probs=118.0

Q ss_pred             cCCCCcc-cCHHHHH-HHHHHHHc-------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          287 ELIDPVI-GRETEIQ-RIIQILCR-------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       287 ~~l~~li-Gr~~~i~-~l~~~L~~-------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      -+|++++ |....+. .....+..       ...++++|+||+|+|||+|++++++.+...       +.++++++...+
T Consensus       108 ~tFdnFv~g~~N~~a~~~a~~~a~~~~~~~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~-------~~~v~yi~~~~f  180 (445)
T PRK12422        108 MTFANFLVTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALRES-------GGKILYVRSELF  180 (445)
T ss_pred             ccccceeeCCcHHHHHHHHHHHHhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHHc-------CCCEEEeeHHHH
Confidence            3577765 6554432 22222221       123678999999999999999999998543       566777776544


Q ss_pred             hhccccCccHHH-HHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHH
Q 005179          358 MAGAKERGELEA-RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHR  436 (710)
Q Consensus       358 ~~g~~~~g~~e~-~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~  436 (710)
                      ...  ....+.. ... .+.... ....+|+|||+|.+.+..       ....++...+..+..++..+++++...+.  
T Consensus       181 ~~~--~~~~l~~~~~~-~f~~~~-~~~dvLiIDDiq~l~~k~-------~~qeelf~l~N~l~~~~k~IIlts~~~p~--  247 (445)
T PRK12422        181 TEH--LVSAIRSGEMQ-RFRQFY-RNVDALFIEDIEVFSGKG-------ATQEEFFHTFNSLHTEGKLIVISSTCAPQ--  247 (445)
T ss_pred             HHH--HHHHHhcchHH-HHHHHc-ccCCEEEEcchhhhcCCh-------hhHHHHHHHHHHHHHCCCcEEEecCCCHH--
Confidence            311  0000000 011 111111 234599999999984431       12445566666556666666666555433  


Q ss_pred             hhhhccHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          437 TQFEKDKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       437 ~~~~~d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      .+..+++.|.+||.   .+.+.+|+.+++..||+..+..    .++.++++++++++....+
T Consensus       248 ~l~~l~~rL~SR~~~Gl~~~l~~pd~e~r~~iL~~k~~~----~~~~l~~evl~~la~~~~~  305 (445)
T PRK12422        248 DLKAMEERLISRFEWGIAIPLHPLTKEGLRSFLERKAEA----LSIRIEETALDFLIEALSS  305 (445)
T ss_pred             HHhhhHHHHHhhhcCCeEEecCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC
Confidence            22357899999994   7999999999999999987764    4789999999998876554

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.52  E-value=3.2e-13  Score=150.90  Aligned_cols=186  Identities=16%  Similarity=0.219  Sum_probs=120.7

Q ss_pred             CCCCcc-cCHHH--HHHHHHHHHcC--CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc
Q 005179          288 LIDPVI-GRETE--IQRIIQILCRR--TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK  362 (710)
Q Consensus       288 ~l~~li-Gr~~~--i~~l~~~L~~~--~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~  362 (710)
                      +|++++ |....  ...+..+....  ..++++|+||+|+|||+|++++++.+....     .+..++.++...+...  
T Consensus       120 tfd~fv~g~~n~~a~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~-----~~~~v~yi~~~~~~~~--  192 (450)
T PRK00149        120 TFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNYILEKN-----PNAKVVYVTSEKFTND--  192 (450)
T ss_pred             cccccccCCCcHHHHHHHHHHHhCcCccCCeEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEEEHHHHHHH--
Confidence            577754 54332  23333333322  235689999999999999999999985431     1566777776655421  


Q ss_pred             cCccHH-HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhc
Q 005179          363 ERGELE-ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEK  441 (710)
Q Consensus       363 ~~g~~e-~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~  441 (710)
                      ....+. .....+.+.+.  ...+|+|||+|.+.+...       ...++..++....+++..++|++..++.  ....+
T Consensus       193 ~~~~~~~~~~~~~~~~~~--~~dlLiiDDi~~l~~~~~-------~~~~l~~~~n~l~~~~~~iiits~~~p~--~l~~l  261 (450)
T PRK00149        193 FVNALRNNTMEEFKEKYR--SVDVLLIDDIQFLAGKER-------TQEEFFHTFNALHEAGKQIVLTSDRPPK--ELPGL  261 (450)
T ss_pred             HHHHHHcCcHHHHHHHHh--cCCEEEEehhhhhcCCHH-------HHHHHHHHHHHHHHCCCcEEEECCCCHH--HHHHH
Confidence            111110 01122223333  245999999999844311       1345666666667777666666655543  12236


Q ss_pred             cHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          442 DKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       442 d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      ++.+.+||.   .+.+.+|+.+++..||+..+..    .++.++++++++++..+.+
T Consensus       262 ~~~l~SRl~~gl~v~i~~pd~~~r~~il~~~~~~----~~~~l~~e~l~~ia~~~~~  314 (450)
T PRK00149        262 EERLRSRFEWGLTVDIEPPDLETRIAILKKKAEE----EGIDLPDEVLEFIAKNITS  314 (450)
T ss_pred             HHHHHhHhcCCeeEEecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHcCcCC
Confidence            799999995   6999999999999999988773    4789999999999877654

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.51  E-value=2.5e-13  Score=148.13  Aligned_cols=200  Identities=21%  Similarity=0.208  Sum_probs=138.8

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc--CceEEEeehh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL--SKRIMSLDMG  355 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~--~~~v~~ld~~  355 (710)
                      .|.+++||.+|++++|++..++.+.+.+..+.. .++||+||||+|||++++.+++.+.+...+....  +..++.++..
T Consensus         6 ~~~~k~rP~~~~~iig~~~~~~~l~~~i~~~~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~~~l~~~   85 (367)
T PRK14970          6 VSARKYRPQTFDDVVGQSHITNTLLNAIENNHLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNIFELDAA   85 (367)
T ss_pred             HHHHHHCCCcHHhcCCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcceEEeccc
Confidence            577899999999999999999999998877544 4788999999999999999999986532221111  2223333211


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEc
Q 005179          356 LLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIAS  429 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~a  429 (710)
                            ...  ....+..+++.+..    .+..|++|||+|.+.             ....+.|...+++  ...++|.+
T Consensus        86 ------~~~--~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~-------------~~~~~~ll~~le~~~~~~~~Il~  144 (367)
T PRK14970         86 ------SNN--SVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLS-------------SAAFNAFLKTLEEPPAHAIFILA  144 (367)
T ss_pred             ------cCC--CHHHHHHHHHHHhhccccCCcEEEEEeChhhcC-------------HHHHHHHHHHHhCCCCceEEEEE
Confidence                  111  11234555555432    335699999999882             2234555555654  34556666


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDL  509 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~l  509 (710)
                      ++...     .+.+++.+|+..+.+.+|+.++...++...+.    .+++.+++++++.++..+.+-      ...++..
T Consensus       145 ~~~~~-----kl~~~l~sr~~~v~~~~~~~~~l~~~l~~~~~----~~g~~i~~~al~~l~~~~~gd------lr~~~~~  209 (367)
T PRK14970        145 TTEKH-----KIIPTILSRCQIFDFKRITIKDIKEHLAGIAV----KEGIKFEDDALHIIAQKADGA------LRDALSI  209 (367)
T ss_pred             eCCcc-----cCCHHHHhcceeEecCCccHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhCCCC------HHHHHHH
Confidence            55433     56789999999999999999998888887766    458899999999999876532      3456666


Q ss_pred             HHHHH
Q 005179          510 VDEAG  514 (710)
Q Consensus       510 l~~a~  514 (710)
                      ++..+
T Consensus       210 lekl~  214 (367)
T PRK14970        210 FDRVV  214 (367)
T ss_pred             HHHHH
Confidence            66554

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.51  E-value=4.3e-13  Score=148.06  Aligned_cols=186  Identities=16%  Similarity=0.239  Sum_probs=118.4

Q ss_pred             CCCC-cccCHHHH-H-HHHHHHHcC--CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc
Q 005179          288 LIDP-VIGRETEI-Q-RIIQILCRR--TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK  362 (710)
Q Consensus       288 ~l~~-liGr~~~i-~-~l~~~L~~~--~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~  362 (710)
                      +|++ ++|.+..+ . .+..+....  ..++++|+||+|+|||+|++++++++....     .+..++.++...+...  
T Consensus       108 tfd~fi~g~~n~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~-----~~~~v~yi~~~~~~~~--  180 (405)
T TIGR00362       108 TFDNFVVGKSNRLAHAAALAVAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILENN-----PNAKVVYVSSEKFTND--  180 (405)
T ss_pred             cccccccCCcHHHHHHHHHHHHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHhC-----CCCcEEEEEHHHHHHH--
Confidence            5666 44655442 2 222222222  235679999999999999999999986431     1466777776654321  


Q ss_pred             cCccHH-HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhc
Q 005179          363 ERGELE-ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEK  441 (710)
Q Consensus       363 ~~g~~e-~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~  441 (710)
                      ....+. ..+..+.+.+..  ..+|+|||+|.+.+..       .....+...+....+++..++|++...+.  ....+
T Consensus       181 ~~~~~~~~~~~~~~~~~~~--~dlLiiDDi~~l~~~~-------~~~~~l~~~~n~~~~~~~~iiits~~~p~--~l~~l  249 (405)
T TIGR00362       181 FVNALRNNKMEEFKEKYRS--VDLLLIDDIQFLAGKE-------RTQEEFFHTFNALHENGKQIVLTSDRPPK--ELPGL  249 (405)
T ss_pred             HHHHHHcCCHHHHHHHHHh--CCEEEEehhhhhcCCH-------HHHHHHHHHHHHHHHCCCCEEEecCCCHH--HHhhh
Confidence            000000 011222223332  3589999999985431       11334566666666666666665554443  22246


Q ss_pred             cHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          442 DKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       442 d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      ++.+.+||.   .+.+.+|+.+++..||+..+..    .++.++++++++++....+
T Consensus       250 ~~~l~SRl~~g~~v~i~~pd~~~r~~il~~~~~~----~~~~l~~e~l~~ia~~~~~  302 (405)
T TIGR00362       250 EERLRSRFEWGLVVDIEPPDLETRLAILQKKAEE----EGLELPDEVLEFIAKNIRS  302 (405)
T ss_pred             hhhhhhhccCCeEEEeCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC
Confidence            789999995   6999999999999999988774    4789999999999877554

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).

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.51  E-value=3.5e-13  Score=153.36  Aligned_cols=188  Identities=20%  Similarity=0.197  Sum_probs=135.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCC---Cccc----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEV---PVFL----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~---p~~l----------  344 (710)
                      -+.+++||.+|++++|++..+..|...+....-.+ +||+||+|||||++|+.+|+.+.+...   |...          
T Consensus         5 ~l~~kyRP~~f~eivGQe~i~~~L~~~i~~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~~~Cg~C   84 (620)
T PRK14954          5 VIARKYRPSKFADITAQEHITHTIQNSLRMDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVTEPCGEC   84 (620)
T ss_pred             HHHHHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccCCCCccC
Confidence            35678999999999999999999999887755555 889999999999999999999966321   1000          


Q ss_pred             ---------cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhH
Q 005179          345 ---------LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI  411 (710)
Q Consensus       345 ---------~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~  411 (710)
                               ....+..+|.      ....+  .+.++.+.+.+.    ....-|+||||+|.+             ....
T Consensus        85 ~sC~~~~~g~~~n~~~~d~------~s~~~--vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~L-------------t~~a  143 (620)
T PRK14954         85 ESCRDFDAGTSLNISEFDA------ASNNS--VDDIRQLRENVRYGPQKGRYRVYIIDEVHML-------------STAA  143 (620)
T ss_pred             HHHHHHhccCCCCeEEecc------cccCC--HHHHHHHHHHHHhhhhcCCCEEEEEeChhhc-------------CHHH
Confidence                     0011222221      11111  223455555542    234568999999999             3445


Q ss_pred             HHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHH
Q 005179          412 SNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAA  489 (710)
Q Consensus       412 ~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l  489 (710)
                      ++.|+.+|++  +..++|.+|+...     .+-+++.+|++.+.+.+++.++....++.++.    ..++.+++++++.+
T Consensus       144 ~naLLK~LEePp~~tv~IL~t~~~~-----kLl~TI~SRc~~vef~~l~~~ei~~~L~~i~~----~egi~I~~eal~~L  214 (620)
T PRK14954        144 FNAFLKTLEEPPPHAIFIFATTELH-----KIPATIASRCQRFNFKRIPLDEIQSQLQMICR----AEGIQIDADALQLI  214 (620)
T ss_pred             HHHHHHHHhCCCCCeEEEEEeCChh-----hhhHHHHhhceEEecCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHH
Confidence            7888888886  4566776665432     56688999999999999999998877776665    34788999999999


Q ss_pred             HHHhhhh
Q 005179          490 VHLSARY  496 (710)
Q Consensus       490 ~~ls~~~  496 (710)
                      +..+.+.
T Consensus       215 a~~s~Gd  221 (620)
T PRK14954        215 ARKAQGS  221 (620)
T ss_pred             HHHhCCC
Confidence            9988754

>TIGR00763 lon ATP-dependent protease La

Probab=99.50  E-value=1.7e-13  Score=162.37  Aligned_cols=180  Identities=20%  Similarity=0.280  Sum_probs=120.9

Q ss_pred             CcccCHHHHHHHHHHHHcC------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-----h
Q 005179          291 PVIGRETEIQRIIQILCRR------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-----A  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-----~  359 (710)
                      +++|.++..+++.+.+...      .+.+++|+||||||||++|+++|..+          +..++.++++.+.     .
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~~~~~~~~lll~GppG~GKT~lAk~iA~~l----------~~~~~~i~~~~~~~~~~i~  390 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKAL----------NRKFVRFSLGGVRDEAEIR  390 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhhcCCCCceEEEECCCCCCHHHHHHHHHHHh----------cCCeEEEeCCCcccHHHHc
Confidence            4889999888888765421      33468999999999999999999998          4455555433221     1


Q ss_pred             c--cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----------------
Q 005179          360 G--AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----------------  420 (710)
Q Consensus       360 g--~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----------------  420 (710)
                      |  ..+.|....++...+..+....+ |+||||||.+.....         .+..+.|.+.++                 
T Consensus       391 g~~~~~~g~~~g~i~~~l~~~~~~~~-villDEidk~~~~~~---------~~~~~aLl~~ld~~~~~~f~d~~~~~~~d  460 (775)
T TIGR00763       391 GHRRTYVGAMPGRIIQGLKKAKTKNP-LFLLDEIDKIGSSFR---------GDPASALLEVLDPEQNNAFSDHYLDVPFD  460 (775)
T ss_pred             CCCCceeCCCCchHHHHHHHhCcCCC-EEEEechhhcCCccC---------CCHHHHHHHhcCHHhcCccccccCCceec
Confidence            1  12333333344455555544444 889999999953211         112233333322                 


Q ss_pred             CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHH-HHHHhhc-----CCCCCHHHHHHHHHHhh
Q 005179          421 RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLR-EKYEAHH-----NCKFTLEAINAAVHLSA  494 (710)
Q Consensus       421 ~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~-~~~~~~~-----~~~i~~~~l~~l~~ls~  494 (710)
                      -+++++|+|+|...     .++++|++||..|.++.|+.+++..|++..+ .+....+     ++.++++++.++++...
T Consensus       461 ~s~v~~I~TtN~~~-----~i~~~L~~R~~vi~~~~~~~~e~~~I~~~~l~~~~~~~~~l~~~~~~~~~~~l~~i~~~~~  535 (775)
T TIGR00763       461 LSKVIFIATANSID-----TIPRPLLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYT  535 (775)
T ss_pred             cCCEEEEEecCCch-----hCCHHHhCCeeEEecCCCCHHHHHHHHHHHHHHHHHHHcCCCcceEEECHHHHHHHHHhcC
Confidence            14678899998864     7899999999999999999999999998644 3333333     35799999999887433


Q ss_pred             h
Q 005179          495 R  495 (710)
Q Consensus       495 ~  495 (710)
                      +
T Consensus       536 ~  536 (775)
T TIGR00763       536 R  536 (775)
T ss_pred             h
Confidence            3

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=99.50  E-value=2.5e-13  Score=137.80  Aligned_cols=179  Identities=12%  Similarity=0.165  Sum_probs=112.4

Q ss_pred             hcCCCCcccCHHHH--HHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc
Q 005179          286 EELIDPVIGRETEI--QRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE  363 (710)
Q Consensus       286 ~~~l~~liGr~~~i--~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~  363 (710)
                      +.+|+++++.+...  ..+.+.......+.++|+||||||||+|++++++.+...       +..+.++++.....    
T Consensus        12 ~~~fd~f~~~~~~~~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~ai~~~~~~~-------~~~~~y~~~~~~~~----   80 (229)
T PRK06893         12 DETLDNFYADNNLLLLDSLRKNFIDLQQPFFYIWGGKSSGKSHLLKAVSNHYLLN-------QRTAIYIPLSKSQY----   80 (229)
T ss_pred             cccccccccCChHHHHHHHHHHhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCCeEEeeHHHhhh----
Confidence            34567777554322  122222222222336899999999999999999987543       33444554432110    


Q ss_pred             CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeE-EEEccChHHHHhhhhcc
Q 005179          364 RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQ-CIASTTQDEHRTQFEKD  442 (710)
Q Consensus       364 ~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~-vI~att~~~~~~~~~~d  442 (710)
                            ....+++.+..  ..+|+|||++.+.+..       .....+.+++....+++..+ ++++++.+..  +-...
T Consensus        81 ------~~~~~~~~~~~--~dlLilDDi~~~~~~~-------~~~~~l~~l~n~~~~~~~~illits~~~p~~--l~~~~  143 (229)
T PRK06893         81 ------FSPAVLENLEQ--QDLVCLDDLQAVIGNE-------EWELAIFDLFNRIKEQGKTLLLISADCSPHA--LSIKL  143 (229)
T ss_pred             ------hhHHHHhhccc--CCEEEEeChhhhcCCh-------HHHHHHHHHHHHHHHcCCcEEEEeCCCChHH--ccccc
Confidence                  11233333332  3599999999984331       11334556666555555544 4555444431  11245


Q ss_pred             HHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          443 KALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       443 ~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +.|.+|+.   .+.+.+|+.+++.+||+..+.    .+++.++++++++++..+.+-
T Consensus       144 ~~L~sRl~~g~~~~l~~pd~e~~~~iL~~~a~----~~~l~l~~~v~~~L~~~~~~d  196 (229)
T PRK06893        144 PDLASRLTWGEIYQLNDLTDEQKIIVLQRNAY----QRGIELSDEVANFLLKRLDRD  196 (229)
T ss_pred             hhHHHHHhcCCeeeCCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhccCC
Confidence            89999986   789999999999999987765    447999999999999887654

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.50  E-value=2.6e-13  Score=145.06  Aligned_cols=200  Identities=18%  Similarity=0.215  Sum_probs=135.7

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      .|.+++||.+|++++|+++.++.+...+......+++|+||||+|||++++.+++.+.....     ...++.++.+...
T Consensus         6 ~w~~kyrP~~~~~~~g~~~~~~~l~~~i~~~~~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~-----~~~~i~~~~~~~~   80 (319)
T PRK00440          6 IWVEKYRPRTLDEIVGQEEIVERLKSYVKEKNMPHLLFAGPPGTGKTTAALALARELYGEDW-----RENFLELNASDER   80 (319)
T ss_pred             ccchhhCCCcHHHhcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCcc-----ccceEEecccccc
Confidence            58899999999999999999999999988776678999999999999999999998843221     1223333221110


Q ss_pred             hccccCccHHHHHHHHHHHHHh--cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHH
Q 005179          359 AGAKERGELEARVTTLISEIQK--SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDE  434 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~~--~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~  434 (710)
                          ....+...+..+......  ....+++|||+|.+.             .+..+.|..+++.  ....+|.+++...
T Consensus        81 ----~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~-------------~~~~~~L~~~le~~~~~~~lIl~~~~~~  143 (319)
T PRK00440         81 ----GIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLT-------------SDAQQALRRTMEMYSQNTRFILSCNYSS  143 (319)
T ss_pred             ----chHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCC-------------HHHHHHHHHHHhcCCCCCeEEEEeCCcc
Confidence                001111222222211101  235699999999982             2233445555542  3345555555432


Q ss_pred             HHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          435 HRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       435 ~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                           .+.+.+.+|+..+.+.+++.++...+++..+.    ..++.+++++++.++..+.+.      +..++..++.++
T Consensus       144 -----~l~~~l~sr~~~~~~~~l~~~ei~~~l~~~~~----~~~~~i~~~al~~l~~~~~gd------~r~~~~~l~~~~  208 (319)
T PRK00440        144 -----KIIDPIQSRCAVFRFSPLKKEAVAERLRYIAE----NEGIEITDDALEAIYYVSEGD------MRKAINALQAAA  208 (319)
T ss_pred             -----ccchhHHHHhheeeeCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC------HHHHHHHHHHHH
Confidence                 45577899999999999999998888887766    447889999999999886643      445677776655


Q ss_pred             h
Q 005179          515 S  515 (710)
Q Consensus       515 ~  515 (710)
                      .
T Consensus       209 ~  209 (319)
T PRK00440        209 A  209 (319)
T ss_pred             H
Confidence            3

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=3.7e-13  Score=154.03  Aligned_cols=188  Identities=20%  Similarity=0.177  Sum_probs=138.1

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCC-CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc-ccCc--------
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRT-KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVF-LLSK--------  347 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~-~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~-l~~~--------  347 (710)
                      .+|.+++|+..|++++|++..+..|...+...+ ..++||+||+|+|||++|+.+|+.+.+...... ...|        
T Consensus         4 ~pl~~kyRP~~f~~liGq~~i~~~L~~~l~~~rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C~~C~~   83 (620)
T PRK14948          4 EPLHHKYRPQRFDELVGQEAIATTLKNALISNRIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKCELCRA   83 (620)
T ss_pred             chHHHHhCCCcHhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCcccHHHHH
Confidence            367889999999999999999999998887654 457899999999999999999999866321100 0011        


Q ss_pred             -------eEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhc
Q 005179          348 -------RIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLK  416 (710)
Q Consensus       348 -------~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~  416 (710)
                             .++.++.      .  .....+.++++++.+..    ....|+||||+|.|             ..+.++.|+
T Consensus        84 i~~g~h~D~~ei~~------~--~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~L-------------t~~a~naLL  142 (620)
T PRK14948         84 IAAGNALDVIEIDA------A--SNTGVDNIRELIERAQFAPVQARWKVYVIDECHML-------------STAAFNALL  142 (620)
T ss_pred             HhcCCCccEEEEec------c--ccCCHHHHHHHHHHHhhChhcCCceEEEEECcccc-------------CHHHHHHHH
Confidence                   1222221      1  11223456677666543    34569999999999             445678888


Q ss_pred             ccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q 005179          417 PSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       417 ~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~  494 (710)
                      ..+++  +.+++|++|+...     .+.+++++||..+.|..++.++....+..++.+    .++.++++++..++..+.
T Consensus       143 K~LEePp~~tvfIL~t~~~~-----~llpTIrSRc~~~~f~~l~~~ei~~~L~~ia~k----egi~is~~al~~La~~s~  213 (620)
T PRK14948        143 KTLEEPPPRVVFVLATTDPQ-----RVLPTIISRCQRFDFRRIPLEAMVQHLSEIAEK----ESIEIEPEALTLVAQRSQ  213 (620)
T ss_pred             HHHhcCCcCeEEEEEeCChh-----hhhHHHHhheeEEEecCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHcC
Confidence            88886  5677777776543     466899999999999999999888777776663    478899999988888876


Q ss_pred             h
Q 005179          495 R  495 (710)
Q Consensus       495 ~  495 (710)
                      +
T Consensus       214 G  214 (620)
T PRK14948        214 G  214 (620)
T ss_pred             C
Confidence            5

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.49  E-value=1.4e-12  Score=142.20  Aligned_cols=209  Identities=21%  Similarity=0.279  Sum_probs=135.1

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------  358 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------  358 (710)
                      +.++||+++++.+...+..    ..+.+++|+||||||||++++.+++.+.... +..-....++.+++....       
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~-~~~~~~~~~v~in~~~~~~~~~~~~   93 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRPSNVFIYGKTGTGKTAVTKYVMKELEEAA-EDRDVRVVTVYVNCQILDTLYQVLV   93 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHh-hccCCceEEEEEECCCCCCHHHHHH
Confidence            3689999999999888753    4557899999999999999999998874311 000001345555542211       


Q ss_pred             ------h--ccc--cCc-cHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc-----ccC
Q 005179          359 ------A--GAK--ERG-ELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS-----LGR  421 (710)
Q Consensus       359 ------~--g~~--~~g-~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~-----l~~  421 (710)
                            .  +.+  ..+ ...+.+..+++.+.. ..+.||+|||+|.+.+.          ..++...|...     +..
T Consensus        94 ~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~----------~~~~L~~l~~~~~~~~~~~  163 (365)
T TIGR02928        94 ELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGD----------DDDLLYQLSRARSNGDLDN  163 (365)
T ss_pred             HHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccC----------CcHHHHhHhccccccCCCC
Confidence                  0  111  111 233445555555543 34688999999999622          11222233332     223


Q ss_pred             CCeEEEEccChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcC
Q 005179          422 GELQCIASTTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       422 ~~v~vI~att~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~  499 (710)
                      .++.+|++++...+..  .+++.+.+||.  .|.+++++.++..+|++......  ..+..+++++++.++..+.+.-+ 
T Consensus       164 ~~v~lI~i~n~~~~~~--~l~~~~~s~~~~~~i~f~p~~~~e~~~il~~r~~~~--~~~~~~~~~~l~~i~~~~~~~~G-  238 (365)
T TIGR02928       164 AKVGVIGISNDLKFRE--NLDPRVKSSLCEEEIIFPPYDAEELRDILENRAEKA--FYDGVLDDGVIPLCAALAAQEHG-  238 (365)
T ss_pred             CeEEEEEEECCcchHh--hcCHHHhccCCcceeeeCCCCHHHHHHHHHHHHHhh--ccCCCCChhHHHHHHHHHHHhcC-
Confidence            6688888888765432  46788999995  69999999999999999876521  12345888888888776654322 


Q ss_pred             CCCcchHHHHHHHHHhh
Q 005179          500 RYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       500 r~~p~~ai~ll~~a~~~  516 (710)
                        .+..++++++.|+..
T Consensus       239 --d~R~al~~l~~a~~~  253 (365)
T TIGR02928       239 --DARKAIDLLRVAGEI  253 (365)
T ss_pred             --CHHHHHHHHHHHHHH
Confidence              356788888877643

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.

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.49  E-value=6.8e-13  Score=146.95  Aligned_cols=186  Identities=18%  Similarity=0.267  Sum_probs=120.3

Q ss_pred             CCCCcc-cCHHHH--HHHHHHHHcC-CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc-
Q 005179          288 LIDPVI-GRETEI--QRIIQILCRR-TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK-  362 (710)
Q Consensus       288 ~l~~li-Gr~~~i--~~l~~~L~~~-~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~-  362 (710)
                      +|++++ |.....  ..+.++.... ..++++||||+|+|||+|++++++.+....     .+..+++++...+..... 
T Consensus       103 tFdnFv~g~~n~~a~~~~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~-----~~~~v~yi~~~~f~~~~~~  177 (440)
T PRK14088        103 TFENFVVGPGNSFAYHAALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNE-----PDLRVMYITSEKFLNDLVD  177 (440)
T ss_pred             cccccccCCchHHHHHHHHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhC-----CCCeEEEEEHHHHHHHHHH
Confidence            566665 544332  2333333322 236799999999999999999999885421     145777777665542110 


Q ss_pred             --cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhh
Q 005179          363 --ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFE  440 (710)
Q Consensus       363 --~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~  440 (710)
                        ..+.    +..+..... ..+.+|+|||++.+.+...       ...++...+..+.+.+..++|++...+.  ..-.
T Consensus       178 ~~~~~~----~~~f~~~~~-~~~dvLlIDDi~~l~~~~~-------~q~elf~~~n~l~~~~k~iIitsd~~p~--~l~~  243 (440)
T PRK14088        178 SMKEGK----LNEFREKYR-KKVDVLLIDDVQFLIGKTG-------VQTELFHTFNELHDSGKQIVICSDREPQ--KLSE  243 (440)
T ss_pred             HHhccc----HHHHHHHHH-hcCCEEEEechhhhcCcHH-------HHHHHHHHHHHHHHcCCeEEEECCCCHH--HHHH
Confidence              0111    112222221 2356999999999854311       1345666666666667666665544443  1224


Q ss_pred             ccHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          441 KDKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       441 ~d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +.+.+.+||.   .+.+.+|+.+.+..||+..+.    ..++.++++++++++....+.
T Consensus       244 l~~rL~SR~~~gl~v~i~~pd~e~r~~IL~~~~~----~~~~~l~~ev~~~Ia~~~~~~  298 (440)
T PRK14088        244 FQDRLVSRFQMGLVAKLEPPDEETRKKIARKMLE----IEHGELPEEVLNFVAENVDDN  298 (440)
T ss_pred             HHHHHhhHHhcCceEeeCCCCHHHHHHHHHHHHH----hcCCCCCHHHHHHHHhccccC
Confidence            5689999996   789999999999999998766    347899999999998876543

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.49  E-value=7.1e-13  Score=152.33  Aligned_cols=211  Identities=21%  Similarity=0.236  Sum_probs=137.7

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      .++.+.+|+..|++++|++..+..+.+.+......+++|+||||||||++|+.++..........+..+..++.+++..+
T Consensus       142 ~~~~~~~rp~~~~~iiGqs~~~~~l~~~ia~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l  221 (615)
T TIGR02903       142 KSAQSLLRPRAFSEIVGQERAIKALLAKVASPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL  221 (615)
T ss_pred             hHHhhhcCcCcHHhceeCcHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence            56667789999999999999999988888766777899999999999999999987663221111112345566655433


Q ss_pred             hhcc-----ccCccH----HHHHHHHHHH----------HHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          358 MAGA-----KERGEL----EARVTTLISE----------IQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       358 ~~g~-----~~~g~~----e~~l~~~~~~----------~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                      ....     ...+..    ....+..+..          +....+.+|||||++.|             +...++.|...
T Consensus       222 ~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~L-------------d~~~Q~~Ll~~  288 (615)
T TIGR02903       222 RWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGEL-------------DPLLQNKLLKV  288 (615)
T ss_pred             cCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccC-------------CHHHHHHHHHH
Confidence            1000     000100    0011111111          11233569999999988             33334444433


Q ss_pred             ccC------------------------------CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHH
Q 005179          419 LGR------------------------------GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLG  468 (710)
Q Consensus       419 l~~------------------------------~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~  468 (710)
                      +++                              ..+++|++|+...    ..++++|++||..+.+++++.++...|++.
T Consensus       289 Le~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~----~~l~~aLrSR~~~i~~~pls~edi~~Il~~  364 (615)
T TIGR02903       289 LEDKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDP----EEINPALRSRCAEVFFEPLTPEDIALIVLN  364 (615)
T ss_pred             HhhCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccc----cccCHHHHhceeEEEeCCCCHHHHHHHHHH
Confidence            332                              2367777776643    157899999999999999999999999998


Q ss_pred             HHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhh
Q 005179          469 LREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       469 l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                      .+.+    .++.+++++++.+..++..       ..++++.|..++..
T Consensus       365 ~a~~----~~v~ls~eal~~L~~ys~~-------gRraln~L~~~~~~  401 (615)
T TIGR02903       365 AAEK----INVHLAAGVEELIARYTIE-------GRKAVNILADVYGY  401 (615)
T ss_pred             HHHH----cCCCCCHHHHHHHHHCCCc-------HHHHHHHHHHHHHH
Confidence            7764    3677899988888766431       24677777666544

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.

>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=99.48  E-value=2.6e-13  Score=136.42  Aligned_cols=185  Identities=20%  Similarity=0.260  Sum_probs=114.7

Q ss_pred             CCCCcc-cCH-HHHHHHHHHHHcCCC---CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc-
Q 005179          288 LIDPVI-GRE-TEIQRIIQILCRRTK---NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA-  361 (710)
Q Consensus       288 ~l~~li-Gr~-~~i~~l~~~L~~~~~---~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~-  361 (710)
                      +|+++| |.. +........+.....   ++++|+||+|+|||+|++++++++....     .+.++++++...+.... 
T Consensus         6 tFdnfv~g~~N~~a~~~~~~ia~~~~~~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~-----~~~~v~y~~~~~f~~~~~   80 (219)
T PF00308_consen    6 TFDNFVVGESNELAYAAAKAIAENPGERYNPLFLYGPSGLGKTHLLQAIANEAQKQH-----PGKRVVYLSAEEFIREFA   80 (219)
T ss_dssp             SCCCS--TTTTHHHHHHHHHHHHSTTTSSSEEEEEESTTSSHHHHHHHHHHHHHHHC-----TTS-EEEEEHHHHHHHHH
T ss_pred             ccccCCcCCcHHHHHHHHHHHHhcCCCCCCceEEECCCCCCHHHHHHHHHHHHHhcc-----ccccceeecHHHHHHHHH
Confidence            577764 642 333334443433322   4589999999999999999999885421     26678888776654211 


Q ss_pred             --ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhh
Q 005179          362 --KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQF  439 (710)
Q Consensus       362 --~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~  439 (710)
                        ...+.    +..+.+.+..  -.+|+|||+|.+.+..       .....+.+++....++++.++|++...+.  ...
T Consensus        81 ~~~~~~~----~~~~~~~~~~--~DlL~iDDi~~l~~~~-------~~q~~lf~l~n~~~~~~k~li~ts~~~P~--~l~  145 (219)
T PF00308_consen   81 DALRDGE----IEEFKDRLRS--ADLLIIDDIQFLAGKQ-------RTQEELFHLFNRLIESGKQLILTSDRPPS--ELS  145 (219)
T ss_dssp             HHHHTTS----HHHHHHHHCT--SSEEEEETGGGGTTHH-------HHHHHHHHHHHHHHHTTSEEEEEESS-TT--TTT
T ss_pred             HHHHccc----chhhhhhhhc--CCEEEEecchhhcCch-------HHHHHHHHHHHHHHhhCCeEEEEeCCCCc--ccc
Confidence              01122    2233333443  3499999999994321       11345666667777777776666644443  233


Q ss_pred             hccHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          440 EKDKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       440 ~~d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      .+++.|.+||.   .+.+.+|+.+++..|++..+.    .+++.++++++++++....+-
T Consensus       146 ~~~~~L~SRl~~Gl~~~l~~pd~~~r~~il~~~a~----~~~~~l~~~v~~~l~~~~~~~  201 (219)
T PF00308_consen  146 GLLPDLRSRLSWGLVVELQPPDDEDRRRILQKKAK----ERGIELPEEVIEYLARRFRRD  201 (219)
T ss_dssp             TS-HHHHHHHHCSEEEEE----HHHHHHHHHHHHH----HTT--S-HHHHHHHHHHTTSS
T ss_pred             ccChhhhhhHhhcchhhcCCCCHHHHHHHHHHHHH----HhCCCCcHHHHHHHHHhhcCC
Confidence            46899999995   799999999999999998777    568899999999998876543

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.

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.48  E-value=1e-12  Score=148.68  Aligned_cols=209  Identities=19%  Similarity=0.145  Sum_probs=137.8

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh------
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM------  358 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~------  358 (710)
                      +.+.||++|+++|...|..    ..++++ +|+|+||||||++++.+.+.+....--..+....++.+++..+.      
T Consensus       755 D~LPhREeEIeeLasfL~paIkgsgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm~Lstp~sIY  834 (1164)
T PTZ00112        755 KYLPCREKEIKEVHGFLESGIKQSGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGMNVVHPNAAY  834 (1164)
T ss_pred             CcCCChHHHHHHHHHHHHHHHhcCCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCCccCCHHHHH
Confidence            5689999999999887653    344455 59999999999999999988743210011113455666653211      


Q ss_pred             -------hcc-ccCc-cHHHHHHHHHHHHHh--cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhc-ccccCCCeEE
Q 005179          359 -------AGA-KERG-ELEARVTTLISEIQK--SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLK-PSLGRGELQC  426 (710)
Q Consensus       359 -------~g~-~~~g-~~e~~l~~~~~~~~~--~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~-~~l~~~~v~v  426 (710)
                             .+. ...| .....+..++..+..  ....||+|||||.|...         ....+.+++. .......+.+
T Consensus       835 qvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK---------~QDVLYnLFR~~~~s~SKLiL  905 (1164)
T PTZ00112        835 QVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITK---------TQKVLFTLFDWPTKINSKLVL  905 (1164)
T ss_pred             HHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCcc---------HHHHHHHHHHHhhccCCeEEE
Confidence                   011 1111 223445666665532  23468999999999542         1222333333 2223567889


Q ss_pred             EEccChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcc
Q 005179          427 IASTTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD  504 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~  504 (710)
                      ||++|..++..  .+++.+.+||.  .|.|++++.+++.+||+..+...    ...+++++++.+++++...-+   -.+
T Consensus       906 IGISNdlDLpe--rLdPRLRSRLg~eeIvF~PYTaEQL~dILk~RAe~A----~gVLdDdAIELIArkVAq~SG---DAR  976 (1164)
T PTZ00112        906 IAISNTMDLPE--RLIPRCRSRLAFGRLVFSPYKGDEIEKIIKERLENC----KEIIDHTAIQLCARKVANVSG---DIR  976 (1164)
T ss_pred             EEecCchhcch--hhhhhhhhccccccccCCCCCHHHHHHHHHHHHHhC----CCCCCHHHHHHHHHhhhhcCC---HHH
Confidence            99998765433  46789999986  59999999999999999877643    346899999999886664332   246


Q ss_pred             hHHHHHHHHHhh
Q 005179          505 KAIDLVDEAGSR  516 (710)
Q Consensus       505 ~ai~ll~~a~~~  516 (710)
                      +|+++|..|+..
T Consensus       977 KALDILRrAgEi  988 (1164)
T PTZ00112        977 KALQICRKAFEN  988 (1164)
T ss_pred             HHHHHHHHHHhh
Confidence            789999988753

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=6.1e-13  Score=152.63  Aligned_cols=187  Identities=19%  Similarity=0.202  Sum_probs=131.6

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCC-Cc--cc----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEV-PV--FL----------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~-p~--~l----------  344 (710)
                      .|.+++||.+|+++||++..++.|...+..+...+ +||+||+|+|||++++.+++.+.+... +.  ..          
T Consensus         5 ~l~~kyRP~~~~eiiGq~~~~~~L~~~i~~~~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~~c~~i~   84 (585)
T PRK14950          5 VLYRKWRSQTFAELVGQEHVVQTLRNAIAEGRVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCEMCRAIA   84 (585)
T ss_pred             HHHHHhCCCCHHHhcCCHHHHHHHHHHHHhCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCHHHHHHh
Confidence            46789999999999999999999988887655544 589999999999999999999864221 10  00          


Q ss_pred             --cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          345 --LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       345 --~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                        .+..++.++..      ...+  ...++.+++.+..    ....|+||||+|.|             ..+..+.|+.+
T Consensus        85 ~~~~~d~~~i~~~------~~~~--vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L-------------~~~a~naLLk~  143 (585)
T PRK14950         85 EGSAVDVIEMDAA------SHTS--VDDAREIIERVQFRPALARYKVYIIDEVHML-------------STAAFNALLKT  143 (585)
T ss_pred             cCCCCeEEEEecc------ccCC--HHHHHHHHHHHhhCcccCCeEEEEEeChHhC-------------CHHHHHHHHHH
Confidence              01122333221      1111  1224455544432    34569999999999             33456777777


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      +++  ...++|.+++...     .+.+.+.+|+..+.|..++..+...+++.++.    ..++.++++++..++..+.+
T Consensus       144 LEepp~~tv~Il~t~~~~-----kll~tI~SR~~~i~f~~l~~~el~~~L~~~a~----~egl~i~~eal~~La~~s~G  213 (585)
T PRK14950        144 LEEPPPHAIFILATTEVH-----KVPATILSRCQRFDFHRHSVADMAAHLRKIAA----AEGINLEPGALEAIARAATG  213 (585)
T ss_pred             HhcCCCCeEEEEEeCChh-----hhhHHHHhccceeeCCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCC
Confidence            775  4566666665433     45688999999999999999998888877766    34788999999988887654

>PRK08727 hypothetical protein; Validated

Probab=99.48  E-value=8.6e-13  Score=134.23  Aligned_cols=177  Identities=14%  Similarity=0.161  Sum_probs=113.3

Q ss_pred             CCCCcccCH-HHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCcc
Q 005179          288 LIDPVIGRE-TEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGE  366 (710)
Q Consensus       288 ~l~~liGr~-~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~  366 (710)
                      +|+++++.. ..+..+.........+.++|+|++|||||+|+++++..+...       +..+.++.+..+.        
T Consensus        17 ~f~~f~~~~~n~~~~~~~~~~~~~~~~l~l~G~~G~GKThL~~a~~~~~~~~-------~~~~~y~~~~~~~--------   81 (233)
T PRK08727         17 RFDSYIAAPDGLLAQLQALAAGQSSDWLYLSGPAGTGKTHLALALCAAAEQA-------GRSSAYLPLQAAA--------   81 (233)
T ss_pred             ChhhccCCcHHHHHHHHHHHhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEEeHHHhh--------
Confidence            455555444 344444333333344569999999999999999999987543       4555565544322        


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHH
Q 005179          367 LEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       367 ~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                        ..+...++.+..  ..+|+|||++.+.+..       .....+.+++....+++ ..+|.+++... ..+...++.|.
T Consensus        82 --~~~~~~~~~l~~--~dlLiIDDi~~l~~~~-------~~~~~lf~l~n~~~~~~-~~vI~ts~~~p-~~l~~~~~dL~  148 (233)
T PRK08727         82 --GRLRDALEALEG--RSLVALDGLESIAGQR-------EDEVALFDFHNRARAAG-ITLLYTARQMP-DGLALVLPDLR  148 (233)
T ss_pred             --hhHHHHHHHHhc--CCEEEEeCcccccCCh-------HHHHHHHHHHHHHHHcC-CeEEEECCCCh-hhhhhhhHHHH
Confidence              223444554443  3489999999884321       11233444444443344 33444444221 12334679999


Q ss_pred             cccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          447 RRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       447 ~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +||.   .+.+++|+.+++..|++..+..    .++.++++++++++..+.|.
T Consensus       149 SRl~~~~~~~l~~~~~e~~~~iL~~~a~~----~~l~l~~e~~~~La~~~~rd  197 (233)
T PRK08727        149 SRLAQCIRIGLPVLDDVARAAVLRERAQR----RGLALDEAAIDWLLTHGERE  197 (233)
T ss_pred             HHHhcCceEEecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhCCCC
Confidence            9973   7899999999999999986653    47899999999999887653

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

Probab=99.48  E-value=7.9e-14  Score=139.84  Aligned_cols=166  Identities=21%  Similarity=0.276  Sum_probs=129.5

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|+.+-|--.+++.+.+.+.-             ..+..++||||||+|||.++++++..+          +...+.+.
T Consensus       129 ~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~m----------g~nfl~v~  198 (388)
T KOG0651|consen  129 ISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATM----------GVNFLKVV  198 (388)
T ss_pred             cCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhc----------CCceEEee
Confidence            3788899988888888876432             234457999999999999999999988          77788887


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------CCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------RGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------~~~v~v  426 (710)
                      .+.+.  .++.|+....+++.+..+....++|||+||||.+.+...+..+  .....++..|..++.       .+++.+
T Consensus       199 ss~lv--~kyiGEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~se~T--s~dreiqrTLMeLlnqmdgfd~l~rVk~  274 (388)
T KOG0651|consen  199 SSALV--DKYIGESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFSEGT--SSDREIQRTLMELLNQMDGFDTLHRVKT  274 (388)
T ss_pred             Hhhhh--hhhcccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEecccc--chhHHHHHHHHHHHHhhccchhcccccE
Confidence            78887  5689999999999999999999999999999998664322111  223444444443332       478999


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHH
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      |.|||.++     .++|+|.|  |++ .++++.|+...|..|++-...
T Consensus       275 ImatNrpd-----tLdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~  317 (388)
T KOG0651|consen  275 IMATNRPD-----TLDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQ  317 (388)
T ss_pred             EEecCCcc-----ccchhhcCCccccceeccCCcchhhceeeEeeccc
Confidence            99999987     78999999  887 799999999999888774433

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.48  E-value=6e-13  Score=152.30  Aligned_cols=200  Identities=20%  Similarity=0.189  Sum_probs=144.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCc---------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPV---------------  342 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~---------------  342 (710)
                      -+.+++||..|++++|+++.++.+...+..+.-.+ +||+||+|+|||++|+.+|+.+.+.....               
T Consensus         6 ~~~~kyRP~~f~~viGq~~~~~~L~~~i~~~~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~sC~~~~   85 (614)
T PRK14971          6 VSARKYRPSTFESVVGQEALTTTLKNAIATNKLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECESCVAFN   85 (614)
T ss_pred             HHHHHHCCCCHHHhcCcHHHHHHHHHHHHcCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcchHHHHHh
Confidence            35678999999999999999999999988766666 68999999999999999999986432110               


Q ss_pred             cccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          343 FLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       343 ~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                      ......++.+|..      ...  -...++.+++.+..    ++.-|++|||+|.|             ..+.++.|+.+
T Consensus        86 ~~~~~n~~~ld~~------~~~--~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~L-------------s~~a~naLLK~  144 (614)
T PRK14971         86 EQRSYNIHELDAA------SNN--SVDDIRNLIEQVRIPPQIGKYKIYIIDEVHML-------------SQAAFNAFLKT  144 (614)
T ss_pred             cCCCCceEEeccc------ccC--CHHHHHHHHHHHhhCcccCCcEEEEEECcccC-------------CHHHHHHHHHH
Confidence            0011233333321      111  12335555555532    33568999999999             44567888888


Q ss_pred             ccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          419 LGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       419 l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      |++  ...++|.+|+...     .+-+++++|+..+.|.+++.++....|+.++.    ..++.+++++++.++..+.+.
T Consensus       145 LEepp~~tifIL~tt~~~-----kIl~tI~SRc~iv~f~~ls~~ei~~~L~~ia~----~egi~i~~~al~~La~~s~gd  215 (614)
T PRK14971        145 LEEPPSYAIFILATTEKH-----KILPTILSRCQIFDFNRIQVADIVNHLQYVAS----KEGITAEPEALNVIAQKADGG  215 (614)
T ss_pred             HhCCCCCeEEEEEeCCch-----hchHHHHhhhheeecCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC
Confidence            886  4567777776533     56789999999999999999998888887766    348899999999999887653


Q ss_pred             hcCCCCcchHHHHHHHHH
Q 005179          497 ISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~  514 (710)
                      +      +.++.+++..+
T Consensus       216 l------r~al~~Lekl~  227 (614)
T PRK14971        216 M------RDALSIFDQVV  227 (614)
T ss_pred             H------HHHHHHHHHHH
Confidence            2      34555555443

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.47  E-value=6.6e-12  Score=138.42  Aligned_cols=207  Identities=16%  Similarity=0.189  Sum_probs=134.5

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh--------
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL--------  357 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l--------  357 (710)
                      +.++||+++++++...+..    ..+.+++|+||||+|||++++.+++.+....     .+..++.+++...        
T Consensus        30 ~~l~~Re~e~~~l~~~l~~~~~~~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~-----~~~~~v~in~~~~~~~~~~~~  104 (394)
T PRK00411         30 ENLPHREEQIEELAFALRPALRGSRPLNVLIYGPPGTGKTTTVKKVFEELEEIA-----VKVVYVYINCQIDRTRYAIFS  104 (394)
T ss_pred             CCCCCHHHHHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhc-----CCcEEEEEECCcCCCHHHHHH
Confidence            4589999999999888743    3457899999999999999999999875432     1344555554221        


Q ss_pred             --h---hc--cccCc-cHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc--ccCCCeEE
Q 005179          358 --M---AG--AKERG-ELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS--LGRGELQC  426 (710)
Q Consensus       358 --~---~g--~~~~g-~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~--l~~~~v~v  426 (710)
                        .   .+  ....+ .+.+.+..+.+.+.. ..+.||+|||+|.+...        .....+..++...  +...++.+
T Consensus       105 ~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~~~--------~~~~~l~~l~~~~~~~~~~~v~v  176 (394)
T PRK00411        105 EIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLFEK--------EGNDVLYSLLRAHEEYPGARIGV  176 (394)
T ss_pred             HHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhhcc--------CCchHHHHHHHhhhccCCCeEEE
Confidence              1   01  01112 234444555555443 34689999999999621        1112233332211  12336778


Q ss_pred             EEccChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcc
Q 005179          427 IASTTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD  504 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~  504 (710)
                      |++++......  .+++.+.+||.  .|.+++++.++..+||+..+...  ..+..+++++++.+++.+.+..+   ...
T Consensus       177 I~i~~~~~~~~--~l~~~~~s~~~~~~i~f~py~~~e~~~il~~r~~~~--~~~~~~~~~~l~~i~~~~~~~~G---d~r  249 (394)
T PRK00411        177 IGISSDLTFLY--ILDPRVKSVFRPEEIYFPPYTADEIFDILKDRVEEG--FYPGVVDDEVLDLIADLTAREHG---DAR  249 (394)
T ss_pred             EEEECCcchhh--hcCHHHHhcCCcceeecCCCCHHHHHHHHHHHHHhh--cccCCCCHhHHHHHHHHHHHhcC---cHH
Confidence            88877654333  36788888884  78999999999999999776431  22446899999999988866432   246


Q ss_pred             hHHHHHHHHHhh
Q 005179          505 KAIDLVDEAGSR  516 (710)
Q Consensus       505 ~ai~ll~~a~~~  516 (710)
                      .+++++..|+..
T Consensus       250 ~a~~ll~~a~~~  261 (394)
T PRK00411        250 VAIDLLRRAGLI  261 (394)
T ss_pred             HHHHHHHHHHHH
Confidence            778888777643

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.46  E-value=1e-12  Score=145.68  Aligned_cols=190  Identities=18%  Similarity=0.171  Sum_probs=119.5

Q ss_pred             cCCCCcc-cCHHH--HHHHHHHHHcC--CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc
Q 005179          287 ELIDPVI-GRETE--IQRIIQILCRR--TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA  361 (710)
Q Consensus       287 ~~l~~li-Gr~~~--i~~l~~~L~~~--~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~  361 (710)
                      -+|++++ |....  ...+..+....  ..++++|+|++|+|||+|++++++.+....     .+..++++....+....
T Consensus       112 ~tFdnFv~g~~n~~A~~aa~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~-----~~~~v~yv~~~~f~~~~  186 (450)
T PRK14087        112 NTFENFVIGSSNEQAFIAVQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNF-----SDLKVSYMSGDEFARKA  186 (450)
T ss_pred             cchhcccCCCcHHHHHHHHHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhC-----CCCeEEEEEHHHHHHHH
Confidence            3666665 54333  22233333222  235688999999999999999999875321     25677787776654221


Q ss_pred             ccCccHH---HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhh
Q 005179          362 KERGELE---ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQ  438 (710)
Q Consensus       362 ~~~g~~e---~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~  438 (710)
                        ...+.   ..+..+.+...  ...+|+|||++.+.+..       .....+..++....+++..++|.+...++.  .
T Consensus       187 --~~~l~~~~~~~~~~~~~~~--~~dvLiIDDiq~l~~k~-------~~~e~lf~l~N~~~~~~k~iIltsd~~P~~--l  253 (450)
T PRK14087        187 --VDILQKTHKEIEQFKNEIC--QNDVLIIDDVQFLSYKE-------KTNEIFFTIFNNFIENDKQLFFSSDKSPEL--L  253 (450)
T ss_pred             --HHHHHHhhhHHHHHHHHhc--cCCEEEEeccccccCCH-------HHHHHHHHHHHHHHHcCCcEEEECCCCHHH--H
Confidence              11111   11222222222  34589999999984321       113456666666666776555554444431  2


Q ss_pred             hhccHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          439 FEKDKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       439 ~~~d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      -.+++.|.+||.   .+.+.+|+.+++.+||+..+...  ...+.++++++++++..+.+.
T Consensus       254 ~~l~~rL~SR~~~Gl~~~L~~pd~e~r~~iL~~~~~~~--gl~~~l~~evl~~Ia~~~~gd  312 (450)
T PRK14087        254 NGFDNRLITRFNMGLSIAIQKLDNKTATAIIKKEIKNQ--NIKQEVTEEAINFISNYYSDD  312 (450)
T ss_pred             hhccHHHHHHHhCCceeccCCcCHHHHHHHHHHHHHhc--CCCCCCCHHHHHHHHHccCCC
Confidence            246899999996   79999999999999999877642  112379999999998886653

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.44  E-value=3.1e-12  Score=132.29  Aligned_cols=191  Identities=19%  Similarity=0.203  Sum_probs=124.7

Q ss_pred             CCcchhHHHhhhhhHHhh---hhc--CCCCcccCHHHHHHHHHHHH--------cCCCCCcEEEcCCCChHHHHHHHHHH
Q 005179          267 RTRASALEQFCVDLTARA---SEE--LIDPVIGRETEIQRIIQILC--------RRTKNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       267 ~~~~~~l~~~~~~l~~~~---~~~--~l~~liGr~~~i~~l~~~L~--------~~~~~nvLL~GppG~GKT~la~~la~  333 (710)
                      +|+.-.+..+-..+.-..   ..|  -|+.+|-.-..-.++..+-.        +..-+|+++|||||||||.+|+.||+
T Consensus       327 ~pw~gsls~~k~~i~~~~~~s~~gk~pl~~ViL~psLe~Rie~lA~aTaNTK~h~apfRNilfyGPPGTGKTm~ArelAr  406 (630)
T KOG0742|consen  327 FPWIGSLSALKHPIQGSRSASSRGKDPLEGVILHPSLEKRIEDLAIATANTKKHQAPFRNILFYGPPGTGKTMFARELAR  406 (630)
T ss_pred             CCCcccHHHHhchhhhhHhhhhcCCCCcCCeecCHHHHHHHHHHHHHhcccccccchhhheeeeCCCCCCchHHHHHHHh
Confidence            345555666655554322   222  37788877655555554321        12237899999999999999999998


Q ss_pred             HHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHH
Q 005179          334 RIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDIS  412 (710)
Q Consensus       334 ~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~  412 (710)
                      ..          +...-.+..+++   .....+-...++.+|+.++++ .+.+|||||.|.++-......- ++......
T Consensus       407 ~S----------GlDYA~mTGGDV---APlG~qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktym-SEaqRsaL  472 (630)
T KOG0742|consen  407 HS----------GLDYAIMTGGDV---APLGAQAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYM-SEAQRSAL  472 (630)
T ss_pred             hc----------CCceehhcCCCc---cccchHHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhh-cHHHHHHH
Confidence            75          222111111111   011123455689999999875 4788999999988754332111 12223333


Q ss_pred             Hhhc-cc-ccCCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhh
Q 005179          413 NLLK-PS-LGRGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAH  476 (710)
Q Consensus       413 ~~L~-~~-l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~  476 (710)
                      |.|+ .. -...+++++.+||.++     .+|.++.+||+ .|+|+.|-.++|..+|...+.+|...
T Consensus       473 NAlLfRTGdqSrdivLvlAtNrpg-----dlDsAV~DRide~veFpLPGeEERfkll~lYlnkyi~~  534 (630)
T KOG0742|consen  473 NALLFRTGDQSRDIVLVLATNRPG-----DLDSAVNDRIDEVVEFPLPGEEERFKLLNLYLNKYILK  534 (630)
T ss_pred             HHHHHHhcccccceEEEeccCCcc-----chhHHHHhhhhheeecCCCChHHHHHHHHHHHHHHhcC
Confidence            4332 11 1256789999999987     88999999997 89999999999999999988888643

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.41  E-value=4.8e-12  Score=135.54  Aligned_cols=163  Identities=18%  Similarity=0.212  Sum_probs=112.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc--ccCccHHHHHHHHHHHHHhcCCeEEEE
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA--KERGELEARVTTLISEIQKSGDVILFI  388 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~--~~~g~~e~~l~~~~~~~~~~~~~IL~I  388 (710)
                      .++++|+|+.|.|||+|+++++.......     .+..++.+....+....  ..+..-.+.++...      .-.+|+|
T Consensus       113 ~nplfi~G~~GlGKTHLl~Aign~~~~~~-----~~a~v~y~~se~f~~~~v~a~~~~~~~~Fk~~y------~~dlllI  181 (408)
T COG0593         113 YNPLFIYGGVGLGKTHLLQAIGNEALANG-----PNARVVYLTSEDFTNDFVKALRDNEMEKFKEKY------SLDLLLI  181 (408)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHhhC-----CCceEEeccHHHHHHHHHHHHHhhhHHHHHHhh------ccCeeee
Confidence            67889999999999999999999885532     24566666554433110  00000001112211      1238999


Q ss_pred             ccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHcccc---ceEecCCCHHHHHHH
Q 005179          389 DEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ---PVLISEPSQEDAVRI  465 (710)
Q Consensus       389 DEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~---~I~v~~Ps~~~~~~I  465 (710)
                      ||++.+.+...       ...++.+.+..+.+.++.+++.+...+.  ..-.+.+.|.+||.   .+.+.+|+.+.+..|
T Consensus       182 DDiq~l~gk~~-------~qeefFh~FN~l~~~~kqIvltsdr~P~--~l~~~~~rL~SR~~~Gl~~~I~~Pd~e~r~ai  252 (408)
T COG0593         182 DDIQFLAGKER-------TQEEFFHTFNALLENGKQIVLTSDRPPK--ELNGLEDRLRSRLEWGLVVEIEPPDDETRLAI  252 (408)
T ss_pred             chHhHhcCChh-------HHHHHHHHHHHHHhcCCEEEEEcCCCch--hhccccHHHHHHHhceeEEeeCCCCHHHHHHH
Confidence            99999965432       2667888888888888755555544433  23346799999996   799999999999999


Q ss_pred             HHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          466 LLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       466 L~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      |+....    ..++.++++++.+++....+-+
T Consensus       253 L~kka~----~~~~~i~~ev~~~la~~~~~nv  280 (408)
T COG0593         253 LRKKAE----DRGIEIPDEVLEFLAKRLDRNV  280 (408)
T ss_pred             HHHHHH----hcCCCCCHHHHHHHHHHhhccH
Confidence            998555    5689999999999987765543

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.41  E-value=1.9e-12  Score=140.51  Aligned_cols=174  Identities=14%  Similarity=0.172  Sum_probs=118.9

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCC----------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc-c------------
Q 005179          288 LIDPVIGRETEIQRIIQILCRRT----------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVF-L------------  344 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~----------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~-l------------  344 (710)
                      .|++++|++..++.|...+..+.          +..+||+||+|+|||++|+.+|+.+.+...... .            
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~~~~   82 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTVLAG   82 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcC
Confidence            46789999999999999887753          455899999999999999999999866431100 0            


Q ss_pred             cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc
Q 005179          345 LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG  420 (710)
Q Consensus       345 ~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~  420 (710)
                      ....+..+...    +. .  -....++.+++.+..    .+..|+||||+|.+             ....+|.|+..|+
T Consensus        83 ~hpD~~~i~~~----~~-~--i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m-------------~~~aanaLLk~LE  142 (394)
T PRK07940         83 THPDVRVVAPE----GL-S--IGVDEVRELVTIAARRPSTGRWRIVVIEDADRL-------------TERAANALLKAVE  142 (394)
T ss_pred             CCCCEEEeccc----cc-c--CCHHHHHHHHHHHHhCcccCCcEEEEEechhhc-------------CHHHHHHHHHHhh
Confidence            00112222111    00 0  112335666666543    34569999999999             4446677888887


Q ss_pred             C---CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          421 R---GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       421 ~---~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +   +.+.+++|++..      .+.|++++||+.+.|++|+.++..++|..   +      ..++++.+..++.++.+.
T Consensus       143 ep~~~~~fIL~a~~~~------~llpTIrSRc~~i~f~~~~~~~i~~~L~~---~------~~~~~~~a~~la~~s~G~  206 (394)
T PRK07940        143 EPPPRTVWLLCAPSPE------DVLPTIRSRCRHVALRTPSVEAVAEVLVR---R------DGVDPETARRAARASQGH  206 (394)
T ss_pred             cCCCCCeEEEEECChH------HChHHHHhhCeEEECCCCCHHHHHHHHHH---h------cCCCHHHHHHHHHHcCCC
Confidence            6   455566666643      67899999999999999999997766652   1      136677777787777664

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.41  E-value=4.4e-12  Score=131.38  Aligned_cols=163  Identities=19%  Similarity=0.249  Sum_probs=108.0

Q ss_pred             HHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh------hhhhhccc-c--CccHHH
Q 005179          299 IQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM------GLLMAGAK-E--RGELEA  369 (710)
Q Consensus       299 i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~------~~l~~g~~-~--~g~~e~  369 (710)
                      ++++...+.  .+.+++|+||||||||++|+++|+.+          +.+++.+++      .+++.... +  ......
T Consensus        11 ~~~~l~~l~--~g~~vLL~G~~GtGKT~lA~~la~~l----------g~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~   78 (262)
T TIGR02640        11 TSRALRYLK--SGYPVHLRGPAGTGKTTLAMHVARKR----------DRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQ   78 (262)
T ss_pred             HHHHHHHHh--cCCeEEEEcCCCCCHHHHHHHHHHHh----------CCCEEEEeCCccCCHHHHhhhhcccchhhHHHH
Confidence            344444444  35789999999999999999999876          445554433      22221100 0  000000


Q ss_pred             HH----------------HHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------
Q 005179          370 RV----------------TTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------  422 (710)
Q Consensus       370 ~l----------------~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------  422 (710)
                      .+                ..++..+.  .+.+|+|||++.+             ..++++.|..+|+.+           
T Consensus        79 ~~~~~~~~~~~~~~~~~~g~l~~A~~--~g~~lllDEi~r~-------------~~~~q~~Ll~~Le~~~~~i~~~~~~~  143 (262)
T TIGR02640        79 FIHNVVKLEDIVRQNWVDNRLTLAVR--EGFTLVYDEFTRS-------------KPETNNVLLSVFEEGVLELPGKRGTS  143 (262)
T ss_pred             HHHHhhhhhcccceeecCchHHHHHH--cCCEEEEcchhhC-------------CHHHHHHHHHHhcCCeEEccCCCCCC
Confidence            00                01111122  3469999999998             456677776666532           


Q ss_pred             -------CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          423 -------ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       423 -------~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                             .+++|+|+|+..|....+++++|.+||..+.++.|+.++..+|++...         .+.++.++.++.+...
T Consensus       144 ~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~R~~~i~i~~P~~~~e~~Il~~~~---------~~~~~~~~~iv~~~~~  214 (262)
T TIGR02640       144 RYVDVHPEFRVIFTSNPVEYAGVHETQDALLDRLITIFMDYPDIDTETAILRAKT---------DVAEDSAATIVRLVRE  214 (262)
T ss_pred             ceEecCCCCEEEEeeCCccccceecccHHHHhhcEEEECCCCCHHHHHHHHHHhh---------CCCHHHHHHHHHHHHH
Confidence                   467999999887776667889999999999999999999888887532         3677788888877665


Q ss_pred             hh
Q 005179          496 YI  497 (710)
Q Consensus       496 ~i  497 (710)
                      .-
T Consensus       215 ~R  216 (262)
T TIGR02640       215 FR  216 (262)
T ss_pred             HH
Confidence            44

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).

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.41  E-value=7.5e-12  Score=126.96  Aligned_cols=188  Identities=15%  Similarity=0.183  Sum_probs=117.2

Q ss_pred             CCCcc--cCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCcc
Q 005179          289 IDPVI--GRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGE  366 (710)
Q Consensus       289 l~~li--Gr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~  366 (710)
                      |++++  +.+..++.+.+++......+++|+||+|||||++++++++.....       +..++.+++..+...      
T Consensus        14 ~~~~~~~~~~~~~~~l~~~~~~~~~~~lll~G~~G~GKT~la~~~~~~~~~~-------~~~~~~i~~~~~~~~------   80 (226)
T TIGR03420        14 FDNFYAGGNAELLAALRQLAAGKGDRFLYLWGESGSGKSHLLQAACAAAEER-------GKSAIYLPLAELAQA------   80 (226)
T ss_pred             hcCcCcCCcHHHHHHHHHHHhcCCCCeEEEECCCCCCHHHHHHHHHHHHHhc-------CCcEEEEeHHHHHHh------
Confidence            44444  245577777777666677899999999999999999999987432       456777777665421      


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHH
Q 005179          367 LEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       367 ~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                          ...++..+..  ..+|+|||+|.+....       .....+..++......+..+++++++...  ......+.|.
T Consensus        81 ----~~~~~~~~~~--~~lLvIDdi~~l~~~~-------~~~~~L~~~l~~~~~~~~~iIits~~~~~--~~~~~~~~L~  145 (226)
T TIGR03420        81 ----DPEVLEGLEQ--ADLVCLDDVEAIAGQP-------EWQEALFHLYNRVREAGGRLLIAGRAAPA--QLPLRLPDLR  145 (226)
T ss_pred             ----HHHHHhhccc--CCEEEEeChhhhcCCh-------HHHHHHHHHHHHHHHcCCeEEEECCCChH--HCCcccHHHH
Confidence                1223332322  3489999999983210       00223344433333334433443333322  1111237888


Q ss_pred             cccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          447 RRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       447 ~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      +||.   .|.+++|+.+++..+++....    ..++.+++++++.++..+.+-      +..+..+++.+.
T Consensus       146 ~r~~~~~~i~l~~l~~~e~~~~l~~~~~----~~~~~~~~~~l~~L~~~~~gn------~r~L~~~l~~~~  206 (226)
T TIGR03420       146 TRLAWGLVFQLPPLSDEEKIAALQSRAA----RRGLQLPDEVADYLLRHGSRD------MGSLMALLDALD  206 (226)
T ss_pred             HHHhcCeeEecCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhccCC------HHHHHHHHHHHH
Confidence            8874   789999999999999876554    347889999998887754432      344555555543

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.

>CHL00195 ycf46 Ycf46; Provisional

Probab=99.40  E-value=9.4e-12  Score=138.33  Aligned_cols=96  Identities=11%  Similarity=0.136  Sum_probs=63.0

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHH
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDA  462 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~  462 (710)
                      +.|+++.|+|.++....       ....+.++....-..++.+||.+.+.       .+++.|.+-+..+.++.|+.+++
T Consensus        82 ~~~~vl~d~h~~~~~~~-------~~r~l~~l~~~~~~~~~~~i~~~~~~-------~~p~el~~~~~~~~~~lP~~~ei  147 (489)
T CHL00195         82 PALFLLKDFNRFLNDIS-------ISRKLRNLSRILKTQPKTIIIIASEL-------NIPKELKDLITVLEFPLPTESEI  147 (489)
T ss_pred             CcEEEEecchhhhcchH-------HHHHHHHHHHHHHhCCCEEEEEcCCC-------CCCHHHHhceeEEeecCcCHHHH
Confidence            68999999999973211       11222222221222344444443322       46677877777889999999999


Q ss_pred             HHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          463 VRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       463 ~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      ..+++.+..    ..++.++++.++.+++.+.++
T Consensus       148 ~~~l~~~~~----~~~~~~~~~~~~~l~~~~~gl  177 (489)
T CHL00195        148 KKELTRLIK----SLNIKIDSELLENLTRACQGL  177 (489)
T ss_pred             HHHHHHHHH----hcCCCCCHHHHHHHHHHhCCC
Confidence            999877664    346788999999888887765

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.38  E-value=1e-11  Score=135.43  Aligned_cols=191  Identities=25%  Similarity=0.316  Sum_probs=121.3

Q ss_pred             cccCHHHHHHHHHHHHc----------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          292 VIGRETEIQRIIQILCR----------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~----------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      ++|+++.++.+...+..                ....|+||+||||||||++|+++|..+          +.+++.+|++
T Consensus        73 ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l----------~~pf~~id~~  142 (412)
T PRK05342         73 VIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL----------DVPFAIADAT  142 (412)
T ss_pred             eeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh----------CCCceecchh
Confidence            89999988877554421                124789999999999999999999887          5667777776


Q ss_pred             hhhhccccCcc-HHHHHHHHHHH----HHhcCCeEEEEccchhhhhCCCCCC-CCCCChHhHHHhhcccccCC-------
Q 005179          356 LLMAGAKERGE-LEARVTTLISE----IQKSGDVILFIDEVHTLIGSGTVGR-GNKGTGLDISNLLKPSLGRG-------  422 (710)
Q Consensus       356 ~l~~g~~~~g~-~e~~l~~~~~~----~~~~~~~IL~IDEid~l~~~~~~~~-~~~~~~~~~~~~L~~~l~~~-------  422 (710)
                      .+.. ..+.|. .+..+..++..    +....+.||||||||.+...+.... +.+-++..+++.|+.+|+..       
T Consensus       143 ~l~~-~gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~~~  221 (412)
T PRK05342        143 TLTE-AGYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQ  221 (412)
T ss_pred             hccc-CCcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeCCC
Confidence            5542 224443 33334444332    2345678999999999975421100 01112335677777766521       


Q ss_pred             --------CeEEEEccCh---------------------------------------HHHHh--------hhhccHHHHc
Q 005179          423 --------ELQCIASTTQ---------------------------------------DEHRT--------QFEKDKALAR  447 (710)
Q Consensus       423 --------~v~vI~att~---------------------------------------~~~~~--------~~~~d~aL~~  447 (710)
                              +.++|.|+|.                                       ..+..        .+.+.|.|..
T Consensus       222 gg~~~~~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEflg  301 (412)
T PRK05342        222 GGRKHPQQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIG  301 (412)
T ss_pred             CCcCcCCCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHhC
Confidence                    1223333332                                       00000        1124688999


Q ss_pred             ccc-ceEecCCCHHHHHHHHH----HHHHHHHh---hc--CCCCCHHHHHHHHHHh
Q 005179          448 RFQ-PVLISEPSQEDAVRILL----GLREKYEA---HH--NCKFTLEAINAAVHLS  493 (710)
Q Consensus       448 Rf~-~I~v~~Ps~~~~~~IL~----~l~~~~~~---~~--~~~i~~~~l~~l~~ls  493 (710)
                      |++ .+.+.+++.++...|+.    .+.++|..   .+  .+.+++++++++++.+
T Consensus       302 Rld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~  357 (412)
T PRK05342        302 RLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKA  357 (412)
T ss_pred             CCCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhC
Confidence            997 78889999999999997    35554432   23  3578999999998864

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.37  E-value=7.6e-12  Score=127.06  Aligned_cols=171  Identities=14%  Similarity=0.175  Sum_probs=107.9

Q ss_pred             cCCCCcc-cCH-HHHHHHHHHHH-cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc
Q 005179          287 ELIDPVI-GRE-TEIQRIIQILC-RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE  363 (710)
Q Consensus       287 ~~l~~li-Gr~-~~i~~l~~~L~-~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~  363 (710)
                      -+|++++ |.+ ..+..+.++.. ....++++|+||+|||||+|++++++.....       +..++.+++..+...   
T Consensus        15 ~~~d~f~~~~~~~~~~~l~~~~~~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~-------~~~~~~i~~~~~~~~---   84 (227)
T PRK08903         15 PTFDNFVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYG-------GRNARYLDAASPLLA---   84 (227)
T ss_pred             hhhcccccCCcHHHHHHHHHHHhccCCCCeEEEECCCCCCHHHHHHHHHHHHHhC-------CCcEEEEehHHhHHH---
Confidence            4566666 333 33344444433 2345789999999999999999999987443       456667766543311   


Q ss_pred             CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccH
Q 005179          364 RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDK  443 (710)
Q Consensus       364 ~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~  443 (710)
                                 +..  .....+|+|||+|.+-.         .....+...+...-+++..++|.+++...  ....+.+
T Consensus        85 -----------~~~--~~~~~~liiDdi~~l~~---------~~~~~L~~~~~~~~~~~~~~vl~~~~~~~--~~~~l~~  140 (227)
T PRK08903         85 -----------FDF--DPEAELYAVDDVERLDD---------AQQIALFNLFNRVRAHGQGALLVAGPAAP--LALPLRE  140 (227)
T ss_pred             -----------Hhh--cccCCEEEEeChhhcCc---------hHHHHHHHHHHHHHHcCCcEEEEeCCCCH--HhCCCCH
Confidence                       011  12345899999998821         11223334443333455544555544332  1223568


Q ss_pred             HHHccc---cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          444 ALARRF---QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       444 aL~~Rf---~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      .|.+||   ..|.+++|+.+++..++..+..    ..++.+++++++.++..+.+
T Consensus       141 ~L~sr~~~~~~i~l~pl~~~~~~~~l~~~~~----~~~v~l~~~al~~L~~~~~g  191 (227)
T PRK08903        141 DLRTRLGWGLVYELKPLSDADKIAALKAAAA----ERGLQLADEVPDYLLTHFRR  191 (227)
T ss_pred             HHHHHHhcCeEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhccC
Confidence            888888   3799999998888888776554    45799999999999876444

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=99.37  E-value=4.4e-12  Score=139.61  Aligned_cols=188  Identities=21%  Similarity=0.307  Sum_probs=128.9

Q ss_pred             CCcccCHHHHHHHHHHHHcCC------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh----
Q 005179          290 DPVIGRETEIQRIIQILCRRT------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA----  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~----  359 (710)
                      ++-+|.++..+++++.+....      +.-+.|+||||||||++++.||+.+          +..++.+.++.+..    
T Consensus       411 eDHYgm~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~kSIA~AL----------nRkFfRfSvGG~tDvAeI  480 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIAKSIARAL----------NRKFFRFSVGGMTDVAEI  480 (906)
T ss_pred             ccccchHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHHHHHHHHh----------CCceEEEeccccccHHhh
Confidence            467899999999999876532      2235789999999999999999999          77777776655532    


Q ss_pred             -ccc--cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----------------
Q 005179          360 -GAK--ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----------------  420 (710)
Q Consensus       360 -g~~--~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----------------  420 (710)
                       |..  |.|.+--++-+.++.+....| +++|||||.+- .|-.|        |-...|+.+|.                
T Consensus       481 kGHRRTYVGAMPGkiIq~LK~v~t~NP-liLiDEvDKlG-~g~qG--------DPasALLElLDPEQNanFlDHYLdVp~  550 (906)
T KOG2004|consen  481 KGHRRTYVGAMPGKIIQCLKKVKTENP-LILIDEVDKLG-SGHQG--------DPASALLELLDPEQNANFLDHYLDVPV  550 (906)
T ss_pred             cccceeeeccCChHHHHHHHhhCCCCc-eEEeehhhhhC-CCCCC--------ChHHHHHHhcChhhccchhhhcccccc
Confidence             211  344444445555555555555 67789999993 22221        22333333332                


Q ss_pred             -CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHH-HHHHHhhcC-----CCCCHHHHHHHHHHh
Q 005179          421 -RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGL-REKYEAHHN-----CKFTLEAINAAVHLS  493 (710)
Q Consensus       421 -~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l-~~~~~~~~~-----~~i~~~~l~~l~~ls  493 (710)
                       =.++.+|+|.|.-+     .+++.|++|+..|+++-+..++...|.+.. ..+....++     ++++++++..+++.-
T Consensus       551 DLSkVLFicTAN~id-----tIP~pLlDRMEvIelsGYv~eEKv~IA~~yLip~a~~~~gl~~e~v~is~~al~~lI~~Y  625 (906)
T KOG2004|consen  551 DLSKVLFICTANVID-----TIPPPLLDRMEVIELSGYVAEEKVKIAERYLIPQALKDCGLKPEQVKISDDALLALIERY  625 (906)
T ss_pred             chhheEEEEeccccc-----cCChhhhhhhheeeccCccHHHHHHHHHHhhhhHHHHHcCCCHHhcCccHHHHHHHHHHH
Confidence             13688999988865     788999999999999999999999998863 344444444     578888887777654


Q ss_pred             hhhhcCCCC
Q 005179          494 ARYISDRYL  502 (710)
Q Consensus       494 ~~~i~~r~~  502 (710)
                      -|-.+-|.+
T Consensus       626 crEaGVRnL  634 (906)
T KOG2004|consen  626 CREAGVRNL  634 (906)
T ss_pred             HHHHhHHHH
Confidence            444444443

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.37  E-value=5.5e-12  Score=139.86  Aligned_cols=199  Identities=20%  Similarity=0.274  Sum_probs=135.3

Q ss_pred             CcccCHHHHHHHHHHHHcC-----CC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-----
Q 005179          291 PVIGRETEIQRIIQILCRR-----TK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-----  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~-----~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-----  359 (710)
                      +-.|-++..+++++.|...     .+ .-++|+||||||||+|++.||+.+          +..++.+.++.+..     
T Consensus       324 dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~al----------~RkfvR~sLGGvrDEAEIR  393 (782)
T COG0466         324 DHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKAL----------GRKFVRISLGGVRDEAEIR  393 (782)
T ss_pred             cccCchhHHHHHHHHHHHHHHhccCCCcEEEEECCCCCCchhHHHHHHHHh----------CCCEEEEecCccccHHHhc
Confidence            5688898999999877542     22 335789999999999999999999          77777777655542     


Q ss_pred             ccc--cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----------------
Q 005179          360 GAK--ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----------------  420 (710)
Q Consensus       360 g~~--~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----------------  420 (710)
                      |..  |.|.+--++-+-+..+....| +++|||||.+...-         .-|-+..|+..|.                 
T Consensus       394 GHRRTYIGamPGrIiQ~mkka~~~NP-v~LLDEIDKm~ss~---------rGDPaSALLEVLDPEQN~~F~DhYLev~yD  463 (782)
T COG0466         394 GHRRTYIGAMPGKIIQGMKKAGVKNP-VFLLDEIDKMGSSF---------RGDPASALLEVLDPEQNNTFSDHYLEVPYD  463 (782)
T ss_pred             cccccccccCChHHHHHHHHhCCcCC-eEEeechhhccCCC---------CCChHHHHHhhcCHhhcCchhhccccCccc
Confidence            211  334443444444444444445 77889999994321         1122333333332                 


Q ss_pred             CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHH-HHHHHHhhcC-----CCCCHHHHHHHHHHhh
Q 005179          421 RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLG-LREKYEAHHN-----CKFTLEAINAAVHLSA  494 (710)
Q Consensus       421 ~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~-l~~~~~~~~~-----~~i~~~~l~~l~~ls~  494 (710)
                      =.++.+|+|.|.-+     .++..|++|...|++.-++.++..+|-+. +..+....|+     +.++++++..+++.-.
T Consensus       464 LS~VmFiaTANsl~-----tIP~PLlDRMEiI~lsgYt~~EKl~IAk~~LiPk~~~~~gL~~~el~i~d~ai~~iI~~YT  538 (782)
T COG0466         464 LSKVMFIATANSLD-----TIPAPLLDRMEVIRLSGYTEDEKLEIAKRHLIPKQLKEHGLKKGELTITDEAIKDIIRYYT  538 (782)
T ss_pred             hhheEEEeecCccc-----cCChHHhcceeeeeecCCChHHHHHHHHHhcchHHHHHcCCCccceeecHHHHHHHHHHHh
Confidence            13688999998865     68999999999999999999999999886 3444444444     5799999999988766


Q ss_pred             hhhcCCCCcchHHHHHHHHH
Q 005179          495 RYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       495 ~~i~~r~~p~~ai~ll~~a~  514 (710)
                      |-.+-|.+-...-.+++.++
T Consensus       539 REAGVR~LeR~i~ki~RK~~  558 (782)
T COG0466         539 REAGVRNLEREIAKICRKAA  558 (782)
T ss_pred             HhhhhhHHHHHHHHHHHHHH
Confidence            66665655444444444443

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=99.36  E-value=3.2e-11  Score=119.87  Aligned_cols=166  Identities=22%  Similarity=0.325  Sum_probs=117.4

Q ss_pred             CCCCcccCHHHHHHHHH----HHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc
Q 005179          288 LIDPVIGRETEIQRIIQ----ILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE  363 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~----~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~  363 (710)
                      .+++++|.+.+.+.|++    .+.....+|+||+|++|||||++++++..++...       +.++++++-..+..    
T Consensus        25 ~l~~L~Gie~Qk~~l~~Nt~~Fl~G~pannvLL~G~rGtGKSSlVkall~~y~~~-------GLRlIev~k~~L~~----   93 (249)
T PF05673_consen   25 RLDDLIGIERQKEALIENTEQFLQGLPANNVLLWGARGTGKSSLVKALLNEYADQ-------GLRLIEVSKEDLGD----   93 (249)
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHHcCCCCcceEEecCCCCCHHHHHHHHHHHHhhc-------CceEEEECHHHhcc----
Confidence            45678999988887776    3455677999999999999999999999998553       67888887655541    


Q ss_pred             CccHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------CCeEEEEccChHHH-
Q 005179          364 RGELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------GELQCIASTTQDEH-  435 (710)
Q Consensus       364 ~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------~~v~vI~att~~~~-  435 (710)
                             +..+++.+.. ..+.|||+||+-  ++.          ...-...|+.+|+.      .++.+.+|+|.-.. 
T Consensus        94 -------l~~l~~~l~~~~~kFIlf~DDLs--Fe~----------~d~~yk~LKs~LeGgle~~P~NvliyATSNRRHLv  154 (249)
T PF05673_consen   94 -------LPELLDLLRDRPYKFILFCDDLS--FEE----------GDTEYKALKSVLEGGLEARPDNVLIYATSNRRHLV  154 (249)
T ss_pred             -------HHHHHHHHhcCCCCEEEEecCCC--CCC----------CcHHHHHHHHHhcCccccCCCcEEEEEecchhhcc
Confidence                   5556666653 357999999864  222          22235666766653      35777777765321 


Q ss_pred             ----Hhhh-----hc--------cHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHH
Q 005179          436 ----RTQF-----EK--------DKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAIN  487 (710)
Q Consensus       436 ----~~~~-----~~--------d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~  487 (710)
                          ....     ++        .-+|..||. .|.|.+|+.++..+|+++++.++    ++.++++.+.
T Consensus       155 ~E~~~d~~~~~~~eih~~d~~eEklSLsDRFGL~l~F~~~~q~~YL~IV~~~~~~~----g~~~~~e~l~  220 (249)
T PF05673_consen  155 PESFSDREDIQDDEIHPSDTIEEKLSLSDRFGLWLSFYPPDQEEYLAIVRHYAERY----GLELDEEELR  220 (249)
T ss_pred             chhhhhccCCCccccCcchHHHHHHhHHHhCCcEEEecCCCHHHHHHHHHHHHHHc----CCCCCHHHHH
Confidence                1100     11        135777998 89999999999999999988754    7888865443

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.36  E-value=2.3e-11  Score=130.04  Aligned_cols=112  Identities=26%  Similarity=0.325  Sum_probs=79.4

Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------CCeEEEEccChHHHHhhhhccHHHHccc
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------GELQCIASTTQDEHRTQFEKDKALARRF  449 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------~~v~vI~att~~~~~~~~~~d~aL~~Rf  449 (710)
                      ...|+||||||.++..+... +.+-.+.-++..|+++++.            .++.+|++..-... +.-.+-|.|..||
T Consensus       249 ~~GIVfiDEiDKIa~~~~~~-~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~-kp~DlIPEl~GR~  326 (443)
T PRK05201        249 QNGIVFIDEIDKIAARGGSS-GPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVS-KPSDLIPELQGRF  326 (443)
T ss_pred             cCCEEEEEcchhhcccCCCC-CCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCC-ChhhccHHHhCcc
Confidence            45699999999998664321 1122334478888888874            46677876542210 1114569999999


Q ss_pred             c-ceEecCCCHHHHHHHHH----HHHHHHHhh-----cCCCCCHHHHHHHHHHhhh
Q 005179          450 Q-PVLISEPSQEDAVRILL----GLREKYEAH-----HNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       450 ~-~I~v~~Ps~~~~~~IL~----~l~~~~~~~-----~~~~i~~~~l~~l~~ls~~  495 (710)
                      . .+.+.+++.++...||.    .+.++|...     ..+.+++++++.+++.+..
T Consensus       327 Pi~v~L~~L~~~dL~~ILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~  382 (443)
T PRK05201        327 PIRVELDALTEEDFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQ  382 (443)
T ss_pred             ceEEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHH
Confidence            7 78999999999999994    477776642     2357899999999998875

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.36  E-value=2.1e-11  Score=130.33  Aligned_cols=112  Identities=24%  Similarity=0.309  Sum_probs=78.5

Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------CCeEEEEccChHHHHhhhhccHHHHccc
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------GELQCIASTTQDEHRTQFEKDKALARRF  449 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------~~v~vI~att~~~~~~~~~~d~aL~~Rf  449 (710)
                      ...|+||||||.++..+... +.+-.+.-++..|+++++.            .++.+|++..-.... .-.+-|.|.-||
T Consensus       247 ~~GIVfiDEiDKIa~~~~~~-~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~k-p~DlIPEl~GR~  324 (441)
T TIGR00390       247 QSGIIFIDEIDKIAKKGESS-GADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAK-PSDLIPELQGRF  324 (441)
T ss_pred             cCCEEEEEchhhhcccCCCC-CCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCC-hhhccHHHhCcc
Confidence            45699999999998664221 1112233478888888874            456777765422111 113569999999


Q ss_pred             c-ceEecCCCHHHHHHHH----HHHHHHHHh---hcC--CCCCHHHHHHHHHHhhh
Q 005179          450 Q-PVLISEPSQEDAVRIL----LGLREKYEA---HHN--CKFTLEAINAAVHLSAR  495 (710)
Q Consensus       450 ~-~I~v~~Ps~~~~~~IL----~~l~~~~~~---~~~--~~i~~~~l~~l~~ls~~  495 (710)
                      . .+.+.+++.++...||    ..+.++|..   ..+  +.+++++++.+++.+..
T Consensus       325 Pi~v~L~~L~~edL~rILteP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~  380 (441)
T TIGR00390       325 PIRVELQALTTDDFERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAYN  380 (441)
T ss_pred             ceEEECCCCCHHHHHHHhcCChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHHHH
Confidence            7 7899999999999999    456666653   223  57899999999998764

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.

>PRK09087 hypothetical protein; Validated

Probab=99.35  E-value=1.3e-11  Score=124.58  Aligned_cols=142  Identities=15%  Similarity=0.097  Sum_probs=101.9

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccch
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVH  392 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid  392 (710)
                      .++|+||+|+|||||+++++...          +..  .++...+.             .+++..+.   ..+|+|||++
T Consensus        46 ~l~l~G~~GsGKThLl~~~~~~~----------~~~--~i~~~~~~-------------~~~~~~~~---~~~l~iDDi~   97 (226)
T PRK09087         46 VVVLAGPVGSGKTHLASIWREKS----------DAL--LIHPNEIG-------------SDAANAAA---EGPVLIEDID   97 (226)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhc----------CCE--EecHHHcc-------------hHHHHhhh---cCeEEEECCC
Confidence            48999999999999999988754          222  33322111             11222222   1378899999


Q ss_pred             hhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccc---cceEecCCCHHHHHHHHHHH
Q 005179          393 TLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRF---QPVLISEPSQEDAVRILLGL  469 (710)
Q Consensus       393 ~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf---~~I~v~~Ps~~~~~~IL~~l  469 (710)
                      .+.          .....+.+++....+++..++|++++.+.+-.  ...+.|++||   ..+.+.+|+.+++.+||+..
T Consensus        98 ~~~----------~~~~~lf~l~n~~~~~g~~ilits~~~p~~~~--~~~~dL~SRl~~gl~~~l~~pd~e~~~~iL~~~  165 (226)
T PRK09087         98 AGG----------FDETGLFHLINSVRQAGTSLLMTSRLWPSSWN--VKLPDLKSRLKAATVVEIGEPDDALLSQVIFKL  165 (226)
T ss_pred             CCC----------CCHHHHHHHHHHHHhCCCeEEEECCCChHHhc--cccccHHHHHhCCceeecCCCCHHHHHHHHHHH
Confidence            872          11445777777777888888888877665221  2368899999   48999999999999999987


Q ss_pred             HHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          470 REKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       470 ~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      +..    .++.++++++++++..+.+-+.
T Consensus       166 ~~~----~~~~l~~ev~~~La~~~~r~~~  190 (226)
T PRK09087        166 FAD----RQLYVDPHVVYYLVSRMERSLF  190 (226)
T ss_pred             HHH----cCCCCCHHHHHHHHHHhhhhHH
Confidence            764    4789999999999998776443

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.34  E-value=4.5e-12  Score=127.88  Aligned_cols=152  Identities=22%  Similarity=0.305  Sum_probs=105.0

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHH---hcCC--eEEEE
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ---KSGD--VILFI  388 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~---~~~~--~IL~I  388 (710)
                      +||+||||||||+|+++||+.+.= .....+....+++++..++.  +++.++..+.+..+|+.+.   +.++  +.++|
T Consensus       180 iLlhGPPGTGKTSLCKaLaQkLSI-R~~~~y~~~~liEinshsLF--SKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLI  256 (423)
T KOG0744|consen  180 ILLHGPPGTGKTSLCKALAQKLSI-RTNDRYYKGQLIEINSHSLF--SKWFSESGKLVAKMFQKIQELVEDRGNLVFVLI  256 (423)
T ss_pred             EEEeCCCCCChhHHHHHHHHhhee-eecCccccceEEEEehhHHH--HHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEe
Confidence            689999999999999999999832 22233445678899888887  4555555555555555543   3333  44669


Q ss_pred             ccchhhhhCCCCCCCC--CCChHhHHHhhccccc----CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHH
Q 005179          389 DEVHTLIGSGTVGRGN--KGTGLDISNLLKPSLG----RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQED  461 (710)
Q Consensus       389 DEid~l~~~~~~~~~~--~~~~~~~~~~L~~~l~----~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~  461 (710)
                      ||++.|..++......  ......+.|.|+..+.    ..++.+.+|.|..+     .+|.+|.+|-+ ...|.+|+...
T Consensus       257 DEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~-----siD~AfVDRADi~~yVG~Pt~~a  331 (423)
T KOG0744|consen  257 DEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTD-----SIDVAFVDRADIVFYVGPPTAEA  331 (423)
T ss_pred             HHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHH-----HHHHHhhhHhhheeecCCccHHH
Confidence            9999997654221111  1224556676665443    35566666666665     78999999998 78999999999


Q ss_pred             HHHHHHHHHHHH
Q 005179          462 AVRILLGLREKY  473 (710)
Q Consensus       462 ~~~IL~~l~~~~  473 (710)
                      +.+|++.-....
T Consensus       332 i~~IlkscieEL  343 (423)
T KOG0744|consen  332 IYEILKSCIEEL  343 (423)
T ss_pred             HHHHHHHHHHHH
Confidence            999999866644

>PRK06620 hypothetical protein; Validated

Probab=99.33  E-value=1.2e-11  Score=123.90  Aligned_cols=135  Identities=11%  Similarity=0.145  Sum_probs=98.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEV  391 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEi  391 (710)
                      ++++|+||||+|||||++++++..          +..  .+.  ...    . .      ....   .  ...+|+||||
T Consensus        45 ~~l~l~Gp~G~GKThLl~a~~~~~----------~~~--~~~--~~~----~-~------~~~~---~--~~d~lliDdi   94 (214)
T PRK06620         45 FTLLIKGPSSSGKTYLTKIWQNLS----------NAY--IIK--DIF----F-N------EEIL---E--KYNAFIIEDI   94 (214)
T ss_pred             ceEEEECCCCCCHHHHHHHHHhcc----------CCE--Ecc--hhh----h-c------hhHH---h--cCCEEEEecc
Confidence            458999999999999999987754          211  111  000    0 0      0111   1  2358999999


Q ss_pred             hhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHcccc---ceEecCCCHHHHHHHHHH
Q 005179          392 HTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ---PVLISEPSQEDAVRILLG  468 (710)
Q Consensus       392 d~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~  468 (710)
                      |.+.            ...+.+++..+.++|..++|++++.+.   .+.+ ++|++||.   .+.+.+|+.+++..+++.
T Consensus        95 ~~~~------------~~~lf~l~N~~~e~g~~ilits~~~p~---~l~l-~~L~SRl~~gl~~~l~~pd~~~~~~~l~k  158 (214)
T PRK06620         95 ENWQ------------EPALLHIFNIINEKQKYLLLTSSDKSR---NFTL-PDLSSRIKSVLSILLNSPDDELIKILIFK  158 (214)
T ss_pred             ccch------------HHHHHHHHHHHHhcCCEEEEEcCCCcc---ccch-HHHHHHHhCCceEeeCCCCHHHHHHHHHH
Confidence            9651            235666777777888888888888776   3346 89999997   899999999999888887


Q ss_pred             HHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          469 LREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       469 l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      .+..    .++.++++++++++..+.+-
T Consensus       159 ~~~~----~~l~l~~ev~~~L~~~~~~d  182 (214)
T PRK06620        159 HFSI----SSVTISRQIIDFLLVNLPRE  182 (214)
T ss_pred             HHHH----cCCCCCHHHHHHHHHHccCC
Confidence            6653    47899999999999887654

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.32  E-value=2.7e-11  Score=129.86  Aligned_cols=200  Identities=16%  Similarity=0.145  Sum_probs=129.5

Q ss_pred             hhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcC----CCcccc----Cce------
Q 005179          284 ASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAE----VPVFLL----SKR------  348 (710)
Q Consensus       284 ~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~----~p~~l~----~~~------  348 (710)
                      ..|..++.++|+++.+..+...+...+..| +||+||+|+|||++|+.+|+.+.+..    .|....    .+.      
T Consensus        17 ~~P~~~~~l~Gh~~a~~~L~~a~~~grl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~~~~~c~~c~~i~   96 (351)
T PRK09112         17 PSPSENTRLFGHEEAEAFLAQAYREGKLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLADPDPASPVWRQIA   96 (351)
T ss_pred             CCCCchhhccCcHHHHHHHHHHHHcCCCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCCCCCCCHHHHHHH
Confidence            467778899999999999999988776555 88999999999999999999987632    121110    010      


Q ss_pred             ------EEEeehhhhhhccc-cCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcc
Q 005179          349 ------IMSLDMGLLMAGAK-ERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP  417 (710)
Q Consensus       349 ------v~~ld~~~l~~g~~-~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~  417 (710)
                            ++.+....-..+.+ ...-..+.++.+.+.+.    ..+..|++|||+|.|             +...+|.|+.
T Consensus        97 ~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l-------------~~~aanaLLk  163 (351)
T PRK09112         97 QGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDM-------------NRNAANAILK  163 (351)
T ss_pred             cCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhc-------------CHHHHHHHHH
Confidence                  11111000000000 00001223444444433    234579999999999             4556777877


Q ss_pred             cccCC--CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          418 SLGRG--ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       418 ~l~~~--~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      .+++.  +..+|..++...     .+.+.+++||..+.+++|+.++...+|.....      ...++++++..++.++.+
T Consensus       164 ~LEEpp~~~~fiLit~~~~-----~llptIrSRc~~i~l~pl~~~~~~~~L~~~~~------~~~~~~~~~~~i~~~s~G  232 (351)
T PRK09112        164 TLEEPPARALFILISHSSG-----RLLPTIRSRCQPISLKPLDDDELKKALSHLGS------SQGSDGEITEALLQRSKG  232 (351)
T ss_pred             HHhcCCCCceEEEEECChh-----hccHHHHhhccEEEecCCCHHHHHHHHHHhhc------ccCCCHHHHHHHHHHcCC
Confidence            77753  344444444443     45699999999999999999999888886321      122678888888777654


Q ss_pred             hhcCCCCcchHHHHHHHH
Q 005179          496 YISDRYLPDKAIDLVDEA  513 (710)
Q Consensus       496 ~i~~r~~p~~ai~ll~~a  513 (710)
                            .|..++.++...
T Consensus       233 ------~pr~Al~ll~~~  244 (351)
T PRK09112        233 ------SVRKALLLLNYG  244 (351)
T ss_pred             ------CHHHHHHHHhcC
Confidence                  466777776543

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.32  E-value=2.9e-11  Score=128.22  Aligned_cols=160  Identities=23%  Similarity=0.314  Sum_probs=97.8

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------cC--------------
Q 005179          288 LIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------LS--------------  346 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l-------~~--------------  346 (710)
                      .|..++|+++.++.+.-.+......|+||+|+||+|||+++++++..+.........       .+              
T Consensus         6 ~f~~i~Gq~~~~~~l~~~~~~~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~   85 (334)
T PRK13407          6 PFSAIVGQEEMKQAMVLTAIDPGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAHVSSTTMIE   85 (334)
T ss_pred             CHHHhCCHHHHHHHHHHHHhccCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcccCCcccccccCCcccc
Confidence            466799999988877754433345789999999999999999999987421100000       00              


Q ss_pred             --ceEEEeehh----hhhhcccc------CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHh
Q 005179          347 --KRIMSLDMG----LLMAGAKE------RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNL  414 (710)
Q Consensus       347 --~~v~~ld~~----~l~~g~~~------~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~  414 (710)
                        .++..+...    .++ |.-+      .|++..+ ..   .+....+.+|||||++.+             ....++.
T Consensus        86 ~~~p~~~~p~~~t~~~l~-G~~d~~~~l~~g~~~~~-~G---~l~~A~~GiL~lDEInrl-------------~~~~q~~  147 (334)
T PRK13407         86 RPTPVVDLPLGVTEDRVV-GALDIERALTRGEKAFE-PG---LLARANRGYLYIDEVNLL-------------EDHIVDL  147 (334)
T ss_pred             cCCccccCCCCCCcceee-cchhhhhhhhcCCeeec-CC---ceEEcCCCeEEecChHhC-------------CHHHHHH
Confidence              000000000    000 1000      0111000 00   111233568999999999             4556777


Q ss_pred             hcccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCH-HHHHHHHHHH
Q 005179          415 LKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQ-EDAVRILLGL  469 (710)
Q Consensus       415 L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~-~~~~~IL~~l  469 (710)
                      |...|+.+               .+++|+++|+.+    ..+.+++..||. .|.+++|.. +++.+|+...
T Consensus       148 Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e----~~l~~aLldRF~~~v~v~~~~~~~e~~~il~~~  215 (334)
T PRK13407        148 LLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEE----GELRPQLLDRFGLSVEVRSPRDVETRVEVIRRR  215 (334)
T ss_pred             HHHHHHcCCeEEEECCeEEecCCCEEEEecCCccc----CCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHh
Confidence            77666544               367788888754    247899999997 788888865 8888888763

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.31  E-value=1.7e-11  Score=144.04  Aligned_cols=176  Identities=16%  Similarity=0.235  Sum_probs=116.2

Q ss_pred             CcccCHHHHHHHHHHHHc------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-----h
Q 005179          291 PVIGRETEIQRIIQILCR------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-----A  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-----~  359 (710)
                      +.+|.++..+++++.+..      ..+..++|+||||+|||++++.++..+          +..++.++++...     .
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~~~~~g~~i~l~GppG~GKTtl~~~ia~~l----------~~~~~~i~~~~~~d~~~i~  392 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKAT----------GRKYVRMALGGVRDEAEIR  392 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhcccCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEEcCCCCCHHHhc
Confidence            489999999998876653      234568999999999999999999987          4445545433321     1


Q ss_pred             cc--ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC----------------
Q 005179          360 GA--KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR----------------  421 (710)
Q Consensus       360 g~--~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~----------------  421 (710)
                      |.  .+.|....++...+..+... +.|++|||+|.+....         ..+..+.|.++++.                
T Consensus       393 g~~~~~~g~~~G~~~~~l~~~~~~-~~villDEidk~~~~~---------~g~~~~aLlevld~~~~~~~~d~~~~~~~d  462 (784)
T PRK10787        393 GHRRTYIGSMPGKLIQKMAKVGVK-NPLFLLDEIDKMSSDM---------RGDPASALLEVLDPEQNVAFSDHYLEVDYD  462 (784)
T ss_pred             cchhccCCCCCcHHHHHHHhcCCC-CCEEEEEChhhccccc---------CCCHHHHHHHHhccccEEEEeccccccccc
Confidence            11  12222222222223322222 3488999999994321         11233444444432                


Q ss_pred             -CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHH-HHHhh-----cCCCCCHHHHHHHHHH
Q 005179          422 -GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLRE-KYEAH-----HNCKFTLEAINAAVHL  492 (710)
Q Consensus       422 -~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~-~~~~~-----~~~~i~~~~l~~l~~l  492 (710)
                       +++.+|+|+|..      .++++|++||..|.+..++.++..+|.+..+. +....     ..+.++++++..+++.
T Consensus       463 ls~v~~i~TaN~~------~i~~aLl~R~~ii~~~~~t~eek~~Ia~~~L~~k~~~~~~l~~~~l~i~~~ai~~ii~~  534 (784)
T PRK10787        463 LSDVMFVATSNSM------NIPAPLLDRMEVIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRY  534 (784)
T ss_pred             CCceEEEEcCCCC------CCCHHHhcceeeeecCCCCHHHHHHHHHHhhhHHHHHHhCCCCCeEEECHHHHHHHHHh
Confidence             578888877652      58999999999999999999999999987653 22222     2367999999999863

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=99.31  E-value=1.1e-10  Score=125.53  Aligned_cols=208  Identities=22%  Similarity=0.264  Sum_probs=142.0

Q ss_pred             CcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh--------
Q 005179          291 PVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM--------  358 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~--------  358 (710)
                      .+.+|+++++++...|..    ..+.|++++|+||||||++++.+++++.....     +..++++++....        
T Consensus        18 ~l~~Re~ei~~l~~~l~~~~~~~~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~-----~~~~~yINc~~~~t~~~i~~~   92 (366)
T COG1474          18 ELPHREEEINQLASFLAPALRGERPSNIIIYGPTGTGKTATVKFVMEELEESSA-----NVEVVYINCLELRTPYQVLSK   92 (366)
T ss_pred             cccccHHHHHHHHHHHHHHhcCCCCccEEEECCCCCCHhHHHHHHHHHHHhhhc-----cCceEEEeeeeCCCHHHHHHH
Confidence            378999999999887643    56678999999999999999999999855321     1114444432221        


Q ss_pred             --h---ccccCc-cHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEEc
Q 005179          359 --A---GAKERG-ELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIAS  429 (710)
Q Consensus       359 --~---g~~~~g-~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~a  429 (710)
                        .   .....| ...+.++.+.+.+.. ....|+++||+|.|+...         +..+.++++ ...  ..++.+|+.
T Consensus        93 i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~---------~~~LY~L~r-~~~~~~~~v~vi~i  162 (366)
T COG1474          93 ILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKD---------GEVLYSLLR-APGENKVKVSIIAV  162 (366)
T ss_pred             HHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhcccc---------chHHHHHHh-hccccceeEEEEEE
Confidence              1   111222 223334555555544 457889999999996541         122333332 222  345678888


Q ss_pred             cChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAI  507 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai  507 (710)
                      +|...+..  .+++.+.++|.  .|.|++++.+|...||....+..  ...-.+++++++.++..+...-+   -..+++
T Consensus       163 ~n~~~~~~--~ld~rv~s~l~~~~I~F~pY~a~el~~Il~~R~~~~--~~~~~~~~~vl~lia~~~a~~~G---DAR~ai  235 (366)
T COG1474         163 SNDDKFLD--YLDPRVKSSLGPSEIVFPPYTAEELYDILRERVEEG--FSAGVIDDDVLKLIAALVAAESG---DARKAI  235 (366)
T ss_pred             eccHHHHH--HhhhhhhhccCcceeeeCCCCHHHHHHHHHHHHHhh--ccCCCcCccHHHHHHHHHHHcCc---cHHHHH
Confidence            88876633  57899999996  68999999999999999876643  34567899999988887776544   346899


Q ss_pred             HHHHHHHhhhhhh
Q 005179          508 DLVDEAGSRAHIE  520 (710)
Q Consensus       508 ~ll~~a~~~~~~~  520 (710)
                      ++++.|+..+...
T Consensus       236 dilr~A~eiAe~~  248 (366)
T COG1474         236 DILRRAGEIAERE  248 (366)
T ss_pred             HHHHHHHHHHHhh
Confidence            9999998766543

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.29  E-value=8.7e-11  Score=124.75  Aligned_cols=165  Identities=22%  Similarity=0.273  Sum_probs=102.0

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCC----ccc--cCceEEEeehhhhhhcc
Q 005179          288 LIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVP----VFL--LSKRIMSLDMGLLMAGA  361 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p----~~l--~~~~v~~ld~~~l~~g~  361 (710)
                      -|..++|+++....|...+..+..+++||.|++|||||++++++++.+...++.    ...  .+...+.-++.....+.
T Consensus        15 pf~~ivGq~~~k~al~~~~~~p~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~~p~~~~~~~~~~~~~~   94 (350)
T CHL00081         15 PFTAIVGQEEMKLALILNVIDPKIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSDPELMSDEVREAIQNG   94 (350)
T ss_pred             CHHHHhChHHHHHHHHHhccCCCCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCCChhhhchhhhhhhccc
Confidence            366899999988888877777777899999999999999999999887653321    100  00000000000000000


Q ss_pred             ----------c----cCccHHHHH------HHHHH---------HHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHH
Q 005179          362 ----------K----ERGELEARV------TTLIS---------EIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDIS  412 (710)
Q Consensus       362 ----------~----~~g~~e~~l------~~~~~---------~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~  412 (710)
                                +    ..+-.+.++      ...+.         .+....+.+|||||++.+             ....+
T Consensus        95 ~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL-------------~~~~Q  161 (350)
T CHL00081         95 ETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLL-------------DDHLV  161 (350)
T ss_pred             ccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhC-------------CHHHH
Confidence                      0    001111111      11111         011334679999999999             44566


Q ss_pred             HhhcccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCC-HHHHHHHHHHH
Q 005179          413 NLLKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPS-QEDAVRILLGL  469 (710)
Q Consensus       413 ~~L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps-~~~~~~IL~~l  469 (710)
                      +.|...|+.+               .+++|++.++.+    -.+.++|..||. .|.+..|+ .+++.+|++..
T Consensus       162 ~~LLeam~e~~~~ier~G~s~~~p~rfiviaT~np~e----g~l~~~LldRf~l~i~l~~~~~~~~e~~il~~~  231 (350)
T CHL00081        162 DILLDSAASGWNTVEREGISIRHPARFVLVGSGNPEE----GELRPQLLDRFGMHAEIRTVKDPELRVKIVEQR  231 (350)
T ss_pred             HHHHHHHHhCCeEEeeCCeeeecCCCEEEEeccCccc----CCCCHHHHHHhCceeecCCCCChHHHHHHHHhh
Confidence            6666655432               456777777654    247899999998 78999997 68999998864

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.28  E-value=7.5e-11  Score=125.36  Aligned_cols=163  Identities=21%  Similarity=0.283  Sum_probs=98.4

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhc----CCCcc---------ccCceEE-----
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQA----EVPVF---------LLSKRIM-----  350 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~----~~p~~---------l~~~~v~-----  350 (710)
                      |..++|+++.+..++-.+-.+...+++|.|++|+|||+++++++..+...    ..|..         ..+++..     
T Consensus         3 f~~ivgq~~~~~al~~~~~~~~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~   82 (337)
T TIGR02030         3 FTAIVGQDEMKLALLLNVIDPKIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPEMMCEEVRIRVDSQE   82 (337)
T ss_pred             ccccccHHHHHHHHHHHhcCCCCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCccccChHHhhhhhccc
Confidence            56789999999887766666667889999999999999999999876321    00100         0001110     


Q ss_pred             ----------EeehhhhhhccccCcc--HHHHHHH---HH--HHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHH
Q 005179          351 ----------SLDMGLLMAGAKERGE--LEARVTT---LI--SEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISN  413 (710)
Q Consensus       351 ----------~ld~~~l~~g~~~~g~--~e~~l~~---~~--~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~  413 (710)
                                ..|+..=.......|.  ++..+..   .+  ..+.+..+.+|||||++.+             ....++
T Consensus        83 ~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L-------------~~~~Q~  149 (337)
T TIGR02030        83 PLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLL-------------EDHLVD  149 (337)
T ss_pred             ccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhC-------------CHHHHH
Confidence                      0111100000001111  1111100   00  0112244579999999998             445666


Q ss_pred             hhcccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCH-HHHHHHHHH
Q 005179          414 LLKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQ-EDAVRILLG  468 (710)
Q Consensus       414 ~L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~-~~~~~IL~~  468 (710)
                      .|...|+++               .+++|+++++.+    -.+.++|..||. .+.+..|.. +++.+|++.
T Consensus       150 ~Ll~~l~~g~~~v~r~G~~~~~~~r~iviat~np~e----g~l~~~LldRf~l~i~l~~p~~~eer~eIL~~  217 (337)
T TIGR02030       150 VLLDVAASGWNVVEREGISIRHPARFVLVGSGNPEE----GELRPQLLDRFGLHAEIRTVRDVELRVEIVER  217 (337)
T ss_pred             HHHHHHHhCCeEEEECCEEEEcCCCEEEEecccccc----CCCCHHHHhhcceEEECCCCCCHHHHHHHHHh
Confidence            666666543               356777777653    247899999998 788888875 888888876

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.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.27  E-value=1.9e-10  Score=125.48  Aligned_cols=152  Identities=18%  Similarity=0.265  Sum_probs=90.2

Q ss_pred             CcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc------ccC
Q 005179          291 PVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA------KER  364 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~------~~~  364 (710)
                      .++|+++.++.+...+.  .+.|+||+||||||||++|++|+..+.... |.....+.+.  ...+++ |.      +..
T Consensus        21 ~i~gre~vI~lll~aal--ag~hVLL~GpPGTGKT~LAraLa~~~~~~~-~F~~~~~~ft--tp~DLf-G~l~i~~~~~~   94 (498)
T PRK13531         21 GLYERSHAIRLCLLAAL--SGESVFLLGPPGIAKSLIARRLKFAFQNAR-AFEYLMTRFS--TPEEVF-GPLSIQALKDE   94 (498)
T ss_pred             hccCcHHHHHHHHHHHc--cCCCEEEECCCChhHHHHHHHHHHHhcccC-cceeeeeeec--CcHHhc-CcHHHhhhhhc
Confidence            48999999999988775  468899999999999999999999874322 2221111110  112222 11      112


Q ss_pred             ccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCC-----------e-EEEEccCh
Q 005179          365 GELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGE-----------L-QCIASTTQ  432 (710)
Q Consensus       365 g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~-----------v-~vI~att~  432 (710)
                      |.+.......+   ..  ..+||+|||+.+             +...++.|...|+.+.           . .++++||+
T Consensus        95 g~f~r~~~G~L---~~--A~lLfLDEI~ra-------------sp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~  156 (498)
T PRK13531         95 GRYQRLTSGYL---PE--AEIVFLDEIWKA-------------GPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNE  156 (498)
T ss_pred             CchhhhcCCcc---cc--ccEEeecccccC-------------CHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCC
Confidence            22221111111   01  228999999877             5567777777775322           2 23444453


Q ss_pred             HHHHhhhhccHHHHcccc-ceEecCCC-HHHHHHHHHH
Q 005179          433 DEHRTQFEKDKALARRFQ-PVLISEPS-QEDAVRILLG  468 (710)
Q Consensus       433 ~~~~~~~~~d~aL~~Rf~-~I~v~~Ps-~~~~~~IL~~  468 (710)
                      .+  ..-...+++..||. .|.+++|+ .++-.+||..
T Consensus       157 LP--E~g~~leAL~DRFliri~vp~l~~~~~e~~lL~~  192 (498)
T PRK13531        157 LP--EADSSLEALYDRMLIRLWLDKVQDKANFRSMLTS  192 (498)
T ss_pred             Cc--ccCCchHHhHhhEEEEEECCCCCchHHHHHHHHc
Confidence            22  11123358999996 68888886 4555777764

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.27  E-value=5.1e-11  Score=128.38  Aligned_cols=196  Identities=15%  Similarity=0.172  Sum_probs=126.4

Q ss_pred             hhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCc-c--------cc--------
Q 005179          284 ASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPV-F--------LL--------  345 (710)
Q Consensus       284 ~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~-~--------l~--------  345 (710)
                      .+|.++++++|++..++.+.+.+.+.+..| +||+||+|+||+++|..+|+.+.+..... .        +.        
T Consensus        13 ~~P~~~~~iiGq~~~~~~L~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~~~l~~~~~c~~c   92 (365)
T PRK07471         13 PHPRETTALFGHAAAEAALLDAYRSGRLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPPTSLAIDPDHPVA   92 (365)
T ss_pred             CCCCchhhccChHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCccccccccccCCCCChHH
Confidence            477888999999999999999988876666 78999999999999999999997643110 0        00        


Q ss_pred             -------CceEEEeehhhhhhccccCcc-HHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHH
Q 005179          346 -------SKRIMSLDMGLLMAGAKERGE-LEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISN  413 (710)
Q Consensus       346 -------~~~v~~ld~~~l~~g~~~~g~-~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~  413 (710)
                             .-.++.+....-..+.+.... ..+.++.+.+.+.    ..++.|++|||+|.+             +...+|
T Consensus        93 ~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m-------------~~~aan  159 (365)
T PRK07471         93 RRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEM-------------NANAAN  159 (365)
T ss_pred             HHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhc-------------CHHHHH
Confidence                   001111111000000000011 1233555555443    245779999999999             556788


Q ss_pred             hhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          414 LLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       414 ~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                      .|+..+++  +..++|.+|+...     .+.+.+++|++.|.+.+|+.++..++|...        .....++.+..++.
T Consensus       160 aLLK~LEepp~~~~~IL~t~~~~-----~llpti~SRc~~i~l~~l~~~~i~~~L~~~--------~~~~~~~~~~~l~~  226 (365)
T PRK07471        160 ALLKVLEEPPARSLFLLVSHAPA-----RLLPTIRSRCRKLRLRPLAPEDVIDALAAA--------GPDLPDDPRAALAA  226 (365)
T ss_pred             HHHHHHhcCCCCeEEEEEECCch-----hchHHhhccceEEECCCCCHHHHHHHHHHh--------cccCCHHHHHHHHH
Confidence            88888886  3455565555544     456899999999999999999988777642        12334444455565


Q ss_pred             HhhhhhcCCCCcchHHHHHH
Q 005179          492 LSARYISDRYLPDKAIDLVD  511 (710)
Q Consensus       492 ls~~~i~~r~~p~~ai~ll~  511 (710)
                      ++.+      .|..++.+++
T Consensus       227 ~s~G------sp~~Al~ll~  240 (365)
T PRK07471        227 LAEG------SVGRALRLAG  240 (365)
T ss_pred             HcCC------CHHHHHHHhc
Confidence            6543      2445555543

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.27  E-value=1.3e-10  Score=123.44  Aligned_cols=136  Identities=18%  Similarity=0.250  Sum_probs=93.5

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEE
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILF  387 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~  387 (710)
                      +..+++-|||||||||||+++.|+|+.+          ++.|+-++++....      ..+  ++.++...  ...+||+
T Consensus       232 kawKRGYLLYGPPGTGKSS~IaAmAn~L----------~ydIydLeLt~v~~------n~d--Lr~LL~~t--~~kSIiv  291 (457)
T KOG0743|consen  232 KAWKRGYLLYGPPGTGKSSFIAAMANYL----------NYDIYDLELTEVKL------DSD--LRHLLLAT--PNKSILL  291 (457)
T ss_pred             cchhccceeeCCCCCCHHHHHHHHHhhc----------CCceEEeeeccccC------cHH--HHHHHHhC--CCCcEEE
Confidence            3567899999999999999999999999          89999988765432      122  66666543  3468999


Q ss_pred             EccchhhhhCCCCCCCC---CC---ChHhH---HHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHc--ccc-ceE
Q 005179          388 IDEVHTLIGSGTVGRGN---KG---TGLDI---SNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALAR--RFQ-PVL  453 (710)
Q Consensus       388 IDEid~l~~~~~~~~~~---~~---~~~~~---~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~  453 (710)
                      |+|||.-+.........   ..   ....+   .|.+--+-+.  +.-++|.|||..+     .+||+|.|  |.+ .|.
T Consensus       292 IEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGLLNfiDGlwSscg~ERIivFTTNh~E-----kLDPALlRpGRmDmhI~  366 (457)
T KOG0743|consen  292 IEDIDCSFDLRERRKKKKENFEGDLSRVTLSGLLNFLDGLWSSCGDERIIVFTTNHKE-----KLDPALLRPGRMDMHIY  366 (457)
T ss_pred             EeecccccccccccccccccccCCcceeehHHhhhhhccccccCCCceEEEEecCChh-----hcCHhhcCCCcceeEEE
Confidence            99999876432111100   01   11222   2222222222  3667888999988     89999999  887 899


Q ss_pred             ecCCCHHHHHHHHHH
Q 005179          454 ISEPSQEDAVRILLG  468 (710)
Q Consensus       454 v~~Ps~~~~~~IL~~  468 (710)
                      +...+.++...++..
T Consensus       367 mgyCtf~~fK~La~n  381 (457)
T KOG0743|consen  367 MGYCTFEAFKTLASN  381 (457)
T ss_pred             cCCCCHHHHHHHHHH
Confidence            999999985555443

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.27  E-value=8.1e-11  Score=133.98  Aligned_cols=222  Identities=11%  Similarity=0.081  Sum_probs=137.2

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCC-----CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccc--cCceEE
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTK-----NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL--LSKRIM  350 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~-----~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l--~~~~v~  350 (710)
                      .+|.++++|..+++++|+++.+..+..++.....     +-++|+||||+|||++++.++..+... +-...  .++...
T Consensus        72 ~pW~eKyrP~~ldel~~~~~ki~~l~~~l~~~~~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~-~~Ew~npv~~~~~  150 (637)
T TIGR00602        72 EPWVEKYKPETQHELAVHKKKIEEVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQ-VQEWSNPTLPDFQ  150 (637)
T ss_pred             CchHHHhCCCCHHHhcCcHHHHHHHHHHHHhcccccCCCcEEEEECCCCCCHHHHHHHHHHHhhhH-HHHHhhhhhhccc
Confidence            4799999999999999999999999888765322     228999999999999999999876321 00000  000000


Q ss_pred             E---eehhhhhhccccCccHHHHHHHHHHHHH----------hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhc-
Q 005179          351 S---LDMGLLMAGAKERGELEARVTTLISEIQ----------KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLK-  416 (710)
Q Consensus       351 ~---ld~~~l~~g~~~~g~~e~~l~~~~~~~~----------~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~-  416 (710)
                      .   .....+.........-.+.++.++..+.          .....||||||++.++..         ....+.++|. 
T Consensus       151 ~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r---------~~~~lq~lLr~  221 (637)
T TIGR00602       151 KNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYR---------DTRALHEILRW  221 (637)
T ss_pred             ccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchh---------hHHHHHHHHHH
Confidence            0   0000000000000111223444444443          124679999999887532         1234566666 


Q ss_pred             ccccCCCeEEEEccChHHH------Hhhhh----ccHHHHc--cccceEecCCCHHHHHHHHHHHHHHHHhh--cCCCC-
Q 005179          417 PSLGRGELQCIASTTQDEH------RTQFE----KDKALAR--RFQPVLISEPSQEDAVRILLGLREKYEAH--HNCKF-  481 (710)
Q Consensus       417 ~~l~~~~v~vI~att~~~~------~~~~~----~d~aL~~--Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~--~~~~i-  481 (710)
                      .+.+.+.+.+|+++|...+      ...+.    +.+++.+  |...|.|.+.+..+..+.|+.++......  ....+ 
T Consensus       222 ~~~e~~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv~~I~FnPia~t~l~K~L~rIl~~E~~~~~~~~~~p  301 (637)
T TIGR00602       222 KYVSIGRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRVSNISFNPIAPTIMKKFLNRIVTIEAKKNGEKIKVP  301 (637)
T ss_pred             HhhcCCCceEEEEecCCccccccccccccchhcccCHhHhcccceeEEEeCCCCHHHHHHHHHHHHHhhhhccccccccC
Confidence            5667777777777664322      11122    3478876  55689999999999999999888754221  12223 


Q ss_pred             CHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          482 TLEAINAAVHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       482 ~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      +++++..++..+.+-+      +.||..|..+|.
T Consensus       302 ~~~~l~~I~~~s~GDi------RsAIn~LQf~~~  329 (637)
T TIGR00602       302 KKTSVELLCQGCSGDI------RSAINSLQFSSS  329 (637)
T ss_pred             CHHHHHHHHHhCCChH------HHHHHHHHHHHh
Confidence            5678888887655543      468888888764

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

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.25  E-value=7.5e-11  Score=116.93  Aligned_cols=193  Identities=16%  Similarity=0.209  Sum_probs=141.8

Q ss_pred             hHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceE--------EE
Q 005179          280 LTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRI--------MS  351 (710)
Q Consensus       280 l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v--------~~  351 (710)
                      |.+++||..++.++++++.-..+........-.|+++|||+|.||-|.+.++.+++....++..-.....        ++
T Consensus         3 Wvdkyrpksl~~l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~~tpS~kklE   82 (351)
T KOG2035|consen    3 WVDKYRPKSLDELIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTFTTPSKKKLE   82 (351)
T ss_pred             chhhcCcchhhhcccHHHHHHHHHHhcccCCCCeEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEEecCCCceEE
Confidence            5678899999999999988888888777666799999999999999999999999866444322111111        11


Q ss_pred             e---------ehhhhhhccccCccHHHHHHHHHHHHHhc---------CCeEEEEccchhhhhCCCCCCCCCCChHhHHH
Q 005179          352 L---------DMGLLMAGAKERGELEARVTTLISEIQKS---------GDVILFIDEVHTLIGSGTVGRGNKGTGLDISN  413 (710)
Q Consensus       352 l---------d~~~l~~g~~~~g~~e~~l~~~~~~~~~~---------~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~  413 (710)
                      +         .++.--.|..++-    .+.++++++.+.         .-.|++|.|+|.|             ..|++.
T Consensus        83 istvsS~yHlEitPSDaG~~DRv----ViQellKevAQt~qie~~~qr~fKvvvi~ead~L-------------T~dAQ~  145 (351)
T KOG2035|consen   83 ISTVSSNYHLEITPSDAGNYDRV----VIQELLKEVAQTQQIETQGQRPFKVVVINEADEL-------------TRDAQH  145 (351)
T ss_pred             EEEecccceEEeChhhcCcccHH----HHHHHHHHHHhhcchhhccccceEEEEEechHhh-------------hHHHHH
Confidence            1         1111112222222    234455544331         2358899999999             778999


Q ss_pred             hhccccc--CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          414 LLKPSLG--RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       414 ~L~~~l~--~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                      .|+..|+  .+..++|..+|.-.     .+-+.+++|+-.|.++.|+.++...+|..++.+.    ++.++.+.+..+++
T Consensus       146 aLRRTMEkYs~~~RlIl~cns~S-----riIepIrSRCl~iRvpaps~eeI~~vl~~v~~kE----~l~lp~~~l~rIa~  216 (351)
T KOG2035|consen  146 ALRRTMEKYSSNCRLILVCNSTS-----RIIEPIRSRCLFIRVPAPSDEEITSVLSKVLKKE----GLQLPKELLKRIAE  216 (351)
T ss_pred             HHHHHHHHHhcCceEEEEecCcc-----cchhHHhhheeEEeCCCCCHHHHHHHHHHHHHHh----cccCcHHHHHHHHH
Confidence            9998888  46777777777654     5668999999999999999999999999888754    78899999999999


Q ss_pred             Hhhhhhc
Q 005179          492 LSARYIS  498 (710)
Q Consensus       492 ls~~~i~  498 (710)
                      .+.|.+.
T Consensus       217 kS~~nLR  223 (351)
T KOG2035|consen  217 KSNRNLR  223 (351)
T ss_pred             HhcccHH
Confidence            9887543

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.25  E-value=1.4e-10  Score=125.89  Aligned_cols=191  Identities=23%  Similarity=0.298  Sum_probs=119.3

Q ss_pred             cccCHHHHHHHHHHHH----c-------C-------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          292 VIGRETEIQRIIQILC----R-------R-------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       292 liGr~~~i~~l~~~L~----~-------~-------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      +||+++.++.+...+.    +       .       .+.++||+||||||||++|+++|..+          +.++..++
T Consensus        79 ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l----------~~pf~~~d  148 (413)
T TIGR00382        79 VIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL----------NVPFAIAD  148 (413)
T ss_pred             ecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc----------CCCeEEec
Confidence            7999998888766552    1       0       13579999999999999999999877          44555566


Q ss_pred             hhhhhhccccCcc-HHHHHHHHHHH----HHhcCCeEEEEccchhhhhCCCCCCC-CCCChHhHHHhhcccccC------
Q 005179          354 MGLLMAGAKERGE-LEARVTTLISE----IQKSGDVILFIDEVHTLIGSGTVGRG-NKGTGLDISNLLKPSLGR------  421 (710)
Q Consensus       354 ~~~l~~g~~~~g~-~e~~l~~~~~~----~~~~~~~IL~IDEid~l~~~~~~~~~-~~~~~~~~~~~L~~~l~~------  421 (710)
                      ...+.. ..+.|. .+..+..++..    +....+.||||||+|.+......... .+-.+..+++.|++.|+.      
T Consensus       149 a~~L~~-~gyvG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~~v~  227 (413)
T TIGR00382       149 ATTLTE-AGYVGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVP  227 (413)
T ss_pred             hhhccc-cccccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchhHHHHHHHHhhccceecc
Confidence            555432 224443 33444444332    23345679999999999753211000 011123567777666631      


Q ss_pred             ---------CCeEEEEccChH-------------------------------------HHH------h--hhhccHHHHc
Q 005179          422 ---------GELQCIASTTQD-------------------------------------EHR------T--QFEKDKALAR  447 (710)
Q Consensus       422 ---------~~v~vI~att~~-------------------------------------~~~------~--~~~~d~aL~~  447 (710)
                               .+.++|.|+|.-                                     ++.      .  .+.+.|.|..
T Consensus       228 ~~~gr~~~~~~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEflg  307 (413)
T TIGR00382       228 PQGGRKHPYQEFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIG  307 (413)
T ss_pred             cCCCccccCCCeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHhC
Confidence                     123345444430                                     000      0  1124588999


Q ss_pred             ccc-ceEecCCCHHHHHHHHHH----HHHHHHhh-----cCCCCCHHHHHHHHHHh
Q 005179          448 RFQ-PVLISEPSQEDAVRILLG----LREKYEAH-----HNCKFTLEAINAAVHLS  493 (710)
Q Consensus       448 Rf~-~I~v~~Ps~~~~~~IL~~----l~~~~~~~-----~~~~i~~~~l~~l~~ls  493 (710)
                      |++ .+.+.+.+.+++.+|+..    +.++|...     ..+.+++++++++++.+
T Consensus       308 Rld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~  363 (413)
T TIGR00382       308 RLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKA  363 (413)
T ss_pred             CCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeEEEECHHHHHHHHHhC
Confidence            997 677889999999999986    45555432     23578999999998874

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.24  E-value=1.9e-10  Score=136.69  Aligned_cols=182  Identities=16%  Similarity=0.207  Sum_probs=124.3

Q ss_pred             CcccCHHHHHHHHHHHHcC--------CC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc-
Q 005179          291 PVIGRETEIQRIIQILCRR--------TK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG-  360 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~--------~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g-  360 (710)
                      .++|+++.+..+.+.+.+.        .+ ..+||+||+|||||.+|++||+.+..+       ...++.+|++.+... 
T Consensus       567 ~v~GQ~~Av~~v~~~i~~~~~gl~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~-------~~~~~~~dmse~~~~~  639 (852)
T TIGR03345       567 RVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETALALAELLYGG-------EQNLITINMSEFQEAH  639 (852)
T ss_pred             eEcChHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCC-------CcceEEEeHHHhhhhh
Confidence            5999999999998877541        11 237999999999999999999998433       346777887766421 


Q ss_pred             -------c--ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------
Q 005179          361 -------A--KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------  422 (710)
Q Consensus       361 -------~--~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------  422 (710)
                             .  .+.|.-+.  ..+.+.++..+.+||+||||+.+             ..++.+.|.+++..|         
T Consensus       640 ~~~~l~g~~~gyvg~~~~--g~L~~~v~~~p~svvllDEieka-------------~~~v~~~Llq~ld~g~l~d~~Gr~  704 (852)
T TIGR03345       640 TVSRLKGSPPGYVGYGEG--GVLTEAVRRKPYSVVLLDEVEKA-------------HPDVLELFYQVFDKGVMEDGEGRE  704 (852)
T ss_pred             hhccccCCCCCccccccc--chHHHHHHhCCCcEEEEechhhc-------------CHHHHHHHHHHhhcceeecCCCcE
Confidence                   1  12221110  11234445567789999999977             556778887777643         


Q ss_pred             ----CeEEEEccChHH--HHh----------------h------hhccHHHHccccceEecCCCHHHHHHHHHHHHHHHH
Q 005179          423 ----ELQCIASTTQDE--HRT----------------Q------FEKDKALARRFQPVLISEPSQEDAVRILLGLREKYE  474 (710)
Q Consensus       423 ----~v~vI~att~~~--~~~----------------~------~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~  474 (710)
                          +.++|.|+|...  |..                .      ....|.|.+|++.|.|.+++.++..+|+...+....
T Consensus       705 vd~~n~iiI~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEflnRi~iI~F~pLs~e~l~~Iv~~~L~~l~  784 (852)
T TIGR03345       705 IDFKNTVILLTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLGRMTVIPYLPLDDDVLAAIVRLKLDRIA  784 (852)
T ss_pred             EeccccEEEEeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhcceeEEEeCCCCHHHHHHHHHHHHHHHH
Confidence                355777766311  000                0      114588899999999999999999999987655432


Q ss_pred             ----hh--cCCCCCHHHHHHHHHHhh
Q 005179          475 ----AH--HNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       475 ----~~--~~~~i~~~~l~~l~~ls~  494 (710)
                          ..  ..+.++++++++++..+.
T Consensus       785 ~rl~~~~gi~l~i~d~a~~~La~~g~  810 (852)
T TIGR03345       785 RRLKENHGAELVYSEALVEHIVARCT  810 (852)
T ss_pred             HHHHHhcCceEEECHHHHHHHHHHcC
Confidence                22  235789999999887753

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.24  E-value=7.6e-11  Score=123.18  Aligned_cols=172  Identities=14%  Similarity=0.166  Sum_probs=108.0

Q ss_pred             ccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHH----
Q 005179          293 IGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELE----  368 (710)
Q Consensus       293 iGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e----  368 (710)
                      +-..+..+.++..+..  +++++|.|+||||||++++.+|..+          +.+++.+++..........|...    
T Consensus        48 ~f~~~~~~~vl~~l~~--~~~ilL~G~pGtGKTtla~~lA~~l----------~~~~~rV~~~~~l~~~DliG~~~~~l~  115 (327)
T TIGR01650        48 LFDKATTKAICAGFAY--DRRVMVQGYHGTGKSTHIEQIAARL----------NWPCVRVNLDSHVSRIDLVGKDAIVLK  115 (327)
T ss_pred             cCCHHHHHHHHHHHhc--CCcEEEEeCCCChHHHHHHHHHHHH----------CCCeEEEEecCCCChhhcCCCceeecc
Confidence            3344455556655543  5689999999999999999999999          55565555433322111111100    


Q ss_pred             -----HH-HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----------------CCCeEE
Q 005179          369 -----AR-VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----------------RGELQC  426 (710)
Q Consensus       369 -----~~-l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----------------~~~v~v  426 (710)
                           .. ....+-.+.. .+.+|++||++..             ..++++.|..+|+                ...+++
T Consensus       116 ~g~~~~~f~~GpL~~A~~-~g~illlDEin~a-------------~p~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~Frv  181 (327)
T TIGR01650       116 DGKQITEFRDGILPWALQ-HNVALCFDEYDAG-------------RPDVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRL  181 (327)
T ss_pred             CCcceeEEecCcchhHHh-CCeEEEechhhcc-------------CHHHHHHHHHHhccCCeEEECCCceEecCCCCeEE
Confidence                 00 1112222222 3678999999988             3334444333333                135779


Q ss_pred             EEccChHH-------HHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhh
Q 005179          427 IASTTQDE-------HRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       427 I~att~~~-------~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~  494 (710)
                      |+|+|+.+       |.....++.++.+||. .+.++.|+.++-.+|+......+    .-..+++.++++++++.
T Consensus       182 iAT~Np~g~Gd~~G~y~Gt~~l~~A~lDRF~i~~~~~Yp~~e~E~~Il~~~~~~~----~~~~~~~i~~~mV~la~  253 (327)
T TIGR01650       182 FATANTIGLGDTTGLYHGTQQINQAQMDRWSIVTTLNYLEHDNEAAIVLAKAKGF----DDTEGKDIINAMVRVAD  253 (327)
T ss_pred             EEeeCCCCcCCCCcceeeeecCCHHHHhheeeEeeCCCCCHHHHHHHHHhhccCC----CccchHHHHHHHHHHHH
Confidence            99999866       7788889999999997 56899999999999987653211    11123456666665543

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=99.21  E-value=4.6e-10  Score=115.21  Aligned_cols=211  Identities=20%  Similarity=0.225  Sum_probs=132.0

Q ss_pred             cccCH---HHHHHHHHHHHcC---CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh-----------
Q 005179          292 VIGRE---TEIQRIIQILCRR---TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM-----------  354 (710)
Q Consensus       292 liGr~---~~i~~l~~~L~~~---~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~-----------  354 (710)
                      .||..   ..++++.+++..+   +..|++|+|++|.|||++++.+.+......-+. ....+|+.+.+           
T Consensus        36 WIgY~~A~~~L~~L~~Ll~~P~~~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~-~~~~PVv~vq~P~~p~~~~~Y~  114 (302)
T PF05621_consen   36 WIGYPRAKEALDRLEELLEYPKRHRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDED-AERIPVVYVQMPPEPDERRFYS  114 (302)
T ss_pred             eecCHHHHHHHHHHHHHHhCCcccCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCC-CccccEEEEecCCCCChHHHHH
Confidence            45544   3445555656543   347899999999999999999887543221111 11235555542           


Q ss_pred             ---hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccC
Q 005179          355 ---GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT  431 (710)
Q Consensus       355 ---~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att  431 (710)
                         ..+....+........-..++..++..+.-+|+|||+|.++....      ....++.|.|+.+-..-++.+|+..+
T Consensus       115 ~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~------~~qr~~Ln~LK~L~NeL~ipiV~vGt  188 (302)
T PF05621_consen  115 AILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSY------RKQREFLNALKFLGNELQIPIVGVGT  188 (302)
T ss_pred             HHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccH------HHHHHHHHHHHHHhhccCCCeEEecc
Confidence               222222222333333333344555566677999999999753311      23667889998887777888888888


Q ss_pred             hHHHHhhhhccHHHHccccceEecCCCH-HHHHHHHHHHHHHHHhhcCCCC-CHHHHHHHHHHhhhhhcCCCCcchHHHH
Q 005179          432 QDEHRTQFEKDKALARRFQPVLISEPSQ-EDAVRILLGLREKYEAHHNCKF-TLEAINAAVHLSARYISDRYLPDKAIDL  509 (710)
Q Consensus       432 ~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~-~~~~~IL~~l~~~~~~~~~~~i-~~~~l~~l~~ls~~~i~~r~~p~~ai~l  509 (710)
                      .+-+. .+..|+.+.+||..+.++.... ++...+|..+...+.....-.+ +++....+...+.+.++      +...+
T Consensus       189 ~~A~~-al~~D~QLa~RF~~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG------~l~~l  261 (302)
T PF05621_consen  189 REAYR-ALRTDPQLASRFEPFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIG------ELSRL  261 (302)
T ss_pred             HHHHH-HhccCHHHHhccCCccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchH------HHHHH
Confidence            87765 5678999999999999988764 3444444444443333333333 45666888888877655      46677


Q ss_pred             HHHHHhh
Q 005179          510 VDEAGSR  516 (710)
Q Consensus       510 l~~a~~~  516 (710)
                      +..|+..
T Consensus       262 l~~aA~~  268 (302)
T PF05621_consen  262 LNAAAIA  268 (302)
T ss_pred             HHHHHHH
Confidence            7776643

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=99.20  E-value=4.6e-10  Score=131.20  Aligned_cols=146  Identities=18%  Similarity=0.314  Sum_probs=96.4

Q ss_pred             HHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-----hcc----ccCccHHH
Q 005179          299 IQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-----AGA----KERGELEA  369 (710)
Q Consensus       299 i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-----~g~----~~~g~~e~  369 (710)
                      +.+++..+..  ..+++|-|.||+|||+|+.+||+..          |..++.++++.-.     .|.    ...|+|..
T Consensus      1533 l~rVlRAmqv--~kpilLEGsPGVGKTSlItaLAr~t----------G~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w 1600 (4600)
T COG5271        1533 LRRVLRAMQV--GKPILLEGSPGVGKTSLITALARKT----------GKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRW 1600 (4600)
T ss_pred             HHHHHHHHhc--CCceeecCCCCccHHHHHHHHHHHh----------cCceEEeeccccchHHHHhCCCCCcccCceeEe
Confidence            3455555544  4679999999999999999999988          6777777654432     121    23355554


Q ss_pred             HHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----------------CCCeEEEEccChH
Q 005179          370 RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----------------RGELQCIASTTQD  433 (710)
Q Consensus       370 ~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----------------~~~v~vI~att~~  433 (710)
                      +=..++..++.  +.++++||+....             ..+..-|...|.                ..+++|.++-|+.
T Consensus      1601 ~dapfL~amr~--G~WVlLDEiNLaS-------------QSVlEGLNacLDhR~eayIPEld~~f~~HpnfrVFAaqNPq 1665 (4600)
T COG5271        1601 MDAPFLHAMRD--GGWVLLDEINLAS-------------QSVLEGLNACLDHRREAYIPELDKTFDVHPNFRVFAAQNPQ 1665 (4600)
T ss_pred             cccHHHHHhhc--CCEEEeehhhhhH-------------HHHHHHHHHHHhhccccccccccceeeccCCeeeeeecCch
Confidence            44445554443  4488899998762             223333322221                2467778877765


Q ss_pred             HHH-hhhhccHHHHccccceEecCCCHHHHHHHHHHHHH
Q 005179          434 EHR-TQFEKDKALARRFQPVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       434 ~~~-~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      .-. +...++..|.+||.+|.++..+.++...|...+..
T Consensus      1666 ~qggGRKgLPkSF~nRFsvV~~d~lt~dDi~~Ia~~~yp 1704 (4600)
T COG5271        1666 DQGGGRKGLPKSFLNRFSVVKMDGLTTDDITHIANKMYP 1704 (4600)
T ss_pred             hcCCCcccCCHHHhhhhheEEecccccchHHHHHHhhCC
Confidence            322 13357899999999999999999998888776543

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.20  E-value=1.8e-10  Score=122.83  Aligned_cols=174  Identities=17%  Similarity=0.216  Sum_probs=117.3

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCcc
Q 005179          288 LIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGE  366 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~  366 (710)
                      .|++++|++..++.+...+..+...|. ||+||+|+|||++|+.+++.+.+......  ...++.+...   .|...  .
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~--h~D~~~~~~~---~~~~i--~   74 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSIIKNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQRE--YVDIIEFKPI---NKKSI--G   74 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHHcCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCC--CCCeEEeccc---cCCCC--C
Confidence            478899999999999999987766665 89999999999999999999865322111  1112222110   11111  1


Q ss_pred             HHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChHHHHhhhh
Q 005179          367 LEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQDEHRTQFE  440 (710)
Q Consensus       367 ~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~~~~~~~~  440 (710)
                       .+.++.+.+.+..    .+.-|++||++|.+             ....+|.|+..+++.  ...+|.+|+..+     .
T Consensus        75 -v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m-------------~~~a~naLLK~LEepp~~t~~il~~~~~~-----~  135 (313)
T PRK05564         75 -VDDIRNIIEEVNKKPYEGDKKVIIIYNSEKM-------------TEQAQNAFLKTIEEPPKGVFIILLCENLE-----Q  135 (313)
T ss_pred             -HHHHHHHHHHHhcCcccCCceEEEEechhhc-------------CHHHHHHHHHHhcCCCCCeEEEEEeCChH-----h
Confidence             1225555554432    34569999999999             556788898888862  344554444433     6


Q ss_pred             ccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          441 KDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       441 ~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      +-+++++|++.+.+.+|+.++....++....        .++++.++.++.++.+
T Consensus       136 ll~TI~SRc~~~~~~~~~~~~~~~~l~~~~~--------~~~~~~~~~l~~~~~g  182 (313)
T PRK05564        136 ILDTIKSRCQIYKLNRLSKEEIEKFISYKYN--------DIKEEEKKSAIAFSDG  182 (313)
T ss_pred             CcHHHHhhceeeeCCCcCHHHHHHHHHHHhc--------CCCHHHHHHHHHHcCC
Confidence            7799999999999999999987666653221        4667777766666543

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.20  E-value=4.6e-10  Score=133.89  Aligned_cols=182  Identities=19%  Similarity=0.256  Sum_probs=121.0

Q ss_pred             CCCcccCHHHHHHHHHHHHcC--------CC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh
Q 005179          289 IDPVIGRETEIQRIIQILCRR--------TK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA  359 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~--------~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~  359 (710)
                      ...++|++..+..+...+.+.        .+ .+++|+||+|||||++|++|++.+...       +..++.++++.+..
T Consensus       567 ~~~viGQ~~ai~~l~~~i~~~~~gl~~~~~p~~~~Lf~Gp~G~GKT~lA~aLa~~l~~~-------~~~~i~id~se~~~  639 (857)
T PRK10865        567 HHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKTELCKALANFMFDS-------DDAMVRIDMSEFME  639 (857)
T ss_pred             CCeEeCCHHHHHHHHHHHHHHHhcccCCCCCCceEEEECCCCCCHHHHHHHHHHHhhcC-------CCcEEEEEhHHhhh
Confidence            346899999999888876542        11 357999999999999999999988432       33466677665532


Q ss_pred             --------cc--ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCC------
Q 005179          360 --------GA--KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGE------  423 (710)
Q Consensus       360 --------g~--~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~------  423 (710)
                              |.  .+.|.-+  -..+.+.+...+..||||||++.+             ..++++.|.++++.|.      
T Consensus       640 ~~~~~~LiG~~pgy~g~~~--~g~l~~~v~~~p~~vLllDEieka-------------~~~v~~~Ll~ile~g~l~d~~g  704 (857)
T PRK10865        640 KHSVSRLVGAPPGYVGYEE--GGYLTEAVRRRPYSVILLDEVEKA-------------HPDVFNILLQVLDDGRLTDGQG  704 (857)
T ss_pred             hhhHHHHhCCCCcccccch--hHHHHHHHHhCCCCeEEEeehhhC-------------CHHHHHHHHHHHhhCceecCCc
Confidence                    11  1111111  011223334455689999999988             5567888887776542      


Q ss_pred             -------eEEEEccChH--HHH------------h------hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh
Q 005179          424 -------LQCIASTTQD--EHR------------T------QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA  475 (710)
Q Consensus       424 -------v~vI~att~~--~~~------------~------~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~  475 (710)
                             .++|.|+|..  .+.            .      .....|.|.+|++ .+.+.+++.++...|++..+.+...
T Consensus       705 r~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELlnRld~iivF~PL~~edl~~Iv~~~L~~l~~  784 (857)
T PRK10865        705 RTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFINRIDEVVVFHPLGEQHIASIAQIQLQRLYK  784 (857)
T ss_pred             eEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHHhCCeeEecCCCCHHHHHHHHHHHHHHHHH
Confidence                   3377777752  111            0      0123588999995 7888999999999999887766432


Q ss_pred             -----hcCCCCCHHHHHHHHHH
Q 005179          476 -----HHNCKFTLEAINAAVHL  492 (710)
Q Consensus       476 -----~~~~~i~~~~l~~l~~l  492 (710)
                           ...+.+++++++.++..
T Consensus       785 rl~~~gi~l~is~~al~~L~~~  806 (857)
T PRK10865        785 RLEERGYEIHISDEALKLLSEN  806 (857)
T ss_pred             HHHhCCCcCcCCHHHHHHHHHc
Confidence                 23457899999888765

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.17  E-value=3.9e-10  Score=111.04  Aligned_cols=160  Identities=19%  Similarity=0.215  Sum_probs=103.5

Q ss_pred             HHHHHHHcCCC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc---------------CceEEEeehhhhhhccccC
Q 005179          301 RIIQILCRRTK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL---------------SKRIMSLDMGLLMAGAKER  364 (710)
Q Consensus       301 ~l~~~L~~~~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~---------------~~~v~~ld~~~l~~g~~~~  364 (710)
                      .+.+.+..+.. ..+||+||+|+|||++++.+++.+.+.. +....               ...+..++..    +.. .
T Consensus         3 ~l~~~i~~~~~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~-~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~----~~~-~   76 (188)
T TIGR00678         3 QLKRALEKGRLAHAYLFAGPEGVGKELLALALAKALLCEQ-PGGGEPCGECPSCRLIEAGNHPDLHRLEPE----GQS-I   76 (188)
T ss_pred             HHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHHcCCC-CCCCCCCCCCHHHHHHHcCCCCcEEEeccc----cCc-C
Confidence            34455555444 4589999999999999999999986531 00000               0011111110    000 1


Q ss_pred             ccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChHHHHhh
Q 005179          365 GELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQDEHRTQ  438 (710)
Q Consensus       365 g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~~~~~~  438 (710)
                        -.+.++.+++.+..    ....|++|||+|.+             ..+.++.|+.++++.  ...+|.+++...    
T Consensus        77 --~~~~i~~i~~~~~~~~~~~~~kviiide~~~l-------------~~~~~~~Ll~~le~~~~~~~~il~~~~~~----  137 (188)
T TIGR00678        77 --KVDQVRELVEFLSRTPQESGRRVVIIEDAERM-------------NEAAANALLKTLEEPPPNTLFILITPSPE----  137 (188)
T ss_pred             --CHHHHHHHHHHHccCcccCCeEEEEEechhhh-------------CHHHHHHHHHHhcCCCCCeEEEEEECChH----
Confidence              12335555655543    34579999999999             344567777777753  355666555432    


Q ss_pred             hhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          439 FEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       439 ~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                       .+.+++.+|+..+.+.+|+.++..++|...        +  +++++++.++..+.+.
T Consensus       138 -~l~~~i~sr~~~~~~~~~~~~~~~~~l~~~--------g--i~~~~~~~i~~~~~g~  184 (188)
T TIGR00678       138 -KLLPTIRSRCQVLPFPPLSEEALLQWLIRQ--------G--ISEEAAELLLALAGGS  184 (188)
T ss_pred             -hChHHHHhhcEEeeCCCCCHHHHHHHHHHc--------C--CCHHHHHHHHHHcCCC
Confidence             578999999999999999999987777643        3  7888888888876643

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.

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=99.16  E-value=4.8e-10  Score=113.74  Aligned_cols=207  Identities=14%  Similarity=0.142  Sum_probs=144.5

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      +.-.++.-+|.+++++..+++++++++.+..+.+......-.|+|+|||||+|||+.+.+.|..+.+.. +   .+..+.
T Consensus        22 p~~~~~~~pwvekyrP~~l~dv~~~~ei~st~~~~~~~~~lPh~L~YgPPGtGktsti~a~a~~ly~~~-~---~~~m~l   97 (360)
T KOG0990|consen   22 PQSPQYPQPWVEKYRPPFLGIVIKQEPIWSTENRYSGMPGLPHLLFYGPPGTGKTSTILANARDFYSPH-P---TTSMLL   97 (360)
T ss_pred             CCCcccCCCCccCCCCchhhhHhcCCchhhHHHHhccCCCCCcccccCCCCCCCCCchhhhhhhhcCCC-C---chhHHH
Confidence            344567789999999999999999999999888887777778999999999999999999999885421 0   011122


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHh-------cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQK-------SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--  421 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-------~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--  421 (710)
                      +++.++    ....+-...++ ..+...+.       ....++++||+|.+             ..++++.|++.++.  
T Consensus        98 elnaSd----~rgid~vr~qi-~~fast~~~~~fst~~~fKlvILDEADaM-------------T~~AQnALRRviek~t  159 (360)
T KOG0990|consen   98 ELNASD----DRGIDPVRQQI-HLFASTQQPTTYSTHAAFKLVILDEADAM-------------TRDAQNALRRVIEKYT  159 (360)
T ss_pred             HhhccC----ccCCcchHHHH-HHHHhhccceeccccCceeEEEecchhHh-------------hHHHHHHHHHHHHHhc
Confidence            222211    11122222222 22222221       24568999999999             67889999887663  


Q ss_pred             CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCC
Q 005179          422 GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRY  501 (710)
Q Consensus       422 ~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~  501 (710)
                      .+++++..+++..     ...|++.+||..+++.+.+..+...++.++++    .....++++...+++.++.+-+.   
T Consensus       160 ~n~rF~ii~n~~~-----ki~pa~qsRctrfrf~pl~~~~~~~r~shi~e----~e~~~~~~~~~~a~~r~s~gDmr---  227 (360)
T KOG0990|consen  160 ANTRFATISNPPQ-----KIHPAQQSRCTRFRFAPLTMAQQTERQSHIRE----SEQKETNPEGYSALGRLSVGDMR---  227 (360)
T ss_pred             cceEEEEeccChh-----hcCchhhcccccCCCCCCChhhhhhHHHHHHh----cchhhcCHHHHHHHHHHhHHHHH---
Confidence            4556666667765     67899999999999999999888888888776    33567788887777666555332   


Q ss_pred             CcchHHHHHHHHH
Q 005179          502 LPDKAIDLVDEAG  514 (710)
Q Consensus       502 ~p~~ai~ll~~a~  514 (710)
                         ++++.|+...
T Consensus       228 ---~a~n~Lqs~~  237 (360)
T KOG0990|consen  228 ---VALNYLQSIL  237 (360)
T ss_pred             ---HHHHHHHHHH
Confidence               3555555433

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.16  E-value=1.3e-10  Score=124.06  Aligned_cols=180  Identities=19%  Similarity=0.266  Sum_probs=109.5

Q ss_pred             cccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--------cc
Q 005179          292 VIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--------GA  361 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--------g~  361 (710)
                      +||.+..++++.+.+.+  ....+|||+|++||||+++|++|.......       +.+++.+||..+..        |.
T Consensus         1 liG~S~~m~~~~~~~~~~a~~~~pVLI~GE~GtGK~~lAr~iH~~s~r~-------~~pfv~vnc~~~~~~~l~~~lfG~   73 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAPLDRPVLIIGERGTGKELIAARLHYLSKRW-------QGPLVKLNCAALSENLLDSELFGH   73 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHhcCcc-------CCCeEEEeCCCCChHHHHHHHhcc
Confidence            47888888777776544  456789999999999999999998765332       44566666654321        10


Q ss_pred             ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEEE
Q 005179          362 KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCIA  428 (710)
Q Consensus       362 ~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI~  428 (710)
                       ..|.+......-...+....+.+||||||+.|             ..+.+..|..+++.+             ++++|+
T Consensus        74 -~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L-------------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~  139 (329)
T TIGR02974        74 -EAGAFTGAQKRHQGRFERADGGTLFLDELATA-------------SLLVQEKLLRVIEYGEFERVGGSQTLQVDVRLVC  139 (329)
T ss_pred             -ccccccCcccccCCchhhCCCCEEEeCChHhC-------------CHHHHHHHHHHHHcCcEEecCCCceeccceEEEE
Confidence             00100000000001122345679999999999             556677776666543             468899


Q ss_pred             ccChHHHH--hhhhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcC----CCCCHHHHHHHHHH
Q 005179          429 STTQDEHR--TQFEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHN----CKFTLEAINAAVHL  492 (710)
Q Consensus       429 att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~----~~i~~~~l~~l~~l  492 (710)
                      +|+.+-..  ..-...+.|..||..+.|..|+.    ++...+++.++.++...++    ..+++++++.+..+
T Consensus       140 at~~~l~~~~~~g~fr~dL~~rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~ls~~a~~~L~~y  213 (329)
T TIGR02974       140 ATNADLPALAAEGRFRADLLDRLAFDVITLPPLRERQEDIMLLAEHFAIRMARELGLPLFPGFTPQAREQLLEY  213 (329)
T ss_pred             echhhHHHHhhcCchHHHHHHHhcchhcCCCchhhhhhhHHHHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHhC
Confidence            88765311  11134577888997556666654    4445555555555544333    46899988877544

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

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

Probab=99.16  E-value=2.9e-11  Score=124.30  Aligned_cols=61  Identities=31%  Similarity=0.453  Sum_probs=53.2

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|.++-++.|..+|        .+-+.|+.+|    .|+|||||||||||+||||+|+.   +...+||+..||+
T Consensus       153 IGGL~~Qi~EirE~VELPL~~PElF~~~GI~PP----KGVLLYGPPGTGKTLLAkAVA~~---T~AtFIrvvgSEl  221 (406)
T COG1222         153 IGGLDEQIQEIREVVELPLKNPELFEELGIDPP----KGVLLYGPPGTGKTLLAKAVANQ---TDATFIRVVGSEL  221 (406)
T ss_pred             ccCHHHHHHHHHHHhcccccCHHHHHHcCCCCC----CceEeeCCCCCcHHHHHHHHHhc---cCceEEEeccHHH
Confidence            677777777777666        5668899877    89999999999999999999999   8889999999998

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.15  E-value=5.5e-10  Score=118.20  Aligned_cols=164  Identities=15%  Similarity=0.160  Sum_probs=110.3

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCC-CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc--------ccCceEEEeehhhhh
Q 005179          288 LIDPVIGRETEIQRIIQILCRRT-KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVF--------LLSKRIMSLDMGLLM  358 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~-~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~--------l~~~~v~~ld~~~l~  358 (710)
                      .|++++|++..++.+...+...+ +...||+||+|+||+++|.++|+.+.+......        .....++.+......
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~~rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~hPDl~~i~p~~~~   81 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQNRIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNHPDLLWVEPTYQH   81 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCCCCEEEEeccccc
Confidence            46789999999999999987765 467899999999999999999999876431100        001112222111001


Q ss_pred             hccc--------------cCcc-HHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          359 AGAK--------------ERGE-LEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       359 ~g~~--------------~~g~-~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                      .|..              ..+. -.+.++++.+.+..    ++..|++||++|.|             ....+|.|+..|
T Consensus        82 ~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m-------------~~~aaNaLLK~L  148 (314)
T PRK07399         82 QGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETM-------------NEAAANALLKTL  148 (314)
T ss_pred             cccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhc-------------CHHHHHHHHHHH
Confidence            1100              0001 01235556555542    45679999999999             556788888888


Q ss_pred             cCC-CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHH
Q 005179          420 GRG-ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGL  469 (710)
Q Consensus       420 ~~~-~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l  469 (710)
                      ++. +.++|..++..+     .+-|++++|++.|.|.+|+.++..++|...
T Consensus       149 EEPp~~~fILi~~~~~-----~Ll~TI~SRcq~i~f~~l~~~~~~~~L~~~  194 (314)
T PRK07399        149 EEPGNGTLILIAPSPE-----SLLPTIVSRCQIIPFYRLSDEQLEQVLKRL  194 (314)
T ss_pred             hCCCCCeEEEEECChH-----hCcHHHHhhceEEecCCCCHHHHHHHHHHh
Confidence            742 334555555544     677999999999999999999988888764

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=99.15  E-value=1.2e-09  Score=112.05  Aligned_cols=113  Identities=19%  Similarity=0.208  Sum_probs=83.3

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-CeEEEEccChH-------HHHhhhhccHHHHccccceEe
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-ELQCIASTTQD-------EHRTQFEKDKALARRFQPVLI  454 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-~v~vI~att~~-------~~~~~~~~d~aL~~Rf~~I~v  454 (710)
                      |.||||||+|.|             +.+...+|...|++. --++|.+||..       ++..-+.++..|.+|+-.|..
T Consensus       292 pGVLFIDEvHmL-------------DIE~FsFlnrAlEse~aPIii~AtNRG~~kiRGTd~~sPhGIP~DlLDRllII~t  358 (450)
T COG1224         292 PGVLFIDEVHML-------------DIECFSFLNRALESELAPIIILATNRGMTKIRGTDIESPHGIPLDLLDRLLIIST  358 (450)
T ss_pred             cceEEEechhhh-------------hHHHHHHHHHHhhcccCcEEEEEcCCceeeecccCCcCCCCCCHhhhhheeEEec
Confidence            789999999999             788899999888754 23455555532       122334678899999989999


Q ss_pred             cCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhh
Q 005179          455 SEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       455 ~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~  517 (710)
                      .+++.++..+|++..+.    ..++.+++++++.++.+...-     .-..++.||.-|...+
T Consensus       359 ~py~~~EireIi~iRa~----ee~i~l~~~Ale~L~~ig~et-----SLRYa~qLL~pa~iiA  412 (450)
T COG1224         359 RPYSREEIREIIRIRAK----EEDIELSDDALEYLTDIGEET-----SLRYAVQLLTPASIIA  412 (450)
T ss_pred             CCCCHHHHHHHHHHhhh----hhccccCHHHHHHHHhhchhh-----hHHHHHHhccHHHHHH
Confidence            99999999999997766    447899999999998875431     1233666766555433

>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=99.14  E-value=8.7e-10  Score=115.14  Aligned_cols=109  Identities=21%  Similarity=0.241  Sum_probs=72.0

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-CeEEEEccChH-------HHHhhhhccHHHHccccceEe
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-ELQCIASTTQD-------EHRTQFEKDKALARRFQPVLI  454 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-~v~vI~att~~-------~~~~~~~~d~aL~~Rf~~I~v  454 (710)
                      |.||||||+|.|             +.+...+|...++.. .-++|.+||..       ++.....++..|.+|+-.|..
T Consensus       279 pGVLFIDEvHmL-------------DiEcFsfLnralEs~~sPiiIlATNRg~~~irGt~~~sphGiP~DlLDRllII~t  345 (398)
T PF06068_consen  279 PGVLFIDEVHML-------------DIECFSFLNRALESELSPIIILATNRGITKIRGTDIISPHGIPLDLLDRLLIIRT  345 (398)
T ss_dssp             E-EEEEESGGGS-------------BHHHHHHHHHHHTSTT--EEEEEES-SEEE-BTTS-EEETT--HHHHTTEEEEEE
T ss_pred             cceEEecchhhc-------------cHHHHHHHHHHhcCCCCcEEEEecCceeeeccCccCcCCCCCCcchHhhcEEEEC
Confidence            789999999999             788899999999864 34555566532       233345677899999999999


Q ss_pred             cCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHH
Q 005179          455 SEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEA  513 (710)
Q Consensus       455 ~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a  513 (710)
                      .+++.++..+|++-.++    ..++.+++++++.+..+....-     -+.|+.|+.-|
T Consensus       346 ~py~~~ei~~Il~iR~~----~E~v~i~~~al~~L~~ig~~~S-----LRYAiqLi~~a  395 (398)
T PF06068_consen  346 KPYSEEEIKQILKIRAK----EEDVEISEDALDLLTKIGVETS-----LRYAIQLITPA  395 (398)
T ss_dssp             ----HHHHHHHHHHHHH----HCT--B-HHHHHHHHHHHHHS------HHHHHHCHHHH
T ss_pred             CCCCHHHHHHHHHhhhh----hhcCcCCHHHHHHHHHHhhhcc-----HHHHHHhhhhh
Confidence            99999999999997776    4589999999999987765421     13355555443

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.

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.13  E-value=2.7e-10  Score=121.72  Aligned_cols=184  Identities=17%  Similarity=0.230  Sum_probs=112.3

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------  359 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------  359 (710)
                      .+++++|.+..++++.+.+.+  ....+|+|+|++||||+++|++|.......       +.+++.+||..+..      
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~~~pVlI~GE~GtGK~~lA~~iH~~s~r~-------~~pfv~v~c~~~~~~~~~~~   76 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPLDKPVLIIGERGTGKELIASRLHYLSSRW-------QGPFISLNCAALNENLLDSE   76 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhCCcc-------CCCeEEEeCCCCCHHHHHHH
Confidence            356799999999988887654  456789999999999999999998654222       34566666654321      


Q ss_pred             --ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------Ce
Q 005179          360 --GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------EL  424 (710)
Q Consensus       360 --g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v  424 (710)
                        |.. .+.+..........+....+..|||||++.|             ....+..|..+++.+             ++
T Consensus        77 lfg~~-~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L-------------~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~  142 (326)
T PRK11608         77 LFGHE-AGAFTGAQKRHPGRFERADGGTLFLDELATA-------------PMLVQEKLLRVIEYGELERVGGSQPLQVNV  142 (326)
T ss_pred             Hcccc-ccccCCcccccCCchhccCCCeEEeCChhhC-------------CHHHHHHHHHHHhcCcEEeCCCCceeeccE
Confidence              100 0000000000011123345678999999999             455666666555432             47


Q ss_pred             EEEEccChHHHH--hhhhccHHHHccccceEecCCCHHHH----HHHHHHHHHHHHhhcC----CCCCHHHHHHHHHH
Q 005179          425 QCIASTTQDEHR--TQFEKDKALARRFQPVLISEPSQEDA----VRILLGLREKYEAHHN----CKFTLEAINAAVHL  492 (710)
Q Consensus       425 ~vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~~~~----~~IL~~l~~~~~~~~~----~~i~~~~l~~l~~l  492 (710)
                      ++|++++.+-..  ..-...+.|..||..+.|..|+..+|    ..++..++.++...++    ..+++++++.+..+
T Consensus       143 RiI~~s~~~l~~l~~~g~f~~dL~~~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~~~~~~~~~~~~s~~al~~L~~y  220 (326)
T PRK11608        143 RLVCATNADLPAMVAEGKFRADLLDRLAFDVVQLPPLRERQSDIMLMAEHFAIQMCRELGLPLFPGFTERARETLLNY  220 (326)
T ss_pred             EEEEeCchhHHHHHHcCCchHHHHHhcCCCEEECCChhhhhhhHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHhC
Confidence            888887764311  11234577888997666666664444    4455555555444433    35788888776543

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

Probab=99.12  E-value=3.4e-10  Score=123.19  Aligned_cols=191  Identities=20%  Similarity=0.319  Sum_probs=125.0

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh-hhccccC
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL-MAGAKER  364 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l-~~g~~~~  364 (710)
                      ...++||+...+.++.+.+.+  ....+|||+|++||||..+|++|.+.-...+-|+...||.-+.-++-.. ..| ..+
T Consensus       139 ~~~~liG~S~am~~l~~~i~kvA~s~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~l~ESELFG-hek  217 (464)
T COG2204         139 LGGELVGESPAMQQLRRLIAKVAPSDASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPENLLESELFG-HEK  217 (464)
T ss_pred             ccCCceecCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHHHHHHHhhc-ccc
Confidence            456899999999999887765  4567899999999999999999998876555454444443333222111 112 123


Q ss_pred             ccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEEEccC
Q 005179          365 GELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCIASTT  431 (710)
Q Consensus       365 g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI~att  431 (710)
                      |.|..-...-....+...+..||||||..|             ..+++..|+..|+.+             +++||++|+
T Consensus       218 GAFTGA~~~r~G~fE~A~GGTLfLDEI~~m-------------pl~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIaaT~  284 (464)
T COG2204         218 GAFTGAITRRIGRFEQANGGTLFLDEIGEM-------------PLELQVKLLRVLQEREFERVGGNKPIKVDVRIIAATN  284 (464)
T ss_pred             cCcCCcccccCcceeEcCCceEEeeccccC-------------CHHHHHHHHHHHHcCeeEecCCCcccceeeEEEeecC
Confidence            322222222222333456789999999998             778888888777643             577999988


Q ss_pred             hHHHHhh--hhccHHHHccccceEecCCC----HHHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          432 QDEHRTQ--FEKDKALARRFQPVLISEPS----QEDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       432 ~~~~~~~--~~~d~aL~~Rf~~I~v~~Ps----~~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      .+-....  -..-..|.-|+.++.+..|+    .++..-++++++.++....+   ..++++++..+..+
T Consensus       285 ~dL~~~v~~G~FReDLyyRLnV~~i~iPpLRER~EDIp~L~~hfl~~~~~~~~~~~~~~s~~a~~~L~~y  354 (464)
T COG2204         285 RDLEEEVAAGRFREDLYYRLNVVPLRLPPLRERKEDIPLLAEHFLKRFAAELGRPPKGFSPEALAALLAY  354 (464)
T ss_pred             cCHHHHHHcCCcHHHHHhhhccceecCCcccccchhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhC
Confidence            7532111  11336677788888888887    45555566667776665544   46888888776543

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.12  E-value=5.8e-10  Score=119.67  Aligned_cols=152  Identities=24%  Similarity=0.286  Sum_probs=103.6

Q ss_pred             CcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHH
Q 005179          291 PVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEAR  370 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~  370 (710)
                      .++|+++.+..+...+..  +.+++|.||||||||++|+.+|+.+          +..++.+.+..-.......|.+...
T Consensus        25 ~~~g~~~~~~~~l~a~~~--~~~vll~G~PG~gKT~la~~lA~~l----------~~~~~~i~~t~~l~p~d~~G~~~~~   92 (329)
T COG0714          25 VVVGDEEVIELALLALLA--GGHVLLEGPPGVGKTLLARALARAL----------GLPFVRIQCTPDLLPSDLLGTYAYA   92 (329)
T ss_pred             eeeccHHHHHHHHHHHHc--CCCEEEECCCCccHHHHHHHHHHHh----------CCCeEEEecCCCCCHHHhcCchhHh
Confidence            388888888887766654  5789999999999999999999998          5666666655444333333332221


Q ss_pred             HHH---HHHHHHhc---CC--eEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--------------CCeEEEE
Q 005179          371 VTT---LISEIQKS---GD--VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--------------GELQCIA  428 (710)
Q Consensus       371 l~~---~~~~~~~~---~~--~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--------------~~v~vI~  428 (710)
                      ...   -.......   ..  .++++|||+..             ..++++.|...|+.              ..+.+|+
T Consensus        93 ~~~~~~~~~~~~~gpl~~~~~~ill~DEInra-------------~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~via  159 (329)
T COG0714          93 ALLLEPGEFRFVPGPLFAAVRVILLLDEINRA-------------PPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIA  159 (329)
T ss_pred             hhhccCCeEEEecCCcccccceEEEEeccccC-------------CHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEE
Confidence            110   00000000   11  39999999987             45677777766653              3456888


Q ss_pred             ccChHHHHhhhhccHHHHccc-cceEecCC-CHHHHHHHHH
Q 005179          429 STTQDEHRTQFEKDKALARRF-QPVLISEP-SQEDAVRILL  467 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf-~~I~v~~P-s~~~~~~IL~  467 (710)
                      |.|+.+|.....++.++.+|| -.+.++.| +.++...++.
T Consensus       160 T~Np~e~~g~~~l~eA~ldRf~~~~~v~yp~~~~e~~~i~~  200 (329)
T COG0714         160 TQNPGEYEGTYPLPEALLDRFLLRIYVDYPDSEEEERIILA  200 (329)
T ss_pred             ccCccccCCCcCCCHHHHhhEEEEEecCCCCchHHHHHHHH
Confidence            889888888888899999999 58999999 4444444444

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.09  E-value=2.1e-10  Score=131.19  Aligned_cols=187  Identities=22%  Similarity=0.318  Sum_probs=118.6

Q ss_pred             hhcCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh---
Q 005179          285 SEELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA---  359 (710)
Q Consensus       285 ~~~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~---  359 (710)
                      +.+.++.+||.+..++++.+.+.+  ....+|+|+|++||||+++|++|.......       +.+++.+||..+..   
T Consensus       191 ~~~~~~~liG~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~lA~~ih~~s~r~-------~~pfv~i~c~~~~~~~~  263 (534)
T TIGR01817       191 RSGKEDGIIGKSPAMRQVVDQARVVARSNSTVLLRGESGTGKELIAKAIHYLSPRA-------KRPFVKVNCAALSETLL  263 (534)
T ss_pred             ccCccCceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCccHHHHHHHHHHhCCCC-------CCCeEEeecCCCCHHHH
Confidence            346788999999999998887654  456789999999999999999999865322       45667777654421   


Q ss_pred             -----ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC------------
Q 005179          360 -----GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG------------  422 (710)
Q Consensus       360 -----g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~------------  422 (710)
                           |. .+|.+..........+....+.+||||||+.|             ..+.+..|..+++.+            
T Consensus       264 ~~~lfg~-~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L-------------~~~~Q~~Ll~~l~~~~~~~~~~~~~~~  329 (534)
T TIGR01817       264 ESELFGH-EKGAFTGAIAQRKGRFELADGGTLFLDEIGEI-------------SPAFQAKLLRVLQEGEFERVGGNRTLK  329 (534)
T ss_pred             HHHHcCC-CCCccCCCCcCCCCcccccCCCeEEEechhhC-------------CHHHHHHHHHHHhcCcEEECCCCceEe
Confidence                 10 01110000000000122334678999999999             556677776666543            


Q ss_pred             -CeEEEEccChHHHH--hhhhccHHHHccccceEecCCC----HHHHHHHHHHHHHHHHhhcC--CCCCHHHHHHHHHH
Q 005179          423 -ELQCIASTTQDEHR--TQFEKDKALARRFQPVLISEPS----QEDAVRILLGLREKYEAHHN--CKFTLEAINAAVHL  492 (710)
Q Consensus       423 -~v~vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps----~~~~~~IL~~l~~~~~~~~~--~~i~~~~l~~l~~l  492 (710)
                       ++++|++|+.+...  ..-...+.|..|+..+.+..|+    .++...+++.++.++...++  +.+++++++.+..+
T Consensus       330 ~~~riI~~s~~~l~~~~~~~~f~~~L~~rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~~  408 (534)
T TIGR01817       330 VDVRLVAATNRDLEEAVAKGEFRADLYYRINVVPIFLPPLRERREDIPLLAEAFLEKFNRENGRPLTITPSAIRVLMSC  408 (534)
T ss_pred             ecEEEEEeCCCCHHHHHHcCCCCHHHHHHhcCCeeeCCCcccccccHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHhC
Confidence             37888887764311  1112456777888755555554    35556666777666654333  67899998877644

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.

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.08  E-value=5.6e-09  Score=101.99  Aligned_cols=191  Identities=19%  Similarity=0.267  Sum_probs=127.1

Q ss_pred             CCCcccCHHHHHHHHH----HHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccC
Q 005179          289 IDPVIGRETEIQRIIQ----ILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKER  364 (710)
Q Consensus       289 l~~liGr~~~i~~l~~----~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~  364 (710)
                      +..++|.+.+-+.+++    .+.....||+||+|..|+|||++++++..++...       +.++++++-.++..     
T Consensus        59 L~~l~Gvd~qk~~L~~NT~~F~~G~pANnVLLwGaRGtGKSSLVKA~~~e~~~~-------glrLVEV~k~dl~~-----  126 (287)
T COG2607          59 LADLVGVDRQKEALVRNTEQFAEGLPANNVLLWGARGTGKSSLVKALLNEYADE-------GLRLVEVDKEDLAT-----  126 (287)
T ss_pred             HHHHhCchHHHHHHHHHHHHHHcCCcccceEEecCCCCChHHHHHHHHHHHHhc-------CCeEEEEcHHHHhh-----
Confidence            3467888877766665    4455667999999999999999999999998554       66788888766652     


Q ss_pred             ccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC------CeEEEEccChHHHHh
Q 005179          365 GELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG------ELQCIASTTQDEHRT  437 (710)
Q Consensus       365 g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~------~v~vI~att~~~~~~  437 (710)
                            +-.+++.++.. .+.|||+||+-.=            .+.+....|+..|+.+      +|.+.+|+|.....+
T Consensus       127 ------Lp~l~~~Lr~~~~kFIlFcDDLSFe------------~gd~~yK~LKs~LeG~ve~rP~NVl~YATSNRRHLl~  188 (287)
T COG2607         127 ------LPDLVELLRARPEKFILFCDDLSFE------------EGDDAYKALKSALEGGVEGRPANVLFYATSNRRHLLP  188 (287)
T ss_pred             ------HHHHHHHHhcCCceEEEEecCCCCC------------CCchHHHHHHHHhcCCcccCCCeEEEEEecCCccccc
Confidence                  45566666653 4799999987432            2334577788887642      566667766432111


Q ss_pred             -h-------h-hcc--------HHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcC
Q 005179          438 -Q-------F-EKD--------KALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       438 -~-------~-~~d--------~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~  499 (710)
                       .       . +++        -+|..||. .+.|.+++.++..+|+.++++    +.++.++++.++.-+....---++
T Consensus       189 e~~~dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~----~~~l~~~~e~l~~eAl~WAt~rg~  264 (287)
T COG2607         189 EDMKDNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAK----HFGLDISDEELHAEALQWATTRGG  264 (287)
T ss_pred             HhhhhCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHHHHhcCC
Confidence             0       0 111        24667998 899999999999999998887    558889887766544433322222


Q ss_pred             CCCcchHHHHHHHHH
Q 005179          500 RYLPDKAIDLVDEAG  514 (710)
Q Consensus       500 r~~p~~ai~ll~~a~  514 (710)
                      | ...-|-.+++...
T Consensus       265 R-SGR~A~QF~~~~~  278 (287)
T COG2607         265 R-SGRVAWQFIRDLA  278 (287)
T ss_pred             C-ccHhHHHHHHHHH
Confidence            2 1234555544433

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=99.08  E-value=3.5e-09  Score=122.83  Aligned_cols=160  Identities=21%  Similarity=0.312  Sum_probs=98.0

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhc----CCCcc---------------------
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQA----EVPVF---------------------  343 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~----~~p~~---------------------  343 (710)
                      |..++|++..+..+.-.+..+...++||.|++|||||++|++|+..+...    ..+..                     
T Consensus         3 f~~ivGq~~~~~al~~~av~~~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~~~~~~~~~~~~~~~   82 (633)
T TIGR02442         3 FTAIVGQEDLKLALLLNAVDPRIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPEEWCEECRRKYRPSE   82 (633)
T ss_pred             cchhcChHHHHHHHHHHhhCCCCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCccccChhhhhcccccc
Confidence            56799999888776655554455679999999999999999999887210    00000                     


Q ss_pred             ccCceEEEeehhhh---hhccccCccHHHHHHH---H--HHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhh
Q 005179          344 LLSKRIMSLDMGLL---MAGAKERGELEARVTT---L--ISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLL  415 (710)
Q Consensus       344 l~~~~v~~ld~~~l---~~g~~~~g~~e~~l~~---~--~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L  415 (710)
                      .....++.+.++..   +.|..   +++..+..   .  -..+....+.||||||++.+             ....++.|
T Consensus        83 ~~~~pfv~~p~~~t~~~l~G~~---d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l-------------~~~~q~~L  146 (633)
T TIGR02442        83 QRPVPFVNLPLGATEDRVVGSL---DIERALREGEKAFQPGLLAEAHRGILYIDEVNLL-------------DDHLVDVL  146 (633)
T ss_pred             cCCCCeeeCCCCCcHHHcCCcc---cHHHHhhcCCeeecCcceeecCCCeEEeChhhhC-------------CHHHHHHH
Confidence            00123333322211   01110   01111100   0  00111234569999999999             55677788


Q ss_pred             cccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCC-HHHHHHHHHH
Q 005179          416 KPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPS-QEDAVRILLG  468 (710)
Q Consensus       416 ~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps-~~~~~~IL~~  468 (710)
                      ...|+.+               .+.+|+++|+.+    ..+.++|..||. .|.++.+. .+++.++++.
T Consensus       147 l~~le~g~~~v~r~g~~~~~~~~~~lIat~np~e----g~l~~~L~dR~~l~i~v~~~~~~~~~~~il~~  212 (633)
T TIGR02442       147 LDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEE----GDLRPQLLDRFGLCVDVAAPRDPEERVEIIRR  212 (633)
T ss_pred             HHHHhcCCEEEEECCceeeecCCeEEEEecCCCC----CCCCHHHHhhcceEEEccCCCchHHHHHHHHH
Confidence            7777655               367889888753    247789999997 57776664 5777777764

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.

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.08  E-value=6.9e-10  Score=123.07  Aligned_cols=149  Identities=20%  Similarity=0.236  Sum_probs=100.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHH--H--hcCCeEEE
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEI--Q--KSGDVILF  387 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~--~--~~~~~IL~  387 (710)
                      .-+||+||||.||||||+-+|+..          |+.+++++.++-..+    ..+++++..++..=  -  ...|.+|+
T Consensus       327 KilLL~GppGlGKTTLAHViAkqa----------GYsVvEINASDeRt~----~~v~~kI~~avq~~s~l~adsrP~CLV  392 (877)
T KOG1969|consen  327 KILLLCGPPGLGKTTLAHVIAKQA----------GYSVVEINASDERTA----PMVKEKIENAVQNHSVLDADSRPVCLV  392 (877)
T ss_pred             ceEEeecCCCCChhHHHHHHHHhc----------CceEEEecccccccH----HHHHHHHHHHHhhccccccCCCcceEE
Confidence            347999999999999999999998          999999987664432    23444444443321  1  14689999


Q ss_pred             EccchhhhhCCCCCCCCCCChHhHHHhhccccc--------------------CC---CeEEEEccChHHHHhhhhccHH
Q 005179          388 IDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--------------------RG---ELQCIASTTQDEHRTQFEKDKA  444 (710)
Q Consensus       388 IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--------------------~~---~v~vI~att~~~~~~~~~~d~a  444 (710)
                      |||||--             ..-+.+.|+.++.                    ++   .-.||+.||..       ..|+
T Consensus       393 iDEIDGa-------------~~~~Vdvilslv~a~~k~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdL-------YaPa  452 (877)
T KOG1969|consen  393 IDEIDGA-------------PRAAVDVILSLVKATNKQATGKQAKKDKKRKKKRSKLLTRPIICICNDL-------YAPA  452 (877)
T ss_pred             EecccCC-------------cHHHHHHHHHHHHhhcchhhcCcccchhhhhhhccccccCCEEEEecCc-------cchh
Confidence            9999743             1112222222221                    00   01256666662       3467


Q ss_pred             HHc--cc-cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          445 LAR--RF-QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       445 L~~--Rf-~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      |+.  -| ..|.|.+|+.....+-|+.++.+    .++..+..++..+++++..-+.
T Consensus       453 LR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~r----E~mr~d~~aL~~L~el~~~DIR  505 (877)
T KOG1969|consen  453 LRPLRPFAEIIAFVPPSQSRLVERLNEICHR----ENMRADSKALNALCELTQNDIR  505 (877)
T ss_pred             hhhcccceEEEEecCCChhHHHHHHHHHHhh----hcCCCCHHHHHHHHHHhcchHH
Confidence            765  23 37899999998888888888774    4899999999999999886554

>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=99.08  E-value=3e-10  Score=115.18  Aligned_cols=198  Identities=20%  Similarity=0.282  Sum_probs=105.6

Q ss_pred             cccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCC-CccccCceEEEe-ehhhh------------
Q 005179          292 VIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEV-PVFLLSKRIMSL-DMGLL------------  357 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~-p~~l~~~~v~~l-d~~~l------------  357 (710)
                      ++||+.+++.|.+.+.......++|+||.|+|||++++.+.+.+..... ..+......... ....+            
T Consensus         1 F~gR~~el~~l~~~l~~~~~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~   80 (234)
T PF01637_consen    1 FFGREKELEKLKELLESGPSQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSE   80 (234)
T ss_dssp             S-S-HHHHHHHHHCHHH--SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHH
T ss_pred             CCCHHHHHHHHHHHHHhhcCcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHH
Confidence            5899999999999998877788999999999999999999988733221 111111110000 00000            


Q ss_pred             -hh-cc----------ccCccHHHHHHHHHHHHHhcC-CeEEEEccchhhh-hCCCCCCCCCCChHhHHHhhcccccCCC
Q 005179          358 -MA-GA----------KERGELEARVTTLISEIQKSG-DVILFIDEVHTLI-GSGTVGRGNKGTGLDISNLLKPSLGRGE  423 (710)
Q Consensus       358 -~~-g~----------~~~g~~e~~l~~~~~~~~~~~-~~IL~IDEid~l~-~~~~~~~~~~~~~~~~~~~L~~~l~~~~  423 (710)
                       .. ..          .........+..+++.+...+ +.||+|||++.+. .....    ......+.+.+.......+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~----~~~~~~l~~~~~~~~~~~~  156 (234)
T PF01637_consen   81 ALGISIPSITLEKISKDLSEDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEED----KDFLKSLRSLLDSLLSQQN  156 (234)
T ss_dssp             HHHHHCCTSTTEEEECTS-GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTT----HHHHHHHHHHHHH----TT
T ss_pred             HHhhhcccccchhhhhcchhhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccch----HHHHHHHHHHHhhccccCC
Confidence             00 00          011234455677777776543 5899999999997 21100    0112234444444444566


Q ss_pred             eEEEEccChHHHH-hhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          424 LQCIASTTQDEHR-TQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       424 v~vI~att~~~~~-~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +.+|.+++...+. ........+..|+..+.+++.+.++..+++.......   .++.++++.++.+..++.++
T Consensus       157 ~~~v~~~S~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~e~~~~~~~~~~~~---~~~~~~~~~~~~i~~~~gG~  227 (234)
T PF01637_consen  157 VSIVITGSSDSLMEEFLDDKSPLFGRFSHIELKPLSKEEAREFLKELFKEL---IKLPFSDEDIEEIYSLTGGN  227 (234)
T ss_dssp             EEEEEEESSHHHHHHTT-TTSTTTT---EEEE----HHHHHHHHHHHHHCC---------HHHHHHHHHHHTT-
T ss_pred             ceEEEECCchHHHHHhhcccCccccccceEEEeeCCHHHHHHHHHHHHHHh---hcccCCHHHHHHHHHHhCCC
Confidence            6655555544322 2233445566777789999999999998888765532   12245899999999888764

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.07  E-value=3.1e-09  Score=113.88  Aligned_cols=153  Identities=20%  Similarity=0.246  Sum_probs=105.2

Q ss_pred             CcccCHHHHHHHHHHHH-cCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc--------------cCceEEEeeh
Q 005179          291 PVIGRETEIQRIIQILC-RRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL--------------LSKRIMSLDM  354 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~-~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l--------------~~~~v~~ld~  354 (710)
                      +++|.+..+.++..... .....+ +||+||||+|||++|.++|+.+.+.......              ....+++++.
T Consensus         2 ~~~~~~~~~~~l~~~~~~~~~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~   81 (325)
T COG0470           2 ELVPWQEAVKRLLVQALESGRLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNP   81 (325)
T ss_pred             CcccchhHHHHHHHHHHhcCCCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhhcCCCceEEecc
Confidence            56778888888877766 444566 9999999999999999999999653321111              1234555554


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEE
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIA  428 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~  428 (710)
                      ++...    ..-..+.++.+.+....    .+.-|++|||+|.|             ..++++.|+..++.  .+.++|.
T Consensus        82 s~~~~----~~i~~~~vr~~~~~~~~~~~~~~~kviiidead~m-------------t~~A~nallk~lEep~~~~~~il  144 (325)
T COG0470          82 SDLRK----IDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKL-------------TEDAANALLKTLEEPPKNTRFIL  144 (325)
T ss_pred             cccCC----CcchHHHHHHHHHHhccCCCCCCceEEEeCcHHHH-------------hHHHHHHHHHHhccCCCCeEEEE
Confidence            33221    11234456666555433    34579999999999             56788888888874  5677888


Q ss_pred             ccChHHHHhhhhccHHHHccccceEecCCCHHHHHHH
Q 005179          429 STTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRI  465 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~I  465 (710)
                      +|+...     .+-+.+++|+..+.|.+|+.......
T Consensus       145 ~~n~~~-----~il~tI~SRc~~i~f~~~~~~~~i~~  176 (325)
T COG0470         145 ITNDPS-----KILPTIRSRCQRIRFKPPSRLEAIAW  176 (325)
T ss_pred             EcCChh-----hccchhhhcceeeecCCchHHHHHHH
Confidence            888554     56679999999999988665544333

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=99.06  E-value=4.4e-10  Score=120.23  Aligned_cols=203  Identities=20%  Similarity=0.294  Sum_probs=122.4

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc-
Q 005179          287 ELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE-  363 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~-  363 (710)
                      ..++.+||.+..++++++.+.+  +...++||+|++||||+.+|+.|.......      ...+++.++|..+...... 
T Consensus        75 ~~~~~LIG~~~~~~~~~eqik~~ap~~~~vLi~GetGtGKel~A~~iH~~s~r~------~~~PFI~~NCa~~~en~~~~  148 (403)
T COG1221          75 EALDDLIGESPSLQELREQIKAYAPSGLPVLIIGETGTGKELFARLIHALSARR------AEAPFIAFNCAAYSENLQEA  148 (403)
T ss_pred             hhhhhhhccCHHHHHHHHHHHhhCCCCCcEEEecCCCccHHHHHHHHHHhhhcc------cCCCEEEEEHHHhCcCHHHH
Confidence            3466799999998888887655  456789999999999999999999443221      2456667776665422100 


Q ss_pred             ------CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------Ce
Q 005179          364 ------RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------EL  424 (710)
Q Consensus       364 ------~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v  424 (710)
                            .|.|.-....-....+...+.+||+|||+.|             ....+..|..+|++|             ++
T Consensus       149 eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~L-------------P~~~Q~kLl~~le~g~~~rvG~~~~~~~dV  215 (403)
T COG1221         149 ELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRL-------------PPEGQEKLLRVLEEGEYRRVGGSQPRPVDV  215 (403)
T ss_pred             HHhccccceeecccCCcCchheecCCCEEehhhhhhC-------------CHhHHHHHHHHHHcCceEecCCCCCcCCCc
Confidence                  1111000000011122345779999999999             555677777777653             57


Q ss_pred             EEEEccChHHHHhhhhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcCCCCC---HHHHHHHHHHhhhhh
Q 005179          425 QCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHNCKFT---LEAINAAVHLSARYI  497 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~~~i~---~~~l~~l~~ls~~~i  497 (710)
                      ++|++|+.+--...+.- ..|.+|...+.|..|+.    +|+..++++++..+....+..+.   ++++..+..+     
T Consensus       216 Rli~AT~~~l~~~~~~g-~dl~~rl~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~~~~~~~~~~a~~~L~~y-----  289 (403)
T COG1221         216 RLICATTEDLEEAVLAG-ADLTRRLNILTITLPPLRERKEDILLLAEHFLKSEARRLGLPLSVDSPEALRALLAY-----  289 (403)
T ss_pred             eeeeccccCHHHHHHhh-cchhhhhcCceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhC-----
Confidence            78999887643333322 36777665566666664    45555666677766666665443   3445444322     


Q ss_pred             cCCCCcc---hHHHHHHHHHhhh
Q 005179          498 SDRYLPD---KAIDLVDEAGSRA  517 (710)
Q Consensus       498 ~~r~~p~---~ai~ll~~a~~~~  517 (710)
                         .+|+   ....+++.+|...
T Consensus       290 ---~~pGNirELkN~Ve~~~~~~  309 (403)
T COG1221         290 ---DWPGNIRELKNLVERAVAQA  309 (403)
T ss_pred             ---CCCCcHHHHHHHHHHHHHHh
Confidence               1233   3455666666544

>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=99.05  E-value=1e-09  Score=102.17  Aligned_cols=144  Identities=24%  Similarity=0.329  Sum_probs=89.8

Q ss_pred             ccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHH-H
Q 005179          293 IGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEAR-V  371 (710)
Q Consensus       293 iGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~-l  371 (710)
                      +|++..+..+...+......+++|+||||+|||++++.+++.+..       .+..++.++................. .
T Consensus         1 ~~~~~~~~~i~~~~~~~~~~~v~i~G~~G~GKT~l~~~i~~~~~~-------~~~~v~~~~~~~~~~~~~~~~~~~~~~~   73 (151)
T cd00009           1 VGQEEAIEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFR-------PGAPFLYLNASDLLEGLVVAELFGHFLV   73 (151)
T ss_pred             CchHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHhhc-------CCCCeEEEehhhhhhhhHHHHHhhhhhH
Confidence            467888888888888777788999999999999999999998842       24567777765544222111100000 0


Q ss_pred             HHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEEEEccChHHHHhhhhccHHHHc
Q 005179          372 TTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQCIASTTQDEHRTQFEKDKALAR  447 (710)
Q Consensus       372 ~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~vI~att~~~~~~~~~~d~aL~~  447 (710)
                      ...........+.+|+|||++.+...         ....+...+.....    ...+.+|++++....   ...++.+.+
T Consensus        74 ~~~~~~~~~~~~~~lilDe~~~~~~~---------~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~---~~~~~~~~~  141 (151)
T cd00009          74 RLLFELAEKAKPGVLFIDEIDSLSRG---------AQNALLRVLETLNDLRIDRENVRVIGATNRPLL---GDLDRALYD  141 (151)
T ss_pred             hHHHHhhccCCCeEEEEeChhhhhHH---------HHHHHHHHHHhcCceeccCCCeEEEEecCcccc---CCcChhHHh
Confidence            11112222345789999999987111         12233344444332    367888888877642   356788889


Q ss_pred             ccc-ceEec
Q 005179          448 RFQ-PVLIS  455 (710)
Q Consensus       448 Rf~-~I~v~  455 (710)
                      ||. .|.++
T Consensus       142 r~~~~i~~~  150 (151)
T cd00009         142 RLDIRIVIP  150 (151)
T ss_pred             hhccEeecC
Confidence            995 55543

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.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.05  E-value=7.7e-10  Score=118.35  Aligned_cols=154  Identities=17%  Similarity=0.170  Sum_probs=106.5

Q ss_pred             CCCccc-CHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCccc--------------cCceEEEe
Q 005179          289 IDPVIG-RETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVFL--------------LSKRIMSL  352 (710)
Q Consensus       289 l~~liG-r~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~l--------------~~~~v~~l  352 (710)
                      ++.++| ++..++.+...+...+..|. ||+||+|+|||++|+.+++.+.+.......              ....+..+
T Consensus         4 ~~~i~~~q~~~~~~L~~~~~~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~~~~~~~hpD~~~i   83 (329)
T PRK08058          4 WEQLTALQPVVVKMLQNSIAKNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCKRIDSGNHPDVHLV   83 (329)
T ss_pred             HHHHHhhHHHHHHHHHHHHHcCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEe
Confidence            456788 78888888888887766665 899999999999999999998654311000              00011121


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQC  426 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~v  426 (710)
                      ...    |...   ..+.++.+.+.+..    ++.-|++|||+|.+             ..+.+|.|+..|++  ....+
T Consensus        84 ~~~----~~~i---~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~-------------~~~a~NaLLK~LEEPp~~~~~  143 (329)
T PRK08058         84 APD----GQSI---KKDQIRYLKEEFSKSGVESNKKVYIIEHADKM-------------TASAANSLLKFLEEPSGGTTA  143 (329)
T ss_pred             ccc----cccC---CHHHHHHHHHHHhhCCcccCceEEEeehHhhh-------------CHHHHHHHHHHhcCCCCCceE
Confidence            110    1110   12335555555432    34569999999999             56678999999986  56677


Q ss_pred             EEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHH
Q 005179          427 IASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                      |.+|+...     .+-+++++|++.+.+.+|+.++..++|+
T Consensus       144 Il~t~~~~-----~ll~TIrSRc~~i~~~~~~~~~~~~~L~  179 (329)
T PRK08058        144 ILLTENKH-----QILPTILSRCQVVEFRPLPPESLIQRLQ  179 (329)
T ss_pred             EEEeCChH-----hCcHHHHhhceeeeCCCCCHHHHHHHHH
Confidence            77666544     6779999999999999999998766664

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=99.04  E-value=1.6e-09  Score=122.82  Aligned_cols=184  Identities=22%  Similarity=0.293  Sum_probs=116.3

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------  359 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------  359 (710)
                      .++.+||++..++++.+.+.+  ....+|+|+|++||||+++|++|.......       +.+++.+||..+..      
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~-------~~p~v~v~c~~~~~~~~e~~  257 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAASDLNVLILGETGVGKELVARAIHAASPRA-------DKPLVYLNCAALPESLAESE  257 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhCCcC-------CCCeEEEEcccCChHHHHHH
Confidence            467899999999988887655  456789999999999999999999875332       44566666654421      


Q ss_pred             --ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------Ce
Q 005179          360 --GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------EL  424 (710)
Q Consensus       360 --g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v  424 (710)
                        |. ..|.+......-...+....+..||||||+.|             ..+.+..|..+++.+             ++
T Consensus       258 lfG~-~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L-------------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~  323 (509)
T PRK05022        258 LFGH-VKGAFTGAISNRSGKFELADGGTLFLDEIGEL-------------PLALQAKLLRVLQYGEIQRVGSDRSLRVDV  323 (509)
T ss_pred             hcCc-cccccCCCcccCCcchhhcCCCEEEecChhhC-------------CHHHHHHHHHHHhcCCEeeCCCCcceecce
Confidence              10 01111000000000122344678999999999             555666666666543             46


Q ss_pred             EEEEccChHHHHh--hhhccHHHHccccceEecCCCHH----HHHHHHHHHHHHHHhhc---CCCCCHHHHHHHHHH
Q 005179          425 QCIASTTQDEHRT--QFEKDKALARRFQPVLISEPSQE----DAVRILLGLREKYEAHH---NCKFTLEAINAAVHL  492 (710)
Q Consensus       425 ~vI~att~~~~~~--~~~~d~aL~~Rf~~I~v~~Ps~~----~~~~IL~~l~~~~~~~~---~~~i~~~~l~~l~~l  492 (710)
                      ++|++|+.+-...  .-.....|..|+..+.|..|+..    +...+++.++.++...+   .+.+++++++.+..+
T Consensus       324 RiI~~t~~~l~~~~~~~~f~~dL~~rl~~~~i~lPpLreR~eDI~~L~~~fl~~~~~~~~~~~~~~s~~a~~~L~~y  400 (509)
T PRK05022        324 RVIAATNRDLREEVRAGRFRADLYHRLSVFPLSVPPLRERGDDVLLLAGYFLEQNRARLGLRSLRLSPAAQAALLAY  400 (509)
T ss_pred             EEEEecCCCHHHHHHcCCccHHHHhcccccEeeCCCchhchhhHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhC
Confidence            8898887653111  11245677778876666666644    44455556666655443   367999998877644

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=99.03  E-value=6.7e-09  Score=121.87  Aligned_cols=149  Identities=15%  Similarity=0.282  Sum_probs=97.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee------hhhhhhc--cccCccHHHHHHHHHHHHHhc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD------MGLLMAG--AKERGELEARVTTLISEIQKS  381 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld------~~~l~~g--~~~~g~~e~~l~~~~~~~~~~  381 (710)
                      ...++||.||..+|||+++..+|+..          +.+++.++      +...+..  +...|.+.-+=..+++.++. 
T Consensus       887 ~~fP~LiQGpTSSGKTSMI~yla~~t----------ghkfVRINNHEHTdlqeYiGTyvTdd~G~lsFkEGvLVeAlR~-  955 (4600)
T COG5271         887 SNFPLLIQGPTSSGKTSMILYLARET----------GHKFVRINNHEHTDLQEYIGTYVTDDDGSLSFKEGVLVEALRR-  955 (4600)
T ss_pred             cCCcEEEecCCCCCcchHHHHHHHHh----------CccEEEecCcccchHHHHhhceeecCCCceeeehhHHHHHHhc-
Confidence            45678999999999999999999987          44555543      2222210  11233222222234444443 


Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------------CeEEEEccChHH-HHhhhhccHH
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------------ELQCIASTTQDE-HRTQFEKDKA  444 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------------~v~vI~att~~~-~~~~~~~d~a  444 (710)
                       +.++++||+...             ..++...|..+|..+                ++.+.+|-|++. |.+...+..+
T Consensus       956 -GyWIVLDELNLA-------------pTDVLEaLNRLLDDNRelfIPETqevV~PHp~F~lFATQNppg~YgGRK~LSrA 1021 (4600)
T COG5271         956 -GYWIVLDELNLA-------------PTDVLEALNRLLDDNRELFIPETQEVVVPHPNFRLFATQNPPGGYGGRKGLSRA 1021 (4600)
T ss_pred             -CcEEEeeccccC-------------cHHHHHHHHHhhccccceecCCcceeeccCCCeeEEeecCCCccccchHHHHHH
Confidence             458999999776             456777776666532                455677767553 5555567899


Q ss_pred             HHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          445 LARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       445 L~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      |++||-.+.|..-..++...||++         ++.|.+.....+++.
T Consensus      1022 FRNRFlE~hFddipedEle~ILh~---------rc~iapSyakKiVeV 1060 (4600)
T COG5271        1022 FRNRFLEMHFDDIPEDELEEILHG---------RCEIAPSYAKKIVEV 1060 (4600)
T ss_pred             HHhhhHhhhcccCcHHHHHHHHhc---------cCccCHHHHHHHHHH
Confidence            999999999999999998888875         345666655555544

>PHA02244 ATPase-like protein

Probab=99.03  E-value=1.4e-09  Score=114.77  Aligned_cols=123  Identities=18%  Similarity=0.268  Sum_probs=78.0

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh--hh-hhcc-ccCccHHHHHHHHHHHHHhcCCeE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG--LL-MAGA-KERGELEARVTTLISEIQKSGDVI  385 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~--~l-~~g~-~~~g~~e~~l~~~~~~~~~~~~~I  385 (710)
                      .+.+++|+||||||||++|++++..+          +.+++.++..  .+ ..|. ...|.|.  -..++..+.  .+.+
T Consensus       118 ~~~PVLL~GppGtGKTtLA~aLA~~l----------g~pfv~In~l~d~~~L~G~i~~~g~~~--dgpLl~A~~--~Ggv  183 (383)
T PHA02244        118 ANIPVFLKGGAGSGKNHIAEQIAEAL----------DLDFYFMNAIMDEFELKGFIDANGKFH--ETPFYEAFK--KGGL  183 (383)
T ss_pred             cCCCEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEecChHHHhhccccccccccc--chHHHHHhh--cCCE
Confidence            45689999999999999999999987          4444444311  11 0110 1122221  112333232  3569


Q ss_pred             EEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-------------CCCeEEEEccChHH------HHhhhhccHHHH
Q 005179          386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-------------RGELQCIASTTQDE------HRTQFEKDKALA  446 (710)
Q Consensus       386 L~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-------------~~~v~vI~att~~~------~~~~~~~d~aL~  446 (710)
                      |||||++.+             ..+++..|..+++             ..++++|+|+|+..      |.....++++++
T Consensus       184 LiLDEId~a-------------~p~vq~~L~~lLd~r~l~l~g~~i~~h~~FRlIATsN~~~~G~~~~y~G~k~L~~All  250 (383)
T PHA02244        184 FFIDEIDAS-------------IPEALIIINSAIANKFFDFADERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATL  250 (383)
T ss_pred             EEEeCcCcC-------------CHHHHHHHHHHhccCeEEecCcEEecCCCEEEEEeeCCCccCcccccCCCcccCHHHH
Confidence            999999987             3344444444443             24678999988742      212346789999


Q ss_pred             ccccceEecCCCH
Q 005179          447 RRFQPVLISEPSQ  459 (710)
Q Consensus       447 ~Rf~~I~v~~Ps~  459 (710)
                      +||..|.++.|+.
T Consensus       251 DRFv~I~~dyp~~  263 (383)
T PHA02244        251 DRFAPIEFDYDEK  263 (383)
T ss_pred             hhcEEeeCCCCcH
Confidence            9999999999973

>TIGR00763 lon ATP-dependent protease La

Probab=99.03  E-value=2.3e-09  Score=127.30  Aligned_cols=104  Identities=19%  Similarity=0.212  Sum_probs=81.1

Q ss_pred             CcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCC
Q 005179          590 AVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTG  669 (710)
Q Consensus       590 ~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpG  669 (710)
                      ..-....+...++.++++|+.+.+.+ ...+..+++.|.+.++||+++++.|...+...+..- .+..|  ++||+||||
T Consensus       282 ~~~~~~~~~~yl~~~~~ip~~~~~~~-~~~~~~~~~~l~~~~~G~~~~k~~i~~~~~~~~~~~-~~~~~--~lll~GppG  357 (775)
T TIGR00763       282 SSSEFTVTRNYLDWLTDLPWGKYSKE-NLDLKRAKEILDEDHYGLKKVKERILEYLAVQKLRG-KMKGP--ILCLVGPPG  357 (775)
T ss_pred             CCchHHHHHHHHHHHHCCCCcccccc-hhhHHHHHHHhhhhcCChHHHHHHHHHHHHHHHhhc-CCCCc--eEEEECCCC
Confidence            34455567889999999999987766 667889999999999999999999988664433211 11111  799999999


Q ss_pred             CcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          670 VGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       670 tGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      ||||++|++||+.+.   ..+++++++.+.+
T Consensus       358 ~GKT~lAk~iA~~l~---~~~~~i~~~~~~~  385 (775)
T TIGR00763       358 VGKTSLGKSIAKALN---RKFVRFSLGGVRD  385 (775)
T ss_pred             CCHHHHHHHHHHHhc---CCeEEEeCCCccc
Confidence            999999999999973   4788888766543

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.

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

Probab=99.03  E-value=5.5e-10  Score=119.61  Aligned_cols=185  Identities=20%  Similarity=0.310  Sum_probs=118.2

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc-----
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG-----  360 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g-----  360 (710)
                      .+..+||+...+.++++.+..  ....+|||.|++||||..+|++|.+.-...+-|       ++.++|..+-..     
T Consensus       221 ~~~~iIG~S~am~~ll~~i~~VA~Sd~tVLi~GETGtGKElvAraIH~~S~R~~kP-------fV~~NCAAlPesLlESE  293 (550)
T COG3604         221 EVGGIIGRSPAMRQLLKEIEVVAKSDSTVLIRGETGTGKELVARAIHQLSPRRDKP-------FVKLNCAALPESLLESE  293 (550)
T ss_pred             ccccceecCHHHHHHHHHHHHHhcCCCeEEEecCCCccHHHHHHHHHhhCcccCCC-------ceeeeccccchHHHHHH
Confidence            456799999999998887654  456789999999999999999999887655444       445554443211     


Q ss_pred             --cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeE
Q 005179          361 --AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQ  425 (710)
Q Consensus       361 --~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~  425 (710)
                        ...+|.|.-.+..=....+-.++..||+|||..|             ...++..|+..|.++             +++
T Consensus       294 LFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGel-------------PL~lQaKLLRvLQegEieRvG~~r~ikVDVR  360 (550)
T COG3604         294 LFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGEL-------------PLALQAKLLRVLQEGEIERVGGDRTIKVDVR  360 (550)
T ss_pred             HhcccccccccchhccCcceeecCCCeEechhhccC-------------CHHHHHHHHHHHhhcceeecCCCceeEEEEE
Confidence              1223333222211111122345778999999888             677888888777754             478


Q ss_pred             EEEccChHHHHhhh--hccHHHHccccceEecCCCHH----HHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          426 CIASTTQDEHRTQF--EKDKALARRFQPVLISEPSQE----DAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       426 vI~att~~~~~~~~--~~d~aL~~Rf~~I~v~~Ps~~----~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      +|++||.+-.....  +.-..|.-|+.++.+..|+.-    +..-+...+++++....+   +.+++++++.+..+
T Consensus       361 iIAATNRDL~~~V~~G~FRaDLYyRLsV~Pl~lPPLRER~~DIplLA~~Fle~~~~~~gr~~l~ls~~Al~~L~~y  436 (550)
T COG3604         361 VIAATNRDLEEMVRDGEFRADLYYRLSVFPLELPPLRERPEDIPLLAGYFLEKFRRRLGRAILSLSAEALELLSSY  436 (550)
T ss_pred             EEeccchhHHHHHHcCcchhhhhhcccccccCCCCcccCCccHHHHHHHHHHHHHHhcCCcccccCHHHHHHHHcC
Confidence            99999986422111  112334447777777777643    333344455555554443   57899998877544

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.02  E-value=2.6e-09  Score=125.80  Aligned_cols=186  Identities=20%  Similarity=0.327  Sum_probs=114.9

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc----
Q 005179          287 ELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG----  360 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g----  360 (710)
                      ..|++++|++..++.+.+.+.+  ....+|+|+|++|||||++|++|.......       +.+++.+||..+..+    
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a~~~~pVLI~GE~GTGK~~lA~~ih~~s~r~-------~~~~v~i~c~~~~~~~~~~  445 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVAQSDSTVLILGETGTGKELIARAIHNLSGRN-------NRRMVKMNCAAMPAGLLES  445 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCC-------CCCeEEEecccCChhHhhh
Confidence            4678899999999888776543  445689999999999999999998765322       456666666544211    


Q ss_pred             ---cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-------------CCe
Q 005179          361 ---AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-------------GEL  424 (710)
Q Consensus       361 ---~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-------------~~v  424 (710)
                         ....|.+..........+....+.+||||||+.+             ..+.+..|..+++.             .++
T Consensus       446 ~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L-------------~~~~Q~~L~~~l~~~~~~~~g~~~~~~~~~  512 (686)
T PRK15429        446 DLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDM-------------PLELQPKLLRVLQEQEFERLGSNKIIQTDV  512 (686)
T ss_pred             hhcCcccccccccccchhhHHHhcCCCeEEEechhhC-------------CHHHHHHHHHHHHhCCEEeCCCCCcccceE
Confidence               0011111100011112233445679999999999             45566666555543             346


Q ss_pred             EEEEccChHHHH--hhhhccHHHHccccceEecCCCHHHHHH----HHHHHHHHHHhhcC--C-CCCHHHHHHHHHH
Q 005179          425 QCIASTTQDEHR--TQFEKDKALARRFQPVLISEPSQEDAVR----ILLGLREKYEAHHN--C-KFTLEAINAAVHL  492 (710)
Q Consensus       425 ~vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~----IL~~l~~~~~~~~~--~-~i~~~~l~~l~~l  492 (710)
                      ++|++|+.+-..  ..-.....|..|+..+.|..|+..+|.+    +++.++.++...++  + .+++++++.+..+
T Consensus       513 RiI~~t~~~l~~~~~~~~f~~~L~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~~s~~al~~L~~y  589 (686)
T PRK15429        513 RLIAATNRDLKKMVADREFRSDLYYRLNVFPIHLPPLRERPEDIPLLVKAFTFKIARRMGRNIDSIPAETLRTLSNM  589 (686)
T ss_pred             EEEEeCCCCHHHHHHcCcccHHHHhccCeeEEeCCChhhhHhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhC
Confidence            899988765311  1112445677788777777777555544    45555555544433  2 4788888776433

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=99.02  E-value=2.4e-09  Score=120.53  Aligned_cols=185  Identities=17%  Similarity=0.254  Sum_probs=113.6

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHh-cCCCccccCceEEEeehhhhhh-----
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQ-AEVPVFLLSKRIMSLDMGLLMA-----  359 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~-~~~p~~l~~~~v~~ld~~~l~~-----  359 (710)
                      .|++++|.+..++++.+.+.+  ....+|||+|++||||+.+|++|...+.. .+.+..-.+.+++.+||..+..     
T Consensus       217 ~f~~iiG~S~~m~~~~~~i~~~A~s~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~inCaal~e~lles  296 (538)
T PRK15424        217 VLGDLLGQSPQMEQVRQTILLYARSSAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAVNCGAIAESLLEA  296 (538)
T ss_pred             chhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEeecccCChhhHHH
Confidence            578899999999988887643  55678999999999999999999886211 1100111255677777765421     


Q ss_pred             ---ccccCccHHHH----HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------
Q 005179          360 ---GAKERGELEAR----VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------  422 (710)
Q Consensus       360 ---g~~~~g~~e~~----l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------  422 (710)
                         |. ..|.|...    -..+++   ...+..||||||+.|             ....+..|..+++++          
T Consensus       297 eLFG~-~~gaftga~~~~~~Gl~e---~A~gGTLfLdeI~~L-------------p~~~Q~kLl~~L~e~~~~r~G~~~~  359 (538)
T PRK15424        297 ELFGY-EEGAFTGSRRGGRAGLFE---IAHGGTLFLDEIGEM-------------PLPLQTRLLRVLEEKEVTRVGGHQP  359 (538)
T ss_pred             HhcCC-ccccccCccccccCCchh---ccCCCEEEEcChHhC-------------CHHHHHHHHhhhhcCeEEecCCCce
Confidence               10 01111000    001222   344678999999999             566777777777653          


Q ss_pred             ---CeEEEEccChHHHHhh--hhccHHHHccccceEecCCCHHHHH----HHHHHHHHHHHhhcCCCCCHHHHHHH
Q 005179          423 ---ELQCIASTTQDEHRTQ--FEKDKALARRFQPVLISEPSQEDAV----RILLGLREKYEAHHNCKFTLEAINAA  489 (710)
Q Consensus       423 ---~v~vI~att~~~~~~~--~~~d~aL~~Rf~~I~v~~Ps~~~~~----~IL~~l~~~~~~~~~~~i~~~~l~~l  489 (710)
                         ++++|++|+.+--...  -...+.|..|+..+.+..|+..+|.    .+++.++.++....+..++++++...
T Consensus       360 ~~~dvRiIaat~~~L~~~v~~g~Fr~dL~yrL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~  435 (538)
T PRK15424        360 VPVDVRVISATHCDLEEDVRQGRFRRDLFYRLSILRLQLPPLRERVADILPLAESFLKQSLAALSAPFSAALRQGL  435 (538)
T ss_pred             eccceEEEEecCCCHHHHHhcccchHHHHHHhcCCeecCCChhhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHhh
Confidence               3478888876531111  1133556678877777777755544    44445555543345666787776433

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.02  E-value=2.3e-09  Score=120.71  Aligned_cols=197  Identities=19%  Similarity=0.244  Sum_probs=120.7

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-----
Q 005179          287 ELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-----  359 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-----  359 (710)
                      ..|++++|.+..++++.+.+.+  ....+|||+|++||||+.+|++|.......       +.+++.+||..+..     
T Consensus       209 ~~f~~iiG~S~~m~~~~~~i~~~A~~~~pVLI~GE~GTGKe~lA~~IH~~S~r~-------~~pfv~inC~~l~e~lles  281 (526)
T TIGR02329       209 YRLDDLLGASAPMEQVRALVRLYARSDATVLILGESGTGKELVAQAIHQLSGRR-------DFPFVAINCGAIAESLLEA  281 (526)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCCCCcEEEECCCCcCHHHHHHHHHHhcCcC-------CCCEEEeccccCChhHHHH
Confidence            4578899999999988887643  456789999999999999999998765333       44566666654321     


Q ss_pred             ---ccccCccHHHH----HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------
Q 005179          360 ---GAKERGELEAR----VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------  422 (710)
Q Consensus       360 ---g~~~~g~~e~~----l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------  422 (710)
                         |. ..|.|...    -..+++   ...+..||||||+.|             +.+.+..|..+++++          
T Consensus       282 eLFG~-~~gaftga~~~~~~Gl~e---~A~gGTLfLdeI~~L-------------p~~~Q~~Ll~~L~~~~~~r~g~~~~  344 (526)
T TIGR02329       282 ELFGY-EEGAFTGARRGGRTGLIE---AAHRGTLFLDEIGEM-------------PLPLQTRLLRVLEEREVVRVGGTEP  344 (526)
T ss_pred             HhcCC-cccccccccccccccchh---hcCCceEEecChHhC-------------CHHHHHHHHHHHhcCcEEecCCCce
Confidence               11 11111000    011222   234678999999999             566777777766543          


Q ss_pred             ---CeEEEEccChHHHHh--hhhccHHHHccccceEecCCCHH----HHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHh
Q 005179          423 ---ELQCIASTTQDEHRT--QFEKDKALARRFQPVLISEPSQE----DAVRILLGLREKYEAHHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       423 ---~v~vI~att~~~~~~--~~~~d~aL~~Rf~~I~v~~Ps~~----~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls  493 (710)
                         ++++|++|+.+-...  .-...+.|..|+..+.+..|+..    +...++..++.++...+++.+++++++.+... 
T Consensus       345 ~~~dvRiIaat~~~l~~~v~~g~fr~dL~~rL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a~~~~~~~-  423 (526)
T TIGR02329       345 VPVDVRVVAATHCALTTAVQQGRFRRDLFYRLSILRIALPPLRERPGDILPLAAEYLVQAAAALRLPDSEAAAQVLAGV-  423 (526)
T ss_pred             eeecceEEeccCCCHHHHhhhcchhHHHHHhcCCcEEeCCCchhchhHHHHHHHHHHHHHHHHcCCCCCHHHHHHhHHH-
Confidence               347888887653111  11234566668876666666644    44455556666655555677888887763322 


Q ss_pred             hhhhcCCCCcchHHH
Q 005179          494 ARYISDRYLPDKAID  508 (710)
Q Consensus       494 ~~~i~~r~~p~~ai~  508 (710)
                      ...+....+|+....
T Consensus       424 ~~~L~~y~WPGNvrE  438 (526)
T TIGR02329       424 ADPLQRYPWPGNVRE  438 (526)
T ss_pred             HHHHHhCCCCchHHH
Confidence            112223345665433

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.

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=99.02  E-value=5.1e-09  Score=106.05  Aligned_cols=175  Identities=22%  Similarity=0.293  Sum_probs=111.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCc-cHHHHHHHHHHHH----HhcCCe
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERG-ELEARVTTLISEI----QKSGDV  384 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g-~~e~~l~~~~~~~----~~~~~~  384 (710)
                      .+.|+||+||.|+|||.||+.||+.+          +.++.-.|...+.. ..|.| +.|..+..+++.+    ......
T Consensus        96 ~KSNILLiGPTGsGKTlLAqTLAk~L----------nVPFaiADATtLTE-AGYVGEDVENillkLlqaadydV~rAerG  164 (408)
T COG1219          96 SKSNILLIGPTGSGKTLLAQTLAKIL----------NVPFAIADATTLTE-AGYVGEDVENILLKLLQAADYDVERAERG  164 (408)
T ss_pred             eeccEEEECCCCCcHHHHHHHHHHHh----------CCCeeeccccchhh-ccccchhHHHHHHHHHHHcccCHHHHhCC
Confidence            35799999999999999999999999          55566666666653 23455 4566666666654    334577


Q ss_pred             EEEEccchhhhhCCCCCCCC-CCChHhHHHhhcccccC-----------------------CCeEEEEccCh--------
Q 005179          385 ILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSLGR-----------------------GELQCIASTTQ--------  432 (710)
Q Consensus       385 IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l~~-----------------------~~v~vI~att~--------  432 (710)
                      |+||||||.+........-. +-.+.-++..|+..++.                       .++.+|+...-        
T Consensus       165 IIyIDEIDKIarkSeN~SITRDVSGEGVQQALLKiiEGTvasVPPqGGRKHP~Qe~iqvDT~NILFIcgGAF~GlekiI~  244 (408)
T COG1219         165 IIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEGTVASVPPQGGRKHPQQEFIQVDTSNILFICGGAFAGLEKIIK  244 (408)
T ss_pred             eEEEechhhhhccCCCCCcccccCchHHHHHHHHHHcCceeccCCCCCCCCCccceEEEcccceeEEeccccccHHHHHH
Confidence            99999999997653211110 11223356666655541                       12333321100        


Q ss_pred             -----------------------HH--------HHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHH----HHHHHHhh
Q 005179          433 -----------------------DE--------HRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLG----LREKYEAH  476 (710)
Q Consensus       433 -----------------------~~--------~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~----l~~~~~~~  476 (710)
                                             .+        ..-.|.+-|.|.-|+. ...+.+.+.++...||..    +.++|+.-
T Consensus       245 ~R~~~~~iGF~a~~~~~~~~~~~~~~l~~vepeDLvkFGLIPEfIGRlPvia~L~~Lde~aLv~ILtePkNAlvKQYq~L  324 (408)
T COG1219         245 KRLGKKGIGFGAEVKSKSKKKEEGELLKQVEPEDLVKFGLIPEFIGRLPVIATLEELDEDALVQILTEPKNALVKQYQKL  324 (408)
T ss_pred             HhccCCcccccccccchhhhhhHHHHHHhcChHHHHHcCCcHHHhcccceeeehhhcCHHHHHHHHhcccHHHHHHHHHH
Confidence                                   01        1112334577888887 567888999999999974    66666542


Q ss_pred             c-----CCCCCHHHHHHHHHHhhh
Q 005179          477 H-----NCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       477 ~-----~~~i~~~~l~~l~~ls~~  495 (710)
                      .     .+.++++++..+++.+-.
T Consensus       325 f~~d~V~L~F~~~AL~~IA~~A~~  348 (408)
T COG1219         325 FEMDGVELEFTEEALKAIAKKAIE  348 (408)
T ss_pred             hcccCceEEEcHHHHHHHHHHHHH
Confidence            2     356899999998877643

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.01  E-value=2.1e-09  Score=116.45  Aligned_cols=162  Identities=22%  Similarity=0.306  Sum_probs=92.8

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe----ehhhhhhccccC
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL----DMGLLMAGAKER  364 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l----d~~~l~~g~~~~  364 (710)
                      ++++++.++.++.+...+..  +.|++|+||||||||++|+.+|..+.....+.   ....+.+    +..+++.|....
T Consensus       174 l~d~~i~e~~le~l~~~L~~--~~~iil~GppGtGKT~lA~~la~~l~~~~~~~---~v~~VtFHpsySYeDFI~G~rP~  248 (459)
T PRK11331        174 LNDLFIPETTIETILKRLTI--KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQ---RVNMVQFHQSYSYEDFIQGYRPN  248 (459)
T ss_pred             hhcccCCHHHHHHHHHHHhc--CCCEEEECCCCCCHHHHHHHHHHHhcCCcccc---eeeEEeecccccHHHHhcccCCC
Confidence            45577888899998888764  67999999999999999999998874322111   1111222    123344333211


Q ss_pred             c-cH--H-HHHHHHHHHHHhc--CCeEEEEccchhhhhCCCCCC------CC-CCChHhHHHhh-----cccccCCCeEE
Q 005179          365 G-EL--E-ARVTTLISEIQKS--GDVILFIDEVHTLIGSGTVGR------GN-KGTGLDISNLL-----KPSLGRGELQC  426 (710)
Q Consensus       365 g-~~--e-~~l~~~~~~~~~~--~~~IL~IDEid~l~~~~~~~~------~~-~~~~~~~~~~L-----~~~l~~~~v~v  426 (710)
                      + .+  . ..+.+++..+...  .+.+||||||++.--..-.|.      .+ ++....+.-..     ..+.--.++.+
T Consensus       249 ~vgy~~~~G~f~~~~~~A~~~p~~~~vliIDEINRani~kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~iP~Nl~I  328 (459)
T PRK11331        249 GVGFRRKDGIFYNFCQQAKEQPEKKYVFIIDEINRANLSKVFGEVMMLMEHDKRGENWSVPLTYSENDEERFYVPENVYI  328 (459)
T ss_pred             CCCeEecCchHHHHHHHHHhcccCCcEEEEehhhccCHHHhhhhhhhhccccccccccceeeeccccccccccCCCCeEE
Confidence            1 00  0 1233444555442  478999999987521110000      00 00000000000     00111246889


Q ss_pred             EEccChHHHHhhhhccHHHHccccceEecC
Q 005179          427 IASTTQDEHRTQFEKDKALARRFQPVLISE  456 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~Rf~~I~v~~  456 (710)
                      |||+|..+ +....+|.+|+|||..|++.+
T Consensus       329 IgTMNt~D-rs~~~lD~AlrRRF~fi~i~p  357 (459)
T PRK11331        329 IGLMNTAD-RSLAVVDYALRRRFSFIDIEP  357 (459)
T ss_pred             EEecCccc-cchhhccHHHHhhhheEEecC
Confidence            99999876 344568999999999888876

>PRK04132 replication factor C small subunit; Provisional

Probab=99.00  E-value=3.5e-09  Score=123.73  Aligned_cols=160  Identities=18%  Similarity=0.224  Sum_probs=121.5

Q ss_pred             cEEEc--CCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhc------CCeE
Q 005179          314 PILLG--ESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS------GDVI  385 (710)
Q Consensus       314 vLL~G--ppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~------~~~I  385 (710)
                      -+..|  |.+.||||+|++||+.+...+     .+..++++|.++..      |  ...++.+++.+...      +..|
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~-----~~~~~lElNASd~r------g--id~IR~iIk~~a~~~~~~~~~~KV  633 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGEN-----WRHNFLELNASDER------G--INVIREKVKEFARTKPIGGASFKI  633 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhccc-----ccCeEEEEeCCCcc------c--HHHHHHHHHHHHhcCCcCCCCCEE
Confidence            35668  999999999999999873311     14567888765421      1  11245555444321      2369


Q ss_pred             EEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHH
Q 005179          386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAV  463 (710)
Q Consensus       386 L~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~  463 (710)
                      +||||+|.|             ..+.++.|+..|+.  +.+.+|++||...     .+.+++++||+.+.|.+|+.++..
T Consensus       634 vIIDEaD~L-------------t~~AQnALLk~lEep~~~~~FILi~N~~~-----kIi~tIrSRC~~i~F~~ls~~~i~  695 (846)
T PRK04132        634 IFLDEADAL-------------TQDAQQALRRTMEMFSSNVRFILSCNYSS-----KIIEPIQSRCAIFRFRPLRDEDIA  695 (846)
T ss_pred             EEEECcccC-------------CHHHHHHHHHHhhCCCCCeEEEEEeCChh-----hCchHHhhhceEEeCCCCCHHHHH
Confidence            999999999             55688999999995  7888999988875     677999999999999999999999


Q ss_pred             HHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          464 RILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       464 ~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      ..|+.++.+    .++.++++++..++..+.+-      +.+++.+|+.++
T Consensus       696 ~~L~~I~~~----Egi~i~~e~L~~Ia~~s~GD------lR~AIn~Lq~~~  736 (846)
T PRK04132        696 KRLRYIAEN----EGLELTEEGLQAILYIAEGD------MRRAINILQAAA  736 (846)
T ss_pred             HHHHHHHHh----cCCCCCHHHHHHHHHHcCCC------HHHHHHHHHHHH
Confidence            888888773    47889999999999887764      356888887665

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

Probab=98.99  E-value=8.3e-10  Score=119.94  Aligned_cols=181  Identities=20%  Similarity=0.321  Sum_probs=117.0

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh------
Q 005179          287 ELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM------  358 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~------  358 (710)
                      -+|+++||...++.++++...+  +...+|||.|++||||..+|++|.+.....+       .+++.++|.++-      
T Consensus       242 y~f~~Iig~S~~m~~~~~~akr~A~tdstVLi~GESGTGKElfA~~IH~~S~R~~-------~PFIaiNCaAiPe~LlES  314 (560)
T COG3829         242 YTFDDIIGESPAMLRVLELAKRIAKTDSTVLILGESGTGKELFARAIHNLSPRAN-------GPFIAINCAAIPETLLES  314 (560)
T ss_pred             cchhhhccCCHHHHHHHHHHHhhcCCCCcEEEecCCCccHHHHHHHHHhcCcccC-------CCeEEEecccCCHHHHHH
Confidence            3689999999999999887765  4557899999999999999999998765554       445555554432      


Q ss_pred             --hccccCccHHHHH----HHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------
Q 005179          359 --AGAKERGELEARV----TTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------  422 (710)
Q Consensus       359 --~g~~~~g~~e~~l----~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------  422 (710)
                        .|. ..|.|.-..    ..+|+.   +.+.-||+|||..|             ...++..|+..|+.+          
T Consensus       315 ELFGy-e~GAFTGA~~~GK~GlfE~---A~gGTLFLDEIgem-------------pl~LQaKLLRVLQEkei~rvG~t~~  377 (560)
T COG3829         315 ELFGY-EKGAFTGASKGGKPGLFEL---ANGGTLFLDEIGEM-------------PLPLQAKLLRVLQEKEIERVGGTKP  377 (560)
T ss_pred             HHhCc-CCccccccccCCCCcceee---ccCCeEEehhhccC-------------CHHHHHHHHHHHhhceEEecCCCCc
Confidence              111 112211111    122222   33568999999988             677888888777643          


Q ss_pred             ---CeEEEEccChHHHHhhhh---ccHHHHccccceEecCCCHHHH----HHHHHHHHHHHHhhcC--CC-CCHHHHHHH
Q 005179          423 ---ELQCIASTTQDEHRTQFE---KDKALARRFQPVLISEPSQEDA----VRILLGLREKYEAHHN--CK-FTLEAINAA  489 (710)
Q Consensus       423 ---~v~vI~att~~~~~~~~~---~d~aL~~Rf~~I~v~~Ps~~~~----~~IL~~l~~~~~~~~~--~~-i~~~~l~~l  489 (710)
                         ++++|+|||.+.- +.++   .-..|.=|+.++.+.-|+..+|    ..+...++.++...++  +. ++++++..+
T Consensus       378 ~~vDVRIIAATN~nL~-~~i~~G~FReDLYYRLNV~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~~~v~~ls~~a~~~L  456 (560)
T COG3829         378 IPVDVRIIAATNRNLE-KMIAEGTFREDLYYRLNVIPITIPPLRERKEDIPLLAEYFLDKFSRRYGRNVKGLSPDALALL  456 (560)
T ss_pred             eeeEEEEEeccCcCHH-HHHhcCcchhhheeeeceeeecCCCcccCcchHHHHHHHHHHHHHHHcCCCcccCCHHHHHHH
Confidence               5789999998641 1111   1233333778888877774444    4444555555554444  33 788888776


Q ss_pred             HHH
Q 005179          490 VHL  492 (710)
Q Consensus       490 ~~l  492 (710)
                      ..+
T Consensus       457 ~~y  459 (560)
T COG3829         457 LRY  459 (560)
T ss_pred             HhC
Confidence            543

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

Probab=98.98  E-value=4.1e-10  Score=110.03  Aligned_cols=61  Identities=33%  Similarity=0.481  Sum_probs=48.3

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|.+--+..|..++        .+...|+.+|    .|+|+|||||||||+||||+|+.   +..++||+..|||
T Consensus       157 iggld~qkqeireavelplt~~~ly~qigidpp----rgvllygppg~gktml~kava~~---t~a~firvvgsef  225 (408)
T KOG0727|consen  157 IGGLDVQKQEIREAVELPLTHADLYKQIGIDPP----RGVLLYGPPGTGKTMLAKAVANH---TTAAFIRVVGSEF  225 (408)
T ss_pred             cccchhhHHHHHHHHhccchHHHHHHHhCCCCC----cceEEeCCCCCcHHHHHHHHhhc---cchheeeeccHHH
Confidence            444444444444444        4556788766    69999999999999999999998   8889999999999

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=98.98  E-value=5.4e-09  Score=116.46  Aligned_cols=105  Identities=23%  Similarity=0.270  Sum_probs=83.1

Q ss_pred             CCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHH--HHhhcCCCCCCCCCeEEE
Q 005179          586 DDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAV--KRSRVGLKDPNRPTAAML  663 (710)
Q Consensus       586 ~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i--~~~r~gl~~p~rp~~~~L  663 (710)
                      .+.+..-....++..+...+.+||.+-+. +...+.+.++.|.+...|.+++++.|.+.+  +.....++.|     -+|
T Consensus       281 ~m~~~SaE~~ViRnYlDwll~lPW~~~sk-~~~Dl~~a~~iLd~dHYGLekVKeRIlEyLAV~~l~~~~kGp-----ILc  354 (782)
T COG0466         281 TMSPMSAEATVIRNYLDWLLDLPWGKRSK-DKLDLKKAEKILDKDHYGLEKVKERILEYLAVQKLTKKLKGP-----ILC  354 (782)
T ss_pred             cCCCCCchHHHHHHHHHHHHhCCCccccc-hhhhHHHHHHHhcccccCchhHHHHHHHHHHHHHHhccCCCc-----EEE
Confidence            34445556667889999999999988766 455788999999999999999999998755  3334344443     689


Q ss_pred             EEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          664 FCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       664 f~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |+||||||||.|++.||+.+   ++.++|+-++=.-
T Consensus       355 LVGPPGVGKTSLgkSIA~al---~RkfvR~sLGGvr  387 (782)
T COG0466         355 LVGPPGVGKTSLGKSIAKAL---GRKFVRISLGGVR  387 (782)
T ss_pred             EECCCCCCchhHHHHHHHHh---CCCEEEEecCccc
Confidence            99999999999999999995   4579998766443

>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=98.98  E-value=2.5e-10  Score=111.33  Aligned_cols=132  Identities=21%  Similarity=0.274  Sum_probs=69.1

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh----hhhhhccccC
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM----GLLMAGAKER  364 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~----~~l~~g~~~~  364 (710)
                      |.+++|++...+.+.-...  .+.|+||+||||||||++|+.+...+........+.-..++++..    ..+.....++
T Consensus         2 f~dI~GQe~aKrAL~iAAa--G~h~lLl~GppGtGKTmlA~~l~~lLP~l~~~e~le~~~i~s~~~~~~~~~~~~~~Pfr   79 (206)
T PF01078_consen    2 FSDIVGQEEAKRALEIAAA--GGHHLLLIGPPGTGKTMLARRLPSLLPPLTEEEALEVSKIYSVAGLGPDEGLIRQRPFR   79 (206)
T ss_dssp             TCCSSSTHHHHHHHHHHHH--CC--EEEES-CCCTHHHHHHHHHHCS--CCEECCESS--S-TT---S---EEEE---EE
T ss_pred             hhhhcCcHHHHHHHHHHHc--CCCCeEEECCCCCCHHHHHHHHHHhCCCCchHHHhhhccccccccCCCCCceecCCCcc
Confidence            6789999987777665444  357999999999999999999987664322111111111111100    0000000000


Q ss_pred             cc-HHHHHHHHH--------HHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------
Q 005179          365 GE-LEARVTTLI--------SEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------  422 (710)
Q Consensus       365 g~-~e~~l~~~~--------~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------  422 (710)
                      .- .......++        .++..+.+.|||+||+..+             ...+.+.|++.++++             
T Consensus        80 ~phhs~s~~~liGgg~~~~PGeislAh~GVLflDE~~ef-------------~~~vld~Lr~ple~g~v~i~R~~~~~~~  146 (206)
T PF01078_consen   80 APHHSASEAALIGGGRPPRPGEISLAHRGVLFLDELNEF-------------DRSVLDALRQPLEDGEVTISRAGGSVTY  146 (206)
T ss_dssp             EE-TT--HHHHHEEGGGEEE-CGGGGTTSEEEECETTTS--------------HHHHHHHHHHHHHSBEEEEETTEEEEE
T ss_pred             cCCCCcCHHHHhCCCcCCCcCHHHHhcCCEEEechhhhc-------------CHHHHHHHHHHHHCCeEEEEECCceEEE
Confidence            00 000011111        1223355779999999888             667888998888765             


Q ss_pred             --CeEEEEccChHHH
Q 005179          423 --ELQCIASTTQDEH  435 (710)
Q Consensus       423 --~v~vI~att~~~~  435 (710)
                        ++++|+|+|+-+.
T Consensus       147 Pa~f~lv~a~NPcpC  161 (206)
T PF01078_consen  147 PARFLLVAAMNPCPC  161 (206)
T ss_dssp             B--EEEEEEE-S---
T ss_pred             ecccEEEEEeccccc
Confidence              4578998887543

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.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=98.98  E-value=2.2e-09  Score=121.88  Aligned_cols=182  Identities=13%  Similarity=0.234  Sum_probs=112.9

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh----
Q 005179          286 EELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA----  359 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~----  359 (710)
                      ...|+.++|.+..++++++.+.+  ....+++|+|++||||+++|+++.......       ..+++.+||..+..    
T Consensus       200 ~~~f~~~ig~s~~~~~~~~~~~~~A~~~~pvlI~GE~GtGK~~lA~aiH~~s~r~-------~~pfv~inca~~~~~~~e  272 (520)
T PRK10820        200 DSAFSQIVAVSPKMRQVVEQARKLAMLDAPLLITGDTGTGKDLLAYACHLRSPRG-------KKPFLALNCASIPDDVVE  272 (520)
T ss_pred             cccccceeECCHHHHHHHHHHHHHhCCCCCEEEECCCCccHHHHHHHHHHhCCCC-------CCCeEEeccccCCHHHHH
Confidence            45789999999988888876643  456789999999999999999987655333       34555666544321    


Q ss_pred             ----ccccCccHH---HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------
Q 005179          360 ----GAKERGELE---ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------  422 (710)
Q Consensus       360 ----g~~~~g~~e---~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------  422 (710)
                          |.. .|.+.   ..-..+++   ...+..||||||+.|             +...+..|..+++++          
T Consensus       273 ~elFG~~-~~~~~~~~~~~~g~~e---~a~~GtL~LdeI~~L-------------~~~~Q~~Ll~~l~~~~~~~~g~~~~  335 (520)
T PRK10820        273 SELFGHA-PGAYPNALEGKKGFFE---QANGGSVLLDEIGEM-------------SPRMQAKLLRFLNDGTFRRVGEDHE  335 (520)
T ss_pred             HHhcCCC-CCCcCCcccCCCChhh---hcCCCEEEEeChhhC-------------CHHHHHHHHHHHhcCCcccCCCCcc
Confidence                110 01000   00011222   234678999999999             445566665555432          


Q ss_pred             ---CeEEEEccChHHH--HhhhhccHHHHccccceEecCCCHH----HHHHHHHHHHHHHHhhcC---CCCCHHHHHHHH
Q 005179          423 ---ELQCIASTTQDEH--RTQFEKDKALARRFQPVLISEPSQE----DAVRILLGLREKYEAHHN---CKFTLEAINAAV  490 (710)
Q Consensus       423 ---~v~vI~att~~~~--~~~~~~d~aL~~Rf~~I~v~~Ps~~----~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~  490 (710)
                         ++++|++|+.+.-  ...-...+.|..|+..+.+..|+..    +...+++.++.++...++   ..+++++++.+.
T Consensus       336 ~~~~vRiI~st~~~l~~l~~~g~f~~dL~~rL~~~~i~lPpLreR~~Di~~L~~~fl~~~~~~~g~~~~~ls~~a~~~L~  415 (520)
T PRK10820        336 VHVDVRVICATQKNLVELVQKGEFREDLYYRLNVLTLNLPPLRDRPQDIMPLTELFVARFADEQGVPRPKLAADLNTVLT  415 (520)
T ss_pred             eeeeeEEEEecCCCHHHHHHcCCccHHHHhhcCeeEEeCCCcccChhHHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHh
Confidence               4678888765421  1111245778888876666666644    444455566666655544   368899887764


Q ss_pred             H
Q 005179          491 H  491 (710)
Q Consensus       491 ~  491 (710)
                      .
T Consensus       416 ~  416 (520)
T PRK10820        416 R  416 (520)
T ss_pred             c
Confidence            3

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.97  E-value=3.1e-08  Score=103.27  Aligned_cols=172  Identities=19%  Similarity=0.251  Sum_probs=97.5

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEE--eehhhhh------hccccCcc----HHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMS--LDMGLLM------AGAKERGE----LEARVTTLISE  377 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~--ld~~~l~------~g~~~~g~----~e~~l~~~~~~  377 (710)
                      ....++|+||+|+|||++++.++..+....+..    ..+..  .+...+.      .|....+.    ....+...+..
T Consensus        42 ~~~~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~----~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~  117 (269)
T TIGR03015        42 REGFILITGEVGAGKTTLIRNLLKRLDQERVVA----AKLVNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIE  117 (269)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHhcCCCCeEE----eeeeCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHH
Confidence            345689999999999999999998874322110    00010  1111111      12111121    11223332222


Q ss_pred             -HHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-CC-CeEEEEccChHHHHhhhh--ccHHHHcccc-c
Q 005179          378 -IQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-RG-ELQCIASTTQDEHRTQFE--KDKALARRFQ-P  451 (710)
Q Consensus       378 -~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-~~-~v~vI~att~~~~~~~~~--~d~aL~~Rf~-~  451 (710)
                       .....+.+|+|||+|.+...          ..+....|..... ++ .+.+|.+.++. +...+.  ....+.+|+. .
T Consensus       118 ~~~~~~~~vliiDe~~~l~~~----------~~~~l~~l~~~~~~~~~~~~vvl~g~~~-~~~~l~~~~~~~l~~r~~~~  186 (269)
T TIGR03015       118 QFAAGKRALLVVDEAQNLTPE----------LLEELRMLSNFQTDNAKLLQIFLVGQPE-FRETLQSPQLQQLRQRIIAS  186 (269)
T ss_pred             HHhCCCCeEEEEECcccCCHH----------HHHHHHHHhCcccCCCCeEEEEEcCCHH-HHHHHcCchhHHHHhheeee
Confidence             23456789999999998211          1222222222221 22 24455555543 322222  1235777864 7


Q ss_pred             eEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          452 VLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       452 I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +.+++++.++...++...+.......+..+++++++.+++.+.++
T Consensus       187 ~~l~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~  231 (269)
T TIGR03015       187 CHLGPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGI  231 (269)
T ss_pred             eeCCCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCc
Confidence            889999999999999887775533334578999999999998775

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.

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=98.95  E-value=7.9e-09  Score=110.00  Aligned_cols=135  Identities=21%  Similarity=0.256  Sum_probs=91.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCc--cc------------cCceEEEeehhhhhhccccCccHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPV--FL------------LSKRIMSLDMGLLMAGAKERGELEARVTTLIS  376 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~--~l------------~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~  376 (710)
                      +..+||+||+|+|||++|+.+|+.+.+.+...  ..            ....++.+...    +.+ ..--.+.++++.+
T Consensus        22 ~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~----~~~-~~i~id~iR~l~~   96 (328)
T PRK05707         22 PHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPE----EAD-KTIKVDQVRELVS   96 (328)
T ss_pred             ceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEecc----CCC-CCCCHHHHHHHHH
Confidence            34478999999999999999999997642110  00            00122222110    000 0011234566665


Q ss_pred             HHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHcccc
Q 005179          377 EIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQ  450 (710)
Q Consensus       377 ~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~  450 (710)
                      .+..    ++.-|++||++|.|             ..+.+|.|+..|++  ++..+|.+|+..+     .+.|++++|++
T Consensus        97 ~~~~~~~~~~~kv~iI~~a~~m-------------~~~aaNaLLK~LEEPp~~~~fiL~t~~~~-----~ll~TI~SRc~  158 (328)
T PRK05707         97 FVVQTAQLGGRKVVLIEPAEAM-------------NRNAANALLKSLEEPSGDTVLLLISHQPS-----RLLPTIKSRCQ  158 (328)
T ss_pred             HHhhccccCCCeEEEECChhhC-------------CHHHHHHHHHHHhCCCCCeEEEEEECChh-----hCcHHHHhhce
Confidence            5543    34568899999999             56788899888986  5677777777765     67899999999


Q ss_pred             ceEecCCCHHHHHHHHHH
Q 005179          451 PVLISEPSQEDAVRILLG  468 (710)
Q Consensus       451 ~I~v~~Ps~~~~~~IL~~  468 (710)
                      .+.|.+|+.++..+.|..
T Consensus       159 ~~~~~~~~~~~~~~~L~~  176 (328)
T PRK05707        159 QQACPLPSNEESLQWLQQ  176 (328)
T ss_pred             eeeCCCcCHHHHHHHHHH
Confidence            999999999987776653

>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=98.95  E-value=7.1e-10  Score=103.47  Aligned_cols=111  Identities=23%  Similarity=0.391  Sum_probs=66.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-----cc-cc-CccHHHHHHHHHHHHHhcCCeE
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-----GA-KE-RGELEARVTTLISEIQKSGDVI  385 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-----g~-~~-~g~~e~~l~~~~~~~~~~~~~I  385 (710)
                      |++|+||||||||++++.+|+.+          +.+++.+.+.....     |. .. .+..+..-..+...+.  .+.|
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~----------~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~--~~~i   68 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL----------GRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMR--KGGI   68 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH----------TCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHH--EEEE
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh----------hcceEEEEeccccccccceeeeeeccccccccccccccccc--ceeE
Confidence            58999999999999999999998          55555555433221     10 00 0100000000111111  4689


Q ss_pred             EEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC---------------C------CeEEEEccChHHHHhhhhccHH
Q 005179          386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR---------------G------ELQCIASTTQDEHRTQFEKDKA  444 (710)
Q Consensus       386 L~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~---------------~------~v~vI~att~~~~~~~~~~d~a  444 (710)
                      +||||++..             ..++.+.|.++++.               .      .+++|+|+|+.. .....++++
T Consensus        69 l~lDEin~a-------------~~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~-~~~~~l~~a  134 (139)
T PF07728_consen   69 LVLDEINRA-------------PPEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRD-KGRKELSPA  134 (139)
T ss_dssp             EEESSCGG---------------HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST---TTTTCHH
T ss_pred             EEECCcccC-------------CHHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCC-CCcCcCCHH
Confidence            999999987             34556666554442               1      288999999876 445578999


Q ss_pred             HHccc
Q 005179          445 LARRF  449 (710)
Q Consensus       445 L~~Rf  449 (710)
                      |.+||
T Consensus       135 l~~Rf  139 (139)
T PF07728_consen  135 LLDRF  139 (139)
T ss_dssp             HHTT-
T ss_pred             HHhhC
Confidence            99998

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.

>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=98.94  E-value=7.1e-10  Score=106.89  Aligned_cols=116  Identities=22%  Similarity=0.295  Sum_probs=69.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFID  389 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~ID  389 (710)
                      ...+++|+||+|||||.+|++|++.+.-      -...+++.+|++.+..+......+...+...-..+......|||||
T Consensus         2 p~~~~ll~GpsGvGKT~la~~la~~l~~------~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllD   75 (171)
T PF07724_consen    2 PKSNFLLAGPSGVGKTELAKALAELLFV------GSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLD   75 (171)
T ss_dssp             -SEEEEEESSTTSSHHHHHHHHHHHHT-------SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEE
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHhcc------CCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhH
Confidence            3567999999999999999999999931      1245888999988875211111111111110001111122399999


Q ss_pred             cchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEEEccChH
Q 005179          390 EVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCIASTTQD  433 (710)
Q Consensus       390 Eid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI~att~~  433 (710)
                      |||.+......+  .+.....+++.|+++++.|             ++++|+|+|-.
T Consensus        76 EidKa~~~~~~~--~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~  130 (171)
T PF07724_consen   76 EIDKAHPSNSGG--ADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFG  130 (171)
T ss_dssp             TGGGCSHTTTTC--SHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSS
T ss_pred             HHhhcccccccc--chhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEecccc
Confidence            999996531110  1122346788888877643             56688887754

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 ....

>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=98.94  E-value=4.5e-09  Score=100.61  Aligned_cols=142  Identities=16%  Similarity=0.145  Sum_probs=91.9

Q ss_pred             cCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc-------------ccCceEEEeehhhhhh
Q 005179          294 GRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF-------------LLSKRIMSLDMGLLMA  359 (710)
Q Consensus       294 Gr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~-------------l~~~~v~~ld~~~l~~  359 (710)
                      |++..++.|...+....-.+ +||+||+|+||+++|..+++.+.+......             .....++.++....  
T Consensus         1 gq~~~~~~L~~~~~~~~l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~--   78 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRLPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKK--   78 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC--SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTS--
T ss_pred             CcHHHHHHHHHHHHcCCcceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccc--
Confidence            67888899999888877676 699999999999999999999866433210             11223333322110  


Q ss_pred             ccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChH
Q 005179          360 GAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQD  433 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~  433 (710)
                         ...-..+.++.+.+.+..    .+.-|++|||+|.|             ..+++|.|+..||+.  .+.+|.+|+..
T Consensus        79 ---~~~i~i~~ir~i~~~~~~~~~~~~~KviiI~~ad~l-------------~~~a~NaLLK~LEepp~~~~fiL~t~~~  142 (162)
T PF13177_consen   79 ---KKSIKIDQIREIIEFLSLSPSEGKYKVIIIDEADKL-------------TEEAQNALLKTLEEPPENTYFILITNNP  142 (162)
T ss_dssp             ---SSSBSHHHHHHHHHHCTSS-TTSSSEEEEEETGGGS--------------HHHHHHHHHHHHSTTTTEEEEEEES-G
T ss_pred             ---cchhhHHHHHHHHHHHHHHHhcCCceEEEeehHhhh-------------hHHHHHHHHHHhcCCCCCEEEEEEECCh
Confidence               001112345566655532    34679999999999             678899999999864  67777777765


Q ss_pred             HHHhhhhccHHHHccccceEecCCC
Q 005179          434 EHRTQFEKDKALARRFQPVLISEPS  458 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~~I~v~~Ps  458 (710)
                      .     .+-+++++|+..|.+.+++
T Consensus       143 ~-----~il~TI~SRc~~i~~~~ls  162 (162)
T PF13177_consen  143 S-----KILPTIRSRCQVIRFRPLS  162 (162)
T ss_dssp             G-----GS-HHHHTTSEEEEE----
T ss_pred             H-----HChHHHHhhceEEecCCCC
Confidence            5     6789999999999988754

...

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=98.94  E-value=2.2e-08  Score=105.61  Aligned_cols=154  Identities=15%  Similarity=0.151  Sum_probs=100.8

Q ss_pred             HHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-----------cCceEEEeehhhhhhcccc
Q 005179          296 ETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-----------LSKRIMSLDMGLLMAGAKE  363 (710)
Q Consensus       296 ~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-----------~~~~v~~ld~~~l~~g~~~  363 (710)
                      +..++++.+.+...+-.| +||+||+|+||+++|..+|+.+.+.......           ..-.++.+....-..|.+.
T Consensus        10 ~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~   89 (319)
T PRK08769         10 QRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKL   89 (319)
T ss_pred             HHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccc
Confidence            346677777777766555 8899999999999999999998774311100           0011222210000001000


Q ss_pred             -CccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChHHHH
Q 005179          364 -RGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQDEHR  436 (710)
Q Consensus       364 -~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~~~~  436 (710)
                       ..-..+.++++.+.+..    ++.-|++||++|.|             ....+|.|+..||+.  +.++|..++..+  
T Consensus        90 ~~~I~idqIR~l~~~~~~~p~~g~~kV~iI~~ae~m-------------~~~AaNaLLKtLEEPp~~~~fiL~~~~~~--  154 (319)
T PRK08769         90 RTEIVIEQVREISQKLALTPQYGIAQVVIVDPADAI-------------NRAACNALLKTLEEPSPGRYLWLISAQPA--  154 (319)
T ss_pred             cccccHHHHHHHHHHHhhCcccCCcEEEEeccHhhh-------------CHHHHHHHHHHhhCCCCCCeEEEEECChh--
Confidence             00123445666655543    33469999999999             566788888889864  566666666654  


Q ss_pred             hhhhccHHHHccccceEecCCCHHHHHHHHH
Q 005179          437 TQFEKDKALARRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       437 ~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                         .+-|++++||+.|.|.+|+.++....|.
T Consensus       155 ---~lLpTIrSRCq~i~~~~~~~~~~~~~L~  182 (319)
T PRK08769        155 ---RLPATIRSRCQRLEFKLPPAHEALAWLL  182 (319)
T ss_pred             ---hCchHHHhhheEeeCCCcCHHHHHHHHH
Confidence               6779999999999999999988776665

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=98.94  E-value=6.3e-09  Score=121.73  Aligned_cols=177  Identities=19%  Similarity=0.258  Sum_probs=114.9

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCc
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERG  365 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g  365 (710)
                      .|+.++|.+..++++.+.+.+  ....+++|+|++||||+++|++|.+.....       +.+++.+||..+...     
T Consensus       323 ~~~~l~g~s~~~~~~~~~~~~~a~~~~pvli~Ge~GtGK~~~A~~ih~~s~r~-------~~pfv~vnc~~~~~~-----  390 (638)
T PRK11388        323 TFDHMPQDSPQMRRLIHFGRQAAKSSFPVLLCGEEGVGKALLAQAIHNESERA-------AGPYIAVNCQLYPDE-----  390 (638)
T ss_pred             cccceEECCHHHHHHHHHHHHHhCcCCCEEEECCCCcCHHHHHHHHHHhCCcc-------CCCeEEEECCCCChH-----
Confidence            688999999999888876654  456779999999999999999998866333       345666666543210     


Q ss_pred             cHHHHHHHHHH------------HHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------
Q 005179          366 ELEARVTTLIS------------EIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------  422 (710)
Q Consensus       366 ~~e~~l~~~~~------------~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------  422 (710)
                      .++   ..+|.            .+....+.+||||||+.|             ..+.+..|..+++.+           
T Consensus       391 ~~~---~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l-------------~~~~Q~~Ll~~l~~~~~~~~~~~~~~  454 (638)
T PRK11388        391 ALA---EEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYL-------------SPELQSALLQVLKTGVITRLDSRRLI  454 (638)
T ss_pred             HHH---HHhcCCCCcCccCCCCCceeECCCCEEEEcChhhC-------------CHHHHHHHHHHHhcCcEEeCCCCceE
Confidence            000   01111            122344678999999999             566777777766543           


Q ss_pred             --CeEEEEccChHHHH--hhhhccHHHHccccceEecCCCHHHH----HHHHHHHHHHHHhhc--CCCCCHHHHHHHHHH
Q 005179          423 --ELQCIASTTQDEHR--TQFEKDKALARRFQPVLISEPSQEDA----VRILLGLREKYEAHH--NCKFTLEAINAAVHL  492 (710)
Q Consensus       423 --~v~vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~~~~----~~IL~~l~~~~~~~~--~~~i~~~~l~~l~~l  492 (710)
                        ++++|++|+.+...  ..-...+.|..|+..+.|..|+..+|    ..+++.++.++...+  .+.+++++++.+..+
T Consensus       455 ~~~~riI~~t~~~l~~~~~~~~f~~dL~~~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~~~~~~~~~~s~~a~~~L~~y  534 (638)
T PRK11388        455 PVDVRVIATTTADLAMLVEQNRFSRQLYYALHAFEITIPPLRMRREDIPALVNNKLRSLEKRFSTRLKIDDDALARLVSY  534 (638)
T ss_pred             EeeEEEEEeccCCHHHHHhcCCChHHHhhhhceeEEeCCChhhhhhHHHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHcC
Confidence              46789888765311  11123466777887777777765544    445555555554332  356899988877544

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=98.94  E-value=2.4e-09  Score=95.76  Aligned_cols=73  Identities=29%  Similarity=0.468  Sum_probs=61.6

Q ss_pred             HHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeC
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFF  694 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d  694 (710)
                      +..|+..|...++||.-|++.|..+++.-... ..|.||+ .+.|.||||||||.+++.||+.||.++  ...|...
T Consensus        16 ~~~L~~~L~~~l~GQhla~~~v~~ai~~~l~~-~~p~KpL-VlSfHG~tGtGKn~v~~liA~~ly~~G~~S~~V~~f   90 (127)
T PF06309_consen   16 ITGLEKDLQRNLFGQHLAVEVVVNAIKGHLAN-PNPRKPL-VLSFHGWTGTGKNFVSRLIAEHLYKSGMKSPFVHQF   90 (127)
T ss_pred             HHHHHHHHHHHccCcHHHHHHHHHHHHHHHcC-CCCCCCE-EEEeecCCCCcHHHHHHHHHHHHHhcccCCCceeee
Confidence            45788899999999999999999999877544 4789997 889999999999999999999999863  3444443

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

>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=98.93  E-value=2.9e-10  Score=109.30  Aligned_cols=139  Identities=23%  Similarity=0.350  Sum_probs=82.8

Q ss_pred             cccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--------cc
Q 005179          292 VIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--------GA  361 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--------g~  361 (710)
                      +||.+..++++++.+.+  ....+|||+|++||||+.+|++|.+.....       +.+++.+||+.+..        |.
T Consensus         1 liG~s~~m~~~~~~~~~~a~~~~pVlI~GE~GtGK~~lA~~IH~~s~r~-------~~pfi~vnc~~~~~~~~e~~LFG~   73 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAASSDLPVLITGETGTGKELLARAIHNNSPRK-------NGPFISVNCAALPEELLESELFGH   73 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTTSTS-EEEECSTTSSHHHHHHHHHHCSTTT-------TS-EEEEETTTS-HHHHHHHHHEB
T ss_pred             CEeCCHHHHHHHHHHHHHhCCCCCEEEEcCCCCcHHHHHHHHHHhhhcc-------cCCeEEEehhhhhcchhhhhhhcc
Confidence            57888888888887655  456889999999999999999998854322       45677777765421        11


Q ss_pred             ccCccHH---HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeE
Q 005179          362 KERGELE---ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQ  425 (710)
Q Consensus       362 ~~~g~~e---~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~  425 (710)
                      . .|.+.   ..-..+   +....+.+||||||+.|             +.+++..|..+|+.+             +++
T Consensus        74 ~-~~~~~~~~~~~~G~---l~~A~~GtL~Ld~I~~L-------------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~R  136 (168)
T PF00158_consen   74 E-KGAFTGARSDKKGL---LEQANGGTLFLDEIEDL-------------PPELQAKLLRVLEEGKFTRLGSDKPVPVDVR  136 (168)
T ss_dssp             C-SSSSTTTSSEBEHH---HHHTTTSEEEEETGGGS--------------HHHHHHHHHHHHHSEEECCTSSSEEE--EE
T ss_pred             c-cccccccccccCCc---eeeccceEEeecchhhh-------------HHHHHHHHHHHHhhchhccccccccccccce
Confidence            0 11000   000122   33455779999999999             666777777666532             578


Q ss_pred             EEEccChHH--HHhhhhccHHHHccccceEe
Q 005179          426 CIASTTQDE--HRTQFEKDKALARRFQPVLI  454 (710)
Q Consensus       426 vI~att~~~--~~~~~~~d~aL~~Rf~~I~v  454 (710)
                      +|++|+.+-  ....-...+.|.-|+..+.+
T Consensus       137 iI~st~~~l~~~v~~g~fr~dLy~rL~~~~i  167 (168)
T PF00158_consen  137 IIASTSKDLEELVEQGRFREDLYYRLNVFTI  167 (168)
T ss_dssp             EEEEESS-HHHHHHTTSS-HHHHHHHTTEEE
T ss_pred             EEeecCcCHHHHHHcCCChHHHHHHhceEec
Confidence            999988642  11111234556556654443

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 ....

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=98.93  E-value=2.2e-09  Score=115.02  Aligned_cols=77  Identities=34%  Similarity=0.475  Sum_probs=63.2

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHHH--hhcCCCCCCC---CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVKR--SRVGLKDPNR---PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~~--~r~gl~~p~r---p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .++.+.|...|+||++|++.+..++..  .|.++.++.+   +..++||+||||||||++|++||+.+   +.+++++|+
T Consensus         7 ~~I~~~Ld~~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l---~~~fi~vD~   83 (443)
T PRK05201          7 REIVSELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLA---NAPFIKVEA   83 (443)
T ss_pred             HHHHHHhccccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHh---CChheeecc
Confidence            456788999999999999999998843  4555543332   12699999999999999999999996   568999999


Q ss_pred             CCCCC
Q 005179          696 SPFNS  700 (710)
Q Consensus       696 se~~~  700 (710)
                      ++|..
T Consensus        84 t~f~e   88 (443)
T PRK05201         84 TKFTE   88 (443)
T ss_pred             hhhcc
Confidence            98865

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.92  E-value=1.6e-08  Score=106.20  Aligned_cols=175  Identities=27%  Similarity=0.376  Sum_probs=113.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCc-cHHHHHHHHHHHH----HhcCCe
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERG-ELEARVTTLISEI----QKSGDV  384 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g-~~e~~l~~~~~~~----~~~~~~  384 (710)
                      .+.|+||.||+|+|||.|++.||+.+          +.++.-.|+..+... .|.| +.|..+..++..+    +++...
T Consensus       225 eKSNvLllGPtGsGKTllaqTLAr~l----------dVPfaIcDcTtLTQA-GYVGeDVEsvi~KLl~~A~~nVekAQqG  293 (564)
T KOG0745|consen  225 EKSNVLLLGPTGSGKTLLAQTLARVL----------DVPFAICDCTTLTQA-GYVGEDVESVIQKLLQEAEYNVEKAQQG  293 (564)
T ss_pred             ecccEEEECCCCCchhHHHHHHHHHh----------CCCeEEecccchhhc-ccccccHHHHHHHHHHHccCCHHHHhcC
Confidence            47899999999999999999999988          677777788777532 2444 5666677777655    345677


Q ss_pred             EEEEccchhhhhCCC-CCCCCCCChHhHHHhhcccccC---------------C--------CeEEEEccCh--------
Q 005179          385 ILFIDEVHTLIGSGT-VGRGNKGTGLDISNLLKPSLGR---------------G--------ELQCIASTTQ--------  432 (710)
Q Consensus       385 IL~IDEid~l~~~~~-~~~~~~~~~~~~~~~L~~~l~~---------------~--------~v~vI~att~--------  432 (710)
                      |+||||+|.+..+.. .+..-+-.+.-++..|+.+++.               +        ++.+|+....        
T Consensus       294 IVflDEvDKi~~~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk~I~  373 (564)
T KOG0745|consen  294 IVFLDEVDKITKKAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDKIIS  373 (564)
T ss_pred             eEEEehhhhhcccCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHHHHH
Confidence            999999999963211 1111011233355666555541               1        2333332100        


Q ss_pred             -----------------------------------HHHH--------hhhhccHHHHcccc-ceEecCCCHHHHHHHHHH
Q 005179          433 -----------------------------------DEHR--------TQFEKDKALARRFQ-PVLISEPSQEDAVRILLG  468 (710)
Q Consensus       433 -----------------------------------~~~~--------~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~  468 (710)
                                                         ++..        -.+.+-|.|.-||. .+.+...+.++...||..
T Consensus       374 rR~~d~slGFg~~s~~~vr~~~~~~s~~~~~~~~~~~lL~~~~~~DLisfGmIPEfVGRfPVlVplh~L~~~~Lv~VLtE  453 (564)
T KOG0745|consen  374 RRLDDKSLGFGAPSSKGVRANMATKSGVENDAEKRDELLEKVESGDLISFGMIPEFVGRFPVLVPLHSLDEDQLVRVLTE  453 (564)
T ss_pred             HhhcchhcccCCCCCccchhhcccccCcchhHHHHHHHHhhccccchhhhcCcHHHhcccceEeeccccCHHHHHHHHhc
Confidence                                               0000        01233477888997 688888999999999874


Q ss_pred             ----HHHHHHhhc-----CCCCCHHHHHHHHHHhhh
Q 005179          469 ----LREKYEAHH-----NCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       469 ----l~~~~~~~~-----~~~i~~~~l~~l~~ls~~  495 (710)
                          +..+|....     .+.+++++++.+++++-.
T Consensus       454 PknaL~~Qyk~lf~~~nV~L~fTe~Al~~IAq~Al~  489 (564)
T KOG0745|consen  454 PKNALGKQYKKLFGMDNVELHFTEKALEAIAQLALK  489 (564)
T ss_pred             chhhHHHHHHHHhccCCeeEEecHHHHHHHHHHHHh
Confidence                566665433     356899999999887643

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.90  E-value=3.3e-08  Score=113.61  Aligned_cols=120  Identities=22%  Similarity=0.277  Sum_probs=78.0

Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------------------CeEEEEccChHHHHhh
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------------------ELQCIASTTQDEHRTQ  438 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------------------~v~vI~att~~~~~~~  438 (710)
                      .+.+|||||++.|             ....+..|+..|+.+                       ++++|++++++.   .
T Consensus       217 ngGtL~Ldei~~L-------------~~~~q~~Ll~~L~~~~i~~~g~~e~~~~~~~~~~~ip~dvrvIa~~~~~~---l  280 (608)
T TIGR00764       217 HKGVLYIDEIKTM-------------PLEVQQYLLTALQDKKFPITGQSENSSGAMVRTEPVPCDFILVASGNLDD---L  280 (608)
T ss_pred             CCCEEEEEChHhC-------------CHHHHHHHHHHHHhCcEEecCccccccccccCCCCCccceEEEEECCHHH---H
Confidence            3467777888777             234555555555321                       567899999864   3


Q ss_pred             hhccHHHHcccc----ceEe--c-CCCHHHHHHHHHHHHHHHHhh-cCCCCCHHHHHHHHHHhhhhhcCCCC----cchH
Q 005179          439 FEKDKALARRFQ----PVLI--S-EPSQEDAVRILLGLREKYEAH-HNCKFTLEAINAAVHLSARYISDRYL----PDKA  506 (710)
Q Consensus       439 ~~~d~aL~~Rf~----~I~v--~-~Ps~~~~~~IL~~l~~~~~~~-~~~~i~~~~l~~l~~ls~~~i~~r~~----p~~a  506 (710)
                      ..+++.|.+||.    .+.+  . +.+.+.+..+++.+....+.+ .-..++++++..+++.+.|...++..    ..+.
T Consensus       281 ~~l~~~l~~rf~~y~v~v~~~~~~~~~~e~~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L  360 (608)
T TIGR00764       281 EGMHPALRSRIRGYGYEVYMKDTMPDTPENRDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLREL  360 (608)
T ss_pred             hhcCHHHHHHhcCCeEEEEeeccCCCCHHHHHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHH
Confidence            468999999997    1333  2 234666777766666655544 23468999999999888877655543    3556


Q ss_pred             HHHHHHHHhhh
Q 005179          507 IDLVDEAGSRA  517 (710)
Q Consensus       507 i~ll~~a~~~~  517 (710)
                      .+++..|...+
T Consensus       361 ~~llR~A~~iA  371 (608)
T TIGR00764       361 GGLVRAAGDIA  371 (608)
T ss_pred             HHHHHHHHHHH
Confidence            66777765443

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>smart00350 MCM minichromosome maintenance proteins

Probab=98.90  E-value=8.3e-09  Score=116.84  Aligned_cols=206  Identities=15%  Similarity=0.164  Sum_probs=121.2

Q ss_pred             CCcccCHHHHHHHHHHHHcCC------------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          290 DPVIGRETEIQRIIQILCRRT------------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~------------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      ..++|.+.....+.-.+....            ..|+||+|+||+|||++++.+++......   +..+..   .+...+
T Consensus       203 p~i~G~~~~k~~l~l~l~gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~---~~~~~~---~~~~~l  276 (509)
T smart00350      203 PSIYGHEDIKKAILLLLFGGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAV---YTTGKG---SSAVGL  276 (509)
T ss_pred             ccccCcHHHHHHHHHHHhCCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcce---EcCCCC---CCcCCc
Confidence            357888876544444443321            13899999999999999999998652210   100000   011111


Q ss_pred             hhc---cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC------------
Q 005179          358 MAG---AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG------------  422 (710)
Q Consensus       358 ~~g---~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~------------  422 (710)
                      ...   ....|++..+-    ..+..+.+.+|+|||++.+             ....+..|...|+++            
T Consensus       277 ~~~~~~~~~~g~~~~~~----G~l~~A~~Gil~iDEi~~l-------------~~~~q~~L~e~me~~~i~i~k~G~~~~  339 (509)
T smart00350      277 TAAVTRDPETREFTLEG----GALVLADNGVCCIDEFDKM-------------DDSDRTAIHEAMEQQTISIAKAGITTT  339 (509)
T ss_pred             cccceEccCcceEEecC----ccEEecCCCEEEEechhhC-------------CHHHHHHHHHHHhcCEEEEEeCCEEEE
Confidence            100   00112211000    0111234679999999998             334455555555432            


Q ss_pred             ---CeEEEEccChHH--HH------hhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhh-------cCCCCC
Q 005179          423 ---ELQCIASTTQDE--HR------TQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAH-------HNCKFT  482 (710)
Q Consensus       423 ---~v~vI~att~~~--~~------~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~-------~~~~i~  482 (710)
                         .+.+|+++|+.+  |.      ..+.+++++.+||+  .+.++.|+.+...+|++++...+...       ....++
T Consensus       340 l~~~~~viAa~NP~~g~y~~~~~~~~n~~l~~~lLsRFdLi~~~~d~~~~~~d~~i~~~i~~~~~~~~~~~~~~~~~~~~  419 (509)
T smart00350      340 LNARCSVLAAANPIGGRYDPKLTPEENIDLPAPILSRFDLLFVVLDEVDEERDRELAKHVVDLHRYSHPEPDEADEVPIS  419 (509)
T ss_pred             ecCCcEEEEEeCCCCcccCCCcChhhccCCChHHhCceeeEEEecCCCChHHHHHHHHHHHHhhcccCccccccccccCC
Confidence               456899988753  11      12478999999998  45667899999999999876543211       112467


Q ss_pred             HHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhh
Q 005179          483 LEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHI  519 (710)
Q Consensus       483 ~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~  519 (710)
                      .+.+...+.+++.++.-. +++.+.+.+.......+.
T Consensus       420 ~~~l~~yi~~ar~~~~P~-ls~~~~~~i~~~y~~~R~  455 (509)
T smart00350      420 QEFLRKYIAYAREKIKPK-LSEEAAEKLVKAYVDLRK  455 (509)
T ss_pred             HHHHHHHHHHHHhcCCCC-CCHHHHHHHHHHHHHhcc
Confidence            778888888888744222 567777777666544443

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.87  E-value=7.4e-08  Score=102.28  Aligned_cols=161  Identities=22%  Similarity=0.250  Sum_probs=99.1

Q ss_pred             CcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEE--eeh--------------
Q 005179          291 PVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMS--LDM--------------  354 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~--ld~--------------  354 (710)
                      -++|++..-.-|....-.+.-.++||-|+.|+||||++++|+..+....+.   .+|++-.  .+.              
T Consensus        18 aivGqd~lk~aL~l~av~P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V---~gc~f~cdP~~P~~~c~~c~~k~~e~   94 (423)
T COG1239          18 AIVGQDPLKLALGLNAVDPQIGGALIAGEKGTAKSTLARALADLLPEIEVV---IGCPFNCDPDDPEEMCDECRAKGDEL   94 (423)
T ss_pred             hhcCchHHHHHHhhhhcccccceeEEecCCCccHHHHHHHHHHhCCcccee---cCCCCCCCCCChhhhhHHHHhhcccc
Confidence            468888555444433333455789999999999999999999887432110   0110000  000              


Q ss_pred             hhhhhc-------cccCccHHHHH------HHHHH---------HHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHH
Q 005179          355 GLLMAG-------AKERGELEARV------TTLIS---------EIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDIS  412 (710)
Q Consensus       355 ~~l~~g-------~~~~g~~e~~l------~~~~~---------~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~  412 (710)
                      ..+...       .-.-|..+.++      ...++         .+.+....||||||+..|             ...++
T Consensus        95 ~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL-------------~d~lv  161 (423)
T COG1239          95 EWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLL-------------DDHLV  161 (423)
T ss_pred             ccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEeccccc-------------cHHHH
Confidence            000000       00011222211      11111         112345679999999999             55678


Q ss_pred             HhhcccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCC-CHHHHHHHHHHHHH
Q 005179          413 NLLKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEP-SQEDAVRILLGLRE  471 (710)
Q Consensus       413 ~~L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~P-s~~~~~~IL~~l~~  471 (710)
                      +.|+..++.|               ++++|+|+|+++    -++-+.|+.||. .|.+..| +.+++.+|++....
T Consensus       162 d~LLd~aaeG~n~vereGisi~hpa~fvligTmNPEe----GeLrpqLlDRfg~~v~~~~~~~~~~rv~Ii~r~~~  233 (423)
T COG1239         162 DALLDVAAEGVNDVEREGISIRHPARFLLIGTMNPEE----GELRPQLLDRFGLEVDTHYPLDLEERVEIIRRRLA  233 (423)
T ss_pred             HHHHHHHHhCCceeeeCceeeccCccEEEEeecCccc----cccchhhHhhhcceeeccCCCCHHHHHHHHHHHHH
Confidence            8888777654               578999999985    367899999997 7888777 58888888886544

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.85  E-value=3.7e-08  Score=105.13  Aligned_cols=168  Identities=14%  Similarity=0.144  Sum_probs=109.5

Q ss_pred             HHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--------------ccCceEEEeehhhhhhc
Q 005179          296 ETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--------------LLSKRIMSLDMGLLMAG  360 (710)
Q Consensus       296 ~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--------------l~~~~v~~ld~~~l~~g  360 (710)
                      +..++++.+.+...+..| .||+||+|+||+++|.++|+.+.+.+....              .....++.+...    +
T Consensus         8 ~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~----~   83 (334)
T PRK07993          8 RPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPE----K   83 (334)
T ss_pred             hHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecc----c
Confidence            346677888777755544 579999999999999999999976421110              001112222110    0


Q ss_pred             cccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHH
Q 005179          361 AKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDE  434 (710)
Q Consensus       361 ~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~  434 (710)
                      .+ ..-..+.++++.+.+.    .++.-|++||++|.|             ...++|.|+..||+  ++.++|..|...+
T Consensus        84 ~~-~~I~idqiR~l~~~~~~~~~~g~~kV~iI~~ae~m-------------~~~AaNaLLKtLEEPp~~t~fiL~t~~~~  149 (334)
T PRK07993         84 GK-SSLGVDAVREVTEKLYEHARLGGAKVVWLPDAALL-------------TDAAANALLKTLEEPPENTWFFLACREPA  149 (334)
T ss_pred             cc-ccCCHHHHHHHHHHHhhccccCCceEEEEcchHhh-------------CHHHHHHHHHHhcCCCCCeEEEEEECChh
Confidence            00 0011234555555553    244579999999999             66788999999986  4566676666655


Q ss_pred             HHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          435 HRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       435 ~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                           .+-|++++|++.+.+++|+.++....|..         ...++++.+..++.++.+
T Consensus       150 -----~lLpTIrSRCq~~~~~~~~~~~~~~~L~~---------~~~~~~~~a~~~~~la~G  196 (334)
T PRK07993        150 -----RLLATLRSRCRLHYLAPPPEQYALTWLSR---------EVTMSQDALLAALRLSAG  196 (334)
T ss_pred             -----hChHHHHhccccccCCCCCHHHHHHHHHH---------ccCCCHHHHHHHHHHcCC
Confidence                 68899999999999999999886666542         123556655566666544

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=98.85  E-value=5.4e-09  Score=114.24  Aligned_cols=78  Identities=35%  Similarity=0.404  Sum_probs=60.9

Q ss_pred             HHHHHHHhhCcccChHHHHHHHHHHH----HHhhcCCC---CCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCccee
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISRAV----KRSRVGLK---DPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYL  692 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~~i----~~~r~gl~---~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~  692 (710)
                      ..++.+.|.+.|+||++|++.++.++    ++.+.+..   +...+.+++||+||||||||++|++||+.+   ...+++
T Consensus        62 p~~i~~~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l---~~pf~~  138 (412)
T PRK05342         62 PKEIKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARIL---DVPFAI  138 (412)
T ss_pred             HHHHHHHHhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHh---CCCcee
Confidence            45678888899999999999998877    33333332   122344789999999999999999999986   457999


Q ss_pred             eCCCCCCC
Q 005179          693 FFPSPFNS  700 (710)
Q Consensus       693 ~d~se~~~  700 (710)
                      +|++++..
T Consensus       139 id~~~l~~  146 (412)
T PRK05342        139 ADATTLTE  146 (412)
T ss_pred             cchhhccc
Confidence            99988753

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.84  E-value=2.7e-08  Score=115.77  Aligned_cols=208  Identities=15%  Similarity=0.157  Sum_probs=121.3

Q ss_pred             CCcccCHHHHHHHHHHHHcCC---------------------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCce
Q 005179          290 DPVIGRETEIQRIIQILCRRT---------------------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKR  348 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~---------------------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~  348 (710)
                      ..++|.+...+.++-.|....                     ..|+||+|+||||||.+++.+++......   +..+..
T Consensus       450 P~I~G~e~vK~ailL~L~gG~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~lspR~~---ytsG~~  526 (915)
T PTZ00111        450 PSIKARNNVKIGLLCQLFSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLLSPRSI---YTSGKS  526 (915)
T ss_pred             CeEECCHHHHHHHHHHHhcCCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHhCCccc---cCCCCC
Confidence            457888877666554442221                     12899999999999999999987542221   111222


Q ss_pred             EEEeehhhhhh-ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----
Q 005179          349 IMSLDMGLLMA-GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----  422 (710)
Q Consensus       349 v~~ld~~~l~~-g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----  422 (710)
                      ...+.+..... -....|+|.....    .+..+.+.+|+|||++.+             ....+..|..+|+++     
T Consensus       527 ~s~vgLTa~~~~~d~~tG~~~le~G----aLvlAdgGtL~IDEidkm-------------s~~~Q~aLlEaMEqqtIsI~  589 (915)
T PTZ00111        527 SSSVGLTASIKFNESDNGRAMIQPG----AVVLANGGVCCIDELDKC-------------HNESRLSLYEVMEQQTVTIA  589 (915)
T ss_pred             CccccccchhhhcccccCcccccCC----cEEEcCCCeEEecchhhC-------------CHHHHHHHHHHHhCCEEEEe
Confidence            22322222211 0011122211000    122344679999999998             444555666666533     


Q ss_pred             ----------CeEEEEccChHHHH--------hhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhc-----
Q 005179          423 ----------ELQCIASTTQDEHR--------TQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHH-----  477 (710)
Q Consensus       423 ----------~v~vI~att~~~~~--------~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~-----  477 (710)
                                ++.||+++|+...+        ..+.+.++|.+||+  .+.++.|+.+.-..|-.+++..+...|     
T Consensus       590 KaGi~~tL~ar~rVIAAaNP~~gryd~~~s~~eni~Lp~~LLSRFDLIf~l~D~~d~~~D~~lA~hI~~~~~~~h~~~~~  669 (915)
T PTZ00111        590 KAGIVATLKAETAILASCNPINSRYNKNKAVIENINISPSLFTRFDLIYLVLDHIDQDTDQLISLSIAKDFLLPHMTGSG  669 (915)
T ss_pred             cCCcceecCCCeEEEEEcCCcccccCcccCcccccCCChHHhhhhcEEEEecCCCChHHHHHHHHHHHHhhccccccccc
Confidence                      46789999985321        34667899999998  456688888877777777765431101     


Q ss_pred             ------------------------CCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhh
Q 005179          478 ------------------------NCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAH  518 (710)
Q Consensus       478 ------------------------~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~  518 (710)
                                              ...++.+.+..-+.+++.++. -.+.+.|.++|.......+
T Consensus       670 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~lLrkYI~YAR~~~~-P~Ls~eA~~~i~~~Yv~mR  733 (915)
T PTZ00111        670 NDEDTYDRSNTMHVEDESLRSEKDYNKNDLDMLRMYIKFSKLHCF-PKLSDEAKKVITREYVKMR  733 (915)
T ss_pred             ccccchhccccccccccccccccccCCCCHHHHHHHHHHHhccCC-CCCCHHHHHHHHHHHHHHh
Confidence                                    012456667777777765533 2345677777766554433

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=98.83  E-value=6.8e-08  Score=110.90  Aligned_cols=182  Identities=20%  Similarity=0.212  Sum_probs=107.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh---hhhhhccccCccHHHHHHH---HH--HHHHhcC
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM---GLLMAGAKERGELEARVTT---LI--SEIQKSG  382 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~---~~l~~g~~~~g~~e~~l~~---~~--~~~~~~~  382 (710)
                      -.++||.|+||||||+++++++..+.. ..|       ++.+..   .+.+.|.-   .++..+..   .+  ..+....
T Consensus        16 ~g~vLl~G~~GtgKs~lar~l~~~~~~-~~p-------fv~i~~~~t~d~L~G~i---dl~~~~~~g~~~~~~G~L~~A~   84 (589)
T TIGR02031        16 LGGVAIRARAGTGKTALARALAEILPP-IMP-------FVELPLGVTEDRLIGGI---DVEESLAGGQRVTQPGLLDEAP   84 (589)
T ss_pred             cceEEEEcCCCcHHHHHHHHHHHhCCc-CCC-------eEecCcccchhhcccch---hhhhhhhcCcccCCCCCeeeCC
Confidence            568999999999999999999987632 111       222221   11111110   00000000   00  0011244


Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------------CeEEEEccChHHHHhhhhccHHHHc
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALAR  447 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~  447 (710)
                      +.+|||||++.+             ....++.|...|+++               .+.+|+++|+.+...  .+.++|..
T Consensus        85 ~GvL~lDEi~rl-------------~~~~q~~Ll~al~~g~v~i~r~G~~~~~p~~f~lIAt~np~e~~g--~L~~~Lld  149 (589)
T TIGR02031        85 RGVLYVDMANLL-------------DDGLSNRLLQALDEGVVIVEREGISVVHPAKFALIATYDPAEGGG--GLPDHLLD  149 (589)
T ss_pred             CCcEeccchhhC-------------CHHHHHHHHHHHHcCCeEEEECCCceeecCceEEEEecCCccccC--CCCHHHHH
Confidence            579999999999             556777777777654               367899888764222  57899999


Q ss_pred             ccc-ceEecC-CCHHHHHHHHHHHHHHHH-------------------hhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          448 RFQ-PVLISE-PSQEDAVRILLGLREKYE-------------------AHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       448 Rf~-~I~v~~-Ps~~~~~~IL~~l~~~~~-------------------~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ||. .|.+.. |+.+++.+|++.....+.                   ....+.++++++++++.++-.+-.  ..+...
T Consensus       150 Rf~l~v~~~~~~~~~er~eil~~~~~~~~~~~~~~~~~~~~~i~~ar~~~~~V~i~~~~~~~l~~~~~~~gv--~s~Ra~  227 (589)
T TIGR02031       150 RLALHVSLEDVASQDLRVEIVRRERCNEVFRMNDELELLRGQIEAARELLPQVTISAEQVKELVLTAASLGI--SGHRAD  227 (589)
T ss_pred             hccCeeecCCCCCHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHHHhcCCccCCHHHHHHHHHHHHHcCC--CCccHH
Confidence            997 455544 567778888887543221                   123466777777777777644321  123445


Q ss_pred             HHHHHHHHhhhhhh
Q 005179          507 IDLVDEAGSRAHIE  520 (710)
Q Consensus       507 i~ll~~a~~~~~~~  520 (710)
                      +.++.-|.+.+.+.
T Consensus       228 i~~~r~ArA~Aal~  241 (589)
T TIGR02031       228 LFAVRAAKAHAALH  241 (589)
T ss_pred             HHHHHHHHHHHHHh
Confidence            55555555544443

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.

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.83  E-value=9.9e-08  Score=97.52  Aligned_cols=111  Identities=25%  Similarity=0.301  Sum_probs=74.9

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------CCeEEEEccChHHHHhhhhccHHHHcccc
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------GELQCIASTTQDEHRTQFEKDKALARRFQ  450 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------~~v~vI~att~~~~~~~~~~d~aL~~Rf~  450 (710)
                      ..|+||||||.++..+..+.+ +-...-++.-|+++++.            .++.+|++..-.- .+--.+-|.|..||.
T Consensus       251 ~GIvFIDEIDKIa~~~~~g~~-dvSREGVQRDlLPlvEGstV~TKyG~VkTdHILFIasGAFh~-sKPSDLiPELQGRfP  328 (444)
T COG1220         251 NGIVFIDEIDKIAKRGGSGGP-DVSREGVQRDLLPLVEGSTVSTKYGPVKTDHILFIASGAFHV-AKPSDLIPELQGRFP  328 (444)
T ss_pred             cCeEEEehhhHHHhcCCCCCC-CcchhhhcccccccccCceeeccccccccceEEEEecCceec-CChhhcChhhcCCCc
Confidence            569999999999877653221 11122356667777763            3567887753211 111256689999997


Q ss_pred             -ceEecCCCHHHHHHHHHH----HHHHHHh-----hcCCCCCHHHHHHHHHHhhh
Q 005179          451 -PVLISEPSQEDAVRILLG----LREKYEA-----HHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       451 -~I~v~~Ps~~~~~~IL~~----l~~~~~~-----~~~~~i~~~~l~~l~~ls~~  495 (710)
                       .|++...+.++...||..    +..+|..     .-.+.+++++++.+++.+-.
T Consensus       329 IRVEL~~Lt~~Df~rILtep~~sLikQY~aLlkTE~v~l~FtddaI~~iAeiA~~  383 (444)
T COG1220         329 IRVELDALTKEDFERILTEPKASLIKQYKALLKTEGVELEFTDDAIKRIAEIAYQ  383 (444)
T ss_pred             eEEEcccCCHHHHHHHHcCcchHHHHHHHHHHhhcCeeEEecHHHHHHHHHHHHH
Confidence             799999999999999874    5566653     22357889999888877543

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=98.82  E-value=7.2e-08  Score=107.06  Aligned_cols=101  Identities=20%  Similarity=0.262  Sum_probs=79.2

Q ss_pred             HHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHH
Q 005179          594 PDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKT  673 (710)
Q Consensus       594 ~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT  673 (710)
                      .......+...+.+||++.+.+ .-.+...+..|.+...|++++++.|...+...+.--..- .  .-+||+||||||||
T Consensus       377 fnvtrNYLdwlt~LPWgk~S~E-n~dl~~Ak~iLdeDHYgm~dVKeRILEfiAV~kLrgs~q-G--kIlCf~GPPGVGKT  452 (906)
T KOG2004|consen  377 FNVTRNYLDWLTSLPWGKSSTE-NLDLARAKEILDEDHYGMEDVKERILEFIAVGKLRGSVQ-G--KILCFVGPPGVGKT  452 (906)
T ss_pred             hhHHHHHHHHHHhCCCCCCChh-hhhHHHHHHhhcccccchHHHHHHHHHHHHHHhhcccCC-C--cEEEEeCCCCCCcc
Confidence            3445667788889999998876 456778899999999999999999998887665421111 1  16899999999999


Q ss_pred             HHHHHHHHHHcCCCCcceeeCCCCCCCc
Q 005179          674 ELAKSLAACYFGSVRIHYLFFPSPFNSV  701 (710)
Q Consensus       674 ~lAkaLA~~lfg~~~~li~~d~se~~~~  701 (710)
                      .+||.||+.|-.   .+.||..+=..+|
T Consensus       453 SI~kSIA~ALnR---kFfRfSvGG~tDv  477 (906)
T KOG2004|consen  453 SIAKSIARALNR---KFFRFSVGGMTDV  477 (906)
T ss_pred             cHHHHHHHHhCC---ceEEEeccccccH
Confidence            999999999744   6889876655554

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=98.81  E-value=8.4e-09  Score=110.54  Aligned_cols=75  Identities=35%  Similarity=0.491  Sum_probs=61.0

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHHH--hhcCCC----CCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVKR--SRVGLK----DPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~~--~r~gl~----~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .++.+.|.+.|+||++|++.++.++..  .|.++.    .+..| .++||+||||||||++|++||+.+   +.+++.+|
T Consensus         4 ~~I~~~Ld~~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p-~~ILLiGppG~GKT~lAraLA~~l---~~~fi~vd   79 (441)
T TIGR00390         4 REIVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTP-KNILMIGPTGVGKTEIARRLAKLA---NAPFIKVE   79 (441)
T ss_pred             HHHHHHHhhhccCHHHHHHHHHHHHHhhhhhhccccccccccCC-ceEEEECCCCCCHHHHHHHHHHHh---CCeEEEee
Confidence            356778899999999999999988853  444443    22334 699999999999999999999996   56899999


Q ss_pred             CCCCC
Q 005179          695 PSPFN  699 (710)
Q Consensus       695 ~se~~  699 (710)
                      +++|.
T Consensus        80 at~~~   84 (441)
T TIGR00390        80 ATKFT   84 (441)
T ss_pred             cceee
Confidence            98774

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.

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

Probab=98.81  E-value=5.3e-09  Score=102.99  Aligned_cols=57  Identities=37%  Similarity=0.415  Sum_probs=44.8

Q ss_pred             ccChHHHHHHHHHHHHHhhc----CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          631 VIGQDEAVAAISRAVKRSRV----GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~----gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      |+||++|+.+-...+++.+-    |-..|    .++|||||||||||++|||||++   ..-.++-+.
T Consensus       123 ViGqEeAK~kcrli~~yLenPe~Fg~WAP----knVLFyGppGTGKTm~Akalane---~kvp~l~vk  183 (368)
T COG1223         123 VIGQEEAKRKCRLIMEYLENPERFGDWAP----KNVLFYGPPGTGKTMMAKALANE---AKVPLLLVK  183 (368)
T ss_pred             hhchHHHHHHHHHHHHHhhChHHhcccCc----ceeEEECCCCccHHHHHHHHhcc---cCCceEEec
Confidence            99999999998888877642    33333    59999999999999999999988   444555544

>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=98.80  E-value=7.8e-09  Score=101.67  Aligned_cols=61  Identities=25%  Similarity=0.342  Sum_probs=42.3

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      +.++||++.+..+.-.++..+.    .+.++.++|||||||||||+||+.||+++-   .++..+..+
T Consensus        24 ~efiGQ~~l~~~l~i~i~aa~~----r~~~l~h~lf~GPPG~GKTTLA~IIA~e~~---~~~~~~sg~   84 (233)
T PF05496_consen   24 DEFIGQEHLKGNLKILIRAAKK----RGEALDHMLFYGPPGLGKTTLARIIANELG---VNFKITSGP   84 (233)
T ss_dssp             CCS-S-HHHHHHHHHHHHHHHC----TTS---EEEEESSTTSSHHHHHHHHHHHCT-----EEEEECC
T ss_pred             HHccCcHHHHhhhHHHHHHHHh----cCCCcceEEEECCCccchhHHHHHHHhccC---CCeEeccch
Confidence            4599999999998877776653    123456999999999999999999999942   345444443

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.

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=98.79  E-value=1.1e-07  Score=100.61  Aligned_cols=148  Identities=16%  Similarity=0.175  Sum_probs=100.0

Q ss_pred             HHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCc--cc------------cCceEEEeehhhhhhcc
Q 005179          297 TEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEVPV--FL------------LSKRIMSLDMGLLMAGA  361 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~--~l------------~~~~v~~ld~~~l~~g~  361 (710)
                      .....+...+.+.+.. ..||+||+|+||+++|+.+|+.+.+.+...  ..            ....++.+...   .| 
T Consensus         9 ~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~---~~-   84 (325)
T PRK06871          9 PTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPI---DN-   84 (325)
T ss_pred             HHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccc---cC-
Confidence            3556677777765544 466899999999999999999997743111  00            01112222110   11 


Q ss_pred             ccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHH
Q 005179          362 KERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEH  435 (710)
Q Consensus       362 ~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~  435 (710)
                      +..  -.+.++++.+.+..    ++.-|++||++|.|             ....+|.|+..||+  .++.+|.+|+..+ 
T Consensus        85 ~~I--~id~iR~l~~~~~~~~~~g~~KV~iI~~a~~m-------------~~~AaNaLLKtLEEPp~~~~fiL~t~~~~-  148 (325)
T PRK06871         85 KDI--GVDQVREINEKVSQHAQQGGNKVVYIQGAERL-------------TEAAANALLKTLEEPRPNTYFLLQADLSA-  148 (325)
T ss_pred             CCC--CHHHHHHHHHHHhhccccCCceEEEEechhhh-------------CHHHHHHHHHHhcCCCCCeEEEEEECChH-
Confidence            111  12345566555532    34568999999999             56788999999985  4566666666655 


Q ss_pred             HhhhhccHHHHccccceEecCCCHHHHHHHHHH
Q 005179          436 RTQFEKDKALARRFQPVLISEPSQEDAVRILLG  468 (710)
Q Consensus       436 ~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~  468 (710)
                          .+-|++++|++.+.+.+|+.++..+.|..
T Consensus       149 ----~llpTI~SRC~~~~~~~~~~~~~~~~L~~  177 (325)
T PRK06871        149 ----ALLPTIYSRCQTWLIHPPEEQQALDWLQA  177 (325)
T ss_pred             ----hCchHHHhhceEEeCCCCCHHHHHHHHHH
Confidence                68899999999999999999987777664

>PRK08116 hypothetical protein; Validated

Probab=98.79  E-value=5.2e-08  Score=101.06  Aligned_cols=130  Identities=17%  Similarity=0.244  Sum_probs=72.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc--cCccHHHHHHHHHHHHHhcCCeEEEEc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK--ERGELEARVTTLISEIQKSGDVILFID  389 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~--~~g~~e~~l~~~~~~~~~~~~~IL~ID  389 (710)
                      .+++|+|++|+|||+|+.++++.+...       +..++.++...++...+  +.+........+++.+...  .+|+||
T Consensus       115 ~gl~l~G~~GtGKThLa~aia~~l~~~-------~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~--dlLviD  185 (268)
T PRK08116        115 VGLLLWGSVGTGKTYLAACIANELIEK-------GVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNA--DLLILD  185 (268)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCC--CEEEEe
Confidence            359999999999999999999998653       45677777766543211  1110011122344444433  489999


Q ss_pred             cchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccc----cceEecCCC
Q 005179          390 EVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRF----QPVLISEPS  458 (710)
Q Consensus       390 Eid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf----~~I~v~~Ps  458 (710)
                      |++.....       ......+.+++.....++. .+|.|||...-.-....+..+.+|+    ..|.+.-++
T Consensus       186 Dlg~e~~t-------~~~~~~l~~iin~r~~~~~-~~IiTsN~~~~eL~~~~~~ri~sRl~e~~~~v~~~g~d  250 (268)
T PRK08116        186 DLGAERDT-------EWAREKVYNIIDSRYRKGL-PTIVTTNLSLEELKNQYGKRIYDRILEMCTPVENEGKS  250 (268)
T ss_pred             cccCCCCC-------HHHHHHHHHHHHHHHHCCC-CEEEECCCCHHHHHHHHhHHHHHHHHHcCEEEEeeCcC
Confidence            99653111       0112334455544444444 4555555432111112467888885    256666665

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.79  E-value=1.9e-08  Score=108.12  Aligned_cols=147  Identities=22%  Similarity=0.290  Sum_probs=88.3

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------cCceEE----
Q 005179          288 LIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------LSKRIM----  350 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------~~~~v~----  350 (710)
                      .|.+++|++...+.+.-.  ...+.|+|++||||||||++++.+...+.....+..+             .+++++    
T Consensus       177 D~~DV~GQ~~AKrAleiA--AAGgHnLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s~~g~~~~~~~~~~~rP  254 (490)
T COG0606         177 DFKDVKGQEQAKRALEIA--AAGGHNLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSLAGDLHEGCPLKIHRP  254 (490)
T ss_pred             chhhhcCcHHHHHHHHHH--HhcCCcEEEecCCCCchHHhhhhhcccCCCCChHHHHHHHHHhhhcccccccCccceeCC
Confidence            456899999766655533  3357899999999999999999876544221111111             001111    


Q ss_pred             ------Eeehhhhhhccc--cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC
Q 005179          351 ------SLDMGLLMAGAK--ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG  422 (710)
Q Consensus       351 ------~ld~~~l~~g~~--~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~  422 (710)
                            +....+++.|..  ..|           ++....+.||||||+-.+             ...+.+.|+.-|++|
T Consensus       255 Fr~PHHsaS~~aLvGGG~~p~PG-----------eIsLAH~GVLFLDElpef-------------~~~iLe~LR~PLE~g  310 (490)
T COG0606         255 FRAPHHSASLAALVGGGGVPRPG-----------EISLAHNGVLFLDELPEF-------------KRSILEALREPLENG  310 (490)
T ss_pred             ccCCCccchHHHHhCCCCCCCCC-----------ceeeecCCEEEeeccchh-------------hHHHHHHHhCccccC
Confidence                  111222222211  011           122345679999999777             567899999999876


Q ss_pred             C---------------eEEEEccChH-----------------HHHhh-hhccHHHHcccc-ceEecCCCHH
Q 005179          423 E---------------LQCIASTTQD-----------------EHRTQ-FEKDKALARRFQ-PVLISEPSQE  460 (710)
Q Consensus       423 ~---------------v~vI~att~~-----------------~~~~~-~~~d~aL~~Rf~-~I~v~~Ps~~  460 (710)
                      +               +++|++||+.                 ....| -.+...|++||+ .|.++.++..
T Consensus       311 ~i~IsRa~~~v~ypa~Fqlv~AmNpcpcG~~~~~~~~C~c~~~~~~~Y~~klSgp~lDRiDl~vev~~~~~~  382 (490)
T COG0606         311 KIIISRAGSKVTYPARFQLVAAMNPCPCGNLGAPLRRCPCSPRQIKRYLNKLSGPFLDRIDLMVEVPRLSAG  382 (490)
T ss_pred             cEEEEEcCCeeEEeeeeEEhhhcCCCCccCCCCCCCCcCCCHHHHHHHHHHhhHHHHhhhhheecccCCCHH
Confidence            4               4466776642                 11112 245678899998 6777776533

>PRK12377 putative replication protein; Provisional

Probab=98.77  E-value=1.7e-08  Score=102.95  Aligned_cols=73  Identities=21%  Similarity=0.368  Sum_probs=49.1

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc---CccHHHHHHHHHHHHHhcCCeEE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE---RGELEARVTTLISEIQKSGDVIL  386 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~---~g~~e~~l~~~~~~~~~~~~~IL  386 (710)
                      ...+++|+||||||||+|+.++++.+...       +..+..+...++...-+.   .+..   ...+++.+..  ..+|
T Consensus       100 ~~~~l~l~G~~GtGKThLa~AIa~~l~~~-------g~~v~~i~~~~l~~~l~~~~~~~~~---~~~~l~~l~~--~dLL  167 (248)
T PRK12377        100 GCTNFVFSGKPGTGKNHLAAAIGNRLLAK-------GRSVIVVTVPDVMSRLHESYDNGQS---GEKFLQELCK--VDLL  167 (248)
T ss_pred             cCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCCeEEEEHHHHHHHHHHHHhccch---HHHHHHHhcC--CCEE
Confidence            34689999999999999999999998643       566677776666532110   1111   2234444433  4599


Q ss_pred             EEccchhh
Q 005179          387 FIDEVHTL  394 (710)
Q Consensus       387 ~IDEid~l  394 (710)
                      +|||++..
T Consensus       168 iIDDlg~~  175 (248)
T PRK12377        168 VLDEIGIQ  175 (248)
T ss_pred             EEcCCCCC
Confidence            99999765

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.77  E-value=5e-08  Score=103.89  Aligned_cols=152  Identities=17%  Similarity=0.183  Sum_probs=98.5

Q ss_pred             HHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCC-Ccc--------------ccCceEEEeehhhhh----
Q 005179          298 EIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEV-PVF--------------LLSKRIMSLDMGLLM----  358 (710)
Q Consensus       298 ~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~-p~~--------------l~~~~v~~ld~~~l~----  358 (710)
                      ..+++... ..+-+..+||+||+|+||+++|+.+|+.+.+... +..              .....++.+......    
T Consensus         9 ~~~~l~~~-~~rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~   87 (342)
T PRK06964          9 DWNRLQAL-RARLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAP   87 (342)
T ss_pred             HHHHHHHh-cCCcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEeccccccccc
Confidence            44555554 3344556789999999999999999999977541 100              001112222111000    


Q ss_pred             -------------hccc---c-CccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcc
Q 005179          359 -------------AGAK---E-RGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP  417 (710)
Q Consensus       359 -------------~g~~---~-~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~  417 (710)
                                   .|.+   . ..-..+.++.+.+.+..    ++.-|++||++|.|             .....|.|+.
T Consensus        88 ~~~~~~~~~~~~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m-------------~~~AaNaLLK  154 (342)
T PRK06964         88 GAADEAKEADADEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEAL-------------NVAAANALLK  154 (342)
T ss_pred             ccccccccchhhcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhc-------------CHHHHHHHHH
Confidence                         0000   0 01112445666655532    34569999999999             5668888888


Q ss_pred             cccC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHH
Q 005179          418 SLGR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLG  468 (710)
Q Consensus       418 ~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~  468 (710)
                      .|++  .++++|.+|+..+     .+.|++++|++.|.|++|+.++..+.|..
T Consensus       155 tLEEPp~~t~fiL~t~~~~-----~LLpTI~SRcq~i~~~~~~~~~~~~~L~~  202 (342)
T PRK06964        155 TLEEPPPGTVFLLVSARID-----RLLPTILSRCRQFPMTVPAPEAAAAWLAA  202 (342)
T ss_pred             HhcCCCcCcEEEEEECChh-----hCcHHHHhcCEEEEecCCCHHHHHHHHHH
Confidence            8985  4566777777665     78899999999999999999987777753

>PRK08181 transposase; Validated

Probab=98.77  E-value=2.5e-08  Score=102.91  Aligned_cols=118  Identities=16%  Similarity=0.262  Sum_probs=69.4

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc---ccCccHHHHHHHHHHHHHhcCCeEE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA---KERGELEARVTTLISEIQKSGDVIL  386 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~---~~~g~~e~~l~~~~~~~~~~~~~IL  386 (710)
                      .+.|++|+||||||||+|+.+++..+...       +..++.+....++..-   ...+.    +...+..+..  ..+|
T Consensus       105 ~~~nlll~Gp~GtGKTHLa~Aia~~a~~~-------g~~v~f~~~~~L~~~l~~a~~~~~----~~~~l~~l~~--~dLL  171 (269)
T PRK08181        105 KGANLLLFGPPGGGKSHLAAAIGLALIEN-------GWRVLFTRTTDLVQKLQVARRELQ----LESAIAKLDK--FDLL  171 (269)
T ss_pred             cCceEEEEecCCCcHHHHHHHHHHHHHHc-------CCceeeeeHHHHHHHHHHHHhCCc----HHHHHHHHhc--CCEE
Confidence            56789999999999999999999988543       5677777776665321   11122    2233444433  4599


Q ss_pred             EEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccC--hHHHHhhhh---ccHHHHccc
Q 005179          387 FIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT--QDEHRTQFE---KDKALARRF  449 (710)
Q Consensus       387 ~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att--~~~~~~~~~---~d~aL~~Rf  449 (710)
                      +|||++.+....       .....+.+++....+++  .+|.++|  ..+|...+.   +..++.+|+
T Consensus       172 IIDDlg~~~~~~-------~~~~~Lf~lin~R~~~~--s~IiTSN~~~~~w~~~~~D~~~a~aildRL  230 (269)
T PRK08181        172 ILDDLAYVTKDQ-------AETSVLFELISARYERR--SILITANQPFGEWNRVFPDPAMTLAAVDRL  230 (269)
T ss_pred             EEeccccccCCH-------HHHHHHHHHHHHHHhCC--CEEEEcCCCHHHHHHhcCCccchhhHHHhh
Confidence            999998873221       11234455555444443  3444444  444544432   223455555

>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=98.77  E-value=8e-09  Score=92.60  Aligned_cols=107  Identities=24%  Similarity=0.343  Sum_probs=57.3

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh------hhhhhcccc----CccHHHHHHHHHHHHHhcC
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM------GLLMAGAKE----RGELEARVTTLISEIQKSG  382 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~------~~l~~g~~~----~g~~e~~l~~~~~~~~~~~  382 (710)
                      |+||.|+||+|||++|+++|+.+          +..+..+.+      +++. |...    .++++-.-.-++       
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~----------~~~f~RIq~tpdllPsDi~-G~~v~~~~~~~f~~~~GPif-------   62 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSL----------GLSFKRIQFTPDLLPSDIL-GFPVYDQETGEFEFRPGPIF-------   62 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHT----------T--EEEEE--TT--HHHHH-EEEEEETTTTEEEEEE-TT--------
T ss_pred             CEeeECCCccHHHHHHHHHHHHc----------CCceeEEEecCCCCcccce-eeeeeccCCCeeEeecChhh-------
Confidence            68999999999999999999987          333333322      1221 1110    111110001111       


Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEEEccChHHHHhhhhccHHHHccc
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCIASTTQDEHRTQFEKDKALARRF  449 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI~att~~~~~~~~~~d~aL~~Rf  449 (710)
                      ..|+++|||++.             ....++.|.+.|+++             .+.||+|.|+.++...+.+..++.+||
T Consensus        63 ~~ill~DEiNra-------------ppktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~DRF  129 (131)
T PF07726_consen   63 TNILLADEINRA-------------PPKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLDRF  129 (131)
T ss_dssp             SSEEEEETGGGS--------------HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHTTS
T ss_pred             hceeeecccccC-------------CHHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhccc
Confidence            248999999998             445677777777643             366899999988888899999999998


Q ss_pred             c
Q 005179          450 Q  450 (710)
Q Consensus       450 ~  450 (710)
                      -
T Consensus       130 ~  130 (131)
T PF07726_consen  130 M  130 (131)
T ss_dssp             S
T ss_pred             c
Confidence            3

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.

>TIGR00368 Mg chelatase-related protein

Probab=98.77  E-value=2.6e-08  Score=111.46  Aligned_cols=150  Identities=19%  Similarity=0.226  Sum_probs=89.5

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe---------------
Q 005179          288 LIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL---------------  352 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l---------------  352 (710)
                      .|++++|++..++.+...+  ..+.+++|+||||+|||++++.++..+........+....+..+               
T Consensus       190 d~~dv~Gq~~~~~al~~aa--~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~~g~~~~~~~~~~~Pf  267 (499)
T TIGR00368       190 DLKDIKGQQHAKRALEIAA--AGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSLVGKLIDRKQIKQRPF  267 (499)
T ss_pred             CHHHhcCcHHHHhhhhhhc--cCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccchhhhccccccccCCc
Confidence            4567899987766555433  34578999999999999999999875532111111111111111               


Q ss_pred             ---e----hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---
Q 005179          353 ---D----MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---  422 (710)
Q Consensus       353 ---d----~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---  422 (710)
                         +    ...++.|..     ..+    -..+....+.+|||||++.+             ...+++.|.+.|+.+   
T Consensus       268 ~~p~~s~s~~~~~ggg~-----~~~----pG~i~lA~~GvLfLDEi~e~-------------~~~~~~~L~~~LE~~~v~  325 (499)
T TIGR00368       268 RSPHHSASKPALVGGGP-----IPL----PGEISLAHNGVLFLDELPEF-------------KRSVLDALREPIEDGSIS  325 (499)
T ss_pred             cccccccchhhhhCCcc-----ccc----hhhhhccCCCeEecCChhhC-------------CHHHHHHHHHHHHcCcEE
Confidence               0    001111100     000    01223345679999999998             556777777777644   


Q ss_pred             ------------CeEEEEccChHH---H--------------Hh-hhhccHHHHcccc-ceEecCCCHHH
Q 005179          423 ------------ELQCIASTTQDE---H--------------RT-QFEKDKALARRFQ-PVLISEPSQED  461 (710)
Q Consensus       423 ------------~v~vI~att~~~---~--------------~~-~~~~d~aL~~Rf~-~I~v~~Ps~~~  461 (710)
                                  ++++|+++|+.+   |              .. ...+...|++||+ .+.+++++.++
T Consensus       326 i~r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllDR~dl~~~~~~~~~~~  395 (499)
T TIGR00368       326 ISRASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLDRIDLSVEVPLLPPEK  395 (499)
T ss_pred             EEecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHhhCCEEEEEcCCCHHH
Confidence                        467899988642   1              11 1247889999998 67787766543

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

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

Probab=98.77  E-value=1.2e-08  Score=105.80  Aligned_cols=86  Identities=28%  Similarity=0.260  Sum_probs=52.3

Q ss_pred             HHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHH
Q 005179          596 DIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTEL  675 (710)
Q Consensus       596 di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~l  675 (710)
                      ++.+++++-.--.-.++.|+|+-++.+.++.|++          +|..++.+.. .++.-.||..|+|++||||||||+|
T Consensus       193 ~Lve~lerdIl~~np~ikW~DIagl~~AK~lL~E----------AVvlPi~mPe-~F~GirrPWkgvLm~GPPGTGKTlL  261 (491)
T KOG0738|consen  193 DLVEALERDILQRNPNIKWDDIAGLHEAKKLLKE----------AVVLPIWMPE-FFKGIRRPWKGVLMVGPPGTGKTLL  261 (491)
T ss_pred             HHHHHHHHHHhccCCCcChHhhcchHHHHHHHHH----------HHhhhhhhHH-HHhhcccccceeeeeCCCCCcHHHH
Confidence            6777775532222226888886665555554442          2222222222 1222346678999999999999999


Q ss_pred             HHHHHHHHcCCCCcceeeCCCC
Q 005179          676 AKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       676 AkaLA~~lfg~~~~li~~d~se  697 (710)
                      |||||.+ .|    -+.||.|.
T Consensus       262 AKAvATE-c~----tTFFNVSs  278 (491)
T KOG0738|consen  262 AKAVATE-CG----TTFFNVSS  278 (491)
T ss_pred             HHHHHHh-hc----CeEEEech
Confidence            9999988 22    45555443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=98.76  E-value=9e-09  Score=104.11  Aligned_cols=60  Identities=30%  Similarity=0.419  Sum_probs=51.4

Q ss_pred             ccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          612 ITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       612 ~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .+|.+..+-..+++     +.||+.++..+.+++.+ +.+        -++|||||||||||..|+++|++||+
T Consensus        24 ~swteKYrPkt~de-----~~gQe~vV~~L~~a~~~-~~l--------p~~LFyGPpGTGKTStalafar~L~~   83 (346)
T KOG0989|consen   24 RSWTEKYRPKTFDE-----LAGQEHVVQVLKNALLR-RIL--------PHYLFYGPPGTGKTSTALAFARALNC   83 (346)
T ss_pred             cchHHHhCCCcHHh-----hcchHHHHHHHHHHHhh-cCC--------ceEEeeCCCCCcHhHHHHHHHHHhcC
Confidence            45666666667777     99999999999999988 422        28999999999999999999999999

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.76  E-value=4.7e-08  Score=109.62  Aligned_cols=184  Identities=22%  Similarity=0.313  Sum_probs=111.8

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------  359 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------  359 (710)
                      .+..++|....+.++.+.+..  ....+++|+|++||||+++|+++.......       +.+++.+++..+..      
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~-------~~~~v~v~c~~~~~~~~~~~  209 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIAPSDITVLLLGESGTGKEVLARALHQLSDRK-------DKRFVAINCAAIPENLLESE  209 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhCCcC-------CCCeEEEECCCCChHHHHHH
Confidence            345688888888777766543  345789999999999999999998765322       34566666654321      


Q ss_pred             --ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------Ce
Q 005179          360 --GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------EL  424 (710)
Q Consensus       360 --g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v  424 (710)
                        |. ..|.+..........+....+.+|||||++.|             ....+..|..+++.+             ++
T Consensus       210 lfg~-~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l-------------~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~  275 (445)
T TIGR02915       210 LFGY-EKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDL-------------PLNLQAKLLRFLQERVIERLGGREEIPVDV  275 (445)
T ss_pred             hcCC-CCCCcCCCccCCCCceeECCCCEEEEechhhC-------------CHHHHHHHHHHHhhCeEEeCCCCceeeece
Confidence              10 00100000000011122345678999999999             455666666666533             46


Q ss_pred             EEEEccChHHHHh--hhhccHHHHccccceEecCCCHHHHH----HHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          425 QCIASTTQDEHRT--QFEKDKALARRFQPVLISEPSQEDAV----RILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       425 ~vI~att~~~~~~--~~~~d~aL~~Rf~~I~v~~Ps~~~~~----~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      ++|++|+.+-...  .-...+.|..||..+.|..|+..+|.    .+++.++.++...++   ..+++++++.+..+
T Consensus       276 rii~~~~~~l~~~~~~~~~~~~L~~~l~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  352 (445)
T TIGR02915       276 RIVCATNQDLKRMIAEGTFREDLFYRIAEISITIPPLRSRDGDAVLLANAFLERFARELKRKTKGFTDDALRALEAH  352 (445)
T ss_pred             EEEEecCCCHHHHHHcCCccHHHHHHhccceecCCCchhchhhHHHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHhC
Confidence            8888887653111  12345667788876777777655444    455556665554433   46899988877544

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).

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.75  E-value=1.5e-07  Score=94.28  Aligned_cols=110  Identities=18%  Similarity=0.188  Sum_probs=78.6

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-CeEEEEccChH--------HHHhhhhccHHHHccccceE
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-ELQCIASTTQD--------EHRTQFEKDKALARRFQPVL  453 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-~v~vI~att~~--------~~~~~~~~d~aL~~Rf~~I~  453 (710)
                      |.||||||+|.|             ..+....|...++.. .-++|.++|..        ....-+.+.+.|.+|+-.|.
T Consensus       297 PGVLFIDEVhML-------------DiEcFTyL~kalES~iaPivifAsNrG~~~irGt~d~~sPhGip~dllDRl~Iir  363 (456)
T KOG1942|consen  297 PGVLFIDEVHML-------------DIECFTYLHKALESPIAPIVIFASNRGMCTIRGTEDILSPHGIPPDLLDRLLIIR  363 (456)
T ss_pred             CcceEeeehhhh-------------hhHHHHHHHHHhcCCCCceEEEecCCcceeecCCcCCCCCCCCCHHHhhheeEEe
Confidence            789999999999             778888888888754 23455554432        11123457799999998899


Q ss_pred             ecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          454 ISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       454 v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      ..+++.++..+|++...+    ..++.++++++..++.+..+     ..-+.++.|+.-+.
T Consensus       364 t~~y~~~e~r~Ii~~Ra~----~E~l~~~e~a~~~l~~~gt~-----tsLRy~vqLl~p~~  415 (456)
T KOG1942|consen  364 TLPYDEEEIRQIIKIRAQ----VEGLQVEEEALDLLAEIGTS-----TSLRYAVQLLTPAS  415 (456)
T ss_pred             eccCCHHHHHHHHHHHHh----hhcceecHHHHHHHHhhccc-----hhHHHHHHhcCHHH
Confidence            999999999999987665    44789999999988876432     11234566655443

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

Probab=98.75  E-value=7.3e-09  Score=107.46  Aligned_cols=78  Identities=28%  Similarity=0.299  Sum_probs=54.6

Q ss_pred             hccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcc
Q 005179          611 QITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIH  690 (710)
Q Consensus       611 ~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~l  690 (710)
                      .++|+|++++..+++.|.+.|+=+      +..+-.+++.++   -+|..|+|||||||||||++|||+|++   .+.++
T Consensus        88 ~v~f~DIggLe~v~~~L~e~VilP------lr~pelF~~g~L---l~p~kGiLL~GPpG~GKTmlAKA~Ake---aga~f  155 (386)
T KOG0737|consen   88 GVSFDDIGGLEEVKDALQELVILP------LRRPELFAKGKL---LRPPKGILLYGPPGTGKTMLAKAIAKE---AGANF  155 (386)
T ss_pred             eeehhhccchHHHHHHHHHHHhhc------ccchhhhccccc---ccCCccceecCCCCchHHHHHHHHHHH---cCCCc
Confidence            467888777777777666444322      111112223333   335569999999999999999999999   77789


Q ss_pred             eeeCCCCCCC
Q 005179          691 YLFFPSPFNS  700 (710)
Q Consensus       691 i~~d~se~~~  700 (710)
                      |-+.||...+
T Consensus       156 Inv~~s~lt~  165 (386)
T KOG0737|consen  156 INVSVSNLTS  165 (386)
T ss_pred             ceeeccccch
Confidence            9999997654

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=98.75  E-value=1.8e-08  Score=109.63  Aligned_cols=76  Identities=29%  Similarity=0.317  Sum_probs=57.5

Q ss_pred             HHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCC----CC-----CCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcc
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKD----PN-----RPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIH  690 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~----p~-----rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~l  690 (710)
                      ..++++.|.++|+||++|++.++.++.....+++.    +.     .+.+++||+||||||||++|++||+.+   ...+
T Consensus        68 p~~i~~~L~~~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l---~~pf  144 (413)
T TIGR00382        68 PKEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARIL---NVPF  144 (413)
T ss_pred             HHHHHHHhcceecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhc---CCCe
Confidence            35788899999999999999999988544333322    11     113689999999999999999999886   2356


Q ss_pred             eeeCCCCC
Q 005179          691 YLFFPSPF  698 (710)
Q Consensus       691 i~~d~se~  698 (710)
                      +.+|++.+
T Consensus       145 ~~~da~~L  152 (413)
T TIGR00382       145 AIADATTL  152 (413)
T ss_pred             EEechhhc
Confidence            66666654

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.

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

Probab=98.73  E-value=9.7e-09  Score=116.77  Aligned_cols=62  Identities=35%  Similarity=0.452  Sum_probs=53.4

Q ss_pred             ccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |.|.++|++.|.+.|       +|.+.|.+.|    .|+||+||||||||+||||+|.+   .+-+++.+..|||-
T Consensus       313 VAG~deAK~El~E~V~fLKNP~~Y~~lGAKiP----kGvLL~GPPGTGKTLLAKAiAGE---AgVPF~svSGSEFv  381 (774)
T KOG0731|consen  313 VAGVDEAKEELMEFVKFLKNPEQYQELGAKIP----KGVLLVGPPGTGKTLLAKAIAGE---AGVPFFSVSGSEFV  381 (774)
T ss_pred             ccCcHHHHHHHHHHHHHhcCHHHHHHcCCcCc----CceEEECCCCCcHHHHHHHHhcc---cCCceeeechHHHH
Confidence            777777777777666       6778888877    79999999999999999999998   88899999999983

>PRK06526 transposase; Provisional

Probab=98.72  E-value=2.3e-08  Score=102.65  Aligned_cols=105  Identities=28%  Similarity=0.396  Sum_probs=60.4

Q ss_pred             CCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccC
Q 005179          267 RTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS  346 (710)
Q Consensus       267 ~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~  346 (710)
                      +|...+|+.|.++....         + ....+..+...-....+.|++|+||||||||+++.+|+..+...       +
T Consensus        64 ~p~~~~le~fd~~~~~~---------~-~~~~~~~l~~~~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~-------g  126 (254)
T PRK06526         64 FPARKSLEEFDFDHQRS---------L-KRDTIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQA-------G  126 (254)
T ss_pred             CCCCCChhhccCccCCC---------c-chHHHHHHhcCchhhcCceEEEEeCCCCchHHHHHHHHHHHHHC-------C
Confidence            44456788776553211         1 11233333322122356789999999999999999999988653       4


Q ss_pred             ceEEEeehhhhhhc---cccCccHHHHHHHHHHHHHhcCCeEEEEccchhh
Q 005179          347 KRIMSLDMGLLMAG---AKERGELEARVTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       347 ~~v~~ld~~~l~~g---~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                      ..+.......++..   ....+...    ..+..+.  ...+|+|||++.+
T Consensus       127 ~~v~f~t~~~l~~~l~~~~~~~~~~----~~l~~l~--~~dlLIIDD~g~~  171 (254)
T PRK06526        127 HRVLFATAAQWVARLAAAHHAGRLQ----AELVKLG--RYPLLIVDEVGYI  171 (254)
T ss_pred             CchhhhhHHHHHHHHHHHHhcCcHH----HHHHHhc--cCCEEEEcccccC
Confidence            45555555444321   11122222    2233332  3469999999987

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.72  E-value=1.6e-07  Score=99.54  Aligned_cols=82  Identities=16%  Similarity=0.159  Sum_probs=54.2

Q ss_pred             hHhHHHhhcccccCC-------------CeEEEEccChHHHHhh--hhccHHHHccccceEecCCC-HHHHHHHHHHHHH
Q 005179          408 GLDISNLLKPSLGRG-------------ELQCIASTTQDEHRTQ--FEKDKALARRFQPVLISEPS-QEDAVRILLGLRE  471 (710)
Q Consensus       408 ~~~~~~~L~~~l~~~-------------~v~vI~att~~~~~~~--~~~d~aL~~Rf~~I~v~~Ps-~~~~~~IL~~l~~  471 (710)
                      ..++.+.|+..++++             +.++|+++|+.+|...  .....+|.+||..|.++.|. ..+-.+|.+..+.
T Consensus       249 ~~~~l~~LL~~~qE~~v~~~~~~~~~~~d~liia~sNe~e~~~~~~~k~~eaf~dR~~~i~vpY~l~~~~E~~Iy~k~~~  328 (361)
T smart00763      249 DIKFLHPLLTATQEGNIKGTGGFAMIPIDGLIIAHSNESEWQRFKSNKKNEALLDRIIKVKVPYCLRVSEEAQIYEKLLR  328 (361)
T ss_pred             CHHHHHHHhhhhhcceEecCCcccccccceEEEEeCCHHHHhhhhccccchhhhhceEEEeCCCcCCHHHHHHHHHHHhc
Confidence            455666666555533             2457899999998765  34579999999999998874 6666777776655


Q ss_pred             HHHhhcCCCCCHHHHHHHH
Q 005179          472 KYEAHHNCKFTLEAINAAV  490 (710)
Q Consensus       472 ~~~~~~~~~i~~~~l~~l~  490 (710)
                      .-. ..+..+.+.+++.++
T Consensus       329 ~s~-~~~~~~aP~~le~aa  346 (361)
T smart00763      329 NSD-LTEAHIAPHTLEMAA  346 (361)
T ss_pred             cCc-CcccccCchHHHHHH
Confidence            221 123556666655544

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=98.72  E-value=1.6e-07  Score=99.11  Aligned_cols=148  Identities=15%  Similarity=0.124  Sum_probs=98.7

Q ss_pred             HHHHHHHHHHHcCCCC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------cCceEEEeehhhhhhccc
Q 005179          297 TEIQRIIQILCRRTKN-NPILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------LSKRIMSLDMGLLMAGAK  362 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------~~~~v~~ld~~~l~~g~~  362 (710)
                      ...+++...+.+.+.. .+||+||.|+||+++|+.+|+.+.+.+.+...             ....++.+....  .| +
T Consensus        10 ~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~--~~-~   86 (319)
T PRK06090         10 PVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEK--EG-K   86 (319)
T ss_pred             HHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCc--CC-C
Confidence            3556677766665544 47899999999999999999998775422100             011222222110  00 1


Q ss_pred             cCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHH
Q 005179          363 ERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHR  436 (710)
Q Consensus       363 ~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~  436 (710)
                      ..  ..+.++.+.+.+..    ++.-|++||++|.|             ....+|.|+..||+  .+..+|..|+..+  
T Consensus        87 ~I--~vdqiR~l~~~~~~~~~~~~~kV~iI~~ae~m-------------~~~AaNaLLKtLEEPp~~t~fiL~t~~~~--  149 (319)
T PRK06090         87 SI--TVEQIRQCNRLAQESSQLNGYRLFVIEPADAM-------------NESASNALLKTLEEPAPNCLFLLVTHNQK--  149 (319)
T ss_pred             cC--CHHHHHHHHHHHhhCcccCCceEEEecchhhh-------------CHHHHHHHHHHhcCCCCCeEEEEEECChh--
Confidence            11  12334555544432    34569999999999             56788999988986  3566666666654  


Q ss_pred             hhhhccHHHHccccceEecCCCHHHHHHHHH
Q 005179          437 TQFEKDKALARRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       437 ~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                         .+-|++++|++.+.|++|+.++..+.|.
T Consensus       150 ---~lLpTI~SRCq~~~~~~~~~~~~~~~L~  177 (319)
T PRK06090        150 ---RLLPTIVSRCQQWVVTPPSTAQAMQWLK  177 (319)
T ss_pred             ---hChHHHHhcceeEeCCCCCHHHHHHHHH
Confidence               6789999999999999999998777665

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.70  E-value=1.2e-06  Score=93.57  Aligned_cols=205  Identities=17%  Similarity=0.154  Sum_probs=121.2

Q ss_pred             CCcccCHHHHHHHHHHH----HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------
Q 005179          290 DPVIGRETEIQRIIQIL----CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L----~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------  359 (710)
                      ..+.||+.++..+.+++    .......+.+.|-||+|||.+...+.......     .....++++++..+..      
T Consensus       150 ~~l~gRe~e~~~v~~F~~~hle~~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~-----~~~~~~v~inc~sl~~~~aiF~  224 (529)
T KOG2227|consen  150 GTLKGRELEMDIVREFFSLHLELNTSGSLYVSGQPGTGKTALLSRVLDSLSKS-----SKSPVTVYINCTSLTEASAIFK  224 (529)
T ss_pred             CCccchHHHHHHHHHHHHhhhhcccCcceEeeCCCCcchHHHHHHHHHhhhhh-----cccceeEEEeeccccchHHHHH
Confidence            45899999998887764    45677889999999999999998877665332     1222344555443221      


Q ss_pred             --------ccccCccHHHHHHHHHHHHHhcC-CeEEEEccchhhhhCCCCCCCCCCChHhHHH-hhcccccCCCeEEEEc
Q 005179          360 --------GAKERGELEARVTTLISEIQKSG-DVILFIDEVHTLIGSGTVGRGNKGTGLDISN-LLKPSLGRGELQCIAS  429 (710)
Q Consensus       360 --------g~~~~g~~e~~l~~~~~~~~~~~-~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~-~L~~~l~~~~v~vI~a  429 (710)
                              +....+...+.+..+-....... ..|+++||+|.|...+..         .+.. +..+.+-...+++||.
T Consensus       225 kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~~~---------vLy~lFewp~lp~sr~iLiGi  295 (529)
T KOG2227|consen  225 KIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRSQT---------VLYTLFEWPKLPNSRIILIGI  295 (529)
T ss_pred             HHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcccc---------eeeeehhcccCCcceeeeeee
Confidence                    11111222222233333333333 789999999999633211         1111 1134455677888888


Q ss_pred             cChHHHHhhhhccHHHHcccc----ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALARRFQ----PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~----~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      .|.-+...  ..-+.|..|..    .+.|++++.+|..+||+..+....   -..+-+-+++.++.....--+   --++
T Consensus       296 ANslDlTd--R~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~---t~~~~~~Aie~~ArKvaa~SG---DlRk  367 (529)
T KOG2227|consen  296 ANSLDLTD--RFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEES---TSIFLNAAIELCARKVAAPSG---DLRK  367 (529)
T ss_pred             hhhhhHHH--HHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhccc---ccccchHHHHHHHHHhccCch---hHHH
Confidence            88755222  22355555543    689999999999999997665432   123333445554444333222   2357


Q ss_pred             HHHHHHHHHhh
Q 005179          506 AIDLVDEAGSR  516 (710)
Q Consensus       506 ai~ll~~a~~~  516 (710)
                      +++++..|...
T Consensus       368 aLdv~R~aiEI  378 (529)
T KOG2227|consen  368 ALDVCRRAIEI  378 (529)
T ss_pred             HHHHHHHHHHH
Confidence            77777777643

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.70  E-value=8.5e-09  Score=96.09  Aligned_cols=130  Identities=22%  Similarity=0.334  Sum_probs=78.8

Q ss_pred             ccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHH
Q 005179          293 IGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEAR  370 (710)
Q Consensus       293 iGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~  370 (710)
                      ||....++++.+.+.+  ....+++|+|++||||+++|+.|...-....       ..++.+++..+.            
T Consensus         1 vG~S~~~~~l~~~l~~~a~~~~pvli~GE~GtGK~~~A~~lh~~~~~~~-------~~~~~~~~~~~~------------   61 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAKSSSPVLITGEPGTGKSLLARALHRYSGRAN-------GPFIVIDCASLP------------   61 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHCSSS-EEEECCTTSSHHHHHHCCHHTTTTCC-------S-CCCCCHHCTC------------
T ss_pred             CCCCHHHHHHHHHHHHHhCCCCcEEEEcCCCCCHHHHHHHHHhhcCccC-------CCeEEechhhCc------------
Confidence            5677777777776554  5667899999999999999999987653221       122223332211            


Q ss_pred             HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc---CCCeEEEEccChHHH--HhhhhccHHH
Q 005179          371 VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG---RGELQCIASTTQDEH--RTQFEKDKAL  445 (710)
Q Consensus       371 l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~---~~~v~vI~att~~~~--~~~~~~d~aL  445 (710)
                       .++++.   ..+..|||+|++.|             +.+.+..|..++.   +.++++|++++.+-.  ...-.+++.|
T Consensus        62 -~~~l~~---a~~gtL~l~~i~~L-------------~~~~Q~~L~~~l~~~~~~~~RlI~ss~~~l~~l~~~~~~~~~L  124 (138)
T PF14532_consen   62 -AELLEQ---AKGGTLYLKNIDRL-------------SPEAQRRLLDLLKRQERSNVRLIASSSQDLEELVEEGRFSPDL  124 (138)
T ss_dssp             -HHHHHH---CTTSEEEEECGCCS--------------HHHHHHHHHHHHHCTTTTSEEEEEECC-CCCHHHHSTHHHHH
T ss_pred             -HHHHHH---cCCCEEEECChHHC-------------CHHHHHHHHHHHHhcCCCCeEEEEEeCCCHHHHhhccchhHHH
Confidence             223332   35679999999999             4455555555554   456788887665421  1223467888


Q ss_pred             HccccceEecCCC
Q 005179          446 ARRFQPVLISEPS  458 (710)
Q Consensus       446 ~~Rf~~I~v~~Ps  458 (710)
                      ..||..+.+..|+
T Consensus       125 ~~~l~~~~i~lPp  137 (138)
T PF14532_consen  125 YYRLSQLEIHLPP  137 (138)
T ss_dssp             HHHCSTCEEEE--
T ss_pred             HHHhCCCEEeCCC
Confidence            8899755555553

>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes

Probab=98.70  E-value=2.4e-08  Score=76.48  Aligned_cols=51  Identities=22%  Similarity=0.334  Sum_probs=46.4

Q ss_pred             HHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhh
Q 005179           96 SQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWH  146 (710)
Q Consensus        96 A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~  146 (710)
                      |+++|++++|.+|++||||+||+.++++  .++|..+|+|++.+++++.+.++
T Consensus         1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~lg   53 (53)
T PF02861_consen    1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKALG   53 (53)
T ss_dssp             HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHHC
T ss_pred             CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence            7899999999999999999999999877  88999999999999999987754

The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=98.69  E-value=9.2e-08  Score=88.05  Aligned_cols=126  Identities=22%  Similarity=0.305  Sum_probs=72.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------------ccccCccHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------------GAKERGELEARVTTLISEI  378 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------------g~~~~g~~e~~l~~~~~~~  378 (710)
                      +.+++|+||||||||++++.++..+....       ..++.++......            ..............++..+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   74 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPG-------GGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALA   74 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCC-------CCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHH
Confidence            46789999999999999999999884321       2355554433211            1112223344556667777


Q ss_pred             HhcCCeEEEEccchhhhhCCCCCCCCCCChHhHH-----HhhcccccCCCeEEEEccChHHHHhhhhccHHHHcccc-ce
Q 005179          379 QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDIS-----NLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ-PV  452 (710)
Q Consensus       379 ~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~-----~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I  452 (710)
                      ....+.+++|||++.+......        ....     .............+|++++..    ....+..+..|++ .+
T Consensus        75 ~~~~~~viiiDei~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~----~~~~~~~~~~~~~~~~  142 (148)
T smart00382       75 RKLKPDVLILDEITSLLDAEQE--------ALLLLLEELRLLLLLKSEKNLTVILTTNDE----KDLGPALLRRRFDRRI  142 (148)
T ss_pred             HhcCCCEEEEECCcccCCHHHH--------HHHHhhhhhHHHHHHHhcCCCEEEEEeCCC----ccCchhhhhhccceEE
Confidence            7666689999999998432110        0000     011222334567788888851    1234455555665 44


Q ss_pred             Eec
Q 005179          453 LIS  455 (710)
Q Consensus       453 ~v~  455 (710)
                      .+.
T Consensus       143 ~~~  145 (148)
T smart00382      143 VLL  145 (148)
T ss_pred             Eec
Confidence            443

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.

>CHL00181 cbbX CbbX; Provisional

Probab=98.69  E-value=3.7e-08  Score=103.10  Aligned_cols=66  Identities=24%  Similarity=0.386  Sum_probs=52.4

Q ss_pred             HHHHHHHHhhCcccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          619 LLVGLEEQLKKRVIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       619 ~l~~l~~~L~~~v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .+.++.+.|.+.++|++++++.|...+       .+.+.|+..|..+ -++||+||||||||++|+++|+.++.
T Consensus        13 ~~~~~~~~l~~~l~Gl~~vK~~i~e~~~~~~~~~~~~~~g~~~~~~~-~~ill~G~pGtGKT~lAr~la~~~~~   85 (287)
T CHL00181         13 QIQEVLDILDEELVGLAPVKTRIREIAALLLIDRLRKNLGLTSSNPG-LHMSFTGSPGTGKTTVALKMADILYK   85 (287)
T ss_pred             CHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCC-ceEEEECCCCCCHHHHHHHHHHHHHH
Confidence            456677888888999999999887654       2345687766443 37999999999999999999999875

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.68  E-value=2.9e-08  Score=96.47  Aligned_cols=84  Identities=20%  Similarity=0.365  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc---ccCccHHHHHHHH
Q 005179          298 EIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA---KERGELEARVTTL  374 (710)
Q Consensus       298 ~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~---~~~g~~e~~l~~~  374 (710)
                      .+..+...-....+.|++|+|++|||||+||.++++++...       +..+..++..+++..-   ...+..+    ..
T Consensus        34 ~~~~l~~~~~~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~-------g~~v~f~~~~~L~~~l~~~~~~~~~~----~~  102 (178)
T PF01695_consen   34 QIAQLAALEFIENGENLILYGPPGTGKTHLAVAIANEAIRK-------GYSVLFITASDLLDELKQSRSDGSYE----EL  102 (178)
T ss_dssp             HHHHHHHH-S-SC--EEEEEESTTSSHHHHHHHHHHHHHHT-------T--EEEEEHHHHHHHHHCCHCCTTHC----HH
T ss_pred             HHHHHhcCCCcccCeEEEEEhhHhHHHHHHHHHHHHHhccC-------CcceeEeecCceeccccccccccchh----hh
Confidence            44444433333467899999999999999999999988653       6778888887776322   1222332    33


Q ss_pred             HHHHHhcCCeEEEEccchhh
Q 005179          375 ISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       375 ~~~~~~~~~~IL~IDEid~l  394 (710)
                      ++.+...  .+|+|||+...
T Consensus       103 ~~~l~~~--dlLilDDlG~~  120 (178)
T PF01695_consen  103 LKRLKRV--DLLILDDLGYE  120 (178)
T ss_dssp             HHHHHTS--SCEEEETCTSS
T ss_pred             cCccccc--cEeccccccee
Confidence            4444443  48999999654

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.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.67  E-value=4e-08  Score=110.95  Aligned_cols=183  Identities=23%  Similarity=0.341  Sum_probs=110.6

Q ss_pred             CCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-------
Q 005179          289 IDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-------  359 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-------  359 (710)
                      +..++|....+.++.+.+.+  ....+++|+|++|||||++|+++.......       +.+++.+||..+..       
T Consensus       137 ~~~lig~s~~~~~l~~~~~~~~~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~-------~~~~i~i~c~~~~~~~~~~~l  209 (469)
T PRK10923        137 TTDIIGEAPAMQDVFRIIGRLSRSSISVLINGESGTGKELVAHALHRHSPRA-------KAPFIALNMAAIPKDLIESEL  209 (469)
T ss_pred             cccceecCHHHHHHHHHHHHHhccCCeEEEEeCCCCcHHHHHHHHHhcCCCC-------CCCeEeeeCCCCCHHHHHHHh
Confidence            45689988888777766543  345679999999999999999998865322       44566666654421       


Q ss_pred             -ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeE
Q 005179          360 -GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQ  425 (710)
Q Consensus       360 -g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~  425 (710)
                       |. ..|.+..........+....+..|||||++.|             ..+.+..|..+++.+             +++
T Consensus       210 fg~-~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l-------------~~~~q~~L~~~l~~~~~~~~~~~~~~~~~~r  275 (469)
T PRK10923        210 FGH-EKGAFTGANTIRQGRFEQADGGTLFLDEIGDM-------------PLDVQTRLLRVLADGQFYRVGGYAPVKVDVR  275 (469)
T ss_pred             cCC-CCCCCCCCCcCCCCCeeECCCCEEEEeccccC-------------CHHHHHHHHHHHhcCcEEeCCCCCeEEeeEE
Confidence             10 00000000000000112334568999999999             455666666666543             357


Q ss_pred             EEEccChHHHH--hhhhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          426 CIASTTQDEHR--TQFEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       426 vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      +|++|+.+-..  ..-...+.|..||..+.+..|+.    ++...++..++.++...++   ..+++++++.+..+
T Consensus       276 ii~~~~~~l~~~~~~~~~~~~L~~~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  351 (469)
T PRK10923        276 IIAATHQNLEQRVQEGKFREDLFHRLNVIRVHLPPLRERREDIPRLARHFLQVAARELGVEAKLLHPETEAALTRL  351 (469)
T ss_pred             EEEeCCCCHHHHHHcCCchHHHHHHhcceeecCCCcccchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhC
Confidence            88887764311  11124577888997666666663    4555566666666554443   25788888776543

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=98.67  E-value=4.2e-08  Score=101.80  Aligned_cols=67  Identities=28%  Similarity=0.350  Sum_probs=49.2

Q ss_pred             ccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC----CCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS----VRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~----~~~li~~d~se~  698 (710)
                      ++|++++++.|...+       .+.+.|+..+.++ .++||+||||||||++|+++|+.++..    ...++.++.+++
T Consensus         8 ~~Gl~~vk~~i~~~~~~~~~~~~~~~~g~~~~~~~-~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~~~l   85 (261)
T TIGR02881         8 MVGLDEVKALIKEIYAWIQINEKRKEEGLKTSKQV-LHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVERADL   85 (261)
T ss_pred             hcChHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCc-ceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecHHHh
Confidence            889999998887543       3345677766554 489999999999999999999998642    234555555444

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.

>PF13173 AAA_14: AAA domain

Probab=98.62  E-value=8.2e-08  Score=88.23  Aligned_cols=123  Identities=23%  Similarity=0.302  Sum_probs=74.9

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEV  391 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEi  391 (710)
                      ..++|+||.||||||+++.+++.+.        ....++.+++.+.......  ...  +.+.+.+....++.+|||||+
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~--------~~~~~~yi~~~~~~~~~~~--~~~--~~~~~~~~~~~~~~~i~iDEi   70 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLL--------PPENILYINFDDPRDRRLA--DPD--LLEYFLELIKPGKKYIFIDEI   70 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhc--------ccccceeeccCCHHHHHHh--hhh--hHHHHHHhhccCCcEEEEehh
Confidence            4578999999999999999998873        1355666665544321100  000  222222222235679999999


Q ss_pred             hhhhhCCCCCCCCCCChHhHHHhhcccccCC-CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHH
Q 005179          392 HTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQED  461 (710)
Q Consensus       392 d~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~  461 (710)
                      +.+           .   +....++.+...+ +..+|.|++..... ..+....+..|...+.+.|++..|
T Consensus        71 q~~-----------~---~~~~~lk~l~d~~~~~~ii~tgS~~~~l-~~~~~~~l~gr~~~~~l~Plsf~E  126 (128)
T PF13173_consen   71 QYL-----------P---DWEDALKFLVDNGPNIKIILTGSSSSLL-SKDIAESLAGRVIEIELYPLSFRE  126 (128)
T ss_pred             hhh-----------c---cHHHHHHHHHHhccCceEEEEccchHHH-hhcccccCCCeEEEEEECCCCHHH
Confidence            998           1   2344555555544 55666655544311 113456677788889999988765

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

Probab=98.62  E-value=3.7e-08  Score=98.85  Aligned_cols=58  Identities=29%  Similarity=0.431  Sum_probs=41.4

Q ss_pred             hhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHH----HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          610 QQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAV----KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       610 ~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i----~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .++.|++..              |.+.|++++..++    ++...+ ....+|..++||||||||||+.||||+|.+
T Consensus       128 PNVkWsDVA--------------GLE~AKeALKEAVILPIKFPqlF-tGkR~PwrgiLLyGPPGTGKSYLAKAVATE  189 (439)
T KOG0739|consen  128 PNVKWSDVA--------------GLEGAKEALKEAVILPIKFPQLF-TGKRKPWRGILLYGPPGTGKSYLAKAVATE  189 (439)
T ss_pred             CCCchhhhc--------------cchhHHHHHHhheeecccchhhh-cCCCCcceeEEEeCCCCCcHHHHHHHHHhh
Confidence            467788754              4455555555444    444432 233567889999999999999999999988

>PRK07952 DNA replication protein DnaC; Validated

Probab=98.62  E-value=1.2e-07  Score=96.58  Aligned_cols=72  Identities=21%  Similarity=0.396  Sum_probs=49.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccH---HHHHHHHHHHHHhcCCeEEEE
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGEL---EARVTTLISEIQKSGDVILFI  388 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~---e~~l~~~~~~~~~~~~~IL~I  388 (710)
                      .+++|+|+||||||+|+.+++..+...       +..++.++...+...-+  +.+   ......+++.+..  ..+|+|
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~-------g~~v~~it~~~l~~~l~--~~~~~~~~~~~~~l~~l~~--~dlLvI  168 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLR-------GKSVLIITVADIMSAMK--DTFSNSETSEEQLLNDLSN--VDLLVI  168 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEEHHHHHHHHH--HHHhhccccHHHHHHHhcc--CCEEEE
Confidence            579999999999999999999998553       56777777777653211  111   0112334444443  459999


Q ss_pred             ccchhh
Q 005179          389 DEVHTL  394 (710)
Q Consensus       389 DEid~l  394 (710)
                      ||++..
T Consensus       169 DDig~~  174 (244)
T PRK07952        169 DEIGVQ  174 (244)
T ss_pred             eCCCCC
Confidence            999876

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.62  E-value=3.3e-07  Score=102.16  Aligned_cols=149  Identities=21%  Similarity=0.286  Sum_probs=89.8

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe---------------
Q 005179          288 LIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL---------------  352 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l---------------  352 (710)
                      .|..++|+...++.+.  +....+.+++|+||||+|||++++.++..+........+-...++++               
T Consensus       189 d~~~v~Gq~~~~~al~--laa~~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~g~~~~~~~~~~rPf  266 (506)
T PRK09862        189 DLSDVIGQEQGKRGLE--ITAAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQWRQRPF  266 (506)
T ss_pred             CeEEEECcHHHHhhhh--eeccCCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhhccccccCCcCCCCc
Confidence            4556788876665543  23345678999999999999999999866532111111111111111               


Q ss_pred             -------ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---
Q 005179          353 -------DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---  422 (710)
Q Consensus       353 -------d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---  422 (710)
                             ....++.|...       .  --..+....+.+|||||++.+             ....++.|.+.|+.+   
T Consensus       267 r~ph~~~s~~~l~GGg~~-------~--~pG~l~~A~gGvLfLDEi~e~-------------~~~~~~~L~~~LE~g~v~  324 (506)
T PRK09862        267 RSPHHSASLTAMVGGGAI-------P--GPGEISLAHNGVLFLDELPEF-------------ERRTLDALREPIESGQIH  324 (506)
T ss_pred             cCCCccchHHHHhCCCce-------e--hhhHhhhccCCEEecCCchhC-------------CHHHHHHHHHHHHcCcEE
Confidence                   11112211100       0  001234455779999999887             556777777766544   


Q ss_pred             ------------CeEEEEccChHHHHh---------------h-hhccHHHHcccc-ceEecCCCHH
Q 005179          423 ------------ELQCIASTTQDEHRT---------------Q-FEKDKALARRFQ-PVLISEPSQE  460 (710)
Q Consensus       423 ------------~v~vI~att~~~~~~---------------~-~~~d~aL~~Rf~-~I~v~~Ps~~  460 (710)
                                  ++++|+++|+.+...               | -.++..+.+||+ .|.+++|+.+
T Consensus       325 I~r~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLDRfdL~v~v~~~~~~  391 (506)
T PRK09862        325 LSRTRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLDRFDLSLEIPLPPPG  391 (506)
T ss_pred             EecCCcceeccCCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHhhccEEEEeCCCCHH
Confidence                        367899998764111               1 246789999998 7888888655

>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=98.61  E-value=1.6e-07  Score=97.51  Aligned_cols=148  Identities=18%  Similarity=0.284  Sum_probs=88.3

Q ss_pred             HHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHH---
Q 005179          302 IIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEI---  378 (710)
Q Consensus       302 l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~---  378 (710)
                      +++.+.. .+.++||+||+|||||++++.+.+.+...       ..-+..+.++....        ...+..+++..   
T Consensus        25 ll~~l~~-~~~pvLl~G~~GtGKT~li~~~l~~l~~~-------~~~~~~~~~s~~Tt--------s~~~q~~ie~~l~k   88 (272)
T PF12775_consen   25 LLDLLLS-NGRPVLLVGPSGTGKTSLIQNFLSSLDSD-------KYLVITINFSAQTT--------SNQLQKIIESKLEK   88 (272)
T ss_dssp             HHHHHHH-CTEEEEEESSTTSSHHHHHHHHHHCSTTC-------CEEEEEEES-TTHH--------HHHHHHCCCTTECE
T ss_pred             HHHHHHH-cCCcEEEECCCCCchhHHHHhhhccCCcc-------ccceeEeeccCCCC--------HHHHHHHHhhcEEc
Confidence            4444443 46789999999999999999876554211       11233333332211        11122222111   


Q ss_pred             --------HhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------------CeEEEEccChHHHH
Q 005179          379 --------QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------------ELQCIASTTQDEHR  436 (710)
Q Consensus       379 --------~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------------~v~vI~att~~~~~  436 (710)
                              ..++..|+||||++.-...       ..+.....++|+++++.+              ++.+|+++++..  
T Consensus        89 ~~~~~~gP~~~k~lv~fiDDlN~p~~d-------~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~--  159 (272)
T PF12775_consen   89 RRGRVYGPPGGKKLVLFIDDLNMPQPD-------KYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTG--  159 (272)
T ss_dssp             CTTEEEEEESSSEEEEEEETTT-S----------TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTT--
T ss_pred             CCCCCCCCCCCcEEEEEecccCCCCCC-------CCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCC--
Confidence                    0134679999999877432       233445677888777642              567889888743  


Q ss_pred             hhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHH
Q 005179          437 TQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYE  474 (710)
Q Consensus       437 ~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~  474 (710)
                      +...+++.|.|.|..+.++.|+.+....|+..++..+.
T Consensus       160 Gr~~is~R~~r~f~i~~~~~p~~~sl~~If~~il~~~l  197 (272)
T PF12775_consen  160 GRNPISPRFLRHFNILNIPYPSDESLNTIFSSILQSHL  197 (272)
T ss_dssp             T--SHHHHHHTTEEEEE----TCCHHHHHHHHHHHHHT
T ss_pred             CCCCCChHHhhheEEEEecCCChHHHHHHHHHHHhhhc
Confidence            33457899999999999999999999999999887653

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=98.60  E-value=9.1e-07  Score=101.54  Aligned_cols=123  Identities=21%  Similarity=0.266  Sum_probs=77.4

Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------------------CeEEEEccChHHHHhh
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------------------ELQCIASTTQDEHRTQ  438 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------------------~v~vI~att~~~~~~~  438 (710)
                      .+.+|||||++.|             ....+..|+..|+.+                       ++++|++++++.   .
T Consensus       226 nGGtL~LDei~~L-------------~~~~q~~Llr~L~~~~i~i~g~~e~~~~~~~~~~~ip~dvrvI~a~~~~l---l  289 (637)
T PRK13765        226 HKGVLFIDEINTL-------------DLESQQSLLTAMQEKKFPITGQSERSSGAMVRTEPVPCDFIMVAAGNLDA---L  289 (637)
T ss_pred             CCcEEEEeChHhC-------------CHHHHHHHHHHHHhCCEEecccccccccccCCCcceeeeeEEEEecCcCH---H
Confidence            3467788888777             334555565555322                       457888888854   3


Q ss_pred             hhccHHHHccccc----eEecC--C-CHHHHHHHHHHHHHHHHhh-cCCCCCHHHHHHHHHHhhhhhcCCC---C-cchH
Q 005179          439 FEKDKALARRFQP----VLISE--P-SQEDAVRILLGLREKYEAH-HNCKFTLEAINAAVHLSARYISDRY---L-PDKA  506 (710)
Q Consensus       439 ~~~d~aL~~Rf~~----I~v~~--P-s~~~~~~IL~~l~~~~~~~-~~~~i~~~~l~~l~~ls~~~i~~r~---~-p~~a  506 (710)
                      ..+++.|..||..    +.+..  + +.+.+..+++.+.+....+ .-..++++++..+++.+.|....+.   + ..+.
T Consensus       290 ~~~dpdL~~rfk~~~v~v~f~~~~~d~~e~~~~~~~~iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l  369 (637)
T PRK13765        290 ENMHPALRSRIKGYGYEVYMRDTMEDTPENRRKLVRFVAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDL  369 (637)
T ss_pred             HhhhHHHHHHhccCeEEEEcccccCCCHHHHHHHHHHHHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHH
Confidence            3568999999852    44432  1 2455555555444444332 2347999999999999988877655   2 3466


Q ss_pred             HHHHHHHHhhhhhh
Q 005179          507 IDLVDEAGSRAHIE  520 (710)
Q Consensus       507 i~ll~~a~~~~~~~  520 (710)
                      .+++..|...++..
T Consensus       370 ~~l~r~a~~~a~~~  383 (637)
T PRK13765        370 GGLVRVAGDIARSE  383 (637)
T ss_pred             HHHHHHHHHHHHhh
Confidence            67787776555443

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

Probab=98.59  E-value=4.3e-08  Score=96.75  Aligned_cols=61  Identities=26%  Similarity=0.409  Sum_probs=50.8

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|..+-++.+...+        ++.+.|+.+|    .|+|+|||||||||++|+|+|+-   ++.-+||+-.||+
T Consensus       179 vggckeqieklrevve~pll~perfv~lgidpp----kgvllygppgtgktl~aravanr---tdacfirvigsel  247 (435)
T KOG0729|consen  179 VGGCKEQIEKLREVVELPLLHPERFVNLGIDPP----KGVLLYGPPGTGKTLCARAVANR---TDACFIRVIGSEL  247 (435)
T ss_pred             ccchHHHHHHHHHHHhccccCHHHHhhcCCCCC----CceEEeCCCCCchhHHHHHHhcc---cCceEEeehhHHH
Confidence            566666666666555        6778898877    79999999999999999999988   8888999999987

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=98.59  E-value=9.4e-08  Score=100.11  Aligned_cols=80  Identities=25%  Similarity=0.301  Sum_probs=58.4

Q ss_pred             HHHHHHHHHhhCcccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC---
Q 005179          618 MLLVGLEEQLKKRVIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV---  687 (710)
Q Consensus       618 ~~l~~l~~~L~~~v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~---  687 (710)
                      ..+.++.+.|...++|++++++.|...+       .+.+.|+..+ .|..++||+||||||||++|+++|+.+....   
T Consensus        11 ~~~~~~~~~l~~~l~Gl~~vk~~i~e~~~~~~~~~~r~~~g~~~~-~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~   89 (284)
T TIGR02880        11 SGITEVLDQLDRELIGLKPVKTRIREIAALLLVERLRQRLGLASA-APTLHMSFTGNPGTGKTTVALRMAQILHRLGYVR   89 (284)
T ss_pred             ccHHHHHHHHHHhccCHHHHHHHHHHHHHHHHHHHHHHHhCCCcC-CCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcc
Confidence            3456677777778999999999987654       2345677643 3445899999999999999999999986522   


Q ss_pred             -CcceeeCCCCC
Q 005179          688 -RIHYLFFPSPF  698 (710)
Q Consensus       688 -~~li~~d~se~  698 (710)
                       ..++.++.+++
T Consensus        90 ~~~~v~v~~~~l  101 (284)
T TIGR02880        90 KGHLVSVTRDDL  101 (284)
T ss_pred             cceEEEecHHHH
Confidence             24666665443

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.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.59  E-value=4.9e-07  Score=96.25  Aligned_cols=152  Identities=18%  Similarity=0.186  Sum_probs=94.5

Q ss_pred             HHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc---------------ccCceEEEeehhhh--hh
Q 005179          297 TEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVF---------------LLSKRIMSLDMGLL--MA  359 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~---------------l~~~~v~~ld~~~l--~~  359 (710)
                      ..++++... ..+-+..+||+||+|+|||++|+.+|+.+.+......               .....++.++...-  -.
T Consensus         8 ~~w~~l~~~-~~r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~   86 (325)
T PRK08699          8 EQWRQIAEH-WERRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPEN   86 (325)
T ss_pred             HHHHHHHHh-cCCcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccc
Confidence            345555544 2334455889999999999999999999876321000               01122333332110  00


Q ss_pred             ccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChH
Q 005179          360 GAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQD  433 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~  433 (710)
                      |.+...--.+.++++.+.+..    .+.-|++||+++.|             +...++.|...+++.  ...+|.+|...
T Consensus        87 g~~~~~I~id~iR~l~~~~~~~p~~~~~kV~iiEp~~~L-------------d~~a~naLLk~LEep~~~~~~Ilvth~~  153 (325)
T PRK08699         87 GRKLLQIKIDAVREIIDNVYLTSVRGGLRVILIHPAESM-------------NLQAANSLLKVLEEPPPQVVFLLVSHAA  153 (325)
T ss_pred             cccCCCcCHHHHHHHHHHHhhCcccCCceEEEEechhhC-------------CHHHHHHHHHHHHhCcCCCEEEEEeCCh
Confidence            100000123446666666643    34568889999999             555677777777643  45566666655


Q ss_pred             HHHhhhhccHHHHccccceEecCCCHHHHHHHHH
Q 005179          434 EHRTQFEKDKALARRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                      +     .+.+.+.+|++.+.|++|+.++..+.|.
T Consensus       154 ~-----~ll~ti~SRc~~~~~~~~~~~~~~~~L~  182 (325)
T PRK08699        154 D-----KVLPTIKSRCRKMVLPAPSHEEALAYLR  182 (325)
T ss_pred             H-----hChHHHHHHhhhhcCCCCCHHHHHHHHH
Confidence            4     5778999999999999999998776665

>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes

Probab=98.59  E-value=8.7e-08  Score=73.32  Aligned_cols=52  Identities=42%  Similarity=0.677  Sum_probs=47.6

Q ss_pred             HHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          182 AVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       182 A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      |.+.|+++|+.+|+++|||+||++++++.+.++|+++|+|.+.+++.+.+.+
T Consensus         1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~~~id~~~l~~~i~~~l   52 (53)
T PF02861_consen    1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKKLGIDPEQLKAAIEKAL   52 (53)
T ss_dssp             HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHHTTCHHHHHHHHHHHHH
T ss_pred             CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            6789999999999999999999999999999999999999999999887654

The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....

>PRK09183 transposase/IS protein; Provisional

Probab=98.57  E-value=1.4e-07  Score=97.48  Aligned_cols=162  Identities=21%  Similarity=0.258  Sum_probs=85.6

Q ss_pred             CCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc
Q 005179          266 GRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL  345 (710)
Q Consensus       266 ~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~  345 (710)
                      ++|...+++.|..+....         +. ...+..+...-....+.|++|+||||||||+|+.+++..+...       
T Consensus        67 ~~p~~~~l~~fd~~~~~~---------~~-~~~i~~L~~~~~i~~~~~v~l~Gp~GtGKThLa~al~~~a~~~-------  129 (259)
T PRK09183         67 AFPAVKTFEEYDFTFATG---------AP-QKQLQSLRSLSFIERNENIVLLGPSGVGKTHLAIALGYEAVRA-------  129 (259)
T ss_pred             CCCCCCcHhhcccccCCC---------CC-HHHHHHHhcCCchhcCCeEEEEeCCCCCHHHHHHHHHHHHHHc-------
Confidence            344557788776553211         11 1244444332223456789999999999999999998876432       


Q ss_pred             CceEEEeehhhhhhcc---ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC
Q 005179          346 SKRIMSLDMGLLMAGA---KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG  422 (710)
Q Consensus       346 ~~~v~~ld~~~l~~g~---~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~  422 (710)
                      +..+..++...+....   ...+.    +..++.... ..+.+|+|||++.+...       ......+.+++....+++
T Consensus       130 G~~v~~~~~~~l~~~l~~a~~~~~----~~~~~~~~~-~~~dlLiiDdlg~~~~~-------~~~~~~lf~li~~r~~~~  197 (259)
T PRK09183        130 GIKVRFTTAADLLLQLSTAQRQGR----YKTTLQRGV-MAPRLLIIDEIGYLPFS-------QEEANLFFQVIAKRYEKG  197 (259)
T ss_pred             CCeEEEEeHHHHHHHHHHHHHCCc----HHHHHHHHh-cCCCEEEEcccccCCCC-------hHHHHHHHHHHHHHHhcC
Confidence            5667776665554211   11122    223333221 23569999999875211       011122344444334455


Q ss_pred             CeEEEEccC--hHHHHhhhhcc----HHHHcccc----ceEecCCC
Q 005179          423 ELQCIASTT--QDEHRTQFEKD----KALARRFQ----PVLISEPS  458 (710)
Q Consensus       423 ~v~vI~att--~~~~~~~~~~d----~aL~~Rf~----~I~v~~Ps  458 (710)
                      .  +|.|+|  ..+|...+.-|    .++.+|+.    .|.+.-.+
T Consensus       198 s--~iiTsn~~~~~w~~~~~~d~~~~~ai~dRl~~~~~~i~~~g~s  241 (259)
T PRK09183        198 S--MILTSNLPFGQWDQTFAGDAALTSAMLDRLLHHSHVVQIKGES  241 (259)
T ss_pred             c--EEEecCCCHHHHHHHhcCchhHHHHHHHHHhcceEEEeecCCC
Confidence            4  344444  44555554222    35555552    45555443

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.57  E-value=2e-07  Score=95.78  Aligned_cols=110  Identities=24%  Similarity=0.312  Sum_probs=69.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc---cCccHHHHHHHHHHHHHhcCCeEE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK---ERGELEARVTTLISEIQKSGDVIL  386 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~---~~g~~e~~l~~~~~~~~~~~~~IL  386 (710)
                      .+.|++|+|+||||||+|+.+|+.++...       +.+++.+...+++.--+   ..|..+..+...   +..  .-+|
T Consensus       104 ~~~nl~l~G~~G~GKThLa~Ai~~~l~~~-------g~sv~f~~~~el~~~Lk~~~~~~~~~~~l~~~---l~~--~dlL  171 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAIAIGNELLKA-------GISVLFITAPDLLSKLKAAFDEGRLEEKLLRE---LKK--VDLL  171 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHc-------CCeEEEEEHHHHHHHHHHHHhcCchHHHHHHH---hhc--CCEE
Confidence            68899999999999999999999999632       78888888877763211   123444443332   333  3399


Q ss_pred             EEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccC--hHHHHhhhh
Q 005179          387 FIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT--QDEHRTQFE  440 (710)
Q Consensus       387 ~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att--~~~~~~~~~  440 (710)
                      ||||+...-..       ......+..++....++...  |.++|  ..++..++.
T Consensus       172 IiDDlG~~~~~-------~~~~~~~~q~I~~r~~~~~~--~~tsN~~~~~~~~~~~  218 (254)
T COG1484         172 IIDDIGYEPFS-------QEEADLLFQLISRRYESRSL--IITSNLSFGEWDELFG  218 (254)
T ss_pred             EEecccCccCC-------HHHHHHHHHHHHHHHhhccc--eeecCCChHHHHhhcc
Confidence            99999876221       11233445555555556666  44444  444444444

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

Probab=98.54  E-value=8.5e-08  Score=103.09  Aligned_cols=63  Identities=37%  Similarity=0.481  Sum_probs=47.5

Q ss_pred             ccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |.|.|+|+..+.+.+       ++.+.|-+-|    .|+||+||||||||+||+|+|.+   .+-.+.-...|||-.
T Consensus       306 VkG~DEAK~ELeEiVefLkdP~kftrLGGKLP----KGVLLvGPPGTGKTlLARAvAGE---A~VPFF~~sGSEFdE  375 (752)
T KOG0734|consen  306 VKGVDEAKQELEEIVEFLKDPTKFTRLGGKLP----KGVLLVGPPGTGKTLLARAVAGE---AGVPFFYASGSEFDE  375 (752)
T ss_pred             ccChHHHHHHHHHHHHHhcCcHHhhhccCcCC----CceEEeCCCCCchhHHHHHhhcc---cCCCeEeccccchhh
Confidence            666666665555555       6667776655    79999999999999999999987   555667777778743

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.53  E-value=2.4e-07  Score=104.41  Aligned_cols=182  Identities=24%  Similarity=0.339  Sum_probs=108.5

Q ss_pred             CCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--------
Q 005179          290 DPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--------  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--------  359 (710)
                      ..++|....+..+.+.+..  ....++++.|++||||+++++++.......       +..++.+|+..+..        
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~-------~~~~~~~~c~~~~~~~~~~~lf  206 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLSRSDITVLINGESGTGKELVARALHRHSPRA-------NGPFIALNMAAIPKDLIESELF  206 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHhCcCCeEEEECCCCCCHHHHHHHHHHhCCCC-------CCCeEEEeCCCCCHHHHHHHhc
Confidence            3577877777666665533  345678999999999999999998765322       34566666544311        


Q ss_pred             ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEE
Q 005179          360 GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQC  426 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~v  426 (710)
                      |. ..|.+...............+..||||||+.|             ..+.+..|..+++.+             ++++
T Consensus       207 g~-~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l-------------~~~~q~~ll~~l~~~~~~~~~~~~~~~~~~ri  272 (463)
T TIGR01818       207 GH-EKGAFTGANTRRQGRFEQADGGTLFLDEIGDM-------------PLDAQTRLLRVLADGEFYRVGGRTPIKVDVRI  272 (463)
T ss_pred             CC-CCCCCCCcccCCCCcEEECCCCeEEEEchhhC-------------CHHHHHHHHHHHhcCcEEECCCCceeeeeeEE
Confidence            10 11111000000011122344678999999999             445566666655543             4578


Q ss_pred             EEccChHHHH--hhhhccHHHHccccceEecCCC----HHHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          427 IASTTQDEHR--TQFEKDKALARRFQPVLISEPS----QEDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       427 I~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps----~~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      |++|+.+--.  ..-...+.|..|+..+.+..|+    .++...+++.++.++...++   ..+++++++.+..+
T Consensus       273 i~~~~~~l~~~~~~~~f~~~L~~rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  347 (463)
T TIGR01818       273 VAATHQNLEALVRQGKFREDLFHRLNVIRIHLPPLRERREDIPRLARHFLALAARELDVEPKLLDPEALERLKQL  347 (463)
T ss_pred             EEeCCCCHHHHHHcCCcHHHHHHHhCcceecCCCcccchhhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhC
Confidence            8887754311  1112346777788755555454    55666667777666655544   46899998877654

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.51  E-value=6e-07  Score=95.45  Aligned_cols=120  Identities=19%  Similarity=0.247  Sum_probs=71.8

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc---cCccHHHHHHHHHHHHHhcCCeEE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK---ERGELEARVTTLISEIQKSGDVIL  386 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~---~~g~~e~~l~~~~~~~~~~~~~IL  386 (710)
                      ...+++|+|++|||||+|+.++|+.+...       +..++.++...++..-.   .....+  ....++.+...  .+|
T Consensus       182 ~~~~Lll~G~~GtGKThLa~aIa~~l~~~-------g~~V~y~t~~~l~~~l~~~~~~~~~~--~~~~~~~l~~~--DLL  250 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLSNCIAKELLDR-------GKSVIYRTADELIEILREIRFNNDKE--LEEVYDLLINC--DLL  250 (329)
T ss_pred             cCCcEEEECCCCCcHHHHHHHHHHHHHHC-------CCeEEEEEHHHHHHHHHHHHhccchh--HHHHHHHhccC--CEE
Confidence            34889999999999999999999998653       67788887766653211   111100  11123444433  489


Q ss_pred             EEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccC--hHHHHhhhhccHHHHcccc
Q 005179          387 FIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTT--QDEHRTQFEKDKALARRFQ  450 (710)
Q Consensus       387 ~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att--~~~~~~~~~~d~aL~~Rf~  450 (710)
                      +|||++......       .....+.+++...+.++.-++| +||  +.++..  .+++.+.+|+.
T Consensus       251 IIDDlG~e~~t~-------~~~~~Lf~iin~R~~~~k~tIi-TSNl~~~el~~--~~~eri~SRL~  306 (329)
T PRK06835        251 IIDDLGTEKITE-------FSKSELFNLINKRLLRQKKMII-STNLSLEELLK--TYSERISSRLL  306 (329)
T ss_pred             EEeccCCCCCCH-------HHHHHHHHHHHHHHHCCCCEEE-ECCCCHHHHHH--HHhHHHHHHHH
Confidence            999998763221       1233455666555555544444 444  344333  24577888773

>PRK15115 response regulator GlrR; Provisional

Probab=98.50  E-value=2.1e-07  Score=104.37  Aligned_cols=181  Identities=20%  Similarity=0.296  Sum_probs=105.8

Q ss_pred             CcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--------c
Q 005179          291 PVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--------G  360 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--------g  360 (710)
                      .++|....+.++.+....  ....+++|+|++|+|||++|+++.+.....       +..++.+++..+..        |
T Consensus       135 ~lig~s~~~~~~~~~~~~~a~~~~~vli~Ge~GtGk~~lA~~ih~~s~r~-------~~~f~~i~c~~~~~~~~~~~lfg  207 (444)
T PRK15115        135 AIVTRSPLMLRLLEQARMVAQSDVSVLINGQSGTGKEILAQAIHNASPRA-------SKPFIAINCGALPEQLLESELFG  207 (444)
T ss_pred             cccccCHHHHHHHHHHHhhccCCCeEEEEcCCcchHHHHHHHHHHhcCCC-------CCCeEEEeCCCCCHHHHHHHhcC
Confidence            367777777666654322  345679999999999999999998765322       44566666654321        1


Q ss_pred             cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEE
Q 005179          361 AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCI  427 (710)
Q Consensus       361 ~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI  427 (710)
                      .. .|.+...............+.+|||||++.|             ..+.+..|..+++.+             ++++|
T Consensus       208 ~~-~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l-------------~~~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii  273 (444)
T PRK15115        208 HA-RGAFTGAVSNREGLFQAAEGGTLFLDEIGDM-------------PAPLQVKLLRVLQERKVRPLGSNRDIDIDVRII  273 (444)
T ss_pred             CC-cCCCCCCccCCCCcEEECCCCEEEEEccccC-------------CHHHHHHHHHHHhhCCEEeCCCCceeeeeEEEE
Confidence            00 0000000000000112234578999999999             455666666666543             46788


Q ss_pred             EccChHHHHh--hhhccHHHHccccceEecCCCHHHHHH----HHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          428 ASTTQDEHRT--QFEKDKALARRFQPVLISEPSQEDAVR----ILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       428 ~att~~~~~~--~~~~d~aL~~Rf~~I~v~~Ps~~~~~~----IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      ++|+.+-...  .-...+.|..|+..+.+..|+..+|.+    +++.++.++...++   ..+++++++.+..+
T Consensus       274 ~~~~~~l~~~~~~~~f~~~l~~~l~~~~i~lPpLr~R~eDi~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  347 (444)
T PRK15115        274 SATHRDLPKAMARGEFREDLYYRLNVVSLKIPALAERTEDIPLLANHLLRQAAERHKPFVRAFSTDAMKRLMTA  347 (444)
T ss_pred             EeCCCCHHHHHHcCCccHHHHHhhceeeecCCChHhccccHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhC
Confidence            8877642111  112346677788777777777665543    44555555543333   25899998887644

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=98.50  E-value=1.6e-06  Score=102.44  Aligned_cols=105  Identities=18%  Similarity=0.184  Sum_probs=80.1

Q ss_pred             CCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCC
Q 005179          589 PAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPT  668 (710)
Q Consensus       589 ~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPp  668 (710)
                      +.......+...+...+.+||...+.+ ...+.+.++.|.+.++|++++++.|...+..... ......|  .++|+|||
T Consensus       283 ~~~~e~~~~~~yl~~~~~~pw~~~~~~-~~~~~~~~~~l~~~~~g~~~vK~~i~~~l~~~~~-~~~~~g~--~i~l~Gpp  358 (784)
T PRK10787        283 PMSAEATVVRGYIDWMVQVPWNARSKV-KKDLRQAQEILDTDHYGLERVKDRILEYLAVQSR-VNKIKGP--ILCLVGPP  358 (784)
T ss_pred             CCCchHHHHHHHHHHHHhCCCCCCCcc-cccHHHHHHHhhhhccCHHHHHHHHHHHHHHHHh-cccCCCc--eEEEECCC
Confidence            344556678888999999999887664 4578899999999999999999999876653321 1111122  68999999


Q ss_pred             CCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          669 GVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       669 GtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |||||++|+.+|+.+-   ..+++++++...+
T Consensus       359 G~GKTtl~~~ia~~l~---~~~~~i~~~~~~d  387 (784)
T PRK10787        359 GVGKTSLGQSIAKATG---RKYVRMALGGVRD  387 (784)
T ss_pred             CCCHHHHHHHHHHHhC---CCEEEEEcCCCCC
Confidence            9999999999999853   4688888776544

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

Probab=98.50  E-value=1.2e-07  Score=93.37  Aligned_cols=48  Identities=33%  Similarity=0.614  Sum_probs=38.4

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      |+|.+.-++.+..+|        ++-..|+++|    .|+|+|||||||||++|+|.|..
T Consensus       173 iGGldkQIqELvEAiVLpmth~ekF~~lgi~pP----KGvLmYGPPGTGKTlmARAcAaq  228 (424)
T KOG0652|consen  173 IGGLDKQIQELVEAIVLPMTHKEKFENLGIRPP----KGVLMYGPPGTGKTLMARACAAQ  228 (424)
T ss_pred             cccHHHHHHHHHHHhccccccHHHHHhcCCCCC----CceEeeCCCCCcHHHHHHHHHHh
Confidence            666666666666555        5667788766    79999999999999999999876

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.50  E-value=2.3e-07  Score=104.52  Aligned_cols=180  Identities=17%  Similarity=0.228  Sum_probs=107.0

Q ss_pred             CCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-------
Q 005179          289 IDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-------  359 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-------  359 (710)
                      +..++|....+..+.+.+..  ....+++++|++||||+++|+++.......       +.+++.+++..+..       
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~a~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~-------~~~~~~i~c~~~~~~~~~~~l  214 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKIALSQASVLISGESGTGKELIARAIHYNSRRA-------KGPFIKVNCAALPESLLESEL  214 (457)
T ss_pred             ccceecccHHHhHHHHHHHHHcCCCcEEEEEcCCCccHHHHHHHHHHhCCCC-------CCCeEEEECCCCCHHHHHHHh
Confidence            34578887777777665433  345789999999999999999998754222       34566666654321       


Q ss_pred             -ccc---cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------
Q 005179          360 -GAK---ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------  422 (710)
Q Consensus       360 -g~~---~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------  422 (710)
                       |..   ..|....+    ........+.+|||||++.|             ....+..|..+++.+             
T Consensus       215 fg~~~~~~~~~~~~~----~g~~~~a~~gtl~ld~i~~l-------------~~~~q~~L~~~l~~~~~~~~~~~~~~~~  277 (457)
T PRK11361        215 FGHEKGAFTGAQTLR----QGLFERANEGTLLLDEIGEM-------------PLVLQAKLLRILQEREFERIGGHQTIKV  277 (457)
T ss_pred             cCCCCCCCCCCCCCC----CCceEECCCCEEEEechhhC-------------CHHHHHHHHHHHhcCcEEeCCCCceeee
Confidence             100   00000000    00122344678999999999             445566666555432             


Q ss_pred             CeEEEEccChHHHH--hhhhccHHHHccccceEecCCCHHHHH----HHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          423 ELQCIASTTQDEHR--TQFEKDKALARRFQPVLISEPSQEDAV----RILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       423 ~v~vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~~~~~----~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      ++++|++|+.+-..  ..-...+.+..|+..+.+..|+..+|.    .++..++.++...++   ..+++++++.+..+
T Consensus       278 ~~rii~~t~~~l~~~~~~g~~~~~l~~~l~~~~i~~ppLreR~~di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  356 (457)
T PRK11361        278 DIRIIAATNRDLQAMVKEGTFREDLFYRLNVIHLILPPLRDRREDISLLANHFLQKFSSENQRDIIDIDPMAMSLLTAW  356 (457)
T ss_pred             ceEEEEeCCCCHHHHHHcCCchHHHHHHhccceecCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHcC
Confidence            36889888764311  111244567778876777777655443    445555555544333   46888888776543

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

Probab=98.48  E-value=2.1e-07  Score=93.47  Aligned_cols=51  Identities=27%  Similarity=0.391  Sum_probs=44.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .+||+++++.+.-.++.++.    .+..+.++|||||||.|||+||..+|++|--
T Consensus        28 fiGQ~~vk~~L~ifI~AAk~----r~e~lDHvLl~GPPGlGKTTLA~IIA~Emgv   78 (332)
T COG2255          28 FIGQEKVKEQLQIFIKAAKK----RGEALDHVLLFGPPGLGKTTLAHIIANELGV   78 (332)
T ss_pred             hcChHHHHHHHHHHHHHHHh----cCCCcCeEEeeCCCCCcHHHHHHHHHHHhcC
Confidence            89999999999999988874    2334579999999999999999999999744

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

Probab=98.48  E-value=9.6e-08  Score=95.59  Aligned_cols=62  Identities=26%  Similarity=0.407  Sum_probs=49.1

Q ss_pred             cccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .|+|.+.-+..|..++        -|-..|+++|    .|++|||+||||||+||||+|+.   +..-++|+-.||+
T Consensus       186 diGGle~QiQEiKEsvELPLthPE~YeemGikpP----KGVIlyG~PGTGKTLLAKAVANq---TSATFlRvvGseL  255 (440)
T KOG0726|consen  186 DIGGLESQIQEIKESVELPLTHPEYYEEMGIKPP----KGVILYGEPGTGKTLLAKAVANQ---TSATFLRVVGSEL  255 (440)
T ss_pred             ccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCC----CeeEEeCCCCCchhHHHHHHhcc---cchhhhhhhhHHH
Confidence            3777777777777776        4567888877    79999999999999999999988   5555666666654

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.48  E-value=5.2e-06  Score=92.78  Aligned_cols=220  Identities=20%  Similarity=0.223  Sum_probs=128.3

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHH----hcCCC
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIV----QAEVP  341 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~----~~~~p  341 (710)
                      +.|..+-..|.-...|   +.+-+|+.+...+-..+..     ..+..+++.|-||||||+.++.+.+.+.    ++++|
T Consensus       380 S~l~~ara~Lhls~vp---~sLpcRe~E~~~I~~f~~~~i~~~~~g~~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p  456 (767)
T KOG1514|consen  380 SELSKARARLHLSAVP---ESLPCRENEFSEIEDFLRSFISDQGLGSCMYISGVPGTGKTATVLEVMKELQTSSAQKELP  456 (767)
T ss_pred             hHHHHHHHHhHHhhcc---ccccchhHHHHHHHHHHHhhcCCCCCceeEEEecCCCCCceehHHHHHHHHHHHHhhcCCC
Confidence            4555555555544444   3578899888887766543     2334688999999999999999988764    35555


Q ss_pred             ccccCceEEEeehhhhhhc-----------cccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCC
Q 005179          342 VFLLSKRIMSLDMGLLMAG-----------AKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKG  406 (710)
Q Consensus       342 ~~l~~~~v~~ld~~~l~~g-----------~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~  406 (710)
                      .+    ..++++.-.+...           ...+-.+...+..+-....    ...++||+|||+|.|+...        
T Consensus       457 ~f----~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~k~~~~~~VvLiDElD~Lvtr~--------  524 (767)
T KOG1514|consen  457 KF----DYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTVPKPKRSTTVVLIDELDILVTRS--------  524 (767)
T ss_pred             Cc----cEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccCCCCCCCEEEEeccHHHHhccc--------
Confidence            43    2333432222100           0111122222222221111    2347899999999997541        


Q ss_pred             ChHhHHHhhc-ccccCCCeEEEEccChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH
Q 005179          407 TGLDISNLLK-PSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTL  483 (710)
Q Consensus       407 ~~~~~~~~L~-~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~  483 (710)
                       +.-++|++. +.+.+.+++||+..|.-+.-.- .+.....+|+.  .|.|.+++.+|..+|+...+...     -.+.+
T Consensus       525 -QdVlYn~fdWpt~~~sKLvvi~IaNTmdlPEr-~l~nrvsSRlg~tRi~F~pYth~qLq~Ii~~RL~~~-----~~f~~  597 (767)
T KOG1514|consen  525 -QDVLYNIFDWPTLKNSKLVVIAIANTMDLPER-LLMNRVSSRLGLTRICFQPYTHEQLQEIISARLKGL-----DAFEN  597 (767)
T ss_pred             -HHHHHHHhcCCcCCCCceEEEEecccccCHHH-HhccchhhhccceeeecCCCCHHHHHHHHHHhhcch-----hhcch
Confidence             223455553 5566788888877654331111 13345555664  89999999999999988765533     23456


Q ss_pred             HHHHHHHHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          484 EAINAAVHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       484 ~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      ++++.++.....-   ..-..+|.++++.|..
T Consensus       598 ~aielvarkVAav---SGDaRraldic~RA~E  626 (767)
T KOG1514|consen  598 KAIELVARKVAAV---SGDARRALDICRRAAE  626 (767)
T ss_pred             hHHHHHHHHHHhc---cccHHHHHHHHHHHHH
Confidence            6655544432221   2223567777777763

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.48  E-value=5.1e-07  Score=82.94  Aligned_cols=109  Identities=18%  Similarity=0.267  Sum_probs=65.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------------ccc--cCccHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------------GAK--ERGELEARVTTLI  375 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------------g~~--~~g~~e~~l~~~~  375 (710)
                      .++.++|+||+|+|||++++.+++.+........  ...++.+++.....            +..  ........+..+.
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~   80 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIKRLARQLNAEAEIKN--HPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLI   80 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHHHHHHHHHHHHHHCC--CEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHHHHHHHhHHhhhccC--CCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHH
Confidence            4567899999999999999999998753210000  34455555433220            111  1123444455556


Q ss_pred             HHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccCh
Q 005179          376 SEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQ  432 (710)
Q Consensus       376 ~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~  432 (710)
                      +.+......+|+|||+|.+.            .....+.|+.++++..+.+|.++++
T Consensus        81 ~~l~~~~~~~lviDe~~~l~------------~~~~l~~l~~l~~~~~~~vvl~G~~  125 (131)
T PF13401_consen   81 DALDRRRVVLLVIDEADHLF------------SDEFLEFLRSLLNESNIKVVLVGTP  125 (131)
T ss_dssp             HHHHHCTEEEEEEETTHHHH------------THHHHHHHHHHTCSCBEEEEEEESS
T ss_pred             HHHHhcCCeEEEEeChHhcC------------CHHHHHHHHHHHhCCCCeEEEEECh
Confidence            66666655699999999983            2356777777777777777776665

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.46  E-value=9.7e-08  Score=96.93  Aligned_cols=63  Identities=37%  Similarity=0.498  Sum_probs=47.5

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHH----HHhhcCCCCCCC--CCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAV----KRSRVGLKDPNR--PTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i----~~~r~gl~~p~r--p~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++++.|.++|+||+.|++.++-++    ++.+....+-.-  --+.+||.||||+|||+||+.||+.|
T Consensus        53 ~eik~~Ld~YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~L  121 (408)
T COG1219          53 KEIKAHLDEYVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKIL  121 (408)
T ss_pred             HHHHHHhhhheecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHh
Confidence            4778899999999999999877555    444322111101  11589999999999999999999996

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.46  E-value=1.8e-06  Score=86.94  Aligned_cols=110  Identities=22%  Similarity=0.261  Sum_probs=78.0

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-CeEEEEccChH-------HHHhhhhccHHHHccccceEe
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-ELQCIASTTQD-------EHRTQFEKDKALARRFQPVLI  454 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-~v~vI~att~~-------~~~~~~~~d~aL~~Rf~~I~v  454 (710)
                      |.||||||+|.|             ..+...+|...+++. ..++|.+||..       .|..-..++-.|..|.-.|..
T Consensus       289 pGVLFIDEvHML-------------DIEcFsFlNrAlE~d~~PiiimaTNrgit~iRGTn~~SphGiP~D~lDR~lII~t  355 (454)
T KOG2680|consen  289 PGVLFIDEVHML-------------DIECFSFLNRALENDMAPIIIMATNRGITRIRGTNYRSPHGIPIDLLDRMLIIST  355 (454)
T ss_pred             cceEEEeeehhh-------------hhHHHHHHHHHhhhccCcEEEEEcCCceEEeecCCCCCCCCCcHHHhhhhheeec
Confidence            789999999999             677888888888753 12233333321       223344677889999888999


Q ss_pred             cCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          455 SEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       455 ~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      .+++.++..+||+..+.    ..++.+.+++++.+......-     .-..++.|+..+.
T Consensus       356 ~py~~~d~~~IL~iRc~----EEdv~m~~~A~d~Lt~i~~~t-----sLRYai~Lit~a~  406 (454)
T KOG2680|consen  356 QPYTEEDIKKILRIRCQ----EEDVEMNPDALDLLTKIGEAT-----SLRYAIHLITAAS  406 (454)
T ss_pred             ccCcHHHHHHHHHhhhh----hhccccCHHHHHHHHHhhhhh-----hHHHHHHHHHHHH
Confidence            99999999999998877    447899999999887664321     1133566665443

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

Probab=98.45  E-value=2.1e-07  Score=101.60  Aligned_cols=61  Identities=33%  Similarity=0.475  Sum_probs=44.9

Q ss_pred             ccChHHHHHHHHHHHH--------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVK--------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~--------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|++..++.|...+.        +.+.|+..|    .++|||||||||||++|+++|+.+   ...++++..+++
T Consensus       147 igGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~p----kgvLL~GppGTGKT~LAkalA~~l---~~~fi~i~~s~l  215 (398)
T PTZ00454        147 IGGLDIQKQEIREAVELPLTCPELYEQIGIDPP----RGVLLYGPPGTGKTMLAKAVAHHT---TATFIRVVGSEF  215 (398)
T ss_pred             cCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCC----ceEEEECCCCCCHHHHHHHHHHhc---CCCEEEEehHHH
Confidence            6777777777766653        345566544    699999999999999999999985   335677665544

>PRK06921 hypothetical protein; Provisional

Probab=98.44  E-value=5.1e-07  Score=93.52  Aligned_cols=124  Identities=19%  Similarity=0.249  Sum_probs=65.8

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFID  389 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~ID  389 (710)
                      ..++++|+|++|+|||+|+.+++..+....      +..++.+....++...  ...+ ..+...++.+..  ..+|+||
T Consensus       116 ~~~~l~l~G~~G~GKThLa~aia~~l~~~~------g~~v~y~~~~~l~~~l--~~~~-~~~~~~~~~~~~--~dlLiID  184 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLLTAAANELMRKK------GVPVLYFPFVEGFGDL--KDDF-DLLEAKLNRMKK--VEVLFID  184 (266)
T ss_pred             CCCeEEEECCCCCcHHHHHHHHHHHHhhhc------CceEEEEEHHHHHHHH--HHHH-HHHHHHHHHhcC--CCEEEEe
Confidence            467899999999999999999999985431      4566676655544211  0111 112223333333  3599999


Q ss_pred             cchh-hhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccc
Q 005179          390 EVHT-LIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRF  449 (710)
Q Consensus       390 Eid~-l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf  449 (710)
                      |++. +.+....   +......+..++.....++..+|| +++... ..+...++.+.+|+
T Consensus       185 Dl~~~~~g~e~~---t~~~~~~lf~iin~R~~~~k~tIi-tsn~~~-~el~~~~~~l~sRi  240 (266)
T PRK06921        185 DLFKPVNGKPRA---TEWQIEQMYSVLNYRYLNHKPILI-SSELTI-DELLDIDEALGSRI  240 (266)
T ss_pred             ccccccCCCccC---CHHHHHHHHHHHHHHHHCCCCEEE-ECCCCH-HHHhhhhhHHHHHH
Confidence            9955 2122111   001122345555555544444444 444321 11222356666654

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=98.42  E-value=2.5e-07  Score=101.32  Aligned_cols=61  Identities=31%  Similarity=0.458  Sum_probs=47.1

Q ss_pred             ccChHHHHHHHHHHHHH--------hhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKR--------SRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~--------~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|.++.++.+...+..        ...|+..|    .++|||||||||||++|+++|+.+-   ..++.++++++
T Consensus       133 i~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p----~gvLL~GppGtGKT~lAkaia~~~~---~~~i~v~~~~l  201 (389)
T PRK03992        133 IGGLEEQIREVREAVELPLKKPELFEEVGIEPP----KGVLLYGPPGTGKTLLAKAVAHETN---ATFIRVVGSEL  201 (389)
T ss_pred             hCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCC----CceEEECCCCCChHHHHHHHHHHhC---CCEEEeehHHH
Confidence            77777777777766532        34566555    6899999999999999999999853   46888888776

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.42  E-value=1.8e-06  Score=97.03  Aligned_cols=213  Identities=14%  Similarity=0.131  Sum_probs=122.9

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCC-----CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRT-----KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~-----~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      ..|.++++|.+++++.-..+-++.+..+|....     ..-+||+|||||||||+++.||+++          +..+.+-
T Consensus         7 ~~W~~ky~P~~~~eLavhkkKv~eV~~wl~~~~~~~~~~~iLlLtGP~G~GKtttv~~La~el----------g~~v~Ew   76 (519)
T PF03215_consen    7 EPWVEKYAPKTLDELAVHKKKVEEVRSWLEEMFSGSSPKRILLLTGPSGCGKTTTVKVLAKEL----------GFEVQEW   76 (519)
T ss_pred             CccchhcCCCCHHHhhccHHHHHHHHHHHHHHhccCCCcceEEEECCCCCCHHHHHHHHHHHh----------CCeeEEe
Confidence            367788899999999888888888888776422     2336889999999999999999998          2222221


Q ss_pred             -ehhh----------hhhccccCccHHHH---HHHH-HHHHH-----------hcCCeEEEEccchhhhhCCCCCCCCCC
Q 005179          353 -DMGL----------LMAGAKERGELEAR---VTTL-ISEIQ-----------KSGDVILFIDEVHTLIGSGTVGRGNKG  406 (710)
Q Consensus       353 -d~~~----------l~~g~~~~g~~e~~---l~~~-~~~~~-----------~~~~~IL~IDEid~l~~~~~~~~~~~~  406 (710)
                       +...          ........+.+..+   +..+ +...+           ...+.||+|||+-.++..        +
T Consensus        77 ~np~~~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~--------~  148 (519)
T PF03215_consen   77 INPVSFRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHR--------D  148 (519)
T ss_pred             cCCCCccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccch--------h
Confidence             0000          00000000111111   1111 11111           124678999999876432        1


Q ss_pred             ChHhHHHhhcccccCC---CeEEEEccC--h---HHHHh-----hhhccHHHHc--cccceEecCCCHHHHHHHHHHHHH
Q 005179          407 TGLDISNLLKPSLGRG---ELQCIASTT--Q---DEHRT-----QFEKDKALAR--RFQPVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       407 ~~~~~~~~L~~~l~~~---~v~vI~att--~---~~~~~-----~~~~d~aL~~--Rf~~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                       ...+.+.|..++..+   .+++|.+-+  .   ..+..     ..-+.+.+..  ++..|.|.+-...-..+.|..++.
T Consensus       149 -~~~f~~~L~~~l~~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i~~I~FNpIa~T~mkKaL~rI~~  227 (519)
T PF03215_consen  149 -TSRFREALRQYLRSSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGITRIKFNPIAPTFMKKALKRILK  227 (519)
T ss_pred             -HHHHHHHHHHHHHcCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCceEEEecCCCHHHHHHHHHHHHH
Confidence             256777777776643   455555511  1   01000     0123456665  345899999999888888888877


Q ss_pred             HHHh-hcC-CCCC--HHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          472 KYEA-HHN-CKFT--LEAINAAVHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       472 ~~~~-~~~-~~i~--~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      .... ..+ ....  .++++.++..+.+.+.      .||.-|...|.
T Consensus       228 ~E~~~~~~~~~~p~~~~~l~~I~~~s~GDIR------sAIn~LQf~~~  269 (519)
T PF03215_consen  228 KEARSSSGKNKVPDKQSVLDSIAESSNGDIR------SAINNLQFWCL  269 (519)
T ss_pred             HHhhhhcCCccCCChHHHHHHHHHhcCchHH------HHHHHHHHHhc
Confidence            5421 112 1222  3468888877665543      36666666654

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

Probab=98.42  E-value=2.4e-07  Score=90.78  Aligned_cols=66  Identities=24%  Similarity=0.380  Sum_probs=53.7

Q ss_pred             HhhCcccChHHHHHHHHHHHH--------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          626 QLKKRVIGQDEAVAAISRAVK--------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       626 ~L~~~v~Gq~~a~~~i~~~i~--------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      .-.+.|+|.+.-+..|...|.        +-..|+..|    .|+|||||||||||+||+|+|..   ++-.+||+..||
T Consensus       144 StYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQP----KGvlLygppgtGktLlaraVahh---t~c~firvsgse  216 (404)
T KOG0728|consen  144 STYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQP----KGVLLYGPPGTGKTLLARAVAHH---TDCTFIRVSGSE  216 (404)
T ss_pred             cHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCC----cceEEecCCCCchhHHHHHHHhh---cceEEEEechHH
Confidence            344558888888877777662        335688776    69999999999999999999999   777899999988


Q ss_pred             C
Q 005179          698 F  698 (710)
Q Consensus       698 ~  698 (710)
                      +
T Consensus       217 l  217 (404)
T KOG0728|consen  217 L  217 (404)
T ss_pred             H
Confidence            7

>PLN03025 replication factor C subunit; Provisional

Probab=98.41  E-value=2.5e-07  Score=98.86  Aligned_cols=71  Identities=21%  Similarity=0.313  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--Ccce
Q 005179          614 ADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHY  691 (710)
Q Consensus       614 ~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li  691 (710)
                      |.+..+...+.+     ++||++++..+...+...+    .     .++||+||||||||++|+++|+++||..  ...+
T Consensus         3 w~~kyrP~~l~~-----~~g~~~~~~~L~~~~~~~~----~-----~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~   68 (319)
T PLN03025          3 WVEKYRPTKLDD-----IVGNEDAVSRLQVIARDGN----M-----PNLILSGPPGTGKTTSILALAHELLGPNYKEAVL   68 (319)
T ss_pred             hhhhcCCCCHHH-----hcCcHHHHHHHHHHHhcCC----C-----ceEEEECCCCCCHHHHHHHHHHHHhcccCcccee
Confidence            444445555556     8999999998876544211    1     2799999999999999999999999864  3456


Q ss_pred             eeCCCCC
Q 005179          692 LFFPSPF  698 (710)
Q Consensus       692 ~~d~se~  698 (710)
                      .++.|+.
T Consensus        69 eln~sd~   75 (319)
T PLN03025         69 ELNASDD   75 (319)
T ss_pred             eeccccc
Confidence            6666654

>TIGR03689 pup_AAA proteasome ATPase

Probab=98.39  E-value=3.5e-07  Score=102.07  Aligned_cols=50  Identities=36%  Similarity=0.547  Sum_probs=38.5

Q ss_pred             ccChHHHHHHHHHHHH--------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          631 VIGQDEAVAAISRAVK--------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~--------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      |+|+++.++.|...+.        +.+.|+..|    .++|||||||||||++||++|+.+.
T Consensus       184 IgGl~~~i~~i~~~v~lp~~~~~l~~~~gl~~p----~GILLyGPPGTGKT~LAKAlA~eL~  241 (512)
T TIGR03689       184 IGGLDSQIEQIRDAVELPFLHPELYREYDLKPP----KGVLLYGPPGCGKTLIAKAVANSLA  241 (512)
T ss_pred             cCChHHHHHHHHHHHHHHhhCHHHHHhccCCCC----cceEEECCCCCcHHHHHHHHHHhhc
Confidence            5666666666666653        345566654    6899999999999999999999974

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.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.38  E-value=3.9e-06  Score=87.02  Aligned_cols=138  Identities=18%  Similarity=0.125  Sum_probs=90.7

Q ss_pred             HHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc------cCceEEEeehhhhhhccccCccHHH
Q 005179          297 TEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL------LSKRIMSLDMGLLMAGAKERGELEA  369 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l------~~~~v~~ld~~~l~~g~~~~g~~e~  369 (710)
                      ..++.+...+...+-.| .||+||+|+||+++|..+|+.+.+...+...      ....++.+..    .+.. ..--.+
T Consensus         4 ~~~~~L~~~i~~~rl~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p----~~~~-~~I~id   78 (290)
T PRK05917          4 AAWEALIQRVRDQKVPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSP----QGKG-RLHSIE   78 (290)
T ss_pred             HHHHHHHHHHHcCCcCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEec----CCCC-CcCcHH
Confidence            35667777777755544 5699999999999999999999775422110      0111222211    0100 000123


Q ss_pred             HHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHHhhhhccH
Q 005179          370 RVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHRTQFEKDK  443 (710)
Q Consensus       370 ~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~  443 (710)
                      .++.+.+.+..    ++.-|++||++|.+             ..+++|.|+..|++  .++++|..|+..+     .+.|
T Consensus        79 qiR~l~~~~~~~p~e~~~kv~ii~~ad~m-------------t~~AaNaLLK~LEEPp~~~~fiL~~~~~~-----~ll~  140 (290)
T PRK05917         79 TPRAIKKQIWIHPYESPYKIYIIHEADRM-------------TLDAISAFLKVLEDPPQHGVIILTSAKPQ-----RLPP  140 (290)
T ss_pred             HHHHHHHHHhhCccCCCceEEEEechhhc-------------CHHHHHHHHHHhhcCCCCeEEEEEeCChh-----hCcH
Confidence            35566655543    34569999999999             66788999999985  3566666666654     6789


Q ss_pred             HHHccccceEecCC
Q 005179          444 ALARRFQPVLISEP  457 (710)
Q Consensus       444 aL~~Rf~~I~v~~P  457 (710)
                      ++++|++.+.|+++
T Consensus       141 TI~SRcq~~~~~~~  154 (290)
T PRK05917        141 TIRSRSLSIHIPME  154 (290)
T ss_pred             HHHhcceEEEccch
Confidence            99999999999775

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

Probab=98.38  E-value=5.3e-07  Score=99.16  Aligned_cols=61  Identities=30%  Similarity=0.465  Sum_probs=46.9

Q ss_pred             ccChHHHHHHHHHHHHH--------hhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKR--------SRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~--------~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|+++.++.|...+..        ...|+..|    .++|||||||||||++|+++|+.+-   ..+++++.+++
T Consensus       185 IgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p----~gVLL~GPPGTGKT~LAraIA~el~---~~fi~V~~seL  253 (438)
T PTZ00361        185 IGGLEQQIQEIKEAVELPLTHPELYDDIGIKPP----KGVILYGPPGTGKTLLAKAVANETS---ATFLRVVGSEL  253 (438)
T ss_pred             hcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCC----cEEEEECCCCCCHHHHHHHHHHhhC---CCEEEEecchh
Confidence            67777777777776642        34566544    6899999999999999999999853   46788887776

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=98.37  E-value=5.4e-07  Score=87.99  Aligned_cols=48  Identities=38%  Similarity=0.593  Sum_probs=33.6

Q ss_pred             CcccCHHHHHHHHHHHH---cCCCCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          291 PVIGRETEIQRIIQILC---RRTKNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~---~~~~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      +++||+++++++...+.   ...+++++|+|++|+|||++++.+...+...
T Consensus         1 ~fvgR~~e~~~l~~~l~~~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~   51 (185)
T PF13191_consen    1 QFVGREEEIERLRDLLDAAQSGSPRNLLLTGESGSGKTSLLRALLDRLAER   51 (185)
T ss_dssp             --TT-HHHHHHHHHTTGGTSS-----EEE-B-TTSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            47999999999999883   2345779999999999999999998887654

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

Probab=98.35  E-value=1.9e-06  Score=92.92  Aligned_cols=138  Identities=20%  Similarity=0.262  Sum_probs=84.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEV  391 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEi  391 (710)
                      ..+||.||||+|||+||-.+|...          +.+++.+--..-+.|.... .--..++.+|+.+.++.-.|+++|||
T Consensus       539 vSvLl~Gp~~sGKTaLAA~iA~~S----------~FPFvKiiSpe~miG~sEs-aKc~~i~k~F~DAYkS~lsiivvDdi  607 (744)
T KOG0741|consen  539 VSVLLEGPPGSGKTALAAKIALSS----------DFPFVKIISPEDMIGLSES-AKCAHIKKIFEDAYKSPLSIIVVDDI  607 (744)
T ss_pred             eEEEEecCCCCChHHHHHHHHhhc----------CCCeEEEeChHHccCccHH-HHHHHHHHHHHHhhcCcceEEEEcch
Confidence            457999999999999999998765          4444444322333333221 11234788888888888899999999


Q ss_pred             hhhhhCCCCCCCCCCChHhHHHhhccccc----CC-CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCH-HHHHH
Q 005179          392 HTLIGSGTVGRGNKGTGLDISNLLKPSLG----RG-ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQ-EDAVR  464 (710)
Q Consensus       392 d~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~-~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~-~~~~~  464 (710)
                      ++|+.-...|-   -.+.-+...|+-++.    .| ++.+++||+..++..    +-.+...|+ .|.|+..+. ++..+
T Consensus       608 ErLiD~vpIGP---RfSN~vlQaL~VllK~~ppkg~kLli~~TTS~~~vL~----~m~i~~~F~~~i~Vpnl~~~~~~~~  680 (744)
T KOG0741|consen  608 ERLLDYVPIGP---RFSNLVLQALLVLLKKQPPKGRKLLIFGTTSRREVLQ----EMGILDCFSSTIHVPNLTTGEQLLE  680 (744)
T ss_pred             hhhhcccccCc---hhhHHHHHHHHHHhccCCCCCceEEEEecccHHHHHH----HcCHHHhhhheeecCccCchHHHHH
Confidence            99986543310   011122223332332    23 566677776655322    234566776 778877654 67666


Q ss_pred             HHH
Q 005179          465 ILL  467 (710)
Q Consensus       465 IL~  467 (710)
                      +|+
T Consensus       681 vl~  683 (744)
T KOG0741|consen  681 VLE  683 (744)
T ss_pred             HHH
Confidence            665

>PHA00729 NTP-binding motif containing protein

Probab=98.33  E-value=3.2e-06  Score=84.20  Aligned_cols=126  Identities=15%  Similarity=0.174  Sum_probs=71.3

Q ss_pred             HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCC------ccccCceEEEeehhhhhhccccCccHHHHHHHH
Q 005179          301 RIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVP------VFLLSKRIMSLDMGLLMAGAKERGELEARVTTL  374 (710)
Q Consensus       301 ~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p------~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~  374 (710)
                      ++++.+......|++|+|+|||||||+|.+|+..+...-.+      ....+...+.++...+.          ..+...
T Consensus         7 ~~~~~l~~~~f~nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll----------~~L~~a   76 (226)
T PHA00729          7 KIVSAYNNNGFVSAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDAL----------EKIQDA   76 (226)
T ss_pred             HHHHHHhcCCeEEEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHH----------HHHHHH
Confidence            34444445555689999999999999999999987311000      00112233333333322          122222


Q ss_pred             HHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEe
Q 005179          375 ISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLI  454 (710)
Q Consensus       375 ~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v  454 (710)
                      ++..  ....+|+|||+..-......       ..+            .           ...++.+.+++++|++.+.+
T Consensus        77 ~~~~--~~~dlLIIDd~G~~~~~~~w-------h~~------------~-----------~~~yf~L~~aLrSR~~l~il  124 (226)
T PHA00729         77 IDND--YRIPLIIFDDAGIWLSKYVW-------YED------------Y-----------MKTFYKIYALIRTRVSAVIF  124 (226)
T ss_pred             HhcC--CCCCEEEEeCCchhhcccch-------hhh------------c-----------cchHHHHHHHHHhhCcEEEE
Confidence            2111  11247899997544211000       000            0           01244677888889999999


Q ss_pred             cCCCHHHHHHHHHH
Q 005179          455 SEPSQEDAVRILLG  468 (710)
Q Consensus       455 ~~Ps~~~~~~IL~~  468 (710)
                      .+++.++....|+.
T Consensus       125 ~~ls~edL~~~Lr~  138 (226)
T PHA00729        125 TTPSPEDLAFYLRE  138 (226)
T ss_pred             ecCCHHHHHHHHHh
Confidence            99999987777775

>COG1220 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=98.32  E-value=8.2e-07  Score=90.96  Aligned_cols=75  Identities=35%  Similarity=0.507  Sum_probs=55.8

Q ss_pred             HHHHHhhCcccChHHHHHHHHHHH--HHhhcCCCCCCC---CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          622 GLEEQLKKRVIGQDEAVAAISRAV--KRSRVGLKDPNR---PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       622 ~l~~~L~~~v~Gq~~a~~~i~~~i--~~~r~gl~~p~r---p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ++-..|.+.|+||++|+.+|+-++  ++-|..+....|   -+..+|..||||||||++|+-||+.   .+.++|.+--.
T Consensus         8 eIV~eLd~yIIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl---~~aPFiKVEAT   84 (444)
T COG1220           8 EIVSELDRYIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKL---AGAPFIKVEAT   84 (444)
T ss_pred             HHHHHHHhHhcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHH---hCCCeEEEEee
Confidence            345567788999999999999888  344444433222   1258999999999999999999999   56677776655


Q ss_pred             CCC
Q 005179          697 PFN  699 (710)
Q Consensus       697 e~~  699 (710)
                      -|-
T Consensus        85 KfT   87 (444)
T COG1220          85 KFT   87 (444)
T ss_pred             eee
Confidence            553

>PF05729 NACHT: NACHT domain

Probab=98.31  E-value=7.7e-06  Score=78.05  Aligned_cols=144  Identities=19%  Similarity=0.214  Sum_probs=78.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHH-----------HH-HHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARV-----------TT-LISEIQK  380 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l-----------~~-~~~~~~~  380 (710)
                      -++|+|+||+|||++++.++..+.....+... ..-++.+.+......... ..+...+           .. +...+..
T Consensus         2 ~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~l~~~l~~~~~~~~~~~~~~~~~~~~~   79 (166)
T PF05729_consen    2 VLWISGEPGSGKSTLLRKLAQQLAEEEPPPSK-FPYPFFFSLRDISDSNNS-RSLADLLFDQLPESIAPIEELLQELLEK   79 (166)
T ss_pred             EEEEECCCCCChHHHHHHHHHHHHhcCccccc-ceEEEEEeehhhhhcccc-chHHHHHHHhhccchhhhHHHHHHHHHc
Confidence            36899999999999999999988765432211 112223333222211100 0111111           11 1112234


Q ss_pred             cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC---CCeEEEEccChHHHHhhhhccHHHHccc---cceEe
Q 005179          381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR---GELQCIASTTQDEHRTQFEKDKALARRF---QPVLI  454 (710)
Q Consensus       381 ~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~---~~v~vI~att~~~~~~~~~~d~aL~~Rf---~~I~v  454 (710)
                      ....+|+||.+|.+......     .........|..++..   .++.+|.++++..+.       .+.+.+   ..+.+
T Consensus        80 ~~~~llilDglDE~~~~~~~-----~~~~~~~~~l~~l~~~~~~~~~~liit~r~~~~~-------~~~~~~~~~~~~~l  147 (166)
T PF05729_consen   80 NKRVLLILDGLDELEEQDQS-----QERQRLLDLLSQLLPQALPPGVKLIITSRPRAFP-------DLRRRLKQAQILEL  147 (166)
T ss_pred             CCceEEEEechHhcccchhh-----hHHHHHHHHHHHHhhhccCCCCeEEEEEcCChHH-------HHHHhcCCCcEEEE
Confidence            56789999999999543211     0112233444444432   345666666654321       133433   36899


Q ss_pred             cCCCHHHHHHHHHHHH
Q 005179          455 SEPSQEDAVRILLGLR  470 (710)
Q Consensus       455 ~~Ps~~~~~~IL~~l~  470 (710)
                      .+.+.++..++++...
T Consensus       148 ~~~~~~~~~~~~~~~f  163 (166)
T PF05729_consen  148 EPFSEEDIKQYLRKYF  163 (166)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            9999999888887654

>KOG1051 consensus Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones]

Probab=98.29  E-value=3.6e-06  Score=98.20  Aligned_cols=121  Identities=25%  Similarity=0.384  Sum_probs=89.7

Q ss_pred             CcccCHHHHHHHHHHHHcCC--------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh---
Q 005179          291 PVIGRETEIQRIIQILCRRT--------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA---  359 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~--------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~---  359 (710)
                      .++|+++.+..+.+.+.+..        ...++|.||.|||||-||++||..+...       ...++.+|++.+..   
T Consensus       563 ~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgs-------e~~~IriDmse~~evsk  635 (898)
T KOG1051|consen  563 RVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGS-------EENFIRLDMSEFQEVSK  635 (898)
T ss_pred             hccchHHHHHHHHHHHHhhhcccCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCC-------ccceEEechhhhhhhhh
Confidence            59999999999998876522        1236899999999999999999998433       56788899886332   


Q ss_pred             --c--cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------
Q 005179          360 --G--AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------  422 (710)
Q Consensus       360 --g--~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------  422 (710)
                        |  ..|+|..+  ...+.+.++..+.+|++||||+..             ..++++.|++++++|             
T Consensus       636 ligsp~gyvG~e~--gg~LteavrrrP~sVVLfdeIEkA-------------h~~v~n~llq~lD~GrltDs~Gr~Vd~k  700 (898)
T KOG1051|consen  636 LIGSPPGYVGKEE--GGQLTEAVKRRPYSVVLFEEIEKA-------------HPDVLNILLQLLDRGRLTDSHGREVDFK  700 (898)
T ss_pred             ccCCCcccccchh--HHHHHHHHhcCCceEEEEechhhc-------------CHHHHHHHHHHHhcCccccCCCcEeecc
Confidence              1  23455432  345666677788899999999987             678899999888865             


Q ss_pred             CeEEEEccChH
Q 005179          423 ELQCIASTTQD  433 (710)
Q Consensus       423 ~v~vI~att~~  433 (710)
                      +.+||.|.|..
T Consensus       701 N~I~IMTsn~~  711 (898)
T KOG1051|consen  701 NAIFIMTSNVG  711 (898)
T ss_pred             ceEEEEecccc
Confidence            45567666653

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=98.29  E-value=1.5e-05  Score=91.10  Aligned_cols=177  Identities=18%  Similarity=0.138  Sum_probs=110.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh----hhhhhccccCccHHHHHHHH---H--HHHHhc
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM----GLLMAGAKERGELEARVTTL---I--SEIQKS  381 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~----~~l~~g~~~~g~~e~~l~~~---~--~~~~~~  381 (710)
                      -.+++|.|++|+|||+++++++..+.. ..|       +..+..    ..++.|    ++++..++.=   +  ..+...
T Consensus        25 ~gGv~i~g~~G~~ks~~~r~l~~llp~-~~p-------~r~~p~~~t~~~L~Gg----~Dl~~~l~~g~~~~~pGlla~A   92 (584)
T PRK13406         25 LGGVVLRARAGPVRDRWLAALRALLPA-GTP-------LRRLPPGIADDRLLGG----LDLAATLRAGRPVAQRGLLAEA   92 (584)
T ss_pred             cceEEEEcCCCcHHHHHHHHHHHhcCC-CCC-------cccCCCCCcHHHccCC----chHHhHhhcCCcCCCCCceeec
Confidence            367999999999999999999987732 112       122111    112211    1122211110   0  112234


Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------------CeEEEEccChHHHHhhhhccHHHH
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                      .+.||||||+..+             ...+++.|.+.|+.|               .+.+|++.+..+|.  ..+.+++.
T Consensus        93 h~GvL~lDe~n~~-------------~~~~~~aLleame~G~vtIeR~G~s~~~Pa~F~LIat~~~~~~~--~~L~~~lL  157 (584)
T PRK13406         93 DGGVLVLAMAERL-------------EPGTAARLAAALDTGEVRLERDGLALRLPARFGLVALDEGAEED--ERAPAALA  157 (584)
T ss_pred             cCCEEEecCcccC-------------CHHHHHHHHHHHhCCcEEEEECCcEEecCCCcEEEecCCChhcc--cCCCHHhH
Confidence            4679999999998             566888888888865               45578875554443  35789999


Q ss_pred             cccc-ceEecCCCHHHHH-------HHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhh
Q 005179          447 RRFQ-PVLISEPSQEDAV-------RILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAH  518 (710)
Q Consensus       447 ~Rf~-~I~v~~Ps~~~~~-------~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~  518 (710)
                      .||. .|.+..|+..+..       .|... ..++   .++.++++.+++++..+..+--  ..+...+.++.-|.+.+.
T Consensus       158 DRf~l~v~v~~~~~~~~~~~~~~~~~I~~A-R~rl---~~v~v~~~~l~~i~~~~~~~gv--~S~Ra~i~llraARa~Aa  231 (584)
T PRK13406        158 DRLAFHLDLDGLALRDAREIPIDADDIAAA-RARL---PAVGPPPEAIAALCAAAAALGI--ASLRAPLLALRAARAAAA  231 (584)
T ss_pred             hheEEEEEcCCCChHHhcccCCCHHHHHHH-HHHH---ccCCCCHHHHHHHHHHHHHhCC--CCcCHHHHHHHHHHHHHH
Confidence            9998 7888888755432       22222 2222   4789999999998888776531  124555667766665555


Q ss_pred             hh
Q 005179          519 IE  520 (710)
Q Consensus       519 ~~  520 (710)
                      +.
T Consensus       232 L~  233 (584)
T PRK13406        232 LA  233 (584)
T ss_pred             Hc
Confidence            44

>smart00763 AAA_PrkA PrkA AAA domain

Probab=98.29  E-value=1.1e-06  Score=93.10  Aligned_cols=69  Identities=25%  Similarity=0.377  Sum_probs=54.3

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC----CCCcceeeCC----CCCCCc
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG----SVRIHYLFFP----SPFNSV  701 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg----~~~~li~~d~----se~~~~  701 (710)
                      .|+|++++++.+...++....|...+.+   .++|+||||||||++|++||+.|=.    .+..+..+..    |++...
T Consensus        52 ~~~G~~~~i~~lv~~l~~~a~g~~~~r~---il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~~~~~sp~~e~  128 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQ---ILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKWNGEESPMHED  128 (361)
T ss_pred             hccCcHHHHHHHHHHHHHHHhcCCCCCc---EEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEecCCCCCCccC
Confidence            5999999999999999888877765433   6899999999999999999999733    2446666665    555443

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

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

Probab=98.28  E-value=6.3e-07  Score=94.27  Aligned_cols=50  Identities=36%  Similarity=0.613  Sum_probs=37.4

Q ss_pred             HHHHHHHHhhCcccChHHHHH---HHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          619 LLVGLEEQLKKRVIGQDEAVA---AISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       619 ~l~~l~~~L~~~v~Gq~~a~~---~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      +..++++     |+||++.+.   .|.+++....         +.+++||||||||||+||++||..
T Consensus        19 RP~~lde-----~vGQ~HLlg~~~~lrr~v~~~~---------l~SmIl~GPPG~GKTTlA~liA~~   71 (436)
T COG2256          19 RPKSLDE-----VVGQEHLLGEGKPLRRAVEAGH---------LHSMILWGPPGTGKTTLARLIAGT   71 (436)
T ss_pred             CCCCHHH-----hcChHhhhCCCchHHHHHhcCC---------CceeEEECCCCCCHHHHHHHHHHh
Confidence            3445555     999988873   4444444333         258999999999999999999997

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.27  E-value=1.8e-06  Score=96.77  Aligned_cols=181  Identities=18%  Similarity=0.298  Sum_probs=105.2

Q ss_pred             CcccCHHHHHHHHHHHH--cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--------c
Q 005179          291 PVIGRETEIQRIIQILC--RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--------G  360 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~--~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--------g  360 (710)
                      .++|....+..+...+.  .....+++++|++|+||+++++++.......       +.+++.+++..+..        |
T Consensus       140 ~lig~s~~~~~~~~~i~~~~~~~~~vli~ge~g~gk~~~a~~ih~~s~~~-------~~~~i~~~c~~~~~~~~~~~lfg  212 (441)
T PRK10365        140 GMVGKSPAMQHLLSEIALVAPSEATVLIHGDSGTGKELVARAIHASSARS-------EKPLVTLNCAALNESLLESELFG  212 (441)
T ss_pred             ceEecCHHHHHHHHHHhhccCCCCeEEEEecCCCCHHHHHHHHHHcCCCC-------CCCeeeeeCCCCCHHHHHHHhcC
Confidence            35666666665554332  2345779999999999999999998765322       34566666654321        1


Q ss_pred             cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEE
Q 005179          361 AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCI  427 (710)
Q Consensus       361 ~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI  427 (710)
                      . ..|.+..........+....+++||||||+.|             ..+.+..|..+++.+             ++++|
T Consensus       213 ~-~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l-------------~~~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii  278 (441)
T PRK10365        213 H-EKGAFTGADKRREGRFVEADGGTLFLDEIGDI-------------SPMMQVRLLRAIQEREVQRVGSNQTISVDVRLI  278 (441)
T ss_pred             C-CCCCcCCCCcCCCCceeECCCCEEEEeccccC-------------CHHHHHHHHHHHccCcEEeCCCCceeeeceEEE
Confidence            0 00100000000001122345678999999999             445566666666543             35688


Q ss_pred             EccChHHHHhh--hhccHHHHccccceEecCCCHHHH----HHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          428 ASTTQDEHRTQ--FEKDKALARRFQPVLISEPSQEDA----VRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       428 ~att~~~~~~~--~~~d~aL~~Rf~~I~v~~Ps~~~~----~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      ++|+.+.....  -...+.|..||..+.+..|+..+|    ..+++.++.++...++   ..+++++++.+..+
T Consensus       279 ~~t~~~~~~~~~~~~~~~~l~~~l~~~~i~~ppLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  352 (441)
T PRK10365        279 AATHRDLAAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFAERNRKAVKGFTPQAMDLLIHY  352 (441)
T ss_pred             EeCCCCHHHHHHcCCchHHHHHHhccceecCCChhhcchhHHHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHhC
Confidence            88776542211  124566677887777777765544    4455555555544333   35888888777544

>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=98.27  E-value=3.3e-06  Score=88.78  Aligned_cols=173  Identities=17%  Similarity=0.240  Sum_probs=90.8

Q ss_pred             CHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh----------hh--hc
Q 005179          295 RETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL----------LM--AG  360 (710)
Q Consensus       295 r~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~----------l~--~g  360 (710)
                      ||.+++++.+.|..  ....-+.|+|++|+|||+||..+++......   .. + .+++++++.          +.  .+
T Consensus         1 re~~~~~l~~~L~~~~~~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~---~f-~-~v~wv~~~~~~~~~~~~~~i~~~l~   75 (287)
T PF00931_consen    1 REKEIEKLKDWLLDNSNEVRVVAIVGMGGIGKTTLARQVARDLRIKN---RF-D-GVIWVSLSKNPSLEQLLEQILRQLG   75 (287)
T ss_dssp             -HHHHHHHHHHHHTTTTSSEEEEEEESTTSSHHHHHHHHHCHHHHCC---CC-T-EEEEEEEES-SCCHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHhhCCCCCeEEEEEEcCCcCCcceeeeeccccccccc---cc-c-ccccccccccccccccccccccccc
Confidence            67899999999987  4455678999999999999999997743111   11 1 223332211          10  01


Q ss_pred             cc-----cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEEccChH
Q 005179          361 AK-----ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIASTTQD  433 (710)
Q Consensus       361 ~~-----~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~att~~  433 (710)
                      ..     ...+.+.....+.+.+ ...+++|++||++...              .+.. +...+.  ..+..+|.||...
T Consensus        76 ~~~~~~~~~~~~~~~~~~l~~~L-~~~~~LlVlDdv~~~~--------------~~~~-l~~~~~~~~~~~kilvTTR~~  139 (287)
T PF00931_consen   76 EPDSSISDPKDIEELQDQLRELL-KDKRCLLVLDDVWDEE--------------DLEE-LREPLPSFSSGSKILVTTRDR  139 (287)
T ss_dssp             CC-STSSCCSSHHHHHHHHHHHH-CCTSEEEEEEEE-SHH--------------HH--------HCHHSS-EEEEEESCG
T ss_pred             ccccccccccccccccccchhhh-ccccceeeeeeecccc--------------cccc-ccccccccccccccccccccc
Confidence            11     1223444344444433 3458999999998762              1211 222221  2235566666554


Q ss_pred             HHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          434 EHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      .      +-..+......+.+...+.++..+++......... ......++..+.+++.+.+
T Consensus       140 ~------v~~~~~~~~~~~~l~~L~~~ea~~L~~~~~~~~~~-~~~~~~~~~~~~i~~~c~g  194 (287)
T PF00931_consen  140 S------VAGSLGGTDKVIELEPLSEEEALELFKKRAGRKES-ESPEDLEDLAKEIVEKCGG  194 (287)
T ss_dssp             G------GGTTHHSCEEEEECSS--HHHHHHHHHHHHTSHS-----TTSCTHHHHHHHHTTT
T ss_pred             c------ccccccccccccccccccccccccccccccccccc-ccccccccccccccccccc
Confidence            2      11122222447999999999999888876442210 0112223455667776654

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.

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.26  E-value=1.2e-06  Score=97.90  Aligned_cols=48  Identities=38%  Similarity=0.561  Sum_probs=40.7

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||++++..+.+++...+        ...++||+||||||||++|+++|+.++..
T Consensus        16 ivGq~~i~~~L~~~i~~~~--------l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~   63 (472)
T PRK14962         16 VVGQDHVKKLIINALKKNS--------ISHAYIFAGPRGTGKTTVARILAKSLNCE   63 (472)
T ss_pred             ccCcHHHHHHHHHHHHcCC--------CCeEEEEECCCCCCHHHHHHHHHHHhccc
Confidence            9999999999888776543        22479999999999999999999998753

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=98.26  E-value=7.9e-06  Score=84.04  Aligned_cols=166  Identities=22%  Similarity=0.283  Sum_probs=99.5

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh------hh--
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG------LL--  357 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~------~l--  357 (710)
                      -++.|..++-..+.+++.+    +..+.++++||.|+|||.++....... + .+.+   +.-++.+|..      .+  
T Consensus        24 ~~l~g~~~~~~~l~~~lkqt~~~gEsnsviiigprgsgkT~li~~~Ls~~-q-~~~E---~~l~v~Lng~~~~dk~al~~   98 (408)
T KOG2228|consen   24 INLFGVQDEQKHLSELLKQTILHGESNSVIIIGPRGSGKTILIDTRLSDI-Q-ENGE---NFLLVRLNGELQTDKIALKG   98 (408)
T ss_pred             cceeehHHHHHHHHHHHHHHHHhcCCCceEEEccCCCCceEeeHHHHhhH-H-hcCC---eEEEEEECccchhhHHHHHH
Confidence            4577776666666555543    678899999999999999876544332 1 1110   1112222211      00  


Q ss_pred             ---------hhccccCccHHHHHHHHHHHHHhc-----CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc-ccCC
Q 005179          358 ---------MAGAKERGELEARVTTLISEIQKS-----GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS-LGRG  422 (710)
Q Consensus       358 ---------~~g~~~~g~~e~~l~~~~~~~~~~-----~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~-l~~~  422 (710)
                               ....+..|.+.+.+..++..++..     .++|+++||+|..++-..        +.-+.|++.-. -++.
T Consensus        99 I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~r--------QtllYnlfDisqs~r~  170 (408)
T KOG2228|consen   99 ITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHSR--------QTLLYNLFDISQSARA  170 (408)
T ss_pred             HHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccchh--------hHHHHHHHHHHhhcCC
Confidence                     122344566777777777766542     356777899999865311        22234443211 1256


Q ss_pred             CeEEEEccChHHHHhhhhccHHHHcccc--ceEecCC-CHHHHHHHHHHHH
Q 005179          423 ELQCIASTTQDEHRTQFEKDKALARRFQ--PVLISEP-SQEDAVRILLGLR  470 (710)
Q Consensus       423 ~v~vI~att~~~~~~~~~~d~aL~~Rf~--~I~v~~P-s~~~~~~IL~~l~  470 (710)
                      .+.+||.|+.-+...+  +...+.+||.  .|.+.++ +.++...+++.++
T Consensus       171 Piciig~Ttrld~lE~--LEKRVKSRFshr~I~m~~~~~l~~yv~l~r~ll  219 (408)
T KOG2228|consen  171 PICIIGVTTRLDILEL--LEKRVKSRFSHRVIFMLPSLPLGDYVDLYRKLL  219 (408)
T ss_pred             CeEEEEeeccccHHHH--HHHHHHhhcccceeeccCCCChHHHHHHHHHHh
Confidence            7889998887664443  4578999996  4666654 4777777777665

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.25  E-value=1.7e-06  Score=91.38  Aligned_cols=72  Identities=19%  Similarity=0.327  Sum_probs=49.0

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc---cCccHHHHHHHHHHHHHhcCCeEE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK---ERGELEARVTTLISEIQKSGDVIL  386 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~---~~g~~e~~l~~~~~~~~~~~~~IL  386 (710)
                      ...+++|+|++|||||+|+.++++.+...       +..+..+.+..++..-+   ..+.    +...++.+..  ..+|
T Consensus       155 ~~~gl~L~G~~G~GKThLa~Aia~~l~~~-------g~~v~~~~~~~l~~~lk~~~~~~~----~~~~l~~l~~--~dlL  221 (306)
T PRK08939        155 KVKGLYLYGDFGVGKSYLLAAIANELAKK-------GVSSTLLHFPEFIRELKNSISDGS----VKEKIDAVKE--APVL  221 (306)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCCEEEEEHHHHHHHHHHHHhcCc----HHHHHHHhcC--CCEE
Confidence            45689999999999999999999999653       56666666665542211   1122    2344444444  3499


Q ss_pred             EEccchhh
Q 005179          387 FIDEVHTL  394 (710)
Q Consensus       387 ~IDEid~l  394 (710)
                      +|||+..-
T Consensus       222 iIDDiG~e  229 (306)
T PRK08939        222 MLDDIGAE  229 (306)
T ss_pred             EEecCCCc
Confidence            99999764

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=98.22  E-value=1.4e-06  Score=94.86  Aligned_cols=62  Identities=32%  Similarity=0.461  Sum_probs=45.6

Q ss_pred             cccChHHHHHHHHHHHHHh--------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRS--------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~--------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .|+|.++.++.|...+...        ..|+..|    .++|||||||||||++|+++|+.+..   .++++..+++
T Consensus       123 di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p----~gvLL~GppGtGKT~lakaia~~l~~---~~~~v~~~~l  192 (364)
T TIGR01242       123 DIGGLEEQIREIREAVELPLKHPELFEEVGIEPP----KGVLLYGPPGTGKTLLAKAVAHETNA---TFIRVVGSEL  192 (364)
T ss_pred             HhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCC----ceEEEECCCCCCHHHHHHHHHHhCCC---CEEecchHHH
Confidence            4788888888887776432        3355443    68999999999999999999998643   4666655443

Many proteins may score above the trusted cutoff because an internal

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=98.22  E-value=1.5e-06  Score=98.50  Aligned_cols=61  Identities=36%  Similarity=0.464  Sum_probs=43.5

Q ss_pred             ccChHHHHHHHHHHHH-------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVK-------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~-------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|++++++.+...+.       +...|...|    .++|||||||||||++|++||..+   .-.++.++.+++
T Consensus        57 i~g~~~~k~~l~~~~~~l~~~~~~~~~g~~~~----~giLL~GppGtGKT~la~alA~~~---~~~~~~i~~~~~  124 (495)
T TIGR01241        57 VAGIDEAKEELMEIVDFLKNPSKFTKLGAKIP----KGVLLVGPPGTGKTLLAKAVAGEA---GVPFFSISGSDF  124 (495)
T ss_pred             hCCHHHHHHHHHHHHHHHHCHHHHHhcCCCCC----CcEEEECCCCCCHHHHHHHHHHHc---CCCeeeccHHHH
Confidence            5666666666655553       333454333    589999999999999999999984   446777776655

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.

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=98.22  E-value=1.7e-06  Score=94.29  Aligned_cols=57  Identities=30%  Similarity=0.508  Sum_probs=46.5

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCC-CeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRP-TAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp-~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .|+||+.+++.+.+++...+.+.....++ ..++||+||||||||++|+++|+.++..
T Consensus         6 ~IiGq~~~~~~L~~~i~~~~~~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~   63 (394)
T PRK07940          6 DLVGQEAVVAELRAAARAARADVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCT   63 (394)
T ss_pred             hccChHHHHHHHHHHHHhccccccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCC
Confidence            49999999999999998776443333332 2479999999999999999999998764

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=98.22  E-value=1.3e-05  Score=82.84  Aligned_cols=178  Identities=13%  Similarity=0.248  Sum_probs=109.8

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh------
Q 005179          287 ELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM------  358 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~------  358 (710)
                      ..|+.+++....++.++.--.+  .--.++||.|+.||||-.+|++-......++.|       ++.++|..+-      
T Consensus       201 ~~F~~~v~~S~~mk~~v~qA~k~AmlDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~p-------FlalNCA~lPe~~aEs  273 (511)
T COG3283         201 SGFEQIVAVSPKMKHVVEQAQKLAMLDAPLLITGETGTGKDLLAKACHLASPRHSKP-------FLALNCASLPEDAAES  273 (511)
T ss_pred             cchHHHhhccHHHHHHHHHHHHhhccCCCeEEecCCCchHHHHHHHHhhcCcccCCC-------eeEeecCCCchhHhHH
Confidence            3577889998888887764433  234678999999999999999987666555444       4444444332      


Q ss_pred             --hccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------C
Q 005179          359 --AGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------E  423 (710)
Q Consensus       359 --~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~  423 (710)
                        .|.. .|.  +--..+|+.+   .+..+|+|||..+             +..++..|+.++..|             +
T Consensus       274 ElFG~a-pg~--~gk~GffE~A---ngGTVlLDeIgEm-------------Sp~lQaKLLRFL~DGtFRRVGee~Ev~vd  334 (511)
T COG3283         274 ELFGHA-PGD--EGKKGFFEQA---NGGTVLLDEIGEM-------------SPRLQAKLLRFLNDGTFRRVGEDHEVHVD  334 (511)
T ss_pred             HHhcCC-CCC--CCccchhhhc---cCCeEEeehhhhc-------------CHHHHHHHHHHhcCCceeecCCcceEEEE
Confidence              1111 110  0012344433   3557899999888             666778888888765             4


Q ss_pred             eEEEEccChH--HHHhhhhccHHHHccccceEecCCCHHHH----HHHHHHHHHHHHhhcCC---CCCHHHHHHHH
Q 005179          424 LQCIASTTQD--EHRTQFEKDKALARRFQPVLISEPSQEDA----VRILLGLREKYEAHHNC---KFTLEAINAAV  490 (710)
Q Consensus       424 v~vI~att~~--~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~----~~IL~~l~~~~~~~~~~---~i~~~~l~~l~  490 (710)
                      ++||++|..+  ++...-+.-..|.-|+.++.+..|...+|    ..+.+.+..++....++   +++++.+.++.
T Consensus       335 VRVIcatq~nL~~lv~~g~fReDLfyRLNVLtl~~PpLRer~~di~pL~e~Fv~q~s~elg~p~pkl~~~~~~~L~  410 (511)
T COG3283         335 VRVICATQVNLVELVQKGKFREDLFYRLNVLTLNLPPLRERPQDIMPLAELFVQQFSDELGVPRPKLAADLLTVLT  410 (511)
T ss_pred             EEEEecccccHHHHHhcCchHHHHHHHhheeeecCCccccCcccchHHHHHHHHHHHHHhCCCCCccCHHHHHHHH
Confidence            6789887653  22222233456666888777777764444    44455555555544443   56777666553

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=98.21  E-value=1.4e-06  Score=93.79  Aligned_cols=72  Identities=33%  Similarity=0.457  Sum_probs=53.6

Q ss_pred             cHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--Ccc
Q 005179          613 TADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIH  690 (710)
Q Consensus       613 ~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~l  690 (710)
                      .|.+..+...+.+     ++|++++++.+...+...+         ..++||+||||||||++|+++|+.+++..  ...
T Consensus         4 ~w~~ky~P~~~~~-----~~g~~~~~~~L~~~~~~~~---------~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~   69 (337)
T PRK12402          4 LWTEKYRPALLED-----ILGQDEVVERLSRAVDSPN---------LPHLLVQGPPGSGKTAAVRALARELYGDPWENNF   69 (337)
T ss_pred             chHHhhCCCcHHH-----hcCCHHHHHHHHHHHhCCC---------CceEEEECCCCCCHHHHHHHHHHHhcCcccccce
Confidence            3444444444444     8899999999888765321         12789999999999999999999998764  457


Q ss_pred             eeeCCCCC
Q 005179          691 YLFFPSPF  698 (710)
Q Consensus       691 i~~d~se~  698 (710)
                      +.++++++
T Consensus        70 ~~i~~~~~   77 (337)
T PRK12402         70 TEFNVADF   77 (337)
T ss_pred             EEechhhh
Confidence            78888765

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.20  E-value=1.3e-06  Score=96.25  Aligned_cols=48  Identities=42%  Similarity=0.599  Sum_probs=41.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.++..+.+++...+.        ...+||+||||||||++|+++|+.++..
T Consensus        20 vVGQe~iv~~L~~~i~~~ri--------~ha~Lf~GP~GtGKTTlAriLAk~Lnce   67 (484)
T PRK14956         20 VIHQDLAIGALQNALKSGKI--------GHAYIFFGPRGVGKTTIARILAKRLNCE   67 (484)
T ss_pred             HhChHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHhcCcc
Confidence            99999999999988876542        1368999999999999999999998763

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.18  E-value=2.3e-06  Score=95.20  Aligned_cols=46  Identities=30%  Similarity=0.586  Sum_probs=39.9

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      |+||+.+++.+.+++...+.        ..++||+||+|||||++|+++|+.|+
T Consensus        15 liGQe~vv~~L~~a~~~~ri--------~ha~Lf~Gp~G~GKTT~ArilAk~Ln   60 (491)
T PRK14964         15 LVGQDVLVRILRNAFTLNKI--------PQSILLVGASGVGKTTCARIISLCLN   60 (491)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CceEEEECCCCccHHHHHHHHHHHHc
Confidence            99999999999888766542        24899999999999999999999874

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.18  E-value=2.2e-05  Score=82.37  Aligned_cols=145  Identities=14%  Similarity=0.128  Sum_probs=92.9

Q ss_pred             HHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCcc---ccCceEEEeehhhhhhccccCccHHHHHHH
Q 005179          298 EIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVF---LLSKRIMSLDMGLLMAGAKERGELEARVTT  373 (710)
Q Consensus       298 ~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~---l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~  373 (710)
                      .++.+...+....-.|+ ||+|+.|+||+.+++.+++.+.+......   .....+..+|..    |...  . .+.++.
T Consensus         4 ~~~~l~~~i~~~~l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~----g~~i--~-vd~Ir~   76 (299)
T PRK07132          4 WIKFLDNSATQNKISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIF----DKDL--S-KSEFLS   76 (299)
T ss_pred             HHHHHHHHHHhCCCCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccC----CCcC--C-HHHHHH
Confidence            44556666666555555 59999999999999999999855321100   001112222210    1110  1 123455


Q ss_pred             HHHHHHh-----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHHhhhhccHHHH
Q 005179          374 LISEIQK-----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       374 ~~~~~~~-----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                      +.+.+..     ++.-|++||+++.+             ....++.|+..+++  ....+|..|+..+     .+-+++.
T Consensus        77 l~~~~~~~~~~~~~~KvvII~~~e~m-------------~~~a~NaLLK~LEEPp~~t~~il~~~~~~-----kll~TI~  138 (299)
T PRK07132         77 AINKLYFSSFVQSQKKILIIKNIEKT-------------SNSLLNALLKTIEEPPKDTYFLLTTKNIN-----KVLPTIV  138 (299)
T ss_pred             HHHHhccCCcccCCceEEEEeccccc-------------CHHHHHHHHHHhhCCCCCeEEEEEeCChH-----hChHHHH
Confidence            5555421     35679999999888             55678888888885  3455555555433     5678999


Q ss_pred             ccccceEecCCCHHHHHHHHH
Q 005179          447 RRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       447 ~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                      +|++.+.+.+|+.++....|.
T Consensus       139 SRc~~~~f~~l~~~~l~~~l~  159 (299)
T PRK07132        139 SRCQVFNVKEPDQQKILAKLL  159 (299)
T ss_pred             hCeEEEECCCCCHHHHHHHHH
Confidence            999999999999998666654

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=98.18  E-value=2.1e-06  Score=91.18  Aligned_cols=50  Identities=26%  Similarity=0.426  Sum_probs=40.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ++||++.++.+...+...+..-    .+..+++|+||||||||++|+++|+.+-
T Consensus         6 ~iG~~~~~~~l~~~l~~~~~~~----~~~~~~ll~Gp~G~GKT~la~~ia~~~~   55 (305)
T TIGR00635         6 FIGQEKVKEQLQLFIEAAKMRQ----EALDHLLLYGPPGLGKTTLAHIIANEMG   55 (305)
T ss_pred             HcCHHHHHHHHHHHHHHHHhcC----CCCCeEEEECCCCCCHHHHHHHHHHHhC
Confidence            9999999999988886554321    2224799999999999999999999964

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.

>PRK04195 replication factor C large subunit; Provisional

Probab=98.16  E-value=2.6e-06  Score=96.29  Aligned_cols=73  Identities=30%  Similarity=0.344  Sum_probs=55.6

Q ss_pred             cHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCccee
Q 005179          613 TADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYL  692 (710)
Q Consensus       613 ~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~  692 (710)
                      .|.+..+...+.+     ++|++++++.+...+.....|.     |..++||+||||||||++|++||+.+.   ..++.
T Consensus         3 ~W~eKyrP~~l~d-----lvg~~~~~~~l~~~l~~~~~g~-----~~~~lLL~GppG~GKTtla~ala~el~---~~~ie   69 (482)
T PRK04195          3 PWVEKYRPKTLSD-----VVGNEKAKEQLREWIESWLKGK-----PKKALLLYGPPGVGKTSLAHALANDYG---WEVIE   69 (482)
T ss_pred             CchhhcCCCCHHH-----hcCCHHHHHHHHHHHHHHhcCC-----CCCeEEEECCCCCCHHHHHHHHHHHcC---CCEEE
Confidence            3555555555666     9999999999998887665332     235899999999999999999999972   35777


Q ss_pred             eCCCCC
Q 005179          693 FFPSPF  698 (710)
Q Consensus       693 ~d~se~  698 (710)
                      +|.|.+
T Consensus        70 lnasd~   75 (482)
T PRK04195         70 LNASDQ   75 (482)
T ss_pred             Eccccc
Confidence            777765

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.12  E-value=4e-06  Score=93.08  Aligned_cols=143  Identities=15%  Similarity=0.196  Sum_probs=82.4

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEV  391 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEi  391 (710)
                      -|+||+|.||||||.+.+.+++....+....   |+.--.+-+...+.-....+++...-    ..+.-+++.|.+|||+
T Consensus       463 INILL~GDPGtsKSqlLqyv~~l~pRg~yTS---GkGsSavGLTayVtrd~dtkqlVLes----GALVLSD~GiCCIDEF  535 (804)
T KOG0478|consen  463 INILLVGDPGTSKSQLLQYCHRLLPRGVYTS---GKGSSAVGLTAYVTKDPDTRQLVLES----GALVLSDNGICCIDEF  535 (804)
T ss_pred             ceEEEecCCCcCHHHHHHHHHHhCCcceeec---CCccchhcceeeEEecCccceeeeec----CcEEEcCCceEEchhh
Confidence            5899999999999999999998774432111   11100000011110011111110000    0011245678999999


Q ss_pred             hhhhhCCCCCCCCCCChHhHHHhhcccccC---------------CCeEEEEccChHH--H------HhhhhccHHHHcc
Q 005179          392 HTLIGSGTVGRGNKGTGLDISNLLKPSLGR---------------GELQCIASTTQDE--H------RTQFEKDKALARR  448 (710)
Q Consensus       392 d~l~~~~~~~~~~~~~~~~~~~~L~~~l~~---------------~~v~vI~att~~~--~------~~~~~~d~aL~~R  448 (710)
                      |.|.             ....+.|.+.|++               .+..|++++|+.+  |      .+.+.+.|.|.+|
T Consensus       536 DKM~-------------dStrSvLhEvMEQQTvSIAKAGII~sLNAR~SVLAaANP~~skynp~k~i~eNI~LpptLLSR  602 (804)
T KOG0478|consen  536 DKMS-------------DSTRSVLHEVMEQQTLSIAKAGIIASLNARCSVLAAANPIRSKYNPNKSIIENINLPPTLLSR  602 (804)
T ss_pred             hhhh-------------HHHHHHHHHHHHHhhhhHhhcceeeeccccceeeeeeccccccCCCCCchhhccCCChhhhhh
Confidence            9992             2334555555543               2344788877532  1      2245678999999


Q ss_pred             cc--ceEecCCCHHHHHHHHHHHHHHHH
Q 005179          449 FQ--PVLISEPSQEDAVRILLGLREKYE  474 (710)
Q Consensus       449 f~--~I~v~~Ps~~~~~~IL~~l~~~~~  474 (710)
                      |+  -+-++.|+...-..+-.++...|.
T Consensus       603 FDLIylllD~~DE~~Dr~La~HivsLy~  630 (804)
T KOG0478|consen  603 FDLIFLLLDKPDERSDRRLADHIVALYP  630 (804)
T ss_pred             hcEEEEEecCcchhHHHHHHHHHHHhcc
Confidence            99  456688887766777777776654

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.12  E-value=3.5e-06  Score=94.82  Aligned_cols=47  Identities=36%  Similarity=0.574  Sum_probs=40.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+++++.+.+.+...+.        ...+|||||||||||++|+++|+.++.
T Consensus        16 vvGq~~v~~~L~~~i~~~~l--------~ha~Lf~GppGtGKTTlA~~lA~~l~c   62 (504)
T PRK14963         16 VVGQEHVKEVLLAALRQGRL--------GHAYLFSGPRGVGKTTTARLIAMAVNC   62 (504)
T ss_pred             hcChHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHHhc
Confidence            99999999999988876432        235799999999999999999999973

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=98.11  E-value=3.1e-06  Score=90.84  Aligned_cols=50  Identities=26%  Similarity=0.408  Sum_probs=41.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ++||++.++.+...+...+..    +.|..++|||||||||||++|+++|+.+-
T Consensus        27 ~vG~~~~~~~l~~~l~~~~~~----~~~~~~~ll~GppG~GKT~la~~ia~~l~   76 (328)
T PRK00080         27 FIGQEKVKENLKIFIEAAKKR----GEALDHVLLYGPPGLGKTTLANIIANEMG   76 (328)
T ss_pred             hcCcHHHHHHHHHHHHHHHhc----CCCCCcEEEECCCCccHHHHHHHHHHHhC
Confidence            899999999998887665422    23445899999999999999999999963

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.11  E-value=2.9e-06  Score=95.65  Aligned_cols=48  Identities=42%  Similarity=0.630  Sum_probs=42.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.+++.+.+++...+.        ...+||+||||||||++|+++|+.|+..
T Consensus        18 ivGq~~v~~~L~~~~~~~~l--------~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~   65 (509)
T PRK14958         18 VIGQAPVVRALSNALDQQYL--------HHAYLFTGTRGVGKTTISRILAKCLNCE   65 (509)
T ss_pred             hcCCHHHHHHHHHHHHhCCC--------CeeEEEECCCCCCHHHHHHHHHHHhcCC
Confidence            99999999999999876552        1368999999999999999999999864

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=98.10  E-value=3.7e-06  Score=93.43  Aligned_cols=51  Identities=27%  Similarity=0.511  Sum_probs=45.4

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|++++++.|...++.+..|+..+.+   .++|+||||+|||+||+.||+.|
T Consensus        77 d~yGlee~ieriv~~l~~Aa~gl~~~~~---IL~LvGPpG~GKSsLa~~la~~l  127 (644)
T PRK15455         77 EFYGMEEAIEQIVSYFRHAAQGLEEKKQ---ILYLLGPVGGGKSSLAERLKSLM  127 (644)
T ss_pred             cccCcHHHHHHHHHHHHHHHHhcCCCCc---eEEEecCCCCCchHHHHHHHHHH
Confidence            3899999999999999888888866433   78999999999999999999986

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.10  E-value=4.2e-06  Score=95.36  Aligned_cols=47  Identities=38%  Similarity=0.600  Sum_probs=40.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.+++.+.+.+...+.        ...+||+||+|||||++|+++|+.|+.
T Consensus        15 ivGq~~i~~~L~~~i~~~r~--------~ha~Lf~Gp~G~GKTt~A~~lAk~l~c   61 (584)
T PRK14952         15 VVGQEHVTEPLSSALDAGRI--------NHAYLFSGPRGCGKTSSARILARSLNC   61 (584)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhcc
Confidence            99999999999998875431        135899999999999999999999984

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.10  E-value=4.8e-05  Score=83.03  Aligned_cols=176  Identities=12%  Similarity=0.145  Sum_probs=101.8

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHH-----cCC-C-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILC-----RRT-K-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~-----~~~-~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ..|.+++.|.+++++-=...-|..+.++|.     .+. + +-+||+||+||||||.++.|+.++          +..+.
T Consensus        70 elW~eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~~~l~~~iLLltGPsGcGKSTtvkvLskel----------g~~~~  139 (634)
T KOG1970|consen   70 ELWVEKYKPRTLEELAVHKKKISEVKQWLKQVAEFTPKLGSRILLLTGPSGCGKSTTVKVLSKEL----------GYQLI  139 (634)
T ss_pred             chhHHhcCcccHHHHhhhHHhHHHHHHHHHHHHHhccCCCceEEEEeCCCCCCchhHHHHHHHhh----------Cceee
Confidence            467788889888888777777777777766     222 2 235788999999999999999987          33333


Q ss_pred             Eee-------hhhhh-----hccccCccHHHHHHHHHHHHH------------hcCCeEEEEccchhhhhCCCCCCCCCC
Q 005179          351 SLD-------MGLLM-----AGAKERGELEARVTTLISEIQ------------KSGDVILFIDEVHTLIGSGTVGRGNKG  406 (710)
Q Consensus       351 ~ld-------~~~l~-----~g~~~~g~~e~~l~~~~~~~~------------~~~~~IL~IDEid~l~~~~~~~~~~~~  406 (710)
                      +-.       ...+.     .+..+... -..++.++..+.            ...+.+|+|||+-..+...        
T Consensus       140 Ew~Npi~~~~~~~~h~~t~~~~~~~~s~-L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d--------  210 (634)
T KOG1970|consen  140 EWSNPINLKEPENLHNETSFLMFPYQSQ-LAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRD--------  210 (634)
T ss_pred             eecCCccccccccccccchhcccchhhH-HHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhh--------
Confidence            221       00000     00011111 111222222221            1235689999998875431        


Q ss_pred             ChHhHHHhhcccccCCCe--EEEEcc-----ChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHH
Q 005179          407 TGLDISNLLKPSLGRGEL--QCIAST-----TQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKY  473 (710)
Q Consensus       407 ~~~~~~~~L~~~l~~~~v--~vI~at-----t~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~  473 (710)
                      ....+.+.|..+...+..  ++|.|-     +...|+. +-.|-....|...|.|.|-...-..+.|+.++...
T Consensus       211 ~~~~f~evL~~y~s~g~~PlIf~iTd~~~~g~nnq~rl-f~~d~q~~~ri~~IsFNPIa~T~MKK~L~ric~~e  283 (634)
T KOG1970|consen  211 DSETFREVLRLYVSIGRCPLIFIITDSLSNGNNNQDRL-FPKDIQEEPRISNISFNPIAPTIMKKFLKRICRIE  283 (634)
T ss_pred             hHHHHHHHHHHHHhcCCCcEEEEEeccccCCCcchhhh-chhhhhhccCcceEeecCCcHHHHHHHHHHHHHHh
Confidence            133456666655555543  333321     2222222 22333444577789999988888788888777654

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.09  E-value=2.8e-05  Score=80.93  Aligned_cols=145  Identities=13%  Similarity=0.149  Sum_probs=92.9

Q ss_pred             CHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--------------ccCceEEEeehhhhhh
Q 005179          295 RETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--------------LLSKRIMSLDMGLLMA  359 (710)
Q Consensus       295 r~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--------------l~~~~v~~ld~~~l~~  359 (710)
                      +...+..+...+...+-.+ .||+||  +||+++|..+|+.+.+.+....              .....++.+...    
T Consensus         7 q~~~~~~L~~~~~~~rl~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~----   80 (290)
T PRK07276          7 QPKVFQRFQTILEQDRLNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQ----   80 (290)
T ss_pred             HHHHHHHHHHHHHcCCcceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCC----
Confidence            3456677777777766554 588895  7899999999999876542110              001112222110    


Q ss_pred             ccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChH
Q 005179          360 GAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQD  433 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~  433 (710)
                      |.   .--.+.++.+...+..    ++.-|++||++|.|             .....|.|+..|++.  +.++|..|+..
T Consensus        81 ~~---~I~idqIR~l~~~~~~~p~~~~~kV~II~~ad~m-------------~~~AaNaLLKtLEEPp~~t~~iL~t~~~  144 (290)
T PRK07276         81 GQ---VIKTDTIRELVKNFSQSGYEGKQQVFIIKDADKM-------------HVNAANSLLKVIEEPQSEIYIFLLTNDE  144 (290)
T ss_pred             CC---cCCHHHHHHHHHHHhhCcccCCcEEEEeehhhhc-------------CHHHHHHHHHHhcCCCCCeEEEEEECCh
Confidence            10   0012345666555543    34569999999999             566789998889863  46666666655


Q ss_pred             HHHhhhhccHHHHccccceEecCCCHHHHHHHHH
Q 005179          434 EHRTQFEKDKALARRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                      +     .+-|++++|++.|.|+. +.++..++|.
T Consensus       145 ~-----~lLpTI~SRcq~i~f~~-~~~~~~~~L~  172 (290)
T PRK07276        145 N-----KVLPTIKSRTQIFHFPK-NEAYLIQLLE  172 (290)
T ss_pred             h-----hCchHHHHcceeeeCCC-cHHHHHHHHH
Confidence            4     67899999999999965 5555444443

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=98.09  E-value=5.4e-06  Score=94.68  Aligned_cols=205  Identities=14%  Similarity=0.187  Sum_probs=109.3

Q ss_pred             CCCcccCHHHHHHHHHHHHcC------------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          289 IDPVIGRETEIQRIIQILCRR------------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~------------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      ...+.|.+...+.+.-.|...            .--|+||+|.||||||.|.+.+++....+-   +..+......-+..
T Consensus       285 aPsIyG~e~VKkAilLqLfgGv~k~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~aPr~v---ytsgkgss~~GLTA  361 (682)
T COG1241         285 APSIYGHEDVKKAILLQLFGGVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGV---YTSGKGSSAAGLTA  361 (682)
T ss_pred             cccccCcHHHHHHHHHHhcCCCcccCCCCcccccceeEEEcCCCchhHHHHHHHHHhhCCceE---EEccccccccCcee
Confidence            456888887444443333221            125899999999999999999987763211   11111111111111


Q ss_pred             hhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCC-------------
Q 005179          357 LMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGE-------------  423 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~-------------  423 (710)
                      .+.-.+..|+|.  +..  ..+.-++++|.+|||+|.+             .......|...|++..             
T Consensus       362 av~rd~~tge~~--Lea--GALVlAD~Gv~cIDEfdKm-------------~~~dr~aihEaMEQQtIsIaKAGI~atLn  424 (682)
T COG1241         362 AVVRDKVTGEWV--LEA--GALVLADGGVCCIDEFDKM-------------NEEDRVAIHEAMEQQTISIAKAGITATLN  424 (682)
T ss_pred             EEEEccCCCeEE--EeC--CEEEEecCCEEEEEeccCC-------------ChHHHHHHHHHHHhcEeeecccceeeecc
Confidence            110011111110  000  0011245779999999988             2233445555555322             


Q ss_pred             --eEEEEccChHH--H------HhhhhccHHHHccccc--eEecCCCHHHHHHHHHHHHHHHHhhcCCCC----------
Q 005179          424 --LQCIASTTQDE--H------RTQFEKDKALARRFQP--VLISEPSQEDAVRILLGLREKYEAHHNCKF----------  481 (710)
Q Consensus       424 --v~vI~att~~~--~------~~~~~~d~aL~~Rf~~--I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i----------  481 (710)
                        ..+++++|+..  |      ...+.+++.|.+||+.  +..+.|+.+.-..+..+++..+.....-..          
T Consensus       425 ARcsvLAAaNP~~Gryd~~~~~~enI~l~~~lLSRFDLifvl~D~~d~~~D~~ia~hil~~h~~~~~~~~~~~~~~~~~~  504 (682)
T COG1241         425 ARCSVLAAANPKFGRYDPKKTVAENINLPAPLLSRFDLIFVLKDDPDEEKDEEIAEHILDKHRGEEPEETISLDGVDEVE  504 (682)
T ss_pred             hhhhhhhhhCCCCCcCCCCCCHHHhcCCChhHHhhCCeeEEecCCCCccchHHHHHHHHHHHhccccccccccccccccc
Confidence              22566666542  1      2346778999999993  455678887777777777765531111111          


Q ss_pred             --CHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          482 --TLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       482 --~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                        +.+.+...+.++++++. -.+.+.+...+....
T Consensus       505 ~~~~~~lrkYI~YAR~~v~-P~lt~ea~e~l~~~Y  538 (682)
T COG1241         505 ERDFELLRKYISYARKNVT-PVLTEEAREELEDYY  538 (682)
T ss_pred             cCcHHHHHHHHHHHhccCC-cccCHHHHHHHHHHH
Confidence              34556666666666532 234556666555444

>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=98.09  E-value=2.5e-06  Score=83.50  Aligned_cols=45  Identities=38%  Similarity=0.562  Sum_probs=34.2

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..|+||+.++.++.-+.    +|.       .++||+||||||||++|+.++..|=
T Consensus         3 ~dI~GQe~aKrAL~iAA----aG~-------h~lLl~GppGtGKTmlA~~l~~lLP   47 (206)
T PF01078_consen    3 SDIVGQEEAKRALEIAA----AGG-------HHLLLIGPPGTGKTMLARRLPSLLP   47 (206)
T ss_dssp             CCSSSTHHHHHHHHHHH----HCC---------EEEES-CCCTHHHHHHHHHHCS-
T ss_pred             hhhcCcHHHHHHHHHHH----cCC-------CCeEEECCCCCCHHHHHHHHHHhCC
Confidence            35999999998876543    342       4899999999999999999998753

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.

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.09  E-value=3.5e-06  Score=91.62  Aligned_cols=47  Identities=40%  Similarity=0.566  Sum_probs=40.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+++++.+.+++...+.        ...+||+||||||||++|+++|+.++.
T Consensus        18 iiGq~~~~~~l~~~~~~~~~--------~h~~L~~Gp~G~GKTtla~~la~~l~c   64 (363)
T PRK14961         18 IIGQKHIVTAISNGLSLGRI--------HHAWLLSGTRGVGKTTIARLLAKSLNC   64 (363)
T ss_pred             ccChHHHHHHHHHHHHcCCC--------CeEEEEecCCCCCHHHHHHHHHHHhcC
Confidence            99999999999888865432        136799999999999999999999975

>CHL00176 ftsH cell division protein; Validated

Probab=98.08  E-value=4.1e-06  Score=96.60  Aligned_cols=62  Identities=34%  Similarity=0.439  Sum_probs=44.4

Q ss_pred             ccChHHHHHHHHHHHHH-------hhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKR-------SRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~-------~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |+|.+++++.+...+..       ...|...|    .++||+||||||||++|++||..+   ...++.+++++|.
T Consensus       185 v~G~~~~k~~l~eiv~~lk~~~~~~~~g~~~p----~gVLL~GPpGTGKT~LAralA~e~---~~p~i~is~s~f~  253 (638)
T CHL00176        185 IAGIEEAKEEFEEVVSFLKKPERFTAVGAKIP----KGVLLVGPPGTGKTLLAKAIAGEA---EVPFFSISGSEFV  253 (638)
T ss_pred             ccChHHHHHHHHHHHHHHhCHHHHhhccCCCC----ceEEEECCCCCCHHHHHHHHHHHh---CCCeeeccHHHHH
Confidence            66666666666555433       33344332    589999999999999999999985   4568888877763

>PRK13531 regulatory ATPase RavA; Provisional

Probab=98.08  E-value=5.5e-06  Score=91.04  Aligned_cols=57  Identities=19%  Similarity=0.316  Sum_probs=48.3

Q ss_pred             HHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          618 MLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       618 ~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..+..+.+.|.+.|+|++++++.+..++...           +++||+||||||||++|++||..+-+
T Consensus         9 ~~i~~l~~~l~~~i~gre~vI~lll~aalag-----------~hVLL~GpPGTGKT~LAraLa~~~~~   65 (498)
T PRK13531          9 ERISRLSSALEKGLYERSHAIRLCLLAALSG-----------ESVFLLGPPGIAKSLIARRLKFAFQN   65 (498)
T ss_pred             HHHHHHHHHHhhhccCcHHHHHHHHHHHccC-----------CCEEEECCCChhHHHHHHHHHHHhcc
Confidence            4566788999999999999999987765432           48999999999999999999998543

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.08  E-value=3.7e-06  Score=92.52  Aligned_cols=48  Identities=27%  Similarity=0.424  Sum_probs=41.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.+++.+...+...+.        ..++||+||||||||++|+++|+.++..
T Consensus        18 iiGq~~~~~~L~~~~~~~~~--------~ha~lf~Gp~G~GKtt~A~~~a~~l~c~   65 (397)
T PRK14955         18 ITAQEHITRTIQNSLRMGRV--------GHGYIFSGLRGVGKTTAARVFAKAVNCQ   65 (397)
T ss_pred             ccChHHHHHHHHHHHHhCCc--------ceeEEEECCCCCCHHHHHHHHHHHhcCC
Confidence            99999999999888765432        1369999999999999999999999863

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.07  E-value=3.4e-06  Score=98.31  Aligned_cols=48  Identities=35%  Similarity=0.558  Sum_probs=41.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.++..+.+++...+.        ...+||+||||||||++|+++|+.|+..
T Consensus        18 IIGQe~Iv~~LknaI~~~rl--------~HAyLFtGPpGtGKTTLARiLAk~Lnce   65 (944)
T PRK14949         18 MVGQSHVLHALTNALTQQRL--------HHAYLFTGTRGVGKTSLARLFAKGLNCE   65 (944)
T ss_pred             hcCcHHHHHHHHHHHHhCCC--------CeEEEEECCCCCCHHHHHHHHHHhccCc
Confidence            99999999999988876542        2357999999999999999999999874

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.07  E-value=7.3e-06  Score=84.81  Aligned_cols=71  Identities=31%  Similarity=0.353  Sum_probs=56.9

Q ss_pred             hCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcch
Q 005179          628 KKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKV  703 (710)
Q Consensus       628 ~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~  703 (710)
                      ..-++||.+|-++---.++..+.|-..-    .++||.||||||||.||-+||++| |.+-+++.+..||.-+...
T Consensus        38 ~dG~VGQ~~AReAaGvIv~mik~gk~aG----rgiLi~GppgTGKTAlA~gIa~eL-G~dvPF~~isgsEiYS~E~  108 (450)
T COG1224          38 GDGLVGQEEAREAAGVIVKMIKQGKMAG----RGILIVGPPGTGKTALAMGIAREL-GEDVPFVAISGSEIYSLEV  108 (450)
T ss_pred             CCcccchHHHHHhhhHHHHHHHhCcccc----cEEEEECCCCCcHHHHHHHHHHHh-CCCCCceeeccceeeeecc
Confidence            4458999999988777777777653221    389999999999999999999996 6677899999999865543

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

Probab=98.06  E-value=3.6e-06  Score=94.51  Aligned_cols=61  Identities=39%  Similarity=0.499  Sum_probs=46.6

Q ss_pred             ccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |.|.|++++.+.+.|       ++.+.|-+-|    .|+||+||||||||+||||+|.+   .+-++...-.|+|
T Consensus       152 VAG~dEakeel~EiVdfLk~p~ky~~lGakiP----kGvlLvGpPGTGKTLLAkAvAgE---A~VPFf~iSGS~F  219 (596)
T COG0465         152 VAGVDEAKEELSELVDFLKNPKKYQALGAKIP----KGVLLVGPPGTGKTLLAKAVAGE---AGVPFFSISGSDF  219 (596)
T ss_pred             hcCcHHHHHHHHHHHHHHhCchhhHhcccccc----cceeEecCCCCCcHHHHHHHhcc---cCCCceeccchhh
Confidence            666677776666666       5556666555    79999999999999999999988   5556666666666

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.06  E-value=5e-06  Score=94.20  Aligned_cols=47  Identities=43%  Similarity=0.697  Sum_probs=41.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.+++.+.+++...+.        ...+||+||+|||||++|+++|+.|+.
T Consensus        17 VIGQe~vv~~L~~aI~~grl--------~HAyLF~GPpGvGKTTlAriLAK~LnC   63 (702)
T PRK14960         17 LVGQNHVSRALSSALERGRL--------HHAYLFTGTRGVGKTTIARILAKCLNC   63 (702)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            99999999999998875432        258899999999999999999999875

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=98.06  E-value=3.7e-06  Score=93.55  Aligned_cols=183  Identities=17%  Similarity=0.241  Sum_probs=109.7

Q ss_pred             ccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh-hhccccCccHHH
Q 005179          293 IGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL-MAGAKERGELEA  369 (710)
Q Consensus       293 iGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l-~~g~~~~g~~e~  369 (710)
                      ++.+..++.+...+.+  ...-+++|.|++||||-.+++++.+.-. ...|....+|..+.-++... ..|. ..|.|..
T Consensus       316 ~~~d~s~a~l~rk~~rv~~~~~pvll~GEtGtGKe~laraiH~~s~-~~gpfvAvNCaAip~~liesELFGy-~~GafTg  393 (606)
T COG3284         316 PLLDPSRATLLRKAERVAATDLPVLLQGETGTGKEVLARAIHQNSE-AAGPFVAVNCAAIPEALIESELFGY-VAGAFTG  393 (606)
T ss_pred             cccCHHHHHHHHHHHHHhhcCCCeEecCCcchhHHHHHHHHHhccc-ccCCeEEEEeccchHHhhhHHHhcc-Ccccccc
Confidence            3556666666555443  3456799999999999999999998775 65565555555444332111 1111 1222211


Q ss_pred             -HHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC------------CeEEEEccChHHHH
Q 005179          370 -RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG------------ELQCIASTTQDEHR  436 (710)
Q Consensus       370 -~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~------------~v~vI~att~~~~~  436 (710)
                       ..+.....+.+..+..||+|||..|             ...++..|+..|+++            +++||++|+.+- .
T Consensus       394 a~~kG~~g~~~~A~gGtlFldeIgd~-------------p~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~dl-~  459 (606)
T COG3284         394 ARRKGYKGKLEQADGGTLFLDEIGDM-------------PLALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRDL-A  459 (606)
T ss_pred             chhccccccceecCCCccHHHHhhhc-------------hHHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcCH-H
Confidence             1111222233455778999999988             677888888888765            467888887652 1


Q ss_pred             hhh---hccHHHHccccceEecCCCHHHH---HHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          437 TQF---EKDKALARRFQPVLISEPSQEDA---VRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       437 ~~~---~~d~aL~~Rf~~I~v~~Ps~~~~---~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      ...   .....|.-|+....|.-|+..+|   ...|..+..++. ..++.++++++..+..+
T Consensus       460 ~lv~~g~fredLyyrL~~~~i~lP~lr~R~d~~~~l~~~~~~~~-~~~~~l~~~~~~~l~~~  520 (606)
T COG3284         460 QLVEQGRFREDLYYRLNAFVITLPPLRERSDRIPLLDRILKREN-DWRLQLDDDALARLLAY  520 (606)
T ss_pred             HHHHcCCchHHHHHHhcCeeeccCchhcccccHHHHHHHHHHcc-CCCccCCHHHHHHHHhC
Confidence            111   11233444777666666664444   445555544443 25688999998877644

>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=98.03  E-value=8.9e-06  Score=85.57  Aligned_cols=69  Identities=29%  Similarity=0.319  Sum_probs=51.7

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcc
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVK  702 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~  702 (710)
                      .-++||.+|-++.--.++..+.|--.-    .++||.||||||||.||-++|++| |.+-+++.+..||..+-.
T Consensus        24 ~GlVGQ~~AReAagiiv~mIk~~K~aG----r~iLiaGppGtGKTAlA~~ia~eL-G~~~PF~~isgSEiyS~e   92 (398)
T PF06068_consen   24 DGLVGQEKAREAAGIIVDMIKEGKIAG----RAILIAGPPGTGKTALAMAIAKEL-GEDVPFVSISGSEIYSSE   92 (398)
T ss_dssp             TTEES-HHHHHHHHHHHHHHHTT--TT-----EEEEEE-TTSSHHHHHHHHHHHC-TTTS-EEEEEGGGG-BTT
T ss_pred             ccccChHHHHHHHHHHHHHHhcccccC----cEEEEeCCCCCCchHHHHHHHHHh-CCCCCeeEcccceeeecc
Confidence            458999999998888777777554211    389999999999999999999995 677789999999986543

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.

>PF14516 AAA_35: AAA-like domain

Probab=98.03  E-value=8.8e-05  Score=79.63  Aligned_cols=180  Identities=18%  Similarity=0.224  Sum_probs=105.0

Q ss_pred             cccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc----------
Q 005179          292 VIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA----------  361 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~----------  361 (710)
                      .|.|...-+.+.+.+.. .+..+.|.||..+|||+++..+.+.+...       +..++.+|+..+....          
T Consensus        13 Yi~R~~~e~~~~~~i~~-~G~~~~I~apRq~GKTSll~~l~~~l~~~-------~~~~v~id~~~~~~~~~~~~~~f~~~   84 (331)
T PF14516_consen   13 YIERPPAEQECYQEIVQ-PGSYIRIKAPRQMGKTSLLLRLLERLQQQ-------GYRCVYIDLQQLGSAIFSDLEQFLRW   84 (331)
T ss_pred             ccCchHHHHHHHHHHhc-CCCEEEEECcccCCHHHHHHHHHHHHHHC-------CCEEEEEEeecCCCcccCCHHHHHHH
Confidence            35566555566666554 36788999999999999999999888554       4555555544331100          


Q ss_pred             ---------ccCcc----H------HHHHHHHHHHH--Hh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          362 ---------KERGE----L------EARVTTLISEI--QK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       362 ---------~~~g~----~------e~~l~~~~~~~--~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                               +....    |      ...+...+++.  .. ..|.||+|||+|.+++...       ...++...|+...
T Consensus        85 ~~~~i~~~L~l~~~l~~~w~~~~~~~~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~-------~~~dF~~~LR~~~  157 (331)
T PF14516_consen   85 FCEEISRQLKLDEKLDEYWDEEIGSKISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQ-------IADDFFGLLRSWY  157 (331)
T ss_pred             HHHHHHHHcCCChhHHHHHHHhcCChhhHHHHHHHHHHhcCCCCEEEEEechhhhccCcc-------hHHHHHHHHHHHH
Confidence                     00000    0      01222233321  22 4689999999999975321       2346777776655


Q ss_pred             cC-------CCeEEEEccChHHHHhhhhcc-HHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          420 GR-------GELQCIASTTQDEHRTQFEKD-KALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       420 ~~-------~~v~vI~att~~~~~~~~~~d-~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                      ++       ..+.+|++...+.|.. .... ..| +-...|.++..+.+|...+++.        ++..+++..++.+..
T Consensus       158 ~~~~~~~~~~~L~li~~~~t~~~~~-~~~~~SPF-NIg~~i~L~~Ft~~ev~~L~~~--------~~~~~~~~~~~~l~~  227 (331)
T PF14516_consen  158 EQRKNNPIWQKLRLILAGSTEDYII-LDINQSPF-NIGQPIELPDFTPEEVQELAQR--------YGLEFSQEQLEQLMD  227 (331)
T ss_pred             HhcccCcccceEEEEEecCcccccc-cCCCCCCc-ccccceeCCCCCHHHHHHHHHh--------hhccCCHHHHHHHHH
Confidence            43       2355555544332211 1111 111 2223788898999996665442        356688888888888


Q ss_pred             Hhhhh
Q 005179          492 LSARY  496 (710)
Q Consensus       492 ls~~~  496 (710)
                      ++.++
T Consensus       228 ~tgGh  232 (331)
T PF14516_consen  228 WTGGH  232 (331)
T ss_pred             HHCCC
Confidence            87764

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=98.03  E-value=4.2e-05  Score=70.90  Aligned_cols=145  Identities=17%  Similarity=0.192  Sum_probs=75.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCC-------cc-----ccCceEEEeehhhh--h----hccccCc-------c
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVP-------VF-----LLSKRIMSLDMGLL--M----AGAKERG-------E  366 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p-------~~-----l~~~~v~~ld~~~l--~----~g~~~~g-------~  366 (710)
                      -.+.++|+||+||||++..++..+....+.       ..     ..+..++.++-..-  .    .+....|       .
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g~kvgGf~t~EVR~gGkR~GF~Ivdl~tg~~~~la~~~~~~~rvGkY~V~v~~   85 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKGYKVGGFITPEVREGGKRIGFKIVDLATGEEGILARVGFSRPRVGKYGVNVEG   85 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHHHhcCceeeeEEeeeeecCCeEeeeEEEEccCCceEEEEEcCCCCcccceEEeeHHH
Confidence            458999999999999999999998664211       11     11333333321110  0    0111111       2


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHH
Q 005179          367 LEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       367 ~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                      ++...-..++.+..+ -.+++||||.-|--          .+..+...+...|..++. +|++--...-.   ..-..+.
T Consensus        86 le~i~~~al~rA~~~-aDvIIIDEIGpMEl----------ks~~f~~~ve~vl~~~kp-liatlHrrsr~---P~v~~ik  150 (179)
T COG1618          86 LEEIAIPALRRALEE-ADVIIIDEIGPMEL----------KSKKFREAVEEVLKSGKP-LIATLHRRSRH---PLVQRIK  150 (179)
T ss_pred             HHHHhHHHHHHHhhc-CCEEEEecccchhh----------ccHHHHHHHHHHhcCCCc-EEEEEecccCC---hHHHHhh
Confidence            333333444444444 24899999988821          244566666666766655 55543221100   0113444


Q ss_pred             ccccceEecCCCHHHHHHHHHHHHHHH
Q 005179          447 RRFQPVLISEPSQEDAVRILLGLREKY  473 (710)
Q Consensus       447 ~Rf~~I~v~~Ps~~~~~~IL~~l~~~~  473 (710)
                      +++..+.+  .+++.|-.|+..++..+
T Consensus       151 ~~~~v~v~--lt~~NR~~i~~~Il~~L  175 (179)
T COG1618         151 KLGGVYVF--LTPENRNRILNEILSVL  175 (179)
T ss_pred             hcCCEEEE--EccchhhHHHHHHHHHh
Confidence            55554443  44444446776665543

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=98.02  E-value=5.5e-06  Score=95.54  Aligned_cols=61  Identities=30%  Similarity=0.508  Sum_probs=47.7

Q ss_pred             cHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          613 TADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       613 ~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .|.+..+...+.+     |+||+.++..+..+++..+.        ...+|||||+|||||++|+++|+.|+..
T Consensus         7 ~l~~KyRP~~f~d-----IiGQe~~v~~L~~aI~~~rl--------~HAYLF~GP~GtGKTt~AriLAk~LnC~   67 (725)
T PRK07133          7 ALYRKYRPKTFDD-----IVGQDHIVQTLKNIIKSNKI--------SHAYLFSGPRGTGKTSVAKIFANALNCS   67 (725)
T ss_pred             hHHHHhCCCCHHH-----hcCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCcHHHHHHHHHHHhccc
Confidence            3444444445555     99999999999998875442        2478999999999999999999999864

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=98.01  E-value=6.1e-06  Score=93.15  Aligned_cols=47  Identities=40%  Similarity=0.638  Sum_probs=40.7

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.++..+.++++..+.        ...+||+||+|||||++|+++|+.|+.
T Consensus        18 iiGq~~~v~~L~~~i~~~rl--------~ha~Lf~Gp~GvGKTTlAr~lAk~L~c   64 (546)
T PRK14957         18 VAGQQHALNSLVHALETQKV--------HHAYLFTGTRGVGKTTLGRLLAKCLNC   64 (546)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            99999999999988865432        236899999999999999999999985

>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=98.00  E-value=7.8e-06  Score=82.64  Aligned_cols=123  Identities=19%  Similarity=0.257  Sum_probs=74.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEcc
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDE  390 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDE  390 (710)
                      .....++||+|||||+.++.+|+.+          ++.++.++++..+.        ...+.+++.-+... ++++++||
T Consensus        32 ~~~~~~~GpagtGKtetik~La~~l----------G~~~~vfnc~~~~~--------~~~l~ril~G~~~~-GaW~cfde   92 (231)
T PF12774_consen   32 NLGGALSGPAGTGKTETIKDLARAL----------GRFVVVFNCSEQMD--------YQSLSRILKGLAQS-GAWLCFDE   92 (231)
T ss_dssp             TTEEEEESSTTSSHHHHHHHHHHCT----------T--EEEEETTSSS---------HHHHHHHHHHHHHH-T-EEEEET
T ss_pred             CCCCCCcCCCCCCchhHHHHHHHHh----------CCeEEEeccccccc--------HHHHHHHHHHHhhc-Cchhhhhh
Confidence            3456799999999999999999988          88899888765442        12356666655554 57999999


Q ss_pred             chhhhhCCCCCCCCCCChHhHHHhh-------cccccC---------------CCeEEEEccChHHHHhhhhccHHHHcc
Q 005179          391 VHTLIGSGTVGRGNKGTGLDISNLL-------KPSLGR---------------GELQCIASTTQDEHRTQFEKDKALARR  448 (710)
Q Consensus       391 id~l~~~~~~~~~~~~~~~~~~~~L-------~~~l~~---------------~~v~vI~att~~~~~~~~~~d~aL~~R  448 (710)
                      +++|-             .++...+       ...+..               ....+..|+|+ .|....++++.|+.-
T Consensus        93 fnrl~-------------~~vLS~i~~~i~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np-~y~gr~~LP~nLk~l  158 (231)
T PF12774_consen   93 FNRLS-------------EEVLSVISQQIQSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNP-GYAGRSELPENLKAL  158 (231)
T ss_dssp             CCCSS-------------HHHHHHHHHHHHHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B--CCCC--S-HHHCTT
T ss_pred             hhhhh-------------HHHHHHHHHHHHHHHHhhcccccccccCCCEEEEccceeEEEeecc-ccCCcccCCHhHHHH
Confidence            99982             2222211       111111               12335555554 455566788999999


Q ss_pred             ccceEecCCCHHHHHHHH
Q 005179          449 FQPVLISEPSQEDAVRIL  466 (710)
Q Consensus       449 f~~I~v~~Ps~~~~~~IL  466 (710)
                      |.+|.+..||.....+++
T Consensus       159 FRpvam~~PD~~~I~ei~  176 (231)
T PF12774_consen  159 FRPVAMMVPDLSLIAEIL  176 (231)
T ss_dssp             EEEEE--S--HHHHHHHH
T ss_pred             hheeEEeCCCHHHHHHHH
Confidence            999999999988755554

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=97.99  E-value=6e-06  Score=93.38  Aligned_cols=59  Identities=27%  Similarity=0.429  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          614 ADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       614 ~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |.+..+...+.+     |+||+.+++.+.+++...+.        ..++||+||+|||||++|+++|+.|+.
T Consensus         6 ~~~KyRP~~F~d-----IIGQe~iv~~L~~aI~~~rl--------~hA~Lf~GP~GvGKTTlA~~lAk~L~C   64 (605)
T PRK05896          6 FYRKYRPHNFKQ-----IIGQELIKKILVNAILNNKL--------THAYIFSGPRGIGKTSIAKIFAKAINC   64 (605)
T ss_pred             HHHHhCCCCHHH-----hcCcHHHHHHHHHHHHcCCC--------CceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            444444444555     99999999999888765432        137999999999999999999999975

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.99  E-value=6.8e-06  Score=92.89  Aligned_cols=47  Identities=38%  Similarity=0.627  Sum_probs=41.9

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+++++.+.+++...+.        ...+||+||+|||||++|++||+.|+.
T Consensus        18 VIGQe~vv~~L~~al~~gRL--------pHA~LFtGP~GvGKTTLAriLAkaLnC   64 (700)
T PRK12323         18 LVGQEHVVRALTHALEQQRL--------HHAYLFTGTRGVGKTTLSRILAKSLNC   64 (700)
T ss_pred             HcCcHHHHHHHHHHHHhCCC--------ceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            99999999999999876653        246899999999999999999999986

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=97.99  E-value=5.9e-06  Score=92.71  Aligned_cols=47  Identities=30%  Similarity=0.407  Sum_probs=40.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ++||+.++..+.+++...+.        ..++||+||||||||++|+++|+.+..
T Consensus        23 liGq~~vv~~L~~ai~~~ri--------~~a~Lf~Gp~G~GKTT~ArilAk~Lnc   69 (507)
T PRK06645         23 LQGQEVLVKVLSYTILNDRL--------AGGYLLTGIRGVGKTTSARIIAKAVNC   69 (507)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CceEEEECCCCCCHHHHHHHHHHHhcC
Confidence            99999999999888765442        248999999999999999999999865

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=97.98  E-value=8.3e-06  Score=87.15  Aligned_cols=72  Identities=31%  Similarity=0.378  Sum_probs=53.4

Q ss_pred             ccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC--c
Q 005179          612 ITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR--I  689 (710)
Q Consensus       612 ~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~--~  689 (710)
                      +.|.+..+...+.+     ++|++++++.+...++...       .  .++||+||||||||++|+++++.+++...  .
T Consensus         5 ~~w~~kyrP~~~~~-----~~g~~~~~~~l~~~i~~~~-------~--~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~   70 (319)
T PRK00440          5 EIWVEKYRPRTLDE-----IVGQEEIVERLKSYVKEKN-------M--PHLLFAGPPGTGKTTAALALARELYGEDWREN   70 (319)
T ss_pred             CccchhhCCCcHHH-----hcCcHHHHHHHHHHHhCCC-------C--CeEEEECCCCCCHHHHHHHHHHHHcCCccccc
Confidence            44666666556666     8899999999988775321       1  26899999999999999999999988653  4


Q ss_pred             ceeeCCCC
Q 005179          690 HYLFFPSP  697 (710)
Q Consensus       690 li~~d~se  697 (710)
                      .+.++.+.
T Consensus        71 ~i~~~~~~   78 (319)
T PRK00440         71 FLELNASD   78 (319)
T ss_pred             eEEecccc
Confidence            45555443

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

Probab=97.98  E-value=7.2e-06  Score=83.34  Aligned_cols=46  Identities=37%  Similarity=0.494  Sum_probs=35.9

Q ss_pred             HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          646 KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       646 ~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ...+.|++.|    .++|+|||||+|||.+|+++|..|-   -+++.+-.|++
T Consensus       157 lf~rvgIk~P----kg~ll~GppGtGKTlla~~Vaa~mg---~nfl~v~ss~l  202 (388)
T KOG0651|consen  157 LFLRVGIKPP----KGLLLYGPPGTGKTLLARAVAATMG---VNFLKVVSSAL  202 (388)
T ss_pred             hccccCCCCC----ceeEEeCCCCCchhHHHHHHHHhcC---CceEEeeHhhh
Confidence            4556777766    7999999999999999999999962   35565555554

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=97.97  E-value=1e-05  Score=92.49  Aligned_cols=48  Identities=35%  Similarity=0.595  Sum_probs=41.4

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .|+||+.+++.+.++++..+.        ...+|||||+|||||++|+++|+.++.
T Consensus        17 ~viGq~~v~~~L~~~i~~~~~--------~hayLf~Gp~GtGKTt~Ak~lAkal~c   64 (559)
T PRK05563         17 DVVGQEHITKTLKNAIKQGKI--------SHAYLFSGPRGTGKTSAAKIFAKAVNC   64 (559)
T ss_pred             hccCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            399999999999999876442        236899999999999999999999874

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=97.96  E-value=7.7e-06  Score=91.16  Aligned_cols=48  Identities=38%  Similarity=0.564  Sum_probs=41.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.++..+.+.++..+.        ..++|||||||||||++|+++|+.++..
T Consensus        19 iiGq~~~v~~L~~~i~~~~i--------~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~   66 (451)
T PRK06305         19 ILGQDAVVAVLKNALRFNRA--------AHAYLFSGIRGTGKTTLARIFAKALNCQ   66 (451)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------ceEEEEEcCCCCCHHHHHHHHHHHhcCC
Confidence            99999999999888876432        2479999999999999999999999864

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.96  E-value=5.9e-05  Score=73.78  Aligned_cols=91  Identities=21%  Similarity=0.303  Sum_probs=63.0

Q ss_pred             HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCc----cHHH-------
Q 005179          301 RIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERG----ELEA-------  369 (710)
Q Consensus       301 ~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g----~~e~-------  369 (710)
                      -++..+......|.|+.|||||||||+.+-||+.+..+..  ....+++.-+|-.+-++|. ..|    ++..       
T Consensus       127 ~li~~ly~~g~lntLiigpP~~GKTTlLRdiaR~~s~g~~--~~l~kkv~IiDersEIag~-~~gvpq~~~g~R~dVld~  203 (308)
T COG3854         127 PLIKDLYQNGWLNTLIIGPPQVGKTTLLRDIARLLSDGIN--QFLPKKVGIIDERSEIAGC-LNGVPQHGRGRRMDVLDP  203 (308)
T ss_pred             HHHHHHHhcCceeeEEecCCCCChHHHHHHHHHHhhcccc--ccCCceEEEEeccchhhcc-ccCCchhhhhhhhhhccc
Confidence            3666677777889999999999999999999998865532  2236677778866666542 222    1111       


Q ss_pred             --HHHHHHHHHHhcCCeEEEEccchhh
Q 005179          370 --RVTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       370 --~l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                        +-..++..++...|-|+++|||...
T Consensus       204 cpk~~gmmmaIrsm~PEViIvDEIGt~  230 (308)
T COG3854         204 CPKAEGMMMAIRSMSPEVIIVDEIGTE  230 (308)
T ss_pred             chHHHHHHHHHHhcCCcEEEEeccccH
Confidence              1123445566677899999999776

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

Probab=97.95  E-value=1e-05  Score=85.42  Aligned_cols=39  Identities=10%  Similarity=0.017  Sum_probs=32.6

Q ss_pred             CCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          657 RPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       657 rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +|..+++||||||||||.+|+++|+.+   +-.+|.++.+|+
T Consensus       146 k~PlgllL~GPPGcGKTllAraiA~el---g~~~i~vsa~eL  184 (413)
T PLN00020        146 KVPLILGIWGGKGQGKSFQCELVFKKM---GIEPIVMSAGEL  184 (413)
T ss_pred             CCCeEEEeeCCCCCCHHHHHHHHHHHc---CCCeEEEEHHHh
Confidence            334799999999999999999999995   346888887665

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.94  E-value=8.1e-06  Score=93.66  Aligned_cols=47  Identities=28%  Similarity=0.431  Sum_probs=40.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.++..+.+++...+.        ..++||+||+|||||++|+++|+.|+.
T Consensus        18 ivGQe~i~~~L~~~i~~~ri--------~ha~Lf~Gp~GvGKttlA~~lAk~L~c   64 (620)
T PRK14954         18 ITAQEHITHTIQNSLRMDRV--------GHGYIFSGLRGVGKTTAARVFAKAVNC   64 (620)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            99999999999888765442        136999999999999999999999976

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=97.94  E-value=5.6e-06  Score=75.85  Aligned_cols=35  Identities=34%  Similarity=0.375  Sum_probs=30.6

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          662 MLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +||+||||||||++|+.+|+.+   +..++.++++++.
T Consensus         1 ill~G~~G~GKT~l~~~la~~l---~~~~~~i~~~~~~   35 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYL---GFPFIEIDGSELI   35 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHT---TSEEEEEETTHHH
T ss_pred             CEEECcCCCCeeHHHHHHHhhc---ccccccccccccc
Confidence            6899999999999999999996   3568888888774

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 ....

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.93  E-value=9e-06  Score=93.04  Aligned_cols=47  Identities=36%  Similarity=0.603  Sum_probs=41.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.++..+.+++...+.        ...+||+||+|||||++|+++|+.|+-
T Consensus        18 viGQe~vv~~L~~~l~~~rl--------~ha~Lf~Gp~GvGKTtlAr~lAk~LnC   64 (618)
T PRK14951         18 MVGQEHVVQALTNALTQQRL--------HHAYLFTGTRGVGKTTVSRILAKSLNC   64 (618)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            89999999999998876552        136899999999999999999999974

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.92  E-value=1e-05  Score=91.98  Aligned_cols=48  Identities=40%  Similarity=0.623  Sum_probs=41.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.+++.+.+++...+.        ...+||+||||||||++|+++|+.|+..
T Consensus        18 ivGq~~v~~~L~~~i~~~~~--------~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~   65 (527)
T PRK14969         18 LVGQEHVVRALTNALEQQRL--------HHAYLFTGTRGVGKTTLARILAKSLNCE   65 (527)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CEEEEEECCCCCCHHHHHHHHHHHhcCC
Confidence            89999999999998876442        2468999999999999999999999763

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=97.91  E-value=1.2e-05  Score=87.24  Aligned_cols=48  Identities=40%  Similarity=0.621  Sum_probs=40.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ++||+++++.+...++..+        ....+|||||||+|||++|+++|+.+++.
T Consensus        16 iig~~~~~~~l~~~~~~~~--------~~~~~Ll~G~~G~GKt~~a~~la~~l~~~   63 (355)
T TIGR02397        16 VIGQEHIVQTLKNAIKNGR--------IAHAYLFSGPRGTGKTSIARIFAKALNCQ   63 (355)
T ss_pred             ccCcHHHHHHHHHHHHcCC--------CCeEEEEECCCCCCHHHHHHHHHHHhcCC
Confidence            8999999999998876432        12478999999999999999999999854

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.

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.91  E-value=1.6e-05  Score=73.65  Aligned_cols=58  Identities=33%  Similarity=0.519  Sum_probs=44.2

Q ss_pred             ChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          633 GQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       633 Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |++..+..+...+...         +..+++++||||||||++++.+++.++......+.++.+++.
T Consensus         2 ~~~~~~~~i~~~~~~~---------~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~   59 (151)
T cd00009           2 GQEEAIEALREALELP---------PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLL   59 (151)
T ss_pred             chHHHHHHHHHHHhCC---------CCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhh
Confidence            5566666665554332         113799999999999999999999998777788888887763

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.

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=97.90  E-value=1e-05  Score=92.58  Aligned_cols=48  Identities=35%  Similarity=0.533  Sum_probs=41.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.++..+.+.+...+        ...++||+||+|||||++|+++|+.|+..
T Consensus        18 IIGQe~vv~~L~~ai~~~r--------l~Ha~Lf~GP~GvGKTTlAriLAk~LnC~   65 (709)
T PRK08691         18 LVGQEHVVKALQNALDEGR--------LHHAYLLTGTRGVGKTTIARILAKSLNCE   65 (709)
T ss_pred             HcCcHHHHHHHHHHHHcCC--------CCeEEEEECCCCCcHHHHHHHHHHHhccc
Confidence            9999999999999877543        22478999999999999999999998864

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=97.90  E-value=1.1e-05  Score=92.54  Aligned_cols=47  Identities=36%  Similarity=0.595  Sum_probs=40.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+++++.|.+.+...+.        ...+||+||+|||||++|++||+.|+.
T Consensus        18 VIGQe~Vv~~L~~aL~~gRL--------~HAyLFtGPpGvGKTTlAriLAKaLnC   64 (830)
T PRK07003         18 LVGQEHVVRALTHALDGGRL--------HHAYLFTGTRGVGKTTLSRIFAKALNC   64 (830)
T ss_pred             HcCcHHHHHHHHHHHhcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            99999999999988764432        236799999999999999999999875

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=97.89  E-value=1.5e-05  Score=77.78  Aligned_cols=71  Identities=24%  Similarity=0.326  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC--CCcce
Q 005179          614 ADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS--VRIHY  691 (710)
Q Consensus       614 ~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~--~~~li  691 (710)
                      |-+..+...+.+     |+|.++.++.+....+-..    -|     +++|.||||||||+-+.+||++|.|+  .+.++
T Consensus        17 wVeKYrP~~l~d-----IVGNe~tv~rl~via~~gn----mP-----~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vL   82 (333)
T KOG0991|consen   17 WVEKYRPSVLQD-----IVGNEDTVERLSVIAKEGN----MP-----NLIISGPPGTGKTTSILCLARELLGDSYKEAVL   82 (333)
T ss_pred             HHHhhCchHHHH-----hhCCHHHHHHHHHHHHcCC----CC-----ceEeeCCCCCchhhHHHHHHHHHhChhhhhHhh
Confidence            555555556666     9999999998876543321    13     89999999999999999999999994  45666


Q ss_pred             eeCCCCC
Q 005179          692 LFFPSPF  698 (710)
Q Consensus       692 ~~d~se~  698 (710)
                      -+|-|.-
T Consensus        83 ELNASde   89 (333)
T KOG0991|consen   83 ELNASDE   89 (333)
T ss_pred             hccCccc
Confidence            6666654

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=97.89  E-value=0.00018  Score=75.56  Aligned_cols=160  Identities=20%  Similarity=0.222  Sum_probs=88.4

Q ss_pred             CCcccCHHHHHHHHHHHHcC---CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh--------
Q 005179          290 DPVIGRETEIQRIIQILCRR---TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM--------  358 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~---~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~--------  358 (710)
                      ..+.+|+.+++.+...+...   .+.+++|+|.+|||||.+++.+.+......+.....++-.+..-+..+.        
T Consensus         6 ~~v~~Re~qi~~L~~Llg~~~~~~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~~~d~   85 (438)
T KOG2543|consen    6 PNVPCRESQIRRLKSLLGNNSCTIPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQLADK   85 (438)
T ss_pred             cCccchHHHHHHHHHHhCCCCcccceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhccCCC
Confidence            35788999999999988653   3456799999999999999999888721111111111111100011111        


Q ss_pred             hccccCccHHHHHHHHHHHHHh-------cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhh---cccccCCCeEEEE
Q 005179          359 AGAKERGELEARVTTLISEIQK-------SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLL---KPSLGRGELQCIA  428 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~~-------~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L---~~~l~~~~v~vI~  428 (710)
                      .|....+. .+.+..++....+       .....|++|++|.+-..          +..+.+.|   ..++....+.+|.
T Consensus        86 dg~~~~~~-~en~~d~i~~l~q~~~~t~~d~~~~liLDnad~lrD~----------~a~ll~~l~~L~el~~~~~i~iil  154 (438)
T KOG2543|consen   86 DGDKVEGD-AENFSDFIYLLVQWPAATNRDQKVFLILDNADALRDM----------DAILLQCLFRLYELLNEPTIVIIL  154 (438)
T ss_pred             chhhhhhH-HHHHHHHHHHHHhhHHhhccCceEEEEEcCHHhhhcc----------chHHHHHHHHHHHHhCCCceEEEE
Confidence            01111221 1223333333322       24678999999999432          22233332   2344455555555


Q ss_pred             ccChHHHHhhhhccHHHH---cccc--ceEecCCCHHHHHHHHHH
Q 005179          429 STTQDEHRTQFEKDKALA---RRFQ--PVLISEPSQEDAVRILLG  468 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~---~Rf~--~I~v~~Ps~~~~~~IL~~  468 (710)
                      .....+        ....   .-+.  ++.++.|+.++...|+..
T Consensus       155 s~~~~e--------~~y~~n~g~~~i~~l~fP~Ys~~e~~~Il~~  191 (438)
T KOG2543|consen  155 SAPSCE--------KQYLINTGTLEIVVLHFPQYSVEETQVILSR  191 (438)
T ss_pred             eccccH--------HHhhcccCCCCceEEecCCCCHHHHHHHHhc
Confidence            433322        1111   1222  688899999999999875

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=97.88  E-value=1.1e-05  Score=92.43  Aligned_cols=48  Identities=38%  Similarity=0.578  Sum_probs=41.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.++..+.+++...+.        ...+||+||+|||||++|+++|+.|+..
T Consensus        18 ivGQe~vv~~L~~~l~~~rl--------~hAyLf~Gp~GvGKTTlAr~lAk~L~c~   65 (647)
T PRK07994         18 VVGQEHVLTALANALDLGRL--------HHAYLFSGTRGVGKTTIARLLAKGLNCE   65 (647)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHhhhhc
Confidence            99999999999988876542        1357999999999999999999999874

>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=97.88  E-value=1.3e-05  Score=74.66  Aligned_cols=40  Identities=35%  Similarity=0.358  Sum_probs=33.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcch
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKV  703 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~  703 (710)
                      ++||+||||||||++|+.+|+.+   ...++.+.++....+..
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~---~~~~~~i~~~~~~~~~d   40 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALL---GRPVIRINCSSDTTEED   40 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH---TCEEEEEE-TTTSTHHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHh---hcceEEEEecccccccc
Confidence            47999999999999999999998   55788888887765544

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.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.88  E-value=1.3e-05  Score=89.92  Aligned_cols=47  Identities=45%  Similarity=0.639  Sum_probs=40.7

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ++||+.++..+.++++..+.        ...+|||||+|||||++|+++|+.++.
T Consensus        18 iiGq~~i~~~L~~~i~~~~i--------~hayLf~Gp~G~GKTtlAr~lAk~L~c   64 (486)
T PRK14953         18 VIGQEIVVRILKNAVKLQRV--------SHAYIFAGPRGTGKTTIARILAKVLNC   64 (486)
T ss_pred             ccChHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            99999999999998866442        136899999999999999999999984

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=97.87  E-value=1.3e-05  Score=94.91  Aligned_cols=47  Identities=40%  Similarity=0.609  Sum_probs=40.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.+++.|.+.+...+.        ...+||+||+|||||++|++||+.|+-
T Consensus        17 iiGqe~v~~~L~~~i~~~ri--------~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C   63 (824)
T PRK07764         17 VIGQEHVTEPLSTALDSGRI--------NHAYLFSGPRGCGKTSSARILARSLNC   63 (824)
T ss_pred             hcCcHHHHHHHHHHHHhCCC--------CceEEEECCCCCCHHHHHHHHHHHhCc
Confidence            99999999999998876542        136899999999999999999999973

>CHL00206 ycf2 Ycf2; Provisional

Probab=97.87  E-value=7.6e-06  Score=100.66  Aligned_cols=40  Identities=30%  Similarity=0.414  Sum_probs=35.5

Q ss_pred             CCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          657 RPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       657 rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +|..|+||+||||||||+||||||..   ..-+++.+.++++-
T Consensus      1628 ~pPKGILLiGPPGTGKTlLAKALA~e---s~VPFIsISgs~fl 1667 (2281)
T CHL00206       1628 SPSRGILVIGSIGTGRSYLVKYLATN---SYVPFITVFLNKFL 1667 (2281)
T ss_pred             CCCCceEEECCCCCCHHHHHHHHHHh---cCCceEEEEHHHHh
Confidence            34479999999999999999999999   66789999999885

>PRK13342 recombination factor protein RarA; Reviewed

Probab=97.87  E-value=1.1e-05  Score=89.43  Aligned_cols=55  Identities=27%  Similarity=0.463  Sum_probs=41.5

Q ss_pred             ccChHHHHHH---HHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          631 VIGQDEAVAA---ISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       631 v~Gq~~a~~~---i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ++||++++..   +...+...+         ..+++|+||||||||++|++||+.+-   ..++.++.+.
T Consensus        14 ~vGq~~~v~~~~~L~~~i~~~~---------~~~ilL~GppGtGKTtLA~~ia~~~~---~~~~~l~a~~   71 (413)
T PRK13342         14 VVGQEHLLGPGKPLRRMIEAGR---------LSSMILWGPPGTGKTTLARIIAGATD---APFEALSAVT   71 (413)
T ss_pred             hcCcHHHhCcchHHHHHHHcCC---------CceEEEECCCCCCHHHHHHHHHHHhC---CCEEEEeccc
Confidence            9999998766   666654321         13899999999999999999999853   3566666553

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.86  E-value=1.4e-05  Score=91.03  Aligned_cols=58  Identities=38%  Similarity=0.507  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          615 DERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       615 ~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .+..+-..+++     |+||+.++..+.+++...+.   .     -.+||+||||||||++|+++|+.++.
T Consensus         7 a~KyRP~sf~d-----IiGQe~v~~~L~~ai~~~ri---~-----ha~Lf~GPpG~GKTtiArilAk~L~C   64 (624)
T PRK14959          7 TARYRPQTFAE-----VAGQETVKAILSRAAQENRV---A-----PAYLFSGTRGVGKTTIARIFAKALNC   64 (624)
T ss_pred             HHHhCCCCHHH-----hcCCHHHHHHHHHHHHcCCC---C-----ceEEEECCCCCCHHHHHHHHHHhccc
Confidence            33334444455     89999999999988865432   1     38999999999999999999999985

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=97.86  E-value=1.8e-06  Score=92.50  Aligned_cols=178  Identities=16%  Similarity=0.204  Sum_probs=88.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh-----hhhhc---cccCccHHHHHHHHHHHHHhcCC
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG-----LLMAG---AKERGELEARVTTLISEIQKSGD  383 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~-----~l~~g---~~~~g~~e~~l~~~~~~~~~~~~  383 (710)
                      -|+||+|+||+|||.|.+.+++....          .++. ...     .+.+.   ....|+|.-.-..    +-...+
T Consensus        58 ihiLlvGdpg~gKS~ll~~~~~~~pr----------~v~~-~g~~~s~~gLta~~~~d~~~~~~~leaGa----lvlad~  122 (331)
T PF00493_consen   58 IHILLVGDPGTGKSQLLKYVAKLAPR----------SVYT-SGKGSSAAGLTASVSRDPVTGEWVLEAGA----LVLADG  122 (331)
T ss_dssp             --EEEECSCHHCHHHHHHCCCCT-SS----------EEEE-ECCGSTCCCCCEEECCCGGTSSECEEE-H----HHHCTT
T ss_pred             cceeeccchhhhHHHHHHHHHhhCCc----------eEEE-CCCCcccCCccceeccccccceeEEeCCc----hhcccC
Confidence            48999999999999999987644311          1111 100     01000   0011221000001    112456


Q ss_pred             eEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------------CeEEEEccChHHHH--------hhhh
Q 005179          384 VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------------ELQCIASTTQDEHR--------TQFE  440 (710)
Q Consensus       384 ~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------------~v~vI~att~~~~~--------~~~~  440 (710)
                      .|++|||++.+             ..+....|...|+++               +..|++++|+...+        ..+.
T Consensus       123 GiccIDe~dk~-------------~~~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~~~~~~~~~~ni~  189 (331)
T PF00493_consen  123 GICCIDEFDKM-------------KEDDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGRYDPNKSLSENIN  189 (331)
T ss_dssp             SEEEECTTTT---------------CHHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--S-TTS-CGCCT-
T ss_pred             ceeeecccccc-------------cchHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhhcchhhhhHHhcc
Confidence            79999999998             223455666666643               34478888875311        1235


Q ss_pred             ccHHHHccccceE--ecCCCHHHHHHHHHHHHHHHHhhc----------CCCCCHHHHHHHHHHhhhhhcCCCCcchHHH
Q 005179          441 KDKALARRFQPVL--ISEPSQEDAVRILLGLREKYEAHH----------NCKFTLEAINAAVHLSARYISDRYLPDKAID  508 (710)
Q Consensus       441 ~d~aL~~Rf~~I~--v~~Ps~~~~~~IL~~l~~~~~~~~----------~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~  508 (710)
                      +++.|.+||+-|.  .+.|+.+.-..+.+++...+....          ...++.+.++..+.+++..+.- .+++.+.+
T Consensus       190 l~~~LLSRFDLif~l~D~~d~~~D~~la~~il~~~~~~~~~~~~~~~~~~~~~~~~~lr~yI~yar~~~~P-~ls~ea~~  268 (331)
T PF00493_consen  190 LPPPLLSRFDLIFLLRDKPDEEEDERLAEHILDSHRNGKKSKEKKIKKNDKPISEDLLRKYIAYARQNIHP-VLSEEAKE  268 (331)
T ss_dssp             S-CCCHCC-SEEECC--TTT-HHHHHHHHHHHTTT---S--------SSS-TT-HCCCHHHHHHHHHHC---EE-HHCHH
T ss_pred             cchhhHhhcCEEEEeccccccccccccceEEEeccccccccccccccccCCccCHHHHHHHHHHHHhhccc-ccCHHHHH
Confidence            6788999999433  467777777777776665443221          1246666677777777644332 34566677


Q ss_pred             HHHHHHhhhh
Q 005179          509 LVDEAGSRAH  518 (710)
Q Consensus       509 ll~~a~~~~~  518 (710)
                      ++.......+
T Consensus       269 ~I~~~Yv~lR  278 (331)
T PF00493_consen  269 LIINYYVELR  278 (331)
T ss_dssp             HHHHHHCCCC
T ss_pred             HHHHHHHHhc
Confidence            7666554433

; 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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=97.86  E-value=1.8e-05  Score=84.61  Aligned_cols=72  Identities=19%  Similarity=0.182  Sum_probs=52.9

Q ss_pred             hhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCc
Q 005179          610 QQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRI  689 (710)
Q Consensus       610 ~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~  689 (710)
                      ..+.|.+..+...+.+     ++||+++++.+...++..+        ....+||+||||+|||++|+++++.+.   ..
T Consensus         7 ~~~~w~~kyrP~~~~~-----~~~~~~~~~~l~~~~~~~~--------~~~~lll~G~~G~GKT~la~~l~~~~~---~~   70 (316)
T PHA02544          7 NEFMWEQKYRPSTIDE-----CILPAADKETFKSIVKKGR--------IPNMLLHSPSPGTGKTTVAKALCNEVG---AE   70 (316)
T ss_pred             CCCcceeccCCCcHHH-----hcCcHHHHHHHHHHHhcCC--------CCeEEEeeCcCCCCHHHHHHHHHHHhC---cc
Confidence            3455666666666666     9999999999888776321        124667799999999999999999862   34


Q ss_pred             ceeeCCCC
Q 005179          690 HYLFFPSP  697 (710)
Q Consensus       690 li~~d~se  697 (710)
                      ++.++.++
T Consensus        71 ~~~i~~~~   78 (316)
T PHA02544         71 VLFVNGSD   78 (316)
T ss_pred             ceEeccCc
Confidence            66666665

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=97.85  E-value=0.00012  Score=74.43  Aligned_cols=122  Identities=13%  Similarity=0.102  Sum_probs=79.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc------------CceEEEeehhhhhhccccCccHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL------------SKRIMSLDMGLLMAGAKERGELEARVTTLISEI  378 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~------------~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~  378 (710)
                      +...||+|++|+||..+|.++|+.+.+.+......            ...++.+..      .. ..-..+.++++.+.+
T Consensus         7 ~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p------~~-~~I~id~ir~l~~~l   79 (261)
T PRK05818          7 THPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFD------QK-NPIKKEDALSIINKL   79 (261)
T ss_pred             CcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecC------Cc-ccCCHHHHHHHHHHH
Confidence            45579999999999999999999987643111000            011111110      00 001123345555444


Q ss_pred             H-----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccc
Q 005179          379 Q-----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQP  451 (710)
Q Consensus       379 ~-----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~  451 (710)
                      .     .++.-|++|+++|.+             ...+.|.|+..+++  .+..+|..|+..+     .+-|++++|++.
T Consensus        80 ~~~s~e~~~~KV~II~~ae~m-------------~~~AaNaLLK~LEEPp~~t~fiLit~~~~-----~lLpTI~SRCq~  141 (261)
T PRK05818         80 NRPSVESNGKKIYIIYGIEKL-------------NKQSANSLLKLIEEPPKNTYGIFTTRNEN-----NILNTILSRCVQ  141 (261)
T ss_pred             ccCchhcCCCEEEEeccHhhh-------------CHHHHHHHHHhhcCCCCCeEEEEEECChH-----hCchHhhhheee
Confidence            2     134579999999999             66788999999986  3566666666555     688999999998


Q ss_pred             eEecCC
Q 005179          452 VLISEP  457 (710)
Q Consensus       452 I~v~~P  457 (710)
                      +.++.+
T Consensus       142 ~~~~~~  147 (261)
T PRK05818        142 YVVLSK  147 (261)
T ss_pred             eecCCh
Confidence            888776

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.84  E-value=1.6e-05  Score=91.84  Aligned_cols=47  Identities=40%  Similarity=0.634  Sum_probs=40.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.+++.+.+.+...+.        ...+|||||+|||||++|+++|+.|+.
T Consensus        18 iiGq~~~~~~L~~~i~~~~i--------~~a~Lf~Gp~G~GKTtlA~~lA~~l~c   64 (585)
T PRK14950         18 LVGQEHVVQTLRNAIAEGRV--------AHAYLFTGPRGVGKTSTARILAKAVNC   64 (585)
T ss_pred             hcCCHHHHHHHHHHHHhCCC--------ceEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            99999999999888875442        136899999999999999999999874

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=97.84  E-value=1.6e-05  Score=90.69  Aligned_cols=48  Identities=33%  Similarity=0.632  Sum_probs=41.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.++..+.+.++..+.        ...+|||||+|+|||++|+++|+.++..
T Consensus        18 iiGqe~iv~~L~~~i~~~~i--------~hayLf~Gp~G~GKTt~Ar~lAk~L~c~   65 (563)
T PRK06647         18 LEGQDFVVETLKHSIESNKI--------ANAYIFSGPRGVGKTSSARAFARCLNCV   65 (563)
T ss_pred             ccCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHhhccc
Confidence            99999999999998875442        2369999999999999999999999863

>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=97.84  E-value=0.00096  Score=71.45  Aligned_cols=85  Identities=20%  Similarity=0.267  Sum_probs=59.0

Q ss_pred             cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhc----------cHHHHcc-c
Q 005179          381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEK----------DKALARR-F  449 (710)
Q Consensus       381 ~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~----------d~aL~~R-f  449 (710)
                      ..+.|+||||+|++-+         +.-.++.+.++.++.-.++++|.+..+......+..          ...+..+ |
T Consensus       171 ~~~iViiIDdLDR~~~---------~~i~~~l~~ik~~~~~~~i~~Il~~D~~~l~~ai~~~~~~~~~~~~~~~yLeKii  241 (325)
T PF07693_consen  171 KKRIVIIIDDLDRCSP---------EEIVELLEAIKLLLDFPNIIFILAFDPEILEKAIEKNYGEGFDEIDGREYLEKII  241 (325)
T ss_pred             CceEEEEEcchhcCCc---------HHHHHHHHHHHHhcCCCCeEEEEEecHHHHHHHHHhhcCcccccccHHHHHHhhc
Confidence            4579999999999922         224567777788888888888888877654443322          1233344 4


Q ss_pred             c-ceEecCCCHHHHHHHHHHHHHHHH
Q 005179          450 Q-PVLISEPSQEDAVRILLGLREKYE  474 (710)
Q Consensus       450 ~-~I~v~~Ps~~~~~~IL~~l~~~~~  474 (710)
                      + .+.+|+|+..+....+......+.
T Consensus       242 q~~~~lP~~~~~~~~~~~~~~~~~~~  267 (325)
T PF07693_consen  242 QVPFSLPPPSPSDLERYLNELLESLE  267 (325)
T ss_pred             CeEEEeCCCCHHHHHHHHHHHHHHhh
Confidence            5 688899998888888887765554

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 [].

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=97.83  E-value=1.6e-05  Score=91.13  Aligned_cols=47  Identities=34%  Similarity=0.522  Sum_probs=41.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.+++.+.+++...+.        ..++||+||+|||||++|+++|+.|+-
T Consensus        26 liGq~~~v~~L~~~~~~gri--------~ha~L~~Gp~GvGKTt~Ar~lAk~L~c   72 (598)
T PRK09111         26 LIGQEAMVRTLTNAFETGRI--------AQAFMLTGVRGVGKTTTARILARALNY   72 (598)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CceEEEECCCCCCHHHHHHHHHHhhCc
Confidence            99999999999998875442        247999999999999999999999874

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.83  E-value=2.4e-05  Score=89.93  Aligned_cols=48  Identities=33%  Similarity=0.502  Sum_probs=41.1

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||++++..+.+.++..+        ....+|||||+|||||++|+++|+.++..
T Consensus        18 iiGq~~v~~~L~~~i~~~~--------~~hayLf~Gp~G~GKtt~A~~lak~l~c~   65 (576)
T PRK14965         18 LTGQEHVSRTLQNAIDTGR--------VAHAFLFTGARGVGKTSTARILAKALNCE   65 (576)
T ss_pred             ccCcHHHHHHHHHHHHcCC--------CCeEEEEECCCCCCHHHHHHHHHHhhcCC
Confidence            9999999999998886543        12478999999999999999999999853

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=97.82  E-value=3.2e-05  Score=84.44  Aligned_cols=56  Identities=23%  Similarity=0.339  Sum_probs=41.5

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +++.++.++.+...+...           .+++|+||||||||++|+.||..+.+. ....++++-+|
T Consensus       177 ~~i~e~~le~l~~~L~~~-----------~~iil~GppGtGKT~lA~~la~~l~~~-~~~~~v~~VtF  232 (459)
T PRK11331        177 LFIPETTIETILKRLTIK-----------KNIILQGPPGVGKTFVARRLAYLLTGE-KAPQRVNMVQF  232 (459)
T ss_pred             ccCCHHHHHHHHHHHhcC-----------CCEEEECCCCCCHHHHHHHHHHHhcCC-cccceeeEEee
Confidence            666677777776655421           388999999999999999999998774 33555655555

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=97.82  E-value=9.9e-05  Score=81.72  Aligned_cols=188  Identities=14%  Similarity=0.226  Sum_probs=103.1

Q ss_pred             CCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          289 IDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      +..+.|.+....-+.-.|..            +.--|++|+|.||+|||-+.++.+.....+-+   ..|...-..-+..
T Consensus       344 ~PsIyGhe~VK~GilL~LfGGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vY---tsGkaSSaAGLTa  420 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILLSLFGGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVY---TSGKASSAAGLTA  420 (764)
T ss_pred             CccccchHHHHhhHHHHHhCCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCCcceE---ecCcccccccceE
Confidence            45677877655555444422            12258999999999999999998876532110   0000000000000


Q ss_pred             hhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------------
Q 005179          357 LMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------------  422 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------------  422 (710)
                      -+......|+|.-.-.    .+.-+++.|.+|||+|.+             ...-+-.|...|++.              
T Consensus       421 aVvkD~esgdf~iEAG----ALmLADnGICCIDEFDKM-------------d~~dqvAihEAMEQQtISIaKAGv~aTLn  483 (764)
T KOG0480|consen  421 AVVKDEESGDFTIEAG----ALMLADNGICCIDEFDKM-------------DVKDQVAIHEAMEQQTISIAKAGVVATLN  483 (764)
T ss_pred             EEEecCCCCceeeecC----cEEEccCceEEechhccc-------------ChHhHHHHHHHHHhheehheecceEEeec
Confidence            0000112222211000    112245779999999999             111123333444431              


Q ss_pred             -CeEEEEccChH--------HHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhh-----cCCCCCHHHH
Q 005179          423 -ELQCIASTTQD--------EHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAH-----HNCKFTLEAI  486 (710)
Q Consensus       423 -~v~vI~att~~--------~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~-----~~~~i~~~~l  486 (710)
                       +..+|+++|+-        ..+..+.+++++.+||+  -|-++.|++..-..|-+++.......     ....++-+.+
T Consensus       484 ARtSIlAAANPv~GhYdR~ktl~eNi~msApimSRFDL~FiLlD~~nE~~D~~ia~hIld~h~~i~~~~~~~~~~~~e~v  563 (764)
T KOG0480|consen  484 ARTSILAAANPVGGHYDRKKTLRENINMSAPIMSRFDLFFILLDDCNEVVDYAIARHILDLHRGIDDATERVCVYTLEQV  563 (764)
T ss_pred             chhhhhhhcCCcCCccccccchhhhcCCCchhhhhhcEEEEEecCCchHHHHHHHHHHHHHhccccccccccccccHHHH
Confidence             23367777753        23345678899999998  57889999888888888877653211     1124555666


Q ss_pred             HHHHHHhhhh
Q 005179          487 NAAVHLSARY  496 (710)
Q Consensus       487 ~~l~~ls~~~  496 (710)
                      ..-+.+++.+
T Consensus       564 rkYi~yAR~~  573 (764)
T KOG0480|consen  564 RKYIRYARNF  573 (764)
T ss_pred             HHHHHHHHhc
Confidence            6666665533

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=97.81  E-value=2.2e-05  Score=88.34  Aligned_cols=48  Identities=33%  Similarity=0.498  Sum_probs=41.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      |+||+.+++.+...++..+.        ...+|||||+|||||++|+++|+.++..
T Consensus        16 iiGqe~v~~~L~~~I~~grl--------~hayLf~Gp~G~GKTt~Ar~LAk~L~c~   63 (535)
T PRK08451         16 LIGQESVSKTLSLALDNNRL--------AHAYLFSGLRGSGKTSSARIFARALVCE   63 (535)
T ss_pred             ccCcHHHHHHHHHHHHcCCC--------CeeEEEECCCCCcHHHHHHHHHHHhcCC
Confidence            99999999999988865431        1367999999999999999999999853

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.80  E-value=2.6e-05  Score=85.19  Aligned_cols=47  Identities=38%  Similarity=0.622  Sum_probs=40.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ++||+.+++.+...++..+        ...++|||||||+|||++|+++|+.++.
T Consensus        19 iig~~~~~~~l~~~i~~~~--------~~~~~L~~G~~G~GKt~~a~~la~~l~~   65 (367)
T PRK14970         19 VVGQSHITNTLLNAIENNH--------LAQALLFCGPRGVGKTTCARILARKINQ   65 (367)
T ss_pred             cCCcHHHHHHHHHHHHcCC--------CCeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            8999999999988876532        1248999999999999999999999986

>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=97.79  E-value=9.4e-05  Score=76.48  Aligned_cols=165  Identities=13%  Similarity=0.214  Sum_probs=88.0

Q ss_pred             cccCHHHHHHHHH---HHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHH
Q 005179          292 VIGRETEIQRIIQ---ILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELE  368 (710)
Q Consensus       292 liGr~~~i~~l~~---~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e  368 (710)
                      ++--++.++.+..   +|. ..+.|.||+|.+|+||+++++..+...          +..++.+.++.    .-...+|.
T Consensus        10 lVlf~~ai~hi~ri~RvL~-~~~Gh~LLvG~~GsGr~sl~rLaa~i~----------~~~~~~i~~~~----~y~~~~f~   74 (268)
T PF12780_consen   10 LVLFDEAIEHIARISRVLS-QPRGHALLVGVGGSGRQSLARLAAFIC----------GYEVFQIEITK----GYSIKDFK   74 (268)
T ss_dssp             ----HHHHHHHHHHHHHHC-STTEEEEEECTTTSCHHHHHHHHHHHT----------TEEEE-TTTST----TTHHHHHH
T ss_pred             eeeHHHHHHHHHHHHHHHc-CCCCCeEEecCCCccHHHHHHHHHHHh----------ccceEEEEeeC----CcCHHHHH
Confidence            3444556665554   444 456899999999999999999776555          77888776432    11234677


Q ss_pred             HHHHHHHHHHH-hcCCeEEEEccch-----------hhhhCCCCCCC-CCCChHhHHHhhccccc---------------
Q 005179          369 ARVTTLISEIQ-KSGDVILFIDEVH-----------TLIGSGTVGRG-NKGTGLDISNLLKPSLG---------------  420 (710)
Q Consensus       369 ~~l~~~~~~~~-~~~~~IL~IDEid-----------~l~~~~~~~~~-~~~~~~~~~~~L~~~l~---------------  420 (710)
                      +.++.++..+- ++.+.+++++|-+           .|+..|....- ..+.-..+.+.+++...               
T Consensus        75 ~dLk~~~~~ag~~~~~~vfll~d~qi~~~~fLe~in~LL~sGeip~LF~~eE~~~i~~~l~~~~~~~~~~~~~~~~~~~F  154 (268)
T PF12780_consen   75 EDLKKALQKAGIKGKPTVFLLTDSQIVDESFLEDINSLLSSGEIPNLFTKEELDNIISSLREEAKAEGISDSRESLYEFF  154 (268)
T ss_dssp             HHHHHHHHHHHCS-S-EEEEEECCCSSSCHHHHHHHHHHHCSS-TTTS-TCHHHHHHHHHHHHHHHCT--SSHHHHHHHH
T ss_pred             HHHHHHHHHHhccCCCeEEEecCcccchHhHHHHHHHHHhCCCCCCCccHHHHHHHHHHhHHHHHHcCCCCchHHHHHHH
Confidence            77888877664 3457888887654           23333322110 00101111222211110               


Q ss_pred             ----CCCeEEEEc--cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHH
Q 005179          421 ----RGELQCIAS--TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       421 ----~~~v~vI~a--tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                          +.++.||.+  ...+.++......|+|.+++....+.+.+.+....+-...+.
T Consensus       155 ~~rvr~nLHivl~~sp~~~~~r~~~~~fPaL~~~ctIdW~~~W~~eaL~~Va~~~l~  211 (268)
T PF12780_consen  155 IERVRKNLHIVLCMSPVGPNFRDRCRSFPALVNCCTIDWFDPWPEEALLSVANKFLS  211 (268)
T ss_dssp             HHHHCCCEEEEEEESTTTTCCCHHHHHHCCHHHHSEEEEEES--HHHHHHHHHHHCC
T ss_pred             HHHHHhheeEEEEECCCCchHHHHHHhCcchhcccEEEeCCcCCHHHHHHHHHHHHH
Confidence                233434433  333334445556677888777788888888776666555444

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.

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=97.78  E-value=2.2e-05  Score=83.63  Aligned_cols=44  Identities=30%  Similarity=0.477  Sum_probs=36.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      |+||+++++.+..+...  .|       .+++||+||||||||++||++|..|
T Consensus        10 i~Gq~~~~~~l~~~~~~--~~-------~~~vLl~G~pG~gKT~lar~la~ll   53 (334)
T PRK13407         10 IVGQEEMKQAMVLTAID--PG-------IGGVLVFGDRGTGKSTAVRALAALL   53 (334)
T ss_pred             hCCHHHHHHHHHHHHhc--cC-------CCcEEEEcCCCCCHHHHHHHHHHHC
Confidence            89999999987654322  12       2589999999999999999999997

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=97.78  E-value=1.2e-05  Score=86.85  Aligned_cols=42  Identities=40%  Similarity=0.562  Sum_probs=34.5

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      |+||+.|+.++.-+    -+|-       -++||+||||||||++|+-+...|
T Consensus       181 V~GQ~~AKrAleiA----AAGg-------HnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         181 VKGQEQAKRALEIA----AAGG-------HNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             hcCcHHHHHHHHHH----HhcC-------CcEEEecCCCCchHHhhhhhcccC
Confidence            99999999987654    3333       279999999999999999887664

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.77  E-value=2.6e-05  Score=90.03  Aligned_cols=48  Identities=33%  Similarity=0.542  Sum_probs=41.6

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ++||++++..+.+.+...+.        ..++||+||+|||||++|+++|+.|+..
T Consensus        18 liGq~~i~~~L~~~l~~~rl--------~~a~Lf~Gp~G~GKttlA~~lAk~L~c~   65 (620)
T PRK14948         18 LVGQEAIATTLKNALISNRI--------APAYLFTGPRGTGKTSSARILAKSLNCL   65 (620)
T ss_pred             ccChHHHHHHHHHHHHcCCC--------CceEEEECCCCCChHHHHHHHHHHhcCC
Confidence            99999999999988876442        1389999999999999999999999874

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.76  E-value=4.7e-05  Score=77.40  Aligned_cols=67  Identities=30%  Similarity=0.432  Sum_probs=57.9

Q ss_pred             HHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      +..|++.|...++||.-|++.|..+++--...-+ |.||+ .+-|.|+|||||..+++.||+.+|.++.
T Consensus        73 ~~~Le~dL~~~lfGQHla~~~Vv~alk~~~~n~~-p~KPL-vLSfHG~tGTGKN~Va~iiA~n~~~~Gl  139 (344)
T KOG2170|consen   73 LDGLEKDLARALFGQHLAKQLVVNALKSHWANPN-PRKPL-VLSFHGWTGTGKNYVAEIIAENLYRGGL  139 (344)
T ss_pred             chHHHHHHHHHhhchHHHHHHHHHHHHHHhcCCC-CCCCe-EEEecCCCCCchhHHHHHHHHHHHhccc
Confidence            4568888999999999999999999987765443 88988 8889999999999999999999998653

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=97.76  E-value=3.3e-05  Score=83.62  Aligned_cols=49  Identities=33%  Similarity=0.506  Sum_probs=42.5

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      |+||++++..+.+++...+.        ..++||+||+|+||+++|.++|+.|+...
T Consensus        21 iiGq~~~~~~L~~~~~~~rl--------~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~   69 (365)
T PRK07471         21 LFGHAAAEAALLDAYRSGRL--------HHAWLIGGPQGIGKATLAYRMARFLLATP   69 (365)
T ss_pred             ccChHHHHHHHHHHHHcCCC--------CceEEEECCCCCCHHHHHHHHHHHHhCCC
Confidence            99999999999988877553        13799999999999999999999998643

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=97.75  E-value=2.8e-05  Score=89.75  Aligned_cols=53  Identities=42%  Similarity=0.594  Sum_probs=44.7

Q ss_pred             HHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          623 LEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       623 l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      +.+.|.+.|+||+++++.+..++...           .+++|+||||||||++|+++|+.+...
T Consensus        12 ~~~~~~~~viG~~~a~~~l~~a~~~~-----------~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        12 VPERLIDQVIGQEEAVEIIKKAAKQK-----------RNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             cchhhHhhccCHHHHHHHHHHHHHcC-----------CCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            34466777999999999988877643           278999999999999999999998776

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=97.74  E-value=5.4e-05  Score=81.35  Aligned_cols=66  Identities=30%  Similarity=0.346  Sum_probs=52.4

Q ss_pred             HHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +..+...+...++|+++++..+..++...           +++||.||||||||++|+++|+.+.   ..++++.+....
T Consensus        15 ~~~~~~~~~~~~~g~~~~~~~~l~a~~~~-----------~~vll~G~PG~gKT~la~~lA~~l~---~~~~~i~~t~~l   80 (329)
T COG0714          15 LGKIRSELEKVVVGDEEVIELALLALLAG-----------GHVLLEGPPGVGKTLLARALARALG---LPFVRIQCTPDL   80 (329)
T ss_pred             HHHHHhhcCCeeeccHHHHHHHHHHHHcC-----------CCEEEECCCCccHHHHHHHHHHHhC---CCeEEEecCCCC
Confidence            34456677777999988888876665554           3899999999999999999999976   478888777653

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.72  E-value=0.00016  Score=68.53  Aligned_cols=24  Identities=38%  Similarity=0.627  Sum_probs=21.6

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++|+|+||+|||+++..++.....
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~   25 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIAT   25 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHh
Confidence            689999999999999999988754

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=97.71  E-value=3.3e-05  Score=70.81  Aligned_cols=41  Identities=27%  Similarity=0.224  Sum_probs=34.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      ..++|+||||||||++++.||..++.....++.++++....
T Consensus         3 ~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~   43 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILE   43 (148)
T ss_pred             CEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccc
Confidence            37899999999999999999999888765688888776543

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.

>PRK06893 DNA replication initiation factor; Validated

Probab=97.70  E-value=4.6e-05  Score=77.37  Aligned_cols=36  Identities=22%  Similarity=0.264  Sum_probs=29.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      .++||||||||||.|+.++|+++.......+.+.++
T Consensus        41 ~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~   76 (229)
T PRK06893         41 FFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLS   76 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHH
Confidence            689999999999999999999987655555555554

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=97.69  E-value=6.6e-05  Score=85.58  Aligned_cols=58  Identities=29%  Similarity=0.464  Sum_probs=44.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH-------cCCCCcceeeCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY-------FGSVRIHYLFFPSP  697 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l-------fg~~~~li~~d~se  697 (710)
                      ++||++++..+..++    .+-    .| .++|||||||||||++|+++.+..       |..+..++.+|++.
T Consensus        67 iiGqs~~i~~l~~al----~~~----~~-~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi~id~~~  131 (531)
T TIGR02902        67 IIGQEEGIKALKAAL----CGP----NP-QHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFVEIDATT  131 (531)
T ss_pred             eeCcHHHHHHHHHHH----hCC----CC-ceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEEEEcccc
Confidence            999999998887553    111    12 378999999999999999998752       44456789999764

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=97.69  E-value=5.3e-05  Score=80.41  Aligned_cols=51  Identities=31%  Similarity=0.533  Sum_probs=44.4

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      ..|+||+++++.+..++...+.        ..++||+||+|+||+++|+++|+.+++..
T Consensus         4 ~~iiGq~~~~~~L~~~i~~~rl--------~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~   54 (314)
T PRK07399          4 ANLIGQPLAIELLTAAIKQNRI--------APAYLFAGPEGVGRKLAALCFIEGLLSQG   54 (314)
T ss_pred             HHhCCHHHHHHHHHHHHHhCCC--------CceEEEECCCCCCHHHHHHHHHHHHcCCC
Confidence            3499999999999999877653        13899999999999999999999999864

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=97.68  E-value=7.9e-05  Score=77.30  Aligned_cols=35  Identities=31%  Similarity=0.301  Sum_probs=29.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+||+||||||||++|++||+.+   +..++++++++-
T Consensus        23 ~vLL~G~~GtGKT~lA~~la~~l---g~~~~~i~~~~~   57 (262)
T TIGR02640        23 PVHLRGPAGTGKTTLAMHVARKR---DRPVMLINGDAE   57 (262)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHh---CCCEEEEeCCcc
Confidence            67999999999999999999975   346788877664

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).

>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]

Probab=97.68  E-value=4e-05  Score=79.42  Aligned_cols=69  Identities=29%  Similarity=0.538  Sum_probs=45.3

Q ss_pred             CCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHH---HHHHHHHhhcCCCCCCCCCeEEEEEcCC
Q 005179          592 VGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAA---ISRAVKRSRVGLKDPNRPTAAMLFCGPT  668 (710)
Q Consensus       592 v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~---i~~~i~~~r~gl~~p~rp~~~~Lf~GPp  668 (710)
                      +...++...+   .+.|     ..+..+-..|.+     ++||++++..   +...|+..+         +-+++|.|||
T Consensus       114 l~~~e~R~~~---qh~P-----LaermRPktL~d-----yvGQ~hlv~q~gllrs~ieq~~---------ipSmIlWGpp  171 (554)
T KOG2028|consen  114 LAAEEIRQML---QHKP-----LAERMRPKTLDD-----YVGQSHLVGQDGLLRSLIEQNR---------IPSMILWGPP  171 (554)
T ss_pred             hhhHHHHHHh---ccCC-----hhhhcCcchHHH-----hcchhhhcCcchHHHHHHHcCC---------CCceEEecCC
Confidence            4555554443   2444     234444555666     8888888854   223333333         2389999999


Q ss_pred             CCcHHHHHHHHHHH
Q 005179          669 GVGKTELAKSLAAC  682 (710)
Q Consensus       669 GtGKT~lAkaLA~~  682 (710)
                      |||||+||+.||..
T Consensus       172 G~GKTtlArlia~t  185 (554)
T KOG2028|consen  172 GTGKTTLARLIAST  185 (554)
T ss_pred             CCchHHHHHHHHhh
Confidence            99999999999987

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.68  E-value=0.00053  Score=68.65  Aligned_cols=175  Identities=19%  Similarity=0.195  Sum_probs=90.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee--hhhhhh--ccccCc----cHHHHHHHHHHHHHhc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD--MGLLMA--GAKERG----ELEARVTTLISEIQKS  381 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld--~~~l~~--g~~~~g----~~e~~l~~~~~~~~~~  381 (710)
                      ...-+.++|+-|+|||.+.+++...+...++-......+.+...  +..++.  ....+.    ..+..-+.+....++.
T Consensus        50 ~qg~~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g  129 (269)
T COG3267          50 GQGILAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKG  129 (269)
T ss_pred             CCceEEEEecCCCchhHHHHHHHHhcCCCceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhC
Confidence            34457899999999999999777766544322211122211110  001110  011111    1222233333334444


Q ss_pred             -CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEEccChHHHHh-hhhccHHHHccccc-eEecC
Q 005179          382 -GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIASTTQDEHRT-QFEKDKALARRFQP-VLISE  456 (710)
Q Consensus       382 -~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~att~~~~~~-~~~~d~aL~~Rf~~-I~v~~  456 (710)
                       .|.++++||+|.+...          ..+....|...-.  .+.+.++....+.-... ....-..+..|+.. |.++|
T Consensus       130 ~r~v~l~vdEah~L~~~----------~le~Lrll~nl~~~~~~~l~ivL~Gqp~L~~~lr~~~l~e~~~R~~ir~~l~P  199 (269)
T COG3267         130 KRPVVLMVDEAHDLNDS----------ALEALRLLTNLEEDSSKLLSIVLIGQPKLRPRLRLPVLRELEQRIDIRIELPP  199 (269)
T ss_pred             CCCeEEeehhHhhhChh----------HHHHHHHHHhhcccccCceeeeecCCcccchhhchHHHHhhhheEEEEEecCC
Confidence             4589999999999322          2333333322222  22333443333311000 00111344558875 88999


Q ss_pred             CCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          457 PSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       457 Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      .+.++....|+..++.-... .--++++++..+...+++
T Consensus       200 ~~~~~t~~yl~~~Le~a~~~-~~l~~~~a~~~i~~~sqg  237 (269)
T COG3267         200 LTEAETGLYLRHRLEGAGLP-EPLFSDDALLLIHEASQG  237 (269)
T ss_pred             cChHHHHHHHHHHHhccCCC-cccCChhHHHHHHHHhcc
Confidence            99998888888877755222 223577777777666665

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=97.66  E-value=7e-05  Score=75.98  Aligned_cols=39  Identities=18%  Similarity=0.128  Sum_probs=34.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|+||||||||.||+++++.++.....++.++++++
T Consensus        43 ~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~   81 (227)
T PRK08903         43 RFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASP   81 (227)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHh
Confidence            378999999999999999999999888888888888765

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=97.66  E-value=4e-05  Score=89.71  Aligned_cols=54  Identities=31%  Similarity=0.507  Sum_probs=38.2

Q ss_pred             ccChHHHHH---HHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          631 VIGQDEAVA---AISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       631 v~Gq~~a~~---~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ++||+..+.   .+...+...+         ..+++||||||||||++|+++|+.+   ...++.++.+
T Consensus        30 ~vGQe~ii~~~~~L~~~i~~~~---------~~slLL~GPpGtGKTTLA~aIA~~~---~~~f~~lna~   86 (725)
T PRK13341         30 FVGQDHILGEGRLLRRAIKADR---------VGSLILYGPPGVGKTTLARIIANHT---RAHFSSLNAV   86 (725)
T ss_pred             hcCcHHHhhhhHHHHHHHhcCC---------CceEEEECCCCCCHHHHHHHHHHHh---cCcceeehhh
Confidence            889999885   3434433211         2489999999999999999999985   2345555544

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=97.66  E-value=6.5e-05  Score=86.73  Aligned_cols=46  Identities=37%  Similarity=0.683  Sum_probs=40.1

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      |+||+.+++.+.+.++..+.        ...+|||||+|+|||++|+++|+.++
T Consensus        19 viGq~~~~~~L~~~i~~~~l--------~hayLf~Gp~G~GKtt~A~~lAk~l~   64 (614)
T PRK14971         19 VVGQEALTTTLKNAIATNKL--------AHAYLFCGPRGVGKTTCARIFAKTIN   64 (614)
T ss_pred             hcCcHHHHHHHHHHHHcCCC--------CeeEEEECCCCCCHHHHHHHHHHHhC
Confidence            99999999999988875432        23699999999999999999999987

>PRK12377 putative replication protein; Provisional

Probab=97.65  E-value=5.7e-05  Score=77.15  Aligned_cols=39  Identities=21%  Similarity=0.337  Sum_probs=31.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|+||||||||.||.|||+.+.......+.+.++++
T Consensus       102 ~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l  140 (248)
T PRK12377        102 TNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDV  140 (248)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHH
Confidence            489999999999999999999999866666665555443

>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=97.64  E-value=8.4e-05  Score=71.52  Aligned_cols=63  Identities=21%  Similarity=0.245  Sum_probs=46.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      ++|.+.++..+.+.++..-.   .+    ..+|++|++||||+.+|++|=+.-...+.++|.+||+.+..
T Consensus         1 liG~s~~m~~~~~~~~~~a~---~~----~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~   63 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS---SD----LPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPE   63 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT---ST----S-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-H
T ss_pred             CEeCCHHHHHHHHHHHHHhC---CC----CCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhc
Confidence            46778888888777666531   11    47899999999999999999998777788999999998843

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 ....

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=97.64  E-value=5.6e-05  Score=76.50  Aligned_cols=40  Identities=15%  Similarity=0.173  Sum_probs=34.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ..++|+||||||||++|+++++.++.....++.++++.+.
T Consensus        39 ~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~   78 (226)
T TIGR03420        39 RFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELA   78 (226)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHH
Confidence            4889999999999999999999988666677777776664

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.

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

Probab=97.63  E-value=3e-05  Score=83.72  Aligned_cols=50  Identities=36%  Similarity=0.627  Sum_probs=34.3

Q ss_pred             cccChHHHHHHHHHHHHHh------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          630 RVIGQDEAVAAISRAVKRS------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .+.|.+.++..+...+.+.      -.|++.|   ..++||.||||+|||+|++|||.+
T Consensus       154 di~gl~~~k~~l~e~vi~p~lr~d~F~glr~p---~rglLLfGPpgtGKtmL~~aiAsE  209 (428)
T KOG0740|consen  154 DIAGLEDAKQSLKEAVILPLLRPDLFLGLREP---VRGLLLFGPPGTGKTMLAKAIATE  209 (428)
T ss_pred             CCcchhhHHHHhhhhhhhcccchHhhhccccc---cchhheecCCCCchHHHHHHHHhh
Confidence            3455555555554444332      2355544   459999999999999999999987

>PRK14700 recombination factor protein RarA; Provisional

Probab=97.60  E-value=0.00018  Score=74.21  Aligned_cols=89  Identities=19%  Similarity=0.217  Sum_probs=74.3

Q ss_pred             ccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHH--hhcCCCCCHHHHHHHHHHhh
Q 005179          417 PSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYE--AHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       417 ~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~--~~~~~~i~~~~l~~l~~ls~  494 (710)
                      +.+++|.+++||+||.++   ++++.++|++|++.+.+.+++.++...+|+..+....  ...++.+++++++.++..+.
T Consensus         2 p~vE~G~i~LIGATTENP---~f~vn~ALlSR~~v~~l~~L~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~   78 (300)
T PRK14700          2 PYVESGKIILIGATTENP---TYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNE   78 (300)
T ss_pred             CCccCCcEEEEeecCCCc---cceecHhhhhhhheeeecCCCHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcC
Confidence            678999999999999987   7899999999999999999999999999998776532  12357899999999999988


Q ss_pred             hhhcCCCCcchHHHHHHHHH
Q 005179          495 RYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       495 ~~i~~r~~p~~ai~ll~~a~  514 (710)
                      +-.      +.++..|+.++
T Consensus        79 GDa------R~aLN~LE~a~   92 (300)
T PRK14700         79 GDC------RKILNLLERMF   92 (300)
T ss_pred             CHH------HHHHHHHHHHH
Confidence            743      35677777765

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=97.59  E-value=0.00011  Score=79.10  Aligned_cols=212  Identities=15%  Similarity=0.201  Sum_probs=115.9

Q ss_pred             CcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          291 PVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      .++|.++..+.|+-+|-.            +..-|++|.|.||+.||.|.+.+.+....+... .-+|..-+.+.  .-+
T Consensus       343 EIyGheDVKKaLLLlLVGgvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYT-TGrGSSGVGLT--AAV  419 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLVGGVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYT-TGRGSSGVGLT--AAV  419 (721)
T ss_pred             hhccchHHHHHHHHHhhCCCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCccccee-cCCCCCccccc--hhh
Confidence            488888777766655532            122478999999999999999988765332211 00111111111  111


Q ss_pred             hccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcc-c--cc--------CCCeEEE
Q 005179          359 AGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP-S--LG--------RGELQCI  427 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~-~--l~--------~~~v~vI  427 (710)
                      ......|++.  +..  ..+--.++.|.+|||+|.+.+....         .+.+.+.+ .  ++        +.+..++
T Consensus       420 mkDpvTgEM~--LEG--GALVLAD~GICCIDEfDKM~e~DRt---------AIHEVMEQQTISIaKAGI~TtLNAR~sIL  486 (721)
T KOG0482|consen  420 MKDPVTGEMV--LEG--GALVLADGGICCIDEFDKMDESDRT---------AIHEVMEQQTISIAKAGINTTLNARTSIL  486 (721)
T ss_pred             hcCCCCCeeE--ecc--ceEEEccCceEeehhhhhhhhhhhH---------HHHHHHHhhhhhhhhhccccchhhhHHhh
Confidence            0011111110  000  0011134668899999999544211         11111110 0  00        2234466


Q ss_pred             EccChHH--------HHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHH--hhcCC---CCCHHHHHHHHHH
Q 005179          428 ASTTQDE--------HRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYE--AHHNC---KFTLEAINAAVHL  492 (710)
Q Consensus       428 ~att~~~--------~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~--~~~~~---~i~~~~l~~l~~l  492 (710)
                      ++.|+.-        ....+.++.+|.+||+  .+..+.|+.+.-..+-+++.--..  .....   .++++.++..+.+
T Consensus       487 aAANPayGRYnprrs~e~NI~LPaALLSRFDll~Li~D~pdrd~D~~LA~HiTyVH~H~~qp~~~fepl~~~~mR~yI~~  566 (721)
T KOG0482|consen  487 AAANPAYGRYNPRRSPEQNINLPAALLSRFDLLWLIQDRPDRDNDLRLAQHITYVHQHEEQPPLDFEPLDPNLMRRYISL  566 (721)
T ss_pred             hhcCccccccCcccChhHhcCCcHHHHHhhhhhhhhccCCcccchHHHHHHhHhhhccCCCCCccCCCCCHHHHHHHHHH
Confidence            6666531        1134677899999998  456688998877777776543221  11111   3678889999999


Q ss_pred             hhhhhcCCCCcchHHHHHHHHHhhhhhh
Q 005179          493 SARYISDRYLPDKAIDLVDEAGSRAHIE  520 (710)
Q Consensus       493 s~~~i~~r~~p~~ai~ll~~a~~~~~~~  520 (710)
                      +.++-+  ..|...-+-+..|....+..
T Consensus       567 ak~~~P--~vp~~l~dyi~~AYv~~Rre  592 (721)
T KOG0482|consen  567 AKRKNP--VVPEALADYITGAYVELRRE  592 (721)
T ss_pred             HhhcCC--CCCHHHHHHHHHHHHHHHHH
Confidence            888755  46677777776666544443

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.58  E-value=4.8e-05  Score=81.70  Aligned_cols=24  Identities=29%  Similarity=0.610  Sum_probs=23.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .|.|||||||||||.+.-|+|++|
T Consensus       236 RGYLLYGPPGTGKSS~IaAmAn~L  259 (457)
T KOG0743|consen  236 RGYLLYGPPGTGKSSFIAAMANYL  259 (457)
T ss_pred             ccceeeCCCCCCHHHHHHHHHhhc
Confidence            599999999999999999999996

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

Probab=97.58  E-value=7.3e-05  Score=88.19  Aligned_cols=44  Identities=36%  Similarity=0.597  Sum_probs=31.8

Q ss_pred             hhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          648 SRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       648 ~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ...++.+|    .|+||+||||||||++|++||...-..++ =|.|+|.
T Consensus       292 ~~~~itpP----rgvL~~GppGTGkTl~araLa~~~s~~~~-kisffmr  335 (1080)
T KOG0732|consen  292 DNFNITPP----RGVLFHGPPGTGKTLMARALAAACSRGNR-KISFFMR  335 (1080)
T ss_pred             hhcccCCC----cceeecCCCCCchhHHHHhhhhhhccccc-ccchhhh
Confidence            34455544    79999999999999999999999543333 4445443

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=97.57  E-value=0.00012  Score=79.90  Aligned_cols=67  Identities=18%  Similarity=0.314  Sum_probs=49.5

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC------CcceeeCCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV------RIHYLFFPSPFNS  700 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~------~~li~~d~se~~~  700 (710)
                      +.++|.++-++.|...+...-.|-..     +.++++||||||||++++++++.+-...      -..+.+|+.+...
T Consensus        15 ~~l~gRe~e~~~l~~~l~~~~~~~~~-----~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~~~~~   87 (365)
T TIGR02928        15 DRIVHRDEQIEELAKALRPILRGSRP-----SNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQILDT   87 (365)
T ss_pred             CCCCCcHHHHHHHHHHHHHHHcCCCC-----CcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECCCCCC
Confidence            34889999999998888765444222     3789999999999999999999874321      2466777766544

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.

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.57  E-value=5.4e-05  Score=87.18  Aligned_cols=50  Identities=38%  Similarity=0.577  Sum_probs=42.2

Q ss_pred             HhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          626 QLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       626 ~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .+.+.|+||+++++.+..++...+           .++|+||||||||++|+++|+.++..
T Consensus        28 ~~~~~vigq~~a~~~L~~~~~~~~-----------~~l~~G~~G~GKttla~~l~~~l~~~   77 (637)
T PRK13765         28 RLIDQVIGQEHAVEVIKKAAKQRR-----------HVMMIGSPGTGKSMLAKAMAELLPKE   77 (637)
T ss_pred             ccHHHcCChHHHHHHHHHHHHhCC-----------eEEEECCCCCcHHHHHHHHHHHcChH
Confidence            444559999999999988776432           78999999999999999999998765

>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=97.55  E-value=0.00012  Score=70.10  Aligned_cols=49  Identities=35%  Similarity=0.565  Sum_probs=38.6

Q ss_pred             ChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCc
Q 005179          633 GQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRI  689 (710)
Q Consensus       633 Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~  689 (710)
                      ||+++++.+...++..+.        ...+||+||+|+||+++|+++|+.+++....
T Consensus         1 gq~~~~~~L~~~~~~~~l--------~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~   49 (162)
T PF13177_consen    1 GQEEIIELLKNLIKSGRL--------PHALLFHGPSGSGKKTLALAFARALLCSNPN   49 (162)
T ss_dssp             S-HHHHHHHHHHHHCTC----------SEEEEECSTTSSHHHHHHHHHHHHC-TT-C
T ss_pred             CcHHHHHHHHHHHHcCCc--------ceeEEEECCCCCCHHHHHHHHHHHHcCCCCC
Confidence            899999999888766543        1378999999999999999999999997653

...

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=97.55  E-value=9.3e-05  Score=78.94  Aligned_cols=49  Identities=29%  Similarity=0.536  Sum_probs=41.0

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .|+||+.+++.+...++..+.        ...+||+||+|+|||++|+++|+.++..
T Consensus         5 ~i~g~~~~~~~l~~~~~~~~~--------~ha~Lf~G~~G~Gk~~la~~~a~~l~c~   53 (313)
T PRK05564          5 TIIGHENIKNRIKNSIIKNRF--------SHAHIIVGEDGIGKSLLAKEIALKILGK   53 (313)
T ss_pred             hccCcHHHHHHHHHHHHcCCC--------CceEEeECCCCCCHHHHHHHHHHHHcCC
Confidence            389999999999888754332        1378999999999999999999999864

>PRK07952 DNA replication protein DnaC; Validated

Probab=97.54  E-value=9.5e-05  Score=75.38  Aligned_cols=39  Identities=21%  Similarity=0.341  Sum_probs=32.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|+||||||||.||.+||+++...+...+.++++++
T Consensus       100 ~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~~l  138 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADI  138 (244)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHHHH
Confidence            489999999999999999999998776666666665544

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.53  E-value=0.00019  Score=77.43  Aligned_cols=97  Identities=21%  Similarity=0.239  Sum_probs=57.4

Q ss_pred             CHHHHHHHHHH-HHcCCCCCcEEEcCCCChHHHHHHHHHHH--HHhcCCCccccCceEEEeehhhhhhccccCccHHHHH
Q 005179          295 RETEIQRIIQI-LCRRTKNNPILLGESGVGKTAIAEGLAIR--IVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARV  371 (710)
Q Consensus       295 r~~~i~~l~~~-L~~~~~~nvLL~GppG~GKT~la~~la~~--l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l  371 (710)
                      ....+..|... -....+.|+++.||+|||||+++.+++..  +.++           ....+..++...      .   
T Consensus       192 ~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~~l~~~~a~~sG-----------~f~T~a~Lf~~L------~---  251 (449)
T TIGR02688       192 ARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYNNLSPYVILISG-----------GTITVAKLFYNI------S---  251 (449)
T ss_pred             hHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHHHHhHHHHHHcC-----------CcCcHHHHHHHH------H---
Confidence            34444444443 12345789999999999999999999877  2222           111222332111      0   


Q ss_pred             HHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC
Q 005179          372 TTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG  422 (710)
Q Consensus       372 ~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~  422 (710)
                      ...+..+.  ...+|+|||+..+.-         ....+..+.|+.+|++|
T Consensus       252 ~~~lg~v~--~~DlLI~DEvgylp~---------~~~~~~v~imK~yMesg  291 (449)
T TIGR02688       252 TRQIGLVG--RWDVVAFDEVATLKF---------AKPKELIGILKNYMESG  291 (449)
T ss_pred             HHHHhhhc--cCCEEEEEcCCCCcC---------CchHHHHHHHHHHHHhC
Confidence            12222222  245899999998621         22456788899888865

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.

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=97.53  E-value=7.5e-05  Score=79.80  Aligned_cols=46  Identities=22%  Similarity=0.371  Sum_probs=38.7

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||++++.++.....-.+         +|++||.||+|||||++|+++++.+-.
T Consensus        19 ivGq~~~k~al~~~~~~p~---------~~~vli~G~~GtGKs~~ar~~~~~l~~   64 (350)
T CHL00081         19 IVGQEEMKLALILNVIDPK---------IGGVMIMGDRGTGKSTTIRALVDLLPE   64 (350)
T ss_pred             HhChHHHHHHHHHhccCCC---------CCeEEEEcCCCCCHHHHHHHHHHHHhh
Confidence            9999999998876544322         379999999999999999999999864

>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=97.52  E-value=0.00039  Score=73.35  Aligned_cols=67  Identities=15%  Similarity=0.185  Sum_probs=47.8

Q ss_pred             eEEEEccChHHHHhhhh--ccHHHHccccceEecCC-CHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          424 LQCIASTTQDEHRTQFE--KDKALARRFQPVLISEP-SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       424 v~vI~att~~~~~~~~~--~d~aL~~Rf~~I~v~~P-s~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                      .++|+.+|..+|..+..  ..++|.+|+..|.|+.. +..+-.+|.+.+..+.. ..+..+.|.+++.++.
T Consensus       275 ~liiAhsNe~E~~~f~~~~~~eAf~DRi~~I~VPY~L~~s~E~kIY~k~~~~s~-l~~~h~aP~~L~~aA~  344 (358)
T PF08298_consen  275 ELIIAHSNEEEYNKFKNNKNNEAFKDRIEVIKVPYCLRVSEEVKIYEKLIGKSD-LRDAHIAPHTLEMAAR  344 (358)
T ss_pred             eeEEecCCHHHHHHHhccccchhhhhheEEEeccccCCHHHHHHHHHHHhhhcc-ccccccCchHHHHHHH
Confidence            46889999999987653  56899999998999875 46666777777665321 1245677777766543

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PLN03210 Resistant to P

Probab=97.51  E-value=0.0012  Score=82.74  Aligned_cols=69  Identities=25%  Similarity=0.384  Sum_probs=52.2

Q ss_pred             cchhHHHhhhhhHHhhh---hcCCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          269 RASALEQFCVDLTARAS---EELIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       269 ~~~~l~~~~~~l~~~~~---~~~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +...+++...+...+..   ...+++++|++..++++...+.-  ....-+-|+|++|+||||||++++..+..
T Consensus       160 E~~~i~~Iv~~v~~~l~~~~~~~~~~~vG~~~~l~~l~~lL~l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~  233 (1153)
T PLN03210        160 EAKMIEEIANDVLGKLNLTPSNDFEDFVGIEDHIAKMSSLLHLESEEVRMVGIWGSSGIGKTTIARALFSRLSR  233 (1153)
T ss_pred             HHHHHHHHHHHHHHhhccccCcccccccchHHHHHHHHHHHccccCceEEEEEEcCCCCchHHHHHHHHHHHhh
Confidence            44567777777666653   23567899999999999887753  23345789999999999999999887743

syringae 6; Provisional

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=97.50  E-value=0.00012  Score=78.91  Aligned_cols=48  Identities=35%  Similarity=0.609  Sum_probs=41.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ++||++++..+..++...+.        ...+||+||+|+|||++|+.+|+.|+..
T Consensus        25 l~Gh~~a~~~L~~a~~~grl--------~ha~L~~G~~G~GKttlA~~lA~~Llc~   72 (351)
T PRK09112         25 LFGHEEAEAFLAQAYREGKL--------HHALLFEGPEGIGKATLAFHLANHILSH   72 (351)
T ss_pred             ccCcHHHHHHHHHHHHcCCC--------CeeEeeECCCCCCHHHHHHHHHHHHcCC
Confidence            99999999999988876542        1379999999999999999999999874

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.50  E-value=9.4e-05  Score=77.79  Aligned_cols=30  Identities=43%  Similarity=0.702  Sum_probs=25.6

Q ss_pred             CCCCCCCeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          653 KDPNRPTAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       653 ~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      +.-..|...+|||||||||||+.||-||..
T Consensus       378 K~h~apfRNilfyGPPGTGKTm~ArelAr~  407 (630)
T KOG0742|consen  378 KKHQAPFRNILFYGPPGTGKTMFARELARH  407 (630)
T ss_pred             ccccchhhheeeeCCCCCCchHHHHHHHhh
Confidence            334456679999999999999999999987

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=97.49  E-value=0.00032  Score=81.38  Aligned_cols=60  Identities=23%  Similarity=0.303  Sum_probs=44.9

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc-------CCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF-------GSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf-------g~~~~li~~d~se~  698 (710)
                      .++||+.++..+...+..     .   .| .+++|+||||||||++|+++.+..-       ..+..++.+|++.+
T Consensus       155 ~iiGqs~~~~~l~~~ia~-----~---~~-~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~i~~~~l  221 (615)
T TIGR02903       155 EIVGQERAIKALLAKVAS-----P---FP-QHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVEVDGTTL  221 (615)
T ss_pred             hceeCcHHHHHHHHHHhc-----C---CC-CeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEEEechhc
Confidence            489999999987554421     1   11 3799999999999999999988762       23457888988765

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.

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=97.48  E-value=0.0001  Score=78.20  Aligned_cols=33  Identities=36%  Similarity=0.374  Sum_probs=26.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      +.+||.||+|+|||.||+.||+.|-   -.+...|+
T Consensus       227 SNvLllGPtGsGKTllaqTLAr~ld---VPfaIcDc  259 (564)
T KOG0745|consen  227 SNVLLLGPTGSGKTLLAQTLARVLD---VPFAICDC  259 (564)
T ss_pred             ccEEEECCCCCchhHHHHHHHHHhC---CCeEEecc
Confidence            4699999999999999999999962   24444444

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=97.48  E-value=0.00019  Score=76.85  Aligned_cols=50  Identities=36%  Similarity=0.447  Sum_probs=35.5

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      ++|+++++..+...+....   +-|    -.+||+||||||||++|.++|+.||+..
T Consensus         3 ~~~~~~~~~~l~~~~~~~~---~~~----halL~~Gp~G~Gktt~a~~lA~~l~~~~   52 (325)
T COG0470           3 LVPWQEAVKRLLVQALESG---RLP----HALLFYGPPGVGKTTAALALAKELLCEN   52 (325)
T ss_pred             cccchhHHHHHHHHHHhcC---CCC----ceeeeeCCCCCCHHHHHHHHHHHHhCCC
Confidence            4555566655544443221   112    1599999999999999999999999866

>PTZ00202 tuzin; Provisional

Probab=97.48  E-value=0.0017  Score=70.12  Aligned_cols=47  Identities=23%  Similarity=0.342  Sum_probs=39.2

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCC---CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          289 IDPVIGRETEIQRIIQILCRRTK---NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~---~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ...++||++++..+..+|.....   .-++|+|++|+|||++++.+...+
T Consensus       261 ~~~FVGReaEla~Lr~VL~~~d~~~privvLtG~~G~GKTTLlR~~~~~l  310 (550)
T PTZ00202        261 IRQFVSREAEESWVRQVLRRLDTAHPRIVVFTGFRGCGKSSLCRSAVRKE  310 (550)
T ss_pred             ccCCCCcHHHHHHHHHHHhccCCCCceEEEEECCCCCCHHHHHHHHHhcC
Confidence            66799999999999999864222   245799999999999999998766

>PF03266 NTPase_1: NTPase; InterPro: IPR004948 This entry represents a family of nucleoside-triphosphatases which have activity towards ATP, GTP, CTP, TTP and UTP and may hydrolyse nucleoside diphosphates with lower efficiency []

Probab=97.44  E-value=4.4e-05  Score=73.43  Aligned_cols=133  Identities=17%  Similarity=0.203  Sum_probs=61.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCc--c------ccC----ceEEEe-ehhh-hhhc---------cccCcc---
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPV--F------LLS----KRIMSL-DMGL-LMAG---------AKERGE---  366 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~--~------l~~----~~v~~l-d~~~-l~~g---------~~~~g~---  366 (710)
                      |++|+|+||+||||+++.+.+.+....++.  +      ..+    ..+..+ +... ..+.         .++.-.   
T Consensus         1 ~i~iTG~pG~GKTTll~k~i~~l~~~~~~v~Gf~t~evr~~g~r~GF~iv~l~~g~~~~la~~~~~~~~~vgky~v~~e~   80 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLLKKVIEELKKKGLPVGGFYTEEVRENGRRIGFDIVDLNSGEEAILARVDFRSGPRVGKYFVDLES   80 (168)
T ss_dssp             EEEEES-TTSSHHHHHHHHHHHHHHTCGGEEEEEEEEEETTSSEEEEEEEET-TS-EEEEEETTSS-SCECTTCEE-HHH
T ss_pred             CEEEECcCCCCHHHHHHHHHHHhhccCCccceEEeecccCCCceEEEEEEECcCCCccccccccccccccCCCEEEcHHH
Confidence            579999999999999999999985433221  0      011    122222 0000 0000         111111   


Q ss_pred             HHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHH
Q 005179          367 LEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALA  446 (710)
Q Consensus       367 ~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~  446 (710)
                      |+......++.+. ....+++||||..|-          -.+..+.+.+..+|. .+..+|++-....   ....-..+.
T Consensus        81 fe~~~~~~L~~~~-~~~~liviDEIG~mE----------l~~~~F~~~v~~~l~-s~~~vi~vv~~~~---~~~~l~~i~  145 (168)
T PF03266_consen   81 FEEIGLPALRNAL-SSSDLIVIDEIGKME----------LKSPGFREAVEKLLD-SNKPVIGVVHKRS---DNPFLEEIK  145 (168)
T ss_dssp             HHCCCCCCCHHHH-HCCHEEEE---STTC----------CC-CHHHHHHHHHHC-TTSEEEEE--SS-----SCCHHHHH
T ss_pred             HHHHHHHHHHhhc-CCCCEEEEeccchhh----------hcCHHHHHHHHHHHc-CCCcEEEEEecCC---CcHHHHHHH
Confidence            1111011122211 345699999999882          224456777777776 5555777644431   112335677


Q ss_pred             ccc--cceEecCCCHH
Q 005179          447 RRF--QPVLISEPSQE  460 (710)
Q Consensus       447 ~Rf--~~I~v~~Ps~~  460 (710)
                      +|-  ..+.+.+=+.+
T Consensus       146 ~~~~~~i~~vt~~NRd  161 (168)
T PF03266_consen  146 RRPDVKIFEVTEENRD  161 (168)
T ss_dssp             TTTTSEEEE--TTTCC
T ss_pred             hCCCcEEEEeChhHHh
Confidence            774  35556554433

It includes proteins from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase []. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme []. The sequence carries both a Walker A and Walker B motif which together are characteristic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue [].; GO: 0005524 ATP binding, 0016740 transferase activity, 0019204 nucleotide phosphatase activity; PDB: 1YE8_A 2I3B_A.

>PF10923 DUF2791: P-loop Domain of unknown function (DUF2791); InterPro: IPR021228 This is a family of proteins found in archaea and bacteria

Probab=97.43  E-value=0.0071  Score=66.01  Aligned_cols=114  Identities=17%  Similarity=0.200  Sum_probs=73.5

Q ss_pred             cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc---C---CCeEEEEccChHHHHh---hhhccHHHHcc---
Q 005179          381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG---R---GELQCIASTTQDEHRT---QFEKDKALARR---  448 (710)
Q Consensus       381 ~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~---~---~~v~vI~att~~~~~~---~~~~d~aL~~R---  448 (710)
                      ..+.+|+|||++.+..-...     .......+.|++++.   .   ..+.+|.+.|++-+..   -+.--++|.+|   
T Consensus       238 y~GLlI~lDE~e~l~kl~~~-----~~R~~~ye~lr~lidd~~~G~~~gL~~~~~gTPef~eD~rrGv~sY~AL~~RL~~  312 (416)
T PF10923_consen  238 YKGLLILLDELENLYKLRND-----QAREKNYEALRQLIDDIDQGRAPGLYFVFAGTPEFFEDGRRGVYSYEALAQRLAE  312 (416)
T ss_pred             CCceEEEEechHHHHhcCCh-----HHHHHHHHHHHHHHHHHhcCCCCceEEEEeeCHHHhhCccccccccHHHHHHHhc
Confidence            45789999999999754321     112234455555443   2   3466777777765410   01112344433   


Q ss_pred             -------c----c-ceEecCCCHHHHHHHHHHHHHHHHhhcC--CCCCHHHHHHHHHHhhhhhcC
Q 005179          449 -------F----Q-PVLISEPSQEDAVRILLGLREKYEAHHN--CKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       449 -------f----~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~--~~i~~~~l~~l~~ls~~~i~~  499 (710)
                             |    . .|.+++.+.++...+++.+..-|....+  ..++++.+..+++.+.+.++.
T Consensus       313 ~~~~~~~~~n~~~pvIrL~~l~~eel~~l~~klr~i~a~~~~~~~~v~d~~l~~~~~~~~~r~G~  377 (416)
T PF10923_consen  313 EFFADDGFDNLRAPVIRLQPLTPEELLELLEKLRDIYAEAYGYESRVDDEELKAFAQHVAGRLGG  377 (416)
T ss_pred             cccccccccCccCceecCCCCCHHHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHhccCc
Confidence                   2    2 6888888999999999999888876654  478999998888877766554

Some of the proteins in this family are annotated as being methyl-accepting chemotaxis proteins and ATP/GTP binding proteins.

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=97.43  E-value=0.00015  Score=77.68  Aligned_cols=50  Identities=28%  Similarity=0.402  Sum_probs=40.9

Q ss_pred             cccC-hHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          630 RVIG-QDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       630 ~v~G-q~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      +|+| |+.+++.+...+...+.        ...+||+||+|+|||++|+++|+.++..+
T Consensus         6 ~i~~~q~~~~~~L~~~~~~~~l--------~ha~Lf~G~~G~gk~~~a~~la~~l~c~~   56 (329)
T PRK08058          6 QLTALQPVVVKMLQNSIAKNRL--------SHAYLFEGAKGTGKKATALWLAKSLFCLE   56 (329)
T ss_pred             HHHhhHHHHHHHHHHHHHcCCC--------CceEEEECCCCCCHHHHHHHHHHHHCCCC
Confidence            3666 99999999888765442        24789999999999999999999998653

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.43  E-value=0.00049  Score=75.63  Aligned_cols=138  Identities=22%  Similarity=0.279  Sum_probs=78.5

Q ss_pred             HHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHH
Q 005179          297 TEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLIS  376 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~  376 (710)
                      .-+.++.+.+..... .++|+||.+|||||+++.+.+.+.          ..++.++..++....   -+..+.+.....
T Consensus        24 ~~~~~l~~~~~~~~~-i~~i~GpR~~GKTtll~~l~~~~~----------~~~iy~~~~d~~~~~---~~l~d~~~~~~~   89 (398)
T COG1373          24 KLLPRLIKKLDLRPF-IILILGPRQVGKTTLLKLLIKGLL----------EEIIYINFDDLRLDR---IELLDLLRAYIE   89 (398)
T ss_pred             hhhHHHHhhcccCCc-EEEEECCccccHHHHHHHHHhhCC----------cceEEEEecchhcch---hhHHHHHHHHHH
Confidence            344555655554443 689999999999999977776551          113333332322111   111111222221


Q ss_pred             HHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCe-EEEEccChHHHHhhhhccHHHHccccceEec
Q 005179          377 EIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGEL-QCIASTTQDEHRTQFEKDKALARRFQPVLIS  455 (710)
Q Consensus       377 ~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v-~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~  455 (710)
                       +.......+|||||+.+              .+....++.+..++.. ++|.+++..-.  ..+....|..|...+.+.
T Consensus        90 -~~~~~~~yifLDEIq~v--------------~~W~~~lk~l~d~~~~~v~itgsss~ll--~~~~~~~L~GR~~~~~l~  152 (398)
T COG1373          90 -LKEREKSYIFLDEIQNV--------------PDWERALKYLYDRGNLDVLITGSSSSLL--SKEISESLAGRGKDLELY  152 (398)
T ss_pred             -hhccCCceEEEecccCc--------------hhHHHHHHHHHccccceEEEECCchhhh--ccchhhhcCCCceeEEEC
Confidence             21124468999999998              1234556666666653 33333333221  224557788898889999


Q ss_pred             CCCHHHHHHH
Q 005179          456 EPSQEDAVRI  465 (710)
Q Consensus       456 ~Ps~~~~~~I  465 (710)
                      |.+..+....
T Consensus       153 PlSF~Efl~~  162 (398)
T COG1373         153 PLSFREFLKL  162 (398)
T ss_pred             CCCHHHHHhh
Confidence            9998887654

>PRK08116 hypothetical protein; Validated

Probab=97.42  E-value=0.00016  Score=75.15  Aligned_cols=37  Identities=24%  Similarity=0.223  Sum_probs=31.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      +++|+||||||||.||.++|+.+.......+.+++++
T Consensus       116 gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~  152 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQ  152 (268)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHH
Confidence            7999999999999999999999876556666666554

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=97.41  E-value=0.00029  Score=72.26  Aligned_cols=46  Identities=28%  Similarity=0.325  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHhhcCCCCC-CCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          638 VAAISRAVKRSRVGLKDP-NRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       638 ~~~i~~~i~~~r~gl~~p-~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .....-+++.++-+.+.- -..-.-+|+.||||||||.|.||||+-|
T Consensus       155 l~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkL  201 (423)
T KOG0744|consen  155 LSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKL  201 (423)
T ss_pred             HHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhh
Confidence            344445556666555422 1111368999999999999999999985

>PRK06835 DNA replication protein DnaC; Validated

Probab=97.40  E-value=7.4e-05  Score=79.62  Aligned_cols=39  Identities=26%  Similarity=0.324  Sum_probs=33.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|+||||||||.||.+||+++...+...+-+.++++
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l  222 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADEL  222 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHH
Confidence            489999999999999999999999887776666665554

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.39  E-value=0.00027  Score=71.99  Aligned_cols=113  Identities=19%  Similarity=0.257  Sum_probs=65.0

Q ss_pred             cccCHHHHHHHHHHHHc----CCCC-Cc--EEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccC
Q 005179          292 VIGRETEIQRIIQILCR----RTKN-NP--ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKER  364 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~----~~~~-nv--LL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~  364 (710)
                      ++|+--..+.++..+..    ..+. ++  =|+|.+||||..+++.||+.+..+..-..+...-+-..+...-..-..|+
T Consensus        84 lfGQHla~~~Vv~alk~~~~n~~p~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~~~ie~Yk  163 (344)
T KOG2170|consen   84 LFGQHLAKQLVVNALKSHWANPNPRKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHASKIEDYK  163 (344)
T ss_pred             hhchHHHHHHHHHHHHHHhcCCCCCCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCChHHHHHHH
Confidence            67777666666665543    2222 22  36799999999999999998865432211111111111111100001122


Q ss_pred             ccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc
Q 005179          365 GELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG  420 (710)
Q Consensus       365 g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~  420 (710)
                      .++.   +.+.+.+..++..++++||+|.|             ...+.+.|+++|+
T Consensus       164 ~eL~---~~v~~~v~~C~rslFIFDE~DKm-------------p~gLld~lkpfLd  203 (344)
T KOG2170|consen  164 EELK---NRVRGTVQACQRSLFIFDEVDKL-------------PPGLLDVLKPFLD  203 (344)
T ss_pred             HHHH---HHHHHHHHhcCCceEEechhhhc-------------CHhHHHHHhhhhc
Confidence            2222   23334455677889999999999             5557788888776

>PRK08939 primosomal protein DnaI; Reviewed

Probab=97.38  E-value=0.0002  Score=75.78  Aligned_cols=39  Identities=23%  Similarity=0.246  Sum_probs=32.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|+||||||||.||.|||+.+...+...+.+.+++|
T Consensus       157 ~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l  195 (306)
T PRK08939        157 KGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEF  195 (306)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHH
Confidence            489999999999999999999999866665665655544

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=97.36  E-value=0.00035  Score=77.02  Aligned_cols=66  Identities=17%  Similarity=0.185  Sum_probs=47.7

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d~se~~~  700 (710)
                      .++|.++-++.+...+...-.|...     ..++++||||||||++++.+++.+-...  -..+.+|+.....
T Consensus        31 ~l~~Re~e~~~l~~~l~~~~~~~~~-----~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in~~~~~~   98 (394)
T PRK00411         31 NLPHREEQIEELAFALRPALRGSRP-----LNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYINCQIDRT   98 (394)
T ss_pred             CCCCHHHHHHHHHHHHHHHhCCCCC-----CeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEECCcCCC
Confidence            3777778888888777654333322     3689999999999999999999875432  3467777766544

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=97.35  E-value=0.0029  Score=63.31  Aligned_cols=149  Identities=11%  Similarity=0.063  Sum_probs=95.5

Q ss_pred             HHHHHHHHcCCC-CCcEEEcCCC-ChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc-CccHHHHHHHHHH
Q 005179          300 QRIIQILCRRTK-NNPILLGESG-VGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE-RGELEARVTTLIS  376 (710)
Q Consensus       300 ~~l~~~L~~~~~-~nvLL~GppG-~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~-~g~~e~~l~~~~~  376 (710)
                      ..+...+...+- ...||.|+.+ +||..++..+++.+.+.+++... ...++.+....-  +.+. ..--.+.++++.+
T Consensus         3 ~~L~~~iq~~kLshAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~-HPD~~~I~pe~~--~~~~~~~I~IdqIReL~~   79 (263)
T PRK06581          3 ERLEFNLKHNKLYNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLEN-NPDYHFIARETS--ATSNAKNISIEQIRKLQD   79 (263)
T ss_pred             HHHHHHHHcCcchheeeEeCCChhhHHHHHHHHHHHHHhccCcccCC-CCCEEEEecccc--ccccCCcccHHHHHHHHH
Confidence            345555555444 4468889997 99999999999888665433221 223333322100  0000 0011334566655


Q ss_pred             HHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChHHHHhhhhccHHHHcccc
Q 005179          377 EIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQDEHRTQFEKDKALARRFQ  450 (710)
Q Consensus       377 ~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~~~~~~~~~d~aL~~Rf~  450 (710)
                      .+..    ++.-|++|+++|.|             ...++|.|+..||+.  ...+|..|+..+     .+.|.+++||+
T Consensus        80 ~l~~~p~~g~~KViII~~ae~m-------------t~~AANALLKtLEEPP~~t~fILit~~~~-----~LLpTIrSRCq  141 (263)
T PRK06581         80 FLSKTSAISGYKVAIIYSAELM-------------NLNAANSCLKILEDAPKNSYIFLITSRAA-----SIISTIRSRCF  141 (263)
T ss_pred             HHhhCcccCCcEEEEEechHHh-------------CHHHHHHHHHhhcCCCCCeEEEEEeCChh-----hCchhHhhceE
Confidence            5542    34579999999999             667889999999863  455555555544     67899999999


Q ss_pred             ceEecCCCHHHHHHHHHHH
Q 005179          451 PVLISEPSQEDAVRILLGL  469 (710)
Q Consensus       451 ~I~v~~Ps~~~~~~IL~~l  469 (710)
                      .+.+..|......+.....
T Consensus       142 ~i~~~~p~~~~~~e~~~~~  160 (263)
T PRK06581        142 KINVRSSILHAYNELYSQF  160 (263)
T ss_pred             EEeCCCCCHHHHHHHHHHh
Confidence            9999999887655555443

>PRK10536 hypothetical protein; Provisional

Probab=97.30  E-value=0.0023  Score=65.08  Aligned_cols=44  Identities=25%  Similarity=0.373  Sum_probs=35.2

Q ss_pred             CCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          290 DPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.++......++..+..  ...++++||+|||||+|+.+++...
T Consensus        55 ~~i~p~n~~Q~~~l~al~~--~~lV~i~G~aGTGKT~La~a~a~~~   98 (262)
T PRK10536         55 SPILARNEAQAHYLKAIES--KQLIFATGEAGCGKTWISAAKAAEA   98 (262)
T ss_pred             ccccCCCHHHHHHHHHHhc--CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            3466777777777777765  3588999999999999999999854

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=97.30  E-value=9.4e-05  Score=71.94  Aligned_cols=38  Identities=26%  Similarity=0.350  Sum_probs=29.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      .+++|+||||||||.||.++|+.+...+....-+++++
T Consensus        48 ~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~   85 (178)
T PF01695_consen   48 ENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASD   85 (178)
T ss_dssp             -EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHH
T ss_pred             eEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCc
Confidence            38999999999999999999999887666555555443

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.

>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.30  E-value=0.00086  Score=64.77  Aligned_cols=25  Identities=44%  Similarity=0.520  Sum_probs=22.7

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      ++|+|+||+||||+++.||+.+.+.
T Consensus         4 iIlTGyPgsGKTtfakeLak~L~~~   28 (261)
T COG4088           4 IILTGYPGSGKTTFAKELAKELRQE   28 (261)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHh
Confidence            6899999999999999999998653

>PHA02774 E1; Provisional

Probab=97.29  E-value=0.0007  Score=75.80  Aligned_cols=38  Identities=18%  Similarity=0.225  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHcCC-CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          298 EIQRIIQILCRRT-KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       298 ~i~~l~~~L~~~~-~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -+..+..++.... +++++|+||||||||+++.+|++.+
T Consensus       420 fl~~lk~~l~~~PKknciv~~GPP~TGKS~fa~sL~~~L  458 (613)
T PHA02774        420 FLTALKDFLKGIPKKNCLVIYGPPDTGKSMFCMSLIKFL  458 (613)
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHh
Confidence            3344455555433 5789999999999999999999987

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=97.29  E-value=0.00035  Score=70.55  Aligned_cols=64  Identities=28%  Similarity=0.376  Sum_probs=45.6

Q ss_pred             CcccChHHHHHHHH---HHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          629 KRVIGQDEAVAAIS---RAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~---~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .-++||+.|-++--   +.++..+.+-       .++||.||||||||.||-+++++| |..-.+.-+-.||..+
T Consensus        38 ~g~vGQ~~AReAagiivdlik~KkmaG-------ravLlaGppgtGKTAlAlaisqEL-G~kvPFcpmvgSEvyS  104 (456)
T KOG1942|consen   38 AGFVGQENAREAAGIIVDLIKSKKMAG-------RAVLLAGPPGTGKTALALAISQEL-GPKVPFCPMVGSEVYS  104 (456)
T ss_pred             cccccchhhhhhhhHHHHHHHhhhccC-------cEEEEecCCCCchhHHHHHHHHHh-CCCCCcccccchhhhh
Confidence            34899988776644   4444443321       289999999999999999999996 5555566666666533

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.28  E-value=0.00073  Score=63.23  Aligned_cols=27  Identities=30%  Similarity=0.364  Sum_probs=23.6

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+..+.|+||+|+|||++.+.+|..+
T Consensus        27 ~~Ge~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          27 RAGEFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             cCCceEEEeCCCCccHHHHHHHHHhcc
Confidence            456678999999999999999999765

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=97.27  E-value=0.00028  Score=72.60  Aligned_cols=39  Identities=23%  Similarity=0.364  Sum_probs=32.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++||||||||||.||-|||+.+...+...+-+...++
T Consensus       106 ~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el  144 (254)
T COG1484         106 ENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDL  144 (254)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHH
Confidence            489999999999999999999999865666666665554

>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=97.27  E-value=0.00021  Score=64.62  Aligned_cols=31  Identities=35%  Similarity=0.563  Sum_probs=25.4

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          662 MLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ++++||||+|||++|+.||+.+ |    +..++|++
T Consensus         2 I~I~G~~gsGKST~a~~La~~~-~----~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL-G----FPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH-T----CEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH-C----CeEEEecc
Confidence            6899999999999999999986 3    55555554

...

>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=97.27  E-value=0.00014  Score=65.59  Aligned_cols=25  Identities=48%  Similarity=0.506  Sum_probs=18.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ++|+.|+||+|||++|+++|+.+-.
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~   25 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGL   25 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT-
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCC
Confidence            5799999999999999999999644

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.

>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=97.27  E-value=0.0011  Score=64.76  Aligned_cols=24  Identities=29%  Similarity=0.372  Sum_probs=20.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++++||||+|||+++..++.....
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~   25 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLA   25 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHH
Confidence            689999999999999988877654

A related protein is found in archaea.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.27  E-value=0.00073  Score=60.82  Aligned_cols=48  Identities=13%  Similarity=0.299  Sum_probs=35.5

Q ss_pred             CcccCHHHHHHHHHHHHc----CCC-CCcE--EEcCCCChHHHHHHHHHHHHHhc
Q 005179          291 PVIGRETEIQRIIQILCR----RTK-NNPI--LLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~----~~~-~nvL--L~GppG~GKT~la~~la~~l~~~  338 (710)
                      .++|+.-..+.++..+..    ..+ .+++  |.|+||||||.+++.||+.+...
T Consensus        26 ~l~GQhla~~~v~~ai~~~l~~~~p~KpLVlSfHG~tGtGKn~v~~liA~~ly~~   80 (127)
T PF06309_consen   26 NLFGQHLAVEVVVNAIKGHLANPNPRKPLVLSFHGWTGTGKNFVSRLIAEHLYKS   80 (127)
T ss_pred             HccCcHHHHHHHHHHHHHHHcCCCCCCCEEEEeecCCCCcHHHHHHHHHHHHHhc
Confidence            388998777777766543    222 2333  78999999999999999997554

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

>KOG1808 consensus AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.27  E-value=0.0021  Score=80.44  Aligned_cols=134  Identities=23%  Similarity=0.290  Sum_probs=83.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe------ehhhhhh--ccccCccHHHHHHHHHHHHHhc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL------DMGLLMA--GAKERGELEARVTTLISEIQKS  381 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l------d~~~l~~--g~~~~g~~e~~l~~~~~~~~~~  381 (710)
                      ++.+++|.||.|+|||.++..+|+..          +.++..+      |+-.++.  -....|.+..+-..++..+.. 
T Consensus       439 ~~~pillqG~tssGKtsii~~la~~~----------g~~~vrinnhehtd~qeyig~y~~~~~g~l~freg~LV~Alr~-  507 (1856)
T KOG1808|consen  439 GKFPILLQGPTSSGKTSIIKELARAT----------GKNIVRINNHEHTDLQEYIGTYVADDNGDLVFREGVLVQALRN-  507 (1856)
T ss_pred             CCCCeEEecCcCcCchhHHHHHHHHh----------ccCceehhccccchHHHHHHhhhcCCCCCeeeehhHHHHHHHh-
Confidence            45689999999999999999999988          3333333      2333332  122344444444455555543 


Q ss_pred             CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------------CeEEEEccChH-HHHhhhhccHH
Q 005179          382 GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------------ELQCIASTTQD-EHRTQFEKDKA  444 (710)
Q Consensus       382 ~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------------~v~vI~att~~-~~~~~~~~d~a  444 (710)
                       +.++|+|+++..             ..++.+.|..++..+                .+.+.++-++. .|.....+..+
T Consensus       508 -G~~~vlD~lnla-------------~~dvL~aLnrllddnRel~ipe~~rlv~~h~~f~lfatqn~~~~y~grk~lsRa  573 (1856)
T KOG1808|consen  508 -GDWIVLDELNLA-------------PHDVLEALNRLLDDNRELFIPETQRLVKAHPEFMLFATQNPPGTYGGRKILSRA  573 (1856)
T ss_pred             -CCEEEecccccc-------------chHHHHHHHhhhhhhccccccccceeeccCcchhhhhhccCccccchhhhhhhc
Confidence             568999999887             445566666555431                22233333332 14444556778


Q ss_pred             HHccccceEecCCCHHHHHHHHHH
Q 005179          445 LARRFQPVLISEPSQEDAVRILLG  468 (710)
Q Consensus       445 L~~Rf~~I~v~~Ps~~~~~~IL~~  468 (710)
                      |.+||..+++..-..++...|+.+
T Consensus       574 ~~~rf~e~~f~~~~e~e~~~i~~~  597 (1856)
T KOG1808|consen  574 LRNRFIELHFDDIGEEELEEILEH  597 (1856)
T ss_pred             ccccchhhhhhhcCchhhhhhhcc
Confidence            888998888877777776666654

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.27  E-value=0.00026  Score=79.02  Aligned_cols=51  Identities=27%  Similarity=0.396  Sum_probs=41.7

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc------CCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          287 ELIDPVIGRETEIQRIIQILCR------RTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~------~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..|++++|.++.++++++.+..      ..+.-++|+||||+|||+|++.|++.+..
T Consensus        73 ~fF~d~yGlee~ieriv~~l~~Aa~gl~~~~~IL~LvGPpG~GKSsLa~~la~~le~  129 (644)
T PRK15455         73 PAFEEFYGMEEAIEQIVSYFRHAAQGLEEKKQILYLLGPVGGGKSSLAERLKSLMER  129 (644)
T ss_pred             cchhcccCcHHHHHHHHHHHHHHHHhcCCCCceEEEecCCCCCchHHHHHHHHHHHh
Confidence            3477899999999999998722      33455789999999999999999998743

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=97.26  E-value=0.00046  Score=76.22  Aligned_cols=24  Identities=25%  Similarity=0.321  Sum_probs=21.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -|+||+|.||||||.+.+.+++..
T Consensus       483 invLL~GDPGTaKSQFLKY~eK~s  506 (854)
T KOG0477|consen  483 INVLLLGDPGTAKSQFLKYAEKTS  506 (854)
T ss_pred             eeEEEecCCCccHHHHHHHHHhcC
Confidence            579999999999999999887654

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=97.26  E-value=0.00028  Score=75.47  Aligned_cols=45  Identities=29%  Similarity=0.459  Sum_probs=37.0

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .|+||++++.++..++--..         ++++|+.||||+|||+++++++..+
T Consensus         5 ~ivgq~~~~~al~~~~~~~~---------~g~vli~G~~G~gKttl~r~~~~~~   49 (337)
T TIGR02030         5 AIVGQDEMKLALLLNVIDPK---------IGGVMVMGDRGTGKSTAVRALAALL   49 (337)
T ss_pred             ccccHHHHHHHHHHHhcCCC---------CCeEEEEcCCCCCHHHHHHHHHHhh
Confidence            48999999988755432211         3799999999999999999999998

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.

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=97.24  E-value=0.0004  Score=81.09  Aligned_cols=36  Identities=36%  Similarity=0.477  Sum_probs=30.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++||+||||||||++|+++|..+   ...++.++.+++
T Consensus       186 ~gill~G~~G~GKt~~~~~~a~~~---~~~f~~is~~~~  221 (644)
T PRK10733        186 KGVLMVGPPGTGKTLLAKAIAGEA---KVPFFTISGSDF  221 (644)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHc---CCCEEEEehHHh
Confidence            579999999999999999999984   346777777665

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=97.24  E-value=0.0019  Score=66.24  Aligned_cols=29  Identities=17%  Similarity=0.324  Sum_probs=24.8

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..+..++|+||+|+|||++++.+++.+..
T Consensus        14 ~~Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            45667999999999999999999987743

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.

>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=97.24  E-value=0.0005  Score=74.25  Aligned_cols=130  Identities=17%  Similarity=0.167  Sum_probs=66.0

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee-hhhhhhc-cccCccHHHHHHHHHHHHHhcCCeEE
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD-MGLLMAG-AKERGELEARVTTLISEIQKSGDVIL  386 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld-~~~l~~g-~~~~g~~e~~l~~~~~~~~~~~~~IL  386 (710)
                      ..+.+++|+|++|+|||+|+-.+...+.-.      ...++-.-. +..+... ....+. ..-+..+.+++... ..||
T Consensus        60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~------~k~R~HFh~Fm~~vh~~l~~~~~~-~~~l~~va~~l~~~-~~lL  131 (362)
T PF03969_consen   60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIK------RKRRVHFHEFMLDVHSRLHQLRGQ-DDPLPQVADELAKE-SRLL  131 (362)
T ss_pred             CCCceEEEECCCCCchhHHHHHHHHhCCcc------ccccccccHHHHHHHHHHHHHhCC-CccHHHHHHHHHhc-CCEE
Confidence            356889999999999999999988776321      111111110 0000000 000000 01133344444332 3499


Q ss_pred             EEccchhhhhCCCCCCCCCCChHhH-HHhhcccccCCCeEEEEccChHHHHhhh---------hccHHHHccccceEecC
Q 005179          387 FIDEVHTLIGSGTVGRGNKGTGLDI-SNLLKPSLGRGELQCIASTTQDEHRTQF---------EKDKALARRFQPVLISE  456 (710)
Q Consensus       387 ~IDEid~l~~~~~~~~~~~~~~~~~-~~~L~~~l~~~~v~vI~att~~~~~~~~---------~~d~aL~~Rf~~I~v~~  456 (710)
                      ++||++.--          -++.-+ ..+|..++ +..+++|+|+|.++-.-+.         ..-..|.++|.++.+..
T Consensus       132 cfDEF~V~D----------iaDAmil~rLf~~l~-~~gvvlVaTSN~~P~~Ly~~gl~r~~Flp~I~~l~~~~~vv~ld~  200 (362)
T PF03969_consen  132 CFDEFQVTD----------IADAMILKRLFEALF-KRGVVLVATSNRPPEDLYKNGLQRERFLPFIDLLKRRCDVVELDG  200 (362)
T ss_pred             EEeeeeccc----------hhHHHHHHHHHHHHH-HCCCEEEecCCCChHHHcCCcccHHHHHHHHHHHHhceEEEEecC
Confidence            999998651          112222 33333334 5668888888865421110         01134555777777766


Q ss_pred             C
Q 005179          457 P  457 (710)
Q Consensus       457 P  457 (710)
                      +
T Consensus       201 ~  201 (362)
T PF03969_consen  201 G  201 (362)
T ss_pred             C
Confidence            5

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

>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=97.23  E-value=0.00029  Score=63.62  Aligned_cols=31  Identities=35%  Similarity=0.553  Sum_probs=26.1

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      ++|+|+||+||||+++.|++.+          +..++.+|-
T Consensus         2 I~I~G~~gsGKST~a~~La~~~----------~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERL----------GFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHH----------TCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH----------CCeEEEecc
Confidence            6899999999999999999998          666665543

...

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=97.23  E-value=0.00017  Score=80.31  Aligned_cols=47  Identities=43%  Similarity=0.699  Sum_probs=41.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |+||+.++.++.+++...|..        -++||.||-|||||++||.+|+.|-=
T Consensus        18 vvGQe~v~~~L~nal~~~ri~--------hAYlfsG~RGvGKTt~Ari~AkalNC   64 (515)
T COG2812          18 VVGQEHVVKTLSNALENGRIA--------HAYLFSGPRGVGKTTIARILAKALNC   64 (515)
T ss_pred             hcccHHHHHHHHHHHHhCcch--------hhhhhcCCCCcCchhHHHHHHHHhcC
Confidence            899999999999999887742        38999999999999999999999743

>PRK08181 transposase; Validated

Probab=97.23  E-value=0.00016  Score=74.83  Aligned_cols=37  Identities=22%  Similarity=0.326  Sum_probs=30.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      +++|+||||||||.||.++|+.+...+...+.+.+++
T Consensus       108 nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~  144 (269)
T PRK08181        108 NLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTD  144 (269)
T ss_pred             eEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHH
Confidence            7999999999999999999998876665555555444

>PRK04296 thymidine kinase; Provisional

Probab=97.23  E-value=0.00064  Score=66.93  Aligned_cols=25  Identities=16%  Similarity=0.141  Sum_probs=21.4

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+++||+|+||||++..++.++...
T Consensus         5 ~litG~~GsGKTT~~l~~~~~~~~~   29 (190)
T PRK04296          5 EFIYGAMNSGKSTELLQRAYNYEER   29 (190)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHc
Confidence            5789999999999999998887543

>TIGR00602 rad24 checkpoint protein rad24

Probab=97.21  E-value=0.0004  Score=79.87  Aligned_cols=63  Identities=19%  Similarity=0.229  Sum_probs=48.3

Q ss_pred             ccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          612 ITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       612 ~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..|.+..+...+++     ++||++.++.|...+.....+.    .|-..++|+||||||||+++++||+.+
T Consensus        72 ~pW~eKyrP~~lde-----l~~~~~ki~~l~~~l~~~~~~~----~~~~illL~GP~GsGKTTl~~~la~~l  134 (637)
T TIGR00602        72 EPWVEKYKPETQHE-----LAVHKKKIEEVETWLKAQVLEN----APKRILLITGPSGCGKSTTIKILSKEL  134 (637)
T ss_pred             CchHHHhCCCCHHH-----hcCcHHHHHHHHHHHHhccccc----CCCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            35777766667777     9999999998887776543322    222358999999999999999999885

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

>PHA02244 ATPase-like protein

Probab=97.21  E-value=0.0007  Score=72.24  Aligned_cols=57  Identities=16%  Similarity=0.274  Sum_probs=37.2

Q ss_pred             hhCcccChHHHHHHHHHHH-HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          627 LKKRVIGQDEAVAAISRAV-KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       627 L~~~v~Gq~~a~~~i~~~i-~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      +....+|...........+ +....+.        .+||+||||||||++|++||..+   ...+++++
T Consensus        94 ~d~~~ig~sp~~~~~~~ri~r~l~~~~--------PVLL~GppGtGKTtLA~aLA~~l---g~pfv~In  151 (383)
T PHA02244         94 IDTTKIASNPTFHYETADIAKIVNANI--------PVFLKGGAGSGKNHIAEQIAEAL---DLDFYFMN  151 (383)
T ss_pred             CCCcccCCCHHHHHHHHHHHHHHhcCC--------CEEEECCCCCCHHHHHHHHHHHh---CCCEEEEe
Confidence            3344566666665444433 3333322        57999999999999999999984   23455554

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=97.20  E-value=0.00045  Score=72.82  Aligned_cols=37  Identities=16%  Similarity=0.069  Sum_probs=30.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +++||.||||||||++|+.||+.|-   ..++++++++-.
T Consensus        65 ~~ilL~G~pGtGKTtla~~lA~~l~---~~~~rV~~~~~l  101 (327)
T TIGR01650        65 RRVMVQGYHGTGKSTHIEQIAARLN---WPCVRVNLDSHV  101 (327)
T ss_pred             CcEEEEeCCCChHHHHHHHHHHHHC---CCeEEEEecCCC
Confidence            3789999999999999999999963   467888776653

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.

>TIGR01817 nifA Nif-specific regulatory protein

Probab=97.19  E-value=0.00051  Score=78.88  Aligned_cols=64  Identities=17%  Similarity=0.214  Sum_probs=52.7

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ..++|+..++..+...++.... .      ...+|++|++|||||++|++|.......+..++.+||+.+.
T Consensus       196 ~~liG~s~~~~~~~~~~~~~a~-~------~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~  259 (534)
T TIGR01817       196 DGIIGKSPAMRQVVDQARVVAR-S------NSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALS  259 (534)
T ss_pred             CceEECCHHHHHHHHHHHHHhC-c------CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCC
Confidence            3488999999888887766531 1      13689999999999999999999987778899999998774

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.

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=97.19  E-value=0.00059  Score=68.50  Aligned_cols=68  Identities=22%  Similarity=0.295  Sum_probs=53.7

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcch
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKV  703 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~  703 (710)
                      ++|.+..++.|..-....-.|.     |..++||+|+.|||||.++|++...+.+.+-.+|-++-..+.+.+.
T Consensus        29 L~Gie~Qk~~l~~Nt~~Fl~G~-----pannvLL~G~rGtGKSSlVkall~~y~~~GLRlIev~k~~L~~l~~   96 (249)
T PF05673_consen   29 LIGIERQKEALIENTEQFLQGL-----PANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVSKEDLGDLPE   96 (249)
T ss_pred             hcCHHHHHHHHHHHHHHHHcCC-----CCcceEEecCCCCCHHHHHHHHHHHHhhcCceEEEECHHHhccHHH
Confidence            7778888888776666665554     3458999999999999999999999988888888887666655443

>PRK06526 transposase; Provisional

Probab=97.17  E-value=0.00015  Score=74.49  Aligned_cols=35  Identities=29%  Similarity=0.346  Sum_probs=28.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      +++|+||||||||.||.+|+..+...+.....+.+
T Consensus       100 nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~  134 (254)
T PRK06526        100 NVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATA  134 (254)
T ss_pred             eEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhH
Confidence            79999999999999999999998765554433333

>PRK13695 putative NTPase; Provisional

Probab=97.16  E-value=0.0026  Score=61.62  Aligned_cols=25  Identities=28%  Similarity=0.357  Sum_probs=21.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +++|+|++|+||||+++.++..+..
T Consensus         2 ~i~ltG~~G~GKTTll~~i~~~l~~   26 (174)
T PRK13695          2 KIGITGPPGVGKTTLVLKIAELLKE   26 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4789999999999999999887653

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.16  E-value=0.0048  Score=75.71  Aligned_cols=46  Identities=15%  Similarity=0.185  Sum_probs=31.1

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          286 EELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      |..-..+|-|...++++...   ...+-++|+||+|.||||++...+..
T Consensus        10 p~~~~~~~~R~rl~~~l~~~---~~~~~~~v~apaG~GKTtl~~~~~~~   55 (903)
T PRK04841         10 PVRLHNTVVRERLLAKLSGA---NNYRLVLVTSPAGYGKTTLISQWAAG   55 (903)
T ss_pred             CCCccccCcchHHHHHHhcc---cCCCeEEEECCCCCCHHHHHHHHHHh
Confidence            33344567777666555432   22345789999999999999887753

>PRK08118 topology modulation protein; Reviewed

Probab=97.15  E-value=0.00087  Score=64.51  Aligned_cols=23  Identities=35%  Similarity=0.661  Sum_probs=21.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++++|+||+||||+++.|++.+
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l   25 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKL   25 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            48999999999999999999998

>PRK05642 DNA replication initiation factor; Validated

Probab=97.11  E-value=0.00063  Score=69.32  Aligned_cols=39  Identities=13%  Similarity=0.198  Sum_probs=31.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ..++||||+|||||.|++++++++.......+-+++.++
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~   84 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAEL   84 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHH
Confidence            368999999999999999999987755556666666555

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=97.11  E-value=0.0013  Score=70.52  Aligned_cols=30  Identities=17%  Similarity=0.293  Sum_probs=25.4

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      ..+.-.+|+||||||||+|++.|++.+...
T Consensus       167 GkGQR~lIvgppGvGKTTLaK~Ian~I~~n  196 (416)
T PRK09376        167 GKGQRGLIVAPPKAGKTVLLQNIANSITTN  196 (416)
T ss_pred             ccCceEEEeCCCCCChhHHHHHHHHHHHhh
Confidence            345668999999999999999999988553

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.09  E-value=0.0041  Score=61.52  Aligned_cols=36  Identities=28%  Similarity=0.412  Sum_probs=26.0

Q ss_pred             HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          301 RIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       301 ~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      .+..++.. ..+-.+|.|+||||||+++..+...+..
T Consensus         9 a~~~~l~~-~~~~~~l~G~aGtGKT~~l~~~~~~~~~   44 (196)
T PF13604_consen    9 AVRAILTS-GDRVSVLQGPAGTGKTTLLKALAEALEA   44 (196)
T ss_dssp             HHHHHHHC-TCSEEEEEESTTSTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhc-CCeEEEEEECCCCCHHHHHHHHHHHHHh
Confidence            33334433 3345678899999999999999888755

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=97.09  E-value=0.0011  Score=66.30  Aligned_cols=79  Identities=19%  Similarity=0.272  Sum_probs=47.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh-----hh--ccc--------------cCccHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL-----MA--GAK--------------ERGELEA  369 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l-----~~--g~~--------------~~g~~e~  369 (710)
                      +.-++|+||||+|||+++..++......       +..+++++...+     ..  ...              ...+...
T Consensus        12 g~i~~i~G~~GsGKT~l~~~~~~~~~~~-------g~~v~yi~~e~~~~~rl~~~~~~~~~~~~~~i~~~~~~~~~~~~~   84 (209)
T TIGR02237        12 GTITQIYGPPGSGKTNICMILAVNAARQ-------GKKVVYIDTEGLSPERFKQIAEDRPERALSNFIVFEVFDFDEQGV   84 (209)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEECCCCCHHHHHHHHHhChHHHhcCEEEEECCCHHHHHH
Confidence            3446899999999999999988776432       345555554321     00  000              0011122


Q ss_pred             HHHHHHHHHHhcCCeEEEEccchhhhh
Q 005179          370 RVTTLISEIQKSGDVILFIDEVHTLIG  396 (710)
Q Consensus       370 ~l~~~~~~~~~~~~~IL~IDEid~l~~  396 (710)
                      .+..+...+....+.+|+||-+..+..
T Consensus        85 ~~~~l~~~~~~~~~~lvVIDSis~l~~  111 (209)
T TIGR02237        85 AIQKTSKFIDRDSASLVVVDSFTALYR  111 (209)
T ss_pred             HHHHHHHHHhhcCccEEEEeCcHHHhH
Confidence            234444444445677999999998864

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

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=97.08  E-value=0.0006  Score=76.99  Aligned_cols=24  Identities=42%  Similarity=0.631  Sum_probs=22.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .-+||+||||||||+++++||++|
T Consensus        46 ~iLlLtGP~G~GKtttv~~La~el   69 (519)
T PF03215_consen   46 RILLLTGPSGCGKTTTVKVLAKEL   69 (519)
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            378899999999999999999996

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=97.07  E-value=0.00038  Score=61.69  Aligned_cols=24  Identities=42%  Similarity=0.708  Sum_probs=21.5

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          662 MLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      +.||||||||||.+|+.||+.+..
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~   24 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLK   24 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHH
Confidence            479999999999999999988763

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

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=97.06  E-value=0.018  Score=69.61  Aligned_cols=139  Identities=17%  Similarity=0.199  Sum_probs=81.7

Q ss_pred             CCCCCcEEEcCCCChHHHHHH-HHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHH--------
Q 005179          309 RTKNNPILLGESGVGKTAIAE-GLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ--------  379 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~-~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~--------  379 (710)
                      ...+.++++||||+|||.+.. +|-.+.          ...+..++.+.-.       ..+..+..+-++..        
T Consensus      1492 nt~R~~i~cGppGSgK~mlM~~sLrs~~----------~~ev~~~Nfs~~t-------~T~s~ls~Ler~t~yy~~tg~~ 1554 (3164)
T COG5245        1492 NTLRSYIYCGPPGSGKEMLMCPSLRSEL----------ITEVKYFNFSTCT-------MTPSKLSVLERETEYYPNTGVV 1554 (3164)
T ss_pred             hccceEEEECCCCCccchhcchhhhhhh----------heeeeEEeecccc-------CCHHHHHHHHhhceeeccCCeE
Confidence            456789999999999999754 343333          3455555432111       01111221111111        


Q ss_pred             ----h--cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--------------CCeEEEEccChHHHHhhh
Q 005179          380 ----K--SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--------------GELQCIASTTQDEHRTQF  439 (710)
Q Consensus       380 ----~--~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--------------~~v~vI~att~~~~~~~~  439 (710)
                          +  -...|||.|||+ | +.+..     -...++.-+|++++++              .++.+.|++|+.....-.
T Consensus      1555 ~l~PK~~vK~lVLFcDeIn-L-p~~~~-----y~~~~vI~FlR~l~e~QGfw~s~~~~wvTI~~i~l~Gacnp~td~gRv 1627 (3164)
T COG5245        1555 RLYPKPVVKDLVLFCDEIN-L-PYGFE-----YYPPTVIVFLRPLVERQGFWSSIAVSWVTICGIILYGACNPGTDEGRV 1627 (3164)
T ss_pred             EEccCcchhheEEEeeccC-C-ccccc-----cCCCceEEeeHHHHHhcccccchhhhHhhhcceEEEccCCCCCCcccC
Confidence                0  124689999998 3 22211     2233445566666664              257788999987644444


Q ss_pred             hccHHHHccccceEecCCCHHHHHHHHHHHHH
Q 005179          440 EKDKALARRFQPVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       440 ~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      .....|.|+-..|.+..|.......|.+.+..
T Consensus      1628 ~~~eRf~r~~v~vf~~ype~~SL~~Iyea~l~ 1659 (3164)
T COG5245        1628 KYYERFIRKPVFVFCCYPELASLRNIYEAVLM 1659 (3164)
T ss_pred             ccHHHHhcCceEEEecCcchhhHHHHHHHHHH
Confidence            45566666655788899998888888876544

>PRK08727 hypothetical protein; Validated

Probab=97.06  E-value=0.00087  Score=68.27  Aligned_cols=38  Identities=29%  Similarity=0.295  Sum_probs=31.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++|+||||||||.|+.+++..+...+...+.+.+.++
T Consensus        43 ~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~   80 (233)
T PRK08727         43 WLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAA   80 (233)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHh
Confidence            58999999999999999999998876666666666554

>PRK08084 DNA replication initiation factor; Provisional

Probab=97.06  E-value=0.00075  Score=68.83  Aligned_cols=34  Identities=15%  Similarity=0.087  Sum_probs=26.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .++||||||||||.|+.++++.+........-+.
T Consensus        47 ~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~   80 (235)
T PRK08084         47 YIYLWSREGAGRSHLLHAACAELSQRGRAVGYVP   80 (235)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            7899999999999999999998764433333333

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=97.05  E-value=0.0004  Score=82.15  Aligned_cols=189  Identities=17%  Similarity=0.251  Sum_probs=107.4

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcC---C------------CC-CcEEEcCCCChHHHHHHHHHHHHHhcCCCc
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRR---T------------KN-NPILLGESGVGKTAIAEGLAIRIVQAEVPV  342 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~---~------------~~-nvLL~GppG~GKT~la~~la~~l~~~~~p~  342 (710)
                      -|++.+++.....+.|.......+...|...   .            .. -++++||||+|||+.++..+..+       
T Consensus       309 ~~~~k~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~-------  381 (871)
T KOG1968|consen  309 GWTEKYQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKEL-------  381 (871)
T ss_pred             ccccccccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhc-------
Confidence            4555556655555666555555555554332   0            01 25899999999999999999988       


Q ss_pred             cccCceEEEeehhhhhhccccC---ccHH--HHHHHHH---HH--HHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHH
Q 005179          343 FLLSKRIMSLDMGLLMAGAKER---GELE--ARVTTLI---SE--IQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDIS  412 (710)
Q Consensus       343 ~l~~~~v~~ld~~~l~~g~~~~---g~~e--~~l~~~~---~~--~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~  412 (710)
                         +..+++.|.+....+....   +++.  ..+...+   ..  .......||++||+|-+.+ +..     ++-..+.
T Consensus       382 ---g~~v~E~Nas~~RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~-~dR-----g~v~~l~  452 (871)
T KOG1968|consen  382 ---GFKVVEKNASDVRSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG-EDR-----GGVSKLS  452 (871)
T ss_pred             ---ccceeecCccccccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc-hhh-----hhHHHHH
Confidence               7788887765443211100   0000  0011111   00  0012345899999999966 211     1122222


Q ss_pred             HhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          413 NLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       413 ~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                      .+    +..-...+|.++|.-.    +.....+.+-+..+.|..|+.+.+..-+..++.    ..++.++++.++.++.+
T Consensus       453 ~l----~~ks~~Piv~~cndr~----~p~sr~~~~~~~~l~f~kP~~~~i~~ri~si~~----se~~ki~~~~l~~~s~~  520 (871)
T KOG1968|consen  453 SL----CKKSSRPLVCTCNDRN----LPKSRALSRACSDLRFSKPSSELIRSRIMSICK----SEGIKISDDVLEEISKL  520 (871)
T ss_pred             HH----HHhccCCeEEEecCCC----CccccchhhhcceeeecCCcHHHHHhhhhhhhc----ccceecCcHHHHHHHHh
Confidence            22    2233334555555432    112234444444699999999987777766655    44678999999988888


Q ss_pred             hhh
Q 005179          493 SAR  495 (710)
Q Consensus       493 s~~  495 (710)
                      +.+
T Consensus       521 ~~~  523 (871)
T KOG1968|consen  521 SGG  523 (871)
T ss_pred             ccc
Confidence            754

>PHA00729 NTP-binding motif containing protein

Probab=97.05  E-value=0.00035  Score=69.82  Aligned_cols=24  Identities=33%  Similarity=0.458  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .++++||||||||+||.+||+.+.
T Consensus        19 nIlItG~pGvGKT~LA~aLa~~l~   42 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKVARDVF   42 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            799999999999999999999864

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.04  E-value=0.00041  Score=67.53  Aligned_cols=62  Identities=18%  Similarity=0.243  Sum_probs=40.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ++|.++.++.+...+. ...+-.    + ..++++||+|+|||.+.+++...+-......+.++++..
T Consensus         2 fvgR~~e~~~l~~~l~-~~~~~~----~-~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    2 FVGREEEIERLRDLLD-AAQSGS----P-RNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             -TT-HHHHHHHHHTTG-GTSS----------EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHH-HHHcCC----C-cEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            6788888888888776 222111    1 389999999999999999998887665445677777666

>PRK06921 hypothetical protein; Provisional

Probab=97.03  E-value=0.00061  Score=70.69  Aligned_cols=36  Identities=22%  Similarity=0.182  Sum_probs=28.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC-CCcceeeCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS-VRIHYLFFP  695 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~-~~~li~~d~  695 (710)
                      .+++|+||||||||.||.+||+.+... ....+-+..
T Consensus       118 ~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~  154 (266)
T PRK06921        118 NSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPF  154 (266)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEH
Confidence            489999999999999999999998764 444444443

>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=97.02  E-value=0.00044  Score=64.37  Aligned_cols=22  Identities=50%  Similarity=0.955  Sum_probs=20.2

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 005179          662 MLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ++++||||+|||++|+.+++.+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHC
Confidence            6899999999999999999763

...

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=97.00  E-value=0.00062  Score=79.42  Aligned_cols=45  Identities=27%  Similarity=0.403  Sum_probs=36.4

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .|+||+.++..+..+..-.+         ++++||.||||||||++|++|++.+
T Consensus         5 ~ivGq~~~~~al~~~av~~~---------~g~vli~G~~GtgKs~lar~l~~~l   49 (633)
T TIGR02442         5 AIVGQEDLKLALLLNAVDPR---------IGGVLIRGEKGTAKSTAARGLAALL   49 (633)
T ss_pred             hhcChHHHHHHHHHHhhCCC---------CCeEEEEcCCCCcHHHHHHHHHHhC
Confidence            49999999977754433221         2689999999999999999999997

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.

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.00  E-value=0.00083  Score=67.20  Aligned_cols=23  Identities=30%  Similarity=0.453  Sum_probs=20.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la  332 (710)
                      .+..+||||+||+|||++|+.++
T Consensus        11 ~~~~~liyG~~G~GKtt~a~~~~   33 (220)
T TIGR01618        11 IPNMYLIYGKPGTGKTSTIKYLP   33 (220)
T ss_pred             CCcEEEEECCCCCCHHHHHHhcC
Confidence            35669999999999999999885

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.

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=96.98  E-value=0.0025  Score=66.03  Aligned_cols=81  Identities=19%  Similarity=0.267  Sum_probs=45.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh-hhhh---hccc--cCcc----H--HHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM-GLLM---AGAK--ERGE----L--EARVTTLISEI  378 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~-~~l~---~g~~--~~g~----~--e~~l~~~~~~~  378 (710)
                      ..|++|+||+|+||||+++.++..+........+.+..+..+|- ..+.   .+..  ..+.    +  ..+...++..+
T Consensus       111 ~~~~~i~g~~g~GKttl~~~l~~~~~~~~G~i~~~g~~v~~~d~~~ei~~~~~~~~q~~~~~r~~v~~~~~k~~~~~~~i  190 (270)
T TIGR02858       111 VLNTLIISPPQCGKTTLLRDLARILSTGISQLGLRGKKVGIVDERSEIAGCVNGVPQHDVGIRTDVLDGCPKAEGMMMLI  190 (270)
T ss_pred             eeEEEEEcCCCCCHHHHHHHHhCccCCCCceEEECCEEeecchhHHHHHHHhcccccccccccccccccchHHHHHHHHH
Confidence            36899999999999999999998874332222233445544431 1211   0100  0000    0  01122344445


Q ss_pred             HhcCCeEEEEccc
Q 005179          379 QKSGDVILFIDEV  391 (710)
Q Consensus       379 ~~~~~~IL~IDEi  391 (710)
                      ....|.++++||+
T Consensus       191 ~~~~P~villDE~  203 (270)
T TIGR02858       191 RSMSPDVIVVDEI  203 (270)
T ss_pred             HhCCCCEEEEeCC
Confidence            5567889999996

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.

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=96.96  E-value=0.0012  Score=65.32  Aligned_cols=99  Identities=28%  Similarity=0.398  Sum_probs=59.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccch
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVH  392 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid  392 (710)
                      -++|+|+.|+|||++++.|......               +.  +.  .....++..   .    +.  ...|+.+||++
T Consensus        54 ~lvl~G~QG~GKStf~~~L~~~~~~---------------d~--~~--~~~~kd~~~---~----l~--~~~iveldEl~  105 (198)
T PF05272_consen   54 VLVLVGKQGIGKSTFFRKLGPEYFS---------------DS--IN--DFDDKDFLE---Q----LQ--GKWIVELDELD  105 (198)
T ss_pred             eeeEecCCcccHHHHHHHHhHHhcc---------------Cc--cc--cCCCcHHHH---H----HH--HhHheeHHHHh
Confidence            4789999999999999998654311               10  00  001112211   1    11  13588899998


Q ss_pred             hhhhCCCCCCCCCCChHhHHHhhcccccC-----------------CCeEEEEccChHHHHhhhhccHHHHccccceEec
Q 005179          393 TLIGSGTVGRGNKGTGLDISNLLKPSLGR-----------------GELQCIASTTQDEHRTQFEKDKALARRFQPVLIS  455 (710)
Q Consensus       393 ~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-----------------~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~  455 (710)
                      .+..+             -.+.||.++.+                 ...++|||||..+    +-.|+.=.|||-.|.+.
T Consensus       106 ~~~k~-------------~~~~lK~~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~----~L~D~TGnRRf~~v~v~  168 (198)
T PF05272_consen  106 GLSKK-------------DVEALKSFITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDD----FLKDPTGNRRFWPVEVS  168 (198)
T ss_pred             hcchh-------------hHHHHHHHhcccceeeecCCcCcceeeceeEEEEeccCCcc----eeeCCCCCeEEEEEEEc
Confidence            87311             12344444331                 2456889999875    34577777899877776


Q ss_pred             C
Q 005179          456 E  456 (710)
Q Consensus       456 ~  456 (710)
                      .
T Consensus       169 ~  169 (198)
T PF05272_consen  169 K  169 (198)
T ss_pred             C
Confidence            6

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=96.96  E-value=0.00064  Score=63.20  Aligned_cols=60  Identities=20%  Similarity=0.272  Sum_probs=42.8

Q ss_pred             cChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          632 IGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       632 ~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +|...++..+...++.... .+      ..+|++|++||||+.+|++|...-......++..++...
T Consensus         1 vG~S~~~~~l~~~l~~~a~-~~------~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~   60 (138)
T PF14532_consen    1 VGKSPAMRRLRRQLERLAK-SS------SPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASL   60 (138)
T ss_dssp             --SCHHHHHHHHHHHHHHC-SS------S-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCT
T ss_pred             CCCCHHHHHHHHHHHHHhC-CC------CcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhC
Confidence            4566677777777766541 11      368999999999999999999987776677777776654

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=96.95  E-value=0.0064  Score=67.29  Aligned_cols=40  Identities=23%  Similarity=0.260  Sum_probs=31.9

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ...++|+||||+|||+++..||..|-..+.....+++..|
T Consensus        95 p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~~  134 (437)
T PRK00771         95 PQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADTY  134 (437)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCCC
Confidence            3589999999999999999999887644455666666655

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=96.95  E-value=0.00081  Score=66.05  Aligned_cols=27  Identities=48%  Similarity=0.692  Sum_probs=25.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ..+|||||+|+|||++|+++|+.+++.
T Consensus        15 ~~~L~~G~~G~gkt~~a~~~~~~l~~~   41 (188)
T TIGR00678        15 HAYLFAGPEGVGKELLALALAKALLCE   41 (188)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHcCC
Confidence            479999999999999999999999874

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.

>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=96.93  E-value=0.0026  Score=66.25  Aligned_cols=74  Identities=19%  Similarity=0.321  Sum_probs=43.1

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee-hhhhhhc--------c-ccCccHHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD-MGLLMAG--------A-KERGELEARVTTLISEIQ  379 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld-~~~l~~g--------~-~~~g~~e~~l~~~~~~~~  379 (710)
                      .+.++++.|++|+||||++.++...+...       ..+++.+. ..++...        . .....    +..++..+-
T Consensus       126 ~~~~ili~G~tGSGKTT~l~all~~i~~~-------~~~iv~iEd~~E~~l~~~~~~~~~~~~~~~~----~~~~l~~~L  194 (270)
T PF00437_consen  126 GRGNILISGPTGSGKTTLLNALLEEIPPE-------DERIVTIEDPPELRLPGPNQIQIQTRRDEIS----YEDLLKSAL  194 (270)
T ss_dssp             TTEEEEEEESTTSSHHHHHHHHHHHCHTT-------TSEEEEEESSS-S--SCSSEEEEEEETTTBS----HHHHHHHHT
T ss_pred             cceEEEEECCCccccchHHHHHhhhcccc-------ccceEEeccccceeecccceEEEEeecCccc----HHHHHHHHh
Confidence            57899999999999999999999887543       12222221 1111100        0 11223    344555555


Q ss_pred             hcCCeEEEEccchhh
Q 005179          380 KSGDVILFIDEVHTL  394 (710)
Q Consensus       380 ~~~~~IL~IDEid~l  394 (710)
                      ...|.+++|+|+-.-
T Consensus       195 R~~pD~iiigEiR~~  209 (270)
T PF00437_consen  195 RQDPDVIIIGEIRDP  209 (270)
T ss_dssp             TS--SEEEESCE-SC
T ss_pred             cCCCCcccccccCCH
Confidence            567889999998543

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 ....

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=96.93  E-value=0.001  Score=67.19  Aligned_cols=152  Identities=20%  Similarity=0.296  Sum_probs=77.5

Q ss_pred             cCHHHHHHHHHHHH---cCCCCCcEEEcCCCChHHHHHHHHHHHHH-hcCCCccccCceEEEeehhhhhhc-------cc
Q 005179          294 GRETEIQRIIQILC---RRTKNNPILLGESGVGKTAIAEGLAIRIV-QAEVPVFLLSKRIMSLDMGLLMAG-------AK  362 (710)
Q Consensus       294 Gr~~~i~~l~~~L~---~~~~~nvLL~GppG~GKT~la~~la~~l~-~~~~p~~l~~~~v~~ld~~~l~~g-------~~  362 (710)
                      -+....+++++.+.   .+...++||.||.|.||+.|++.+-..-. ..+     ..-++++++|..+...       ..
T Consensus       188 trnp~fnrmieqierva~rsr~p~ll~gptgagksflarriyelk~arhq-----~sg~fvevncatlrgd~amsalfgh  262 (531)
T COG4650         188 TRNPHFNRMIEQIERVAIRSRAPILLNGPTGAGKSFLARRIYELKQARHQ-----FSGAFVEVNCATLRGDTAMSALFGH  262 (531)
T ss_pred             ccChHHHHHHHHHHHHHhhccCCeEeecCCCcchhHHHHHHHHHHHHHHh-----cCCceEEEeeeeecCchHHHHHHhh
Confidence            34455555554433   35567899999999999999998764321 111     1334555555433211       11


Q ss_pred             cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-------------CCeEEEEc
Q 005179          363 ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-------------GELQCIAS  429 (710)
Q Consensus       363 ~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-------------~~v~vI~a  429 (710)
                      .+|.|...-..--..++..++.+||+|||..|             +.+-+.+|+..++.             .++++|+-
T Consensus       263 vkgaftga~~~r~gllrsadggmlfldeigel-------------gadeqamllkaieekrf~pfgsdr~v~sdfqliag  329 (531)
T COG4650         263 VKGAFTGARESREGLLRSADGGMLFLDEIGEL-------------GADEQAMLLKAIEEKRFYPFGSDRQVSSDFQLIAG  329 (531)
T ss_pred             hccccccchhhhhhhhccCCCceEehHhhhhc-------------CccHHHHHHHHHHhhccCCCCCccccccchHHhhh
Confidence            11211110011111223456789999999988             23334455444442             24556655


Q ss_pred             cChHHHHhhhh---ccHHHHccccceEecCCCHHHHHH
Q 005179          430 TTQDEHRTQFE---KDKALARRFQPVLISEPSQEDAVR  464 (710)
Q Consensus       430 tt~~~~~~~~~---~d~aL~~Rf~~I~v~~Ps~~~~~~  464 (710)
                      |..+ .++...   ....|..|+....+..|-..+|.+
T Consensus       330 tvrd-lrq~vaeg~fredl~arinlwtf~lpgl~qr~e  366 (531)
T COG4650         330 TVRD-LRQLVAEGKFREDLYARINLWTFTLPGLRQRQE  366 (531)
T ss_pred             hHHH-HHHHHhccchHHHHHHhhheeeeeccccccCcc
Confidence            4432 222111   123444466656666676555444

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=96.92  E-value=0.001  Score=72.25  Aligned_cols=80  Identities=16%  Similarity=0.313  Sum_probs=48.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh---------ccccCc---cHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA---------GAKERG---ELEARVTTLISEI  378 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~---------g~~~~g---~~e~~l~~~~~~~  378 (710)
                      +.-++|+|+||+|||+++..++..+...       +.++++++......         +.....   ..+..+..+++.+
T Consensus        82 GslvLI~G~pG~GKStLllq~a~~~a~~-------g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i  154 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQVAARLAKR-------GGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASI  154 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHhc-------CCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHH
Confidence            3457899999999999999999877543       23444443211100         000000   0011244555556


Q ss_pred             HhcCCeEEEEccchhhhhC
Q 005179          379 QKSGDVILFIDEVHTLIGS  397 (710)
Q Consensus       379 ~~~~~~IL~IDEid~l~~~  397 (710)
                      ...++.+|+||+++.+...
T Consensus       155 ~~~~~~lVVIDSIq~l~~~  173 (372)
T cd01121         155 EELKPDLVIIDSIQTVYSS  173 (372)
T ss_pred             HhcCCcEEEEcchHHhhcc
Confidence            6667889999999998643

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.

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=96.92  E-value=0.0019  Score=67.01  Aligned_cols=91  Identities=13%  Similarity=0.203  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee-hhhhhh-c---cccCccHHHH
Q 005179          296 ETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD-MGLLMA-G---AKERGELEAR  370 (710)
Q Consensus       296 ~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld-~~~l~~-g---~~~~g~~e~~  370 (710)
                      ++.++.+..++. .....++|+|++|+||||+++++...+...       +..++.+. ..++.. +   .....+....
T Consensus        66 ~~~~~~l~~~~~-~~~GlilisG~tGSGKTT~l~all~~i~~~-------~~~iitiEdp~E~~~~~~~q~~v~~~~~~~  137 (264)
T cd01129          66 PENLEIFRKLLE-KPHGIILVTGPTGSGKTTTLYSALSELNTP-------EKNIITVEDPVEYQIPGINQVQVNEKAGLT  137 (264)
T ss_pred             HHHHHHHHHHHh-cCCCEEEEECCCCCcHHHHHHHHHhhhCCC-------CCeEEEECCCceecCCCceEEEeCCcCCcC
Confidence            334445544443 345679999999999999999998877431       22222221 111100 0   0000010112


Q ss_pred             HHHHHHHHHhcCCeEEEEccchhh
Q 005179          371 VTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       371 l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                      +...+..+...+|.+++|+|+-.-
T Consensus       138 ~~~~l~~~lR~~PD~i~vgEiR~~  161 (264)
T cd01129         138 FARGLRAILRQDPDIIMVGEIRDA  161 (264)
T ss_pred             HHHHHHHHhccCCCEEEeccCCCH
Confidence            444555555567889999998543

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.

>COG3899 Predicted ATPase [General function prediction only]

Probab=96.91  E-value=0.0094  Score=71.75  Aligned_cols=48  Identities=35%  Similarity=0.613  Sum_probs=40.0

Q ss_pred             CcccCHHHHHHHHHHHHcCCC---CCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          291 PVIGRETEIQRIIQILCRRTK---NNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~---~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      +++||+.++..|.+.+.+..+   .-+++.|.+|.|||.+++.+.+.+.+.
T Consensus         1 ~l~GRe~ev~~Ll~~f~~v~~g~~~~~lv~G~sGIGKsalv~ev~~~i~~~   51 (849)
T COG3899           1 PLYGRETELAQLLAAFDRVSKGRGEVVLVAGESGIGKSALVNEVHKPITQQ   51 (849)
T ss_pred             CCCchHhHHHHHHHHHHHHhCCCeEEEEEeecCCCcHHHHHHHHHHHHhcc
Confidence            479999999999998876333   347888999999999999999987653

>PRK09183 transposase/IS protein; Provisional

Probab=96.91  E-value=0.00051  Score=71.05  Aligned_cols=37  Identities=27%  Similarity=0.292  Sum_probs=28.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      +++|+||||||||.||.+|+..+...+.....+++++
T Consensus       104 ~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~  140 (259)
T PRK09183        104 NIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAAD  140 (259)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHH
Confidence            7899999999999999999988655444444444443

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=96.90  E-value=0.0017  Score=69.55  Aligned_cols=62  Identities=23%  Similarity=0.214  Sum_probs=48.1

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ++|...++..+...++..-. . +     ..+|++|+|||||+.+|++|-..-......++.+|++...
T Consensus         1 liG~S~~m~~~~~~~~~~a~-~-~-----~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~   62 (329)
T TIGR02974         1 LIGESNAFLEVLEQVSRLAP-L-D-----RPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALS   62 (329)
T ss_pred             CCcCCHHHHHHHHHHHHHhC-C-C-----CCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCC
Confidence            46777778777776665531 1 1     3689999999999999999988766667899999998663

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

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=96.89  E-value=0.0015  Score=74.48  Aligned_cols=64  Identities=22%  Similarity=0.303  Sum_probs=52.9

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ..++|+..++..+...++....  .+     ..+|++|++|||||++|++|-..-...+..++.+||+.+.
T Consensus       187 ~~iig~s~~~~~~~~~i~~~a~--~~-----~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~  250 (509)
T PRK05022        187 GEMIGQSPAMQQLKKEIEVVAA--SD-----LNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALP  250 (509)
T ss_pred             CceeecCHHHHHHHHHHHHHhC--CC-----CcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCC
Confidence            3489999999999888877532  11     3789999999999999999999877677899999998874

>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=96.88  E-value=0.0029  Score=58.78  Aligned_cols=22  Identities=45%  Similarity=0.684  Sum_probs=20.5

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      ++++|+||+||||+++.+++.+
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~   23 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRL   23 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHC
Confidence            5899999999999999999887

...

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.88  E-value=0.0006  Score=76.55  Aligned_cols=39  Identities=18%  Similarity=0.308  Sum_probs=30.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC--CCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS--VRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~--~~~li~~d~se~  698 (710)
                      .+++||||||||||.|++++|+.+...  +...+.++..+|
T Consensus       149 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~  189 (450)
T PRK00149        149 NPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKF  189 (450)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHH
Confidence            468999999999999999999998654  334555555444

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.87  E-value=0.0006  Score=75.48  Aligned_cols=39  Identities=18%  Similarity=0.289  Sum_probs=30.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC--CCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS--VRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~--~~~li~~d~se~  698 (710)
                      ..++||||||||||.|++++++++...  +...+.++.++|
T Consensus       137 n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~  177 (405)
T TIGR00362       137 NPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKF  177 (405)
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHH
Confidence            468999999999999999999998754  345556665544

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).

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=96.84  E-value=0.0035  Score=65.39  Aligned_cols=27  Identities=33%  Similarity=0.578  Sum_probs=24.2

Q ss_pred             CCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          656 NRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       656 ~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+|+ .+++.||||||||++|..||+.|
T Consensus        90 ~~p~-iIlI~G~sgsGKStlA~~La~~l  116 (301)
T PRK04220         90 KEPI-IILIGGASGVGTSTIAFELASRL  116 (301)
T ss_pred             CCCE-EEEEECCCCCCHHHHHHHHHHHh
Confidence            3565 79999999999999999999997

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.83  E-value=0.012  Score=61.26  Aligned_cols=42  Identities=29%  Similarity=0.305  Sum_probs=32.2

Q ss_pred             CCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          657 RPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       657 rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ++...++|+||||+|||+++..||..+-..+.....+|+..|
T Consensus        70 ~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~  111 (272)
T TIGR00064        70 NKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTF  111 (272)
T ss_pred             CCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCC
Confidence            334689999999999999999999887665555655665544

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.

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.83  E-value=0.009  Score=65.65  Aligned_cols=41  Identities=27%  Similarity=0.343  Sum_probs=31.3

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +...++|+||+|+|||+++..||..|-..+.....+++..|
T Consensus        99 ~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D~~  139 (429)
T TIGR01425        99 KQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTF  139 (429)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCccc
Confidence            34689999999999999999999987654545555555444

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=96.83  E-value=0.0056  Score=62.33  Aligned_cols=26  Identities=15%  Similarity=0.342  Sum_probs=22.0

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..++++|+||+|||+++..++...
T Consensus        24 ~g~~~~i~G~~GsGKt~l~~~~~~~~   49 (234)
T PRK06067         24 FPSLILIEGDHGTGKSVLSQQFVYGA   49 (234)
T ss_pred             CCcEEEEECCCCCChHHHHHHHHHHH
Confidence            45567899999999999999997664

>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=96.82  E-value=0.0015  Score=52.78  Aligned_cols=22  Identities=36%  Similarity=0.555  Sum_probs=20.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 005179          662 MLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      +.+.|+||+|||+++++|++.|
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999997

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.

>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=96.81  E-value=0.0023  Score=67.68  Aligned_cols=66  Identities=26%  Similarity=0.426  Sum_probs=51.2

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ..+.|.+++++.+...++.+..|+...+|   .++|.||+|+||+++++.|-+.|  .+-.+..+..|...
T Consensus        61 ~~~~G~~~~i~~lV~~fk~AA~g~~~~kr---Il~L~GPvg~GKSsl~~~Lk~~l--e~y~~Y~l~~~Pm~  126 (358)
T PF08298_consen   61 DEFYGMEETIERLVNYFKSAAQGLEERKR---ILLLLGPVGGGKSSLAELLKRGL--EEYPIYTLKGCPMH  126 (358)
T ss_pred             ccccCcHHHHHHHHHHHHHHHhccCccce---EEEEECCCCCCHHHHHHHHHHHh--heEEEEEecCCccc
Confidence            34899999999999999998888865544   78999999999999999998876  22245555444443

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>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=96.80  E-value=0.001  Score=60.42  Aligned_cols=22  Identities=41%  Similarity=0.514  Sum_probs=20.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHH
Q 005179          662 MLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      +++.|+||+|||++|+.|++.+
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            5799999999999999999996

...

>PRK06620 hypothetical protein; Validated

Probab=96.79  E-value=0.00088  Score=67.19  Aligned_cols=22  Identities=36%  Similarity=0.510  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .++||||||||||.|++++++.
T Consensus        46 ~l~l~Gp~G~GKThLl~a~~~~   67 (214)
T PRK06620         46 TLLIKGPSSSGKTYLTKIWQNL   67 (214)
T ss_pred             eEEEECCCCCCHHHHHHHHHhc
Confidence            6899999999999999999886

>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=96.79  E-value=0.0037  Score=58.99  Aligned_cols=41  Identities=34%  Similarity=0.386  Sum_probs=33.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG  360 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g  360 (710)
                      -+.|+|.||+||||||++|.+.+...       +.+++.+|...+..+
T Consensus         4 vIwltGlsGsGKtTlA~~L~~~L~~~-------g~~~~~LDgD~lR~~   44 (156)
T PF01583_consen    4 VIWLTGLSGSGKTTLARALERRLFAR-------GIKVYLLDGDNLRHG   44 (156)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHT-------TS-EEEEEHHHHCTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEecCcchhhc
Confidence            36899999999999999999999654       778888988777643

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 ....

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.77  E-value=0.031  Score=59.38  Aligned_cols=102  Identities=20%  Similarity=0.298  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHh--c-CCeEEEEccchhhhhCCCCCCCC----CCChHhHHHhhccccc------CCCeEE-EEccChHHH
Q 005179          370 RVTTLISEIQK--S-GDVILFIDEVHTLIGSGTVGRGN----KGTGLDISNLLKPSLG------RGELQC-IASTTQDEH  435 (710)
Q Consensus       370 ~l~~~~~~~~~--~-~~~IL~IDEid~l~~~~~~~~~~----~~~~~~~~~~L~~~l~------~~~v~v-I~att~~~~  435 (710)
                      .+..+++++..  . .|+++-||++..++........+    ......+...|+.+++      +|.+++ +++|....-
T Consensus       141 ~~~~l~~EL~~~~~~~PVL~avD~~n~l~~~S~Y~~~~~~~I~~~~L~l~~~f~~~~s~~~~~~nG~~v~~l~~t~~~~~  220 (309)
T PF10236_consen  141 VFQALIRELKAQSKRPPVLVAVDGFNALFGPSAYRDPDFKPIHPHDLTLVRLFLDLLSGKRDFKNGAVVTALAATSVSNA  220 (309)
T ss_pred             HHHHHHHHHHhcccCCceEEEehhhHHhhCCccccCCCCccccHHHhhHHHHHHHHhcCccccCCCeEEEEEeccccccc
Confidence            45666666654  2 47888899999998764322111    1112334555666533      343332 444332211


Q ss_pred             Hhhhhc-------------------cHHHHccc---cceEecCCCHHHHHHHHHHHHH
Q 005179          436 RTQFEK-------------------DKALARRF---QPVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       436 ~~~~~~-------------------d~aL~~Rf---~~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      .....+                   |+.+...+   ..|.++..+.+|...+++....
T Consensus       221 ~~~~~l~~~L~~~~~~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~  278 (309)
T PF10236_consen  221 PKSPTLPVALGGKEGFPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYAD  278 (309)
T ss_pred             cCCccchhhhccccCCCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHH
Confidence            110112                   22222222   2788888899987777665443

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).

>PHA02624 large T antigen; Provisional

Probab=96.77  E-value=0.0063  Score=68.66  Aligned_cols=27  Identities=22%  Similarity=0.215  Sum_probs=24.2

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.++.++|+||||||||+++.+|++.+
T Consensus       429 PKk~~il~~GPpnTGKTtf~~sLl~~L  455 (647)
T PHA02624        429 PKRRYWLFKGPVNSGKTTLAAALLDLC  455 (647)
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHc
Confidence            445678999999999999999999988

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=96.76  E-value=0.0034  Score=58.53  Aligned_cols=22  Identities=36%  Similarity=0.492  Sum_probs=20.4

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      +.+.|+|||||||+++.||+.+
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~   24 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHL   24 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHh
Confidence            4678999999999999999998

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=96.74  E-value=0.0017  Score=72.32  Aligned_cols=38  Identities=21%  Similarity=0.225  Sum_probs=29.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      .+++||||||||||.|++++|+.+.......+-++..+
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~  179 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSEL  179 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHH
Confidence            36899999999999999999999865444455554433

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=96.74  E-value=0.0026  Score=68.22  Aligned_cols=64  Identities=19%  Similarity=0.214  Sum_probs=50.3

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +.++|...++..+...+++.-. .   +   ..+|++|++||||+.+|++|-..-......++.+|++.+.
T Consensus         6 ~~liG~S~~~~~~~~~i~~~a~-~---~---~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~   69 (326)
T PRK11608          6 DNLLGEANSFLEVLEQVSRLAP-L---D---KPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALN   69 (326)
T ss_pred             CccEECCHHHHHHHHHHHHHhC-C---C---CCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCC
Confidence            3478888888888877766531 1   1   3689999999999999999987655556789999999874

>PRK06696 uridine kinase; Validated

Probab=96.74  E-value=0.0031  Score=63.75  Aligned_cols=57  Identities=21%  Similarity=0.159  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          636 EAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       636 ~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +.++.|...+....     +.+|. -+.+.|+||+|||++|+.||+.|-..+...+.+-|..|
T Consensus         5 ~~~~~la~~~~~~~-----~~~~~-iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf   61 (223)
T PRK06696          5 QLIKELAEHILTLN-----LTRPL-RVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDF   61 (223)
T ss_pred             HHHHHHHHHHHHhC-----CCCce-EEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeccccc
Confidence            34455555554322     23343 78899999999999999999998543345565554444

>PRK13947 shikimate kinase; Provisional

Probab=96.74  E-value=0.0036  Score=60.24  Aligned_cols=24  Identities=33%  Similarity=0.594  Sum_probs=22.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .|++|+|+||+|||++++.||+.+
T Consensus         2 ~~I~l~G~~GsGKst~a~~La~~l   25 (171)
T PRK13947          2 KNIVLIGFMGTGKTTVGKRVATTL   25 (171)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHh
Confidence            379999999999999999999998

>PRK11823 DNA repair protein RadA; Provisional

Probab=96.74  E-value=0.0018  Score=72.25  Aligned_cols=112  Identities=13%  Similarity=0.186  Sum_probs=59.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc----ccCc--------cHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA----KERG--------ELEARVTTLISEI  378 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~----~~~g--------~~e~~l~~~~~~~  378 (710)
                      +.-++|+|+||+|||+++..++..+...       +.++++++........    ...|        ..+..+..+++.+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~~~a~~-------g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i  152 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAARLAAA-------GGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATI  152 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHH
Confidence            3457899999999999999999877532       3444444432111000    0000        0011234555556


Q ss_pred             HhcCCeEEEEccchhhhhCCCCCCCCCC-ChHhHHHhhcccccCCCeEEEEc
Q 005179          379 QKSGDVILFIDEVHTLIGSGTVGRGNKG-TGLDISNLLKPSLGRGELQCIAS  429 (710)
Q Consensus       379 ~~~~~~IL~IDEid~l~~~~~~~~~~~~-~~~~~~~~L~~~l~~~~v~vI~a  429 (710)
                      ...++.+++||.+..+......+..++. .-..+...|..+..+.++.+|.+
T Consensus       153 ~~~~~~lVVIDSIq~l~~~~~~~~~g~~~qvr~~~~~L~~~ak~~~itvilv  204 (446)
T PRK11823        153 EEEKPDLVVIDSIQTMYSPELESAPGSVSQVRECAAELMRLAKQRGIAVFLV  204 (446)
T ss_pred             HhhCCCEEEEechhhhccccccCCCCCHHHHHHHHHHHHHHHHHcCCEEEEE
Confidence            6667789999999998653211000000 11223344555555555555544

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=96.73  E-value=0.00036  Score=71.75  Aligned_cols=59  Identities=31%  Similarity=0.395  Sum_probs=42.4

Q ss_pred             cHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          613 TADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       613 ~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .|.+..+-..+.+     ++++++.+..+.+.     .+.  +.-|  ++|||||||+|||....+.|+.|++
T Consensus        30 pwvekyrP~~l~d-----v~~~~ei~st~~~~-----~~~--~~lP--h~L~YgPPGtGktsti~a~a~~ly~   88 (360)
T KOG0990|consen   30 PWVEKYRPPFLGI-----VIKQEPIWSTENRY-----SGM--PGLP--HLLFYGPPGTGKTSTILANARDFYS   88 (360)
T ss_pred             CCccCCCCchhhh-----HhcCCchhhHHHHh-----ccC--CCCC--cccccCCCCCCCCCchhhhhhhhcC
Confidence            3444444444444     78888888777554     222  2222  8999999999999999999999998

>PHA02624 large T antigen; Provisional

Probab=96.73  E-value=0.0028  Score=71.43  Aligned_cols=27  Identities=41%  Similarity=0.486  Sum_probs=25.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ..+|||||||||||+++++|.+.|-|.
T Consensus       432 ~~il~~GPpnTGKTtf~~sLl~~L~G~  458 (647)
T PHA02624        432 RYWLFKGPVNSGKTTLAAALLDLCGGK  458 (647)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCe
Confidence            489999999999999999999999784

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.72  E-value=0.0014  Score=71.12  Aligned_cols=23  Identities=35%  Similarity=0.518  Sum_probs=21.3

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -+++.|.||||||.|+-.++..+
T Consensus         3 v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             EEEEEecCCcCHHHHHHHHHHHh
Confidence            46889999999999999999988

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	710
3pxi_A	758	Structure Of Meca108:clpc Length = 758		1e-114
1qvr_A	854	Crystal Structure Analysis Of Clpb Length = 854		6e-99
3pxg_A	468	Structure Of Meca121 And Clpc1-485 Complex Length =		1e-92
4hse_A	397	Crystal Structure Of Clpb Nbd1 In Complex With Guan		9e-76
1ksf_X	758	Crystal Structure Of Clpa, An Hsp100 Chaperone And		2e-75
1ksf_X	758	Crystal Structure Of Clpa, An Hsp100 Chaperone And		4e-12
1jbk_A	195	Crystal Structure Of The First Nucelotide Binding D		1e-55
2p65_A	187	Crystal Structure Of The First Nucleotide Binding D		2e-55
4fct_A	308	Crystal Structure Of The C-Terminal Domain Of Clpb		2e-17
4fcv_A	311	Crystal Structure Of The C-Terminal Domain Of Clpb		2e-17
3fh2_A	146	The Crystal Structure Of The Probable Atp-Dependent		4e-14
2y1r_A	149	Structure Of Meca121 & Clpc N-Domain Complex Length		8e-14
2k77_A	146	Nmr Solution Structure Of The Bacillus Subtilis Clp		8e-14
2y1q_A	150	Crystal Structure Of Clpc N-Terminal Domain Length		2e-13
3fes_A	145	Crystal Structure Of The Atp-Dependent Clp Protease		6e-09

>pdb|3PXI|A Chain A, Structure Of Meca108:clpc Length = 758

Iteration: 1
 Score =  408 bits (1049), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 257/610 (42%), Positives = 354/610 (58%), Gaps = 69/610 (11%)
Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E          GI   KA +A
Sbjct: 2   MFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREG--------EGIAA-KALQA 52
Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
           +  +      ++ +    +G+  S    + ++   K+V E +++ +R  G++++  EHI 
Sbjct: 53  L-GLGSEKIQKEVESLIGRGQEMSQT--IHYTPRAKKVIELSMDEARKLGHSYVGTEHIL 109
Query: 201 LGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTA 260
           LGL    +G A RVL  LGV +N  A   V +L G                 N      A
Sbjct: 110 LGLIREGEGVAARVLNNLGVSLNK-ARQQVLQLLGS----------------NETGSSAA 152
Query: 261 ALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGES 320
              S   T    L+    DLTA A E+ +DPVIGR  EIQR+I++L RRTKNNP+L+GE 
Sbjct: 153 GTNSNANT--PTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEP 210
Query: 321 GVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK 380
           GVGKTAIAEGLA +I+  EVP  L  KR+M+LDMG      K RGE E R+  ++ EI++
Sbjct: 211 GVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-----TKYRGEFEDRLKKVMDEIRQ 265
Query: 381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFE 440
           +G++ILFID                   +D SN+LKPSL RGELQCI +TT DE+R   E
Sbjct: 266 AGNIILFID-----------------AAIDASNILKPSLARGELQCIGATTLDEYRKYIE 308
Query: 441 KDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDR 500
           KD AL RRFQP+ + +PS +++++IL GLR++YEAHH    T +AI AAV LS RYISDR
Sbjct: 309 KDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDR 368
Query: 501 YLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLK 560
           +LPDKAIDL+DEAGS+  +  F           + PP+    E +  +   E     + +
Sbjct: 369 FLPDKAIDLIDEAGSKVRLRSF-----------TTPPNLKELEQKLDEVRKEKDAAVQSQ 417
Query: 561 YDDVVASMGDTSEIV---VESSLPSASDD--DEPAVVGPDDIAAVASLWSGIPVQQITAD 615
             +  AS+ DT + +   VE +  S  +    E + V  DDIA V S W+G+PV +I   
Sbjct: 418 EFEKAASLRDTEQRLREQVEDTKKSWKEKQGQENSEVTVDDIAMVVSSWTGVPVSKIAQT 477
Query: 616 ERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTEL 675
           E   L+ +E  L  RVIGQDEAV A+++AV+R+R GLKDP RP  + +F GPTGVGKTEL
Sbjct: 478 ETDKLLNMENILHSRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTEL 537
Query: 676 AKSLAACYFG 685
           A++LA   FG
Sbjct: 538 ARALAESIFG 547

>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb Length = 854

Iteration: 1
 Score =  358 bits (919), Expect = 6e-99,   Method: Compositional matrix adjust.
 Identities = 219/472 (46%), Positives = 295/472 (62%), Gaps = 63/472 (13%)
Query: 271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEG 330
           +ALEQ+ +DLT  A+E  +DPVIGR+ EI+R+IQIL RRTKNNP+L+GE GVGKTAI EG
Sbjct: 151 NALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEG 210
Query: 331 LAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISE-IQKSGDVILFID 389
           LA RIV+ +VP  L  KRI+SL MG L+AGAK RGE E R+  +I E +Q  G+VILFID
Sbjct: 211 LAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFID 270
Query: 390 EVHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARR 448
           E+HT++G+G      K  G +D  N+LKP+L RGEL+ I +TT DE+R + EKD AL RR
Sbjct: 271 ELHTVVGAG------KAEGAVDAGNMLKPALARGELRLIGATTLDEYR-EIEKDPALERR 323
Query: 449 FQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID 508
           FQPV + EP+ E+ + IL GL+EKYE HH  + +  AI AA  LS RYI++R LPDKAID
Sbjct: 324 FQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAID 383
Query: 509 LVDEAGSR---------AHIELFKRKK-----EQQTCILSKPPDDY-------------- 540
           L+DEA +R           I+  +RKK     E++     K PD                
Sbjct: 384 LIDEAAARLRMALESAPEEIDALERKKLQLEIEREALKKEKDPDSQERLKAIEAEIAKLT 443
Query: 541 ---------WQEIRTV-----QAMHEV------VQGSRLKYDDVVASMGDTSEI-VVESS 579
                    W+  R +     +A H +      ++ +  +YD   A+     E+  +E+ 
Sbjct: 444 EEIAKLRAEWEREREILRKLREAQHRLDEVRREIELAERQYDLNRAAELRYGELPKLEAE 503
Query: 580 LPSASDDDEPA-----VVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQ 634
           + + S+    A      V  +DIA + S W+GIPV ++   ER  L+ LEE+L KRV+GQ
Sbjct: 504 VEALSEKLRGARFVRLEVTEEDIAEIVSRWTGIPVSKLLEGEREKLLRLEEELHKRVVGQ 563
Query: 635 DEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           DEA+ A++ A++R+R GLKDPNRP  + LF GPTGVGKTELAK+LAA  F +
Sbjct: 564 DEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT 615

>pdb|3PXG|A Chain A, Structure Of Meca121 And Clpc1-485 Complex Length = 468

Iteration: 1
 Score =  337 bits (865), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 213/531 (40%), Positives = 297/531 (55%), Gaps = 69/531 (12%)
Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E          GI   KA +A
Sbjct: 2   MFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREG--------EGIAA-KALQA 52
Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
           +  +      ++ +    +G+  S    + ++   K+V E +++ +R  G++++  EHI 
Sbjct: 53  L-GLGSEKIQKEVESLIGRGQEMSQT--IHYTPRAKKVIELSMDEARKLGHSYVGTEHIL 109
Query: 201 LGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTA 260
           LGL    +G A RVL  LGV +N  A   V +L G                 N      A
Sbjct: 110 LGLIREGEGVAARVLNNLGVSLNK-ARQQVLQLLGS----------------NETGSSAA 152
Query: 261 ALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGES 320
              S   T    L+    DLTA A E+ +DPVIGR  EIQR+I++L RRTKNNP+L+GE 
Sbjct: 153 GTNSNANT--PTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGEP 210
Query: 321 GVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK 380
           GVGKTAIAEGLA +I+  EVP  L  KR+M+LDMG      K RGE E R+  ++ EI++
Sbjct: 211 GVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-----TKYRGEFEDRLKKVMDEIRQ 265
Query: 381 SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFE 440
           +G++ILFID                   +D SN+LKPSL RGELQCI +TT DE+R   E
Sbjct: 266 AGNIILFID-----------------AAIDASNILKPSLARGELQCIGATTLDEYRKYIE 308
Query: 441 KDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDR 500
           KD AL RRFQP+ + +PS +++++IL GLR++YEAHH    T +AI AAV LS RYISDR
Sbjct: 309 KDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDR 368
Query: 501 YLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLK 560
           +LPDKAIDL+DEAGS+  +  F           + PP+    E +  +   E     + +
Sbjct: 369 FLPDKAIDLIDEAGSKVRLRSF-----------TTPPNLKELEQKLDEVRKEKDAAVQSQ 417
Query: 561 YDDVVASMGDTSEIV---VESSLPSASDD--DEPAVVGPDDIAAVASLWSG 606
             +  AS+ DT + +   VE +  S  +    E + V  DDIA V S W+G
Sbjct: 418 EFEKAASLRDTEQRLREQVEDTKKSWKEKQGQENSEVTVDDIAMVVSSWTG 468

>pdb|4HSE|A Chain A, Crystal Structure Of Clpb Nbd1 In Complex With Guanidinium Chloride And Adp Length = 397

Iteration: 1
 Score =  281 bits (719), Expect = 9e-76,   Method: Compositional matrix adjust.
 Identities = 153/284 (53%), Positives = 197/284 (69%), Gaps = 23/284 (8%)
Query: 271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEG 330
           +ALEQ+ +DLT  A+E  +DPVIGR+ EI+R+IQIL RRTKNNP+L+GE GVGKTAI EG
Sbjct: 14  NALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEG 73
Query: 331 LAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISE-IQKSGDVILFID 389
           LA RIV+ +VP  L  KRI+SL MG L+AGAK RGE E R+  +I E +Q  G+VILFID
Sbjct: 74  LAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFID 133
Query: 390 EVHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARR 448
           E+HT++G+G      K  G +D  N+LKP+L RGEL+ I +TT DE+R + EKD AL RR
Sbjct: 134 ELHTVVGAG------KAEGAVDAGNMLKPALARGELRLIGATTLDEYR-EIEKDPALERR 186
Query: 449 FQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID 508
           FQPV + EP+ E+ + IL GL+EKYE HH  + +  AI AA  LS RYI++R LPDKAID
Sbjct: 187 FQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAID 246
Query: 509 LVDEAGSR---------AHIELFKRKK-----EQQTCILSKPPD 538
           L+DEA +R           I+  +RKK     E++     K PD
Sbjct: 247 LIDEAAARLRMALESAPEEIDALERKKLQLEIEREALKKEKDPD 290

>pdb|1KSF|X Chain X, Crystal Structure Of Clpa, An Hsp100 Chaperone And Regulator Of Clpap Protease: Structural Basis Of Differences In Function Of The Two Aaa+ Atpase Domains Length = 758

Iteration: 1
 Score =  280 bits (715), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 154/360 (42%), Positives = 227/360 (63%), Gaps = 26/360 (7%)
Query: 172 SISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVS 231
           ++S +RV + AV + +S G N +   ++ + +F+  +  A  +L++   +V+ L  V   
Sbjct: 81  TLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKH--EVSRLDVVNF- 137
Query: 232 RLQGELAKEGREPSLAKGVRENSISGKTAALKSPGRTRASA----LEQFCVDLTARASEE 287
                         ++ G R++  +  +     P     +     LE F  +L   A   
Sbjct: 138 --------------ISHGTRKDEPTQSSDPGSQPNSEEQAGGEERLENFTTNLNQLARVG 183
Query: 288 LIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSK 347
            IDP+IGRE E++R IQ+LCRR KNNP+L+GESGVGKTAIAEGLA RIVQ +VP  +   
Sbjct: 184 GIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADC 243
Query: 348 RIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGT 407
            I SLD+G L+AG K RG+ E R   L+ ++++  + ILFIDE+HT+IG+G    G    
Sbjct: 244 TIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQ--- 300
Query: 408 GLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILL 467
            +D +NL+KP L  G+++ I STT  E    FEKD+ALARRFQ + I+EPS E+ V+I+ 
Sbjct: 301 -VDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIIN 359
Query: 468 GLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHI-ELFKRKK 526
           GL+ KYEAHH+ ++T +A+ AAV L+ +YI+DR+LPDKAID++DEAG+RA +  + KRKK
Sbjct: 360 GLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKK 419

>pdb|1KSF|X Chain X, Crystal Structure Of Clpa, An Hsp100 Chaperone And Regulator Of Clpap Protease: Structural Basis Of Differences In Function Of The Two Aaa+ Atpase Domains Length = 758

Iteration: 1
 Score = 70.1 bits (170), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 34/85 (40%), Positives = 54/85 (63%)
Query: 596 DIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDP 655
           DI +V +  + IP + ++  +R  L  L ++LK  V GQD+A+ A++ A+K +R GL   
Sbjct: 425 DIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHE 484
Query: 656 NRPTAAMLFCGPTGVGKTELAKSLA 680
           ++P  + LF GPTGVGKTE+   L+
Sbjct: 485 HKPVGSFLFAGPTGVGKTEVTVQLS 509

>pdb|1JBK|A Chain A, Crystal Structure Of The First Nucelotide Binding Domain Of Clpb Length = 195

Iteration: 1
 Score =  214 bits (545), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 109/197 (55%), Positives = 146/197 (74%), Gaps = 8/197 (4%)
Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           AL+++ +DLT RA +  +DPVIGR+ EI+R IQ+L RRTKNNP+L+GE GVGKTAI EGL
Sbjct: 4   ALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGL 63
Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDE 390
           A RI+  EVP  L  +R+++LDMG L+AGAK RGE E R+  +++++ K  G+VILFIDE
Sbjct: 64  AQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDE 123
Query: 391 VHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRF 449
           +HT++G+G      K  G +D  N+LKP+L RGEL C+ +TT DE+R   EKD AL RRF
Sbjct: 124 LHTMVGAG------KADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRF 177
Query: 450 QPVLISEPSQEDAVRIL 466
           Q V ++EPS ED + IL
Sbjct: 178 QKVFVAEPSVEDTIAIL 194

>pdb|2P65|A Chain A, Crystal Structure Of The First Nucleotide Binding Domain Of Chaperone Clpb1, Putative, (Pv089580) From Plasmodium Vivax Length = 187

Iteration: 1
 Score =  214 bits (544), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 107/188 (56%), Positives = 141/188 (75%), Gaps = 5/188 (2%)
Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           ALE++  DLTA A    +DPVIGR+TEI+R IQIL RRTKNNPILLG+ GVGKTAI EGL
Sbjct: 4   ALEKYSRDLTALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGL 63
Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDE 390
           AI+IVQ +VP  L  ++++SLD+  L+AGAK RG+ E R+ +++ E+Q + G V++FIDE
Sbjct: 64  AIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDE 123
Query: 391 VHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ 450
           +HT++G+G V  G     LD  N+LKP L RGEL+CI +TT  E+R   EKDKAL RRFQ
Sbjct: 124 IHTVVGAGAVAEG----ALDAGNILKPMLARGELRCIGATTVSEYRQFIEKDKALERRFQ 179
Query: 451 PVLISEPS 458
            +L+ +PS
Sbjct: 180 QILVEQPS 187

>pdb|4FCT|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb Length = 308

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/58 (65%), Positives = 48/58 (82%)
Query: 629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           KRV+GQDEA+ A++ A++R+R GLKDPNRP  + LF GPTGVGKTELAK+LAA  F +
Sbjct: 14  KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT 71

>pdb|4FCV|A Chain A, Crystal Structure Of The C-Terminal Domain Of Clpb Length = 311

Iteration: 1
 Score = 87.4 bits (215), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/58 (65%), Positives = 48/58 (82%)
Query: 629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           KRV+GQDEA+ A++ A++R+R GLKDPNRP  + LF GPTGVGKTELAK+LAA  F +
Sbjct: 17  KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT 74

>pdb|3FH2|A Chain A, The Crystal Structure Of The Probable Atp-Dependent Protease (Heat Shock Protein) From Corynebacterium Glutamicum Length = 146

Iteration: 1
 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 49/159 (30%), Positives = 81/159 (50%), Gaps = 15/159 (9%)
Query: 79  SSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNG-FLES-GITIDK 136
            ++FERFT+RA + ++ +Q EA+ L  + + T+H+LLGLI E        LES GI++D 
Sbjct: 1   QAMFERFTDRARRVIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDA 60
Query: 137 AREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAP 196
            R            Q+ ++   QG    +   +PF+   K+V E ++      G+ +I  
Sbjct: 61  VR------------QEVEEIIGQGSQ-PTTGHIPFTPRAKKVLELSLREGLQMGHKYIGT 107
Query: 197 EHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQG 235
           E + LGL    +G A +VL +LG D+  +    +  L G
Sbjct: 108 EFLLLGLIREGEGVAAQVLVKLGADLPRVRQQVIQLLSG 146

>pdb|2Y1R|A Chain A, Structure Of Meca121 & Clpc N-Domain Complex Length = 149

Iteration: 1
 Score = 75.9 bits (185), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 47/143 (32%), Positives = 77/143 (53%), Gaps = 12/143 (8%)
Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E          GI   KA +A
Sbjct: 2   MFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREG--------EGIA-AKALQA 52
Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
           +  +      ++ +    +G+  S    + ++   K+V E +++ +R  G++++  EHI 
Sbjct: 53  L-GLGSEKIQKEVESLIGRGQEMSQT--IHYTPRAKKVIELSMDEARKLGHSYVGTEHIL 109
Query: 201 LGLFTVDDGSAGRVLKRLGVDVN 223
           LGL    +G A RVL  LGV +N
Sbjct: 110 LGLIREGEGVAARVLNNLGVSLN 132

>pdb|2K77|A Chain A, Nmr Solution Structure Of The Bacillus Subtilis Clpc N- Domain Length = 146

Iteration: 1
 Score = 75.9 bits (185), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 47/143 (32%), Positives = 77/143 (53%), Gaps = 12/143 (8%)
Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E          GI   KA +A
Sbjct: 3   MFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREG--------EGIA-AKALQA 53
Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
           +  +      ++ +    +G+  S    + ++   K+V E +++ +R  G++++  EHI 
Sbjct: 54  L-GLGSEKIQKEVESLIGRGQEMSQT--IHYTPRAKKVIELSMDEARKLGHSYVGTEHIL 110
Query: 201 LGLFTVDDGSAGRVLKRLGVDVN 223
           LGL    +G A RVL  LGV +N
Sbjct: 111 LGLIREGEGVAARVLNNLGVSLN 133

>pdb|2Y1Q|A Chain A, Crystal Structure Of Clpc N-Terminal Domain Length = 150

Iteration: 1
 Score = 74.3 bits (181), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 45/143 (31%), Positives = 76/143 (53%), Gaps = 12/143 (8%)
Query: 81  VFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREA 140
           +F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E          GI    A +A
Sbjct: 2   MFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREG--------EGI----AAKA 49
Query: 141 VVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIA 200
           + ++   +     +  +  G+    +  + ++   K+V E +++ +R  G++++  EHI 
Sbjct: 50  LQALGLGSEKIQKEVESLIGRAQEMSQTIHYTPRAKKVIELSMDEARKLGHSYVGTEHIL 109
Query: 201 LGLFTVDDGSAGRVLKRLGVDVN 223
           LGL    +G A RVL  LGV +N
Sbjct: 110 LGLIREGEGVAARVLNNLGVSLN 132

>pdb|3FES|A Chain A, Crystal Structure Of The Atp-Dependent Clp Protease Clpc From Clostridium Difficile Length = 145

Iteration: 1
 Score = 59.7 bits (143), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 42/149 (28%), Positives = 73/149 (48%), Gaps = 12/149 (8%)
Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAV 141
           F RFT+RA KA+  +   AKSLG ++V ++H+LLGL+ E        E GI    A + +
Sbjct: 5   FNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLRE--------EEGI----AAKVL 52
Query: 142 VSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIAL 201
             +  +    +      +GK    +  +  S  +K++ E +  ++     N+I  EHI L
Sbjct: 53  SKVGFTEAYLEGKIVDXEGKGEEISEDIVLSPRSKQILELSGXFANKLKTNYIGTEHILL 112
Query: 202 GLFTVDDGSAGRVLKRLGVDVNHLAAVAV 230
            +    +G A ++L   GV+   LA + +
Sbjct: 113 AIIQEGEGIANKILNYAGVNDRTLAQLTI 141

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	710
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	0.0
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	1e-179
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	1e-169
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	1e-134
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	9e-38
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	1e-89
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	2e-87
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	1e-64
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	3e-34
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	1e-31
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	9e-31
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	3e-28
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	6e-10
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-12
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-06
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	4e-11
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	8e-11
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	2e-10
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	1e-05
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	3e-07
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	2e-05
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	3e-06
2chg_A	226	Replication factor C small subunit; DNA-binding pr	2e-05
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	4e-05
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	4e-05
2chq_A	319	Replication factor C small subunit; DNA-binding pr	5e-05
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	9e-05
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	9e-05
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	1e-04
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	2e-04
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	4e-04
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	5e-04

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis} Length = 758

 Score =  693 bits (1790), Expect = 0.0
 Identities = 245/614 (39%), Positives = 342/614 (55%), Gaps = 67/614 (10%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHP--NGFLESGITIDKARE 139
           F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E            G+  +K ++
Sbjct: 3   FGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQK 62

Query: 140 AVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHI 199
            V S+               G+    +  + ++   K+V E +++ +R  G++++  EHI
Sbjct: 63  EVESLI--------------GRGQEMSQTIHYTPRAKKVIELSMDEARKLGHSYVGTEHI 108

Query: 200 ALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKT 259
            LGL    +G A RVL  LGV +N      +  L                         +
Sbjct: 109 LLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSN-------------------ETGS 149

Query: 260 AALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGE 319
           +A  +        L+    DLTA A E+ +DPVIGR  EIQR+I++L RRTKNNP+L+GE
Sbjct: 150 SAAGTNSNANTPTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGE 209

Query: 320 SGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ 379
            GVGKTAIAEGLA +I+  EVP  L  KR+M+LDMG      K RGE E R+  ++ EI+
Sbjct: 210 PGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-----TKYRGEFEDRLKKVMDEIR 264

Query: 380 KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQF 439
           ++G++ILFID                   +D SN+LKPSL RGELQCI +TT DE+R   
Sbjct: 265 QAGNIILFIDA-----------------AIDASNILKPSLARGELQCIGATTLDEYRKYI 307

Query: 440 EKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD 499
           EKD AL RRFQP+ + +PS +++++IL GLR++YEAHH    T +AI AAV LS RYISD
Sbjct: 308 EKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISD 367

Query: 500 RYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRL 559
           R+LPDKAIDL+DEAGS+  +  F      +   L +  D+  +E        E  + + L
Sbjct: 368 RFLPDKAIDLIDEAGSKVRLRSFTTPPNLKE--LEQKLDEVRKEKDAAVQSQEFEKAASL 425

Query: 560 KYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERML 619
           +  +         ++             E + V  DDIA V S W+G+PV +I   E   
Sbjct: 426 RDTEQRL----REQVEDTKKSWKEKQGQENSEVTVDDIAMVVSSWTGVPVSKIAQTETDK 481

Query: 620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSL 679
           L+ +E  L  RVIGQDEAV A+++AV+R+R GLKDP RP  + +F GPTGVGKTELA++L
Sbjct: 482 LLNMENILHSRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARAL 541

Query: 680 AACYFGS----VRI 689
           A   FG     +RI
Sbjct: 542 AESIFGDEESMIRI 555

>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* Length = 758

 Score =  530 bits (1367), Expect = e-179
 Identities = 187/606 (30%), Positives = 291/606 (48%), Gaps = 89/606 (14%)

Query: 85  FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSI 144
             +    ++  +   A+    + +  +HLLL L++            + +   R+ + + 
Sbjct: 2   LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAF 61

Query: 145 WHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLF 204
              T          +    + + +        RV + AV + +S G N +   ++ + +F
Sbjct: 62  IEQTTPVLPASEEERDTQPTLSFQ--------RVLQRAVFHVQSSGRNEVTGANVLVAIF 113

Query: 205 TVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKTAALKS 264
           +  +  A  +L++  V    +    V+ +     K+    S   G + N           
Sbjct: 114 SEQESQAAYLLRKHEVSRLDV----VNFISHGTRKDEPTQSSDPGSQPN---------SE 160

Query: 265 PGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGK 324
                   LE F  +L   A    IDP+IGRE E++R IQ+LCRR KNNP+L+GESGVGK
Sbjct: 161 EQAGGEERLENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGK 220

Query: 325 TAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDV 384
           TAIAEGLA RIVQ +VP  +    I SLD+G L+AG K RG+ E R   L+ ++++  + 
Sbjct: 221 TAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNS 280

Query: 385 ILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKA 444
           ILFIDE+HT+IG+G       G  +D +NL+KP L  G+++ I STT  E    FEKD+A
Sbjct: 281 ILFIDEIHTIIGAGAAS----GGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRA 336

Query: 445 LARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD 504
           LARRFQ + I+EPS E+ V+I+ GL+ KYEAHH+ ++T +A+ AAV L+ +YI+DR+LPD
Sbjct: 337 LARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPD 396

Query: 505 KAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDV 564
           KAID++DEAG+RA +    ++K+               +I +V A    +    +   D 
Sbjct: 397 KAIDVIDEAGARARLMPVSKRKKTVNV----------ADIESVVARIARIPEKSVSQSD- 445

Query: 565 VASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLE 624
                         +L +  D  +  V G D   A+ +L   I         +M   GL 
Sbjct: 446 ------------RDTLKNLGDRLKMLVFGQDK--AIEALTEAI---------KMARAGLG 482

Query: 625 EQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF 684
              + + +G                           + LF GPTGVGKTE+   L+    
Sbjct: 483 H--EHKPVG---------------------------SFLFAGPTGVGKTEVTVQLSKALG 513

Query: 685 GS-VRI 689
              +R 
Sbjct: 514 IELLRF 519

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis} Length = 468

 Score =  493 bits (1271), Expect = e-169
 Identities = 202/532 (37%), Positives = 284/532 (53%), Gaps = 73/532 (13%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKARE 139
           F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E            G+  +K ++
Sbjct: 3   FGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQK 62

Query: 140 AVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHI 199
            V            +    +G+  S    + ++   K+V E +++ +R  G++++  EHI
Sbjct: 63  EV------------ESLIGRGQEMSQ--TIHYTPRAKKVIELSMDEARKLGHSYVGTEHI 108

Query: 200 ALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISGKT 259
            LGL    +G A RVL  LGV +N      V +L G                        
Sbjct: 109 LLGLIREGEGVAARVLNNLGVSLNKARQ-QVLQLLGSNETGSSAAG-------------- 153

Query: 260 AALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGE 319
               +        L+    DLTA A E+ +DPVIGR  EIQR+I++L RRTKNNP+L+GE
Sbjct: 154 ----TNSNANTPTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLIGE 209

Query: 320 SGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ 379
            GVGKTAIAEGLA +I+  EVP  L  KR+M+LDMG      K RGE E R+  ++ EI+
Sbjct: 210 PGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-----TKYRGEFEDRLKKVMDEIR 264

Query: 380 KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQF 439
           ++G++ILFID       +           +D SN+LKPSL RGELQCI +TT DE+R   
Sbjct: 265 QAGNIILFID------AA-----------IDASNILKPSLARGELQCIGATTLDEYRKYI 307

Query: 440 EKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD 499
           EKD AL RRFQP+ + +PS +++++IL GLR++YEAHH    T +AI AAV LS RYISD
Sbjct: 308 EKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISD 367

Query: 500 RYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRL 559
           R+LPDKAIDL+DEAGS+  +              + PP+    E +  +   E     + 
Sbjct: 368 RFLPDKAIDLIDEAGSKVRLR-----------SFTTPPNLKELEQKLDEVRKEKDAAVQS 416

Query: 560 KYDDVVASMGDT-----SEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSG 606
           +  +  AS+ DT      ++             E + V  DDIA V S W+G
Sbjct: 417 QEFEKAASLRDTEQRLREQVEDTKKSWKEKQGQENSEVTVDDIAMVVSSWTG 468

>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 Length = 854

 Score =  415 bits (1069), Expect = e-134
 Identities = 173/446 (38%), Positives = 241/446 (54%), Gaps = 58/446 (13%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFL--ESGITIDKARE 139
            ER+T+ A +A+  +Q  A+ +    +   HL   L+ ++R     L  ++G      +E
Sbjct: 3   LERWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADPKALKE 62

Query: 140 AVVSIWHSTNNQDTDDAAAQGKPFSS--AAKMPFSISTKRVFEAAVEYSRSRGYNFIAPE 197
                          +      P           +         A          ++A +
Sbjct: 63  LQ-------------ERELARLPKVEGAEVGQYLTSRLSGALNRAEGLMEELKDRYVAVD 109

Query: 198 HIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEGREPSLAKGVRENSISG 257
            + L L   +       L+ L        A+                   K +R     G
Sbjct: 110 TLVLALA--EATPGLPGLEAL------KGAL-------------------KELR----GG 138

Query: 258 KTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILL 317
           +T   +    T  +ALEQ+ +DLT  A+E  +DPVIGR+ EI+R+IQIL RRTKNNP+L+
Sbjct: 139 RTVQTEHAESTY-NALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLI 197

Query: 318 GESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISE 377
           GE GVGKTAI EGLA RIV+ +VP  L  KRI+SL MG L+AGAK RGE E R+  +I E
Sbjct: 198 GEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQE 257

Query: 378 IQKS-GDVILFIDEVHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQDEH 435
           + +S G+VILFIDE+HT++G+G      K  G +D  N+LKP+L RGEL+ I +TT DE+
Sbjct: 258 VVQSQGEVILFIDELHTVVGAG------KAEGAVDAGNMLKPALARGELRLIGATTLDEY 311

Query: 436 RTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR 495
           R + EKD AL RRFQPV + EP+ E+ + IL GL+EKYE HH  + +  AI AA  LS R
Sbjct: 312 R-EIEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHR 370

Query: 496 YISDRYLPDKAIDLVDEAGSRAHIEL 521
           YI++R LPDKAIDL+DEA +R  + L
Sbjct: 371 YITERRLPDKAIDLIDEAAARLRMAL 396

>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 Length = 854

 Score =  150 bits (380), Expect = 9e-38
 Identities = 57/102 (55%), Positives = 75/102 (73%), Gaps = 4/102 (3%)

Query: 592 VGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVG 651
           V  +DIA + S W+GIPV ++   ER  L+ LEE+L KRV+GQDEA+ A++ A++R+R G
Sbjct: 521 VTEEDIAEIVSRWTGIPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAG 580

Query: 652 LKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS----VRI 689
           LKDPNRP  + LF GPTGVGKTELAK+LAA  F +    +RI
Sbjct: 581 LKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRI 622

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20 Length = 195

 Score =  277 bits (710), Expect = 1e-89
 Identities = 109/197 (55%), Positives = 146/197 (74%), Gaps = 8/197 (4%)

Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           AL+++ +DLT RA +  +DPVIGR+ EI+R IQ+L RRTKNNP+L+GE GVGKTAI EGL
Sbjct: 4   ALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGL 63

Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDE 390
           A RI+  EVP  L  +R+++LDMG L+AGAK RGE E R+  +++++ K  G+VILFIDE
Sbjct: 64  AQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDE 123

Query: 391 VHTLIGSGTVGRGNKGTG-LDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRF 449
           +HT++G+G      K  G +D  N+LKP+L RGEL C+ +TT DE+R   EKD AL RRF
Sbjct: 124 LHTMVGAG------KADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRF 177

Query: 450 QPVLISEPSQEDAVRIL 466
           Q V ++EPS ED + IL
Sbjct: 178 QKVFVAEPSVEDTIAIL 194

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum} Length = 187

 Score =  271 bits (694), Expect = 2e-87
 Identities = 107/188 (56%), Positives = 141/188 (75%), Gaps = 5/188 (2%)

Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           ALE++  DLTA A    +DPVIGR+TEI+R IQIL RRTKNNPILLG+ GVGKTAI EGL
Sbjct: 4   ALEKYSRDLTALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGL 63

Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDE 390
           AI+IVQ +VP  L  ++++SLD+  L+AGAK RG+ E R+ +++ E+Q + G V++FIDE
Sbjct: 64  AIKIVQGDVPDSLKGRKLVSLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDE 123

Query: 391 VHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ 450
           +HT++G+G V  G     LD  N+LKP L RGEL+CI +TT  E+R   EKDKAL RRFQ
Sbjct: 124 IHTVVGAGAVAEG----ALDAGNILKPMLARGELRCIGATTVSEYRQFIEKDKALERRFQ 179

Query: 451 PVLISEPS 458
            +L+ +PS
Sbjct: 180 QILVEQPS 187

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A* Length = 359

 Score =  217 bits (553), Expect = 1e-64
 Identities = 48/289 (16%), Positives = 88/289 (30%), Gaps = 43/289 (14%)

Query: 292 VIGRETEIQRIIQILCRRTKNN----PILLGESGVGKTAIAEGLAIRIVQ---------- 337
           ++        ++Q+L  R ++N     IL+G  G GK+ IAE L   I +          
Sbjct: 1   MVDTHKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQIINEKYHTFLSEHP 60

Query: 338 -------AEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDE 390
                     P+  L   + +L    +    + +G  +  V  +  +  K   +    +E
Sbjct: 61  NVIEVNDRLKPMVNLVDSLKTLQPNKVAEMIENQGLFKDHVEDVNFQPVKYSALTSNNEE 120

Query: 391 VHTLIGSGTVGRGNKGTGLDISNLLKP----SLGRGELQCIASTTQDEH-------RTQF 439
              ++  G            I+ +  P     L +  +        D             
Sbjct: 121 CTAVVARGGTA---NAI--RIAAVDNPVNVNKLAQDSINIAQIVPMDGFHLSRRCLDLFK 175

Query: 440 EKDKALARRFQPVLISEPSQEDAVRILL-GLREKYEAHHNCKFTLEAINAAVHLSARYIS 498
           +   A  RR  P      +     +IL      K  +HH    T           ++ I 
Sbjct: 176 DPQTAHKRRGSPSTFDSNNFLQLCKILAKTSLCKVSSHHKFYSTSSVFEKLSKTFSQTIP 235

Query: 499 DRYLPDKAIDLVDEAGSRAHIELFKR--KKEQQTCILSKPPDDYWQEIR 545
           D ++P     L D    +  I  F R    E    +  +     W++I 
Sbjct: 236 DIFVPGFNHALKDPTPDQYCISKFTRIVILEGLYLLYDQEN---WKKIY 281

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum} Length = 146

 Score =  126 bits (319), Expect = 3e-34
 Identities = 44/158 (27%), Positives = 75/158 (47%), Gaps = 15/158 (9%)

Query: 80  SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKA 137
           ++FERFT+RA + ++ +Q EA+ L  + + T+H+LLGLI E            GI++D  
Sbjct: 2   AMFERFTDRARRVIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDAV 61

Query: 138 REAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPE 197
           R+ V             +         +   +PF+   K+V E ++      G+ +I  E
Sbjct: 62  RQEV-------------EEIIGQGSQPTTGHIPFTPRAKKVLELSLREGLQMGHKYIGTE 108

Query: 198 HIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQG 235
            + LGL    +G A +VL +LG D+  +    +  L G
Sbjct: 109 FLLLGLIREGEGVAAQVLVKLGADLPRVRQQVIQLLSG 146

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A* Length = 311

 Score =  124 bits (314), Expect = 1e-31
 Identities = 47/78 (60%), Positives = 60/78 (76%), Gaps = 4/78 (5%)

Query: 616 ERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTEL 675
           ER  L+ LEE+L KRV+GQDEA+ A++ A++R+R GLKDPNRP  + LF GPTGVGKTEL
Sbjct: 4   EREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTEL 63

Query: 676 AKSLAACYFGS----VRI 689
           AK+LAA  F +    +RI
Sbjct: 64  AKTLAATLFDTEEAMIRI 81

>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural genomics, PSI-2, protein S initiative; HET: PG4 EPE; 1.82A {Clostridium difficile} Length = 145

 Score =  116 bits (293), Expect = 9e-31
 Identities = 41/157 (26%), Positives = 74/157 (47%), Gaps = 16/157 (10%)

Query: 79  SSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDK 136
           ++ F RFT+RA KA+  +   AKSLG ++V ++H+LLGL+ E+         + G T   
Sbjct: 2   NANFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAY 61

Query: 137 AREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAP 196
               +V +              +GK    +  +  S  +K++ E +  ++     N+I  
Sbjct: 62  LEGKIVDM--------------EGKGEEISEDIVLSPRSKQILELSGMFANKLKTNYIGT 107

Query: 197 EHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL 233
           EHI L +    +G A ++L   GV+   LA + +  +
Sbjct: 108 EHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDMM 144

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A Length = 150

 Score =  110 bits (276), Expect = 3e-28
 Identities = 45/146 (30%), Positives = 73/146 (50%), Gaps = 16/146 (10%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDR--HPNGFLESGITIDKARE 139
           F RFTERA K +  +Q EA  LG + + T+H+LLGL+ E            G+  +K ++
Sbjct: 3   FGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQK 62

Query: 140 AVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHI 199
            V S+               G+    +  + ++   K+V E +++ +R  G++++  EHI
Sbjct: 63  EVESLI--------------GRAQEMSQTIHYTPRAKKVIELSMDEARKLGHSYVGTEHI 108

Query: 200 ALGLFTVDDGSAGRVLKRLGVDVNHL 225
            LGL    +G A RVL  LGV +N  
Sbjct: 109 LLGLIREGEGVAARVLNNLGVSLNKA 134

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A Length = 150

 Score = 57.3 bits (139), Expect = 6e-10
 Identities = 26/88 (29%), Positives = 39/88 (44%), Gaps = 4/88 (4%)

Query: 171 FSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAV 230
           F+   ++V   A E +   G+N I  EHI LGL    +G A + L+ LG+    +    V
Sbjct: 6   FTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQK-EV 64

Query: 231 SRLQGELAKEGREPSL---AKGVRENSI 255
             L G   +  +       AK V E S+
Sbjct: 65  ESLIGRAQEMSQTIHYTPRAKKVIELSM 92

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 69.1 bits (168), Expect = 4e-12
 Identities = 63/459 (13%), Positives = 139/459 (30%), Gaps = 131/459 (28%)

Query: 273 LEQFCVDLTARASEELIDPVIG------------RETEIQRIIQILCRRTKNNPILLGES 320
            + F  +   +  +++   ++               +   R+   L  +         E 
Sbjct: 26  EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSK--------QEE 77

Query: 321 GVGKTAIAEGLAIRIVQAEVPVFLLSK-----RIMSLDMGLLMAG-----------AK-- 362
            V +  + E L     +     FL+S      R  S+   + +             AK  
Sbjct: 78  MV-QKFVEEVL-----RINYK-FLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130

Query: 363 -ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR 421
             R +   ++   + E++ + +V+     +  ++GSG      K      + +       
Sbjct: 131 VSRLQPYLKLRQALLELRPAKNVL-----IDGVLGSG------K------TWVALDVCLS 173

Query: 422 GELQC--------IASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILL-----G 468
            ++QC        +     +   T  E  + L  +  P   S       +++ +      
Sbjct: 174 YKVQCKMDFKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAE 233

Query: 469 LRE--KYEAHHNCKFTLEAINAAVHLSARYISDRYL---PDKAI-DLVDEAGSRAHIELF 522
           LR   K + + NC   L  +  A   +A  +S + L     K + D +  A +  HI L 
Sbjct: 234 LRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLS-AATTTHISLD 292

Query: 523 KRKK---EQQTC-ILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASM---------- 568
                    +   +L K     + + R      EV+  +  +   +  S+          
Sbjct: 293 HHSMTLTPDEVKSLLLK-----YLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNW 347

Query: 569 ----GDTSEIVVESSLPSASDDD-----EPAVVGPDDI---AAV-ASLWSGIPVQQITAD 615
                D    ++ESSL      +     +   V P        + + +W  +       D
Sbjct: 348 KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKS----D 403

Query: 616 ERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKD 654
             +++  L    K  ++ +           K S + +  
Sbjct: 404 VMVVVNKLH---KYSLVEKQP---------KESTISIPS 430

>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 = 51.4 bits (122), Expect = 1e-06
 Identities = 37/233 (15%), Positives = 72/233 (30%), Gaps = 65/233 (27%)

Query: 476 HHNCKFTLEAINAAVHLSARYISDRYLPD--KAIDLVDEAGSRAHIELFKRKKEQQTCIL 533
           HH+  F             + I   +        D  D       ++   +       IL
Sbjct: 4   HHHMDFET----GEHQYQYKDILSVFEDAFVDNFDCKD-------VQDMPKS------IL 46

Query: 534 SKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSL---------PSAS 584
           SK      +EI  +    + V G+   +  +++   +  +  VE  L         P  +
Sbjct: 47  SK------EEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKT 100

Query: 585 DDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRA 644
           +  +P+++    I     L++   V                   K  + + +    + +A
Sbjct: 101 EQRQPSMMTRMYIEQRDRLYNDNQV-----------------FAKYNVSRLQPYLKLRQA 143

Query: 645 VKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAA-----CYFGSVRIHYL 692
           +      L    RP   +L  G  G GKT +A  +       C     +I +L
Sbjct: 144 LLE----L----RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDF-KIFWL 187

>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone, ATPase, adaptor binding, X-RAY, structure, N-domain, hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB: 1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A 1mbu_A* Length = 143

 Score = 60.8 bits (147), Expect = 4e-11
 Identities = 19/137 (13%), Positives = 51/137 (37%), Gaps = 8/137 (5%)

Query: 85  FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSI 144
             +    ++  +   A+    + +  +HLLL L++            + +   R+ + + 
Sbjct: 2   LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAF 61

Query: 145 WHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLF 204
                    +                 ++S +RV + AV + +S G N +   ++ + +F
Sbjct: 62  --------IEQTTPVLPASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIF 113

Query: 205 TVDDGSAGRVLKRLGVD 221
           +  +  A  +L++  V 
Sbjct: 114 SEQESQAAYLLRKHEVS 130

>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 = 63.8 bits (154), Expect = 8e-11
 Identities = 33/256 (12%), Positives = 77/256 (30%), Gaps = 26/256 (10%)

Query: 290 DPVIGRETEIQRIIQILCRRTKNNP---------ILLGESGVGKTAIA------------ 328
             +  R  E + + +I   R  +             +G  G+GKT +A            
Sbjct: 22  PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAA 81

Query: 329 -EGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGD--VI 385
            EGL ++              I+SL +       + RG     +   + +     +  ++
Sbjct: 82  KEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLL 141

Query: 386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIA-STTQDEHRTQFEKDKA 444
           + +DE  +++ S  +   +  T L +   +    G   +  +  ++         EK   
Sbjct: 142 VILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQ 201

Query: 445 LARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD 504
           +  +    L     +   +  +L  R +     +  +    +     +            
Sbjct: 202 VESQIGFKLHLPAYKSRELYTILEQRAE-LGLRDTVWEPRHLELISDVYGEDKGGDGSAR 260

Query: 505 KAIDLVDEAGSRAHIE 520
           +AI  +  A   A   
Sbjct: 261 RAIVALKMACEMAEAM 276

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1 Length = 148

 Score = 58.4 bits (142), Expect = 2e-10
 Identities = 28/151 (18%), Positives = 51/151 (33%), Gaps = 18/151 (11%)

Query: 82  FERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFL--ESGITIDKARE 139
            +R T +   A+  +Q  A       +   HL+  L+ ++      L   +GI   + R 
Sbjct: 3   LDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRT 62

Query: 140 AVVSIWHSTNNQDTDDAAAQGKP--FSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPE 197
            +             + A    P    +   +  S    RV     + ++ RG NFI+ E
Sbjct: 63  DI-------------NQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSE 109

Query: 198 HIALGLFTVDDGSAGRVLKRLGVDVNHLAAV 228
              L       G+   +LK  G    ++   
Sbjct: 110 LFVLAALE-SRGTLADILKAAGATTANITQA 139

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1 Length = 148

 Score = 44.9 bits (107), Expect = 1e-05
 Identities = 12/69 (17%), Positives = 23/69 (33%), Gaps = 4/69 (5%)

Query: 171 FSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAV 230
            +   +     A   +      FI P H+   L   + GS   +L   G++   L     
Sbjct: 6   LTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLR---- 61

Query: 231 SRLQGELAK 239
           + +   L +
Sbjct: 62  TDINQALNR 70

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A Length = 171

 Score = 49.9 bits (119), Expect = 3e-07
 Identities = 22/167 (13%), Positives = 48/167 (28%), Gaps = 23/167 (13%)

Query: 76  IPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFL--ESGIT 133
           I + ++  +   ++  A+  +           V  +H L  L+         +  ++G+ 
Sbjct: 16  IELPTLIAKLNAQSKLALEQAASLCIERQHPEVTLEHYLDVLLDNPLSDVRLVLKQAGLE 75

Query: 134 IDKAREAVVSIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEY-SRSRGYN 192
           +D+ ++A+              A+   +         FS     + + A    S      
Sbjct: 76  VDQVKQAI--------------ASTYSREQVLDTYPAFSPLLVELLQEAWLLSSTELEQA 121

Query: 193 FIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAK 239
            +    I L   T  D      L  L         +    L+   A 
Sbjct: 122 ELRSGAIFLAALTRADRYLSFKLISL------FEGINRENLKKHFAM 162

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A Length = 171

 Score = 44.5 bits (105), Expect = 2e-05
 Identities = 16/82 (19%), Positives = 29/82 (35%), Gaps = 1/82 (1%)

Query: 171 FSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAV 230
            +  +K   E A      R +  +  EH    L          VLK+ G++V+ +     
Sbjct: 25  LNAQSKLALEQAASLCIERQHPEVTLEHYLDVLLDNPLSDVRLVLKQAGLEVDQVKQAIA 84

Query: 231 SRLQGELAKEGREPSLAKGVRE 252
           S    E   +   P+ +  + E
Sbjct: 85  STYSREQVLDTY-PAFSPLLVE 105

>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 = 45.3 bits (108), Expect = 2e-05
 Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 9/56 (16%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           V+GQDE +  +   V+R  +    P+     +LF GP G GKT  A +LA   FG 
Sbjct: 19  VVGQDEVIQRLKGYVERKNI----PH-----LLFSGPPGTGKTATAIALARDLFGE 65

>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 = 45.5 bits (107), Expect = 4e-05
 Identities = 37/250 (14%), Positives = 85/250 (34%), Gaps = 37/250 (14%)

Query: 290 DPVIGRETEIQRIIQIL----CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVP---- 341
             +  RE  ++     +        K + + LG +G GKT +++ +   I + +      
Sbjct: 20  KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEY 79

Query: 342 -----VFLLSKRIMSLDMGLLMAGAK--------ERGELEARVTTLISEIQKSGDVILFI 388
                 ++  + +      +L + A         + G         I    ++   I+++
Sbjct: 80  KDVKQAYVNCREVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYL 139

Query: 389 DEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARR 448
           DEV TL+         +  G  +   L  S     +  I++            +  +   
Sbjct: 140 DEVDTLV--------KRRGGDIVLYQLLRSDANISVIMISNDINVRDYM----EPRVLSS 187

Query: 449 FQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID 508
             P +I +P   + ++ +L    +        +  E ++    +SA+   D     KA++
Sbjct: 188 LGPSVIFKPYDAEQLKFILSKYAE-YGLIKGTYDDEILSYIAAISAKEHGD---ARKAVN 243

Query: 509 LVDEAGSRAH 518
           L+  A   A 
Sbjct: 244 LLFRAAQLAS 253

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A* Length = 309

 Score = 45.1 bits (106), Expect = 4e-05
 Identities = 22/80 (27%), Positives = 35/80 (43%), Gaps = 5/80 (6%)

Query: 606 GIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFC 665
           G   +++  +    L+GL+  +K R+    E  A +     R ++GL     PT  M F 
Sbjct: 19  GSGAKEVLEELDRELIGLKP-VKDRI---RETAALLLVERARQKLGLAHE-TPTLHMSFT 73

Query: 666 GPTGVGKTELAKSLAACYFG 685
           G  G GKT +A  +A     
Sbjct: 74  GNPGTGKTTVALKMAGLLHR 93

>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 = 45.0 bits (107), Expect = 5e-05
 Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 9/56 (16%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           V+GQDE +  +   V+R  +    P+     +LF GP G GKT  A +LA   FG 
Sbjct: 19  VVGQDEVIQRLKGYVERKNI----PH-----LLFSGPPGTGKTATAIALARDLFGE 65

>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* Length = 250

 Score = 43.7 bits (104), Expect = 9e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC 682
           V+GQ+  + A++  +   R+          A LF G  GVGKT +A+ LA  
Sbjct: 25  VVGQEHVLTALANGLSLGRIH--------HAYLFSGTRGVGKTSIARLLAKG 68

>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 = 44.3 bits (105), Expect = 9e-05
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 9/56 (16%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS 686
           ++GQ+  V  +   VK   +    P+     +LF GP GVGKT  A +LA   FG 
Sbjct: 27  IVGQEHIVKRLKHYVKTGSM----PH-----LLFAGPPGVGKTTAALALARELFGE 73

>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* Length = 373

 Score = 43.8 bits (104), Expect = 1e-04
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 8/52 (15%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC 682
           V+GQ+  + A++  +   R+          A LF G  GVGKT +A+ LA  
Sbjct: 18  VVGQEHVLTALANGLSLGRIH--------HAYLFSGTRGVGKTSIARLLAKG 61

>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 Length = 363

 Score = 43.3 bits (103), Expect = 2e-04
 Identities = 24/62 (38%), Positives = 31/62 (50%), Gaps = 6/62 (9%)

Query: 625 EQLKKRVIGQDEAVAAISRAV----KRSRVGLKDPNRPTAA--MLFCGPTGVGKTELAKS 678
             L   VIGQ++A   ++ AV    KR R G            +L  GPTG GKT LA++
Sbjct: 11  NHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAET 70

Query: 679 LA 680
           LA
Sbjct: 71  LA 72

>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 Length = 376

 Score = 42.2 bits (100), Expect = 4e-04
 Identities = 23/77 (29%), Positives = 29/77 (37%), Gaps = 21/77 (27%)

Query: 625 EQLKKRVIGQDEAVAAISRAV----KRSRVGLKDPNRPTAAM-----------------L 663
             L   VIGQ++A    S AV    KR     K   +                      L
Sbjct: 17  AVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNIL 76

Query: 664 FCGPTGVGKTELAKSLA 680
             GPTG GKT +A++LA
Sbjct: 77  LIGPTGSGKTLMAQTLA 93

>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 = 42.2 bits (99), Expect = 5e-04
 Identities = 13/58 (22%), Positives = 21/58 (36%), Gaps = 8/58 (13%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTA--------AMLFCGPTGVGKTELAKSLA 680
           V G   +V  +   +       K+  +           A +  GP G+GKT  A  +A
Sbjct: 41  VCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVA 98

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	710
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	100.0
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	100.0
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	100.0
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.97
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	99.93
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	99.91
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.91
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	99.9
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	99.9
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	99.89
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	99.88
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.88
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	99.87
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	99.87
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	99.86
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	99.86
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	99.86
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.86
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	99.85
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	99.83
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.83
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	99.83
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.83
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	99.81
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.8
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.78
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.78
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.77
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	99.77
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	99.76
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.76
3pvs_A	447	Replication-associated recombination protein A; ma	99.76
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.74
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.74
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.74
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.73
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.72
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.72
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.69
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.68
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.67
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.67
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.64
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.64
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	99.64
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.64
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.64
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.63
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.63
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.62
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.61
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.61
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.6
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.6
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.59
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.59
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.59
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.57
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.56
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.55
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.55
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.54
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.54
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.54
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.53
3bos_A	242	Putative DNA replication factor; P-loop containing	99.53
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.51
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.51
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.5
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.5
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.5
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.5
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.5
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.48
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.47
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.46
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.46
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.45
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.44
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.35
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.33
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.32
3co5_A	143	Putative two-component system transcriptional RES	99.29
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.29
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.27
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.26
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.21
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.21
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.2
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	99.16
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.11
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.07
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	99.07
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	99.03
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	98.99
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	98.95
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	98.94
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	98.93
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	98.93
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	98.91
2fna_A	357	Conserved hypothetical protein; structural genomic	98.9
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.86
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.83
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	98.77
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	98.73
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	98.72
3fes_A	145	ATP-dependent CLP endopeptidase; alpha-helical bun	98.72
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	98.69
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	98.69
3fh2_A	146	Probable ATP-dependent protease (heat shock prote;	98.68
3f8t_A	506	Predicted ATPase involved in replication control,	98.68
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	98.67
1khy_A	148	CLPB protein; alpha helix, chaperone; 1.95A {Esche	98.65
3zri_A	171	CLPB protein, CLPV; chaperone, HSP100 proteins, AA	98.62
2y1q_A	150	CLPC N-domain, negative regulator of genetic compe	98.61
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	98.58
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	98.58
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	98.56
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	98.5
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	98.5
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	98.49
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	98.48
2qgz_A	308	Helicase loader, putative primosome component; str	98.46
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	98.46
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.44
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	98.43
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	98.42
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	98.42
1k6k_A	143	ATP-dependent CLP protease ATP-binding subunit CLP	98.41
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	98.39
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	98.37
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	98.35
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	98.35
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	98.35
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.33
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	98.32
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	98.29
2r44_A	331	Uncharacterized protein; putative ATPase, structur	98.26
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	98.25
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	98.24
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	98.22
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	98.21
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	98.2
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	98.19
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	98.17
3co5_A	143	Putative two-component system transcriptional RES	98.15
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	98.13
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	98.13
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	98.11
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	98.09
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.03
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	98.02
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	98.01
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	98.0
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	98.0
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.0
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	97.97
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	97.97
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	97.93
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	97.93
2chg_A	226	Replication factor C small subunit; DNA-binding pr	97.91
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	97.91
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	97.91
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	97.9
3pvs_A	447	Replication-associated recombination protein A; ma	97.89
2chq_A	319	Replication factor C small subunit; DNA-binding pr	97.89
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	97.89
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	97.87
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	97.85
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	97.83
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	97.8
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	97.79
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	97.79
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	97.77
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	97.77
3bos_A	242	Putative DNA replication factor; P-loop containing	97.76
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	97.74
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	97.72
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	97.71
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	97.7
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.69
1tue_A	212	Replication protein E1; helicase, replication, E1E	97.67
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	97.65
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	97.6
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	97.58
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	97.57
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	97.54
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	97.54
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.5
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	97.49
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.49
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	97.47
2qgz_A	308	Helicase loader, putative primosome component; str	97.42
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.41
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	97.39
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	97.37
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.3
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.27
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	97.26
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	97.24
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	97.2
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.13
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.11
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	97.08
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.97
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	96.92
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	96.89
2cvh_A	220	DNA repair and recombination protein RADB; filamen	96.88
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	96.82
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	96.8
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.74
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	96.64
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	96.64
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.63
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	96.61
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.61
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.59
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.57
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.53
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	96.49
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.46
1xp8_A	366	RECA protein, recombinase A; recombination, radior	96.45
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	96.41
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.4
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	96.39
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	96.37
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	96.36
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	96.36
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.34
1via_A	175	Shikimate kinase; structural genomics, transferase	96.3
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.3
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.28
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.28
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	96.27
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	96.27
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.25
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.25
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	96.24
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	96.23
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.16
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.15
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.15
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.14
3lxw_A	247	GTPase IMAP family member 1; immunity, structural	96.14
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	96.13
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	96.12
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.12
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	96.11
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.11
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	96.1
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	96.09
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	96.08
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	96.08
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	96.08
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	96.08
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.05
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	96.04
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	96.01
1u94_A	356	RECA protein, recombinase A; homologous recombinat	96.0
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	95.99
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.99
3f8t_A	506	Predicted ATPase involved in replication control,	95.98
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	95.98
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	95.97
4a74_A	231	DNA repair and recombination protein RADA; hydrola	95.96
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	95.96
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	95.94
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	95.92
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	95.92
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	95.89
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	95.89
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	95.89
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	95.88
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	95.88
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	95.85
2r6a_A	454	DNAB helicase, replicative helicase; replication,	95.85
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	95.84
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.83
2z43_A	324	DNA repair and recombination protein RADA; archaea	95.83
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	95.81
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	95.79
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	95.79
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	95.77
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.76
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	95.75
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	95.75
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	95.71
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.7
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	95.69
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	95.68
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	95.68
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	95.67
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.67
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	95.67
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	95.67
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.67
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	95.64
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	95.64
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	95.64
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	95.63
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	95.63
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	95.62
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	95.62
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	95.6
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	95.6
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	95.59
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	95.58
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.57
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	95.56
2fna_A	357	Conserved hypothetical protein; structural genomic	95.56
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	95.56
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	95.56
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	95.54
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	95.52
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	95.51
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	95.49
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	95.48
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	95.48
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	95.46
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.42
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.42
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	95.42
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.42
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	95.41
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	95.41
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	95.39
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	95.37
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	95.36
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	95.35
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	95.35
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.34
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	95.32
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	95.31
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.3
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	95.29
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	95.28
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	95.26
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	95.23
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	95.23
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	95.22
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.19
2og2_A	359	Putative signal recognition particle receptor; nuc	95.19
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.18
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	95.17
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	95.16
2vli_A	183	Antibiotic resistance protein; transferase, tunica	95.16
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.13
2cvh_A	220	DNA repair and recombination protein RADB; filamen	95.09
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	95.08
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	95.08
3kta_A	182	Chromosome segregation protein SMC; structural mai	95.08
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.06
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	95.06
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	95.05
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.05
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	95.03
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	95.03
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.01
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.01
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	94.99
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	94.97
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	94.95
4a74_A	231	DNA repair and recombination protein RADA; hydrola	94.94
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	94.94
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	94.94
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	94.91
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	94.89
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	94.88
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	94.87
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	94.84
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	94.81
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	94.8
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	94.8
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	94.79
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	94.79
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	94.77
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	94.76
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	94.75
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	94.74
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	94.74
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	94.73
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	94.72
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	94.7
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	94.69
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	94.69
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	94.64
3b6e_A	216	Interferon-induced helicase C domain-containing P;	94.64
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	94.62
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	94.59
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.57
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.57
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	94.57
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	94.56
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.54
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	94.54
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	94.51
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	94.51
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	94.49
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	94.49
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	94.49
1sky_E	473	F1-ATPase, F1-ATP synthase; F1FO ATP synthase, alp	94.45
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.45
2ewv_A	372	Twitching motility protein PILT; pilus retraction	94.44
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	94.42
1u94_A	356	RECA protein, recombinase A; homologous recombinat	94.39
3io5_A	333	Recombination and repair protein; storage dimer, i	94.39
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	94.38
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	94.37
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	94.36
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.35
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	94.35
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	94.34
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	94.34
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	94.31
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	94.31
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	94.3
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	94.29
2xxa_A	433	Signal recognition particle protein; protein trans	94.28
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	94.27
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	94.25
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	94.23
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	94.22
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	94.21
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	94.19
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	94.13
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.13
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	94.09
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	94.07
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	94.05
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	94.0
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.98
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	93.97
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	93.89
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	93.88
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.82
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	93.81
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.81
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	93.78
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	93.74
3io5_A	333	Recombination and repair protein; storage dimer, i	93.7
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	93.7
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	93.69
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	93.68
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	93.66
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	93.66
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	93.64
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	93.62
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.56
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	93.55
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.54
2hf9_A	226	Probable hydrogenase nickel incorporation protein	93.54
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	93.52
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.51
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	93.49
1xp8_A	366	RECA protein, recombinase A; recombination, radior	93.48
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.48
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	93.47
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	93.47
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.42
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	93.42
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	93.37
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	93.34
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	93.33
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	93.31
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	93.28
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	93.27
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	93.26
2z43_A	324	DNA repair and recombination protein RADA; archaea	93.26
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.24
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	93.21
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	93.2
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	93.18
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	93.18
2xxa_A	433	Signal recognition particle protein; protein trans	93.17
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.16
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	93.15
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	93.15
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	93.11
3ice_A	422	Transcription termination factor RHO; transcriptio	93.11
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	93.09
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	93.08
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	93.07
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	93.07
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.06
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	93.05
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	93.05
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	93.03
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	93.02
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	93.0
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	92.99
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	92.98
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	92.96
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	92.92
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	92.91
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	92.91
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	92.89
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	92.89
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	92.89
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	92.88

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=100.00  E-value=3.1e-73  Score=673.40  Aligned_cols=560  Identities=44%  Similarity=0.690  Sum_probs=438.7

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      |||++||++++++|..|+++|+++||++|+|||||+|||.++++  .++|..+|+|++.+++++...+++.+..      
T Consensus         1 mm~~~~t~~a~~~l~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL~~~gvd~~~l~~~l~~~l~~~~~~------   74 (758)
T 3pxi_A            1 MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEM------   74 (758)
T ss_dssp             --CCCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSCCSHHHHHHHHHTCCHHHHHHHHHTTSCCCCTT------
T ss_pred             CchhhhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhccCCCC------
Confidence            58999999999999999999999999999999999999999877  7899999999999999999888776431      


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGEL  237 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~  237 (710)
                              ...++||+.+++||+.|+.+|+++|+.||+++|||+||++++++.++++|+++|++.+.+++.+.+...+. 
T Consensus        75 --------~~~~~~s~~~~~vl~~A~~~A~~~~~~~I~~ehlLlall~~~~~~a~~~L~~~gv~~~~l~~~i~~~~~~~-  145 (758)
T 3pxi_A           75 --------SQTIHYTPRAKKVIELSMDEARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSN-  145 (758)
T ss_dssp             --------CSSCEECHHHHHHHHHHHHHHHTTTCSSBCHHHHHHHHHHTCCSHHHHHHHHTTCCHHHHHHHHHTTCCCC-
T ss_pred             --------CCCCCCCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhcCCcHHHHHHHHcCCCHHHHHHHHHHHhcCC-
Confidence                    23688999999999999999999999999999999999999999999999999999999998877654321 


Q ss_pred             cccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEE
Q 005179          238 AKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILL  317 (710)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~  317 (710)
                       ..  .+.   .      .+      .......+.|++|+.+|++.+++++++++||++++++++.+++.++.++|+||+
T Consensus       146 -~~--~~~---~------~~------~~~~~~~~~l~~~~~~l~~~~~~~~ld~iiG~~~~i~~l~~~l~~~~~~~vLL~  207 (758)
T 3pxi_A          146 -ET--GSS---A------AG------TNSNANTPTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLI  207 (758)
T ss_dssp             -CT--TC--------------------CCSTHHHHHHSSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEE
T ss_pred             -cc--ccc---c------cc------cccchhhhHHHHHHHHHHHHHhhCCCCCccCchHHHHHHHHHHhCCCCCCeEEE
Confidence             00  000   0      00      001124578999999999999999999999999999999999999999999999


Q ss_pred             cCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhC
Q 005179          318 GESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGS  397 (710)
Q Consensus       318 GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~  397 (710)
                      ||||||||++|+++|+.+.++++|..+.++.++.+++     |.++.|+++.+++.++..+....++|||||        
T Consensus       208 G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~~~~-----g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD--------  274 (758)
T 3pxi_A          208 GEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDM-----GTKYRGEFEDRLKKVMDEIRQAGNIILFID--------  274 (758)
T ss_dssp             SCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC---------------CTTHHHHHHHHHTCCCCEEEEC--------
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEEecc-----cccccchHHHHHHHHHHHHHhcCCEEEEEc--------
Confidence            9999999999999999999999999999999999987     677899999999999999998889999999        


Q ss_pred             CCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhc
Q 005179          398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHH  477 (710)
Q Consensus       398 ~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~  477 (710)
                      +         ..+.++.|++.++++.+++|++||..+|.+++.++++|.+||+.|.|++|+.+++..||+.+..+++.++
T Consensus       275 ~---------~~~~~~~L~~~l~~~~v~~I~at~~~~~~~~~~~d~al~rRf~~i~v~~p~~~~~~~il~~~~~~~~~~~  345 (758)
T 3pxi_A          275 A---------AIDASNILKPSLARGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHH  345 (758)
T ss_dssp             C-----------------CCCTTSSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGS
T ss_pred             C---------chhHHHHHHHHHhcCCEEEEeCCChHHHHHHhhccHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHhc
Confidence            1         3457889999999999999999999999999999999999999999999999999999999999888889


Q ss_pred             CCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhc
Q 005179          478 NCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGS  557 (710)
Q Consensus       478 ~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  557 (710)
                      ++.++++++..++.++.+|+.++++|++++++++.|++.+++.....+.+.  ..+......+..+........++..+.
T Consensus       346 ~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~a~~~~~~~~~~~p~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~  423 (758)
T 3pxi_A          346 RVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSKVRLRSFTTPPNL--KELEQKLDEVRKEKDAAVQSQEFEKAA  423 (758)
T ss_dssp             SCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHHHHHHTTC--CCT--HHHHHHHHHHHHHHHHHHHHCCSHHHH
T ss_pred             CCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHHHHHHHHhhccCCCcch--hhHHHHHHHHHHHHHHHHhCcCHHHHH
Confidence            999999999999999999999999999999999999999888765544321  011111111111111111111111111


Q ss_pred             cccchhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHH
Q 005179          558 RLKYDDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEA  637 (710)
Q Consensus       558 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a  637 (710)
                      .+.+....+..    .+......+..........++.+++..+++.|+|+|+..+..++...+..+++.|.+.|+||+++
T Consensus       424 ~l~~~~~~~~~----~l~~~~~~~~~~~~~~~~~v~~~~i~~~v~~~~~ip~~~~~~~~~~~l~~l~~~l~~~viGq~~a  499 (758)
T 3pxi_A          424 SLRDTEQRLRE----QVEDTKKSWKEKQGQENSEVTVDDIAMVVSSWTGVPVSKIAQTETDKLLNMENILHSRVIGQDEA  499 (758)
T ss_dssp             HHHHHHHHHHH----HHHHHHSGGGHHHHCC---CCTHHHHHHHHTTC-------CHHHHSCC-CHHHHHHTTSCSCHHH
T ss_pred             HHHHHHHHHHH----HHHHHHHHHHHhhcccCcccCHHHHHHHHHHHhCCChHHhhHHHHHHHHHHHHHHhCcCcChHHH
Confidence            11110000000    00000000000001124578899999999999999999999999888999999999999999999


Q ss_pred             HHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          638 VAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       638 ~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      ++.+..+++..+.|+.+|.+|++++||+||||||||++|++||+.+|+++..++++|||+|..
T Consensus       500 ~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~  562 (758)
T 3pxi_A          500 VVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYME  562 (758)
T ss_dssp             HHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCS
T ss_pred             HHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccc
Confidence            999999999999999999999999999999999999999999999999999999999999965

>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=100.00  E-value=9.8e-69  Score=635.85  Aligned_cols=530  Identities=37%  Similarity=0.577  Sum_probs=456.2

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCcHHHHHHCCCCHHHHHHHHHHHhhc-CCCCCCchhhhcCCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHS-TNNQDTDDAAAQGKPF  163 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~l~~~gv~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~  163 (710)
                      ||++++++|..|+++|+++||++|+|||||+|||.+++..++|..+|+|++.+++++...+++ .+..           .
T Consensus         2 ~t~~a~~~l~~A~~~A~~~~h~~i~~eHLLlaLl~~~~~~~iL~~~gvd~~~l~~~l~~~l~~~~p~~-----------~   70 (758)
T 1r6b_X            2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVL-----------P   70 (758)
T ss_dssp             BCHHHHHHHHHHHHHHHHTTBSEECHHHHHHHHTTSHHHHHHHHHTTCCHHHHHHHHHHHHHHHSCBC-----------C
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHcCcHHHHHHHHcCCCHHHHHHHHHHHHhccCCCC-----------C
Confidence            899999999999999999999999999999999987555889999999999999999999887 4321           1


Q ss_pred             C--CCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhhcccC
Q 005179          164 S--SAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGELAKEG  241 (710)
Q Consensus       164 ~--~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~~~~~  241 (710)
                      +  ....++||+.++++|+.|+.+|+.+|+.||+++|||+||++++++.+.++|+++|++.+.+.+.+.+.....-... 
T Consensus        71 ~~~~~~~~~~s~~~~~vl~~A~~~a~~~~~~~I~~ehlLlall~~~~~~a~~~L~~~gi~~~~l~~~i~~~~~~~~~~~-  149 (758)
T 1r6b_X           71 ASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFISHGTRKDEPTQ-  149 (758)
T ss_dssp             CSSSCCCCEECHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHTTCTTCHHHHHHHHTTCCHHHHHHHHHTC---------
T ss_pred             CccccCCCCcCHHHHHHHHHHHHHHHHcCCCEeeHHHHHHHHhccccchHHHHHHHcCCCHHHHHHHHHHhhccccccc-
Confidence            1  1246899999999999999999999999999999999999998888999999999999988776544221100000 


Q ss_pred             CCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCC
Q 005179          242 REPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESG  321 (710)
Q Consensus       242 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG  321 (710)
                      ...   .+. . . +.+      +.....+.|++|+.+|++++++++|++++|++++++++++++.+..++|+||+||||
T Consensus       150 ~~~---~~~-~-~-~~~------~~~~~~~~l~~~~~~l~~~~~~~~~d~~iGr~~~i~~l~~~l~~~~~~~vlL~G~~G  217 (758)
T 1r6b_X          150 SSD---PGS-Q-P-NSE------EQAGGEERLENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESG  217 (758)
T ss_dssp             -------------------------------CCSSSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTT
T ss_pred             ccc---ccc-c-c-ccc------ccccchhHHHHHhHhHHHHHhcCCCCCccCCHHHHHHHHHHHhccCCCCeEEEcCCC
Confidence            000   000 0 0 000      001134679999999999999999999999999999999999999999999999999


Q ss_pred             ChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCC
Q 005179          322 VGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVG  401 (710)
Q Consensus       322 ~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~  401 (710)
                      ||||++++++++.+.++.+|..+.++.++.+++..+..+.++.|+++.+++.+++.+....+.||||||+|.+++.+.. 
T Consensus       218 tGKT~la~~la~~l~~~~v~~~~~~~~~~~~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~-  296 (758)
T 1r6b_X          218 VGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAA-  296 (758)
T ss_dssp             SSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCS-
T ss_pred             CCHHHHHHHHHHHHHhCCCChhhcCCEEEEEcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCC-
Confidence            9999999999999999999999999999999999999888899999999999999998777899999999999877543 


Q ss_pred             CCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCC
Q 005179          402 RGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKF  481 (710)
Q Consensus       402 ~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i  481 (710)
                         ..+..++.+.|+++++++.+++|++|+.++|.+.+..|++|.+||+.|.|++|+.+++.+||+.+...+..++++.+
T Consensus       297 ---~~~~~~~~~~L~~~l~~~~~~~I~at~~~~~~~~~~~d~aL~~Rf~~i~v~~p~~~e~~~il~~l~~~~~~~~~v~~  373 (758)
T 1r6b_X          297 ---SGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRY  373 (758)
T ss_dssp             ---SSCHHHHHHHHSSCSSSCCCEEEEEECHHHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCC
T ss_pred             ---CcchHHHHHHHHHHHhCCCeEEEEEeCchHHhhhhhcCHHHHhCceEEEcCCCCHHHHHHHHHHHHHHHHHhcCCCC
Confidence               13477889999999999999999999999998888999999999999999999999999999999999988899999


Q ss_pred             CHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccc
Q 005179          482 TLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKY  561 (710)
Q Consensus       482 ~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  561 (710)
                      +++++..++.++.+|+.++++|+++++++++|++..++...                                       
T Consensus       374 ~~~al~~~~~~s~~~i~~~~lp~~~i~lld~a~~~~~~~~~---------------------------------------  414 (758)
T 1r6b_X          374 TAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPV---------------------------------------  414 (758)
T ss_dssp             CHHHHHHHHHHHHHHCTTSCTTHHHHHHHHHHHHHHHHSSS---------------------------------------
T ss_pred             CHHHHHHHHHHhhhhcccccCchHHHHHHHHHHHHHhcccc---------------------------------------
Confidence            99999999999999999999999999999999865443200                                       


Q ss_pred             hhhhhccCCcchhhhhccCCCCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHH
Q 005179          562 DDVVASMGDTSEIVVESSLPSASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAI  641 (710)
Q Consensus       562 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i  641 (710)
                                              ......|+.++|..+++.|+++|+..+.+++...+..+++.|...|+||+++++.|
T Consensus       415 ------------------------~~~~~~v~~~di~~~~~~~~~ip~~~~~~~~~~~l~~l~~~l~~~v~g~~~~~~~l  470 (758)
T 1r6b_X          415 ------------------------SKRKKTVNVADIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEAL  470 (758)
T ss_dssp             ------------------------CCCCCSCCHHHHHHHHHHHSCCCCCCSSSSHHHHHHHHHHHHTTTSCSCHHHHHHH
T ss_pred             ------------------------cccCCccCHHHHHHHHHHhcCCCccccchhHHHHHHHHHHHHHhhccCHHHHHHHH
Confidence                                    00124689999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          642 SRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       642 ~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      ..+++..+.|+.+|++|++++||+||||||||++|++||+.+   +..++++|||+|+. ++++++++
T Consensus       471 ~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l---~~~~~~i~~s~~~~-~~~~~~l~  534 (758)
T 1r6b_X          471 TEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL---GIELLRFDMSEYME-RHTVSRLI  534 (758)
T ss_dssp             HHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH---TCEEEEEEGGGCSS-SSCCSSSC
T ss_pred             HHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh---cCCEEEEechhhcc-hhhHhhhc
Confidence            999999999999999999999999999999999999999998   36899999999965 56777664

>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=100.00  E-value=2.2e-68  Score=638.36  Aligned_cols=579  Identities=41%  Similarity=0.567  Sum_probs=443.1

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      |||++||++++++|..|+.+|+++||++|+|||||+|||.++++  .++|..+|+|++.++.++...+++.+..      
T Consensus         1 ~~~~~~t~~a~~al~~A~~~A~~~~h~~i~~eHLLlaLl~~~~~~~~~iL~~~gvd~~~l~~~l~~~l~~~p~~------   74 (854)
T 1qvr_A            1 MNLERWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADPKALKELQERELARLPKV------   74 (854)
T ss_dssp             ---CCSCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHHTTSSCHHHHHHHHHHHHHTSCCC------
T ss_pred             CChhhhCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHHHHHhhCCCC------
Confidence            57899999999999999999999999999999999999999887  7899999999999999999999987642      


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGEL  237 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~  237 (710)
                           .+....++||+.++++|+.|+.+|+.+|+.||+++|||+||++++++ +        ++...++..+.+.. +. 
T Consensus        75 -----~~~~~~~~~S~~~~~vL~~A~~~a~~~g~~~I~~ehlLlall~~~~~-~--------~~~~~~~~~~~~~~-~~-  138 (854)
T 1qvr_A           75 -----EGAEVGQYLTSRLSGALNRAEGLMEELKDRYVAVDTLVLALAEATPG-L--------PGLEALKGALKELR-GG-  138 (854)
T ss_dssp             -----CGGGTTCEECHHHHHHHHHHHHHHHTTTCSSCCHHHHHHHHHHHSTT-S--------CCHHHHHHHHTSSC-SC-
T ss_pred             -----CCCCCCCCCCHHHHHHHHHHHHHHHHcCCcEeeHHHHHHHHHhcccc-c--------CCHHHHHHHHHHhc-cc-
Confidence                 12234689999999999999999999999999999999999997764 2        88888776543321 10 


Q ss_pred             cccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEE
Q 005179          238 AKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILL  317 (710)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~  317 (710)
                          .. ..          .     ..+ ....+.|++|+.+|++.+++++|+++||++++++++++++.++.++|++|+
T Consensus       139 ----~~-~~----------~-----~~~-~~~~~~l~~~~~~l~~~~r~~~ld~viGr~~~i~~l~~~l~~~~~~~vlL~  197 (854)
T 1qvr_A          139 ----RT-VQ----------T-----EHA-ESTYNALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLI  197 (854)
T ss_dssp             ----CS-SC----------S-----SCC-CCCCSHHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEE
T ss_pred             ----cc-cc----------c-----ccc-cccchhHHHHHHhHHHHHhcCCCcccCCcHHHHHHHHHHHhcCCCCceEEE
Confidence                00 00          0     000 113468999999999999999999999999999999999999999999999


Q ss_pred             cCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhh
Q 005179          318 GESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIG  396 (710)
Q Consensus       318 GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~  396 (710)
                      ||||||||++++++++.+..+.+|..+.+..++.++++.+..|.++.|+++.+++.++..+... ++.||||||+|.+.+
T Consensus       198 G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~  277 (854)
T 1qvr_A          198 GEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVG  277 (854)
T ss_dssp             ECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC-----
T ss_pred             cCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEEeehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhc
Confidence            9999999999999999999999999888999999999999988889999999999999998875 678999999999986


Q ss_pred             CCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhh
Q 005179          397 SGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAH  476 (710)
Q Consensus       397 ~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~  476 (710)
                      .+..     .+..++.+.|+++++++.+.+|++||.++|.. +.++++|.+||+.|.|++|+.+++..||+.+..+++.+
T Consensus       278 ~~~~-----~g~~~~~~~L~~~l~~~~i~~I~at~~~~~~~-~~~d~aL~rRf~~i~l~~p~~~e~~~iL~~~~~~~~~~  351 (854)
T 1qvr_A          278 AGKA-----EGAVDAGNMLKPALARGELRLIGATTLDEYRE-IEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVH  351 (854)
T ss_dssp             -------------------HHHHHTTCCCEEEEECHHHHHH-HTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHH
T ss_pred             cCCc-----cchHHHHHHHHHHHhCCCeEEEEecCchHHhh-hccCHHHHhCCceEEeCCCCHHHHHHHHHhhhhhhhhh
Confidence            6543     33567888999999999999999999999887 78999999999999999999999999999999999989


Q ss_pred             cCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchhhH------------HhhhhCCCC-------
Q 005179          477 HNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKKEQ------------QTCILSKPP-------  537 (710)
Q Consensus       477 ~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~~~------------~~~~l~~~~-------  537 (710)
                      |++.++++++..++.++.+|+.++++|+++++++++|++.+++.....|.+.            +...+.++.       
T Consensus       352 ~~~~i~~~al~~~~~ls~r~i~~~~lp~kai~lldea~a~~~~~~~~~p~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~  431 (854)
T 1qvr_A          352 HGVRISDSAIIAAATLSHRYITERRLPDKAIDLIDEAAARLRMALESAPEEIDALERKKLQLEIEREALKKEKDPDSQER  431 (854)
T ss_dssp             TTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHSC
T ss_pred             cCCCCCHHHHHHHHHHHhhhcccccChHHHHHHHHHHHHHHHhhccCCchhHHHHHHHHHHHHHHHHHHHhccccccHHH
Confidence            9999999999999999999999999999999999999999998766655431            112233322       


Q ss_pred             -hHHHHHHHHHHH-------hhH-----------H-----------Hhhccccchh--hhhccC----CcchhhhhccCC
Q 005179          538 -DDYWQEIRTVQA-------MHE-----------V-----------VQGSRLKYDD--VVASMG----DTSEIVVESSLP  581 (710)
Q Consensus       538 -~~~~~~~~~~~~-------~~~-----------~-----------~~~~~~~~~~--~~~~~~----~~~~~~~~~~~~  581 (710)
                       ..+.+++.+++.       .++           .           ..+....+..  ..+...    ...++...... 
T Consensus       432 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-  510 (854)
T 1qvr_A          432 LKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQHRLDEVRREIELAERQYDLNRAAELRYGELPKLEAEVEALSEK-  510 (854)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHTTHHHHHHHHHHHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHhcccHHHHHHHhhhhhHHHHHHHHHHHhh-
Confidence             111111111110       000           0           0000000000  000000    00000000000 


Q ss_pred             CCCCCCCCCcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeE
Q 005179          582 SASDDDEPAVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAA  661 (710)
Q Consensus       582 ~~~~~~~~~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~  661 (710)
                      ..........++.+++..+++.|+|+|..++...+...+.++++.+.+.|+||++++..+...++..+.|+.+|++|+++
T Consensus       511 ~~~~~~~~~~v~~~~l~~~v~~~~~ip~~~~~~~~~~~l~~l~~~l~~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~  590 (854)
T 1qvr_A          511 LRGARFVRLEVTEEDIAEIVSRWTGIPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGS  590 (854)
T ss_dssp             SSSCSSCCSEECHHHHHHHHHTTSSCHHHHTTCCHHHHHHSHHHHHHHHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEE
T ss_pred             hcccccccCCcCHHHHHHHHHHHhCCChHhhcHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHhcccCCCCCCceE
Confidence            01112234679999999999999999999988778888888999999999999999999999999999999999999999


Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCCcchhhhccc
Q 005179          662 MLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      +||+||||||||++|++||+.+|+++..++++||+++.. .+++++++
T Consensus       591 vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~-~~~~s~l~  637 (854)
T 1qvr_A          591 FLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYME-KHAVSRLI  637 (854)
T ss_dssp             EEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCS-SGGGGGC-
T ss_pred             EEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccc-hhHHHHHc
Confidence            999999999999999999999999999999999999954 45566543

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=100.00  E-value=9.8e-60  Score=526.42  Aligned_cols=392  Identities=47%  Similarity=0.759  Sum_probs=335.0

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      |||++||++++++|..|+++|+++||++|+|||||+|||.++++  .++|..+|+|++.+++++...+++.+..      
T Consensus         1 mm~~~ft~~a~~al~~A~~~A~~~~h~~v~~eHLLlaLl~~~~~~~~~iL~~~gvd~~~l~~~l~~~l~~~~~~------   74 (468)
T 3pxg_A            1 MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRGQEM------   74 (468)
T ss_dssp             --CCCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSCCSHHHHHHHHHTCCHHHHHHHHHTTSCCCCTT------
T ss_pred             CcchhhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHhcccCCC------
Confidence            49999999999999999999999999999999999999999887  7899999999999999999887765421      


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhhhhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGEL  237 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~~~~  237 (710)
                              ...++||+.++++|+.|+.+|+++|+.||+++|||+||++++++.++++|.++|++.+.++..+.+...+. 
T Consensus        75 --------~~~~~~S~~~~~vL~~A~~~A~~~g~~~I~teHLLlaLl~~~~~~a~~iL~~~gv~~~~l~~~i~~~~~~~-  145 (468)
T 3pxg_A           75 --------SQTIHYTPRAKKVIELSMDEARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLLGSN-  145 (468)
T ss_dssp             --------CSSCEECHHHHHHHHHHHHHHHTTTCSSBCHHHHHHHHHHTCCSHHHHHHHHTTCCHHHHHHHHHTTCCCC-
T ss_pred             --------CCCCCCCHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHhcccchHHHHHHHcCCCHHHHHHHHHHHhccC-
Confidence                    23588999999999999999999999999999999999999999999999999999999998876654221 


Q ss_pred             cccCCCCccccccccccccccccccCCCCCCcchhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEE
Q 005179          238 AKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILL  317 (710)
Q Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~  317 (710)
                          ....  ..    . .       .......+.|++|+.+|++++++++++++||++++++++++++.++.++|+||+
T Consensus       146 ----~~~~--~~----~-~-------~~~~~~~~~l~~~~~~l~~~~r~~~ld~iiGr~~~i~~l~~~l~r~~~~~~LL~  207 (468)
T 3pxg_A          146 ----ETGS--SA----A-G-------TNSNANTPTLDSLARDLTAIAKEDSLDPVIGRSKEIQRVIEVLSRRTKNNPVLI  207 (468)
T ss_dssp             ----CTTC-------------------CCSTHHHHHHSSCCBHHHHTTSSCSCCCCCCHHHHHHHHHHHHCSSSCEEEEE
T ss_pred             ----cccc--cc----c-C-------cCCccCchHHHHHHHHHHHHHhcCCCCCccCcHHHHHHHHHHHhccCCCCeEEE
Confidence                0000  00    0 0       001124578999999999999999999999999999999999999999999999


Q ss_pred             cCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhC
Q 005179          318 GESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGS  397 (710)
Q Consensus       318 GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~  397 (710)
                      ||||||||++|+++++.+..+.+|..+.+..++.++++     .++.|+++.+++.++..+...++.|||||        
T Consensus       208 G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~l~~~-----~~~~g~~e~~~~~~~~~~~~~~~~iLfiD--------  274 (468)
T 3pxg_A          208 GEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMTLDMG-----TKYRGEFEDRLKKVMDEIRQAGNIILFID--------  274 (468)
T ss_dssp             SCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEECC---------------CTTHHHHHHHHHTCCCCEEEEC--------
T ss_pred             CCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEeeCC-----ccccchHHHHHHHHHHHHHhcCCeEEEEe--------
Confidence            99999999999999999999999999999999999886     45778888889999999988888999999        


Q ss_pred             CCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhc
Q 005179          398 GTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHH  477 (710)
Q Consensus       398 ~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~  477 (710)
                      +         ..++++.|++.++++.+++|++||..+|.+++.++++|.+||+.|.|++|+.+++..||+.+..+|+.+|
T Consensus       275 ~---------~~~a~~~L~~~L~~g~v~vI~at~~~e~~~~~~~~~al~~Rf~~i~v~~p~~e~~~~iL~~~~~~~~~~~  345 (468)
T 3pxg_A          275 A---------AIDASNILKPSLARGELQCIGATTLDEYRKYIEKDAALERRFQPIQVDQPSVDESIQILQGLRDRYEAHH  345 (468)
T ss_dssp             C-----------------CCCTTSSSCEEEEECCTTTTHHHHTTCSHHHHSEEEEECCCCCHHHHHHHHHHTTTTSGGGS
T ss_pred             C---------chhHHHHHHHhhcCCCEEEEecCCHHHHHHHhhcCHHHHHhCccceeCCCCHHHHHHHHHHHHHHHHHhc
Confidence            1         3457899999999999999999999999999999999999999999999999999999999999888889


Q ss_pred             CCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhhhhhhchh
Q 005179          478 NCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHIELFKRKK  526 (710)
Q Consensus       478 ~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~~~~~~~~  526 (710)
                      ++.++++++..++.++.+|+.++++|++++++++.+++++++.....|.
T Consensus       346 ~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~a~~~~~~~~~~~p~  394 (468)
T 3pxg_A          346 RVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDEAGSKVRLRSFTTPP  394 (468)
T ss_dssp             SCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred             CCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHHHHHHHHhccCCCch
Confidence            9999999999999999999999999999999999999988887665554

>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=99.97  E-value=3.3e-32  Score=316.11  Aligned_cols=315  Identities=23%  Similarity=0.271  Sum_probs=214.1

Q ss_pred             cCCCCcccCHHHHHHHHHHHH----c---------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC----R---------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~----~---------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|+++.|.++.++.|.+++.    .         ..+.++|||||||||||++|+++|.++          +.+++.++
T Consensus       201 v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~el----------g~~~~~v~  270 (806)
T 3cf2_A          201 VGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET----------GAFFFLIN  270 (806)
T ss_dssp             CCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTT----------TCEEEEEE
T ss_pred             CChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHh----------CCeEEEEE
Confidence            357789998877777766532    1         345789999999999999999999988          88999999


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc----cCCCeEEEEc
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL----GRGELQCIAS  429 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l----~~~~v~vI~a  429 (710)
                      +..+.  .++.|+.+..++.+|..+....|+||||||+|.|+.....+.+  +....+.+.|+..|    +++.+.||++
T Consensus       271 ~~~l~--sk~~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~--~~~~riv~~LL~~mdg~~~~~~V~VIaa  346 (806)
T 3cf2_A          271 GPEIM--SKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHG--EVERRIVSQLLTLMDGLKQRAHVIVMAA  346 (806)
T ss_dssp             HHHHH--SSCTTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCC--TTHHHHHHHHHTHHHHCCGGGCEEEEEE
T ss_pred             hHHhh--cccchHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCC--hHHHHHHHHHHHHHhcccccCCEEEEEe
Confidence            99988  5688999999999999999999999999999999876543221  33344555554444    4578999999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ||..+     .+|++|+|  ||+ .|.|+.|+.++|.+||+.+....      .+.++ .+..++..+.+|.+     .+
T Consensus       347 TN~~d-----~LD~ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~------~~~~dvdl~~lA~~T~Gfsg-----aD  410 (806)
T 3cf2_A          347 TNRPN-----SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNM------KLADDVDLEQVANETHGHVG-----AD  410 (806)
T ss_dssp             CSSTT-----TSCTTTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSS------EECTTCCHHHHHHHCCSCCH-----HH
T ss_pred             cCChh-----hcCHHHhCCcccceEEecCCCCHHHHHHHHHHHhcCC------CCCcccCHHHHHHhcCCCCH-----HH
Confidence            99987     79999999  997 89999999999999998765422      22222 36778888777754     55


Q ss_pred             HHHHHHHHHhhhhhhhhhchhhHHhhhhCCCChHHHHHHHHHHHhhHHHhhccccchhhhhccCCcchhhhhccCCCCCC
Q 005179          506 AIDLVDEAGSRAHIELFKRKKEQQTCILSKPPDDYWQEIRTVQAMHEVVQGSRLKYDDVVASMGDTSEIVVESSLPSASD  585 (710)
Q Consensus       506 ai~ll~~a~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  585 (710)
                      ...++++|+..+..+......      +...                                ....+  .         
T Consensus       411 L~~Lv~eA~~~A~~r~~~~i~------~~~~--------------------------------~~~~e--~---------  441 (806)
T 3cf2_A          411 LAALCSEAALQAIRKKMDLID------LEDE--------------------------------TIDAE--V---------  441 (806)
T ss_dssp             HHHHHHHHHHHHHHHHHHHGG------GTCC--------------------------------CCSHH--H---------
T ss_pred             HHHHHHHHHHHHHHhcccccc------cccc--------------------------------ccchh--h---------
Confidence            666777776443222110000      0000                                00000  0         


Q ss_pred             CCCCCcCCHHHHHHHHHhhhC-------CChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHH----hhcCCCC
Q 005179          586 DDEPAVVGPDDIAAVASLWSG-------IPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKR----SRVGLKD  654 (710)
Q Consensus       586 ~~~~~~v~~~di~~~~s~~~g-------ip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~----~r~gl~~  654 (710)
                       .....|+.+|+..++.....       +...+++|++              |+|++++++.+...+.+    .....+.
T Consensus       442 -~~~~~v~~~Df~~Al~~~~ps~~r~~~~~~p~v~w~d--------------iggl~~~k~~l~e~v~~p~~~p~~f~~~  506 (806)
T 3cf2_A          442 -MNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWED--------------IGGLEDVKRELQELVQYPVEHPDKFLKF  506 (806)
T ss_dssp             -HHHCEECTTHHHHHHSSSSCCCCCCCCCBCCCCCSTT--------------CCSCHHHHHHHTTTTTTTTTCSGGGSSS
T ss_pred             -hccceeeHHHHHHHHHhCCCcccccccccCCCCCHHH--------------hCCHHHHHHHHHHHHHhhhhCHHHHHhc
Confidence             00134566666666644321       1223566665              55555666555554432    2211111


Q ss_pred             CCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          655 PNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       655 p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ..+|..++|||||||||||++||+||.+   .+.+++.++.+++
T Consensus       507 g~~~~~gvLl~GPPGtGKT~lAkaiA~e---~~~~f~~v~~~~l  547 (806)
T 3cf2_A          507 GMTPSKGVLFYGPPGCGKTLLAKAIANE---CQANFISIKGPEL  547 (806)
T ss_dssp             CCCCCSCCEEESSTTSSHHHHHHHHHHT---TTCEEEECCHHHH
T ss_pred             CCCCCceEEEecCCCCCchHHHHHHHHH---hCCceEEeccchh
Confidence            2234468999999999999999999999   4567888876654

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=99.93  E-value=3.2e-25  Score=207.66  Aligned_cols=141  Identities=31%  Similarity=0.559  Sum_probs=130.9

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      .||++||++++++|..|+++|+++||++|+|||||+||+.++++  .++|..+|+|++.+++++...+++.+.       
T Consensus         2 ~m~~~~t~~~~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~~~gv~~~~l~~~l~~~l~~~~~-------   74 (146)
T 3fh2_A            2 AMFERFTDRARRVIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDAVRQEVEEIIGQGSQ-------   74 (146)
T ss_dssp             GGGGGBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCSHHHHHHHHTTCCHHHHHHHHHHHHCCCSC-------
T ss_pred             chhhhcCHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHhCCCChHHHHHHHcCCCHHHHHHHHHHHhccCCC-------
Confidence            69999999999999999999999999999999999999998776  789999999999999999999987753       


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                            +.+..+++|+.++++|+.|+.+|+++|+.||+++|||+||++++++.+.++|+++||+.+.+++.+.+.+
T Consensus        75 ------~~~~~~~~s~~~~~vL~~A~~~a~~~~~~~i~~eHlLlall~~~~~~a~~iL~~~gv~~~~l~~~l~~~~  144 (146)
T 3fh2_A           75 ------PTTGHIPFTPRAKKVLELSLREGLQMGHKYIGTEFLLLGLIREGEGVAAQVLVKLGADLPRVRQQVIQLL  144 (146)
T ss_dssp             ------CCCSCCCBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCSSHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             ------CCcCCCcCCHHHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHHHHh
Confidence                  2235689999999999999999999999999999999999999889999999999999999998887655

>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural genomics, PSI-2, protein S initiative; HET: PG4 EPE; 1.82A {Clostridium difficile}

Probab=99.91  E-value=1.8e-24  Score=202.35  Aligned_cols=140  Identities=28%  Similarity=0.442  Sum_probs=128.3

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      ..|++||++++++|..|+++|+++||++|+|||||+|||.++++  .++|..+|+|++.+++.+...+++.+.       
T Consensus         3 ~~~~~~T~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~~~gvd~~~l~~~l~~~l~~~~~-------   75 (145)
T 3fes_A            3 ANFNRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDMEGKGEE-------   75 (145)
T ss_dssp             -CCCCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHHHHTCCHHHHHHHHHHHHCCCSC-------
T ss_pred             CcccccCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCChHHHHHHHcCCCHHHHHHHHHHHHhcCCC-------
Confidence            46789999999999999999999999999999999999999877  789999999999999999999987642       


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                             .+..++||+.++++|+.|..+|+++|+.||+++|||+||++++++.+.++|+++||+.+.+++.+.+.+
T Consensus        76 -------~~~~~~~s~~~~~vl~~A~~~A~~~~~~~v~~eHlLlAll~~~~~~a~~iL~~~gv~~~~l~~~i~~~~  144 (145)
T 3fes_A           76 -------ISEDIVLSPRSKQILELSGMFANKLKTNYIGTEHILLAIIQEGEGIANKILNYAGVNDRTLAQLTIDMM  144 (145)
T ss_dssp             -------CCSCCEECHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCHHHHHHHHHHTCHHHHHHHHHHHTC
T ss_pred             -------CCCCCCCCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHHHHh
Confidence                   124689999999999999999999999999999999999999989999999999999999998876543

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=99.90  E-value=1.6e-23  Score=197.15  Aligned_cols=140  Identities=32%  Similarity=0.524  Sum_probs=124.7

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      |||++||++++++|..|+++|+++||++|+|||||+|||.++++  .++|..+|+|++.++.++...+++.+..      
T Consensus         1 M~~~~~t~~~~~al~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL~~~g~~~~~l~~~l~~~l~~~~~~------   74 (150)
T 2y1q_A            1 MMFGRFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLIGRAQEM------   74 (150)
T ss_dssp             ---CCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHHHTTCCHHHHHHHHHHHHCCC---------
T ss_pred             CcchhhCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCCHHHHHHHHcCCCHHHHHHHHHHHhccCCcc------
Confidence            57899999999999999999999999999999999999999887  7899999999999999999999877532      


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                              .+.++||+.++++|+.|+.+|+++|+.||+++|||+||++++++.+.++|+.+|++.+.++..+....
T Consensus        75 --------~~~~~~s~~~~~vL~~A~~~A~~~~~~~i~~ehlLlall~~~~~~a~~~L~~~gi~~~~l~~~i~~~~  142 (150)
T 2y1q_A           75 --------SQTIHYTPRAKKVIELSMDEARKLGHSYVGTEHILLGLIREGEGVAARVLNNLGVSLNKARQQVLQLL  142 (150)
T ss_dssp             ----------CCEECHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCSHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             --------cccCCCCHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHhCCCcHHHHHHHHcCCCHHHHHHHHHHHH
Confidence                    13688999999999999999999999999999999999998888888999999999999988776554

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1

Probab=99.90  E-value=3e-23  Score=194.88  Aligned_cols=140  Identities=18%  Similarity=0.237  Sum_probs=121.2

Q ss_pred             hhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhh
Q 005179           80 SVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAA  157 (710)
Q Consensus        80 ~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~  157 (710)
                      |||++||++++++|..|+.+|+++||++|+|||||+|||.++++  .++|..+|+|++.++..+...+++.|..      
T Consensus         1 M~~~~~t~~~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~~~~~~iL~~~g~~~~~l~~~l~~~l~~~p~~------   74 (148)
T 1khy_A            1 MRLDRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQV------   74 (148)
T ss_dssp             ---CCBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHHHHTCCHHHHHHHHHHHHTTSCCC------
T ss_pred             CChhhhhHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHcCCCchHHHHHHHcCCCHHHHHHHHHHHHHhCCCC------
Confidence            57899999999999999999999999999999999999999877  7899999999999999999999887642      


Q ss_pred             hcCCCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHH
Q 005179          158 AQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVS  231 (710)
Q Consensus       158 ~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~  231 (710)
                           .+....++||+.++++|+.|+.+|+.+|+.||+++|||+||+ ++++.+.++|+.+|++.+.++..+..
T Consensus        75 -----~~~~~~~~~s~~~~~vl~~A~~~a~~~~~~~i~~ehlLlall-~~~~~~~~~L~~~gi~~~~l~~~l~~  142 (148)
T 1khy_A           75 -----EGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAAL-ESRGTLADILKAAGATTANITQAIEQ  142 (148)
T ss_dssp             ------------CBCHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHH-TSCHHHHHHHHHTTCCHHHHHHHHHC
T ss_pred             -----CCCCCCcCcCHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH-cCCcHHHHHHHHcCCCHHHHHHHHHH
Confidence                 122246899999999999999999999999999999999999 45678899999999999999876543

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.89  E-value=1.6e-22  Score=216.65  Aligned_cols=200  Identities=23%  Similarity=0.275  Sum_probs=155.5

Q ss_pred             hcCCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          286 EELIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      .-+|+++.|.++.++.|.+.+             ....++++|||||||||||++|+++|.++          +..++.+
T Consensus       144 ~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~----------~~~f~~v  213 (405)
T 4b4t_J          144 DSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHT----------DCKFIRV  213 (405)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHH----------TCEEEEE
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhh----------CCCceEE
Confidence            347899999999888877643             22456889999999999999999999999          8899999


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH---HHhhcccc----cCCCeE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI---SNLLKPSL----GRGELQ  425 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~---~~~L~~~l----~~~~v~  425 (710)
                      +.+.+.  .++.|+.+..++.+|..++...|+||||||+|.+++.+..+.+  ++....   .+.|+..|    ....+.
T Consensus       214 ~~s~l~--sk~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~--~~~~~~~~~l~~lL~~lDg~~~~~~V~  289 (405)
T 4b4t_J          214 SGAELV--QKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSG--GGDSEVQRTMLELLNQLDGFETSKNIK  289 (405)
T ss_dssp             EGGGGS--CSSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSS--GGGGHHHHHHHHHHHHHHTTTCCCCEE
T ss_pred             EhHHhh--ccccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCC--CCcHHHHHHHHHHHHhhhccCCCCCeE
Confidence            999888  6789999999999999999999999999999999876543222  122222   22333222    356789


Q ss_pred             EEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCC
Q 005179          426 CIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRY  501 (710)
Q Consensus       426 vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~  501 (710)
                      ||+|||.++     .+|++|.|  ||+ .|.|+.|+.++|.+||+.+.++.      .++++ .++.++..+.+|.+   
T Consensus       290 vIaATNrpd-----~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~------~l~~dvdl~~lA~~t~G~SG---  355 (405)
T 4b4t_J          290 IIMATNRLD-----ILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKM------NLTRGINLRKVAEKMNGCSG---  355 (405)
T ss_dssp             EEEEESCSS-----SSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTS------BCCSSCCHHHHHHHCCSCCH---
T ss_pred             EEeccCChh-----hCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCC------CCCccCCHHHHHHHCCCCCH---
Confidence            999999987     89999999  998 89999999999999998776532      23222 26778888777644   


Q ss_pred             CcchHHHHHHHHHh
Q 005179          502 LPDKAIDLVDEAGS  515 (710)
Q Consensus       502 ~p~~ai~ll~~a~~  515 (710)
                        .+...++.+|+.
T Consensus       356 --ADi~~l~~eA~~  367 (405)
T 4b4t_J          356 --ADVKGVCTEAGM  367 (405)
T ss_dssp             --HHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHH
Confidence              455666776653

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.88  E-value=3.4e-22  Score=214.55  Aligned_cols=200  Identities=24%  Similarity=0.292  Sum_probs=154.6

Q ss_pred             hcCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          286 EELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      .-+|+++.|.++.++.|.+.+.             .+.+.++|||||||||||++|+++|.++          +..++.+
T Consensus       178 ~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~----------~~~fi~v  247 (437)
T 4b4t_I          178 TESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQT----------SATFLRI  247 (437)
T ss_dssp             CCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHH----------TCEEEEE
T ss_pred             CCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHh----------CCCEEEE
Confidence            3478899999998888776532             2456789999999999999999999999          8899999


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHH---Hhhcccc----cCCCeE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDIS---NLLKPSL----GRGELQ  425 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~---~~L~~~l----~~~~v~  425 (710)
                      +.+.+.  .++.|+.+..++.+|..+....|+||||||+|.++..+..+..  .+.....   +.|+..+    ..++++
T Consensus       248 ~~s~l~--sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~--~~~~~~~~~l~~LL~~lDg~~~~~~Vi  323 (437)
T 4b4t_I          248 VGSELI--QKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNS--GGEREIQRTMLELLNQLDGFDDRGDVK  323 (437)
T ss_dssp             ESGGGC--CSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSC--SSCCHHHHHHHHHHHHHHHCCCSSSEE
T ss_pred             EHHHhh--hccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCC--CccHHHHHHHHHHHHHhhCcCCCCCEE
Confidence            998888  6789999999999999999999999999999999876543222  1222222   2222222    256799


Q ss_pred             EEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCC
Q 005179          426 CIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRY  501 (710)
Q Consensus       426 vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~  501 (710)
                      ||+|||.++     .+|++|.|  ||+ .|.|+.|+.++|.+||+.++.+.      .++++ .++.++..+.+|.+   
T Consensus       324 VIaATNrpd-----~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~------~l~~dvdl~~LA~~T~GfSG---  389 (437)
T 4b4t_I          324 VIMATNKIE-----TLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKM------NLSEDVNLETLVTTKDDLSG---  389 (437)
T ss_dssp             EEEEESCST-----TCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTS------CBCSCCCHHHHHHHCCSCCH---
T ss_pred             EEEeCCChh-----hcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCC------CCCCcCCHHHHHHhCCCCCH---
Confidence            999999987     89999999  998 89999999999999998776532      33332 26778888777644   


Q ss_pred             CcchHHHHHHHHHh
Q 005179          502 LPDKAIDLVDEAGS  515 (710)
Q Consensus       502 ~p~~ai~ll~~a~~  515 (710)
                        .+...++.+|+.
T Consensus       390 --ADI~~l~~eA~~  401 (437)
T 4b4t_I          390 --ADIQAMCTEAGL  401 (437)
T ss_dssp             --HHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHH
Confidence              455566666653

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.88  E-value=3.1e-22  Score=194.76  Aligned_cols=191  Identities=56%  Similarity=0.930  Sum_probs=161.6

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      +.|++++.+|.+.+++..+++++|++++++++.+.+....+.+++|+||||||||++++.+++.+.....+....+..++
T Consensus         3 ~~l~~~~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~   82 (195)
T 1jbk_A            3 QALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVL   82 (195)
T ss_dssp             HHHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEE
T ss_pred             hHHHHHhHHHHHHHhhccccccccchHHHHHHHHHHhcCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEE
Confidence            56899999999999999999999999999999999988778899999999999999999999999887777666788999


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEc
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAS  429 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~a  429 (710)
                      .+++..+..+....+.+...+..++..+.. ..+.||||||+|.+...+..     ....++.+.|+.+++.+++.+|++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~-----~~~~~~~~~l~~~~~~~~~~~i~~  157 (195)
T 1jbk_A           83 ALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKA-----DGAMDAGNMLKPALARGELHCVGA  157 (195)
T ss_dssp             EECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT-----------CCCCHHHHHHHHHTTSCCEEEE
T ss_pred             EeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcc-----cchHHHHHHHHHhhccCCeEEEEe
Confidence            999988887666777788888888887754 45779999999999654321     123345677778888889999999


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRIL  466 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL  466 (710)
                      ++..++.....+++++.+||..|.+++|+.+++.+||
T Consensus       158 ~~~~~~~~~~~~~~~l~~r~~~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          158 TTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             ECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTC
T ss_pred             CCHHHHHHHHhcCHHHHHHhceeecCCCCHHHHHHHh
Confidence            9998887777889999999999999999999988775

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.87  E-value=1.3e-21  Score=212.21  Aligned_cols=199  Identities=21%  Similarity=0.233  Sum_probs=154.0

Q ss_pred             cCCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|+++.|.++.++.|.+.+             ....++++|||||||||||++|+++|.++          +..++.++
T Consensus       206 vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~----------~~~fi~vs  275 (467)
T 4b4t_H          206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRT----------DATFIRVI  275 (467)
T ss_dssp             CCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHH----------TCEEEEEE
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhcc----------CCCeEEEE
Confidence            47899999999888887642             22467889999999999999999999999          88999999


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH---HHhhccc----ccCCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI---SNLLKPS----LGRGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~---~~~L~~~----l~~~~v~v  426 (710)
                      .+.+.  .++.|+.+..++.+|..+....|+||||||+|.++..+..+.+  +.....   .+.|+..    -..+.++|
T Consensus       276 ~s~L~--sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~--~~~~~~~~~l~~lL~~lDg~~~~~~ViV  351 (467)
T 4b4t_H          276 GSELV--QKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGA--GGDNEVQRTMLELITQLDGFDPRGNIKV  351 (467)
T ss_dssp             GGGGC--CCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSC--GGGGHHHHHHHHHHHHHHSSCCTTTEEE
T ss_pred             hHHhh--cccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCC--CccHHHHHHHHHHHHHhhccCCCCcEEE
Confidence            99888  6789999999999999999999999999999999876543211  112222   2222222    23567999


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCCC
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRYL  502 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~~  502 (710)
                      |+|||.++     .+|++|.|  ||+ .|.|+.|+.++|.+||+.+++..      .+..+ .++.++..+.+|.+    
T Consensus       352 IaATNrpd-----~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~------~l~~dvdl~~LA~~T~GfSG----  416 (467)
T 4b4t_H          352 MFATNRPN-----TLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSM------SVERGIRWELISRLCPNSTG----  416 (467)
T ss_dssp             EEECSCTT-----SBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTS------CBCSSCCHHHHHHHCCSCCH----
T ss_pred             EeCCCCcc-----cCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCC------CCCCCCCHHHHHHHCCCCCH----
Confidence            99999987     89999999  998 89999999999999999776633      22222 25677888777644    


Q ss_pred             cchHHHHHHHHHh
Q 005179          503 PDKAIDLVDEAGS  515 (710)
Q Consensus       503 p~~ai~ll~~a~~  515 (710)
                       .+...++.+|+.
T Consensus       417 -ADI~~l~~eAa~  428 (467)
T 4b4t_H          417 -AELRSVCTEAGM  428 (467)
T ss_dssp             -HHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHH
Confidence             455667776653

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.87  E-value=1.1e-21  Score=213.47  Aligned_cols=201  Identities=19%  Similarity=0.256  Sum_probs=154.5

Q ss_pred             hcCCCCcccCHHHHHHHHHHH-------------HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          286 EELIDPVIGRETEIQRIIQIL-------------CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L-------------~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      .-+|+++.|.++.++.|.+.+             ..+.++++|||||||||||++|+++|.++          +..++.+
T Consensus       177 ~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~----------~~~f~~v  246 (434)
T 4b4t_M          177 TETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQT----------NATFLKL  246 (434)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH----------TCEEEEE
T ss_pred             CCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHh----------CCCEEEE
Confidence            347899999999888887642             12456789999999999999999999999          8899999


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH---HHhhcccc----cCCCeE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI---SNLLKPSL----GRGELQ  425 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~---~~~L~~~l----~~~~v~  425 (710)
                      +.+.+.  .++.|+.+..++.+|..+....|+||||||+|.++..+..+.+  .+....   .+.|+..|    ....+.
T Consensus       247 ~~s~l~--~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~--~~~~~~~~~~~~lL~~ldg~~~~~~Vi  322 (434)
T 4b4t_M          247 AAPQLV--QMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEK--SGDREVQRTMLELLNQLDGFSSDDRVK  322 (434)
T ss_dssp             EGGGGC--SSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGG--GTTHHHHHHHHHHHHHHTTSCSSCSSE
T ss_pred             ehhhhh--hcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCC--CCchHHHHHHHHHHHHhhccCCCCCEE
Confidence            999888  6789999999999999999999999999999999876543221  112222   22233222    346789


Q ss_pred             EEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCC
Q 005179          426 CIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYL  502 (710)
Q Consensus       426 vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~  502 (710)
                      ||+|||.++     .+|++|.|  ||+ .|.|+.|+.++|.+||+.+..+.....++     .++.++..+.+|.+    
T Consensus       323 VIaaTNrp~-----~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dv-----dl~~lA~~t~G~sG----  388 (434)
T 4b4t_M          323 VLAATNRVD-----VLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDI-----NWQELARSTDEFNG----  388 (434)
T ss_dssp             EEEECSSCC-----CCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCC-----CHHHHHHHCSSCCH----
T ss_pred             EEEeCCCch-----hcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcC-----CHHHHHHhCCCCCH----
Confidence            999999987     89999988  998 89999999999999999887754222122     25677777777644    


Q ss_pred             cchHHHHHHHHHh
Q 005179          503 PDKAIDLVDEAGS  515 (710)
Q Consensus       503 p~~ai~ll~~a~~  515 (710)
                       .+...++.+|+.
T Consensus       389 -ADi~~l~~eA~~  400 (434)
T 4b4t_M          389 -AQLKAVTVEAGM  400 (434)
T ss_dssp             -HHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHHH
Confidence             455566666653

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.86  E-value=1.1e-20  Score=205.45  Aligned_cols=201  Identities=18%  Similarity=0.197  Sum_probs=154.6

Q ss_pred             cCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|+++.|.++.++.|.+.+.             ...++++|||||||||||++|+++|..+          +.+++.++
T Consensus       169 v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~----------~~~~~~v~  238 (428)
T 4b4t_K          169 VTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANST----------KAAFIRVN  238 (428)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHH----------TCEEEEEE
T ss_pred             CCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCeEEEe
Confidence            468899999998888877542             2456789999999999999999999999          88999999


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCC-hHhHHHhhccc----ccCCCeEEEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGT-GLDISNLLKPS----LGRGELQCIA  428 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~-~~~~~~~L~~~----l~~~~v~vI~  428 (710)
                      ++.+.  .++.|+.+..++.+|..++...|+|+||||+|.++..+..+...... ...+.+.|+..    -...++.||+
T Consensus       239 ~~~l~--~~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~~~~v~vI~  316 (428)
T 4b4t_K          239 GSEFV--HKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQSTNVKVIM  316 (428)
T ss_dssp             GGGTC--CSSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCSSCSEEEEE
T ss_pred             cchhh--ccccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCCCCCEEEEE
Confidence            98887  57899999999999999999999999999999998765332221111 11222333322    2356799999


Q ss_pred             ccChHHHHhhhhccHHHHc--ccc-ceEec-CCCHHHHHHHHHHHHHHHHhhcCCCCCHH-HHHHHHHHhhhhhcCCCCc
Q 005179          429 STTQDEHRTQFEKDKALAR--RFQ-PVLIS-EPSQEDAVRILLGLREKYEAHHNCKFTLE-AINAAVHLSARYISDRYLP  503 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~--Rf~-~I~v~-~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~-~l~~l~~ls~~~i~~r~~p  503 (710)
                      |||.++     .+|++|.|  ||+ .|.|+ .|+.++|..||+.+..+.      .+.++ .++.++..+.+|.+     
T Consensus       317 aTN~~~-----~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~------~l~~~~dl~~lA~~t~G~sg-----  380 (428)
T 4b4t_K          317 ATNRAD-----TLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKM------SLAPEADLDSLIIRNDSLSG-----  380 (428)
T ss_dssp             EESCSS-----SCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSS------CBCTTCCHHHHHHHTTTCCH-----
T ss_pred             ecCChh-----hcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCC------CCCcccCHHHHHHHCCCCCH-----
Confidence            999987     89999999  997 79996 799999999999877632      33332 26778888877744     


Q ss_pred             chHHHHHHHHHh
Q 005179          504 DKAIDLVDEAGS  515 (710)
Q Consensus       504 ~~ai~ll~~a~~  515 (710)
                      .+...++.+|+.
T Consensus       381 adi~~l~~eA~~  392 (428)
T 4b4t_K          381 AVIAAIMQEAGL  392 (428)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            455666776653

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.86  E-value=2.6e-21  Score=210.70  Aligned_cols=201  Identities=22%  Similarity=0.258  Sum_probs=152.9

Q ss_pred             cCCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|+++.|.++.++.|.+.+.             ...++++|||||||||||++|+++|.++          +.+++.++
T Consensus       178 v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~----------~~~~~~v~  247 (437)
T 4b4t_L          178 ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATI----------GANFIFSP  247 (437)
T ss_dssp             SCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHH----------TCEEEEEE
T ss_pred             CChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEe
Confidence            468999999998888776532             2456889999999999999999999999          88999999


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCCh-HhHHHhhcccc----cCCCeEEEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTG-LDISNLLKPSL----GRGELQCIA  428 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~-~~~~~~L~~~l----~~~~v~vI~  428 (710)
                      ++.+.  .++.|+.+..++.+|..+....|+||||||+|.++..+..+....... ....+.|+..|    ..+.++||+
T Consensus       248 ~s~l~--sk~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~~~~vivI~  325 (437)
T 4b4t_L          248 ASGIV--DKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDNLGQTKIIM  325 (437)
T ss_dssp             GGGTC--CSSSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSCTTSSEEEE
T ss_pred             hhhhc--cccchHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccCCCCeEEEE
Confidence            99887  678999999999999999999999999999999987653322111111 11222333323    246789999


Q ss_pred             ccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH-HHHHHHHHHhhhhhcCCCCcc
Q 005179          429 STTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTL-EAINAAVHLSARYISDRYLPD  504 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~-~~l~~l~~ls~~~i~~r~~p~  504 (710)
                      |||.++     .+||+|.|  ||+ .|.|+.|+.++|.+||+.++.+.      ..++ ..++.++..+.+|.+     .
T Consensus       326 ATNrp~-----~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~------~~~~d~dl~~lA~~t~G~sG-----A  389 (437)
T 4b4t_L          326 ATNRPD-----TLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKV------KKTGEFDFEAAVKMSDGFNG-----A  389 (437)
T ss_dssp             EESSTT-----SSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTS------CBCSCCCHHHHHHTCCSCCH-----H
T ss_pred             ecCCch-----hhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCC------CCCcccCHHHHHHhCCCCCH-----H
Confidence            999987     79999998  597 89999999999999999877643      2221 126677777777644     4


Q ss_pred             hHHHHHHHHHh
Q 005179          505 KAIDLVDEAGS  515 (710)
Q Consensus       505 ~ai~ll~~a~~  515 (710)
                      +...++.+|+.
T Consensus       390 Di~~l~~eA~~  400 (437)
T 4b4t_L          390 DIRNCATEAGF  400 (437)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            55566666653

>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone, ATPase, adaptor binding, X-RAY, structure, N-domain, hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB: 1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A 1mbu_A*

Probab=99.86  E-value=2.2e-21  Score=181.01  Aligned_cols=135  Identities=16%  Similarity=0.218  Sum_probs=121.8

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCcHHHHHHCCCCHHHHHHHHHHHhhcC-CCCCCchhhhcCCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHST-NNQDTDDAAAQGKPF  163 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~l~~~gv~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~  163 (710)
                      ||++++++|..|+++|+++||.+|+|||||+|||.+++..++|..+|+|++.++..+...+++. |..           .
T Consensus         2 ~t~~~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~~~~iL~~~g~~~~~l~~~l~~~l~~~~p~~-----------~   70 (143)
T 1k6k_A            2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVL-----------P   70 (143)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHHHHHHHHHTTCCHHHHHHHHHHHHHHHSCBC-----------C
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHcCchHHHHHHHcCCCHHHHHHHHHHHHHhcCCCC-----------C
Confidence            8999999999999999999999999999999999877558899999999999999999998876 431           1


Q ss_pred             -C-CCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHH
Q 005179          164 -S-SAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAV  230 (710)
Q Consensus       164 -~-~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~  230 (710)
                       + ..+.++||+.++++|+.|+.+|+.+|+.||+++|||+||++++++.+.++|+++||+.+.++..+.
T Consensus        71 ~~~~~~~~~~s~~~~~~l~~A~~~A~~~~~~~i~~ehLLlall~~~~~~~~~iL~~~gi~~~~l~~~i~  139 (143)
T 1k6k_A           71 ASEEERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS  139 (143)
T ss_dssp             SSCSCCSCEECHHHHHHHHHHHHHHHSSSCSCBCHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHhCcCcHHHHHHHHcCCCHHHHHHHHH
Confidence             1 124689999999999999999999999999999999999998888889999999999999987654

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.86  E-value=1.4e-21  Score=189.47  Aligned_cols=184  Identities=58%  Similarity=0.927  Sum_probs=156.3

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      +.|++|+.+|.+++++..+++++|++++++.+.+.+......+++|+||||||||++++.+++.+.....|....+..++
T Consensus         3 ~~l~~~~~~l~~~~~~~~~~~~~g~~~~~~~l~~~l~~~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~   82 (187)
T 2p65_A            3 QALEKYSRDLTALARAGKLDPVIGRDTEIRRAIQILSRRTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLV   82 (187)
T ss_dssp             CCTTTTEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEE
T ss_pred             hHHHHHHHHHHHHHhccccchhhcchHHHHHHHHHHhCCCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEE
Confidence            45788999999999999999999999999999999988778899999999999999999999999877777776788999


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEc
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAS  429 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~a  429 (710)
                      .+++..+..+..+.+.+...+..++..+... .+.+|||||+|.+...+..    .....++.+.|+..++++.+.+|++
T Consensus        83 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~----~~~~~~~~~~l~~~~~~~~~~ii~~  158 (187)
T 2p65_A           83 SLDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAV----AEGALDAGNILKPMLARGELRCIGA  158 (187)
T ss_dssp             EECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSS----CTTSCCTHHHHHHHHHTTCSCEEEE
T ss_pred             EEeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccc----cccchHHHHHHHHHHhcCCeeEEEe
Confidence            9999888776667777888888888877665 5789999999999654321    1223456778888888899999999


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCC
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPS  458 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps  458 (710)
                      ++..++.....+++++.+||..|.+++|+
T Consensus       159 ~~~~~~~~~~~~~~~l~~R~~~i~i~~p~  187 (187)
T 2p65_A          159 TTVSEYRQFIEKDKALERRFQQILVEQPS  187 (187)
T ss_dssp             ECHHHHHHHTTTCHHHHHHEEEEECCSCC
T ss_pred             cCHHHHHHHHhccHHHHHhcCcccCCCCC
Confidence            99988777778899999999999999885

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A

Probab=99.85  E-value=4.1e-21  Score=183.26  Aligned_cols=140  Identities=14%  Similarity=0.107  Sum_probs=117.1

Q ss_pred             CCcchhHHHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCC
Q 005179           76 IPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDT  153 (710)
Q Consensus        76 ~~~~~~~~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~  153 (710)
                      ....+||++||++++++|..|+++|+++||++|+|||||+|||.++++  .++|..+|||++.+++++. .+++.+.   
T Consensus        16 ~~l~~~~~kfT~~a~~aL~~A~~~A~~~~h~~I~~EHLLlaLL~~~~~~a~~iL~~~gvd~~~l~~~l~-~l~~~p~---   91 (171)
T 3zri_A           16 IELPTLIAKLNAQSKLALEQAASLCIERQHPEVTLEHYLDVLLDNPLSDVRLVLKQAGLEVDQVKQAIA-STYSREQ---   91 (171)
T ss_dssp             CCHHHHHHHBCHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH-HHSCCCC---
T ss_pred             hhHHHHHHHcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHccCcHHHHHHHHcCCCHHHHHHHHH-HHhcCCC---
Confidence            347789999999999999999999999999999999999999999887  7899999999999999999 8887653   


Q ss_pred             chhhhcCCCCCCCCCCCCCHHHHHHHHHHHHHHH-HcCCCccCHHHHHHHhhhcCCch-HHHHHHH-hcCCHHHHHHHH
Q 005179          154 DDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSR-SRGYNFIAPEHIALGLFTVDDGS-AGRVLKR-LGVDVNHLAAVA  229 (710)
Q Consensus       154 ~~~~~~~~~~~~~~~~~~s~~~~~vl~~A~~~a~-~~g~~~I~~ehlLlall~~~~~~-a~~iL~~-~gv~~~~l~~~~  229 (710)
                                +....++||+.++++|+.|+.+|+ ++|+.||+++|||+||++++... ...+-.. ..|+.+.|++.+
T Consensus        92 ----------~~~~~~~~S~~l~~vL~~A~~~A~l~~gd~~I~teHLLLALl~~~~~~~~~~~~~~l~~i~~~~L~~~~  160 (171)
T 3zri_A           92 ----------VLDTYPAFSPLLVELLQEAWLLSSTELEQAELRSGAIFLAALTRADRYLSFKLISLFEGINRENLKKHF  160 (171)
T ss_dssp             ----------CCSSCCEECHHHHHHHHHHHHHHHTTTCCSSBCHHHHHHHHHHTHHHHSCHHHHHHTTTSCHHHHHHTH
T ss_pred             ----------CCCCCCCcCHHHHHHHHHHHHHHHHHcCCCEEcHHHHHHHHHhChhhhHHHHhhHHHHcCCHHHHHHHH
Confidence                      223568999999999999999999 99999999999999999765210 1111111 346777776544

>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=99.83  E-value=1.4e-19  Score=194.62  Aligned_cols=211  Identities=20%  Similarity=0.258  Sum_probs=152.9

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL  345 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~  345 (710)
                      ..+.....+..|++++|.+..++.|.+.+.            .....++||+||||||||++|+++|..+          
T Consensus        39 ~~~~~~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~----------  108 (355)
T 2qp9_X           39 SAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA----------  108 (355)
T ss_dssp             --------CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCSSCCCCCCEEEECSTTSCHHHHHHHHHHHH----------
T ss_pred             hhhcccCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHh----------
Confidence            344445566789999999999888887652            1234679999999999999999999998          


Q ss_pred             CceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----
Q 005179          346 SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----  420 (710)
Q Consensus       346 ~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----  420 (710)
                      +..++.+++..+.  ..+.|+.+..++.++..+....++||||||+|.+......+.  ......+.+.|...+.     
T Consensus       109 ~~~~~~v~~~~l~--~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~--~~~~~~~~~~ll~~l~~~~~~  184 (355)
T 2qp9_X          109 NSTFFSVSSSDLV--SKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE--SEASRRIKTELLVQMNGVGND  184 (355)
T ss_dssp             TCEEEEEEHHHHH--SCC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC--------CTHHHHHHHHHHHHHHHCC--
T ss_pred             CCCEEEeeHHHHh--hhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCc--chHHHHHHHHHHHHhhccccc
Confidence            7788899988876  345677788889999988888899999999999975432211  1222334444444332     


Q ss_pred             CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcC
Q 005179          421 RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISD  499 (710)
Q Consensus       421 ~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~  499 (710)
                      ...+++|++||.++     .+++++.+||+ .+.++.|+.++|..||+.++.    ..+..+++..++.++..+.+|.+ 
T Consensus       185 ~~~v~vI~atn~~~-----~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~----~~~~~~~~~~l~~la~~t~G~sg-  254 (355)
T 2qp9_X          185 SQGVLVLGATNIPW-----QLDSAIRRRFERRIYIPLPDLAARTTMFEINVG----DTPSVLTKEDYRTLGAMTEGYSG-  254 (355)
T ss_dssp             -CCEEEEEEESCGG-----GSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHT----TSCBCCCHHHHHHHHHHTTTCCH-
T ss_pred             CCCeEEEeecCCcc-----cCCHHHHcccCEEEEeCCcCHHHHHHHHHHHHh----hCCCCCCHHHHHHHHHHcCCCCH-
Confidence            45789999999876     78999999996 899999999999999997765    33556789999999999887643 


Q ss_pred             CCCcchHHHHHHHHHhh
Q 005179          500 RYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       500 r~~p~~ai~ll~~a~~~  516 (710)
                          .+...++++|+..
T Consensus       255 ----~dl~~l~~~A~~~  267 (355)
T 2qp9_X          255 ----SDIAVVVKDALMQ  267 (355)
T ss_dssp             ----HHHHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHHH
Confidence                4556677776644

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.83  E-value=1.3e-19  Score=197.75  Aligned_cols=198  Identities=21%  Similarity=0.336  Sum_probs=147.2

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL  345 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~  345 (710)
                      ..|....++..|++++|++..++.+.+.+.            .....++||+||||||||++|++++..+          
T Consensus       103 ~~~~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~----------  172 (389)
T 3vfd_A          103 NEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES----------  172 (389)
T ss_dssp             GTTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT----------
T ss_pred             hhhhccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh----------
Confidence            355556677789999999999999888762            2335789999999999999999999987          


Q ss_pred             CceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----
Q 005179          346 SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----  420 (710)
Q Consensus       346 ~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----  420 (710)
                      +..++.+++..+.  ..+.|..+..+..++..+....++||||||||.++.....+.  ......+.+.|...+.     
T Consensus       173 ~~~~~~v~~~~l~--~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~--~~~~~~~~~~ll~~l~~~~~~  248 (389)
T 3vfd_A          173 NATFFNISAASLT--SKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGE--HDASRRLKTEFLIEFDGVQSA  248 (389)
T ss_dssp             TCEEEEECSCCC---------CHHHHHHHHHHHHHSSSEEEEEETGGGGC----------CTHHHHHHHHHHHHHHHC--
T ss_pred             cCcEEEeeHHHhh--ccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCcc--chHHHHHHHHHHHHhhccccc
Confidence            7788898887766  345667778888999988888889999999999976533211  1223344444443333     


Q ss_pred             -CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          421 -RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       421 -~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                       ...++||++||..+     .+++++.+||. .|.++.|+.+++..||+.++.    .++..++++.+..++..+.+|..
T Consensus       249 ~~~~v~vI~atn~~~-----~l~~~l~~R~~~~i~i~~p~~~~r~~il~~~~~----~~~~~l~~~~~~~la~~~~g~~~  319 (389)
T 3vfd_A          249 GDDRVLVMGATNRPQ-----ELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLC----KQGSPLTQKELAQLARMTDGYSG  319 (389)
T ss_dssp             ---CEEEEEEESCGG-----GCCHHHHTTCCEEEECCCCCHHHHHHHHHHHHT----TSCCCSCHHHHHHHHHHTTTCCH
T ss_pred             CCCCEEEEEecCCch-----hcCHHHHcCcceEEEcCCcCHHHHHHHHHHHHH----hcCCCCCHHHHHHHHHHcCCCCH
Confidence             45689999999865     78999999997 799999999999999987766    45778999999999988877643

>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=99.83  E-value=8.1e-20  Score=194.14  Aligned_cols=202  Identities=21%  Similarity=0.285  Sum_probs=155.8

Q ss_pred             hhcCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          285 SEELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       285 ~~~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      .+-+|++++|.++.++.+.+.+.            .....++||+||||||||++|+++++.+          +..++.+
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~----------~~~~~~v   82 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA----------NSTFFSV   82 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHH----------TCEEEEE
T ss_pred             CCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHH----------CCCEEEE
Confidence            34467889999999998888662            1234679999999999999999999988          7789999


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-----cCCCeEEE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-----GRGELQCI  427 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-----~~~~v~vI  427 (710)
                      +++.+.  .++.|+.+..++.++..+....++||||||+|.+......+.  ......+.+.|...+     ....+++|
T Consensus        83 ~~~~l~--~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~--~~~~~~~~~~ll~~l~~~~~~~~~v~vi  158 (322)
T 3eie_A           83 SSSDLV--SKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGE--SEASRRIKTELLVQMNGVGNDSQGVLVL  158 (322)
T ss_dssp             EHHHHH--TTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC--------CCTHHHHHHHHHHHGGGGTSCCCEEEE
T ss_pred             chHHHh--hcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCc--chHHHHHHHHHHHHhccccccCCceEEE
Confidence            988877  456788999999999999988899999999999976532211  122333444443333     34678999


Q ss_pred             EccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          428 ASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       428 ~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ++||...     .+++++.+||. .|.++.|+.++|.+||+.++.    ..+..+++..++.++..+.+|.+     .+.
T Consensus       159 ~atn~~~-----~ld~al~~Rf~~~i~~~~p~~~~r~~il~~~~~----~~~~~~~~~~l~~la~~t~g~sg-----~di  224 (322)
T 3eie_A          159 GATNIPW-----QLDSAIRRRFERRIYIPLPDLAARTTMFEINVG----DTPCVLTKEDYRTLGAMTEGYSG-----SDI  224 (322)
T ss_dssp             EEESCGG-----GSCHHHHHHCCEEEECCCCCHHHHHHHHHHHHT----TCCCCCCHHHHHHHHHTTTTCCH-----HHH
T ss_pred             EecCChh-----hCCHHHHcccCeEEEeCCCCHHHHHHHHHHHhc----cCCCCCCHHHHHHHHHHcCCCCH-----HHH
Confidence            9999876     68999999997 799999999999999998765    44667889999999988877644     455


Q ss_pred             HHHHHHHH
Q 005179          507 IDLVDEAG  514 (710)
Q Consensus       507 i~ll~~a~  514 (710)
                      ..++..|.
T Consensus       225 ~~l~~~a~  232 (322)
T 3eie_A          225 AVVVKDAL  232 (322)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHH
Confidence            55666654

>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=99.83  E-value=3.6e-19  Score=191.79  Aligned_cols=216  Identities=22%  Similarity=0.324  Sum_probs=163.8

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      ..++.....+.....+..|++++|++..++.+.+.+.            .....++||+||||||||++|++++..+   
T Consensus        65 ~~~~~i~~~i~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---  141 (357)
T 3d8b_A           65 KMIELIMNEIMDHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS---  141 (357)
T ss_dssp             HHHHHHHHHTBCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT---
T ss_pred             HHHHHHHhhcccCCCCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc---
Confidence            4455556666666677889999999999999888763            2356789999999999999999999987   


Q ss_pred             CCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc
Q 005179          339 EVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS  418 (710)
Q Consensus       339 ~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~  418 (710)
                             +..++.++++.+.  ..+.|+.+..++.++..+....+.||||||+|.+......+.  ......+.+.|...
T Consensus       142 -------~~~~~~i~~~~l~--~~~~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~--~~~~~~~~~~lL~~  210 (357)
T 3d8b_A          142 -------GATFFSISASSLT--SKWVGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGE--HESSRRIKTEFLVQ  210 (357)
T ss_dssp             -------TCEEEEEEGGGGC--CSSTTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC--------CHHHHHHHHHHHH
T ss_pred             -------CCeEEEEehHHhh--ccccchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCc--chHHHHHHHHHHHH
Confidence                   7788899888776  456778888889999888888889999999999976532211  11223344444333


Q ss_pred             cc------CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHH
Q 005179          419 LG------RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVH  491 (710)
Q Consensus       419 l~------~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~  491 (710)
                      +.      ...+++|++||...     .+++++.+||. .+.++.|+.+++..|++.++.    ..++.++++.++.++.
T Consensus       211 l~~~~~~~~~~v~vI~atn~~~-----~l~~~l~~Rf~~~i~i~~p~~~~r~~il~~~~~----~~~~~l~~~~l~~la~  281 (357)
T 3d8b_A          211 LDGATTSSEDRILVVGATNRPQ-----EIDEAARRRLVKRLYIPLPEASARKQIVINLMS----KEQCCLSEEEIEQIVQ  281 (357)
T ss_dssp             HHC----CCCCEEEEEEESCGG-----GBCHHHHTTCCEEEECCCCCHHHHHHHHHHHHH----TSCBCCCHHHHHHHHH
T ss_pred             HhcccccCCCCEEEEEecCChh-----hCCHHHHhhCceEEEeCCcCHHHHHHHHHHHHh----hcCCCccHHHHHHHHH
Confidence            32      35789999998875     68999999997 789999999999999998776    3466789999999999


Q ss_pred             HhhhhhcCCCCcchHHHHHHHHH
Q 005179          492 LSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       492 ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      .+.+|.+     .+...+++.|.
T Consensus       282 ~t~G~s~-----~dl~~l~~~a~  299 (357)
T 3d8b_A          282 QSDAFSG-----ADMTQLCREAS  299 (357)
T ss_dssp             HTTTCCH-----HHHHHHHHHHH
T ss_pred             HcCCCCH-----HHHHHHHHHHH
Confidence            8877643     44445555554

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=99.81  E-value=4.1e-19  Score=188.48  Aligned_cols=202  Identities=20%  Similarity=0.228  Sum_probs=153.1

Q ss_pred             cCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|++++|.++.++.|.+.+.            ...+.++||+||||||||++|+++|+.+         .+..++.+++
T Consensus         9 ~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~iLL~GppGtGKT~la~ala~~~---------~~~~~~~i~~   79 (322)
T 1xwi_A            9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA---------NNSTFFSISS   79 (322)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCTTCCCCSEEEEESSSSSCHHHHHHHHHHHT---------TSCEEEEEEC
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhCCCCCCceEEEECCCCccHHHHHHHHHHHc---------CCCcEEEEEh
Confidence            467899999998888887653            1234679999999999999999999987         1456777777


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-----cCCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-----GRGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-----~~~~v~vI~a  429 (710)
                      ..+.  .++.|+.+..++.++..+....++||||||+|.+......+.  ......+.+.|...+     ....+++|++
T Consensus        80 ~~l~--~~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~--~~~~~~~~~~ll~~ld~~~~~~~~v~vI~a  155 (322)
T 1xwi_A           80 SDLV--SKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE--SEAARRIKTEFLVQMQGVGVDNDGILVLGA  155 (322)
T ss_dssp             CSSC--CSSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCC--TTHHHHHHHHHHHHHHCSSSCCTTEEEEEE
T ss_pred             HHHH--hhhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhcccccccc--chHHHHHHHHHHHHHhcccccCCCEEEEEe
Confidence            7665  456777888899999999888899999999999976543311  122223333333332     2467899999


Q ss_pred             cChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID  508 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~  508 (710)
                      ||.+.     .+++++.|||+ .+.++.|+.++|..||+.++.    ..+..+++..++.++..+.+|.+     .+...
T Consensus       156 tn~~~-----~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~----~~~~~l~~~~l~~la~~t~G~sg-----adl~~  221 (322)
T 1xwi_A          156 TNIPW-----VLDSAIRRRFEKRIYIPLPEPHARAAMFKLHLG----TTQNSLTEADFRELGRKTDGYSG-----ADISI  221 (322)
T ss_dssp             ESCTT-----TSCHHHHHTCCEEEECCCCCHHHHHHHHHHHHT----TCCBCCCHHHHHHHHHTCTTCCH-----HHHHH
T ss_pred             cCCcc-----cCCHHHHhhcCeEEEeCCcCHHHHHHHHHHHHh----cCCCCCCHHHHHHHHHHcCCCCH-----HHHHH
Confidence            99875     78999999996 899999999999999998765    33556789999999988877744     44555


Q ss_pred             HHHHHHh
Q 005179          509 LVDEAGS  515 (710)
Q Consensus       509 ll~~a~~  515 (710)
                      ++++|+.
T Consensus       222 l~~~A~~  228 (322)
T 1xwi_A          222 IVRDALM  228 (322)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHH
Confidence            6666653

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.80  E-value=2.3e-18  Score=180.57  Aligned_cols=208  Identities=20%  Similarity=0.318  Sum_probs=152.4

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccC
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS  346 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~  346 (710)
                      .+.....+..|++++|+++.++.+.+.+..            ....+++|+||||||||++|++++..+          +
T Consensus        10 ~~~~~~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vll~Gp~GtGKT~la~~la~~~----------~   79 (297)
T 3b9p_A           10 EIVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAKGLLLFGPPGNGKTLLARAVATEC----------S   79 (297)
T ss_dssp             TTBCCSSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGGCCCSEEEEESSSSSCHHHHHHHHHHHT----------T
T ss_pred             HhccCCCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCCCCCCeEEEECcCCCCHHHHHHHHHHHh----------C
Confidence            344444566789999999999988876532            235789999999999999999999987          6


Q ss_pred             ceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc------
Q 005179          347 KRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG------  420 (710)
Q Consensus       347 ~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~------  420 (710)
                      ..++.++++.+.  ..+.|..+..++.++..+....+.||||||+|.+........  ......+.+.|...+.      
T Consensus        80 ~~~~~i~~~~l~--~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~--~~~~~~~~~~ll~~l~~~~~~~  155 (297)
T 3b9p_A           80 ATFLNISAASLT--SKYVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSE--HEASRRLKTEFLVEFDGLPGNP  155 (297)
T ss_dssp             CEEEEEESTTTS--SSSCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-------CCSHHHHHHHHHHHHHCC---
T ss_pred             CCeEEeeHHHHh--hcccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCc--chHHHHHHHHHHHHHhcccccC
Confidence            778888877765  345677788888889888888899999999999976533211  1112233333332222      


Q ss_pred             -CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          421 -RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       421 -~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                       ...+++|++|+.++     .+++++.+||. .+.++.|+.+++..|++.++.    ..+..++++.++.++..+.+|..
T Consensus       156 ~~~~v~vi~~tn~~~-----~l~~~l~~R~~~~i~~~~p~~~~r~~il~~~~~----~~~~~~~~~~~~~la~~~~g~~~  226 (297)
T 3b9p_A          156 DGDRIVVLAATNRPQ-----ELDEAALRRFTKRVYVSLPDEQTRELLLNRLLQ----KQGSPLDTEALRRLAKITDGYSG  226 (297)
T ss_dssp             ---CEEEEEEESCGG-----GBCHHHHHHCCEEEECCCCCHHHHHHHHHHHHG----GGSCCSCHHHHHHHHHHTTTCCH
T ss_pred             CCCcEEEEeecCChh-----hCCHHHHhhCCeEEEeCCcCHHHHHHHHHHHHH----hcCCCCCHHHHHHHHHHcCCCCH
Confidence             24688999999875     68999999996 899999999999999987765    34667899999999888776533


Q ss_pred             CCCCcchHHHHHHHHH
Q 005179          499 DRYLPDKAIDLVDEAG  514 (710)
Q Consensus       499 ~r~~p~~ai~ll~~a~  514 (710)
                           .....+++.|+
T Consensus       227 -----~~l~~l~~~a~  237 (297)
T 3b9p_A          227 -----SDLTALAKDAA  237 (297)
T ss_dssp             -----HHHHHHHHHHT
T ss_pred             -----HHHHHHHHHHH
Confidence                 23345555554

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.78  E-value=5.3e-18  Score=176.70  Aligned_cols=200  Identities=22%  Similarity=0.308  Sum_probs=146.2

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -.|++++|.++.++.+.+.+..             ..+.++||+||||||||++|++++..+          +..++.++
T Consensus        14 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~----------~~~~~~v~   83 (285)
T 3h4m_A           14 VRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATET----------NATFIRVV   83 (285)
T ss_dssp             CCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHT----------TCEEEEEE
T ss_pred             CCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEe
Confidence            3567899999999888876543             456789999999999999999999988          77888888


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc-------cCCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL-------GRGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l-------~~~~v~v  426 (710)
                      +..+.  ..+.|..+..+..++..+....+.||||||+|.+.........  .........|..++       ..+.+++
T Consensus        84 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~--~~~~~~~~~l~~ll~~~~~~~~~~~~~v  159 (285)
T 3h4m_A           84 GSELV--KKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALT--GGDREVQRTLMQLLAEMDGFDARGDVKI  159 (285)
T ss_dssp             GGGGC--CCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCC--GGGGHHHHHHHHHHHHHHTTCSSSSEEE
T ss_pred             hHHHH--HhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccC--CccHHHHHHHHHHHHHhhCCCCCCCEEE
Confidence            87776  4467788888999999988888899999999999765432111  12223333333222       2467899


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      |++|+..+     .+++++.+  ||. .+.++.|+.+++.+|++.....+    ++. .+..+..++..+.+|     .+
T Consensus       160 I~ttn~~~-----~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~----~~~-~~~~~~~l~~~~~g~-----~~  224 (285)
T 3h4m_A          160 IGATNRPD-----ILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKM----NLA-EDVNLEEIAKMTEGC-----VG  224 (285)
T ss_dssp             EEECSCGG-----GBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTS----CBC-TTCCHHHHHHHCTTC-----CH
T ss_pred             EEeCCCch-----hcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcC----CCC-CcCCHHHHHHHcCCC-----CH
Confidence            99999875     68999999  997 89999999999999998765532    221 122356666666655     33


Q ss_pred             chHHHHHHHHHh
Q 005179          504 DKAIDLVDEAGS  515 (710)
Q Consensus       504 ~~ai~ll~~a~~  515 (710)
                      .+...+++.|..
T Consensus       225 ~~i~~l~~~a~~  236 (285)
T 3h4m_A          225 AELKAICTEAGM  236 (285)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            455556666653

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.78  E-value=6.8e-17  Score=191.03  Aligned_cols=177  Identities=18%  Similarity=0.264  Sum_probs=126.1

Q ss_pred             CCcccCHHHHHHHHHHHHcCC-------C--CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc
Q 005179          290 DPVIGRETEIQRIIQILCRRT-------K--NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG  360 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~-------~--~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g  360 (710)
                      +.++|++..++.+...+.+..       +  .++||+||||||||++|+++++.+...       +..++.++++.+...
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~~~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~-------~~~~i~i~~s~~~~~  563 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLKDPKRPIGSFIFLGPTGVGKTELARALAESIFGD-------EESMIRIDMSEYMEK  563 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCSCTTSCSEEEEEESCTTSSHHHHHHHHHHHHHSC-------TTCEEEEEGGGGCSS
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC-------CcceEEEechhcccc
Confidence            358999999988888776422       1  259999999999999999999988432       567888999887643


Q ss_pred             cccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeEEE
Q 005179          361 AKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQCI  427 (710)
Q Consensus       361 ~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~vI  427 (710)
                      ....      -..+...+....+.|||||||+.+             ..++++.|.+.++.+             ++++|
T Consensus       564 ~~~~------~~~l~~~~~~~~~~vl~lDEi~~~-------------~~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI  624 (758)
T 3pxi_A          564 HSTS------GGQLTEKVRRKPYSVVLLDAIEKA-------------HPDVFNILLQVLEDGRLTDSKGRTVDFRNTILI  624 (758)
T ss_dssp             CCCC---------CHHHHHHCSSSEEEEECGGGS-------------CHHHHHHHHHHHHHSBCC-----CCBCTTCEEE
T ss_pred             cccc------cchhhHHHHhCCCeEEEEeCcccc-------------CHHHHHHHHHHhccCeEEcCCCCEeccCCeEEE
Confidence            2221      111223344456789999999988             556788888777653             45788


Q ss_pred             EccChH-----HHHh--hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhh-----cCCCCCHHHHHHHHHH
Q 005179          428 ASTTQD-----EHRT--QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAH-----HNCKFTLEAINAAVHL  492 (710)
Q Consensus       428 ~att~~-----~~~~--~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~-----~~~~i~~~~l~~l~~l  492 (710)
                      +|||..     ....  .-.+.|.|.+||+ .|.|++|+.+++..|++..+..+...     ..+.+++++++.++..
T Consensus       625 ~ttn~~~~~~~~~~~~~~~~f~p~l~~Rl~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~a~~~l~~~  702 (758)
T 3pxi_A          625 MTSNVGASEKDKVMGELKRAFRPEFINRIDEIIVFHSLEKKHLTEIVSLMSDQLTKRLKEQDLSIELTDAAKAKVAEE  702 (758)
T ss_dssp             EEESSSTTCCHHHHHHHHHHSCHHHHTTSSEEEECC--CHHHHHHHHHHHHHHHHHHHHTTTCEEEECHHHHHHHHGG
T ss_pred             EeCCCChhhHHHHHHHHHhhCCHHHHhhCCeEEecCCCCHHHHHHHHHHHHHHHHHHHHhCCCeEEECHHHHHHHHHh
Confidence            888831     1111  1126799999995 89999999999999999887765432     2467899999888765

>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=99.77  E-value=3.8e-18  Score=190.17  Aligned_cols=204  Identities=22%  Similarity=0.265  Sum_probs=152.7

Q ss_pred             hhhcCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          284 ASEELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       284 ~~~~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ..+..|++++|.+..++++.+.+..             ..+.++||+||||||||++|++++..+          +..++
T Consensus       198 ~~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~----------~~~fv  267 (489)
T 3hu3_A          198 LNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET----------GAFFF  267 (489)
T ss_dssp             HTCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHC----------SSEEE
T ss_pred             cCCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHh----------CCCEE
Confidence            3455788999999999998876542             456789999999999999999999987          77899


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEE
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQC  426 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~v  426 (710)
                      .+++..+.  ..+.|+.+..++.+|..+....+++|||||||.+........  .+....+++.|...++    ..++++
T Consensus       268 ~vn~~~l~--~~~~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~--~~~~~~~~~~LL~~ld~~~~~~~v~v  343 (489)
T 3hu3_A          268 LINGPEIM--SKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTH--GEVERRIVSQLLTLMDGLKQRAHVIV  343 (489)
T ss_dssp             EEEHHHHH--TSCTTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCC--CHHHHHHHHHHHHHHHHSCTTSCEEE
T ss_pred             EEEchHhh--hhhcchhHHHHHHHHHHHHhcCCcEEEecchhhhcccccccc--chHHHHHHHHHHHHhhccccCCceEE
Confidence            99998887  456788888899999999888899999999999976543211  1223345555555543    567999


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      |++||.++     .+++++.+  ||. .|.++.|+.++|.+||+.+...+    .+. .+..+..++..+.+|..     
T Consensus       344 IaaTn~~~-----~Ld~al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~----~l~-~~~~l~~la~~t~g~s~-----  408 (489)
T 3hu3_A          344 MAATNRPN-----SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNM----KLA-DDVDLEQVANETHGHVG-----  408 (489)
T ss_dssp             EEEESCGG-----GBCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTS----CBC-TTCCHHHHHHTCTTCCH-----
T ss_pred             EEecCCcc-----ccCHHHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcC----CCc-chhhHHHHHHHccCCcH-----
Confidence            99999876     68899999  887 79999999999999998765532    111 12234566666555533     


Q ss_pred             chHHHHHHHHHhh
Q 005179          504 DKAIDLVDEAGSR  516 (710)
Q Consensus       504 ~~ai~ll~~a~~~  516 (710)
                      .+...+++.|+..
T Consensus       409 ~dL~~L~~~A~~~  421 (489)
T 3hu3_A          409 ADLAALCSEAALQ  421 (489)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            4555566666543

>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=99.77  E-value=3.1e-18  Score=189.62  Aligned_cols=206  Identities=19%  Similarity=0.224  Sum_probs=149.7

Q ss_pred             hhhhcCCCCcccCHHHHHHHHHHHH------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          283 RASEELIDPVIGRETEIQRIIQILC------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       283 ~~~~~~l~~liGr~~~i~~l~~~L~------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ...+-.|++++|.+...+.+.+.+.            .....++||+||||||||++|+++|..+         .+..++
T Consensus       127 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~~~~~~~~vLL~GppGtGKT~lA~aia~~~---------~~~~~~  197 (444)
T 2zan_A          127 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAVATEA---------NNSTFF  197 (444)
T ss_dssp             CCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSGGGCCCSEEEEECSTTSSHHHHHHHHHHHC---------CSSEEE
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHc---------CCCCEE
Confidence            3445678999999999988887662            2345789999999999999999999987         145677


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----CCCeE
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----RGELQ  425 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----~~~v~  425 (710)
                      .++++.+..  .+.|+.+..++.++..+....++||||||+|.+......+.  ......+.+.|...+.     ...++
T Consensus       198 ~v~~~~l~~--~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~--~~~~~~~~~~lL~~l~~~~~~~~~v~  273 (444)
T 2zan_A          198 SISSSDLVS--KWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENE--SEAARRIKTEFLVQMQGVGVDNDGIL  273 (444)
T ss_dssp             EECCC-----------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCC--CGGGHHHHHHHHTTTTCSSCCCSSCE
T ss_pred             EEeHHHHHh--hhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCcc--ccHHHHHHHHHHHHHhCcccCCCCEE
Confidence            777776652  34455555678888888888899999999999976543211  1223345555544443     46789


Q ss_pred             EEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcc
Q 005179          426 CIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD  504 (710)
Q Consensus       426 vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~  504 (710)
                      ||++||.+.     .+++++.|||+ .+.++.|+.+++..||+.++.    ..+..+++..++.++..+.+|.+     .
T Consensus       274 vI~atn~~~-----~ld~al~rRf~~~i~i~~P~~~~r~~il~~~l~----~~~~~l~~~~l~~la~~t~G~sg-----a  339 (444)
T 2zan_A          274 VLGATNIPW-----VLDSAIRRRFEKRIYIPLPEAHARAAMFRLHLG----STQNSLTEADFQELGRKTDGYSG-----A  339 (444)
T ss_dssp             EEEEESCGG-----GSCHHHHTTCCEEEECCCCCHHHHHHHHHHHHT----TSCEECCHHHHHHHHHHTTTCCH-----H
T ss_pred             EEecCCCcc-----ccCHHHHhhcceEEEeCCcCHHHHHHHHHHHHh----cCCCCCCHHHHHHHHHHcCCCCH-----H
Confidence            999999875     78999999997 899999999999999987765    33556789999999999887744     4


Q ss_pred             hHHHHHHHHHh
Q 005179          505 KAIDLVDEAGS  515 (710)
Q Consensus       505 ~ai~ll~~a~~  515 (710)
                      +...+++.|+.
T Consensus       340 dl~~l~~~a~~  350 (444)
T 2zan_A          340 DISIIVRDALM  350 (444)
T ss_dssp             HHHHHHHHHHT
T ss_pred             HHHHHHHHHHH
Confidence            55566666653

>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=99.76  E-value=9.9e-18  Score=176.24  Aligned_cols=203  Identities=18%  Similarity=0.261  Sum_probs=141.2

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc-------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          287 ELIDPVIGRETEIQRIIQILCR-------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~-------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      -+|++++|.++.++.+.+.+..             ..+.+++|+||||||||++|++++..+          +..++.++
T Consensus        12 ~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~----------~~~~i~v~   81 (301)
T 3cf0_A           12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC----------QANFISIK   81 (301)
T ss_dssp             CCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHT----------TCEEEEEC
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHh----------CCCEEEEE
Confidence            4567899999988888776542             345679999999999999999999987          67788888


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC-CCCChHhHHHhhcccc----cCCCeEEEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG-NKGTGLDISNLLKPSL----GRGELQCIA  428 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~-~~~~~~~~~~~L~~~l----~~~~v~vI~  428 (710)
                      +..+..  .+.|+.+..+..+|..+....++||||||+|.+........+ ..+....+.+.|...+    ...++++|+
T Consensus        82 ~~~l~~--~~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~~~~v~vi~  159 (301)
T 3cf0_A           82 GPELLT--MWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIG  159 (301)
T ss_dssp             HHHHHH--HHHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCTTSSEEEEE
T ss_pred             hHHHHh--hhcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccCCCCEEEEE
Confidence            877753  234444566788888888888999999999999754221100 0011222333333333    346799999


Q ss_pred             ccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcch
Q 005179          429 STTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      +||.++     .+++++.+  ||. .|.++.|+.++|.+||+.++.....  ...++   ++.++..+.+|.     +.+
T Consensus       160 atn~~~-----~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~--~~~~~---~~~la~~~~g~s-----g~d  224 (301)
T 3cf0_A          160 ATNRPD-----IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPV--AKDVD---LEFLAKMTNGFS-----GAD  224 (301)
T ss_dssp             EESCGG-----GSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCB--CSSCC---HHHHHHTCSSCC-----HHH
T ss_pred             ecCCcc-----ccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCC--Cccch---HHHHHHHcCCCC-----HHH
Confidence            999876     68899998  997 8999999999999999877654311  11222   345555554442     345


Q ss_pred             HHHHHHHHHhh
Q 005179          506 AIDLVDEAGSR  516 (710)
Q Consensus       506 ai~ll~~a~~~  516 (710)
                      ...+++.|+..
T Consensus       225 l~~l~~~a~~~  235 (301)
T 3cf0_A          225 LTEICQRACKL  235 (301)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            56667766643

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.76  E-value=1.6e-17  Score=174.98  Aligned_cols=209  Identities=18%  Similarity=0.215  Sum_probs=154.6

Q ss_pred             CcccCHHHHHHHHHHHH---------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          291 PVIGRETEIQRIIQILC---------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~---------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +++|+++.++.+.+.+.               .....++||+||||||||++|+++++.+....   ......++.++..
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~---~~~~~~~~~~~~~  108 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLVERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLG---YVRKGHLVSVTRD  108 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTT---SSSSCCEEEECGG
T ss_pred             HccChHHHHHHHHHHHHHHHhHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcC---CcCCCcEEEEcHH
Confidence            59999998888876643               23445799999999999999999999985532   1224467888877


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChH
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQD  433 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~  433 (710)
                      .+.  ..+.|.....+..++..+   .+.||||||+|.+......    .....++++.|...++.  .++++|++++..
T Consensus       109 ~l~--~~~~g~~~~~~~~~~~~~---~~~vl~iDEid~l~~~~~~----~~~~~~~~~~Ll~~l~~~~~~~~~i~~~~~~  179 (309)
T 3syl_A          109 DLV--GQYIGHTAPKTKEVLKRA---MGGVLFIDEAYYLYRPDNE----RDYGQEAIEILLQVMENNRDDLVVILAGYAD  179 (309)
T ss_dssp             GTC--CSSTTCHHHHHHHHHHHH---TTSEEEEETGGGSCCCC-------CCTHHHHHHHHHHHHHCTTTCEEEEEECHH
T ss_pred             Hhh--hhcccccHHHHHHHHHhc---CCCEEEEEChhhhccCCCc----ccccHHHHHHHHHHHhcCCCCEEEEEeCChH
Confidence            775  345666777777777655   3679999999999754321    12355677777777764  478999999988


Q ss_pred             HHHhhhhccHHHHccc-cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCC--cchHHHHH
Q 005179          434 EHRTQFEKDKALARRF-QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYL--PDKAIDLV  510 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf-~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~--p~~ai~ll  510 (710)
                      .+..++.++|+|.+|| ..|.|++|+.+++..|++.++..    .++.+++++++.++.+..+.......  ...+..++
T Consensus       180 ~~~~~~~~~~~l~~R~~~~i~~~~~~~~~~~~il~~~l~~----~~~~~~~~~~~~l~~~~~~~~~~~~~gn~r~l~~~l  255 (309)
T 3syl_A          180 RMENFFQSNPGFRSRIAHHIEFPDYSDEELFEIAGHMLDD----QNYQMTPEAETALRAYIGLRRNQPHFANARSIRNAL  255 (309)
T ss_dssp             HHHHHHHHSTTHHHHEEEEEEECCCCHHHHHHHHHHHHHH----TTCEECHHHHHHHHHHHHHHTTSSSCCHHHHHHHHH
T ss_pred             HHHHHHhhCHHHHHhCCeEEEcCCcCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence            7777777899999999 59999999999999999988774    46889999999998887654332221  23455566


Q ss_pred             HHHHh
Q 005179          511 DEAGS  515 (710)
Q Consensus       511 ~~a~~  515 (710)
                      +.++.
T Consensus       256 ~~a~~  260 (309)
T 3syl_A          256 DRARL  260 (309)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            66654

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.76  E-value=3.5e-18  Score=188.70  Aligned_cols=200  Identities=24%  Similarity=0.308  Sum_probs=152.4

Q ss_pred             hhhHHhhhhcCCCCcccCHHHH---HHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          278 VDLTARASEELIDPVIGRETEI---QRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i---~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .+|.+++|+.+|++++|+++.+   ..+...+......++||+||||||||++|+.|++.+          +..++.++.
T Consensus        14 ~pla~r~rP~~l~~ivGq~~~~~~~~~L~~~i~~~~~~~vLL~GppGtGKTtlAr~ia~~~----------~~~f~~l~a   83 (447)
T 3pvs_A           14 QPLAARMRPENLAQYIGQQHLLAAGKPLPRAIEAGHLHSMILWGPPGTGKTTLAEVIARYA----------NADVERISA   83 (447)
T ss_dssp             CCHHHHTCCCSTTTCCSCHHHHSTTSHHHHHHHHTCCCEEEEECSTTSSHHHHHHHHHHHT----------TCEEEEEET
T ss_pred             CChHHHhCCCCHHHhCCcHHHHhchHHHHHHHHcCCCcEEEEECCCCCcHHHHHHHHHHHh----------CCCeEEEEe
Confidence            4788899999999999999998   778888888777889999999999999999999988          556666653


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~at  430 (710)
                      ...  +   ..+    ++.++..+.    ...+.||||||+|.+             ....++.|++.++++.+++|++|
T Consensus        84 ~~~--~---~~~----ir~~~~~a~~~~~~~~~~iLfIDEI~~l-------------~~~~q~~LL~~le~~~v~lI~at  141 (447)
T 3pvs_A           84 VTS--G---VKE----IREAIERARQNRNAGRRTILFVDEVHRF-------------NKSQQDAFLPHIEDGTITFIGAT  141 (447)
T ss_dssp             TTC--C---HHH----HHHHHHHHHHHHHTTCCEEEEEETTTCC-------------------CCHHHHHTTSCEEEEEE
T ss_pred             ccC--C---HHH----HHHHHHHHHHhhhcCCCcEEEEeChhhh-------------CHHHHHHHHHHHhcCceEEEecC
Confidence            221  1   112    333443332    346789999999999             22346778888899999999998


Q ss_pred             ChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhh---cCCCCCHHHHHHHHHHhhhhhcCCCCcchHH
Q 005179          431 TQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAH---HNCKFTLEAINAAVHLSARYISDRYLPDKAI  507 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~---~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai  507 (710)
                      +.+.   .+.++++|.+||..+.+.+|+.+++..+++..+..+...   .++.+++++++.++..+.+.      ...++
T Consensus       142 t~n~---~~~l~~aL~sR~~v~~l~~l~~edi~~il~~~l~~~~~~~~~~~~~i~~~al~~L~~~~~Gd------~R~ll  212 (447)
T 3pvs_A          142 TENP---SFELNSALLSRARVYLLKSLSTEDIEQVLTQAMEDKTRGYGGQDIVLPDETRRAIAELVNGD------ARRAL  212 (447)
T ss_dssp             SSCG---GGSSCHHHHTTEEEEECCCCCHHHHHHHHHHHHHCTTTSSTTSSEECCHHHHHHHHHHHCSC------HHHHH
T ss_pred             CCCc---ccccCHHHhCceeEEeeCCcCHHHHHHHHHHHHHHHhhhhccccCcCCHHHHHHHHHHCCCC------HHHHH
Confidence            7654   357889999999999999999999999999887754322   45779999999999886543      35677


Q ss_pred             HHHHHHHhhhh
Q 005179          508 DLVDEAGSRAH  518 (710)
Q Consensus       508 ~ll~~a~~~~~  518 (710)
                      .+++.++..+.
T Consensus       213 n~Le~a~~~a~  223 (447)
T 3pvs_A          213 NTLEMMADMAE  223 (447)
T ss_dssp             HHHHHHHHHSC
T ss_pred             HHHHHHHHhcc
Confidence            78887775543

>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=99.74  E-value=9.1e-19  Score=203.63  Aligned_cols=201  Identities=18%  Similarity=0.270  Sum_probs=132.4

Q ss_pred             CCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +++++.|.++..+.|.+.+.             ...+.++|||||||||||++|+++|.++          +..++.++.
T Consensus       475 ~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~----------~~~f~~v~~  544 (806)
T 3cf2_A          475 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC----------QANFISIKG  544 (806)
T ss_dssp             CSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTT----------TCEEEECCH
T ss_pred             CHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHh----------CCceEEecc
Confidence            56788898888887776542             1345679999999999999999999998          888999999


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC-CCChHhHHHhhccccc----CCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSLG----RGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l~----~~~v~vI~a  429 (710)
                      +.++  .++.|+.+..++.+|+.++...|+||||||+|.++..+..+.++ .+....+.+.|+..|.    ...+.||++
T Consensus       545 ~~l~--s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~~~~V~vi~a  622 (806)
T 3cf2_A          545 PELL--TMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGA  622 (806)
T ss_dssp             HHHH--TTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCSSSSEEEECC
T ss_pred             chhh--ccccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCCCCCEEEEEe
Confidence            9988  67889999999999999999999999999999998764322111 1112234444444333    467899999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCC-HHHHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFT-LEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~-~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ||.++     .+|+++.|  ||+ .|+|+.|+.++|.+||+.++++.      .+. +-.++.+++.+.+|.+     .+
T Consensus       623 TN~p~-----~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~------~~~~~~dl~~la~~t~g~SG-----ad  686 (806)
T 3cf2_A          623 TNRPD-----IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKS------PVAKDVDLEFLAKMTNGFSG-----AD  686 (806)
T ss_dssp             -CCSS-----SSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--------CCC---------------------C
T ss_pred             CCCch-----hCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCC------CCCCCCCHHHHHHhCCCCCH-----HH
Confidence            99986     79999999  998 89999999999999998765432      222 2236778888887754     44


Q ss_pred             HHHHHHHHHhh
Q 005179          506 AIDLVDEAGSR  516 (710)
Q Consensus       506 ai~ll~~a~~~  516 (710)
                      ...++.+|+..
T Consensus       687 i~~l~~~A~~~  697 (806)
T 3cf2_A          687 LTEICQRACKL  697 (806)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            56677776643

>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=99.74  E-value=4.5e-17  Score=167.25  Aligned_cols=204  Identities=20%  Similarity=0.250  Sum_probs=136.6

Q ss_pred             CCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          288 LIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      .|++++|.++.++.+.+++..            ..++++||+||||||||++|+++++.+          +.+++.+++.
T Consensus         4 ~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~----------~~~~~~~~~~   73 (262)
T 2qz4_A            4 SFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEA----------QVPFLAMAGA   73 (262)
T ss_dssp             CTTSSCSCHHHHHHHHHHHHHHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHH----------TCCEEEEETT
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEechH
Confidence            578999999888777665421            345679999999999999999999988          6678888887


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC---CCCChHhHHHhhcc---cccCCCeEEEEc
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG---NKGTGLDISNLLKP---SLGRGELQCIAS  429 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~---~~~~~~~~~~~L~~---~l~~~~v~vI~a  429 (710)
                      .+.  ..+.+.....+..++..+....+.||||||+|.+.........   +......+..+|..   .-....+++|++
T Consensus        74 ~~~--~~~~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~~~~~vi~~  151 (262)
T 2qz4_A           74 EFV--EVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGTTDHVIVLAS  151 (262)
T ss_dssp             TTS--SSSTTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCTTCCEEEEEE
T ss_pred             HHH--hhccChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCCCCCEEEEec
Confidence            765  3456667777888998888778899999999999654321000   00111112222221   112357889999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ||..+     .+++++.+  ||. .+.++.|+.+++.+|++.++...    ++....+. ...++..+.+|     .+.+
T Consensus       152 tn~~~-----~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~----~~~~~~~~~~~~l~~~~~g~-----~~~~  217 (262)
T 2qz4_A          152 TNRAD-----ILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSL----KLTQSSTFYSQRLAELTPGF-----SGAD  217 (262)
T ss_dssp             ESCGG-----GGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHT----TCCBTHHHHHHHHHHTCTTC-----CHHH
T ss_pred             CCChh-----hcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhC----CCCcchhhHHHHHHHHCCCC-----CHHH
Confidence            98875     67899999  996 89999999999999999887643    45555553 45566555444     2345


Q ss_pred             HHHHHHHHHhhh
Q 005179          506 AIDLVDEAGSRA  517 (710)
Q Consensus       506 ai~ll~~a~~~~  517 (710)
                      ...+++.|+..+
T Consensus       218 l~~l~~~a~~~a  229 (262)
T 2qz4_A          218 IANICNEAALHA  229 (262)
T ss_dssp             HHHHHHHHHTC-
T ss_pred             HHHHHHHHHHHH
Confidence            566777766443

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.74  E-value=2.6e-17  Score=168.94  Aligned_cols=204  Identities=19%  Similarity=0.277  Sum_probs=137.0

Q ss_pred             hhhcCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEE
Q 005179          284 ASEELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMS  351 (710)
Q Consensus       284 ~~~~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~  351 (710)
                      ..+..|++++|.++.++.+.+++..            ..+.+++|+||||||||+++++++..+          +.+++.
T Consensus         6 ~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~----------~~~~~~   75 (257)
T 1lv7_A            6 QIKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA----------KVPFFT   75 (257)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH----------TCCEEE
T ss_pred             CCCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHc----------CCCEEE
Confidence            3455788999999888776654321            235679999999999999999999987          456677


Q ss_pred             eehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC-CCChHhHHHhhcccc----cCCCeEE
Q 005179          352 LDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSL----GRGELQC  426 (710)
Q Consensus       352 ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l----~~~~v~v  426 (710)
                      +++..+.  ..+.|..+..+..+++.+....++++||||+|.+........+. ........+.+...+    ....+++
T Consensus        76 i~~~~~~--~~~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~v  153 (257)
T 1lv7_A           76 ISGSDFV--EMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIV  153 (257)
T ss_dssp             ECSCSST--TSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEE
T ss_pred             EeHHHHH--HHhhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCcccCCCEEE
Confidence            7766654  23445566778888988887778999999999997643321110 011112233332222    3567899


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCC
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYL  502 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~  502 (710)
                      |++|+.++     .+++++.+  ||. .+.++.|+.++|.+|++.+..+      ..+.+++ +..++..+.+|     .
T Consensus       154 I~~tn~~~-----~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~------~~l~~~~~~~~la~~~~G~-----~  217 (257)
T 1lv7_A          154 IAATNRPD-----VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRR------VPLAPDIDAAIIARGTPGF-----S  217 (257)
T ss_dssp             EEEESCTT-----TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTT------SCBCTTCCHHHHHHTCTTC-----C
T ss_pred             EEeeCCch-----hCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhc------CCCCccccHHHHHHHcCCC-----C
Confidence            99999875     68899988  997 7999999999999999876543      2333332 34444443332     3


Q ss_pred             cchHHHHHHHHHh
Q 005179          503 PDKAIDLVDEAGS  515 (710)
Q Consensus       503 p~~ai~ll~~a~~  515 (710)
                      +.+...++..|..
T Consensus       218 ~~dl~~l~~~a~~  230 (257)
T 1lv7_A          218 GADLANLVNEAAL  230 (257)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            3455566666653

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.73  E-value=1.2e-16  Score=170.68  Aligned_cols=192  Identities=21%  Similarity=0.284  Sum_probs=137.6

Q ss_pred             hhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          276 FCVDLTARASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       276 ~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      -..+|.+++++..|++++|++..++.+...+..     ....++||+||||||||++|+++++.+          +..++
T Consensus        15 ~~~~~~~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~ia~~~----------~~~~~   84 (338)
T 3pfi_A           15 FDETYETSLRPSNFDGYIGQESIKKNLNVFIAAAKKRNECLDHILFSGPAGLGKTTLANIISYEM----------SANIK   84 (338)
T ss_dssp             --------CCCCSGGGCCSCHHHHHHHHHHHHHHHHTTSCCCCEEEECSTTSSHHHHHHHHHHHT----------TCCEE
T ss_pred             hhhhhhhccCCCCHHHhCChHHHHHHHHHHHHHHHhcCCCCCeEEEECcCCCCHHHHHHHHHHHh----------CCCeE
Confidence            334677888999999999999999988887754     345689999999999999999999887          56677


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------  422 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------  422 (710)
                      .+++..+.    ..+.    +...+..  ...+.+|||||+|.+             ..+.++.|...++++        
T Consensus        85 ~~~~~~~~----~~~~----~~~~~~~--~~~~~vl~lDEi~~l-------------~~~~~~~Ll~~l~~~~~~~~~~~  141 (338)
T 3pfi_A           85 TTAAPMIE----KSGD----LAAILTN--LSEGDILFIDEIHRL-------------SPAIEEVLYPAMEDYRLDIIIGS  141 (338)
T ss_dssp             EEEGGGCC----SHHH----HHHHHHT--CCTTCEEEEETGGGC-------------CHHHHHHHHHHHHTSCC------
T ss_pred             Eecchhcc----chhH----HHHHHHh--ccCCCEEEEechhhc-------------CHHHHHHHHHHHHhccchhhccc
Confidence            77665432    1112    2233322  245789999999998             344556665555543        


Q ss_pred             ------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHH
Q 005179          423 ------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAA  489 (710)
Q Consensus       423 ------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l  489 (710)
                                  .+++|++|+...     .++++|.+||. .+.+++|+.+++..+++.....    .++.+++++++.+
T Consensus       142 ~~~~~~~~~~~~~~~~i~atn~~~-----~l~~~L~~R~~~~i~l~~~~~~e~~~il~~~~~~----~~~~~~~~~~~~l  212 (338)
T 3pfi_A          142 GPAAQTIKIDLPKFTLIGATTRAG-----MLSNPLRDRFGMQFRLEFYKDSELALILQKAALK----LNKTCEEKAALEI  212 (338)
T ss_dssp             ---CCCCCCCCCCCEEEEEESCGG-----GSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHH----TTCEECHHHHHHH
T ss_pred             CccccceecCCCCeEEEEeCCCcc-----ccCHHHHhhcCEEeeCCCcCHHHHHHHHHHHHHh----cCCCCCHHHHHHH
Confidence                        278999999865     58899999994 8999999999999999877663    4678999999988


Q ss_pred             HHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          490 VHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       490 ~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      +..+.++      +..+..+++.+..
T Consensus       213 ~~~~~G~------~r~l~~~l~~~~~  232 (338)
T 3pfi_A          213 AKRSRST------PRIALRLLKRVRD  232 (338)
T ss_dssp             HHTTTTC------HHHHHHHHHHHHH
T ss_pred             HHHHCcC------HHHHHHHHHHHHH
Confidence            8765543      4456666666543

>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=99.72  E-value=3.2e-16  Score=185.52  Aligned_cols=181  Identities=16%  Similarity=0.217  Sum_probs=128.6

Q ss_pred             CCcccCHHHHHHHHHHHHcC---------CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc
Q 005179          290 DPVIGRETEIQRIIQILCRR---------TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG  360 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~---------~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g  360 (710)
                      ..++|+++.++.+...+...         ...++||+||||||||++|+++++.+          +..++.++++.+...
T Consensus       458 ~~v~g~~~~~~~l~~~i~~~~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l----------~~~~~~i~~s~~~~~  527 (758)
T 1r6b_X          458 MLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL----------GIELLRFDMSEYMER  527 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH----------TCEEEEEEGGGCSSS
T ss_pred             hhccCHHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHh----------cCCEEEEechhhcch
Confidence            45899999998888776532         12368999999999999999999988          567888888776431


Q ss_pred             c---c----cCccHHH-HHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------
Q 005179          361 A---K----ERGELEA-RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------  422 (710)
Q Consensus       361 ~---~----~~g~~e~-~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------  422 (710)
                      .   .    ..|.... .-..+...+....+.||||||++.+             ..++++.|++.++.+          
T Consensus       528 ~~~~~l~g~~~g~~g~~~~~~l~~~~~~~~~~vl~lDEi~~~-------------~~~~~~~Ll~~le~~~~~~~~g~~~  594 (758)
T 1r6b_X          528 HTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKA-------------HPDVFNILLQVMDNGTLTDNNGRKA  594 (758)
T ss_dssp             SCCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGS-------------CHHHHHHHHHHHHHSEEEETTTEEE
T ss_pred             hhHhhhcCCCCCCcCccccchHHHHHHhCCCcEEEEeCcccc-------------CHHHHHHHHHHhcCcEEEcCCCCEE
Confidence            0   0    0111111 1112334455566889999999988             567888888888754          


Q ss_pred             ---CeEEEEccChHH---------HH---------h--hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhh--
Q 005179          423 ---ELQCIASTTQDE---------HR---------T--QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAH--  476 (710)
Q Consensus       423 ---~v~vI~att~~~---------~~---------~--~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~--  476 (710)
                         ++++|+|+|...         |.         .  .-.++|.|.+||+ .|.|++|+.+++..|++.++.++...  
T Consensus       595 ~~~~~~iI~tsN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~R~~~~i~~~~l~~~~~~~i~~~~l~~~~~~~~  674 (758)
T 1r6b_X          595 DFRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQLD  674 (758)
T ss_dssp             ECTTEEEEEEECSSCC-----------------CHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             ecCCeEEEEecCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHhhCCcceeeCCCCHHHHHHHHHHHHHHHHHHHH
Confidence               356888888621         00         0  0146799999995 89999999999999999887755321  


Q ss_pred             ---cCCCCCHHHHHHHHHHh
Q 005179          477 ---HNCKFTLEAINAAVHLS  493 (710)
Q Consensus       477 ---~~~~i~~~~l~~l~~ls  493 (710)
                         ..+.+++++++.++..+
T Consensus       675 ~~~~~~~~~~~a~~~l~~~~  694 (758)
T 1r6b_X          675 QKGVSLEVSQEARNWLAEKG  694 (758)
T ss_dssp             HTTEEEEECHHHHHHHHHHH
T ss_pred             HCCcEEEeCHHHHHHHHHhC
Confidence               13578999999888653

>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=99.72  E-value=8.1e-17  Score=178.05  Aligned_cols=201  Identities=21%  Similarity=0.284  Sum_probs=141.4

Q ss_pred             CCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          288 LIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +|++++|.++.++.+.+++..            ..+.+++|+||||||||+++++++..+          +.+++.++++
T Consensus        14 ~f~di~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~----------~~~f~~is~~   83 (476)
T 2ce7_A           14 TFKDVGGAEEAIEELKEVVEFLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEA----------NVPFFHISGS   83 (476)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHH----------TCCEEEEEGG
T ss_pred             CHHHhCCcHHHHHHHHHHHHHhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHc----------CCCeeeCCHH
Confidence            577899999887777665432            234679999999999999999999987          6678888887


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC-CCCChHhHHHhhcccc----cCCCeEEEEcc
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG-NKGTGLDISNLLKPSL----GRGELQCIAST  430 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~-~~~~~~~~~~~L~~~l----~~~~v~vI~at  430 (710)
                      .+.  ..+.|....+++.+|..+....|+||||||+|.+......+.+ .........+.|...+    ....+++|++|
T Consensus        84 ~~~--~~~~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~~~~viVIaaT  161 (476)
T 2ce7_A           84 DFV--ELFVGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDSKEGIIVMAAT  161 (476)
T ss_dssp             GTT--TCCTTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCGGGTEEEEEEE
T ss_pred             HHH--HHHhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCCCCCEEEEEec
Confidence            776  3456667788899999998888999999999999654322111 0011122334443333    24578999999


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCCcchH
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      |.++     .+|+++.+  ||+ .|.|+.|+.++|.+|++.+.++.      .+.+++ +..++..+.+|.+     .+.
T Consensus       162 n~~~-----~Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~------~l~~~v~l~~la~~t~G~sg-----adL  225 (476)
T 2ce7_A          162 NRPD-----ILDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNK------PLAEDVNLEIIAKRTPGFVG-----ADL  225 (476)
T ss_dssp             SCGG-----GSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTS------CBCTTCCHHHHHHTCTTCCH-----HHH
T ss_pred             CChh-----hhchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhC------CCcchhhHHHHHHhcCCCcH-----HHH
Confidence            9876     68899988  998 89999999999999998665532      233322 5566666655542     455


Q ss_pred             HHHHHHHHhh
Q 005179          507 IDLVDEAGSR  516 (710)
Q Consensus       507 i~ll~~a~~~  516 (710)
                      ..++++|+..
T Consensus       226 ~~lv~~Aal~  235 (476)
T 2ce7_A          226 ENLVNEAALL  235 (476)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            6677776543

>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=99.69  E-value=1.4e-16  Score=169.27  Aligned_cols=195  Identities=15%  Similarity=0.159  Sum_probs=148.6

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCc-EEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNP-ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nv-LL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      ..|.++++|.+|++++|+++.++.+...+......++ |++||||||||++++++++.+          +..++.++.+.
T Consensus        14 ~~~~~k~rP~~~~~ivg~~~~~~~l~~~l~~~~~~~~~L~~G~~G~GKT~la~~la~~l----------~~~~~~i~~~~   83 (324)
T 3u61_B           14 HILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDV----------NADMMFVNGSD   83 (324)
T ss_dssp             SSHHHHSCCCSTTTSCCCHHHHHHHHHHHHTTCCCSEEEECSSTTSSHHHHHHHHHHHT----------TEEEEEEETTT
T ss_pred             chHHHhhCCCCHHHHhCcHHHHHHHHHHHHcCCCCeEEEeeCcCCCCHHHHHHHHHHHh----------CCCEEEEcccc
Confidence            3688889999999999999999999999887666565 556779999999999999988          67788877543


Q ss_pred             hhhccccCccHHHHHHHHHHHHHhc-----CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEc
Q 005179          357 LMAGAKERGELEARVTTLISEIQKS-----GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIAS  429 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~~-----~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~a  429 (710)
                      .       +  ...+...+......     .+.||||||+|.+.+            .+.++.|..+++.  .++++|++
T Consensus        84 ~-------~--~~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~------------~~~~~~L~~~le~~~~~~~iI~~  142 (324)
T 3u61_B           84 C-------K--IDFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL------------AESQRHLRSFMEAYSSNCSIIIT  142 (324)
T ss_dssp             C-------C--HHHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG------------HHHHHHHHHHHHHHGGGCEEEEE
T ss_pred             c-------C--HHHHHHHHHHHHhhcccCCCCeEEEEECCcccCc------------HHHHHHHHHHHHhCCCCcEEEEE
Confidence            1       1  22344444443322     568999999999920            4456777777764  56788888


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHH---hhcCCCCCH-HHHHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYE---AHHNCKFTL-EAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~---~~~~~~i~~-~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      |+...     .+++++.+||..+.+++|+.+++.+|++.+...+.   ...++.+++ ++++.++..+.+.      ...
T Consensus       143 ~n~~~-----~l~~~l~sR~~~i~~~~~~~~e~~~il~~~~~~l~~~~~~~~~~~~~~~~~~~l~~~~~gd------~R~  211 (324)
T 3u61_B          143 ANNID-----GIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPD------FRK  211 (324)
T ss_dssp             ESSGG-----GSCTTHHHHSEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHTCCBSCHHHHHHHHHHTCSC------TTH
T ss_pred             eCCcc-----ccCHHHHhhCcEEEeCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHhCCCC------HHH
Confidence            88865     68899999999999999999999888777655433   356788988 9999998886654      345


Q ss_pred             HHHHHHHHH
Q 005179          506 AIDLVDEAG  514 (710)
Q Consensus       506 ai~ll~~a~  514 (710)
                      ++..++.++
T Consensus       212 a~~~L~~~~  220 (324)
T 3u61_B          212 TIGELDSYS  220 (324)
T ss_dssp             HHHHHHHHG
T ss_pred             HHHHHHHHh
Confidence            777777765

>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=99.68  E-value=2.3e-15  Score=149.56  Aligned_cols=195  Identities=22%  Similarity=0.266  Sum_probs=139.9

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      +|.+.+++..+++++|+++.++.+.+.+......+++|+||+|||||++++.+++.+....     ....++.++.....
T Consensus         6 ~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~-----~~~~~~~~~~~~~~   80 (226)
T 2chg_A            6 IWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-----WRDNFIEMNASDER   80 (226)
T ss_dssp             CHHHHTSCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-----GGGGEEEEETTCTT
T ss_pred             hHHHhcCCCCHHHHcCcHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHhccc-----cccceEEecccccc
Confidence            4666778889999999999999999999887777899999999999999999999874321     12334444432211


Q ss_pred             hccccCccHHHHHHHHHHHHH------hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEEcc
Q 005179          359 AGAKERGELEARVTTLISEIQ------KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIAST  430 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~------~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~at  430 (710)
                            + . ..+...+....      ...+.+|||||+|.+.             .+..+.|..+++  ...+.+|+++
T Consensus        81 ------~-~-~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~-------------~~~~~~l~~~l~~~~~~~~~i~~~  139 (226)
T 2chg_A           81 ------G-I-DVVRHKIKEFARTAPIGGAPFKIIFLDEADALT-------------ADAQAALRRTMEMYSKSCRFILSC  139 (226)
T ss_dssp             ------C-H-HHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSC-------------HHHHHHHHHHHHHTTTTEEEEEEE
T ss_pred             ------C-h-HHHHHHHHHHhcccCCCccCceEEEEeChhhcC-------------HHHHHHHHHHHHhcCCCCeEEEEe
Confidence                  1 1 11222222222      2457899999999982             233455555554  3467778777


Q ss_pred             ChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHH
Q 005179          431 TQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLV  510 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll  510 (710)
                      +...     .+++.+.+||..+.+++|+.++...+++..+..    .++.+++++++.++..+.+.      +..++.++
T Consensus       140 ~~~~-----~~~~~l~~r~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~~~~l~~~~~g~------~r~l~~~l  204 (226)
T 2chg_A          140 NYVS-----RIIEPIQSRCAVFRFKPVPKEAMKKRLLEICEK----EGVKITEDGLEALIYISGGD------FRKAINAL  204 (226)
T ss_dssp             SCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHH----HTCCBCHHHHHHHHHHHTTC------HHHHHHHH
T ss_pred             CChh-----hcCHHHHHhCceeecCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC------HHHHHHHH
Confidence            7654     578999999999999999999999998877653    36789999999888776542      45566666


Q ss_pred             HHHH
Q 005179          511 DEAG  514 (710)
Q Consensus       511 ~~a~  514 (710)
                      +.++
T Consensus       205 ~~~~  208 (226)
T 2chg_A          205 QGAA  208 (226)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            6655

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.67  E-value=1.1e-15  Score=165.04  Aligned_cols=205  Identities=20%  Similarity=0.280  Sum_probs=133.8

Q ss_pred             hhHHhhhhcC-CCCcccCHHHHHHH---HHHHHcCCC--CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          279 DLTARASEEL-IDPVIGRETEIQRI---IQILCRRTK--NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       279 ~l~~~~~~~~-l~~liGr~~~i~~l---~~~L~~~~~--~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      .+.+.+++.. |++++|++..++.+   ...+.....  .++||+||||||||++|+++++.+.. ..|       ++.+
T Consensus        32 ~l~~~~~p~~~~~~ivG~~~~~~~l~~l~~~~~~~~~~~~~vLl~GppGtGKT~la~~la~~l~~-~~~-------~~~~  103 (368)
T 3uk6_A           32 GLDDALEPRQASQGMVGQLAARRAAGVVLEMIREGKIAGRAVLIAGQPGTGKTAIAMGMAQALGP-DTP-------FTAI  103 (368)
T ss_dssp             CBCTTSCBCSEETTEESCHHHHHHHHHHHHHHHTTCCTTCEEEEEESTTSSHHHHHHHHHHHHCS-SCC-------EEEE
T ss_pred             CcccccCcCcchhhccChHHHHHHHHHHHHHHHcCCCCCCEEEEECCCCCCHHHHHHHHHHHhcc-cCC-------cccc
Confidence            3445667777 89999999887664   444444333  58999999999999999999999832 122       2222


Q ss_pred             ehhhhhh-----------------------------------------------ccccCccHHHHHHHHHHHHHh----c
Q 005179          353 DMGLLMA-----------------------------------------------GAKERGELEARVTTLISEIQK----S  381 (710)
Q Consensus       353 d~~~l~~-----------------------------------------------g~~~~g~~e~~l~~~~~~~~~----~  381 (710)
                      ++..+..                                               -....|++...++..+..+..    .
T Consensus       104 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~  183 (368)
T 3uk6_A          104 AGSEIFSLEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREE  183 (368)
T ss_dssp             EGGGGSCSSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHH
T ss_pred             cchhhhhcccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhh
Confidence            2111000                                               001122333344444443321    1


Q ss_pred             C-----CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEcc---------ChHHHHhhhhccHHH
Q 005179          382 G-----DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIAST---------TQDEHRTQFEKDKAL  445 (710)
Q Consensus       382 ~-----~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~at---------t~~~~~~~~~~d~aL  445 (710)
                      +     +.||||||+|.+             ..+.++.|...++..  .++++++.         +...   ...++++|
T Consensus       184 g~~~~~~~vl~IDEi~~l-------------~~~~~~~L~~~le~~~~~~~ii~t~~~~~~i~~t~~~~---~~~l~~~l  247 (368)
T 3uk6_A          184 GKAEIIPGVLFIDEVHML-------------DIESFSFLNRALESDMAPVLIMATNRGITRIRGTSYQS---PHGIPIDL  247 (368)
T ss_dssp             TC---CBCEEEEESGGGS-------------BHHHHHHHHHHTTCTTCCEEEEEESCSEEECBTSSCEE---ETTCCHHH
T ss_pred             ccccccCceEEEhhcccc-------------ChHHHHHHHHHhhCcCCCeeeeecccceeeeeccCCCC---cccCCHHH
Confidence            2     469999999999             445667777666643  23333332         2111   23678999


Q ss_pred             HccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhh
Q 005179          446 ARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       446 ~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                      .+||..+.+++|+.+++..|++..+..    .++.+++++++.++.++.+     ..+..++.+++.++..
T Consensus       248 ~sR~~~i~~~~~~~~e~~~il~~~~~~----~~~~~~~~~l~~l~~~~~~-----G~~r~~~~ll~~a~~~  309 (368)
T 3uk6_A          248 LDRLLIVSTTPYSEKDTKQILRIRCEE----EDVEMSEDAYTVLTRIGLE-----TSLRYAIQLITAASLV  309 (368)
T ss_dssp             HTTEEEEEECCCCHHHHHHHHHHHHHH----TTCCBCHHHHHHHHHHHHH-----SCHHHHHHHHHHHHHH
T ss_pred             HhhccEEEecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHhcC-----CCHHHHHHHHHHHHHH
Confidence            999999999999999999999987663    4688999999999998874     2356788888887644

>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=99.67  E-value=1.4e-15  Score=161.19  Aligned_cols=184  Identities=21%  Similarity=0.194  Sum_probs=131.4

Q ss_pred             HhhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          282 ARASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       282 ~~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      +++++..|++++|++..++.+...+..     ....+++|+||||||||++|+++++.+          +..++.+++..
T Consensus         4 ~~~~p~~~~~~ig~~~~~~~l~~~l~~~~~~~~~~~~vll~G~~GtGKT~la~~i~~~~----------~~~~~~~~~~~   73 (324)
T 1hqc_A            4 LALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL----------GVNLRVTSGPA   73 (324)
T ss_dssp             -CCCCCSTTTCCSCHHHHHHHHHHHHHHHHHCSCCCCCEEECCTTCCCHHHHHHHHHHH----------TCCEEEECTTT
T ss_pred             cccCcccHHHhhCHHHHHHHHHHHHHHHHccCCCCCcEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEeccc
Confidence            456788899999999998888877653     345789999999999999999999987          45566665543


Q ss_pred             hhhccccCccHHHHHHHHHHHHHh--cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-------------
Q 005179          357 LMAGAKERGELEARVTTLISEIQK--SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-------------  421 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~--~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-------------  421 (710)
                      +..           ...++..+..  ..+.+|||||+|.+.             ...++.|...++.             
T Consensus        74 ~~~-----------~~~l~~~l~~~~~~~~~l~lDEi~~l~-------------~~~~~~L~~~l~~~~~~~v~~~~~~~  129 (324)
T 1hqc_A           74 IEK-----------PGDLAAILANSLEEGDILFIDEIHRLS-------------RQAEEHLYPAMEDFVMDIVIGQGPAA  129 (324)
T ss_dssp             CCS-----------HHHHHHHHTTTCCTTCEEEETTTTSCC-------------HHHHHHHHHHHHHSEEEECCSSSSSC
T ss_pred             cCC-----------hHHHHHHHHHhccCCCEEEEECCcccc-------------cchHHHHHHHHHhhhhHHhccccccc
Confidence            321           1122222322  457799999999982             2334444443332             


Q ss_pred             -------CCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHh
Q 005179          422 -------GELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       422 -------~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls  493 (710)
                             .++++|++|+...     .++++|.+||. .+.+++|+.+++..+++....    ..++.+++++++.++..+
T Consensus       130 ~~~~~~~~~~~~i~~t~~~~-----~~~~~l~~R~~~~i~l~~~~~~e~~~~l~~~~~----~~~~~~~~~~~~~l~~~~  200 (324)
T 1hqc_A          130 RTIRLELPRFTLIGATTRPG-----LITAPLLSRFGIVEHLEYYTPEELAQGVMRDAR----LLGVRITEEAALEIGRRS  200 (324)
T ss_dssp             CCEEEECCCCEEEEEESCCS-----SCSCSTTTTCSCEEECCCCCHHHHHHHHHHHHH----TTTCCCCHHHHHHHHHHS
T ss_pred             cccccCCCCEEEEEeCCCcc-----cCCHHHHhcccEEEecCCCCHHHHHHHHHHHHH----hcCCCCCHHHHHHHHHHc
Confidence                   2467889888764     56788999995 899999999998888877665    346789999999888775


Q ss_pred             hhhhcCCCCcchHHHHHHHHH
Q 005179          494 ARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       494 ~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      .+      .|..+..+++.+.
T Consensus       201 ~G------~~r~l~~~l~~~~  215 (324)
T 1hqc_A          201 RG------TMRVAKRLFRRVR  215 (324)
T ss_dssp             CS------CHHHHHHHHHHHT
T ss_pred             cC------CHHHHHHHHHHHH
Confidence            43      3455666666554

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.64  E-value=2.7e-15  Score=159.71  Aligned_cols=162  Identities=17%  Similarity=0.301  Sum_probs=114.5

Q ss_pred             HhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          275 QFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       275 ~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .|..++.+++++..++.++|+++.++.+...+..  +.+++|+||||||||++++++++.+          +..++.+++
T Consensus        12 ~~~~~~~~~~~~~~~~~i~g~~~~~~~l~~~l~~--~~~vll~G~pGtGKT~la~~la~~~----------~~~~~~i~~   79 (331)
T 2r44_A           12 LYYRNKIKEVIDEVGKVVVGQKYMINRLLIGICT--GGHILLEGVPGLAKTLSVNTLAKTM----------DLDFHRIQF   79 (331)
T ss_dssp             HHHHHHHHHHHHHHTTTCCSCHHHHHHHHHHHHH--TCCEEEESCCCHHHHHHHHHHHHHT----------TCCEEEEEC
T ss_pred             HHHHHHHHHHHHHhccceeCcHHHHHHHHHHHHc--CCeEEEECCCCCcHHHHHHHHHHHh----------CCCeEEEec
Confidence            3456788888888899999999999988887765  4689999999999999999999987          334444443


Q ss_pred             h------hhhhccc---cCccHHHHHHHHHHHHHhcC---CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-
Q 005179          355 G------LLMAGAK---ERGELEARVTTLISEIQKSG---DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-  421 (710)
Q Consensus       355 ~------~l~~g~~---~~g~~e~~l~~~~~~~~~~~---~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-  421 (710)
                      .      .+.....   ..|.+.         . ..+   ..||||||++.+             ....++.|.+.++. 
T Consensus        80 ~~~~~~~~l~g~~~~~~~~~~~~---------~-~~g~l~~~vl~iDEi~~~-------------~~~~~~~Ll~~l~~~  136 (331)
T 2r44_A           80 TPDLLPSDLIGTMIYNQHKGNFE---------V-KKGPVFSNFILADEVNRS-------------PAKVQSALLECMQEK  136 (331)
T ss_dssp             CTTCCHHHHHEEEEEETTTTEEE---------E-EECTTCSSEEEEETGGGS-------------CHHHHHHHHHHHHHS
T ss_pred             CCCCChhhcCCceeecCCCCceE---------e-ccCcccccEEEEEccccC-------------CHHHHHHHHHHHhcC
Confidence            1      1111000   011110         0 011   269999999998             33455555555543 


Q ss_pred             ------------CCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHH
Q 005179          422 ------------GELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       422 ------------~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                                  ..+++|+++|+.++.....++++|.+||. .+.+++|+.+++.+||+....
T Consensus       137 ~~~~~g~~~~~~~~~~viat~np~~~~~~~~l~~~l~~Rf~~~i~i~~p~~~~~~~il~~~~~  199 (331)
T 2r44_A          137 QVTIGDTTYPLDNPFLVLATQNPVEQEGTYPLPEAQVDRFMMKIHLTYLDKESELEVMRRVSN  199 (331)
T ss_dssp             EEEETTEEEECCSSCEEEEEECTTCCSCCCCCCHHHHTTSSEEEECCCCCHHHHHHHHHHHHC
T ss_pred             ceeeCCEEEECCCCEEEEEecCCCcccCcccCCHHHHhheeEEEEcCCCCHHHHHHHHHhccc
Confidence                        35678888887654343458999999998 699999999999999987653

>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=99.64  E-value=3.4e-15  Score=157.82  Aligned_cols=195  Identities=18%  Similarity=0.257  Sum_probs=145.6

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      +|.++++|..+++++|++..++.+...+......+++|+||+|+|||++++.+++.+.+..     ....++.++.... 
T Consensus        10 ~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-----~~~~~~~~~~~~~-   83 (323)
T 1sxj_B           10 PWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-----YADGVLELNASDD-   83 (323)
T ss_dssp             CHHHHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-----HHHHEEEECTTSC-
T ss_pred             cHHHhcCCCCHHHHHCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-----ccCCEEEecCccc-
Confidence            5677889999999999999999999999887767799999999999999999999874321     0223455543221 


Q ss_pred             hccccCccHHHHHHHHHHHHH-------hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEc
Q 005179          359 AGAKERGELEARVTTLISEIQ-------KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIAS  429 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~-------~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~a  429 (710)
                           .+  ...++.+++.+.       ...+.|+||||+|.+             .....+.|..+++.  ....+|++
T Consensus        84 -----~~--~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l-------------~~~~~~~L~~~le~~~~~~~~il~  143 (323)
T 1sxj_B           84 -----RG--IDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSM-------------TAGAQQALRRTMELYSNSTRFAFA  143 (323)
T ss_dssp             -----CS--HHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGS-------------CHHHHHTTHHHHHHTTTTEEEEEE
T ss_pred             -----cC--hHHHHHHHHHHHhccccCCCCCceEEEEECcccC-------------CHHHHHHHHHHHhccCCCceEEEE
Confidence                 11  223445555444       233789999999998             33456667766664  55777777


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDL  509 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~l  509 (710)
                      |+...     .+.+++.+||..+.+++|+.++...+++..+..    .++.+++++++.++..+.+.      +..++.+
T Consensus       144 ~~~~~-----~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~~----~~~~~~~~~~~~l~~~~~G~------~r~a~~~  208 (323)
T 1sxj_B          144 CNQSN-----KIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKL----EDVKYTNDGLEAIIFTAEGD------MRQAINN  208 (323)
T ss_dssp             ESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHH----HTCCBCHHHHHHHHHHHTTC------HHHHHHH
T ss_pred             eCChh-----hchhHHHhhceEEeecCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHcCCC------HHHHHHH
Confidence            77644     678999999999999999999999999877663    47789999999998887543      4567777


Q ss_pred             HHHHH
Q 005179          510 VDEAG  514 (710)
Q Consensus       510 l~~a~  514 (710)
                      ++.++
T Consensus       209 l~~~~  213 (323)
T 1sxj_B          209 LQSTV  213 (323)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            76654

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=99.64  E-value=1.4e-15  Score=157.30  Aligned_cols=202  Identities=21%  Similarity=0.244  Sum_probs=130.9

Q ss_pred             CCCCcccCHHHHHHHHHHHH-------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQILC-------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~-------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +|+++.|.++..+.+.+.+.             -..+.+++|+||||||||+++++++..+          +...+.++.
T Consensus         8 ~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~----------~~~~i~i~g   77 (274)
T 2x8a_A            8 TWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANES----------GLNFISVKG   77 (274)
T ss_dssp             ----CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHT----------TCEEEEEET
T ss_pred             CHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHc----------CCCEEEEEc
Confidence            56778888777666655321             1234559999999999999999999987          455677776


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~vI~at  430 (710)
                      ..+.  ..+.++.+..+..+++.+....++++|+||++.+........  ........+.+...|+    +..++++++|
T Consensus        78 ~~l~--~~~~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~--~~~~~~~~~~~l~~Lsgg~~~~~~i~ia~t  153 (274)
T 2x8a_A           78 PELL--NMYVGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRE--TGASVRVVNQLLTEMDGLEARQQVFIMAAT  153 (274)
T ss_dssp             TTTC--SSTTHHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC-----------CTTHHHHHHHHHHTCCSTTCEEEEEEE
T ss_pred             HHHH--hhhhhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCc--chHHHHHHHHHHHhhhcccccCCEEEEeec
Confidence            6654  345677788899999988777789999999999864321100  0111223333333333    3457788888


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCC-HHHHHHHHHH--hhhhhcCCCCcc
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFT-LEAINAAVHL--SARYISDRYLPD  504 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~-~~~l~~l~~l--s~~~i~~r~~p~  504 (710)
                      +.++     .+|+++.|  ||+ .|.++.|+.++|.+||+.+....   ....+. +-.++.++..  +.+|     .+.
T Consensus       154 n~p~-----~LD~al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~---~~~~~~~~~~~~~la~~~~~~g~-----sga  220 (274)
T 2x8a_A          154 NRPD-----IIDPAILRPGRLDKTLFVGLPPPADRLAILKTITKNG---TKPPLDADVNLEAIAGDLRCDCY-----TGA  220 (274)
T ss_dssp             SCGG-----GSCHHHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTT---BTTBBCTTCCHHHHHTCSGGGSC-----CHH
T ss_pred             CChh-----hCCHhhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcc---cCCCCccccCHHHHHHhhccCCc-----CHH
Confidence            8876     67999999  998 89999999999999999765421   112222 1124444443  2244     345


Q ss_pred             hHHHHHHHHHhh
Q 005179          505 KAIDLVDEAGSR  516 (710)
Q Consensus       505 ~ai~ll~~a~~~  516 (710)
                      +...++.+|+..
T Consensus       221 dl~~l~~~a~~~  232 (274)
T 2x8a_A          221 DLSALVREASIC  232 (274)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            667777777643

>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=99.64  E-value=2.1e-15  Score=159.21  Aligned_cols=199  Identities=20%  Similarity=0.241  Sum_probs=144.9

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      +|.++++|..|++++|++..++.+...+......+++|+||||||||++++.+++.+....     .+..++.++.+...
T Consensus         6 ~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKt~la~~l~~~l~~~~-----~~~~~~~~~~~~~~   80 (319)
T 2chq_A            6 IWVEKYRPRTLDEVVGQDEVIQRLKGYVERKNIPHLLFSGPPGTGKTATAIALARDLFGEN-----WRDNFIEMNASDER   80 (319)
T ss_dssp             CTTTTTSCSSGGGSCSCHHHHHHHHTTTTTTCCCCEEEESSSSSSHHHHHHHHHHHHHTTC-----HHHHCEEEETTSTT
T ss_pred             cHHHhcCCCCHHHHhCCHHHHHHHHHHHhCCCCCeEEEECcCCcCHHHHHHHHHHHhcCCc-----ccCCeEEEeCcccc
Confidence            6778899999999999999999999888877767899999999999999999999874321     02234555544322


Q ss_pred             hccccCccHHHHHHHHHHHH--HhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHH
Q 005179          359 AGAKERGELEARVTTLISEI--QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDE  434 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~--~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~  434 (710)
                       +   .......+..+....  ....+.|+||||+|.+             ..+.++.|..+++.  ..+.+|++++...
T Consensus        81 -~---~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l-------------~~~~~~~L~~~le~~~~~~~~i~~~~~~~  143 (319)
T 2chq_A           81 -G---IDVVRHKIKEFARTAPIGGAPFKIIFLDEADAL-------------TADAQAALRRTMEMYSKSCRFILSCNYVS  143 (319)
T ss_dssp             -C---TTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGS-------------CHHHHHTTGGGTSSSSSSEEEEEEESCGG
T ss_pred             -C---hHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcC-------------CHHHHHHHHHHHHhcCCCCeEEEEeCChh
Confidence             1   111112222221110  1134789999999999             34567788888875  5678888887754


Q ss_pred             HHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          435 HRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       435 ~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                           .+.+++.+||..+.+.+|+.+++..++...+.    ..++.+++++++.++..+.+.      +..++.+++.++
T Consensus       144 -----~l~~~l~sr~~~i~~~~~~~~~~~~~l~~~~~----~~~~~i~~~~l~~l~~~~~G~------~r~~~~~l~~~~  208 (319)
T 2chq_A          144 -----RIIEPIQSRCAVFRFKPVPKEAMKKRLLEICE----KEGVKITEDGLEALIYISGGD------FRKAINALQGAA  208 (319)
T ss_dssp             -----GSCHHHHTTCEEEECCCCCHHHHHHHHHHHHH----TTCCCBCHHHHHHHHHTTTTC------HHHHHHHHHHHH
T ss_pred             -----hcchHHHhhCeEEEecCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCCC------HHHHHHHHHHHH
Confidence                 67899999999999999999999888887665    457889999999988776543      345666666554

>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=3.7e-15  Score=157.81  Aligned_cols=207  Identities=17%  Similarity=0.244  Sum_probs=148.2

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ..+.....+|.++++|..|++++|+++.++.+...+......+++|+||||+|||++++.+++.+....     ....++
T Consensus         6 ~~~~~~~~~~~~k~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~l~~~l~~~~-----~~~~~~   80 (327)
T 1iqp_A            6 REVKVLEKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-----WRHNFL   80 (327)
T ss_dssp             HHHHHTTSCHHHHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-----HHHHEE
T ss_pred             hhhcccCCchhhccCCCCHHHhhCCHHHHHHHHHHHHcCCCCeEEEECcCCCCHHHHHHHHHHHhcCCc-----ccCceE
Confidence            345556678999999999999999999999999999887777899999999999999999999874321     012345


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHH--HHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEE
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISE--IQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQC  426 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~--~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~v  426 (710)
                      .++.+.....    ..+...+......  ....++.+++|||+|.+             ..+.++.|...++.  ..+.+
T Consensus        81 ~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l-------------~~~~~~~L~~~le~~~~~~~~  143 (327)
T 1iqp_A           81 ELNASDERGI----NVIREKVKEFARTKPIGGASFKIIFLDEADAL-------------TQDAQQALRRTMEMFSSNVRF  143 (327)
T ss_dssp             EEETTCHHHH----HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGS-------------CHHHHHHHHHHHHHTTTTEEE
T ss_pred             EeeccccCch----HHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcC-------------CHHHHHHHHHHHHhcCCCCeE
Confidence            5554322110    0111112222110  01145789999999999             33456666666653  56778


Q ss_pred             EEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          427 IASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      |++++...     .+.+++.+||..+.+++|+.++...+++..+.    ..++.+++++++.++..+.+      .+..+
T Consensus       144 i~~~~~~~-----~l~~~l~sr~~~~~~~~l~~~~~~~~l~~~~~----~~~~~~~~~~~~~l~~~~~g------~~r~~  208 (327)
T 1iqp_A          144 ILSCNYSS-----KIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAE----NEGLELTEEGLQAILYIAEG------DMRRA  208 (327)
T ss_dssp             EEEESCGG-----GSCHHHHHTEEEEECCCCCHHHHHHHHHHHHH----TTTCEECHHHHHHHHHHHTT------CHHHH
T ss_pred             EEEeCCcc-----ccCHHHHhhCcEEEecCCCHHHHHHHHHHHHH----hcCCCCCHHHHHHHHHHCCC------CHHHH
Confidence            88777654     57899999999999999999998888887665    45788999999999887654      24566


Q ss_pred             HHHHHHHH
Q 005179          507 IDLVDEAG  514 (710)
Q Consensus       507 i~ll~~a~  514 (710)
                      +.+++.+.
T Consensus       209 ~~~l~~~~  216 (327)
T 1iqp_A          209 INILQAAA  216 (327)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            77776554

>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=99.63  E-value=2.3e-17  Score=170.30  Aligned_cols=169  Identities=24%  Similarity=0.323  Sum_probs=111.2

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          286 EELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      +..|++++|.++.++.+.+++..            ..+.++||+||||||||++|++++..+          +..++.++
T Consensus         7 ~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~----------~~~~~~v~   76 (268)
T 2r62_A            7 NVRFKDMAGNEEAKEEVVEIVDFLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEA----------HVPFFSMG   76 (268)
T ss_dssp             CCCSTTSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHH----------TCCCCCCC
T ss_pred             CCCHHHhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHh----------CCCEEEec
Confidence            44678899998877777665431            345679999999999999999999987          33444455


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCC--CCCCChHhHHHhhccccc-----CCCeEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGR--GNKGTGLDISNLLKPSLG-----RGELQC  426 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~--~~~~~~~~~~~~L~~~l~-----~~~v~v  426 (710)
                      +..+...  +.|.....+..++..+....+.||||||+|.+......+.  ..........+.|...+.     ...+++
T Consensus        77 ~~~~~~~--~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~v~v  154 (268)
T 2r62_A           77 GSSFIEM--FVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSENAPVIV  154 (268)
T ss_dssp             SCTTTTS--CSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCSCSCCEE
T ss_pred             hHHHHHh--hcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccCCCCEEE
Confidence            4444321  1222122344566666666788999999999965421100  000111122333333332     235889


Q ss_pred             EEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHH
Q 005179          427 IASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLRE  471 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~  471 (710)
                      |++|+..+     .+++++.+  ||. .|.++.|+.+++.+||+.++.
T Consensus       155 i~ttn~~~-----~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~  197 (268)
T 2r62_A          155 LAATNRPE-----ILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIK  197 (268)
T ss_dssp             EECBSCCT-----TSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTS
T ss_pred             EEecCCch-----hcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHh
Confidence            99999875     57889988  896 799999999999999987654

>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=99.63  E-value=2.9e-15  Score=157.49  Aligned_cols=213  Identities=21%  Similarity=0.274  Sum_probs=137.4

Q ss_pred             CcccCHHHHHHHHHHHHc--------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          291 PVIGRETEIQRIIQILCR--------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~--------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      .++|+++.++.+...+..              ..+.+++|+||||||||++|+++++.+          +..++.++++.
T Consensus        16 ~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l----------~~~~~~i~~~~   85 (310)
T 1ofh_A           16 HIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATK   85 (310)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH----------TCCEEEEEGGG
T ss_pred             hcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEcchh
Confidence            489999999988877654              356789999999999999999999988          56778888877


Q ss_pred             hhhccccCc-cHHHHHHHHHHHH----Hh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------
Q 005179          357 LMAGAKERG-ELEARVTTLISEI----QK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------  422 (710)
Q Consensus       357 l~~g~~~~g-~~e~~l~~~~~~~----~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------  422 (710)
                      +... .+.| .....+..++...    .. ..+.||||||+|.+......... ......+++.|.++++.+        
T Consensus        86 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~-~~~~~~~~~~Ll~~le~~~~~~~~~~  163 (310)
T 1ofh_A           86 FTEV-GYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGA-DVSREGVQRDLLPLVEGSTVSTKHGM  163 (310)
T ss_dssp             GSSC-CSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSS-HHHHHHHHHHHHHHHHCCEEEETTEE
T ss_pred             cccC-CccCccHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCcccccccc-chhHHHHHHHHHHHhcCCeEeccccc
Confidence            6531 1211 1122344444321    11 22569999999999654321000 001112356666666543        


Q ss_pred             ----CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHH----HHHHHHHh---hcC--CCCCHHHHHH
Q 005179          423 ----ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILL----GLREKYEA---HHN--CKFTLEAINA  488 (710)
Q Consensus       423 ----~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~----~l~~~~~~---~~~--~~i~~~~l~~  488 (710)
                          .+++|++++.... ....++++|.+||. .|.|++|+.+++..|++    .+..++..   ..+  +.+++++++.
T Consensus       164 ~~~~~~~~i~~~~~~~~-~~~~l~~~l~~R~~~~i~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~  242 (310)
T 1ofh_A          164 VKTDHILFIASGAFQVA-RPSDLIPELQGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKK  242 (310)
T ss_dssp             EECTTCEEEEEECCSSS-CGGGSCHHHHHTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHHTTCEEEECHHHHHH
T ss_pred             ccCCcEEEEEcCCcccC-CcccCCHHHHhhCCceEEcCCcCHHHHHHHHHhhHHHHHHHHHHHHHhcCCeeccCHHHHHH
Confidence                6778887532100 11268899999997 69999999999999998    44443321   123  4789999999


Q ss_pred             HHHHhhhhh--cCCCCcchHHHHHHHHHhh
Q 005179          489 AVHLSARYI--SDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       489 l~~ls~~~i--~~r~~p~~ai~ll~~a~~~  516 (710)
                      ++..+...-  .....+..+..+++.+...
T Consensus       243 l~~~~~~~~~~~~~g~~R~l~~~l~~~~~~  272 (310)
T 1ofh_A          243 IAEAAFRVNEKTENIGARRLHTVMERLMDK  272 (310)
T ss_dssp             HHHHHHHHHHHSCCCTTHHHHHHHHHHSHH
T ss_pred             HHHHhhhhcccccccCcHHHHHHHHHHHHh
Confidence            998874321  1122345667777766543

>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=99.62  E-value=2.7e-15  Score=150.98  Aligned_cols=200  Identities=19%  Similarity=0.180  Sum_probs=139.3

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.+++++..+++++|++.+++.+...+..... ..++|+||+|+|||++++.+++.+.........             
T Consensus        12 ~~~~~~~p~~~~~~~g~~~~~~~l~~~l~~~~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (250)
T 1njg_A           12 VLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQ   91 (250)
T ss_dssp             CHHHHTCCCSGGGCCSCHHHHHHHHHHHHHTCCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHT
T ss_pred             HHhhccCCccHHHHhCcHHHHHHHHHHHHcCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHHHHHHhc
Confidence            456778888999999999999999998877543 358999999999999999999987542211000             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++..        .......+..++..+.    ...+.+|||||+|.+             ..+..+.|...+
T Consensus        92 ~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l-------------~~~~~~~l~~~l  150 (250)
T 1njg_A           92 GRFVDLIEIDAA--------SRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHML-------------SRHSFNALLKTL  150 (250)
T ss_dssp             TCCSSEEEEETT--------CGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGS-------------CHHHHHHHHHHH
T ss_pred             cCCcceEEecCc--------ccccHHHHHHHHHHhhhchhcCCceEEEEECcccc-------------cHHHHHHHHHHH
Confidence             00012222211        0111223445554432    234689999999998             233445555555


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+.+|++|+...     .+++.+.+|+..+.+++|+.++..++++..+..    .++.+++++++.+++.+.+  
T Consensus       151 ~~~~~~~~~i~~t~~~~-----~~~~~l~~r~~~i~l~~l~~~e~~~~l~~~~~~----~~~~~~~~~~~~l~~~~~G--  219 (250)
T 1njg_A          151 EEPPEHVKFLLATTDPQ-----KLPVTILSRCLQFHLKALDVEQIRHQLEHILNE----EHIAHEPRALQLLARAAEG--  219 (250)
T ss_dssp             HSCCTTEEEEEEESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHH----TTCCBCHHHHHHHHHHHTT--
T ss_pred             hcCCCceEEEEEeCChH-----hCCHHHHHHhhhccCCCCCHHHHHHHHHHHHHh----cCCCCCHHHHHHHHHHcCC--
Confidence            43  4677888777654     577899999989999999999999998877653    4678999999999888755  


Q ss_pred             cCCCCcchHHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~  514 (710)
                          .|..+..+++.++
T Consensus       220 ----~~~~~~~~~~~~~  232 (250)
T 1njg_A          220 ----SLRDALSLTDQAI  232 (250)
T ss_dssp             ----CHHHHHHHHHHHH
T ss_pred             ----CHHHHHHHHHHHH
Confidence                3566777777664

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.61  E-value=2.8e-15  Score=156.77  Aligned_cols=161  Identities=16%  Similarity=0.166  Sum_probs=106.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHH----HhcCCeE
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEI----QKSGDVI  385 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~----~~~~~~I  385 (710)
                      .+.++||+||||||||++|+++|+.+          +.+++.++++.+.  ..+.|..+..++.++..+    +...++|
T Consensus        35 ~p~~lLl~GppGtGKT~la~aiA~~l----------~~~~i~v~~~~l~--~~~~g~~~~~i~~~f~~a~~~~~~~~~~v  102 (293)
T 3t15_A           35 VPLILGIWGGKGQGKSFQCELVFRKM----------GINPIMMSAGELE--SGNAGEPAKLIRQRYREAAEIIRKGNMCC  102 (293)
T ss_dssp             CCSEEEEEECTTSCHHHHHHHHHHHH----------TCCCEEEEHHHHH--CC---HHHHHHHHHHHHHHHHHTTSSCCC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEeHHHhh--hccCchhHHHHHHHHHHHHHHHhcCCCeE
Confidence            34578999999999999999999999          7888999998887  446788888888888877    4567899


Q ss_pred             EEEccchhhhhCCCCCCCCCCChHhHHHhhccccc---------------CCCeEEEEccChHHHHhhhhccHHHHc--c
Q 005179          386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG---------------RGELQCIASTTQDEHRTQFEKDKALAR--R  448 (710)
Q Consensus       386 L~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~---------------~~~v~vI~att~~~~~~~~~~d~aL~~--R  448 (710)
                      |||||||.+.+..............+.+.|...+.               ..++.+|+|||..+     .+++++.|  |
T Consensus       103 l~iDEiD~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~-----~ld~al~R~~R  177 (293)
T 3t15_A          103 LFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFS-----TLYAPLIRDGR  177 (293)
T ss_dssp             EEEECCC--------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCC-----C--CHHHHHHH
T ss_pred             EEEechhhhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcc-----cCCHHHhCCCC
Confidence            99999999976322110001123345566655542               35688999999875     68899987  8


Q ss_pred             ccc-eEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          449 FQP-VLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       449 f~~-I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      |+. |.  .|+.+++.+|++.+..    ..  .++.   +.+..++.+|..
T Consensus       178 ~d~~i~--~P~~~~r~~Il~~~~~----~~--~~~~---~~l~~~~~~~~~  217 (293)
T 3t15_A          178 MEKFYW--APTREDRIGVCTGIFR----TD--NVPA---EDVVKIVDNFPG  217 (293)
T ss_dssp             EEEEEE--CCCHHHHHHHHHHHHG----GG--CCCH---HHHHHHHHHSCS
T ss_pred             CceeEe--CcCHHHHHHHHHHhcc----CC--CCCH---HHHHHHhCCCCc
Confidence            873 43  5899999999986554    22  3343   345556666643

>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=99.61  E-value=2.3e-15  Score=161.35  Aligned_cols=203  Identities=16%  Similarity=0.193  Sum_probs=141.4

Q ss_pred             hhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          277 CVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       277 ~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      ..+|.++++|..|++++|+++.++.+...+......+++|+||||||||++++++++.+....    .....+..++.+.
T Consensus        24 ~~~~~~k~~p~~~~~i~g~~~~~~~l~~~l~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~----~~~~~~~~~~~~~   99 (353)
T 1sxj_D           24 QQPWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPD----LMKSRILELNASD   99 (353)
T ss_dssp             --CHHHHTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHH----HHTTSEEEECSSS
T ss_pred             CccHHHhcCCCCHHHhhCCHHHHHHHHHHHhcCCCCEEEEECCCCCCHHHHHHHHHHHhCCCc----ccccceEEEcccc
Confidence            458889999999999999999999999988877667799999999999999999999874310    0023345554432


Q ss_pred             hhhccccCccHHHHHHHHHHH-----------H-HhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--C
Q 005179          357 LMAGAKERGELEARVTTLISE-----------I-QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--G  422 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~-----------~-~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~  422 (710)
                      .. +   .+.+...+......           . ....+.||||||+|.+             ....++.|...++.  .
T Consensus       100 ~~-~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l-------------~~~~~~~Ll~~le~~~~  162 (353)
T 1sxj_D          100 ER-G---ISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSM-------------TADAQSALRRTMETYSG  162 (353)
T ss_dssp             CC-C---HHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGS-------------CHHHHHHHHHHHHHTTT
T ss_pred             cc-c---hHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCcc-------------CHHHHHHHHHHHHhcCC
Confidence            21 0   01111111111110           0 0123569999999999             33345666666653  3


Q ss_pred             CeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCC
Q 005179          423 ELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYL  502 (710)
Q Consensus       423 ~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~  502 (710)
                      ...+|.+++...     .+.+++.+||..+.+.+|+.++...+++..+.    ..++.+++++++.++.++.+.      
T Consensus       163 ~~~~il~~~~~~-----~l~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~----~~~~~i~~~~l~~l~~~~~G~------  227 (353)
T 1sxj_D          163 VTRFCLICNYVT-----RIIDPLASQCSKFRFKALDASNAIDRLRFISE----QENVKCDDGVLERILDISAGD------  227 (353)
T ss_dssp             TEEEEEEESCGG-----GSCHHHHHHSEEEECCCCCHHHHHHHHHHHHH----TTTCCCCHHHHHHHHHHTSSC------
T ss_pred             CceEEEEeCchh-----hCcchhhccCceEEeCCCCHHHHHHHHHHHHH----HhCCCCCHHHHHHHHHHcCCC------
Confidence            456666666654     57899999999999999999999988887665    357889999999999887643      


Q ss_pred             cchHHHHHHHHHh
Q 005179          503 PDKAIDLVDEAGS  515 (710)
Q Consensus       503 p~~ai~ll~~a~~  515 (710)
                      +..++.+++.+..
T Consensus       228 ~r~~~~~l~~~~~  240 (353)
T 1sxj_D          228 LRRGITLLQSASK  240 (353)
T ss_dssp             HHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHH
Confidence            4567777776553

>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=99.60  E-value=5.7e-14  Score=149.68  Aligned_cols=191  Identities=19%  Similarity=0.243  Sum_probs=129.3

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      .|.+.+++..|+.++|++..++.+...+..     ....+++|+||||+||||+++.++..+          ++.+....
T Consensus        14 ~~~~~lr~~~l~~~~g~~~~~~~l~~~i~~~~~~~~~~~~~ll~Gp~G~GKTTLa~~ia~~l----------~~~~~~~s   83 (334)
T 1in4_A           14 SGVQFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL----------QTNIHVTS   83 (334)
T ss_dssp             ---CTTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH----------TCCEEEEE
T ss_pred             HHHHHcCCccHHHccCcHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEe
Confidence            456778899999999999888777666543     234789999999999999999999988          33333332


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------  421 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------  421 (710)
                      ...+..     +   ..+..++...  ....|+||||+|.+..             ...+.|...++.            
T Consensus        84 g~~~~~-----~---~~l~~~~~~~--~~~~v~~iDE~~~l~~-------------~~~e~L~~~~~~~~~~i~~~~~~~  140 (334)
T 1in4_A           84 GPVLVK-----Q---GDMAAILTSL--ERGDVLFIDEIHRLNK-------------AVEELLYSAIEDFQIDIMIGKGPS  140 (334)
T ss_dssp             TTTCCS-----H---HHHHHHHHHC--CTTCEEEEETGGGCCH-------------HHHHHHHHHHHTSCCCC-------
T ss_pred             chHhcC-----H---HHHHHHHHHc--cCCCEEEEcchhhcCH-------------HHHHHHHHHHHhcccceeeccCcc
Confidence            211111     1   1122222221  2356999999999832             122222222211            


Q ss_pred             --------CCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHH
Q 005179          422 --------GELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHL  492 (710)
Q Consensus       422 --------~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~l  492 (710)
                              ..+.+|++++...     .+++.+++||. .+.+++|+.+++.+||+.....    .++.++++++..++..
T Consensus       141 ~~~i~~~l~~~~li~at~~~~-----~Ls~~l~sR~~l~~~Ld~~~~~~l~~iL~~~~~~----~~~~~~~~~~~~ia~~  211 (334)
T 1in4_A          141 AKSIRIDIQPFTLVGATTRSG-----LLSSPLRSRFGIILELDFYTVKELKEIIKRAASL----MDVEIEDAAAEMIAKR  211 (334)
T ss_dssp             --------CCCEEEEEESCGG-----GSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHH----TTCCBCHHHHHHHHHT
T ss_pred             cccccccCCCeEEEEecCCcc-----cCCHHHHHhcCceeeCCCCCHHHHHHHHHHHHHH----cCCCcCHHHHHHHHHh
Confidence                    1356777777764     68899999997 6889999999999999987663    4688999999888876


Q ss_pred             hhhhhcCCCCcchHHHHHHHHHhhh
Q 005179          493 SARYISDRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       493 s~~~i~~r~~p~~ai~ll~~a~~~~  517 (710)
                      +.+      .|..+..+++.+...+
T Consensus       212 ~~G------~~R~a~~ll~~~~~~a  230 (334)
T 1in4_A          212 SRG------TPRIAIRLTKRVRDML  230 (334)
T ss_dssp             STT------CHHHHHHHHHHHHHHH
T ss_pred             cCC------ChHHHHHHHHHHHHHH
Confidence            543      3567788888765443

>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=99.60  E-value=1.2e-14  Score=157.11  Aligned_cols=200  Identities=19%  Similarity=0.181  Sum_probs=142.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc-------------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL-------------  344 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l-------------  344 (710)
                      .|.++++|..|++++|++++++.+...+......+ ++|+||+|+|||++++.+++.+.........             
T Consensus         5 ~l~~k~rp~~~~~~vg~~~~~~~L~~~l~~~~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~~~~~   84 (373)
T 1jr3_A            5 VLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQ   84 (373)
T ss_dssp             CHHHHTCCCSTTTSCSCHHHHHHHHHHHHHTCCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHHHHHHHT
T ss_pred             HHHHhhCCCchhhccCcHHHHHHHHHHHHhCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHHHHHHhc
Confidence            57788999999999999999999999887755444 6899999999999999999988542211000             


Q ss_pred             -cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          345 -LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       345 -~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                       ....++.++...    ......    ++.+++.+..    .++.||||||+|.+             .....+.|...+
T Consensus        85 ~~~~~~~~~~~~~----~~~~~~----~~~l~~~~~~~~~~~~~~vliiDe~~~l-------------~~~~~~~Ll~~l  143 (373)
T 1jr3_A           85 GRFVDLIEIDAAS----RTKVED----TRDLLDNVQYAPARGRFKVYLIDEVHML-------------SRHSFNALLKTL  143 (373)
T ss_dssp             SCCSSCEEEETTC----SCCSSC----HHHHHHHTTSCCSSSSSEEEEEECGGGS-------------CHHHHHHHHHHH
T ss_pred             cCCCceEEecccc----cCCHHH----HHHHHHHHhhccccCCeEEEEEECcchh-------------cHHHHHHHHHHH
Confidence             001223332211    011122    4445555432    34689999999999             334556666666


Q ss_pred             cC--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhh
Q 005179          420 GR--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYI  497 (710)
Q Consensus       420 ~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i  497 (710)
                      ++  ..+++|++++...     .+.+.+.+|+..+.+.+|+.++...+++..+..    .++.+++++++.++..+.+. 
T Consensus       144 e~~~~~~~~Il~~~~~~-----~l~~~l~sr~~~i~~~~l~~~~~~~~l~~~~~~----~~~~~~~~a~~~l~~~~~G~-  213 (373)
T 1jr3_A          144 EEPPEHVKFLLATTDPQ-----KLPVTILSRCLQFHLKALDVEQIRHQLEHILNE----EHIAHEPRALQLLARAAEGS-  213 (373)
T ss_dssp             HSCCSSEEEEEEESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHH----HTCCBCHHHHHHHHHHSSSC-
T ss_pred             hcCCCceEEEEEeCChH-----hCcHHHHhheeEeeCCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHHCCCC-
Confidence            64  5677787777654     567899999999999999999999998877664    47889999999988886543 


Q ss_pred             cCCCCcchHHHHHHHHH
Q 005179          498 SDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       498 ~~r~~p~~ai~ll~~a~  514 (710)
                           +..+..+++.+.
T Consensus       214 -----~r~~~~~l~~~~  225 (373)
T 1jr3_A          214 -----LRDALSLTDQAI  225 (373)
T ss_dssp             -----HHHHHHHHHHHH
T ss_pred             -----HHHHHHHHHHHH
Confidence                 456777777665

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.59  E-value=6.7e-15  Score=154.16  Aligned_cols=213  Identities=10%  Similarity=0.066  Sum_probs=141.2

Q ss_pred             cccCHHHHHHHHHHHH----cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh---------
Q 005179          292 VIGRETEIQRIIQILC----RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM---------  358 (710)
Q Consensus       292 liGr~~~i~~l~~~L~----~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~---------  358 (710)
                      +.||++|+..+...|.    ...+++++|+||||||||++++.+++.+........+....++.+++..+.         
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I  101 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKI  101 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHH
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHH
Confidence            7889999998886654    467788999999999999999999999854211111113456666653321         


Q ss_pred             ----hccc-cCccHHHHHHHHHHHH--HhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhc-ccccCCCeEEEEcc
Q 005179          359 ----AGAK-ERGELEARVTTLISEI--QKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLK-PSLGRGELQCIAST  430 (710)
Q Consensus       359 ----~g~~-~~g~~e~~l~~~~~~~--~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~-~~l~~~~v~vI~at  430 (710)
                          .|.. ..+.....+..+|..+  ....+.|+||||+|.+. .          ..-+.+++. ......++.+|+++
T Consensus       102 ~~~L~g~~~~~~~~~~~L~~~f~~~~~~~~~~~ii~lDE~d~l~-~----------q~~L~~l~~~~~~~~s~~~vI~i~  170 (318)
T 3te6_A          102 WFAISKENLCGDISLEALNFYITNVPKAKKRKTLILIQNPENLL-S----------EKILQYFEKWISSKNSKLSIICVG  170 (318)
T ss_dssp             HHHHSCCC--CCCCHHHHHHHHHHSCGGGSCEEEEEEECCSSSC-C----------THHHHHHHHHHHCSSCCEEEEEEC
T ss_pred             HHHhcCCCCCchHHHHHHHHHHHHhhhccCCceEEEEecHHHhh-c----------chHHHHHHhcccccCCcEEEEEEe
Confidence                1111 1233345567777665  23457899999999994 1          222223221 11246678888887


Q ss_pred             ChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhh-------------------------------c
Q 005179          431 TQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAH-------------------------------H  477 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~-------------------------------~  477 (710)
                      |..++.. ..+++++.+||.  .|.|++++.+|...||+..+......                               .
T Consensus       171 n~~d~~~-~~L~~~v~SR~~~~~i~F~pYt~~el~~Il~~Rl~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  249 (318)
T 3te6_A          171 GHNVTIR-EQINIMPSLKAHFTEIKLNKVDKNELQQMIITRLKSLLKPFHVKVNDKKEMTIYNNIREGQNQKIPDNVIVI  249 (318)
T ss_dssp             CSSCCCH-HHHHTCHHHHTTEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEECTTCCEEECCCC--------CTTEEEE
T ss_pred             cCcccch-hhcchhhhccCCceEEEeCCCCHHHHHHHHHHHHHhhhcccccccccccccccccccccccccccccccccc
Confidence            7643211 235677888985  69999999999999999988765321                               0


Q ss_pred             CCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhhhh
Q 005179          478 NCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRAHI  519 (710)
Q Consensus       478 ~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~~~  519 (710)
                      .+.+++++++.+++....--++   .++|++++..|+..+..
T Consensus       250 ~~~i~~~ai~~~A~~vA~~~GD---~R~Al~ilr~A~~~ae~  288 (318)
T 3te6_A          250 NHKINNKITQLIAKNVANVSGS---TEKAFKICEAAVEISKK  288 (318)
T ss_dssp             CEECCHHHHHHHHHHHHHHHCS---HHHHHHHHHHHHHHHHH
T ss_pred             ccccCHHHHHHHHHHHHhhCCh---HHHHHHHHHHHHHHHHH
Confidence            1257999999998875554333   46889999988755433

>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=99.59  E-value=8.5e-15  Score=149.80  Aligned_cols=202  Identities=21%  Similarity=0.271  Sum_probs=130.5

Q ss_pred             cCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|++++|.++....+.++...            ..+.+++|+||||||||+++++++..+          +...+.++.
T Consensus        13 ~~~~~i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~----------~~~~i~~~~   82 (254)
T 1ixz_A           13 VTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA----------RVPFITASG   82 (254)
T ss_dssp             CCGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEH
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHh----------CCCEEEeeH
Confidence            3567788888766555443221            123458999999999999999999887          345666776


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC-CCCChHhHHHhhccccc----CCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG-NKGTGLDISNLLKPSLG----RGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~-~~~~~~~~~~~L~~~l~----~~~v~vI~a  429 (710)
                      ..+..  ...+.....+..+++.+....+.++|+||+|.+......+.+ .........+.+...++    +..++++++
T Consensus        83 ~~~~~--~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~~~~~i~~a~  160 (254)
T 1ixz_A           83 SDFVE--MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAA  160 (254)
T ss_dssp             HHHHH--SCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEE
T ss_pred             HHHHH--HHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCCCCCEEEEEc
Confidence            66542  234556667788888776666889999999998643221000 00111122333333332    234677788


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCCcch
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~p~~  505 (710)
                      ++.++     .+|+++.+  ||. .|.++.|+.++|.+||+.+..      +..+.+++ +..++..+.+|.+     .+
T Consensus       161 t~~p~-----~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~------~~~~~~~~~~~~la~~~~G~~~-----~d  224 (254)
T 1ixz_A          161 TNRPD-----ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR------GKPLAEDVDLALLAKRTPGFVG-----AD  224 (254)
T ss_dssp             ESCGG-----GSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHT------TSCBCTTCCHHHHHHTCTTCCH-----HH
T ss_pred             cCCch-----hCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHc------CCCCCcccCHHHHHHHcCCCCH-----HH
Confidence            88775     58899998  786 799999999999999986543      23444433 6667666666543     45


Q ss_pred             HHHHHHHHHhh
Q 005179          506 AIDLVDEAGSR  516 (710)
Q Consensus       506 ai~ll~~a~~~  516 (710)
                      ...++..|+..
T Consensus       225 l~~~~~~a~~~  235 (254)
T 1ixz_A          225 LENLLNEAALL  235 (254)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            56677766543

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.59  E-value=3e-15  Score=166.52  Aligned_cols=204  Identities=22%  Similarity=0.271  Sum_probs=137.3

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          286 EELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      .-+|++++|.++.+..+.++...            ..+.+++|+||||||||+|+++++..+          +..++.++
T Consensus        27 ~~~f~dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~----------~~~~i~i~   96 (499)
T 2dhr_A           27 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA----------RVPFITAS   96 (499)
T ss_dssp             CCCTTSSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHT----------TCCEEEEE
T ss_pred             CCCHHHcCCcHHHHHHHHHHHHHhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHh----------CCCEEEEe
Confidence            44688999999887777665421            123568999999999999999999887          45677888


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCC-CCChHhHHHhhccccc----CCCeEEEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGN-KGTGLDISNLLKPSLG----RGELQCIA  428 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~-~~~~~~~~~~L~~~l~----~~~v~vI~  428 (710)
                      ...+.  ..+.|....++..+|+.+....++++||||||.+......+.+. ........+.|...|+    +..+++|+
T Consensus        97 g~~~~--~~~~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~~~~viviA  174 (499)
T 2dhr_A           97 GSDFV--EMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA  174 (499)
T ss_dssp             GGGGT--SSCTTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCSSCCCEEEE
T ss_pred             hhHHH--HhhhhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhcccccCccEEEEE
Confidence            77765  34566677778888877665567899999999986543211000 0011122333333333    34578888


Q ss_pred             ccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCCcc
Q 005179          429 STTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYLPD  504 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~p~  504 (710)
                      +|+.++     .+|+++.|  ||+ .|.|+.|+.++|.+||+.+.+      ++.+++++ +..++..+.+|.     +.
T Consensus       175 atn~p~-----~LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~------~~~l~~dv~l~~lA~~t~G~~-----ga  238 (499)
T 2dhr_A          175 ATNRPD-----ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR------GKPLAEDVDLALLAKRTPGFV-----GA  238 (499)
T ss_dssp             CCSCGG-----GSCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTS------SSCCCCSSTTHHHHTTSCSCC-----HH
T ss_pred             ecCChh-----hcCcccccccccceEEecCCCCHHHHHHHHHHHHh------cCCCChHHHHHHHHHhcCCCC-----HH
Confidence            888876     48999998  786 899999999999999975433      33444433 555555554443     24


Q ss_pred             hHHHHHHHHHhhh
Q 005179          505 KAIDLVDEAGSRA  517 (710)
Q Consensus       505 ~ai~ll~~a~~~~  517 (710)
                      +...++.+|+..+
T Consensus       239 dL~~lv~~Aa~~A  251 (499)
T 2dhr_A          239 DLENLLNEAALLA  251 (499)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            5566777766443

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.57  E-value=3.9e-14  Score=146.99  Aligned_cols=202  Identities=21%  Similarity=0.277  Sum_probs=131.2

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHc------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          286 EELIDPVIGRETEIQRIIQILCR------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      +-+|++++|.++....+.++...            ..+.+++|+||||||||+++++++..+          ....+.++
T Consensus        36 ~~~~~~i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~----------~~~~i~~~  105 (278)
T 1iy2_A           36 KVTFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA----------RVPFITAS  105 (278)
T ss_dssp             CCCGGGSSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEE
T ss_pred             CCCHHHhCChHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHc----------CCCEEEec
Confidence            34577899998777666554321            123458999999999999999999887          34566677


Q ss_pred             hhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCC-CCCChHhHHHhhccccc----CCCeEEEE
Q 005179          354 MGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRG-NKGTGLDISNLLKPSLG----RGELQCIA  428 (710)
Q Consensus       354 ~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~-~~~~~~~~~~~L~~~l~----~~~v~vI~  428 (710)
                      ...+..  ...+.....+..+++.+....+.++|+||++.+......+.+ .........+.+...++    +..+++++
T Consensus       106 ~~~~~~--~~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~~~~~i~~a  183 (278)
T 1iy2_A          106 GSDFVE--MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMA  183 (278)
T ss_dssp             HHHHHH--STTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCTTCCEEEEE
T ss_pred             HHHHHH--HHhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCCCCCEEEEE
Confidence            665542  234556667788888877667889999999988643211000 00001122233333333    23467778


Q ss_pred             ccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH-HHHHHHHhhhhhcCCCCcc
Q 005179          429 STTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA-INAAVHLSARYISDRYLPD  504 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~-l~~l~~ls~~~i~~r~~p~  504 (710)
                      +++.++     .+|+++.+  ||. .|.++.|+.++|.+||+.+..      +..+++++ +..++..+.+|..     .
T Consensus       184 ~t~~p~-----~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~------~~~~~~~~~~~~la~~~~G~~~-----~  247 (278)
T 1iy2_A          184 ATNRPD-----ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHAR------GKPLAEDVDLALLAKRTPGFVG-----A  247 (278)
T ss_dssp             EESCTT-----SSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHT------TSCBCTTCCHHHHHHTCTTCCH-----H
T ss_pred             ecCCch-----hCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHc------cCCCCcccCHHHHHHHcCCCCH-----H
Confidence            888775     58999998  786 799999999999999986543      23444443 5566666655532     4


Q ss_pred             hHHHHHHHHHh
Q 005179          505 KAIDLVDEAGS  515 (710)
Q Consensus       505 ~ai~ll~~a~~  515 (710)
                      +...++..|+.
T Consensus       248 dl~~l~~~a~~  258 (278)
T 1iy2_A          248 DLENLLNEAAL  258 (278)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            45556776654

>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=99.56  E-value=1.9e-15  Score=170.65  Aligned_cols=198  Identities=15%  Similarity=0.193  Sum_probs=133.7

Q ss_pred             hhhhHHhhhhcCCCCcccCHHHHHHHHHHHHc-----------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcC
Q 005179          277 CVDLTARASEELIDPVIGRETEIQRIIQILCR-----------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAE  339 (710)
Q Consensus       277 ~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~-----------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~  339 (710)
                      ...|+++++|.+|++++|++..++.+.+++..                 ...+++||+||||||||++|+++++.+    
T Consensus        26 ~~lW~ekyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l----  101 (516)
T 1sxj_A           26 DKLWTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL----  101 (516)
T ss_dssp             CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT----
T ss_pred             CCCcccccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc----
Confidence            34688899999999999999999999988765                 134689999999999999999999988    


Q ss_pred             CCccccCceEEEeehhhhhhccccCccHHHH---------HHHHHHHH-----HhcCCeEEEEccchhhhhCCCCCCCCC
Q 005179          340 VPVFLLSKRIMSLDMGLLMAGAKERGELEAR---------VTTLISEI-----QKSGDVILFIDEVHTLIGSGTVGRGNK  405 (710)
Q Consensus       340 ~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~---------l~~~~~~~-----~~~~~~IL~IDEid~l~~~~~~~~~~~  405 (710)
                            +..++.++++.+....    ..+..         +..++..+     ....+.||||||+|.+...        
T Consensus       102 ------~~~~i~in~s~~~~~~----~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~--------  163 (516)
T 1sxj_A          102 ------GYDILEQNASDVRSKT----LLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGG--------  163 (516)
T ss_dssp             ------TCEEEEECTTSCCCHH----HHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTT--------
T ss_pred             ------CCCEEEEeCCCcchHH----HHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchh--------
Confidence                  6778887765432110    00000         01111111     1245789999999999542        


Q ss_pred             CChHhHHHhhcccccCCC--eEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCH
Q 005179          406 GTGLDISNLLKPSLGRGE--LQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTL  483 (710)
Q Consensus       406 ~~~~~~~~~L~~~l~~~~--v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~  483 (710)
                        .....+.|..+++..+  +++|+++....     .+ +.+.+|+..|.|++|+.+++.++|..++.+    .++.+++
T Consensus       164 --~~~~l~~L~~~l~~~~~~iIli~~~~~~~-----~l-~~l~~r~~~i~f~~~~~~~~~~~L~~i~~~----~~~~i~~  231 (516)
T 1sxj_A          164 --DRGGVGQLAQFCRKTSTPLILICNERNLP-----KM-RPFDRVCLDIQFRRPDANSIKSRLMTIAIR----EKFKLDP  231 (516)
T ss_dssp             --STTHHHHHHHHHHHCSSCEEEEESCTTSS-----TT-GGGTTTSEEEECCCCCHHHHHHHHHHHHHH----HTCCCCT
T ss_pred             --hHHHHHHHHHHHHhcCCCEEEEEcCCCCc-----cc-hhhHhceEEEEeCCCCHHHHHHHHHHHHHH----cCCCCCH
Confidence              1122344555555444  44444433221     12 347778889999999999999999877663    3678999


Q ss_pred             HHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          484 EAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       484 ~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      ++++.++..+.+.      ...++.++..++
T Consensus       232 ~~l~~la~~s~Gd------iR~~i~~L~~~~  256 (516)
T 1sxj_A          232 NVIDRLIQTTRGD------IRQVINLLSTIS  256 (516)
T ss_dssp             THHHHHHHHTTTC------HHHHHHHHTHHH
T ss_pred             HHHHHHHHHcCCc------HHHHHHHHHHHH
Confidence            9999998886542      234566655443

>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=6.6e-15  Score=158.08  Aligned_cols=204  Identities=12%  Similarity=0.135  Sum_probs=137.5

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHH-HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccc-c-----------
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQIL-CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL-L-----------  345 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L-~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l-~-----------  345 (710)
                      .|.++++|.+|++++|+++.++.+...+ ......+++|+||+|+||||+++.++..+......... .           
T Consensus         3 ~w~~kyrP~~~~~~vg~~~~~~~l~~~~~~~~~~~~~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~~~~~~~~~~   82 (354)
T 1sxj_E            3 LWVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRK   82 (354)
T ss_dssp             -CTTTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC---------------
T ss_pred             cchhccCCCCHHHhcCCHHHHHHHHHHHhhCCCCCeEEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecceeeccccccc
Confidence            5788999999999999999999998887 66555669999999999999999999976332111000 0           


Q ss_pred             -------CceEEEeehhhhhhccccCccHHHHHHHHHHHHH--------------hcCCeEEEEccchhhhhCCCCCCCC
Q 005179          346 -------SKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ--------------KSGDVILFIDEVHTLIGSGTVGRGN  404 (710)
Q Consensus       346 -------~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~--------------~~~~~IL~IDEid~l~~~~~~~~~~  404 (710)
                             ...++.++....  +.   .. ...++..++.+.              ..++.|++|||++.+          
T Consensus        83 ~~~~~~~~~~~~~~~~~~~--~~---~~-~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L----------  146 (354)
T 1sxj_E           83 LELNVVSSPYHLEITPSDM--GN---ND-RIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSL----------  146 (354)
T ss_dssp             ---CCEECSSEEEECCC---------CC-HHHHHHHHHHHTTTTC------------CCEEEEEECTTSS----------
T ss_pred             ceeeeecccceEEecHhhc--CC---cc-hHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCcccc----------
Confidence                   011122221110  00   01 012333443332              124669999999997          


Q ss_pred             CCChHhHHHhhccccc--CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCC
Q 005179          405 KGTGLDISNLLKPSLG--RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFT  482 (710)
Q Consensus       405 ~~~~~~~~~~L~~~l~--~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~  482 (710)
                         .....+.|...++  ..+..+|.+|+...     .+.+++.+||..+.+++|+.++...+|+.++..    .++.++
T Consensus       147 ---~~~~~~~L~~~le~~~~~~~~Il~t~~~~-----~l~~~l~sR~~~~~~~~~~~~~~~~~l~~~~~~----~~~~~~  214 (354)
T 1sxj_E          147 ---TKDAQAALRRTMEKYSKNIRLIMVCDSMS-----PIIAPIKSQCLLIRCPAPSDSEISTILSDVVTN----ERIQLE  214 (354)
T ss_dssp             ---CHHHHHHHHHHHHHSTTTEEEEEEESCSC-----SSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHH----HTCEEC
T ss_pred             ---CHHHHHHHHHHHHhhcCCCEEEEEeCCHH-----HHHHHHHhhceEEecCCcCHHHHHHHHHHHHHH----cCCCCC
Confidence               3334555555554  23466666666544     577899999999999999999999999887764    378889


Q ss_pred             -HHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhh
Q 005179          483 -LEAINAAVHLSARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       483 -~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                       +++++.++..+.+.      ++.++.+++.+...
T Consensus       215 ~~~~l~~i~~~~~G~------~r~a~~~l~~~~~~  243 (354)
T 1sxj_E          215 TKDILKRIAQASNGN------LRVSLLMLESMALN  243 (354)
T ss_dssp             CSHHHHHHHHHHTTC------HHHHHHHHTHHHHT
T ss_pred             cHHHHHHHHHHcCCC------HHHHHHHHHHHHHh
Confidence             99999999887553      45677787766543

>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=99.55  E-value=7.4e-14  Score=148.15  Aligned_cols=196  Identities=14%  Similarity=0.146  Sum_probs=125.7

Q ss_pred             CCCCcc-cC--HHHHHHHHHHHHcC--CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc
Q 005179          288 LIDPVI-GR--ETEIQRIIQILCRR--TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK  362 (710)
Q Consensus       288 ~l~~li-Gr--~~~i~~l~~~L~~~--~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~  362 (710)
                      +|++++ |.  ......+..++...  ..++++|+||||||||++++++++.+...       +..++.+++..+...  
T Consensus         9 ~f~~fv~g~~~~~a~~~~~~~~~~~~~~~~~lll~G~~GtGKT~la~~i~~~~~~~-------~~~~~~i~~~~~~~~--   79 (324)
T 1l8q_A            9 TLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-------GYRVIYSSADDFAQA--   79 (324)
T ss_dssp             CSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-------TCCEEEEEHHHHHHH--
T ss_pred             CcccCCCCCcHHHHHHHHHHHHhCcCCCCCeEEEECCCCCcHHHHHHHHHHHHHHC-------CCEEEEEEHHHHHHH--
Confidence            567776 43  33444455555443  35789999999999999999999988543       456777777665321  


Q ss_pred             cCccHHHH-HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhc
Q 005179          363 ERGELEAR-VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEK  441 (710)
Q Consensus       363 ~~g~~e~~-l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~  441 (710)
                      ..+.+... ...+....  ..+.+|||||+|.+.+..       .....+...+....+.+..++|++++...  ....+
T Consensus        80 ~~~~~~~~~~~~~~~~~--~~~~vL~iDEi~~l~~~~-------~~~~~l~~~l~~~~~~~~~iii~~~~~~~--~l~~l  148 (324)
T 1l8q_A           80 MVEHLKKGTINEFRNMY--KSVDLLLLDDVQFLSGKE-------RTQIEFFHIFNTLYLLEKQIILASDRHPQ--KLDGV  148 (324)
T ss_dssp             HHHHHHHTCHHHHHHHH--HTCSEEEEECGGGGTTCH-------HHHHHHHHHHHHHHHTTCEEEEEESSCGG--GCTTS
T ss_pred             HHHHHHcCcHHHHHHHh--cCCCEEEEcCcccccCCh-------HHHHHHHHHHHHHHHCCCeEEEEecCChH--HHHHh
Confidence            11111110 11122222  236799999999994321       11334445555555566666666655433  22357


Q ss_pred             cHHHHccc---cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          442 DKALARRF---QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       442 d~aL~~Rf---~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      +++|.+||   ..+.+++ +.+++..|++..+.    ..++.+++++++.++..+ +.      ...+..+++.++.
T Consensus       149 ~~~L~sR~~~~~~i~l~~-~~~e~~~il~~~~~----~~~~~l~~~~l~~l~~~~-g~------~r~l~~~l~~~~~  213 (324)
T 1l8q_A          149 SDRLVSRFEGGILVEIEL-DNKTRFKIIKEKLK----EFNLELRKEVIDYLLENT-KN------VREIEGKIKLIKL  213 (324)
T ss_dssp             CHHHHHHHHTSEEEECCC-CHHHHHHHHHHHHH----HTTCCCCHHHHHHHHHHC-SS------HHHHHHHHHHHHH
T ss_pred             hhHhhhcccCceEEEeCC-CHHHHHHHHHHHHH----hcCCCCCHHHHHHHHHhC-CC------HHHHHHHHHHHHH
Confidence            89999999   4789999 99999999998776    357899999999988876 33      2345555655553

>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=99.54  E-value=2e-13  Score=151.66  Aligned_cols=67  Identities=12%  Similarity=0.043  Sum_probs=56.1

Q ss_pred             hccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHh-hhhhcCCCCcchHHHHHHHHHhh
Q 005179          440 EKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLS-ARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       440 ~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls-~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                      .+++++++||..+.+++|+.++..++|+..+..    .++.++++++..++.++ .+      .+..++.+++.|...
T Consensus       349 ~l~~~i~sR~~~~~~~~~~~~e~~~iL~~~~~~----~~~~~~~~~~~~i~~~a~~g------~~r~a~~ll~~a~~~  416 (456)
T 2c9o_A          349 GIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQT----EGINISEEALNHLGEIGTKT------TLRYSVQLLTPANLL  416 (456)
T ss_dssp             TCCHHHHTTEEEEECCCCCHHHHHHHHHHHHHH----HTCCBCHHHHHHHHHHHHHS------CHHHHHHTHHHHHHH
T ss_pred             cCChhHHhhcceeeCCCCCHHHHHHHHHHHHHH----hCCCCCHHHHHHHHHHccCC------CHHHHHHHHHHHHHH
Confidence            678999999999999999999999999987763    36789999999999887 43      467888888877543

>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=99.54  E-value=4.3e-14  Score=146.09  Aligned_cols=197  Identities=15%  Similarity=0.120  Sum_probs=125.4

Q ss_pred             CCcccCHHHHHHHHH-------HHH---cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh
Q 005179          290 DPVIGRETEIQRIIQ-------ILC---RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~-------~L~---~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~  359 (710)
                      +.++|++..++.++.       .+.   .....++||+||||||||++|+++++.+          +..++.+++.....
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~----------~~~~~~i~~~~~~~  102 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES----------NFPFIKICSPDKMI  102 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH----------TCSEEEEECGGGCT
T ss_pred             cCCCCccHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHh----------CCCEEEEeCHHHhc
Confidence            357787777665554       332   3445689999999999999999999987          56677776655443


Q ss_pred             ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc-----CCCeEEEEccChHH
Q 005179          360 GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG-----RGELQCIASTTQDE  434 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~-----~~~v~vI~att~~~  434 (710)
                      |. ..+.....+..++..+....+.+|||||+|.+++....+   ......+.+.|...+.     ...+++|++|+.++
T Consensus       103 g~-~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~---~~~~~~~l~~L~~~~~~~~~~~~~~~ii~ttn~~~  178 (272)
T 1d2n_A          103 GF-SETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIG---PRFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKD  178 (272)
T ss_dssp             TC-CHHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTT---TBCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHH
T ss_pred             CC-chHHHHHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCC---hhHHHHHHHHHHHHhcCccCCCCCEEEEEecCChh
Confidence            32 122334556777877776778899999999997653321   1224455666655554     23567888888875


Q ss_pred             HHhhhhccH-HHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHH
Q 005179          435 HRTQFEKDK-ALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDE  512 (710)
Q Consensus       435 ~~~~~~~d~-aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~  512 (710)
                           .+++ .+.+||. .|.+++++.  +.+|...+..      ...++++.+..++..+.+|-.... ...++++++.
T Consensus       179 -----~l~~~~l~~rf~~~i~~p~l~~--r~~i~~i~~~------~~~~~~~~~~~l~~~~~g~~~~g~-ir~l~~~l~~  244 (272)
T 1d2n_A          179 -----VLQEMEMLNAFSTTIHVPNIAT--GEQLLEALEL------LGNFKDKERTTIAQQVKGKKVWIG-IKKLLMLIEM  244 (272)
T ss_dssp             -----HHHHTTCTTTSSEEEECCCEEE--HHHHHHHHHH------HTCSCHHHHHHHHHHHTTSEEEEC-HHHHHHHHHH
T ss_pred             -----hcchhhhhcccceEEcCCCccH--HHHHHHHHHh------cCCCCHHHHHHHHHHhcCCCcccc-HHHHHHHHHH
Confidence                 3445 5778985 566655543  3333332222      135789999999988877532111 2345555555


Q ss_pred             HH
Q 005179          513 AG  514 (710)
Q Consensus       513 a~  514 (710)
                      +.
T Consensus       245 a~  246 (272)
T 1d2n_A          245 SL  246 (272)
T ss_dssp             HT
T ss_pred             Hh
Confidence            54

>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=99.54  E-value=1.2e-13  Score=147.58  Aligned_cols=184  Identities=20%  Similarity=0.244  Sum_probs=135.9

Q ss_pred             hhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          277 CVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       277 ~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      ..+|.++++|..|++++|++..++.+...+......+++|+||||+|||++++++++.+.....     ...+..++.+.
T Consensus        12 ~~~~~~k~rp~~~~~~~g~~~~~~~L~~~i~~g~~~~~ll~Gp~G~GKTtla~~la~~l~~~~~-----~~~~~~~~~~~   86 (340)
T 1sxj_C           12 NLPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY-----SNMVLELNASD   86 (340)
T ss_dssp             CCCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSH-----HHHEEEECTTS
T ss_pred             CCchHHHhCCCcHHHhcCcHHHHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHcCCCc-----cceEEEEcCcc
Confidence            3478889999999999999999999998888776677999999999999999999999853210     12344444322


Q ss_pred             hhhccccCccHHHHHHHHHHHHHh------cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEE
Q 005179          357 LMAGAKERGELEARVTTLISEIQK------SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIA  428 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~------~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~  428 (710)
                            ..+  ...++..+..+..      .+..|++|||+|.+             ..+.++.|..+++.  ....+|.
T Consensus        87 ------~~~--~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l-------------~~~~~~~L~~~le~~~~~~~~il  145 (340)
T 1sxj_C           87 ------DRG--IDVVRNQIKDFASTRQIFSKGFKLIILDEADAM-------------TNAAQNALRRVIERYTKNTRFCV  145 (340)
T ss_dssp             ------CCS--HHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGS-------------CHHHHHHHHHHHHHTTTTEEEEE
T ss_pred             ------ccc--HHHHHHHHHHHHhhcccCCCCceEEEEeCCCCC-------------CHHHHHHHHHHHhcCCCCeEEEE
Confidence                  112  1223333433331      23679999999998             33456667666663  4566777


Q ss_pred             ccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          429 STTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      +++...     .+.+++.+||..+.+.+++.++...++..++.    ..++.+++++++.++.++.+
T Consensus       146 ~~n~~~-----~i~~~i~sR~~~~~~~~l~~~~~~~~l~~~~~----~~~~~i~~~~~~~i~~~s~G  203 (340)
T 1sxj_C          146 LANYAH-----KLTPALLSQCTRFRFQPLPQEAIERRIANVLV----HEKLKLSPNAEKALIELSNG  203 (340)
T ss_dssp             EESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHH----TTTCCBCHHHHHHHHHHHTT
T ss_pred             EecCcc-----ccchhHHhhceeEeccCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHcCC
Confidence            777654     67899999999999999999998888877664    34788999999999988765

>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=99.53  E-value=5.9e-14  Score=155.00  Aligned_cols=203  Identities=17%  Similarity=0.211  Sum_probs=128.3

Q ss_pred             CCCCcc-cCHH--HHHHHHHHHHcCC-CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc
Q 005179          288 LIDPVI-GRET--EIQRIIQILCRRT-KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE  363 (710)
Q Consensus       288 ~l~~li-Gr~~--~i~~l~~~L~~~~-~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~  363 (710)
                      +|+.++ |...  ....+..+...+. .++++|+||||+|||++++++++.+....     .+..++.+++..+...  .
T Consensus       103 tfd~fv~g~~n~~a~~~~~~~a~~~~~~~~lll~Gp~G~GKTtLa~aia~~l~~~~-----~~~~v~~v~~~~~~~~--~  175 (440)
T 2z4s_A          103 TFENFVVGPGNSFAYHAALEVAKHPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNE-----PDLRVMYITSEKFLND--L  175 (440)
T ss_dssp             SGGGCCCCTTTHHHHHHHHHHHHSTTSSCCEEEECSSSSSHHHHHHHHHHHHHHHC-----CSSCEEEEEHHHHHHH--H
T ss_pred             ChhhcCCCCchHHHHHHHHHHHhCCCCCCeEEEECCCCCCHHHHHHHHHHHHHHhC-----CCCeEEEeeHHHHHHH--H
Confidence            566776 5433  3334444444433 67899999999999999999999885431     1456777776655311  1


Q ss_pred             CccHHHH-HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhcc
Q 005179          364 RGELEAR-VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKD  442 (710)
Q Consensus       364 ~g~~e~~-l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d  442 (710)
                      .+.+... ...+ .......+.||||||+|.+.+..       .....+...+....+.+..++|++.++..  ....++
T Consensus       176 ~~~~~~~~~~~~-~~~~~~~~~vL~IDEi~~l~~~~-------~~q~~l~~~l~~l~~~~~~iIitt~~~~~--~l~~l~  245 (440)
T 2z4s_A          176 VDSMKEGKLNEF-REKYRKKVDILLIDDVQFLIGKT-------GVQTELFHTFNELHDSGKQIVICSDREPQ--KLSEFQ  245 (440)
T ss_dssp             HHHHHTTCHHHH-HHHHTTTCSEEEEECGGGGSSCH-------HHHHHHHHHHHHHHTTTCEEEEEESSCGG--GCSSCC
T ss_pred             HHHHHcccHHHH-HHHhcCCCCEEEEeCcccccCCh-------HHHHHHHHHHHHHHHCCCeEEEEECCCHH--HHHHHH
Confidence            0001000 1111 11111256799999999994321       11334455555555667666666555433  122378


Q ss_pred             HHHHccc---cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhhh
Q 005179          443 KALARRF---QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       443 ~aL~~Rf---~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~~  517 (710)
                      +.|.+||   ..+.+++|+.+++..||+..+..    .++.+++++++.++..+.+      .+..+..+++.+...+
T Consensus       246 ~~L~sR~~~g~~i~l~~p~~e~r~~iL~~~~~~----~~~~i~~e~l~~la~~~~g------n~R~l~~~L~~~~~~a  313 (440)
T 2z4s_A          246 DRLVSRFQMGLVAKLEPPDEETRKSIARKMLEI----EHGELPEEVLNFVAENVDD------NLRRLRGAIIKLLVYK  313 (440)
T ss_dssp             HHHHHHHHSSBCCBCCCCCHHHHHHHHHHHHHH----HTCCCCTTHHHHHHHHCCS------CHHHHHHHHHHHHHHH
T ss_pred             HHHHhhccCCeEEEeCCCCHHHHHHHHHHHHHH----cCCCCCHHHHHHHHHhcCC------CHHHHHHHHHHHHHHH
Confidence            9999999   47999999999999999987763    4788999999988876543      2455666777666544

>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=99.53  E-value=8.3e-14  Score=140.36  Aligned_cols=192  Identities=13%  Similarity=0.094  Sum_probs=125.8

Q ss_pred             cCCCCcccC---HHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcccc
Q 005179          287 ELIDPVIGR---ETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKE  363 (710)
Q Consensus       287 ~~l~~liGr---~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~  363 (710)
                      ..|++++|.   +..+..+...+......+++|+||||||||++++.+++.+...       +..++.+++..+..... 
T Consensus        25 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ll~G~~G~GKT~la~~l~~~~~~~-------~~~~~~~~~~~~~~~~~-   96 (242)
T 3bos_A           25 ETFTSYYPAAGNDELIGALKSAASGDGVQAIYLWGPVKSGRTHLIHAACARANEL-------ERRSFYIPLGIHASIST-   96 (242)
T ss_dssp             CSTTTSCC--CCHHHHHHHHHHHHTCSCSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEGGGGGGSCG-
T ss_pred             CChhhccCCCCCHHHHHHHHHHHhCCCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEHHHHHHHHH-
Confidence            467788873   4667777777766667899999999999999999999988543       45667777666542210 


Q ss_pred             CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccH
Q 005179          364 RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDK  443 (710)
Q Consensus       364 ~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~  443 (710)
                               ..+..+  ..+.+|||||++.+....       .....+...+....+.+.+.+|.+++... ......++
T Consensus        97 ---------~~~~~~--~~~~vliiDe~~~~~~~~-------~~~~~l~~~l~~~~~~~~~~ii~~~~~~~-~~~~~~~~  157 (242)
T 3bos_A           97 ---------ALLEGL--EQFDLICIDDVDAVAGHP-------LWEEAIFDLYNRVAEQKRGSLIVSASASP-MEAGFVLP  157 (242)
T ss_dssp             ---------GGGTTG--GGSSEEEEETGGGGTTCH-------HHHHHHHHHHHHHHHHCSCEEEEEESSCT-TTTTCCCH
T ss_pred             ---------HHHHhc--cCCCEEEEeccccccCCH-------HHHHHHHHHHHHHHHcCCCeEEEEcCCCH-HHHHHhhh
Confidence                     111111  236799999999983220       00222334444334455553444444221 01123458


Q ss_pred             HHHccc---cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHh
Q 005179          444 ALARRF---QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       444 aL~~Rf---~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      .+.+||   ..+.+++|+.+++.++++..+.    ..++.+++++++.++..+.+.      +..+..+++.++.
T Consensus       158 ~l~~r~~~~~~i~l~~~~~~~~~~~l~~~~~----~~~~~~~~~~~~~l~~~~~g~------~r~l~~~l~~~~~  222 (242)
T 3bos_A          158 DLVSRMHWGLTYQLQPMMDDEKLAALQRRAA----MRGLQLPEDVGRFLLNRMARD------LRTLFDVLDRLDK  222 (242)
T ss_dssp             HHHHHHHHSEEEECCCCCGGGHHHHHHHHHH----HTTCCCCHHHHHHHHHHTTTC------HHHHHHHHHHHHH
T ss_pred             hhhhHhhcCceEEeCCCCHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHccCC------HHHHHHHHHHHHH
Confidence            999999   6899999999999999988776    347889999999888776442      3455666666553

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.51  E-value=9.4e-14  Score=146.19  Aligned_cols=180  Identities=21%  Similarity=0.265  Sum_probs=123.1

Q ss_pred             CcccCHHHHHHHHHHHHcCC---------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc-
Q 005179          291 PVIGRETEIQRIIQILCRRT---------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG-  360 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~---------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g-  360 (710)
                      .++|++..++.+...+....         ..+++|+||||||||++|++++..+...       +..++.++++.+... 
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~-------~~~~~~~~~~~~~~~~   90 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT-------EEAMIRIDMTEYMEKH   90 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSC-------GGGEEEEEGGGCCSTT
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCC-------CcceEEeecccccccc
Confidence            48899999998888776531         2468999999999999999999988543       334566666543211 


Q ss_pred             -------cc--cCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC---------
Q 005179          361 -------AK--ERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG---------  422 (710)
Q Consensus       361 -------~~--~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~---------  422 (710)
                             ..  +.|.-.  ...+...+....+.||||||++.+             ..++++.|..+++.+         
T Consensus        91 ~~~~l~g~~~~~~~~~~--~~~~~~~~~~~~~~vl~lDEi~~l-------------~~~~~~~Ll~~le~~~~~~~~~~~  155 (311)
T 4fcw_A           91 AVSRLIGAPPGYVGYEE--GGQLTEAVRRRPYSVILFDAIEKA-------------HPDVFNILLQMLDDGRLTDSHGRT  155 (311)
T ss_dssp             HHHHHHCCCTTSTTTTT--CCHHHHHHHHCSSEEEEEETGGGS-------------CHHHHHHHHHHHHHSEEECTTSCE
T ss_pred             cHHHhcCCCCccccccc--cchHHHHHHhCCCeEEEEeChhhc-------------CHHHHHHHHHHHhcCEEEcCCCCE
Confidence                   00  001000  012233344455689999999998             445667776666532         


Q ss_pred             ----CeEEEEccChH---------------HHHh------hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhh
Q 005179          423 ----ELQCIASTTQD---------------EHRT------QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAH  476 (710)
Q Consensus       423 ----~v~vI~att~~---------------~~~~------~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~  476 (710)
                          +.++|++||..               +...      .-.+++.|.+||. .+.+.+|+.+++..|++.++.++...
T Consensus       156 ~~~~~~iiI~ttn~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~R~~~~~~~~p~~~~~~~~i~~~~l~~~~~~  235 (311)
T 4fcw_A          156 VDFRNTVIIMTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQMSYLRAR  235 (311)
T ss_dssp             EECTTEEEEEEESTTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHTTCSEEEECCCCCHHHHHHHHHHHTHHHHHH
T ss_pred             EECCCcEEEEecccCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHhcCCeEEEeCCCCHHHHHHHHHHHHHHHHHH
Confidence                45588888872               1111      1146899999996 78899999999999999977766432


Q ss_pred             -----cCCCCCHHHHHHHHHH
Q 005179          477 -----HNCKFTLEAINAAVHL  492 (710)
Q Consensus       477 -----~~~~i~~~~l~~l~~l  492 (710)
                           ..+.+++++++.++..
T Consensus       236 ~~~~~~~~~~~~~~~~~l~~~  256 (311)
T 4fcw_A          236 LAEKRISLELTEAAKDFLAER  256 (311)
T ss_dssp             HHTTTCEEEECHHHHHHHHHH
T ss_pred             HHhCCcEEEeCHHHHHHHHHh
Confidence                 2467899999988875

>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=99.51  E-value=3.6e-13  Score=145.93  Aligned_cols=209  Identities=19%  Similarity=0.159  Sum_probs=138.0

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcccc-CceEEEeehhhhh-h----
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLL-SKRIMSLDMGLLM-A----  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~-~~~v~~ld~~~l~-~----  359 (710)
                      +.++|++++++.+...+..    ..+.+++|+||||||||++++.+++.+.......... +..++.+++.... .    
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~   99 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREVGGTPQAV   99 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHHCSCHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccCCCCHHHH
Confidence            6799999999998877654    3456799999999999999999999874421000001 4567777755432 0    


Q ss_pred             ---------cc--ccCc-cHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH-HHhhcccccCCCeEE
Q 005179          360 ---------GA--KERG-ELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI-SNLLKPSLGRGELQC  426 (710)
Q Consensus       360 ---------g~--~~~g-~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~-~~~L~~~l~~~~v~v  426 (710)
                               +.  ...+ .....+..+...+...+ .||||||+|.+....         ..+. ...|....  .++.+
T Consensus       100 ~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~-~vlilDEi~~l~~~~---------~~~~~l~~l~~~~--~~~~i  167 (384)
T 2qby_B          100 LSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIR-AIIYLDEVDTLVKRR---------GGDIVLYQLLRSD--ANISV  167 (384)
T ss_dssp             HHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSC-EEEEEETTHHHHHST---------TSHHHHHHHHTSS--SCEEE
T ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCC-CEEEEECHHHhccCC---------CCceeHHHHhcCC--cceEE
Confidence                     00  0011 11222344444443333 399999999995431         1223 33444333  67889


Q ss_pred             EEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcch
Q 005179          427 IASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       427 I~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                      |++++..++.  ..+++.+.+||. .|.+++|+.++..+|++..+...  ..+..+++++++.++..+.++-+   .+..
T Consensus       168 I~~t~~~~~~--~~l~~~l~sr~~~~i~l~~l~~~~~~~il~~~~~~~--~~~~~~~~~~~~~i~~~~~~~~G---~~r~  240 (384)
T 2qby_B          168 IMISNDINVR--DYMEPRVLSSLGPSVIFKPYDAEQLKFILSKYAEYG--LIKGTYDDEILSYIAAISAKEHG---DARK  240 (384)
T ss_dssp             EEECSSTTTT--TTSCHHHHHTCCCEEEECCCCHHHHHHHHHHHHHHT--SCTTSCCSHHHHHHHHHHHTTCC---CHHH
T ss_pred             EEEECCCchH--hhhCHHHHhcCCCeEEECCCCHHHHHHHHHHHHHhh--cccCCcCHHHHHHHHHHHHhccC---CHHH
Confidence            9988876421  256899999984 89999999999999999876521  23467899999999988873322   3567


Q ss_pred             HHHHHHHHHhhh
Q 005179          506 AIDLVDEAGSRA  517 (710)
Q Consensus       506 ai~ll~~a~~~~  517 (710)
                      +++++..+...+
T Consensus       241 a~~~l~~a~~~a  252 (384)
T 2qby_B          241 AVNLLFRAAQLA  252 (384)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHh
Confidence            788888876544

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.50  E-value=8e-14  Score=150.94  Aligned_cols=212  Identities=19%  Similarity=0.201  Sum_probs=138.6

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------  359 (710)
                      +.++|++++++.+...+..    ..+.+++|+||||||||++++.+++.+..... ....+..++.+++.....      
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~-~~~~~~~~~~i~~~~~~~~~~~~~   97 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARAS-SLGVLVKPIYVNARHRETPYRVAS   97 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHH-HHTCCEEEEEEETTTSCSHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHh-ccCCCeEEEEEECCcCCCHHHHHH
Confidence            6799999999999988743    45678999999999999999999988743200 000134566666433110      


Q ss_pred             ------cc--ccCcc-HHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc----CCCeE
Q 005179          360 ------GA--KERGE-LEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG----RGELQ  425 (710)
Q Consensus       360 ------g~--~~~g~-~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~----~~~v~  425 (710)
                            +.  ...|. ....+..++..+... .+.||||||+|.+....        ...+....+...+.    ..++.
T Consensus        98 ~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~--------~~~~~l~~l~~~~~~~~~~~~~~  169 (387)
T 2v1u_A           98 AIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRP--------GGQDLLYRITRINQELGDRVWVS  169 (387)
T ss_dssp             HHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHST--------THHHHHHHHHHGGGCC-----CE
T ss_pred             HHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccC--------CCChHHHhHhhchhhcCCCceEE
Confidence                  00  01121 333344555544433 37799999999995431        02233333333333    56788


Q ss_pred             EEEccChHHHHhhhhccHHHHccc--cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          426 CIASTTQDEHRTQFEKDKALARRF--QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       426 vI~att~~~~~~~~~~d~aL~~Rf--~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      +|++++..++.  ..+++.+.+||  ..+.+++|+.++...|++..+...  ..+..+++++++.++..+.+.   ...|
T Consensus       170 ~I~~t~~~~~~--~~l~~~l~~r~~~~~i~l~~l~~~~~~~il~~~~~~~--~~~~~~~~~~~~~l~~~~~~~---~G~~  242 (387)
T 2v1u_A          170 LVGITNSLGFV--ENLEPRVKSSLGEVELVFPPYTAPQLRDILETRAEEA--FNPGVLDPDVVPLCAALAARE---HGDA  242 (387)
T ss_dssp             EEEECSCSTTS--SSSCHHHHTTTTSEECCBCCCCHHHHHHHHHHHHHHH--BCTTTBCSSHHHHHHHHHHSS---SCCH
T ss_pred             EEEEECCCchH--hhhCHHHHhcCCCeEEeeCCCCHHHHHHHHHHHHHhh--ccCCCCCHHHHHHHHHHHHHh---ccCH
Confidence            99988876422  25689999999  479999999999999999877532  235678999999988887732   2235


Q ss_pred             chHHHHHHHHHhhh
Q 005179          504 DKAIDLVDEAGSRA  517 (710)
Q Consensus       504 ~~ai~ll~~a~~~~  517 (710)
                      ..+++++..++..+
T Consensus       243 r~~~~~l~~a~~~a  256 (387)
T 2v1u_A          243 RRALDLLRVAGEIA  256 (387)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            67788888776443

>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=99.50  E-value=3.5e-13  Score=144.17  Aligned_cols=204  Identities=20%  Similarity=0.254  Sum_probs=121.3

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhc----CCCcccc----------------
Q 005179          286 EELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQA----EVPVFLL----------------  345 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~----~~p~~l~----------------  345 (710)
                      +..|++++|++..++.+...+......++||+||||||||++|+++++.+...    ..|....                
T Consensus        20 ~~~f~~i~G~~~~~~~l~~~~~~~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (350)
T 1g8p_A           20 VFPFSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNV   99 (350)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCE
T ss_pred             CCCchhccChHHHHHHHHHHhhCCCCceEEEECCCCccHHHHHHHHHHhCccccccccccccccccccccchhhhhcccc
Confidence            44677899999876665444444456789999999999999999999977321    1111000                


Q ss_pred             ---CceEEEeehh----hhhhccccCccHHHHHHHHHHH---------HHhcCCeEEEEccchhhhhCCCCCCCCCCChH
Q 005179          346 ---SKRIMSLDMG----LLMAGAKERGELEARVTTLISE---------IQKSGDVILFIDEVHTLIGSGTVGRGNKGTGL  409 (710)
Q Consensus       346 ---~~~v~~ld~~----~l~~g~~~~g~~e~~l~~~~~~---------~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~  409 (710)
                         ...++.+..+    .+. |..   .+    ...+..         +....+.+|||||+|.+             ..
T Consensus       100 ~~~~~~~~~~~~~~~~~~l~-g~~---~~----~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l-------------~~  158 (350)
T 1g8p_A          100 IRKPTPVVDLPLGVSEDRVV-GAL---DI----ERAISKGEKAFEPGLLARANRGYLYIDECNLL-------------ED  158 (350)
T ss_dssp             EEECCCEEEECTTCCHHHHH-CEE---CH----HHHHHHCGGGEECCHHHHHTTEEEEETTGGGS-------------CH
T ss_pred             ccCCCcccccCCCcchhhhe-eec---hh----hhhhcCCceeecCceeeecCCCEEEEeChhhC-------------CH
Confidence               0011111110    111 000   00    111110         11123679999999998             33


Q ss_pred             hHHHhhcccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCC-CHHHHHHHHHHHHHH
Q 005179          410 DISNLLKPSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEP-SQEDAVRILLGLREK  472 (710)
Q Consensus       410 ~~~~~L~~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~P-s~~~~~~IL~~l~~~  472 (710)
                      +.++.|...++.+               .+++|+++|+.+    ..++++|.+||. .+.+++| +.+++..|++.....
T Consensus       159 ~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~----~~l~~~L~~R~~~~~~l~~~~~~~~~~~il~~~~~~  234 (350)
T 1g8p_A          159 HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEE----GDLRPQLLDRFGLSVEVLSPRDVETRVEVIRRRDTY  234 (350)
T ss_dssp             HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCS----CCCCHHHHTTCSEEEECCCCCSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCC----CCCCHHHHhhcceEEEcCCCCcHHHHHHHHHHHHhc
Confidence            4556666555533               688899988643    257899999998 4999999 577777888763211


Q ss_pred             -------------------------HHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHHHHhh
Q 005179          473 -------------------------YEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       473 -------------------------~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                                               .....++.+++++++.++.++.+.-..  .+..+..+++.|...
T Consensus       235 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~ls~~~~~~l~~~~~~~~~~--~~R~~~~ll~~a~~~  301 (350)
T 1g8p_A          235 DADPKAFLEEWRPKDMDIRNQILEARERLPKVEAPNTALYDCAALCIALGSD--GLRGELTLLRSARAL  301 (350)
T ss_dssp             HHCHHHHHHHHHHHHHHHHHHHHHHHHHGGGCBCCHHHHHHHHHHHHHSSSC--SHHHHHHHHHHHHHH
T ss_pred             ccCchhhccccccchHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHhCCC--CccHHHHHHHHHHHH
Confidence                                     011235678888888887776553110  234556666655433

>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=99.50  E-value=6.9e-14  Score=150.88  Aligned_cols=191  Identities=23%  Similarity=0.294  Sum_probs=124.1

Q ss_pred             cccCHHHHHHHHHHHHc---------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          292 VIGRETEIQRIIQILCR---------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~---------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      ++|++..++.+...+..               ..+.++||+||||||||++|+++|+.+          +.+++.++++.
T Consensus        17 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~----------~~~~~~~~~~~   86 (363)
T 3hws_A           17 VIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL----------DVPFTMADATT   86 (363)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc----------CCCEEEechHH
Confidence            79999999988877631               145789999999999999999999988          67888888877


Q ss_pred             hhhccccCccH-HHHHHHHHHHH----HhcCCeEEEEccchhhhhCCCCCCCCCC-ChHhHHHhhcccccC---------
Q 005179          357 LMAGAKERGEL-EARVTTLISEI----QKSGDVILFIDEVHTLIGSGTVGRGNKG-TGLDISNLLKPSLGR---------  421 (710)
Q Consensus       357 l~~g~~~~g~~-e~~l~~~~~~~----~~~~~~IL~IDEid~l~~~~~~~~~~~~-~~~~~~~~L~~~l~~---------  421 (710)
                      +... .+.|.. ...+..++..+    ....++||||||+|.+.........+.. ....+++.|++.|+.         
T Consensus        87 l~~~-~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~  165 (363)
T 3hws_A           87 LTEA-GYVGEDVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQG  165 (363)
T ss_dssp             HTTC-HHHHHHHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC--------
T ss_pred             hccc-ccccccHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCcc
Confidence            6521 122322 33445555443    3334679999999999654322110000 111267777777661         


Q ss_pred             --------------CCeEEEEccChHHHHh----------------------------------------hhhccHHHHc
Q 005179          422 --------------GELQCIASTTQDEHRT----------------------------------------QFEKDKALAR  447 (710)
Q Consensus       422 --------------~~v~vI~att~~~~~~----------------------------------------~~~~d~aL~~  447 (710)
                                    .++.+|++++......                                        ...+.|.|.+
T Consensus       166 ~~~~~~~~~~~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~  245 (363)
T 3hws_A          166 GRKHPQQEFLQVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG  245 (363)
T ss_dssp             --------CCCCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT
T ss_pred             ccccCCCceEEEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc
Confidence                          1223344433211111                                        0115799999


Q ss_pred             ccc-ceEecCCCHHHHHHHHHH----HHHHHHhh-----cCCCCCHHHHHHHHHHh
Q 005179          448 RFQ-PVLISEPSQEDAVRILLG----LREKYEAH-----HNCKFTLEAINAAVHLS  493 (710)
Q Consensus       448 Rf~-~I~v~~Ps~~~~~~IL~~----l~~~~~~~-----~~~~i~~~~l~~l~~ls  493 (710)
                      ||. .+.+.+|+.+++..|+..    +..++...     ..+.+++++++.++..+
T Consensus       246 R~~~~~~~~pl~~~~~~~I~~~~~~~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~  301 (363)
T 3hws_A          246 RLPVVATLNELSEEALIQILKEPKNALTKQYQALFNLEGVDLEFRDEALDAIAKKA  301 (363)
T ss_dssp             TCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHH
T ss_pred             ccCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhcCceEEECHHHHHHHHHhh
Confidence            998 566889999999999986    66555432     23568999999998764

>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=99.50  E-value=3.9e-13  Score=145.38  Aligned_cols=209  Identities=19%  Similarity=0.240  Sum_probs=139.2

Q ss_pred             CCCcccCHHHHHHHHHHHHc----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-----
Q 005179          289 IDPVIGRETEIQRIIQILCR----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-----  359 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-----  359 (710)
                      .+.++||+++++.+...+..    ..+.+++|+||+|||||++++.+++.+......    +..++.+++.....     
T Consensus        19 p~~~~gr~~e~~~l~~~l~~~~~~~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~----~~~~~~i~~~~~~~~~~~~   94 (386)
T 2qby_A           19 PDELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLG----KFKHVYINTRQIDTPYRVL   94 (386)
T ss_dssp             CSCCTTCHHHHHHHHHSSGGGGGTCCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCS----SCEEEEEEHHHHCSHHHHH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcC----CceEEEEECCCCCCHHHHH
Confidence            36799999999999987763    456789999999999999999999987542100    34566666543210     


Q ss_pred             -------cc--ccCc-cHHHHHHHHHHHHHhcC-CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc---cCCCeE
Q 005179          360 -------GA--KERG-ELEARVTTLISEIQKSG-DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL---GRGELQ  425 (710)
Q Consensus       360 -------g~--~~~g-~~e~~l~~~~~~~~~~~-~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l---~~~~v~  425 (710)
                             +.  ...+ .....+..+...+...+ +.||+|||++.+.....         .+....|...+   ...++.
T Consensus        95 ~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~~---------~~~l~~l~~~~~~~~~~~~~  165 (386)
T 2qby_A           95 ADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKYN---------DDILYKLSRINSEVNKSKIS  165 (386)
T ss_dssp             HHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSSC---------STHHHHHHHHHHSCCC--EE
T ss_pred             HHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccCc---------CHHHHHHhhchhhcCCCeEE
Confidence                   00  0111 23333455555555443 88999999999965421         12333333333   456788


Q ss_pred             EEEccChHHHHhhhhccHHHHccc--cceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCc
Q 005179          426 CIASTTQDEHRTQFEKDKALARRF--QPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLP  503 (710)
Q Consensus       426 vI~att~~~~~~~~~~d~aL~~Rf--~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p  503 (710)
                      +|++++..++..  .+++.+.+||  ..|.+++++.++..+++...+...  .....+++++++.++.++...   ...|
T Consensus       166 ~I~~~~~~~~~~--~~~~~~~~r~~~~~i~l~~l~~~~~~~il~~~~~~~--~~~~~~~~~~~~~l~~~~~~~---~G~~  238 (386)
T 2qby_A          166 FIGITNDVKFVD--LLDPRVKSSLSEEEIIFPPYNAEELEDILTKRAQMA--FKPGVLPDNVIKLCAALAARE---HGDA  238 (386)
T ss_dssp             EEEEESCGGGGG--GCTTHHHHTTTTEEEEECCCCHHHHHHHHHHHHHHH--BCSSCSCHHHHHHHHHHHHHT---TCCH
T ss_pred             EEEEECCCChHh--hhCHHHhccCCCeeEEeCCCCHHHHHHHHHHHHHhh--ccCCCCCHHHHHHHHHHHHHh---cCCH
Confidence            888888765322  4678888999  479999999999999998866532  234678999999998887632   1235


Q ss_pred             chHHHHHHHHHhhh
Q 005179          504 DKAIDLVDEAGSRA  517 (710)
Q Consensus       504 ~~ai~ll~~a~~~~  517 (710)
                      ..++++++.++..+
T Consensus       239 r~~~~ll~~a~~~a  252 (386)
T 2qby_A          239 RRALDLLRVSGEIA  252 (386)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            67788888776443

>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=99.50  E-value=3.1e-14  Score=146.52  Aligned_cols=184  Identities=16%  Similarity=0.200  Sum_probs=110.7

Q ss_pred             CCCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh------
Q 005179          288 LIDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA------  359 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~------  359 (710)
                      +|+.++|++..+.++.+.+..  ....+++|+||||||||++|+++++.+...       +.+++.++++.+..      
T Consensus         4 ~f~~~ig~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKt~la~~i~~~~~~~-------~~~~~~v~~~~~~~~~~~~~   76 (265)
T 2bjv_A            4 YKDNLLGEANSFLEVLEQVSHLAPLDKPVLIIGERGTGKELIASRLHYLSSRW-------QGPFISLNCAALNENLLDSE   76 (265)
T ss_dssp             ------CCCHHHHHHHHHHHHHTTSCSCEEEECCTTSCHHHHHHHHHHTSTTT-------TSCEEEEEGGGSCHHHHHHH
T ss_pred             ccccceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCcHHHHHHHHHHhcCcc-------CCCeEEEecCCCChhHHHHH
Confidence            578899999999988876643  456789999999999999999999876322       34567777665421      


Q ss_pred             --ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-------------CCe
Q 005179          360 --GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-------------GEL  424 (710)
Q Consensus       360 --g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-------------~~v  424 (710)
                        |. ..|.+..........+....+.+|||||++.+             ..+.++.|...++.             .++
T Consensus        77 l~g~-~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l-------------~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~~  142 (265)
T 2bjv_A           77 LFGH-EAGAFTGAQKRHPGRFERADGGTLFLDELATA-------------PMMVQEKLLRVIEYGELERVGGSQPLQVNV  142 (265)
T ss_dssp             HHCC-C---------CCCCHHHHTTTSEEEEESGGGS-------------CHHHHHHHHHHHHHCEECCCCC--CEECCC
T ss_pred             hcCC-cccccccccccccchhhhcCCcEEEEechHhc-------------CHHHHHHHHHHHHhCCeecCCCcccccCCe
Confidence              10 01111100000000112234579999999999             33455566555543             257


Q ss_pred             EEEEccChHHHH--hhhhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcCC----CCCHHHHHHHHHH
Q 005179          425 QCIASTTQDEHR--TQFEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHNC----KFTLEAINAAVHL  492 (710)
Q Consensus       425 ~vI~att~~~~~--~~~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~~----~i~~~~l~~l~~l  492 (710)
                      ++|++|+.+...  ..-.+.+.|.+||..+.+..|+.    ++...+++.++.++....+.    .+++++++.+..+
T Consensus       143 ~iI~atn~~~~~~~~~~~~~~~L~~Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~~~~~~~~~~~~~~~a~~~L~~~  220 (265)
T 2bjv_A          143 RLVCATNADLPAMVNEGTFRADLLDALAFDVVQLPPLRERESDIMLMAEYFAIQMCREIKLPLFPGFTERARETLLNY  220 (265)
T ss_dssp             EEEEEESSCHHHHHHHTSSCHHHHHHHCSEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCSSCCCBCHHHHHHHHHS
T ss_pred             EEEEecCcCHHHHHHcCCccHHHHHhhcCcEEeCCChhhhhHHHHHHHHHHHHHHHHHhCCCcccCcCHHHHHHHHhC
Confidence            889988874321  11235789999997655555554    45555666666555544443    6899998877643

>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=99.48  E-value=5.9e-13  Score=144.26  Aligned_cols=211  Identities=23%  Similarity=0.266  Sum_probs=128.0

Q ss_pred             CcccCHHHHHHHHHHHH----c--------------------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCC
Q 005179          291 PVIGRETEIQRIIQILC----R--------------------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEV  340 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~----~--------------------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~  340 (710)
                      .++|++..++.+...+.    +                          ....++||+||||||||++|+++++.+     
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~la~~l-----   96 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL-----   96 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT-----
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHHHHHHh-----
Confidence            48999998888876652    1                          135789999999999999999999988     


Q ss_pred             CccccCceEEEeehhhhhhccccCcc-HHHHHHHHHHH----HHhcCCeEEEEccchhhhhCCCCCC-CCCCChHhHHHh
Q 005179          341 PVFLLSKRIMSLDMGLLMAGAKERGE-LEARVTTLISE----IQKSGDVILFIDEVHTLIGSGTVGR-GNKGTGLDISNL  414 (710)
Q Consensus       341 p~~l~~~~v~~ld~~~l~~g~~~~g~-~e~~l~~~~~~----~~~~~~~IL~IDEid~l~~~~~~~~-~~~~~~~~~~~~  414 (710)
                           +.+++.+++..+... .+.|. .+..+..++..    +....+.||||||+|.+...+.... ..+.....+++.
T Consensus        97 -----~~~~~~~~~~~~~~~-~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~~~  170 (376)
T 1um8_A           97 -----DIPIAISDATSLTEA-GYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQA  170 (376)
T ss_dssp             -----TCCEEEEEGGGCC---------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHH
T ss_pred             -----CCCEEEecchhhhhc-CcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCceecccchHHHHHH
Confidence                 567777777665421 12221 12234444432    2234578999999999965421100 000112236777


Q ss_pred             hcccccCC-----------------------CeEEEEccChHHHHh----------------------------------
Q 005179          415 LKPSLGRG-----------------------ELQCIASTTQDEHRT----------------------------------  437 (710)
Q Consensus       415 L~~~l~~~-----------------------~v~vI~att~~~~~~----------------------------------  437 (710)
                      |+.+++.+                       ++.+|++++......                                  
T Consensus       171 Ll~~le~~~~~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~  250 (376)
T 1um8_A          171 LLKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHD  250 (376)
T ss_dssp             HHHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHH
T ss_pred             HHHHhhccceecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHH
Confidence            77766643                       346677665311110                                  


Q ss_pred             --hhhccHHHHcccc-ceEecCCCHHHHHHHHH----HHHHHHHhh-----cCCCCCHHHHHHHHHHhhhhhcCCCCcch
Q 005179          438 --QFEKDKALARRFQ-PVLISEPSQEDAVRILL----GLREKYEAH-----HNCKFTLEAINAAVHLSARYISDRYLPDK  505 (710)
Q Consensus       438 --~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~----~l~~~~~~~-----~~~~i~~~~l~~l~~ls~~~i~~r~~p~~  505 (710)
                        ...+.+.|.+||. .+.+++++.++...|+.    .+..++...     .++.+++++++.++..+...   ..-...
T Consensus       251 l~~~~~~p~l~~R~~~~i~~~~l~~~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~---~~~~R~  327 (376)
T 1um8_A          251 LVTYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALER---KTGARG  327 (376)
T ss_dssp             HHHTTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHT---TCTGGG
T ss_pred             HhhcCCChHHhcCCCceeeccCCCHHHHHHHHhhhHHHHHHHHHHHHhhcCceEEECHHHHHHHHHHhccc---ccCcHH
Confidence              1235799999995 89999999999999997    354444322     24679999999998874321   111244


Q ss_pred             HHHHHHHHHh
Q 005179          506 AIDLVDEAGS  515 (710)
Q Consensus       506 ai~ll~~a~~  515 (710)
                      ...+++.++.
T Consensus       328 L~~~le~~~~  337 (376)
T 1um8_A          328 LRAIIEDFCL  337 (376)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5556665554

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.47  E-value=4.3e-14  Score=148.50  Aligned_cols=179  Identities=21%  Similarity=0.314  Sum_probs=114.4

Q ss_pred             CCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh--------h
Q 005179          290 DPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM--------A  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~--------~  359 (710)
                      ++++|++..+.++.+.+.+  ....++||+||||||||++|++++......+.       +++.++++.+.        .
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~-------~~v~v~~~~~~~~l~~~~lf   74 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVAPSDATVLIHGDSGTGKELVARALHACSARSDR-------PLVTLNCAALNESLLESELF   74 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHCSTTSCEEEESCTTSCHHHHHHHHHHHSSCSSS-------CCCEEECSSCCHHHHHHHHT
T ss_pred             CCcEECCHHHHHHHHHHHHHhCCCCcEEEECCCCchHHHHHHHHHHhCcccCC-------CeEEEeCCCCChHHHHHHhc
Confidence            3589999999998887765  56788999999999999999999987643333       34444443321        1


Q ss_pred             ccccCccHHHH---HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------C
Q 005179          360 GAKERGELEAR---VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------E  423 (710)
Q Consensus       360 g~~~~g~~e~~---l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~  423 (710)
                      |. ..|.+...   ....+..   ..+.+||||||+.+             ..+.+..|...++.+             +
T Consensus        75 g~-~~g~~tg~~~~~~g~~~~---a~~g~L~LDEi~~l-------------~~~~q~~Ll~~l~~~~~~~~g~~~~~~~~  137 (304)
T 1ojl_A           75 GH-EKGAFTGADKRREGRFVE---ADGGTLFLDEIGDI-------------SPLMQVRLLRAIQEREVQRVGSNQTISVD  137 (304)
T ss_dssp             CC-CSSCCC---CCCCCHHHH---HTTSEEEEESCTTC-------------CHHHHHHHHHHHHSSBCCBTTBCCCCBCC
T ss_pred             Cc-cccccCchhhhhcCHHHh---cCCCEEEEeccccC-------------CHHHHHHHHHHHhcCEeeecCCcccccCC
Confidence            11 11111000   1112222   23568999999999             344566666655543             4


Q ss_pred             eEEEEccChHHHHh--hhhccHHHHccccceEecCCC----HHHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          424 LQCIASTTQDEHRT--QFEKDKALARRFQPVLISEPS----QEDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       424 v~vI~att~~~~~~--~~~~d~aL~~Rf~~I~v~~Ps----~~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      +++|++||.+....  .-..++.|..||..+.+..|+    .++...+++.++.++...++   ..+++++++.+..+
T Consensus       138 ~riI~atn~~l~~~v~~g~fr~~L~~Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~~~~~~~~~~~s~~a~~~L~~~  215 (304)
T 1ojl_A          138 VRLIAATHRDLAEEVSAGRFRQDLYYRLNVVAIEMPSLRQRREDIPLLADHFLRRFAERNRKVVKGFTPQAMDLLIHY  215 (304)
T ss_dssp             CEEEEEESSCHHHHHHHTSSCHHHHHHHSSEEEECCCSGGGGGGHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHHC
T ss_pred             eEEEEecCccHHHHHHhCCcHHHHHhhcCeeEEeccCHHHhHhhHHHHHHHHHHHHHHHhccCccCCCHHHHHHHHcC
Confidence            78999988753211  113568899999866665555    45566677777666654433   57899999887655

>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=99.46  E-value=1.1e-12  Score=142.15  Aligned_cols=205  Identities=16%  Similarity=0.173  Sum_probs=136.9

Q ss_pred             CCcccCHHHHHHHHHHHHc----CCCC--CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh----
Q 005179          290 DPVIGRETEIQRIIQILCR----RTKN--NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA----  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~----~~~~--nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~----  359 (710)
                      +.++||+++++++...+..    ..+.  +++|+||||+|||++++.++..+....      +..++.+++.....    
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~------~~~~~~i~~~~~~~~~~~   90 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT------TARFVYINGFIYRNFTAI   90 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC------CCEEEEEETTTCCSHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCCCCCCeEEEECCCCCCHHHHHHHHHHHHhhhc------CeeEEEEeCccCCCHHHH
Confidence            6799999999999888765    3334  799999999999999999999874321      34556665432210    


Q ss_pred             --------cc--ccCc-cHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------
Q 005179          360 --------GA--KERG-ELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------  421 (710)
Q Consensus       360 --------g~--~~~g-~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------  421 (710)
                              +.  ...+ .....+..+...+.. ..+.||||||+|.+             ..+....|..++++      
T Consensus        91 ~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l-------------~~~~~~~L~~~~~~~~~~~~  157 (389)
T 1fnn_A           91 IGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL-------------APDILSTFIRLGQEADKLGA  157 (389)
T ss_dssp             HHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS-------------CHHHHHHHHHHTTCHHHHSS
T ss_pred             HHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc-------------chHHHHHHHHHHHhCCCCCc
Confidence                    00  0011 222333333333333 34789999999998             23345555555532      


Q ss_pred             CCeEEEEccChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc-
Q 005179          422 GELQCIASTTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS-  498 (710)
Q Consensus       422 ~~v~vI~att~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~-  498 (710)
                      .++.+|++++..++..  .+++.+.+||.  .+.+++++.++..+++...+...  .....+++++++.++..+.+... 
T Consensus       158 ~~~~iI~~~~~~~~~~--~l~~~~~~r~~~~~i~~~pl~~~~~~~~l~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~  233 (389)
T 1fnn_A          158 FRIALVIVGHNDAVLN--NLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAG--LAEGSYSEDILQMIADITGAQTPL  233 (389)
T ss_dssp             CCEEEEEEESSTHHHH--TSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHH--BCTTSSCHHHHHHHHHHHSBSSTT
T ss_pred             CCEEEEEEECCchHHH--HhCHHhhhcCCCceEEeCCCCHHHHHHHHHHHHHhh--cCCCCCCHHHHHHHHHHHhhcccC
Confidence            5788888877664333  46788999997  69999999999999998876542  12347899999999988743311 


Q ss_pred             --CCCCcchHHHHHHHHHhhh
Q 005179          499 --DRYLPDKAIDLVDEAGSRA  517 (710)
Q Consensus       499 --~r~~p~~ai~ll~~a~~~~  517 (710)
                        ....+..+++++..++..+
T Consensus       234 ~~~~G~~r~~~~~l~~a~~~a  254 (389)
T 1fnn_A          234 DTNRGDARLAIDILYRSAYAA  254 (389)
T ss_dssp             CTTSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCcHHHHHHHHHHHHHHH
Confidence              0234667888888776543

>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=99.46  E-value=1.3e-13  Score=156.26  Aligned_cols=176  Identities=19%  Similarity=0.243  Sum_probs=112.2

Q ss_pred             CcccCHHHHHHHHHHHHc------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc---
Q 005179          291 PVIGRETEIQRIIQILCR------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA---  361 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~---  361 (710)
                      +++|.++....+.+.+..      ..+.+++|+||||||||+++++++..+          +.....+++..+....   
T Consensus        82 di~G~~~vk~~i~~~~~l~~~~~~~~g~~vll~Gp~GtGKTtlar~ia~~l----------~~~~~~i~~~~~~~~~~~~  151 (543)
T 3m6a_A           82 EHHGLEKVKERILEYLAVQKLTKSLKGPILCLAGPPGVGKTSLAKSIAKSL----------GRKFVRISLGGVRDESEIR  151 (543)
T ss_dssp             HCSSCHHHHHHHHHHHHHHHHSSSCCSCEEEEESSSSSSHHHHHHHHHHHH----------TCEEEEECCCC--------
T ss_pred             HhccHHHHHHHHHHHHHHHHhcccCCCCEEEEECCCCCCHHHHHHHHHHhc----------CCCeEEEEecccchhhhhh
Confidence            478888877776554321      235578999999999999999999988          4445555443322110   


Q ss_pred             ----ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC----------------
Q 005179          362 ----KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR----------------  421 (710)
Q Consensus       362 ----~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~----------------  421 (710)
                          .+.|.....+...+..+.... .||||||+|.+....         ..+.++.|...++.                
T Consensus       152 g~~~~~ig~~~~~~~~~~~~a~~~~-~vl~lDEid~l~~~~---------~~~~~~~LL~~ld~~~~~~~~~~~~~~~~~  221 (543)
T 3m6a_A          152 GHRRTYVGAMPGRIIQGMKKAGKLN-PVFLLDEIDKMSSDF---------RGDPSSAMLEVLDPEQNSSFSDHYIEETFD  221 (543)
T ss_dssp             ------------CHHHHHHTTCSSS-EEEEEEESSSCC------------------CCGGGTCTTTTTBCCCSSSCCCCB
T ss_pred             hHHHHHhccCchHHHHHHHHhhccC-CEEEEhhhhhhhhhh---------ccCHHHHHHHHHhhhhcceeecccCCeeec
Confidence                223333333444444443333 499999999995431         11234555555532                


Q ss_pred             -CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHH-HHHHhhc-----CCCCCHHHHHHHHH
Q 005179          422 -GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLR-EKYEAHH-----NCKFTLEAINAAVH  491 (710)
Q Consensus       422 -~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~-~~~~~~~-----~~~i~~~~l~~l~~  491 (710)
                       .++++|+|||...     .++++|++||..|.++.|+.+++..|++..+ .++...+     ++.++++++..++.
T Consensus       222 ~~~v~iI~ttN~~~-----~l~~aL~~R~~vi~~~~~~~~e~~~Il~~~l~~~~~~~~~~~~~~i~i~~~~l~~l~~  293 (543)
T 3m6a_A          222 LSKVLFIATANNLA-----TIPGPLRDRMEIINIAGYTEIEKLEIVKDHLLPKQIKEHGLKKSNLQLRDQAILDIIR  293 (543)
T ss_dssp             CSSCEEEEECSSTT-----TSCHHHHHHEEEEECCCCCHHHHHHHHHHTHHHHHHHHTTCCGGGCEECHHHHHHHHH
T ss_pred             ccceEEEeccCccc-----cCCHHHHhhcceeeeCCCCHHHHHHHHHHHHHHHHHHHcCCCcccccCCHHHHHHHHH
Confidence             4578999999865     7899999999999999999999999998744 3333333     35678999888776

>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=99.45  E-value=1.1e-12  Score=169.30  Aligned_cols=140  Identities=14%  Similarity=0.185  Sum_probs=95.0

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHH-H---------
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEI-Q---------  379 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~-~---------  379 (710)
                      .+.++||+||||||||++|+.+....         .+..++.++++.....        ..+...++.. .         
T Consensus      1266 ~~~~vLL~GPpGtGKT~la~~~l~~~---------~~~~~~~infsa~ts~--------~~~~~~i~~~~~~~~~~~g~~ 1328 (2695)
T 4akg_A         1266 SKRGIILCGPPGSGKTMIMNNALRNS---------SLYDVVGINFSKDTTT--------EHILSALHRHTNYVTTSKGLT 1328 (2695)
T ss_dssp             HTCEEEEECSTTSSHHHHHHHHHHSC---------SSCEEEEEECCTTCCH--------HHHHHHHHHHBCCEEETTTEE
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHhcC---------CCCceEEEEeecCCCH--------HHHHHHHHHHhhhccccCCcc
Confidence            35789999999999999997665432         1455666665443321        1133333322 0         


Q ss_pred             -----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------------CeEEEEccChHHHHhhhh
Q 005179          380 -----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------------ELQCIASTTQDEHRTQFE  440 (710)
Q Consensus       380 -----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------------~v~vI~att~~~~~~~~~  440 (710)
                           ...+.||||||++.....       ..+.....++|+++++.+              ++++|+|||++...+...
T Consensus      1329 ~~P~~~gk~~VlFiDEinmp~~d-------~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~ 1401 (2695)
T 4akg_A         1329 LLPKSDIKNLVLFCDEINLPKLD-------KYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIP 1401 (2695)
T ss_dssp             EEEBSSSSCEEEEEETTTCSCCC-------SSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCC
T ss_pred             ccCCCCCceEEEEeccccccccc-------ccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCcc
Confidence                 123479999999864221       122344666777666532              478999999874234457


Q ss_pred             ccHHHHccccceEecCCCHHHHHHHHHHHHHHH
Q 005179          441 KDKALARRFQPVLISEPSQEDAVRILLGLREKY  473 (710)
Q Consensus       441 ~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~  473 (710)
                      ++++|.|||..|.++.|+.+++..|+..+...+
T Consensus      1402 l~~rllRrf~vi~i~~P~~~~l~~I~~~il~~~ 1434 (2695)
T 4akg_A         1402 MSERFTRHAAILYLGYPSGKSLSQIYEIYYKAI 1434 (2695)
T ss_dssp             CCHHHHTTEEEEECCCCTTTHHHHHHHHHHHHH
T ss_pred             CChhhhheeeEEEeCCCCHHHHHHHHHHHHHHH
Confidence            899999999999999999999999999887654

>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=99.35  E-value=5.3e-12  Score=137.60  Aligned_cols=105  Identities=27%  Similarity=0.334  Sum_probs=71.5

Q ss_pred             CeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------CCeEEEEcc-----ChHHHHhhhhccHHH
Q 005179          383 DVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------GELQCIAST-----TQDEHRTQFEKDKAL  445 (710)
Q Consensus       383 ~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------~~v~vI~at-----t~~~~~~~~~~d~aL  445 (710)
                      ..||++||+|.+...+.. .+.+-+..-+++.|++.++.            .++.+|+++     ++.      .+.|.|
T Consensus       251 ~~il~~DEidki~~~~~~-~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~~~~~------dlipel  323 (444)
T 1g41_A          251 NGIVFIDEIDKICKKGEY-SGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQVARPS------DLIPEL  323 (444)
T ss_dssp             HCEEEEETGGGGSCCSSC-SSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSSCCGG------GSCHHH
T ss_pred             CCeeeHHHHHHHhhccCC-CCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEeccccccCChh------hcchHH
Confidence            458999999999754321 11001111255677776653            356788776     443      355899


Q ss_pred             Hcccc-ceEecCCCHHHHHHHHH----HHHHHHHhh-----cCCCCCHHHHHHHHHHhh
Q 005179          446 ARRFQ-PVLISEPSQEDAVRILL----GLREKYEAH-----HNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       446 ~~Rf~-~I~v~~Ps~~~~~~IL~----~l~~~~~~~-----~~~~i~~~~l~~l~~ls~  494 (710)
                      .+||. .|.++.++.++...|+.    .+..+|...     ..+.++++++..+++.+.
T Consensus       324 ~~R~~i~i~l~~lt~~e~~~Il~~~~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~  382 (444)
T 1g41_A          324 QGRLPIRVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAF  382 (444)
T ss_dssp             HTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHH
T ss_pred             hcccceeeeCCCCCHHHHHHHHHHHHHhHHHHHHHHhcccCceEEECHHHHHHHHHHHH
Confidence            99998 48999999999999994    355555432     235799999999998754

>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=99.33  E-value=5.8e-12  Score=150.56  Aligned_cols=182  Identities=20%  Similarity=0.260  Sum_probs=125.9

Q ss_pred             CCcccCHHHHHHHHHHHHcCC---------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc
Q 005179          290 DPVIGRETEIQRIIQILCRRT---------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG  360 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~---------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g  360 (710)
                      +.++|++..++.+...+.+..         ..++||+||||||||++|++|++.+...       +..++.++++.+...
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~~~~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~-------~~~~i~i~~~~~~~~  630 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT-------EEAMIRIDMTEYMEK  630 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS-------GGGEEEECTTTCCSS
T ss_pred             cccCCcHHHHHHHHHHHHHHhcccCCCCCCceEEEEECCCCCCHHHHHHHHHHHhcCC-------CCcEEEEechhccch
Confidence            357999999998888775421         1368999999999999999999988543       345666666554321


Q ss_pred             c----------ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------
Q 005179          361 A----------KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------  422 (710)
Q Consensus       361 ~----------~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------  422 (710)
                      .          .+.|.-+  ...+...+....+.||||||++.+             ..++++.|.++++.+        
T Consensus       631 ~~~s~l~g~~~~~~G~~~--~g~l~~~~~~~~~~vl~lDEi~~l-------------~~~~~~~Ll~~l~~~~~~~~~g~  695 (854)
T 1qvr_A          631 HAVSRLIGAPPGYVGYEE--GGQLTEAVRRRPYSVILFDEIEKA-------------HPDVFNILLQILDDGRLTDSHGR  695 (854)
T ss_dssp             GGGGGC----------------CHHHHHHHCSSEEEEESSGGGS-------------CHHHHHHHHHHHTTTEECCSSSC
T ss_pred             hHHHHHcCCCCCCcCccc--cchHHHHHHhCCCeEEEEeccccc-------------CHHHHHHHHHHhccCceECCCCC
Confidence            0          0111100  122333344556789999999988             567888898888765        


Q ss_pred             -----CeEEEEccChHH---------------HHhh------hhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh
Q 005179          423 -----ELQCIASTTQDE---------------HRTQ------FEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA  475 (710)
Q Consensus       423 -----~v~vI~att~~~---------------~~~~------~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~  475 (710)
                           ++++|+|||...               ....      -...|.|.+||+ .+.+.+|+.+++..|++.++.++..
T Consensus       696 ~vd~~~~iiI~tsn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~Rl~~~i~~~pl~~edi~~i~~~~l~~~~~  775 (854)
T 1qvr_A          696 TVDFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRA  775 (854)
T ss_dssp             CEECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHH
T ss_pred             EeccCCeEEEEecCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHHhcCeEEeCCCCCHHHHHHHHHHHHHHHHH
Confidence                 456888888621               1111      134688999995 7888889999999999988776653


Q ss_pred             hc-----CCCCCHHHHHHHHHHh
Q 005179          476 HH-----NCKFTLEAINAAVHLS  493 (710)
Q Consensus       476 ~~-----~~~i~~~~l~~l~~ls  493 (710)
                      ..     .+.+++++++.++..+
T Consensus       776 ~~~~~~~~~~~~~~a~~~L~~~~  798 (854)
T 1qvr_A          776 RLAEKRISLELTEAAKDFLAERG  798 (854)
T ss_dssp             HHHTTTCEEEECHHHHHHHHHHH
T ss_pred             HHHhCCceEEECHHHHHHHHHcC
Confidence            22     3578999999988763

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.32  E-value=1e-12  Score=122.30  Aligned_cols=135  Identities=16%  Similarity=0.039  Sum_probs=88.2

Q ss_pred             CcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHH
Q 005179          291 PVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELE  368 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e  368 (710)
                      .++|++..++++.+.+.+  ....+++|+||||||||++|+++++.....       +..++ +++..+...    ..  
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~~~~~vll~G~~GtGKt~lA~~i~~~~~~~-------~~~~v-~~~~~~~~~----~~--   67 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNA-------QGEFV-YRELTPDNA----PQ--   67 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTTCCSCEEEESSTTSSHHHHHHHHHHSSTTT-------TSCCE-EEECCTTTS----SC--
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCCEEEECCCCCCHHHHHHHHHHhCCcc-------CCCEE-EECCCCCcc----hh--
Confidence            579999999998887654  566789999999999999999999865332       34455 666554432    11  


Q ss_pred             HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEEccChHHHH--hhhhccHH
Q 005179          369 ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIASTTQDEHR--TQFEKDKA  444 (710)
Q Consensus       369 ~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~att~~~~~--~~~~~d~a  444 (710)
                        ....+..+   .+.+|||||+|.+             ..+.+..|..++.  ..++++|++||.+...  ..-...+.
T Consensus        68 --~~~~~~~a---~~g~l~ldei~~l-------------~~~~q~~Ll~~l~~~~~~~~~I~~t~~~~~~~~~~~~~~~~  129 (145)
T 3n70_A           68 --LNDFIALA---QGGTLVLSHPEHL-------------TREQQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNHIIAE  129 (145)
T ss_dssp             --HHHHHHHH---TTSCEEEECGGGS-------------CHHHHHHHHHHHHSSSCSSCEEEEESSCHHHHHHHSCCCHH
T ss_pred             --hhcHHHHc---CCcEEEEcChHHC-------------CHHHHHHHHHHHhhcCCCEEEEEECCcCHHHHHHcCCCCHH
Confidence              23333333   3568999999999             3344555555544  3457888888865321  12235678


Q ss_pred             HHccccceEecCC
Q 005179          445 LARRFQPVLISEP  457 (710)
Q Consensus       445 L~~Rf~~I~v~~P  457 (710)
                      |..||..+.+..|
T Consensus       130 L~~rl~~~~i~lP  142 (145)
T 3n70_A          130 LYYCFAMTQIACL  142 (145)
T ss_dssp             HHHHHHHHEEECC
T ss_pred             HHHHhcCCEEeCC
Confidence            8888874444444

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.29  E-value=5.9e-13  Score=123.65  Aligned_cols=131  Identities=15%  Similarity=0.190  Sum_probs=86.7

Q ss_pred             CcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHH
Q 005179          291 PVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELE  368 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e  368 (710)
                      +++|+++.++++.+.+..  ....+++|+||||||||++|++++...          . +++.+++..+....       
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~~~~~vll~G~~GtGKt~lA~~i~~~~----------~-~~~~~~~~~~~~~~-------   66 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAKRTSPVFLTGEAGSPFETVARYFHKNG----------T-PWVSPARVEYLIDM-------   66 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHTCSSCEEEEEETTCCHHHHHGGGCCTT----------S-CEECCSSTTHHHHC-------
T ss_pred             CceeCCHHHHHHHHHHHHHhCCCCcEEEECCCCccHHHHHHHHHHhC----------C-CeEEechhhCChHh-------
Confidence            478999999888887654  566789999999999999999998755          2 56666665543211       


Q ss_pred             HHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC---CCeEEEEccChHHHH-hhhhccHH
Q 005179          369 ARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR---GELQCIASTTQDEHR-TQFEKDKA  444 (710)
Q Consensus       369 ~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~---~~v~vI~att~~~~~-~~~~~d~a  444 (710)
                        ...++..   ..+.+|||||++.+             ..+.+..|...+++   .++++|++||.+... ..- .++.
T Consensus        67 --~~~~~~~---a~~~~l~lDei~~l-------------~~~~q~~Ll~~l~~~~~~~~~iI~~tn~~~~~~~~~-~~~~  127 (143)
T 3co5_A           67 --PMELLQK---AEGGVLYVGDIAQY-------------SRNIQTGITFIIGKAERCRVRVIASCSYAAGSDGIS-CEEK  127 (143)
T ss_dssp             --HHHHHHH---TTTSEEEEEECTTC-------------CHHHHHHHHHHHHHHTTTTCEEEEEEEECTTTC--C-HHHH
T ss_pred             --hhhHHHh---CCCCeEEEeChHHC-------------CHHHHHHHHHHHHhCCCCCEEEEEecCCCHHHHHhC-ccHH
Confidence              2333332   33579999999999             34455666666653   458899988865311 111 5677


Q ss_pred             HHccccceEecCCC
Q 005179          445 LARRFQPVLISEPS  458 (710)
Q Consensus       445 L~~Rf~~I~v~~Ps  458 (710)
                      |..||..+.+..|+
T Consensus       128 L~~rl~~~~i~lPp  141 (143)
T 3co5_A          128 LAGLFSESVVRIPP  141 (143)
T ss_dssp             HHHHSSSEEEEECC
T ss_pred             HHHHhcCcEEeCCC
Confidence            88888755554443

>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=99.29  E-value=3.8e-11  Score=155.00  Aligned_cols=124  Identities=14%  Similarity=0.210  Sum_probs=89.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEcc
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDE  390 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDE  390 (710)
                      ..+.++.||+|||||++++.+|+.+          +..++.++++.-...        ..+..++..+... +.++++||
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~l----------g~~~v~~nc~e~ld~--------~~lg~~~~g~~~~-Gaw~~~DE  705 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNL----------GRVVVVFNCDDSFDY--------QVLSRLLVGITQI-GAWGCFDE  705 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTT----------TCCCEEEETTSSCCH--------HHHHHHHHHHHHH-TCEEEEET
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHh----------CCcEEEEECCCCCCh--------hHhhHHHHHHHhc-CCEeeehh
Confidence            4568999999999999999999998          788888887653321        2245556555544 47999999


Q ss_pred             chhhhhCCCCCCCCCCChHhHHHhh-------cccc--------c-------CCCeEEEEccChHHHHhhhhccHHHHcc
Q 005179          391 VHTLIGSGTVGRGNKGTGLDISNLL-------KPSL--------G-------RGELQCIASTTQDEHRTQFEKDKALARR  448 (710)
Q Consensus       391 id~l~~~~~~~~~~~~~~~~~~~~L-------~~~l--------~-------~~~v~vI~att~~~~~~~~~~d~aL~~R  448 (710)
                      ++.+             ..++...+       ...+        .       .....+++|+|+ .|....+++++|++|
T Consensus       706 ~nr~-------------~~evLs~l~~~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NP-gy~g~~eLP~~Lk~~  771 (2695)
T 4akg_A          706 FNRL-------------DEKVLSAVSANIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNP-GYNGRSELPENLKKS  771 (2695)
T ss_dssp             TTSS-------------CHHHHHHHHHHHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECC-CSSSSCCCCHHHHTT
T ss_pred             hhhc-------------ChHHHHHHHHHHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCC-CccCcccccHHHHhh
Confidence            9987             22232222       1111        1       134557788887 476677899999999


Q ss_pred             ccceEecCCCHHHHHHHHH
Q 005179          449 FQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       449 f~~I~v~~Ps~~~~~~IL~  467 (710)
                      |..|.+..|+.+...+|+-
T Consensus       772 Fr~v~m~~Pd~~~i~ei~l  790 (2695)
T 4akg_A          772 FREFSMKSPQSGTIAEMIL  790 (2695)
T ss_dssp             EEEEECCCCCHHHHHHHHH
T ss_pred             eEEEEeeCCCHHHHHHHHH
Confidence            9999999999988777753

>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=99.27  E-value=2.5e-11  Score=129.15  Aligned_cols=170  Identities=16%  Similarity=0.177  Sum_probs=116.5

Q ss_pred             CHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCcc--c------------cCceEEEeehhhhhh
Q 005179          295 RETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVF--L------------LSKRIMSLDMGLLMA  359 (710)
Q Consensus       295 r~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~--l------------~~~~v~~ld~~~l~~  359 (710)
                      +++.++.+...+......+ +||+||+|+|||++|+.+++.+.+......  .            ....++.++...   
T Consensus         7 ~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~---   83 (334)
T 1a5t_A            7 LRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEK---   83 (334)
T ss_dssp             GHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCT---
T ss_pred             hHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccc---
Confidence            3556777787777766555 899999999999999999999865331110  0            001233333210   


Q ss_pred             ccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChH
Q 005179          360 GAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQD  433 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~  433 (710)
                      +....  -...++.+++.+..    .+..|++|||+|.+             ..+.++.|...+++  .++++|.+|+..
T Consensus        84 ~~~~~--~i~~ir~l~~~~~~~~~~~~~kvviIdead~l-------------~~~a~naLLk~lEep~~~~~~Il~t~~~  148 (334)
T 1a5t_A           84 GKNTL--GVDAVREVTEKLNEHARLGGAKVVWVTDAALL-------------TDAAANALLKTLEEPPAETWFFLATREP  148 (334)
T ss_dssp             TCSSB--CHHHHHHHHHHTTSCCTTSSCEEEEESCGGGB-------------CHHHHHHHHHHHTSCCTTEEEEEEESCG
T ss_pred             cCCCC--CHHHHHHHHHHHhhccccCCcEEEEECchhhc-------------CHHHHHHHHHHhcCCCCCeEEEEEeCCh
Confidence            00111  12335666666543    34689999999999             44567778888875  357777777765


Q ss_pred             HHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          434 EHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       434 ~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                      +     .+.+++++|++.+.+++|+.++..++|+...         .+++++++.++.++.+.
T Consensus       149 ~-----~l~~ti~SRc~~~~~~~~~~~~~~~~L~~~~---------~~~~~~~~~l~~~s~G~  197 (334)
T 1a5t_A          149 E-----RLLATLRSRCRLHYLAPPPEQYAVTWLSREV---------TMSQDALLAALRLSAGS  197 (334)
T ss_dssp             G-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHC---------CCCHHHHHHHHHHTTTC
T ss_pred             H-----hCcHHHhhcceeeeCCCCCHHHHHHHHHHhc---------CCCHHHHHHHHHHcCCC
Confidence            4     6789999999999999999999888776432         67889988888887553

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.26  E-value=6.2e-11  Score=136.22  Aligned_cols=219  Identities=22%  Similarity=0.277  Sum_probs=131.2

Q ss_pred             HhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccc--------cCceEEEee
Q 005179          282 ARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFL--------LSKRIMSLD  353 (710)
Q Consensus       282 ~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l--------~~~~v~~ld  353 (710)
                      .++++..|+.++|++..++.+...+..  +.+++|+||||||||+++++|+..+.........        ....+..+.
T Consensus        33 ~~~rp~~l~~i~G~~~~l~~l~~~i~~--g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~~~~~~~~~~~~~~p~i~~~p  110 (604)
T 3k1j_A           33 IEVPEKLIDQVIGQEHAVEVIKTAANQ--KRHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPEDENMPRIKTVP  110 (604)
T ss_dssp             SCCCSSHHHHCCSCHHHHHHHHHHHHT--TCCEEEECCTTSSHHHHHHHHHHTSCCSSCEEEEEECCTTCTTSCEEEEEE
T ss_pred             ccccccccceEECchhhHhhccccccC--CCEEEEEeCCCCCHHHHHHHHhccCCcccCCeEEEeCCcccccCCcEEEEe
Confidence            355677788899999999888877765  3689999999999999999999876322100000        000000000


Q ss_pred             hhh---------------------------------hh------hccccCccHHHHHHHHHH------------------
Q 005179          354 MGL---------------------------------LM------AGAKERGELEARVTTLIS------------------  376 (710)
Q Consensus       354 ~~~---------------------------------l~------~g~~~~g~~e~~l~~~~~------------------  376 (710)
                      ...                                 +.      .+.............++.                  
T Consensus       111 ~g~~~~~~e~~~~~~~~~~~~r~~~~~~~~~~~~~nl~v~~~~~~~~~~v~~~~~~~~~L~G~~~~~~~~~g~~~~g~~~  190 (604)
T 3k1j_A          111 ACQGRRIVEKYREKAKSQESVKSSNMRLKSTVLVPKLLVDNCGRTKAPFIDATGAHAGALLGDVRHDPFQSGGLGTPAHE  190 (604)
T ss_dssp             TTHHHHHHHHHHHHHHHHTCC-----------CCCEEEECCTTCSSCCEEECTTCCHHHHHCEECCCCC----CCCCGGG
T ss_pred             cchHHHHHHHHHHhhccchhhhhhcccccccccccceeeccccCCCCCEEEcCCCCHHhcCceEEechhhcCCccccccc
Confidence            000                                 00      000000000000011110                  


Q ss_pred             -----HHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------------------CeEEEE
Q 005179          377 -----EIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------------------ELQCIA  428 (710)
Q Consensus       377 -----~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------------------~v~vI~  428 (710)
                           .+....+.+|||||++.+             ...+++.|+..|+++                       ++++|+
T Consensus       191 ~i~~g~~~~a~~gvL~LDEi~~l-------------~~~~q~~Ll~~Le~~~~~~~g~~~~~~~~~l~~~~~p~~~~vI~  257 (604)
T 3k1j_A          191 RVEPGMIHRAHKGVLFIDEIATL-------------SLKMQQSLLTAMQEKKFPITGQSEMSSGAMVRTEPVPCDFVLVA  257 (604)
T ss_dssp             GEECCHHHHTTTSEEEETTGGGS-------------CHHHHHHHHHHHHHSEECCBCSCTTSGGGGCBCSCEECCCEEEE
T ss_pred             cccCceeeecCCCEEEEechhhC-------------CHHHHHHHHHHHHcCcEEecccccccccccCCCCccceeEEEEE
Confidence                 112234679999999998             345666666655522                       467999


Q ss_pred             ccChHHHHhhhhccHHHHccccc--eEecCC-----CHHHHHHHHHHHHHHHHhh-cCCCCCHHHHHHHHHHhhhhhcCC
Q 005179          429 STTQDEHRTQFEKDKALARRFQP--VLISEP-----SQEDAVRILLGLREKYEAH-HNCKFTLEAINAAVHLSARYISDR  500 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~~--I~v~~P-----s~~~~~~IL~~l~~~~~~~-~~~~i~~~~l~~l~~ls~~~i~~r  500 (710)
                      +||++..   ..++++|.+||..  +.++.+     ..+....+++.+...+... ....++++++..++..+.++-..+
T Consensus       258 atn~~~~---~~l~~~l~~R~~v~~i~i~l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ls~eAl~~Li~~~~r~~g~r  334 (604)
T 3k1j_A          258 AGNLDTV---DKMHPALRSRIRGYGYEVYMRTTMPDTIENRRKLVQFVAQEVKRDGKIPHFTKEAVEEIVREAQKRAGRK  334 (604)
T ss_dssp             EECHHHH---HHSCHHHHHHHHHHSEEEECCSEEECCHHHHHHHHHHHHHHHHHHCSSCCBBHHHHHHHHHHHHHTTCST
T ss_pred             ecCHHHH---hhcCHHHHHHhhccceEeeccccccCCHHHHHHHHHHHHHHHhhccCcccCCHHHHHHHHHHHhhhhccc
Confidence            9998742   2589999999962  334322     3555666666655554432 335799999999999887776655


Q ss_pred             C----CcchHHHHHHHHHhhhh
Q 005179          501 Y----LPDKAIDLVDEAGSRAH  518 (710)
Q Consensus       501 ~----~p~~ai~ll~~a~~~~~  518 (710)
                      .    .+..+.+++..|...+.
T Consensus       335 ~~l~~~~R~l~~llr~A~~~A~  356 (604)
T 3k1j_A          335 GHLTLRLRDLGGIVRAAGDIAV  356 (604)
T ss_dssp             TEEECCHHHHHHHHHHHHHHHH
T ss_pred             cccccCHHHHHHHHHHHHHHHH
Confidence            4    45677778887765443

>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=99.21  E-value=2.9e-10  Score=124.11  Aligned_cols=214  Identities=14%  Similarity=0.115  Sum_probs=130.5

Q ss_pred             CCcccCHHHHHHHHHHH-Hc------CCCCCcEE--EcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh---
Q 005179          290 DPVIGRETEIQRIIQIL-CR------RTKNNPIL--LGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL---  357 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L-~~------~~~~nvLL--~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l---  357 (710)
                      +.++||+++++.+...+ ..      ..+.+++|  +||+|+|||++++.+++.+.... +....+..++.+++...   
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~  100 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAA-AKEGLTVKQAYVNAFNAPNL  100 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHH-HHTTCCEEEEEEEGGGCCSH
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHH-hccCCceeEEEEECCCCCCH
Confidence            56999999999998887 42      24567888  99999999999999998874310 00001234555553211   


Q ss_pred             ---h----h--ccc--cCc-cHHHHHHHHHHHHH-hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc---c-
Q 005179          358 ---M----A--GAK--ERG-ELEARVTTLISEIQ-KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL---G-  420 (710)
Q Consensus       358 ---~----~--g~~--~~g-~~e~~l~~~~~~~~-~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l---~-  420 (710)
                         .    .  +..  ..+ .....+..+...+. ...+.||+|||+|.+.....       ...+....|...+   . 
T Consensus       101 ~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~-------~~~~~l~~l~~~~~~~~~  173 (412)
T 1w5s_A          101 YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPR-------IAAEDLYTLLRVHEEIPS  173 (412)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTT-------SCHHHHHHHHTHHHHSCC
T ss_pred             HHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccC-------cchHHHHHHHHHHHhccc
Confidence               0    0  110  011 12222333333333 24578999999999953210       0122333222222   2 


Q ss_pred             -C--CCeEEEEccChHHHHhhhhcc---HHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHh
Q 005179          421 -R--GELQCIASTTQDEHRTQFEKD---KALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       421 -~--~~v~vI~att~~~~~~~~~~d---~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls  493 (710)
                       .  .++.+|++++..++..  .++   +.+.++|. .+.+++++.++..+++.......  ..+..+++++++.++..+
T Consensus       174 ~~~~~~v~lI~~~~~~~~~~--~l~~~~~~~~~~~~~~i~l~~l~~~e~~~ll~~~~~~~--~~~~~~~~~~~~~i~~~~  249 (412)
T 1w5s_A          174 RDGVNRIGFLLVASDVRALS--YMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELG--LRDTVWEPRHLELISDVY  249 (412)
T ss_dssp             TTSCCBEEEEEEEEETHHHH--HHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHH--BCTTSCCHHHHHHHHHHH
T ss_pred             CCCCceEEEEEEeccccHHH--HHhhhcchhhhhcCCeeeeCCCCHHHHHHHHHHHHHhc--CCCCCCChHHHHHHHHHH
Confidence             3  5778888876554322  234   66777775 59999999999999998765533  223468899999998888


Q ss_pred             hhhhcCCCCcchHHHHHHHHHh
Q 005179          494 ARYISDRYLPDKAIDLVDEAGS  515 (710)
Q Consensus       494 ~~~i~~r~~p~~ai~ll~~a~~  515 (710)
                      .+..+....|..+..++..++.
T Consensus       250 ~~~~~~~G~p~~~~~l~~~a~~  271 (412)
T 1w5s_A          250 GEDKGGDGSARRAIVALKMACE  271 (412)
T ss_dssp             CGGGTSCCCHHHHHHHHHHHHH
T ss_pred             HHhccCCCcHHHHHHHHHHHHH
Confidence            7443222456777788776654

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.21  E-value=2.7e-11  Score=127.29  Aligned_cols=86  Identities=52%  Similarity=0.795  Sum_probs=80.5

Q ss_pred             HHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          615 DERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       615 ~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      ++...+.++++.|.+.++||+++++.+...+...+.|+..|.+|.+.+||+||||||||++|++||+.++.....++.+|
T Consensus         3 ~~~~~l~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~   82 (311)
T 4fcw_A            3 GEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRID   82 (311)
T ss_dssp             HHHHHHHTHHHHHHTTCCSCHHHHHHHHHHHHHHHHTCSCTTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEE
T ss_pred             cHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEee
Confidence            45677889999999999999999999999999999999999999999999999999999999999999999888999999


Q ss_pred             CCCCCC
Q 005179          695 PSPFNS  700 (710)
Q Consensus       695 ~se~~~  700 (710)
                      ++++..
T Consensus        83 ~~~~~~   88 (311)
T 4fcw_A           83 MTEYME   88 (311)
T ss_dssp             GGGCCS
T ss_pred             cccccc
Confidence            998754

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.20  E-value=3.4e-11  Score=134.03  Aligned_cols=208  Identities=13%  Similarity=0.096  Sum_probs=120.2

Q ss_pred             CcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHH
Q 005179          291 PVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEAR  370 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~  370 (710)
                      .++|+++.++.+...+..  +.|+||+||||||||++|++++..+.. ..|.....+.+  ...+.+. |. ..+.... 
T Consensus        23 ~ivGq~~~i~~l~~al~~--~~~VLL~GpPGtGKT~LAraLa~~l~~-~~~f~~~~~~~--~t~~dL~-G~-~~~~~~~-   94 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALS--GESVFLLGPPGIAKSLIARRLKFAFQN-ARAFEYLMTRF--STPEEVF-GP-LSIQALK-   94 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHH--TCEEEEECCSSSSHHHHHHHGGGGBSS-CCEEEEECCTT--CCHHHHH-CC-BC------
T ss_pred             hhHHHHHHHHHHHHHHhc--CCeeEeecCchHHHHHHHHHHHHHHhh-hhHHHHHHHhc--CCHHHhc-Cc-ccHHHHh-
Confidence            489999999988877665  468999999999999999999987621 11111101110  0112222 11 0000000 


Q ss_pred             HHHHHHHHHhc---CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCC------------eEEEEccChHHH
Q 005179          371 VTTLISEIQKS---GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGE------------LQCIASTTQDEH  435 (710)
Q Consensus       371 l~~~~~~~~~~---~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~------------v~vI~att~~~~  435 (710)
                      -...+..+...   .+.|||||||+.+             ....++.|...|+++.            ..+|++||+.+ 
T Consensus        95 ~~g~~~~~~~g~l~~~~IL~IDEI~r~-------------~~~~q~~LL~~lee~~v~i~G~~~~~~~~~iI~ATN~lp-  160 (500)
T 3nbx_X           95 DEGRYERLTSGYLPEAEIVFLDEIWKA-------------GPAILNTLLTAINERQFRNGAHVEKIPMRLLVAASNELP-  160 (500)
T ss_dssp             -----CBCCTTSGGGCSEEEEESGGGC-------------CHHHHHHHHHHHHSSEEECSSSEEECCCCEEEEEESSCC-
T ss_pred             hchhHHhhhccCCCcceeeeHHhHhhh-------------cHHHHHHHHHHHHHHhccCCCCcCCcchhhhhhccccCC-
Confidence            00111111111   2458999999887             4456677776665432            13466666422 


Q ss_pred             HhhhhccHHHHcccc-ceEecCCCH-HHHHHHHHHHH-------------------HHHHhhcCCCCCHHHHHHHHHHhh
Q 005179          436 RTQFEKDKALARRFQ-PVLISEPSQ-EDAVRILLGLR-------------------EKYEAHHNCKFTLEAINAAVHLSA  494 (710)
Q Consensus       436 ~~~~~~d~aL~~Rf~-~I~v~~Ps~-~~~~~IL~~l~-------------------~~~~~~~~~~i~~~~l~~l~~ls~  494 (710)
                       ......+++.+||. .|.+++|+. +++..|+....                   .......++.++++++++++.+..
T Consensus       161 -e~~~~~~aLldRF~~~i~v~~p~~~ee~~~IL~~~~~~~~~~~~~~~~~~~e~l~~~~~~~~~v~v~d~v~e~i~~l~~  239 (500)
T 3nbx_X          161 -EADSSLEALYDRMLIRLWLDKVQDKANFRSMLTSQQDENDNPVPDALQVTDEEYERWQKEIGEITLPDHVFELIFMLRQ  239 (500)
T ss_dssp             -CTTCTTHHHHTTCCEEEECCSCCCHHHHHHHHTCCCCTTSCCSCTTTSBCHHHHHHHHHHHTTCBCCHHHHHHHHHHHH
T ss_pred             -CccccHHHHHHHHHHHHHHHHhhhhhhHHHHHhcccccCCCCCCccceecHHHHHHHHhcCCcccCchHHHHHHHHHHH
Confidence             11123479999997 688999986 67788886432                   111123468899999999988874


Q ss_pred             hhhc----CCCCcchHHHHHHHHHhhhhhhh
Q 005179          495 RYIS----DRYLPDKAIDLVDEAGSRAHIEL  521 (710)
Q Consensus       495 ~~i~----~r~~p~~ai~ll~~a~~~~~~~~  521 (710)
                      ..-.    ....+...+.++..|.+.+.+..
T Consensus       240 ~lr~~r~~~~iS~R~~~~llr~A~A~A~l~g  270 (500)
T 3nbx_X          240 QLDKLPDAPYVSDRRWKKAIRLLQASAFFSG  270 (500)
T ss_dssp             HHHHCSSSCCCCHHHHHHHHHHHHHHHHHTT
T ss_pred             HhhcCCCCCccchhHHHHHHHHHHHHHhhcC
Confidence            3111    12234566667776666655543

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=99.16  E-value=1.4e-10  Score=150.46  Aligned_cols=157  Identities=13%  Similarity=0.172  Sum_probs=98.8

Q ss_pred             cccCHHHHH--HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHH
Q 005179          292 VIGRETEIQ--RIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEA  369 (710)
Q Consensus       292 liGr~~~i~--~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~  369 (710)
                      +|.--+.++  .++..+.. .+.++||+||||||||+++..+...+         .+..++.++++.-...        .
T Consensus      1284 lVPT~DTvR~~~ll~~ll~-~~~pvLL~GptGtGKT~li~~~L~~l---------~~~~~~~infS~~Tta--------~ 1345 (3245)
T 3vkg_A         1284 VIPTVDTTRHVDVLHAWLS-EHRPLILCGPPGSGKTMTLTSTLRAF---------PDFEVVSLNFSSATTP--------E 1345 (3245)
T ss_dssp             CCCCHHHHHHHHHHHHHHH-TTCCCEEESSTTSSHHHHHHHHGGGC---------TTEEEEEECCCTTCCH--------H
T ss_pred             eecchHHHHHHHHHHHHHH-CCCcEEEECCCCCCHHHHHHHHHHhC---------CCCceEEEEeeCCCCH--------H
Confidence            444444443  23333332 46789999999999998876654333         1345566665443311        1


Q ss_pred             HHHHHHHH-H---H------------hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC------------
Q 005179          370 RVTTLISE-I---Q------------KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR------------  421 (710)
Q Consensus       370 ~l~~~~~~-~---~------------~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~------------  421 (710)
                      .+...++. +   .            .++..|+||||++.-...       ..+......+|+++++.            
T Consensus      1346 ~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDiNmp~~D-------~yGtQ~~ielLrqlld~~g~yd~~~~~~~ 1418 (3245)
T 3vkg_A         1346 LLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEINLPSTD-------KYGTQRVITFIRQMVEKGGFWRTSDHTWI 1418 (3245)
T ss_dssp             HHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTTTCCCCC-------TTSCCHHHHHHHHHHHHSEEEETTTTEEE
T ss_pred             HHHHHHhhcceEEeccCCCcccCCCcCCceEEEEecccCCCCcc-------ccccccHHHHHHHHHHcCCeEECCCCeEE
Confidence            12222221 0   0            022369999999864211       12344566777666652            


Q ss_pred             --CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHH
Q 005179          422 --GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKY  473 (710)
Q Consensus       422 --~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~  473 (710)
                        .++++|+|++++...+...++++|.|||..+.++.|+.++...|+..+...+
T Consensus      1419 ~i~d~~~vaamnPp~~gGr~~l~~Rf~r~F~vi~i~~ps~esL~~If~til~~~ 1472 (3245)
T 3vkg_A         1419 KLDKIQFVGACNPPTDAGRVQLTHRFLRHAPILLVDFPSTSSLTQIYGTFNRAL 1472 (3245)
T ss_dssp             EESSEEEEEEECCTTSTTCCCCCHHHHTTCCEEECCCCCHHHHHHHHHHHHHHH
T ss_pred             EecCeEEEEEcCCCCCCCCccCCHHHHhhceEEEeCCCCHHHHHHHHHHHHHHH
Confidence              2467899998864334457899999999999999999999999988776544

>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=99.11  E-value=2.7e-10  Score=119.22  Aligned_cols=146  Identities=10%  Similarity=0.089  Sum_probs=102.5

Q ss_pred             cCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHH
Q 005179          294 GRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTT  373 (710)
Q Consensus       294 Gr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~  373 (710)
                      |+++.+..+...+..+...+.||+||||+|||++++++++.+..  ...  ....++.++...     ...+  ...++.
T Consensus         1 g~~~~~~~L~~~i~~~~~~~~Lf~Gp~G~GKtt~a~~la~~~~~--~~~--~~~d~~~l~~~~-----~~~~--id~ir~   69 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEK--FPP--KASDVLEIDPEG-----ENIG--IDDIRT   69 (305)
T ss_dssp             ---CHHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHT--SCC--CTTTEEEECCSS-----SCBC--HHHHHH
T ss_pred             ChHHHHHHHHHHHHCCCCcEEEEECCCCCCHHHHHHHHHHhCch--hhc--cCCCEEEEcCCc-----CCCC--HHHHHH
Confidence            56778888888888766667899999999999999999986421  100  123445554321     1111  233566


Q ss_pred             HHHHHHhc----CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--CeEEEEccChHHHHhhhhccHHHHc
Q 005179          374 LISEIQKS----GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--ELQCIASTTQDEHRTQFEKDKALAR  447 (710)
Q Consensus       374 ~~~~~~~~----~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--~v~vI~att~~~~~~~~~~d~aL~~  447 (710)
                      +++.+...    +..|+||||+|.+             ..+.++.|+..+++.  ..++|.+|+...     .+.+++.+
T Consensus        70 li~~~~~~p~~~~~kvviIdead~l-------------t~~a~naLLk~LEep~~~t~fIl~t~~~~-----kl~~tI~S  131 (305)
T 2gno_A           70 IKDFLNYSPELYTRKYVIVHDCERM-------------TQQAANAFLKALEEPPEYAVIVLNTRRWH-----YLLPTIKS  131 (305)
T ss_dssp             HHHHHTSCCSSSSSEEEEETTGGGB-------------CHHHHHHTHHHHHSCCTTEEEEEEESCGG-----GSCHHHHT
T ss_pred             HHHHHhhccccCCceEEEeccHHHh-------------CHHHHHHHHHHHhCCCCCeEEEEEECChH-----hChHHHHc
Confidence            77766532    3579999999999             455688898999863  677777776643     67899999


Q ss_pred             cccceEecCCCHHHHHHHHHHHH
Q 005179          448 RFQPVLISEPSQEDAVRILLGLR  470 (710)
Q Consensus       448 Rf~~I~v~~Ps~~~~~~IL~~l~  470 (710)
                      |  .+.+.+|+.++..+.|+...
T Consensus       132 R--~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A          132 R--VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             T--SEEEECCCCHHHHHHHHHHH
T ss_pred             e--eEeCCCCCHHHHHHHHHHHh
Confidence            9  89999999999888887654

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.07  E-value=9e-12  Score=142.29  Aligned_cols=203  Identities=10%  Similarity=0.127  Sum_probs=114.6

Q ss_pred             CCcccCHHHHHHHHHHHHcCC-----------CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCcc--ccCceEEEeehhh
Q 005179          290 DPVIGRETEIQRIIQILCRRT-----------KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVF--LLSKRIMSLDMGL  356 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~-----------~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~--l~~~~v~~ld~~~  356 (710)
                      ..++|++...+.+...+....           ..|+||+||||||||++|+++++.+.....+..  .....+.......
T Consensus       295 ~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~~~  374 (595)
T 3f9v_A          295 PSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVVRE  374 (595)
T ss_dssp             STTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECSSG
T ss_pred             chhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceeeec
Confidence            458999986666654444331           128999999999999999999987632221110  0001111111111


Q ss_pred             hhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC--------------
Q 005179          357 LMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG--------------  422 (710)
Q Consensus       357 l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~--------------  422 (710)
                      ...     |.+.... ..+.   ...+.||||||++.+             ..+.++.|.+.|+++              
T Consensus       375 ~~~-----g~~~~~~-G~l~---~A~~gil~IDEid~l-------------~~~~q~~Ll~~le~~~i~i~~~g~~~~~~  432 (595)
T 3f9v_A          375 KGT-----GEYYLEA-GALV---LADGGIAVIDEIDKM-------------RDEDRVAIHEAMEQQTVSIAKAGIVAKLN  432 (595)
T ss_dssp             GGT-----SSCSEEE-CHHH---HHSSSEECCTTTTCC-------------CSHHHHHHHHHHHSSSEEEESSSSEEEEC
T ss_pred             ccc-----ccccccC-CeeE---ecCCCcEEeehhhhC-------------CHhHhhhhHHHHhCCEEEEecCCcEEEec
Confidence            111     1110000 0111   123579999999998             334556666666543              


Q ss_pred             -CeEEEEccChHH--HHh------hhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHh-hcCCCCCHHHHHHHH
Q 005179          423 -ELQCIASTTQDE--HRT------QFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEA-HHNCKFTLEAINAAV  490 (710)
Q Consensus       423 -~v~vI~att~~~--~~~------~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~-~~~~~i~~~~l~~l~  490 (710)
                       ++.+|+|+|+..  |..      .+.++++|.+||+  .+..+.|+.+ ...|++++...... .....++.+.+...+
T Consensus       433 ~~~~vIaatNp~~G~~~~~~~~~~ni~l~~aLl~RFDl~~~~~~~~~~e-~~~i~~~il~~~~~~~~~~~l~~~~l~~~i  511 (595)
T 3f9v_A          433 ARAAVIAAGNPKFGRYISERPVSDNINLPPTILSRFDLIFILKDQPGEQ-DRELANYILDVHSGKSTKNIIDIDTLRKYI  511 (595)
T ss_dssp             CCCEEEEEECCTTCCSCTTSCSCTTTCSCSSSGGGCSCCEEECCTTHHH-HHHHHHHHHTTTCCCSSSSTTCCTTTHHHH
T ss_pred             CceEEEEEcCCcCCccCcccCchhccCCCHHHHhhCeEEEEeCCCCCHH-HHHHHHHHHHHhhccccccCCCHHHHHHHH
Confidence             356899999863  111      1278899999996  3444556666 67777666543211 112345666677777


Q ss_pred             HHhhhhhcCCCCcchHHHHHHHHHhh
Q 005179          491 HLSARYISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       491 ~ls~~~i~~r~~p~~ai~ll~~a~~~  516 (710)
                      .++..++.. .+++.+.+.+......
T Consensus       512 ~~ar~~~~p-~ls~ea~~~l~~~y~~  536 (595)
T 3f9v_A          512 AYARKYVTP-KITSEAKNLITDFFVE  536 (595)
T ss_dssp             HHHHHHHCC-CCCCCTHHHHHHHHTT
T ss_pred             HHHHHhCCC-CCCHHHHHHHHHHHHH
Confidence            776665443 3456677777666543

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=99.07  E-value=1.9e-09  Score=114.70  Aligned_cols=183  Identities=19%  Similarity=0.182  Sum_probs=112.7

Q ss_pred             CCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-----------
Q 005179          290 DPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-----------  358 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-----------  358 (710)
                      +.++||+++++.+.+.+...  ..++|+||+|+|||++++.+++..          +  ++.+++....           
T Consensus        12 ~~~~gR~~el~~L~~~l~~~--~~v~i~G~~G~GKT~Ll~~~~~~~----------~--~~~~~~~~~~~~~~~~~~~~~   77 (350)
T 2qen_A           12 EDIFDREEESRKLEESLENY--PLTLLLGIRRVGKSSLLRAFLNER----------P--GILIDCRELYAERGHITREEL   77 (350)
T ss_dssp             GGSCSCHHHHHHHHHHHHHC--SEEEEECCTTSSHHHHHHHHHHHS----------S--EEEEEHHHHHHTTTCBCHHHH
T ss_pred             HhcCChHHHHHHHHHHHhcC--CeEEEECCCcCCHHHHHHHHHHHc----------C--cEEEEeecccccccCCCHHHH
Confidence            45899999999999988763  689999999999999999998764          1  3333332210           


Q ss_pred             -----h-------------------cccc---CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhH
Q 005179          359 -----A-------------------GAKE---RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDI  411 (710)
Q Consensus       359 -----~-------------------g~~~---~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~  411 (710)
                           .                   +...   ...+...+..+...+...++.+|+|||+|.+.....      ....++
T Consensus        78 ~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~------~~~~~~  151 (350)
T 2qen_A           78 IKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGS------RGGKEL  151 (350)
T ss_dssp             HHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTT------TTTHHH
T ss_pred             HHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCc------cchhhH
Confidence                 0                   0000   112333333332222323489999999999943100      012344


Q ss_pred             HHhhcccccC-CCeEEEEccChHHH-Hhh---hhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHH
Q 005179          412 SNLLKPSLGR-GELQCIASTTQDEH-RTQ---FEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEA  485 (710)
Q Consensus       412 ~~~L~~~l~~-~~v~vI~att~~~~-~~~---~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~  485 (710)
                      ...|...+.. .++.+|.+++...+ ...   ......+..|+. .+.+.+.+.++..+++.....    ..+..++++.
T Consensus       152 ~~~L~~~~~~~~~~~~il~g~~~~~l~~~l~~~~~~~~l~~~~~~~i~l~pl~~~e~~~~l~~~~~----~~~~~~~~~~  227 (350)
T 2qen_A          152 LALFAYAYDSLPNLKIILTGSEVGLLHDFLKITDYESPLYGRIAGEVLVKPFDKDTSVEFLKRGFR----EVNLDVPENE  227 (350)
T ss_dssp             HHHHHHHHHHCTTEEEEEEESSHHHHHHHHCTTCTTSTTTTCCCEEEECCCCCHHHHHHHHHHHHH----TTTCCCCHHH
T ss_pred             HHHHHHHHHhcCCeEEEEECCcHHHHHHHHhhcCCCCccccCccceeeCCCCCHHHHHHHHHHHHH----HcCCCCCHHH
Confidence            5555544432 46777776665432 121   122223444553 799999999998888875443    3456788888


Q ss_pred             HHHHHHHhhhh
Q 005179          486 INAAVHLSARY  496 (710)
Q Consensus       486 l~~l~~ls~~~  496 (710)
                      +..++..+.++
T Consensus       228 ~~~i~~~tgG~  238 (350)
T 2qen_A          228 IEEAVELLDGI  238 (350)
T ss_dssp             HHHHHHHHTTC
T ss_pred             HHHHHHHhCCC
Confidence            88888887764

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=99.03  E-value=2.7e-08  Score=129.47  Aligned_cols=123  Identities=13%  Similarity=0.183  Sum_probs=87.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEV  391 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEi  391 (710)
                      .+..+.||+|||||.+++.+|+.+          +..++.++++.-+..        ..+..++..+.+. +.+.++||+
T Consensus       605 ~gg~~~GPaGtGKTet~k~La~~l----------gr~~~vfnC~~~~d~--------~~~g~i~~G~~~~-GaW~cfDEf  665 (3245)
T 3vkg_A          605 MGGNPFGPAGTGKTETVKALGSQL----------GRFVLVFCCDEGFDL--------QAMSRIFVGLCQC-GAWGCFDEF  665 (3245)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHT----------TCCEEEEECSSCCCH--------HHHHHHHHHHHHH-TCEEEEETT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHh----------CCeEEEEeCCCCCCH--------HHHHHHHhhHhhc-CcEEEehhh
Confidence            345799999999999999999999          778888877543311        2245555555544 578999999


Q ss_pred             hhhhhCCCCCCCCCCChHhHHHhhcc----------------ccc-------CCCeEEEEccChHHHHhhhhccHHHHcc
Q 005179          392 HTLIGSGTVGRGNKGTGLDISNLLKP----------------SLG-------RGELQCIASTTQDEHRTQFEKDKALARR  448 (710)
Q Consensus       392 d~l~~~~~~~~~~~~~~~~~~~~L~~----------------~l~-------~~~v~vI~att~~~~~~~~~~d~aL~~R  448 (710)
                      +++             ..++...+.+                .+.       +....++.|+|+ .|.+..+++..|..|
T Consensus       666 Nrl-------------~~~vLSvv~~qi~~I~~a~~~~~~~~~~~~G~~i~l~~~~~vfiTmNp-gY~gr~eLP~nLk~l  731 (3245)
T 3vkg_A          666 NRL-------------EERILSAVSQQIQTIQVALKENSKEVELLGGKNISLHQDMGIFVTMNP-GYAGRSNLPDNLKKL  731 (3245)
T ss_dssp             TSS-------------CHHHHHHHHHHHHHHHHHHHHTCSEECCC---CEECCTTCEEEECBCC-CGGGCCCSCHHHHTT
T ss_pred             hcC-------------CHHHHHHHHHHHHHHHHHHHcCCCeEEecCCCEEeecCCeEEEEEeCC-CccCcccChHHHHhh
Confidence            988             2222222111                011       124567888887 677777899999999


Q ss_pred             ccceEecCCCHHHHHHHHH
Q 005179          449 FQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       449 f~~I~v~~Ps~~~~~~IL~  467 (710)
                      |..|.+..|+.+...+|+-
T Consensus       732 Fr~v~m~~Pd~~~i~ei~L  750 (3245)
T 3vkg_A          732 FRSMAMIKPDREMIAQVML  750 (3245)
T ss_dssp             EEEEECCSCCHHHHHHHHH
T ss_pred             cEEEEEeCCCHHHHHHHHH
Confidence            9999999999998777753

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.99  E-value=2.5e-10  Score=122.45  Aligned_cols=63  Identities=22%  Similarity=0.330  Sum_probs=49.0

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|..+|        .+.+.|+..|    .|+|||||||||||++|||||.++   +..++.++.|++.+
T Consensus       150 IgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~p----rGvLL~GPPGTGKTllAkAiA~e~---~~~f~~v~~s~l~s  220 (405)
T 4b4t_J          150 VGGLTKQIKEIKEVIELPVKHPELFESLGIAQP----KGVILYGPPGTGKTLLARAVAHHT---DCKFIRVSGAELVQ  220 (405)
T ss_dssp             SCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCC----CCEEEESCSSSSHHHHHHHHHHHH---TCEEEEEEGGGGSC
T ss_pred             hCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCC----CceEEeCCCCCCHHHHHHHHHHhh---CCCceEEEhHHhhc
Confidence            666666666666555        3446687665    799999999999999999999994   45899999887743

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.95  E-value=6.3e-10  Score=121.18  Aligned_cols=63  Identities=32%  Similarity=0.424  Sum_probs=49.4

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|...+        .+.+.|+..|    .|+|||||||||||++|+|||.++   +..++.++.|++.+
T Consensus       183 igGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~p----rGvLL~GPPGtGKTllAkAiA~e~---~~~~~~v~~s~l~s  253 (437)
T 4b4t_L          183 IGGLTEQIRELREVIELPLKNPEIFQRVGIKPP----KGVLLYGPPGTGKTLLAKAVAATI---GANFIFSPASGIVD  253 (437)
T ss_dssp             GCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCC----CEEEEESCTTSSHHHHHHHHHHHH---TCEEEEEEGGGTCC
T ss_pred             hCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCC----CeEEEECCCCCcHHHHHHHHHHHh---CCCEEEEehhhhcc
Confidence            677777776666655        3446677655    799999999999999999999995   45788998887743

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.94  E-value=6.8e-10  Score=119.37  Aligned_cols=63  Identities=25%  Similarity=0.397  Sum_probs=50.0

Q ss_pred             ccChHHHHHHHHHHHH--------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVK--------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~--------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|.+.+.        +.+.|+..|    .|+|||||||||||++|+|||.++   ...++.++.|++.+
T Consensus       184 IgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~p----rGvLLyGPPGTGKTlLAkAiA~e~---~~~fi~v~~s~l~s  254 (437)
T 4b4t_I          184 IGGLESQIQEIKESVELPLTHPELYEEMGIKPP----KGVILYGAPGTGKTLLAKAVANQT---SATFLRIVGSELIQ  254 (437)
T ss_dssp             TCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCC----SEEEEESSTTTTHHHHHHHHHHHH---TCEEEEEESGGGCC
T ss_pred             cCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCC----CCCceECCCCchHHHHHHHHHHHh---CCCEEEEEHHHhhh
Confidence            7777777777776663        345677655    799999999999999999999994   45789999887743

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.93  E-value=6.5e-10  Score=120.95  Aligned_cols=63  Identities=29%  Similarity=0.424  Sum_probs=49.6

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|.+++++.|...+        .+.+.|+..|    .|+|||||||||||++|+|||.++   +..++.++.|++.+
T Consensus       183 igGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~p----rGvLLyGPPGTGKTllAkAiA~e~---~~~f~~v~~s~l~~  253 (434)
T 4b4t_M          183 VGGLDKQIEELVEAIVLPMKRADKFKDMGIRAP----KGALMYGPPGTGKTLLARACAAQT---NATFLKLAAPQLVQ  253 (434)
T ss_dssp             SCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCC----CEEEEESCTTSSHHHHHHHHHHHH---TCEEEEEEGGGGCS
T ss_pred             cCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCC----CeeEEECcCCCCHHHHHHHHHHHh---CCCEEEEehhhhhh
Confidence            677777777766554        3456677655    799999999999999999999994   45788998887743

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.93  E-value=8e-10  Score=120.14  Aligned_cols=63  Identities=32%  Similarity=0.423  Sum_probs=50.4

Q ss_pred             ccChHHHHHHHHHHHH--------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVK--------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~--------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|...+.        +.+.|+..|    .|+|||||||||||++|+|||+++   +..++.++++++.+
T Consensus       174 igGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~p----rGiLL~GPPGtGKT~lakAiA~~~---~~~~~~v~~~~l~~  244 (428)
T 4b4t_K          174 VGGLDMQKQEIREAVELPLVQADLYEQIGIDPP----RGVLLYGPPGTGKTMLVKAVANST---KAAFIRVNGSEFVH  244 (428)
T ss_dssp             SCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCC----CEEEEESCTTTTHHHHHHHHHHHH---TCEEEEEEGGGTCC
T ss_pred             hccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCC----ceEEEECCCCCCHHHHHHHHHHHh---CCCeEEEecchhhc
Confidence            7777777777776653        445687655    699999999999999999999995   45899999888643

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.91  E-value=7.4e-10  Score=120.24  Aligned_cols=63  Identities=24%  Similarity=0.379  Sum_probs=49.3

Q ss_pred             ccChHHHHHHHHHHH--------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAV--------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i--------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|.+.|        .+.+.|+..|    .|+|||||||||||++|+|||.++   ...++.++.+++.+
T Consensus       211 IgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pp----rGILLyGPPGTGKTlLAkAiA~e~---~~~fi~vs~s~L~s  281 (467)
T 4b4t_H          211 VGGCKDQIEKLREVVELPLLSPERFATLGIDPP----KGILLYGPPGTGKTLCARAVANRT---DATFIRVIGSELVQ  281 (467)
T ss_dssp             CTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCC----SEEEECSCTTSSHHHHHHHHHHHH---TCEEEEEEGGGGCC
T ss_pred             hccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCC----CceEeeCCCCCcHHHHHHHHHhcc---CCCeEEEEhHHhhc
Confidence            666667666666554        3456687655    799999999999999999999995   45789998888744

>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=98.90  E-value=4.5e-09  Score=111.92  Aligned_cols=177  Identities=18%  Similarity=0.207  Sum_probs=102.8

Q ss_pred             CCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-----------
Q 005179          290 DPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-----------  358 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-----------  358 (710)
                      +.++||+++++.+.. +..   ..++|+||+|+|||++++.+++.+.          ...+.+++....           
T Consensus        13 ~~~~gR~~el~~L~~-l~~---~~v~i~G~~G~GKT~L~~~~~~~~~----------~~~~~~~~~~~~~~~~~~~~~~~   78 (357)
T 2fna_A           13 KDFFDREKEIEKLKG-LRA---PITLVLGLRRTGKSSIIKIGINELN----------LPYIYLDLRKFEERNYISYKDFL   78 (357)
T ss_dssp             GGSCCCHHHHHHHHH-TCS---SEEEEEESTTSSHHHHHHHHHHHHT----------CCEEEEEGGGGTTCSCCCHHHHH
T ss_pred             HHhcChHHHHHHHHH-hcC---CcEEEECCCCCCHHHHHHHHHHhcC----------CCEEEEEchhhccccCCCHHHHH
Confidence            458999999999998 655   5889999999999999999998762          123334432210           


Q ss_pred             ---------------------h---ccccCc---c------HHHHHHHHHHHHHhc--CCeEEEEccchhhhhCCCCCCC
Q 005179          359 ---------------------A---GAKERG---E------LEARVTTLISEIQKS--GDVILFIDEVHTLIGSGTVGRG  403 (710)
Q Consensus       359 ---------------------~---g~~~~g---~------~e~~l~~~~~~~~~~--~~~IL~IDEid~l~~~~~~~~~  403 (710)
                                           .   +....+   .      ....+..+++.+...  ++.+|+|||+|.+....     
T Consensus        79 ~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~~~-----  153 (357)
T 2fna_A           79 LELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLR-----  153 (357)
T ss_dssp             HHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCT-----
T ss_pred             HHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhccC-----
Confidence                                 0   000000   0      001133444444432  48899999999995420     


Q ss_pred             CCCChHhHHHhhcccccC-CCeEEEEccChHHH-Hhh---hhccHHHHccc-cceEecCCCHHHHHHHHHHHHHHHHhhc
Q 005179          404 NKGTGLDISNLLKPSLGR-GELQCIASTTQDEH-RTQ---FEKDKALARRF-QPVLISEPSQEDAVRILLGLREKYEAHH  477 (710)
Q Consensus       404 ~~~~~~~~~~~L~~~l~~-~~v~vI~att~~~~-~~~---~~~d~aL~~Rf-~~I~v~~Ps~~~~~~IL~~l~~~~~~~~  477 (710)
                          ..++...|..+... .++.+|.+++.... ...   ......+..|+ ..+.+.+++.++..+++.......    
T Consensus       154 ----~~~~~~~l~~~~~~~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~~r~~~~i~l~~l~~~e~~~~l~~~~~~~----  225 (357)
T 2fna_A          154 ----GVNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEA----  225 (357)
T ss_dssp             ----TCCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHH----
T ss_pred             ----chhHHHHHHHHHHcCCCeEEEEEcCchHHHHHHHhccCCCCccccCccceeecCCCCHHHHHHHHHHHHHHc----
Confidence                11223333333322 35667776665431 221   11222344465 479999999999999888755422    


Q ss_pred             CCCCCHHHHHHHHHHhhh
Q 005179          478 NCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       478 ~~~i~~~~l~~l~~ls~~  495 (710)
                      +...++.  ..++..+.+
T Consensus       226 ~~~~~~~--~~i~~~t~G  241 (357)
T 2fna_A          226 DIDFKDY--EVVYEKIGG  241 (357)
T ss_dssp             TCCCCCH--HHHHHHHCS
T ss_pred             CCCCCcH--HHHHHHhCC
Confidence            3444432  555566554

>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=98.86  E-value=2.3e-09  Score=116.27  Aligned_cols=180  Identities=18%  Similarity=0.268  Sum_probs=115.0

Q ss_pred             CCCcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-------
Q 005179          289 IDPVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-------  359 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-------  359 (710)
                      +..++|....++++.+.+..  ....+++|+|++|||||++|+.+.......       +.+++.+|+..+..       
T Consensus       136 ~~~~ig~s~~m~~l~~~i~~~a~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~-------~~~fv~v~~~~~~~~~~~~el  208 (387)
T 1ny5_A          136 EEEYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRS-------KEPFVALNVASIPRDIFEAEL  208 (387)
T ss_dssp             CCCCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTT-------TSCEEEEETTTSCHHHHHHHH
T ss_pred             chhhhhccHHhhHHHHHHHHhcCCCCCeEEecCCCcCHHHHHHHHHHhcCCC-------CCCeEEEecCCCCHHHHHHHh
Confidence            45788988888888776544  445678999999999999999998765322       44667777655421       


Q ss_pred             -ccccCccHHHH---HHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------
Q 005179          360 -GAKERGELEAR---VTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------  422 (710)
Q Consensus       360 -g~~~~g~~e~~---l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------  422 (710)
                       |. ..|.|...   -...+.   ...+.+||||||+.+             ..+.+..|..+++.+             
T Consensus       209 fg~-~~g~~tga~~~~~g~~~---~a~~gtlfldei~~l-------------~~~~q~~Ll~~l~~~~~~~~g~~~~~~~  271 (387)
T 1ny5_A          209 FGY-EKGAFTGAVSSKEGFFE---LADGGTLFLDEIGEL-------------SLEAQAKLLRVIESGKFYRLGGRKEIEV  271 (387)
T ss_dssp             HCB-CTTSSTTCCSCBCCHHH---HTTTSEEEEESGGGC-------------CHHHHHHHHHHHHHSEECCBTCCSBEEC
T ss_pred             cCC-CCCCCCCcccccCCcee---eCCCcEEEEcChhhC-------------CHHHHHHHHHHHhcCcEEeCCCCceeec
Confidence             11 11110000   011222   234679999999999             556777777666532             


Q ss_pred             CeEEEEccChHHHHh--hhhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          423 ELQCIASTTQDEHRT--QFEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       423 ~v~vI~att~~~~~~--~~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      ++++|++||.+-...  .-...+.|..|+..+.+..|+.    ++...+++.++.++...++   ..+++++++.+..+
T Consensus       272 ~~rii~at~~~l~~~~~~g~fr~dl~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~l~~~  350 (387)
T 1ny5_A          272 NVRILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSY  350 (387)
T ss_dssp             CCEEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHS
T ss_pred             cEEEEEeCCCCHHHHHHcCCccHHHHHhhcCCeecCCcchhccccHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHhC
Confidence            567999988743211  1124567777888777776764    5556666666666654444   34889988877643

>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=98.83  E-value=2.4e-08  Score=107.35  Aligned_cols=178  Identities=19%  Similarity=0.264  Sum_probs=112.2

Q ss_pred             CcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc-------
Q 005179          291 PVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA-------  361 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~-------  361 (710)
                      .++|....+.++...+..  ....+++++|++||||+.+++.+.......       + .++.+++..+....       
T Consensus       130 ~~ig~s~~~~~~~~~~~~~a~~~~~vli~GesGtGKe~lAr~ih~~s~r~-------~-~fv~vnc~~~~~~~~~~~lfg  201 (368)
T 3dzd_A          130 EFVGEHPKILEIKRLIPKIAKSKAPVLITGESGTGKEIVARLIHRYSGRK-------G-AFVDLNCASIPQELAESELFG  201 (368)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHTSCSCEEEECCTTSSHHHHHHHHHHHHCCC-------S-CEEEEESSSSCTTTHHHHHHE
T ss_pred             cccccchHHHHHHhhhhhhhccchhheEEeCCCchHHHHHHHHHHhcccc-------C-CcEEEEcccCChHHHHHHhcC
Confidence            578887777766655432  455779999999999999999998765221       1 26777776542100       


Q ss_pred             ccCccHHH---HHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-------------CeE
Q 005179          362 KERGELEA---RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-------------ELQ  425 (710)
Q Consensus       362 ~~~g~~e~---~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-------------~v~  425 (710)
                      ...|.|..   .-...++   ...+.+||||||+.|             ..+.+..|.++++.+             +++
T Consensus       202 ~~~g~~tga~~~~~g~~~---~a~~gtlfldei~~l-------------~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~r  265 (368)
T 3dzd_A          202 HEKGAFTGALTRKKGKLE---LADQGTLFLDEVGEL-------------DQRVQAKLLRVLETGSFTRLGGNQKIEVDIR  265 (368)
T ss_dssp             ECSCSSSSCCCCEECHHH---HTTTSEEEEETGGGS-------------CHHHHHHHHHHHHHSEECCBTCCCBEECCCE
T ss_pred             ccccccCCcccccCChHh---hcCCCeEEecChhhC-------------CHHHHHHHHHHHHhCCcccCCCCcceeeeeE
Confidence            00110000   0001222   234568999999999             566777777777643             467


Q ss_pred             EEEccChHHHHhh--hhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          426 CIASTTQDEHRTQ--FEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       426 vI~att~~~~~~~--~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      +|++|+.+.....  -...+.|..|+..+.+..|+.    ++...+++.++.++....+   ..+++++++.+..+
T Consensus       266 ii~at~~~l~~~v~~g~fr~dL~~rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~~~~~a~~~L~~~  341 (368)
T 3dzd_A          266 VISATNKNLEEEIKKGNFREDLYYRLSVFQIYLPPLRERGKDVILLAEYFLKKFAKEYKKNCFELSEETKEYLMKQ  341 (368)
T ss_dssp             EEEEESSCHHHHHHTTSSCHHHHHHHTSEEEECCCGGGSTTHHHHHHHHHHHHHHHHTTCCCCCBCHHHHHHHHTC
T ss_pred             EEEecCCCHHHHHHcCCccHHHHHHhCCeEEeCCChhhchhhHHHHHHHHHHHHHHHcCCCCCCcCHHHHHHHHhC
Confidence            9999887542211  123467888888666555543    5667777777777665444   45899998877543

>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=98.77  E-value=4.5e-09  Score=113.54  Aligned_cols=77  Identities=31%  Similarity=0.345  Sum_probs=60.2

Q ss_pred             HHHHHHHhhCcccChHHHHHHHHHHH----HHhhcCC-------CCC----------CCCCeEEEEEcCCCCcHHHHHHH
Q 005179          620 LVGLEEQLKKRVIGQDEAVAAISRAV----KRSRVGL-------KDP----------NRPTAAMLFCGPTGVGKTELAKS  678 (710)
Q Consensus       620 l~~l~~~L~~~v~Gq~~a~~~i~~~i----~~~r~gl-------~~p----------~rp~~~~Lf~GPpGtGKT~lAka  678 (710)
                      +.++.+.|.+.|+||+++++.|..++    ++.+.|+       ++|          .++..++||+||||||||++|++
T Consensus        12 ~~~l~~~L~~~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~~~~~~~~ill~Gp~GtGKT~la~~   91 (376)
T 1um8_A           12 PKELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQT   91 (376)
T ss_dssp             HHHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHH
T ss_pred             HHHHHHHHhhHccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccccccCCCCEEEECCCCCCHHHHHHH
Confidence            35678889999999999999999888    5555544       111          12335899999999999999999


Q ss_pred             HHHHHcCCCCcceeeCCCCCC
Q 005179          679 LAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       679 LA~~lfg~~~~li~~d~se~~  699 (710)
                      ||+.+   ...++.++++.+.
T Consensus        92 la~~l---~~~~~~~~~~~~~  109 (376)
T 1um8_A           92 LAKHL---DIPIAISDATSLT  109 (376)
T ss_dssp             HHHHT---TCCEEEEEGGGCC
T ss_pred             HHHHh---CCCEEEecchhhh
Confidence            99997   3468888887764

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=98.73  E-value=1.4e-08  Score=99.36  Aligned_cols=99  Identities=15%  Similarity=0.169  Sum_probs=60.6

Q ss_pred             hhhhcCCCCcccCHH----HHHHHHHHHHcCC----CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          283 RASEELIDPVIGRET----EIQRIIQILCRRT----KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       283 ~~~~~~l~~liGr~~----~i~~l~~~L~~~~----~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .+++.+|+++++.+.    .+..+...+....    +.+++|+||||||||+++++++..+...       +..++.+++
T Consensus        18 ~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~-------~~~~~~~~~   90 (202)
T 2w58_A           18 EILRASLSDVDLNDDGRIKAIRFAERFVAEYEPGKKMKGLYLHGSFGVGKTYLLAAIANELAKR-------NVSSLIVYV   90 (202)
T ss_dssp             GGGCCCTTSSCCSSHHHHHHHHHHHHHHHHCCSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTT-------TCCEEEEEH
T ss_pred             HHHcCCHhhccCCChhHHHHHHHHHHHHHHhhhccCCCeEEEECCCCCCHHHHHHHHHHHHHHc-------CCeEEEEEh
Confidence            345567788887543    3444455554432    2789999999999999999999988543       445666666


Q ss_pred             hhhhhcc---ccCccHHHHHHHHHHHHHhcCCeEEEEccchhh
Q 005179          355 GLLMAGA---KERGELEARVTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       355 ~~l~~g~---~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                      ..+....   ...+.    +..++..+...  .+|||||++..
T Consensus        91 ~~~~~~~~~~~~~~~----~~~~~~~~~~~--~~lilDei~~~  127 (202)
T 2w58_A           91 PELFRELKHSLQDQT----MNEKLDYIKKV--PVLMLDDLGAE  127 (202)
T ss_dssp             HHHHHHHHHC---CC----CHHHHHHHHHS--SEEEEEEECCC
T ss_pred             HHHHHHHHHHhccch----HHHHHHHhcCC--CEEEEcCCCCC
Confidence            5543211   01111    12233333333  49999999765

>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=98.72  E-value=9.5e-09  Score=110.46  Aligned_cols=76  Identities=30%  Similarity=0.357  Sum_probs=58.8

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHH----HhhcCCCCCC--CCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVK----RSRVGLKDPN--RPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~----~~r~gl~~p~--rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .++++.|.+.|+||+++++.+..++.    +.+.+.....  .+..++||+||||||||++|++||+.+   ...++.++
T Consensus         7 ~~l~~~l~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~---~~~~~~~~   83 (363)
T 3hws_A            7 HEIRNHLDDYVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLL---DVPFTMAD   83 (363)
T ss_dssp             HHHHHHHHHHCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHT---TCCEEEEE
T ss_pred             HHHHHHHHhhccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHc---CCCEEEec
Confidence            45677788889999999999998883    4444443222  244689999999999999999999997   35788888


Q ss_pred             CCCCC
Q 005179          695 PSPFN  699 (710)
Q Consensus       695 ~se~~  699 (710)
                      ++++.
T Consensus        84 ~~~l~   88 (363)
T 3hws_A           84 ATTLT   88 (363)
T ss_dssp             HHHHT
T ss_pred             hHHhc
Confidence            87654

>3fes_A ATP-dependent CLP endopeptidase; alpha-helical bundles, structural genomics, PSI-2, protein S initiative; HET: PG4 EPE; 1.82A {Clostridium difficile}

Probab=98.72  E-value=2.2e-08  Score=92.75  Aligned_cols=65  Identities=31%  Similarity=0.473  Sum_probs=61.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          169 MPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       169 ~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      -+||+.++++|+.|.++|+++||.+|++||||+||++++++.+.++|+++|+|.+.++..+...+
T Consensus         6 ~~~T~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~~~gvd~~~l~~~l~~~l   70 (145)
T 3fes_A            6 NRFTQRAKKAIDLAFESAKSLGHNIVGSEHILLGLLREEEGIAAKVLSKVGFTEAYLEGKIVDME   70 (145)
T ss_dssp             CCBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cccCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCChHHHHHHHcCCCHHHHHHHHHHHH
Confidence            35999999999999999999999999999999999999999999999999999999998887766

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=98.69  E-value=2.5e-08  Score=104.46  Aligned_cols=80  Identities=23%  Similarity=0.246  Sum_probs=61.1

Q ss_pred             HHHHHHHHhhCcccChHHHHHHHHHHHHH-------hhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC----
Q 005179          619 LLVGLEEQLKKRVIGQDEAVAAISRAVKR-------SRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV----  687 (710)
Q Consensus       619 ~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~-------~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~----  687 (710)
                      .+.++.+.|...|+|++++++.|...+..       .+.|+..+ ++..++||+||||||||++|+++|+.+....    
T Consensus        21 ~~~~~~~~l~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~~~-~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~   99 (309)
T 3syl_A           21 GAKEVLEELDRELIGLKPVKDRIRETAALLLVERARQKLGLAHE-TPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRK   99 (309)
T ss_dssp             THHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHHHTCCSS-CCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSS
T ss_pred             cHHHHHHHHHHHccChHHHHHHHHHHHHHHHhHHHHHHcCCCCC-CCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCC
Confidence            34566677777899999999999877643       34566654 4445899999999999999999999985532    


Q ss_pred             CcceeeCCCCCC
Q 005179          688 RIHYLFFPSPFN  699 (710)
Q Consensus       688 ~~li~~d~se~~  699 (710)
                      ..++.++++++.
T Consensus       100 ~~~~~~~~~~l~  111 (309)
T 3syl_A          100 GHLVSVTRDDLV  111 (309)
T ss_dssp             CCEEEECGGGTC
T ss_pred             CcEEEEcHHHhh
Confidence            367888877763

>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=98.69  E-value=1.6e-08  Score=105.62  Aligned_cols=77  Identities=31%  Similarity=0.488  Sum_probs=59.7

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHHH--hhcCCCCC---CCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVKR--SRVGLKDP---NRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~~--~r~gl~~p---~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .++.+.|.+.|+||+++++.+..++..  .+.++..+   .++..++||+||||||||++|+++|+.+   ...++.+++
T Consensus         7 ~~l~~~l~~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l---~~~~~~i~~   83 (310)
T 1ofh_A            7 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA---NAPFIKVEA   83 (310)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH---TCCEEEEEG
T ss_pred             HHHHHHHhhhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHh---CCCEEEEcc
Confidence            456778889999999999999988865  33333211   1122589999999999999999999997   347889999


Q ss_pred             CCCCC
Q 005179          696 SPFNS  700 (710)
Q Consensus       696 se~~~  700 (710)
                      +++..
T Consensus        84 ~~~~~   88 (310)
T 1ofh_A           84 TKFTE   88 (310)
T ss_dssp             GGGSS
T ss_pred             hhccc
Confidence            88754

>3fh2_A Probable ATP-dependent protease (heat shock prote; struct genomics, PSI2, MCSG, protein structure initiative; 1.60A {Corynebacterium glutamicum}

Probab=98.68  E-value=3.8e-08  Score=91.30  Aligned_cols=64  Identities=28%  Similarity=0.457  Sum_probs=60.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++++|+.|.++|+++||.||++||||+||++++++.+.++|+++|+|.+.++..+...+
T Consensus         6 ~~t~~~~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~~iL~~~gv~~~~l~~~l~~~l   69 (146)
T 3fh2_A            6 RFTDRARRVIVLAQEEARMLNHNYIGTEHILLGLIHEGEGVAAKALESMGISLDAVRQEVEEII   69 (146)
T ss_dssp             GBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHCCSHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             hcCHHHHHHHHHHHHHHHHcCCCCchHHHHHHHHHhCCCChHHHHHHHcCCCHHHHHHHHHHHh
Confidence            4899999999999999999999999999999999999899999999999999999998887766

>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=98.68  E-value=1.2e-07  Score=102.58  Aligned_cols=145  Identities=19%  Similarity=0.172  Sum_probs=80.9

Q ss_pred             CCCCcccCHHHHHHHHHHHHcCC-----CCCcEEEcCCCChHHHHHHHH-HHHHHhcCCCccccCceEEEeeh----hhh
Q 005179          288 LIDPVIGRETEIQRIIQILCRRT-----KNNPILLGESGVGKTAIAEGL-AIRIVQAEVPVFLLSKRIMSLDM----GLL  357 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L~~~~-----~~nvLL~GppG~GKT~la~~l-a~~l~~~~~p~~l~~~~v~~ld~----~~l  357 (710)
                      .+.+++|++...+.+.-.+....     .-|+||+|+||+ ||.+++++ ++.+.          ..++..+.    ..+
T Consensus       211 sIapI~G~e~vK~aLll~L~GG~~k~rgdihVLL~G~PGt-KS~Lar~i~~~i~p----------R~~ft~g~~ss~~gL  279 (506)
T 3f8t_A          211 AIAPLPGAEEVGKMLALQLFSCVGKNSERLHVLLAGYPVV-CSEILHHVLDHLAP----------RGVYVDLRRTELTDL  279 (506)
T ss_dssp             HHCCSTTCHHHHHHHHHHHTTCCSSGGGCCCEEEESCHHH-HHHHHHHHHHHTCS----------SEEEEEGGGCCHHHH
T ss_pred             HhcccCCCHHHHHHHHHHHcCCccccCCceeEEEECCCCh-HHHHHHHHHHHhCC----------CeEEecCCCCCccCc
Confidence            34459999875444444443321     128999999999 99999999 65431          11121111    011


Q ss_pred             hhcccc-CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------CeE
Q 005179          358 MAGAKE-RGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------ELQ  425 (710)
Q Consensus       358 ~~g~~~-~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------~v~  425 (710)
                      ...... .| +.-+-..    +..+.+.+|||||++.+             ....+..|.+.|+++           ++.
T Consensus       280 t~s~r~~tG-~~~~~G~----l~LAdgGvl~lDEIn~~-------------~~~~qsaLlEaMEe~~VtI~G~~lparf~  341 (506)
T 3f8t_A          280 TAVLKEDRG-WALRAGA----AVLADGGILAVDHLEGA-------------PEPHRWALMEAMDKGTVTVDGIALNARCA  341 (506)
T ss_dssp             SEEEEESSS-EEEEECH----HHHTTTSEEEEECCTTC-------------CHHHHHHHHHHHHHSEEEETTEEEECCCE
T ss_pred             eEEEEcCCC-cccCCCe----eEEcCCCeeehHhhhhC-------------CHHHHHHHHHHHhCCcEEECCEEcCCCeE
Confidence            100000 01 1000001    11234579999999998             556677777777754           467


Q ss_pred             EEEccChHHHH------hhhhccHHHHcccc--ceEecCCCHHH
Q 005179          426 CIASTTQDEHR------TQFEKDKALARRFQ--PVLISEPSQED  461 (710)
Q Consensus       426 vI~att~~~~~------~~~~~d~aL~~Rf~--~I~v~~Ps~~~  461 (710)
                      +|+|+|+.+..      ..+.+.+++.+||+  .+.++.|+.+.
T Consensus       342 VIAA~NP~~~yd~~~s~~~~~Lp~alLDRFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          342 VLAAINPGEQWPSDPPIARIDLDQDFLSHFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             EEEEECCCC--CCSCGGGGCCSCHHHHTTCSEEEETTC------
T ss_pred             EEEEeCcccccCCCCCccccCCChHHhhheeeEEEecCCCChhH
Confidence            89999986511      12478899999997  34456666443

>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=98.67  E-value=2.3e-08  Score=108.90  Aligned_cols=77  Identities=31%  Similarity=0.488  Sum_probs=58.3

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHHHh--hcCCCCC---CCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVKRS--RVGLKDP---NRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~~~--r~gl~~p---~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .++.+.|.+.|+||+++++.+..++...  +.++...   ..+.+++||+||||||||++|++||+.+   ...++.+|+
T Consensus         7 ~~i~~~Ld~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l---~~~~~~v~~   83 (444)
T 1g41_A            7 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA---NAPFIKVEA   83 (444)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT---TCCEEEEEG
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHc---CCCceeecc
Confidence            3567788899999999999999887332  2222111   1234689999999999999999999996   447899998


Q ss_pred             CCCCC
Q 005179          696 SPFNS  700 (710)
Q Consensus       696 se~~~  700 (710)
                      +.+.+
T Consensus        84 ~~~~~   88 (444)
T 1g41_A           84 TKFTE   88 (444)
T ss_dssp             GGGC-
T ss_pred             hhhcc
Confidence            87654

>1khy_A CLPB protein; alpha helix, chaperone; 1.95A {Escherichia coli} SCOP: a.174.1.1

Probab=98.65  E-value=5.4e-08  Score=90.39  Aligned_cols=64  Identities=19%  Similarity=0.301  Sum_probs=61.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++++|+.|..+|+++||.+|+++|||+||++++++.+..+|+++|+|.+.++..+...+
T Consensus         5 ~~t~~~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~~~~~~iL~~~g~~~~~l~~~l~~~l   68 (148)
T 1khy_A            5 RLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQAL   68 (148)
T ss_dssp             CBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHcCCCchHHHHHHHcCCCHHHHHHHHHHHH
Confidence            5999999999999999999999999999999999999999999999999999999999887766

>3zri_A CLPB protein, CLPV; chaperone, HSP100 proteins, AAA+ proteins, T6SS, secretion,; 1.80A {Vibrio cholerae} PDB: 3zrj_A

Probab=98.62  E-value=6.2e-08  Score=92.02  Aligned_cols=63  Identities=19%  Similarity=0.180  Sum_probs=60.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++++|+.|.++|+++|+.+|++||||+||++++++.+.++|+++|+|.+.++..+. .+
T Consensus        24 kfT~~a~~aL~~A~~~A~~~~h~~I~~EHLLlaLL~~~~~~a~~iL~~~gvd~~~l~~~l~-~l   86 (171)
T 3zri_A           24 KLNAQSKLALEQAASLCIERQHPEVTLEHYLDVLLDNPLSDVRLVLKQAGLEVDQVKQAIA-ST   86 (171)
T ss_dssp             HBCHHHHHHHHHHHHHHHHHTCSEECHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH-HH
T ss_pred             HcCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHccCcHHHHHHHHcCCCHHHHHHHHH-HH
Confidence            4999999999999999999999999999999999999999999999999999999998887 66

>2y1q_A CLPC N-domain, negative regulator of genetic competence CLPC/MEC; transcription, proteolysis; 1.50A {Bacillus subtilis} PDB: 2y1r_A* 2k77_A

Probab=98.61  E-value=6.8e-08  Score=89.95  Aligned_cols=64  Identities=30%  Similarity=0.414  Sum_probs=61.0

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++++|+.|.++|+++||.+|+++|||+||++++++.+..+|+++|+|.+.++..+...+
T Consensus         5 ~~t~~~~~al~~A~~~A~~~~h~~i~~eHlLlaLl~~~~~~~~~iL~~~g~~~~~l~~~l~~~l   68 (150)
T 2y1q_A            5 RFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLI   68 (150)
T ss_dssp             CBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHHCSSHHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             hhCHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHhCCCCHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            5999999999999999999999999999999999999999999999999999999998887766

>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=98.58  E-value=2.5e-08  Score=95.84  Aligned_cols=100  Identities=19%  Similarity=0.246  Sum_probs=58.4

Q ss_pred             hhhhcCCCCcccCH----HHHHHHHHHHHc---CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          283 RASEELIDPVIGRE----TEIQRIIQILCR---RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       283 ~~~~~~l~~liGr~----~~i~~l~~~L~~---~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      ++++.+|+++++.+    ..+..+.+.+..   ..+.+++|+||+|+||||++++++..+....      +..++.++..
T Consensus         3 r~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~------g~~~~~~~~~   76 (180)
T 3ec2_A            3 RYWNANLDTYHPKNVSQNRALLTIRVFVHNFNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKK------GIRGYFFDTK   76 (180)
T ss_dssp             SCTTCCSSSCCCCSHHHHHHHHHHHHHHHSCCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHS------CCCCCEEEHH
T ss_pred             hhhhCccccccCCCHHHHHHHHHHHHHHHhccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHc------CCeEEEEEHH
Confidence            45667888888742    333444443332   3467899999999999999999999885211      3344445554


Q ss_pred             hhhhccc---cCccHHHHHHHHHHHHHhcCCeEEEEccchhh
Q 005179          356 LLMAGAK---ERGELEARVTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       356 ~l~~g~~---~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                      .+.....   ..+..    ..++..+.  .+.+|+|||++..
T Consensus        77 ~~~~~~~~~~~~~~~----~~~~~~~~--~~~llilDE~~~~  112 (180)
T 3ec2_A           77 DLIFRLKHLMDEGKD----TKFLKTVL--NSPVLVLDDLGSE  112 (180)
T ss_dssp             HHHHHHHHHHHHTCC----SHHHHHHH--TCSEEEEETCSSS
T ss_pred             HHHHHHHHHhcCchH----HHHHHHhc--CCCEEEEeCCCCC
Confidence            4431100   00000    02222222  3569999999754

>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=98.58  E-value=5.9e-08  Score=107.56  Aligned_cols=67  Identities=27%  Similarity=0.252  Sum_probs=56.0

Q ss_pred             hCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          628 KKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       628 ~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .+.|+||+++++.+...+...+.|...|    .++|||||||||||++|+++|+.+- ..-.++.++++++.
T Consensus        36 ~~~iiG~~~~~~~l~~~~~~~~~~~~~~----~~iLl~GppGtGKT~la~ala~~l~-~~~~~~~~~~~~~~  102 (456)
T 2c9o_A           36 ASGLVGQENAREACGVIVELIKSKKMAG----RAVLLAGPPGTGKTALALAIAQELG-SKVPFCPMVGSEVY  102 (456)
T ss_dssp             ETTEESCHHHHHHHHHHHHHHHTTCCTT----CEEEEECCTTSSHHHHHHHHHHHHC-TTSCEEEEEGGGGC
T ss_pred             hhhccCHHHHHHHHHHHHHHHHhCCCCC----CeEEEECCCcCCHHHHHHHHHHHhC-CCceEEEEeHHHHH
Confidence            4559999999999999888888776543    6899999999999999999999963 34678888888764

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=98.56  E-value=9e-08  Score=101.02  Aligned_cols=66  Identities=27%  Similarity=0.312  Sum_probs=49.6

Q ss_pred             ccChHHHHHHHHHHHHHh----hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRS----RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~----r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |+|++++++.+...+...    ...- ...+|..++|||||||||||++|+++|+.+.  ...++.++++++.
T Consensus        14 i~G~~~~k~~l~~~v~~p~~~~~~~~-~~~~~~~~iLL~GppGtGKT~la~ala~~~~--~~~~~~i~~~~l~   83 (322)
T 1xwi_A           14 VAGLEGAKEALKEAVILPIKFPHLFT-GKRTPWRGILLFGPPGTGKSYLAKAVATEAN--NSTFFSISSSDLV   83 (322)
T ss_dssp             SCSCHHHHHHHHHHHHHHHHCGGGSC-TTCCCCSEEEEESSSSSCHHHHHHHHHHHTT--SCEEEEEECCSSC
T ss_pred             hcCHHHHHHHHHHHHHHHHhCHHHHh-CCCCCCceEEEECCCCccHHHHHHHHHHHcC--CCcEEEEEhHHHH
Confidence            889999998888777442    2211 1134456999999999999999999999962  4568888887764

>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=98.50  E-value=8.1e-08  Score=100.37  Aligned_cols=61  Identities=25%  Similarity=0.380  Sum_probs=48.1

Q ss_pred             ccChHHHHHHHHHHHHHh--------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRS--------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~--------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|++++++.+...+.+.        ..|+..+    .++|||||||||||++|++||+.+   ...++.++++++
T Consensus        17 i~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~----~~vLL~Gp~GtGKT~la~ala~~~---~~~~i~v~~~~l   85 (301)
T 3cf0_A           17 IGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS----KGVLFYGPPGCGKTLLAKAIANEC---QANFISIKGPEL   85 (301)
T ss_dssp             SCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCC----SEEEEECSSSSSHHHHHHHHHHHT---TCEEEEECHHHH
T ss_pred             hCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCC----ceEEEECCCCcCHHHHHHHHHHHh---CCCEEEEEhHHH
Confidence            889999998888877653        4455433    589999999999999999999995   356777776554

>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=98.50  E-value=7.1e-08  Score=109.06  Aligned_cols=102  Identities=21%  Similarity=0.195  Sum_probs=75.4

Q ss_pred             cCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCC
Q 005179          591 VVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGV  670 (710)
Q Consensus       591 ~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGt  670 (710)
                      ......+...++.++++|+...+.+. ..+.+.++.|.+.++|+++++..+...+.........+   ...+||+|||||
T Consensus        44 ~~e~~~~~~~l~~~~~lp~~~~~~~~-~~~~~~~~~l~~di~G~~~vk~~i~~~~~l~~~~~~~~---g~~vll~Gp~Gt  119 (543)
T 3m6a_A           44 SAESSVIRNYIDWLVALPWTDETDDK-LDLKEAGRLLDEEHHGLEKVKERILEYLAVQKLTKSLK---GPILCLAGPPGV  119 (543)
T ss_dssp             CTTTTHHHHHHHHHHHSCSSCCCCCC-CCTTTGGGTHHHHCSSCHHHHHHHHHHHHHHHHSSSCC---SCEEEEESSSSS
T ss_pred             CchHhHHHHHHHHHhcCCCCcccccc-ccHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhcccCC---CCEEEEECCCCC
Confidence            33445677888888899987765432 22445667788889999999999988776665554442   348999999999


Q ss_pred             cHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          671 GKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       671 GKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |||++|++||..+   ...+++++++.+.
T Consensus       120 GKTtlar~ia~~l---~~~~~~i~~~~~~  145 (543)
T 3m6a_A          120 GKTSLAKSIAKSL---GRKFVRISLGGVR  145 (543)
T ss_dssp             SHHHHHHHHHHHH---TCEEEEECCCC--
T ss_pred             CHHHHHHHHHHhc---CCCeEEEEecccc
Confidence            9999999999997   3467778776643

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=98.49  E-value=9.6e-08  Score=98.35  Aligned_cols=76  Identities=25%  Similarity=0.290  Sum_probs=44.2

Q ss_pred             hccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcc
Q 005179          611 QITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIH  690 (710)
Q Consensus       611 ~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~l  690 (710)
                      .++|++++.+.++++.|.+.|+..      +...-.+...|+..|    .|+||+||||||||+||++||..+-   ..+
T Consensus         6 ~~~~~di~g~~~~~~~l~~~i~~~------~~~~~~l~~~~l~~~----~GvlL~Gp~GtGKTtLakala~~~~---~~~   72 (274)
T 2x8a_A            6 NVTWADIGALEDIREELTMAILAP------VRNPDQFKALGLVTP----AGVLLAGPPGCGKTLLAKAVANESG---LNF   72 (274)
T ss_dssp             ------CCHHHHHHHHHHHHHTHH------HHSHHHHHHTTCCCC----SEEEEESSTTSCHHHHHHHHHHHTT---CEE
T ss_pred             CCCHHHhCCHHHHHHHHHHHHHHH------hhCHHHHHHcCCCCC----CeEEEECCCCCcHHHHHHHHHHHcC---CCE
Confidence            556666555554444444332211      111112344566554    4699999999999999999999852   257


Q ss_pred             eeeCCCCCC
Q 005179          691 YLFFPSPFN  699 (710)
Q Consensus       691 i~~d~se~~  699 (710)
                      +.++.+++.
T Consensus        73 i~i~g~~l~   81 (274)
T 2x8a_A           73 ISVKGPELL   81 (274)
T ss_dssp             EEEETTTTC
T ss_pred             EEEEcHHHH
Confidence            888877764

>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=98.48  E-value=1.9e-07  Score=95.09  Aligned_cols=65  Identities=31%  Similarity=0.328  Sum_probs=50.3

Q ss_pred             CcccChHHHHHHHHHHHHHhhc-------CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRV-------GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~-------gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      +.|+|++++++.+...+...+.       |+.    +..++||+||||||||++|+++|+.+-   ..++.++++++.+
T Consensus         6 ~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g~~----~~~~vll~G~~GtGKT~la~~la~~~~---~~~~~~~~~~~~~   77 (262)
T 2qz4_A            6 KDVAGMHEAKLEVREFVDYLKSPERFLQLGAK----VPKGALLLGPPGCGKTLLAKAVATEAQ---VPFLAMAGAEFVE   77 (262)
T ss_dssp             TSSCSCHHHHHHHHHHHHHHHCCC------CC----CCCEEEEESCTTSSHHHHHHHHHHHHT---CCEEEEETTTTSS
T ss_pred             HHhCCHHHHHHHHHHHHHHHHCHHHHHHcCCC----CCceEEEECCCCCCHHHHHHHHHHHhC---CCEEEechHHHHh
Confidence            4589999999999887755332       222    235899999999999999999999963   4688888887743

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=98.46  E-value=1.5e-07  Score=98.58  Aligned_cols=96  Identities=15%  Similarity=0.249  Sum_probs=56.3

Q ss_pred             hcCCCCcccCH----HHHHHHHHHHHcC---CCCCcEEEcCCCChHHHHHHHHHHHHH-hcCCCccccCceEEEeehhhh
Q 005179          286 EELIDPVIGRE----TEIQRIIQILCRR---TKNNPILLGESGVGKTAIAEGLAIRIV-QAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       286 ~~~l~~liGr~----~~i~~l~~~L~~~---~~~nvLL~GppG~GKT~la~~la~~l~-~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      +.+|+++++.+    ..+..+..++...   ...+++|+||||||||+|+.+++..+. ..       +..+..+....+
T Consensus       120 ~~tfd~f~~~~~~~~~~~~~~~~~i~~~~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~-------g~~v~~~~~~~l  192 (308)
T 2qgz_A          120 HIHLSDIDVNNASRMEAFSAILDFVEQYPSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKK-------GVSTTLLHFPSF  192 (308)
T ss_dssp             SCCGGGSCCCSHHHHHHHHHHHHHHHHCSCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHS-------CCCEEEEEHHHH
T ss_pred             hCCHhhCcCCChHHHHHHHHHHHHHHhccccCCceEEEECCCCCCHHHHHHHHHHHHHHhc-------CCcEEEEEHHHH
Confidence            34555665432    2334444555542   257899999999999999999999886 43       456666666555


Q ss_pred             hhc---cccCccHHHHHHHHHHHHHhcCCeEEEEccchhh
Q 005179          358 MAG---AKERGELEARVTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       358 ~~g---~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                      ...   ....+.    +..++..+..  ..+|||||++..
T Consensus       193 ~~~l~~~~~~~~----~~~~~~~~~~--~~lLiiDdig~~  226 (308)
T 2qgz_A          193 AIDVKNAISNGS----VKEEIDAVKN--VPVLILDDIGAE  226 (308)
T ss_dssp             HHHHHCCCC--------CCTTHHHHT--SSEEEEETCCC-
T ss_pred             HHHHHHHhccch----HHHHHHHhcC--CCEEEEcCCCCC
Confidence            421   111111    1222333333  349999999654

>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=98.46  E-value=1e-07  Score=100.60  Aligned_cols=65  Identities=31%  Similarity=0.400  Sum_probs=48.8

Q ss_pred             ccChHHHHHHHHHHHHHhhc---CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRV---GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~---gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|++++++.+...+.....   -.....+|..++|||||||||||++|++||+.+   ...++.++++++
T Consensus        20 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~~~~~v~~~~l   87 (322)
T 3eie_A           20 VAGLEGAKEALKEAVILPVKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAVATEA---NSTFFSVSSSDL   87 (322)
T ss_dssp             SCSCHHHHHHHHHHTHHHHHCGGGCCTTCCCCCEEEEECSSSSCHHHHHHHHHHHH---TCEEEEEEHHHH
T ss_pred             hcChHHHHHHHHHHHHHHHhCHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHH---CCCEEEEchHHH
Confidence            89999999999887744321   112234455699999999999999999999995   346777777654

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.44  E-value=5.9e-08  Score=90.31  Aligned_cols=105  Identities=15%  Similarity=0.159  Sum_probs=64.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFID  389 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~ID  389 (710)
                      .+.+++|+||+|+|||+|+++++..+...       +..++.++...+...            .+     ...+.+|+||
T Consensus        35 ~g~~~~l~G~~G~GKTtL~~~i~~~~~~~-------g~~~~~~~~~~~~~~------------~~-----~~~~~lLilD   90 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLLQAWVAQALEA-------GKNAAYIDAASMPLT------------DA-----AFEAEYLAVD   90 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHHHHHHHHHHTT-------TCCEEEEETTTSCCC------------GG-----GGGCSEEEEE
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHhc-------CCcEEEEcHHHhhHH------------HH-----HhCCCEEEEe
Confidence            56779999999999999999999988531       445666665444311            01     1235699999


Q ss_pred             cchhhhhCCCCCCCCCCChHhHHHhhcccccCCCe-EEEEccChHHHHhhhhccHHHHcccc
Q 005179          390 EVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGEL-QCIASTTQDEHRTQFEKDKALARRFQ  450 (710)
Q Consensus       390 Eid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v-~vI~att~~~~~~~~~~d~aL~~Rf~  450 (710)
                      |++.+...         ....+.+++....+++.. ++|.+...+.  .+... +.|.+||.
T Consensus        91 E~~~~~~~---------~~~~l~~li~~~~~~g~~~iiits~~~p~--~l~~~-~~L~SRl~  140 (149)
T 2kjq_A           91 QVEKLGNE---------EQALLFSIFNRFRNSGKGFLLLGSEYTPQ--QLVIR-EDLRTRMA  140 (149)
T ss_dssp             STTCCCSH---------HHHHHHHHHHHHHHHTCCEEEEEESSCTT--TSSCC-HHHHHHGG
T ss_pred             CccccChH---------HHHHHHHHHHHHHHcCCcEEEEECCCCHH--Hcccc-HHHHHHHh
Confidence            99886211         123345555555555554 4444332222  12223 89999986

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=98.43  E-value=1.4e-07  Score=98.13  Aligned_cols=60  Identities=10%  Similarity=0.069  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          635 DEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       635 ~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +..++.+...+.+..........| .++|||||||||||++|++||+.+   +..+++++++++
T Consensus        13 ~~~~~~~~~~~~k~~l~~~~~~~p-~~lLl~GppGtGKT~la~aiA~~l---~~~~i~v~~~~l   72 (293)
T 3t15_A           13 PAFMDKLVVHITKNFLKLPNIKVP-LILGIWGGKGQGKSFQCELVFRKM---GINPIMMSAGEL   72 (293)
T ss_dssp             HHHHHHHHHHHHHTTSCCTTCCCC-SEEEEEECTTSCHHHHHHHHHHHH---TCCCEEEEHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCC-eEEEEECCCCCCHHHHHHHHHHHh---CCCEEEEeHHHh
Confidence            344555555555555544444444 489999999999999999999997   457899987765

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=98.42  E-value=3.8e-07  Score=92.79  Aligned_cols=64  Identities=34%  Similarity=0.382  Sum_probs=48.5

Q ss_pred             cccChHHHHHHHHHHHHHhhc-------CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRV-------GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~-------gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .|+|++++++.+...+.+...       |..    +..++||+||||||||++|++||+.+-   ..++.++++++.+
T Consensus        13 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~----~~~~vll~G~~GtGKT~la~~la~~~~---~~~~~i~~~~~~~   83 (257)
T 1lv7_A           13 DVAGCDEAKEEVAELVEYLREPSRFQKLGGK----IPKGVLMVGPPGTGKTLLAKAIAGEAK---VPFFTISGSDFVE   83 (257)
T ss_dssp             GSCSCHHHHHHTHHHHHHHHCGGGC-----C----CCCEEEEECCTTSCHHHHHHHHHHHHT---CCEEEECSCSSTT
T ss_pred             HhcCcHHHHHHHHHHHHHHhCHHHHHHcCCC----CCCeEEEECcCCCCHHHHHHHHHHHcC---CCEEEEeHHHHHH
Confidence            489999999988877655321       222    225799999999999999999999963   3578888887643

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=98.42  E-value=2.1e-07  Score=86.01  Aligned_cols=63  Identities=16%  Similarity=0.199  Sum_probs=49.8

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .++|++.++..+...++....    ..   ..+||+||||||||++|++|++.....+..++ +|++.+.+
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a~----~~---~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~   64 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLSE----TD---IAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDN   64 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHTT----CC---SCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTT
T ss_pred             CceeCCHHHHHHHHHHHHHhC----CC---CCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCc
Confidence            478999999999888766531    11   36899999999999999999998777777888 99887754

>1k6k_A ATP-dependent CLP protease ATP-binding subunit CLPA; chaperone, ATPase, adaptor binding, X-RAY, structure, N-domain, hydrolase; 1.80A {Escherichia coli} SCOP: a.174.1.1 PDB: 1r6c_X 1r6o_A* 1r6q_A* 1mg9_B* 1lzw_B* 1mbx_A* 1mbv_A 1mbu_A*

Probab=98.41  E-value=2.9e-07  Score=84.86  Aligned_cols=62  Identities=19%  Similarity=0.255  Sum_probs=57.5

Q ss_pred             CCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhh
Q 005179          171 FSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQ  234 (710)
Q Consensus       171 ~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~  234 (710)
                      ||+.++++|+.|.++|+++||.+|+++|||+||+++++  +.++|+++|+|.+.++..+...+.
T Consensus         2 ~t~~~~~~l~~A~~~A~~~~~~~i~~eHlLlaLl~~~~--~~~iL~~~g~~~~~l~~~l~~~l~   63 (143)
T 1k6k_A            2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPS--AREALEACSVDLVALRQELEAFIE   63 (143)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHH--HHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHcCch--HHHHHHHcCCCHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999998654  899999999999999998877764

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=98.39  E-value=3.2e-07  Score=94.73  Aligned_cols=62  Identities=29%  Similarity=0.443  Sum_probs=48.3

Q ss_pred             ccChHHHHHHHHHHHHHh--------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRS--------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~--------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ++|++++++.+...+...        ..|+..+    .++||+||||||||++|+++|+.+   ...++.++++++.
T Consensus        19 i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~ll~G~~GtGKT~la~~la~~~---~~~~~~v~~~~~~   88 (285)
T 3h4m_A           19 IGGLEKQMQEIREVVELPLKHPELFEKVGIEPP----KGILLYGPPGTGKTLLAKAVATET---NATFIRVVGSELV   88 (285)
T ss_dssp             SCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCC----SEEEEESSSSSSHHHHHHHHHHHT---TCEEEEEEGGGGC
T ss_pred             hcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCC----CeEEEECCCCCcHHHHHHHHHHHh---CCCEEEEehHHHH
Confidence            889999998888777543        2344333    589999999999999999999995   4468888877663

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=98.37  E-value=4.2e-07  Score=94.52  Aligned_cols=63  Identities=32%  Similarity=0.470  Sum_probs=49.2

Q ss_pred             ccChHHHHHHHHHHHHHhhc------CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRV------GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~------gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |+|++++++.+...+.....      ++.   .|..++||+||||||||++|+++|+.+   ...++.++++++.
T Consensus        23 i~G~~~~~~~l~~~i~~~~~~~~~~~~~~---~~~~~vll~Gp~GtGKT~la~~la~~~---~~~~~~i~~~~l~   91 (297)
T 3b9p_A           23 IAGQDVAKQALQEMVILPSVRPELFTGLR---APAKGLLLFGPPGNGKTLLARAVATEC---SATFLNISAASLT   91 (297)
T ss_dssp             SCCCHHHHHHHHHHTHHHHHCGGGSCGGG---CCCSEEEEESSSSSCHHHHHHHHHHHT---TCEEEEEESTTTS
T ss_pred             hCChHHHHHHHHHHHHhhhhCHHHHhcCC---CCCCeEEEECcCCCCHHHHHHHHHHHh---CCCeEEeeHHHHh
Confidence            89999999999888755321      222   233589999999999999999999996   3468888887764

>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=98.35  E-value=4.1e-07  Score=100.33  Aligned_cols=66  Identities=27%  Similarity=0.319  Sum_probs=47.8

Q ss_pred             ccChHHHHHHHHHHHHHh----hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRS----RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~----r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |+|++++++.+...+...    ... ....+|..++|||||||||||++|++||+.+.  ...++.++++++.
T Consensus       136 i~G~~~~k~~l~~~v~~p~~~~~~~-~~~~~~~~~vLL~GppGtGKT~lA~aia~~~~--~~~~~~v~~~~l~  205 (444)
T 2zan_A          136 VAGLEGAKEALKEAVILPIKFPHLF-TGKRTPWRGILLFGPPGTGKSYLAKAVATEAN--NSTFFSISSSDLV  205 (444)
T ss_dssp             SCSCHHHHHHHHHHHTHHHHCTTTT-SGGGCCCSEEEEECSTTSSHHHHHHHHHHHCC--SSEEEEECCC---
T ss_pred             hcCHHHHHHHHHHHHHHHhhCHHHh-hccCCCCceEEEECCCCCCHHHHHHHHHHHcC--CCCEEEEeHHHHH
Confidence            899999999988877432    211 11123446999999999999999999999972  3568888888763

>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=98.35  E-value=1.7e-07  Score=100.24  Aligned_cols=65  Identities=29%  Similarity=0.382  Sum_probs=48.1

Q ss_pred             cccChHHHHHHHHHHHHHh----hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRS----RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~----r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .|+|++++++.+...+.+.    ..... ..+|..++|||||||||||++|++||+.+   ...++.++++++
T Consensus        52 di~G~~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~---~~~~~~v~~~~l  120 (355)
T 2qp9_X           52 DVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEA---NSTFFSVSSSDL  120 (355)
T ss_dssp             GSCCGGGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHH---TCEEEEEEHHHH
T ss_pred             HhCCHHHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHh---CCCEEEeeHHHH
Confidence            3899999999988877443    22111 23445689999999999999999999997   346777776554

>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=98.35  E-value=1.6e-06  Score=107.89  Aligned_cols=79  Identities=14%  Similarity=0.133  Sum_probs=46.8

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------hcc-------ccCccHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------AGA-------KERGELEARVTTLI  375 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------~g~-------~~~g~~e~~l~~~~  375 (710)
                      .+..++|+||||+|||+|+..++..+...       +..+..++.....       .|.       ......++.+..+-
T Consensus       731 ~G~lVlI~G~PG~GKTtLal~lA~~aa~~-------g~~VlyiS~Ees~~ql~A~~lGvd~~~L~i~~~~~leei~~~l~  803 (1706)
T 3cmw_A          731 MGRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICD  803 (1706)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHH
T ss_pred             CCceEEEECCCCCCcHHHHHHHHHHHHHc-------CCCeEEEeccchHHHHHHHHcCCChhheEEecCCcHHHHHHHHH
Confidence            34568999999999999999999887543       2334444332111       010       00112332222222


Q ss_pred             HHHHhcCCeEEEEccchhhh
Q 005179          376 SEIQKSGDVILFIDEVHTLI  395 (710)
Q Consensus       376 ~~~~~~~~~IL~IDEid~l~  395 (710)
                      ..+....+.+||||.+..+.
T Consensus       804 ~lv~~~~~~lVVIDsLq~l~  823 (1706)
T 3cmw_A          804 ALARSGAVDVIVVDSVAALT  823 (1706)
T ss_dssp             HHHHHTCCSEEEESCSTTCC
T ss_pred             HHHHccCCCEEEEechhhhc
Confidence            22334678899999999986

>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=98.33  E-value=1.6e-06  Score=92.15  Aligned_cols=156  Identities=15%  Similarity=0.082  Sum_probs=102.3

Q ss_pred             HHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHH----hc
Q 005179          306 LCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQ----KS  381 (710)
Q Consensus       306 L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~----~~  381 (710)
                      +..+..+..||+||+|.||++.+..+++.+.+....    .+.++.++      +.   .+    ++.+++.+.    .+
T Consensus        13 l~~~~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~----~~~~~~~~------~~---~~----~~~l~~~~~~~plf~   75 (343)
T 1jr3_D           13 LNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFE----EHHTFSID------PN---TD----WNAIFSLCQAMSLFA   75 (343)
T ss_dssp             HHHCCCSEEEEEESCHHHHHHHHHHHHHHHHHHTCC----EEEEEECC------TT---CC----HHHHHHHHHHHHHCC
T ss_pred             HhcCCCcEEEEECCcHHHHHHHHHHHHHHHHhCCCC----eeEEEEec------CC---CC----HHHHHHHhcCcCCcc
Confidence            333445567899999999999999999987643211    11223332      11   22    334444443    24


Q ss_pred             CCeEEEEccchh-hhhCCCCCCCCCCChHhHHHhhcccccC--CCeE-EEEccChHHHHhhhhccHHHHccccceEecCC
Q 005179          382 GDVILFIDEVHT-LIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQ-CIASTTQDEHRTQFEKDKALARRFQPVLISEP  457 (710)
Q Consensus       382 ~~~IL~IDEid~-l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~-vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~P  457 (710)
                      +.-|++|||+|. +             ..+..+.|..++++  ...+ |+.+++.+...+...+-+++.+|+..+.+.++
T Consensus        76 ~~kvvii~~~~~kl-------------~~~~~~aLl~~le~p~~~~~~il~~~~~~~~~~~~k~~~~i~sr~~~~~~~~l  142 (343)
T 1jr3_D           76 SRQTLLLLLPENGP-------------NAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTP  142 (343)
T ss_dssp             SCEEEEEECCSSCC-------------CTTHHHHHHHHHTTCBTTEEEEEEESCCCTTTTTSHHHHHHTTTCEEEEECCC
T ss_pred             CCeEEEEECCCCCC-------------ChHHHHHHHHHHhcCCCCeEEEEEcCCCChhhHhhHHHHHHHhCceEEEeeCC
Confidence            567999999998 7             22356667777775  2344 44444322111122455889999999999999


Q ss_pred             CHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          458 SQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       458 s~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      +..+....++..+.    ..++.+++++++.++..+.+
T Consensus       143 ~~~~l~~~l~~~~~----~~g~~i~~~a~~~l~~~~~g  176 (343)
T 1jr3_D          143 EQAQLPRWVAARAK----QLNLELDDAANQVLCYCYEG  176 (343)
T ss_dssp             CTTHHHHHHHHHHH----HTTCEECHHHHHHHHHSSTT
T ss_pred             CHHHHHHHHHHHHH----HcCCCCCHHHHHHHHHHhch
Confidence            99998877776665    45899999999999888654

>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=98.32  E-value=2.8e-07  Score=94.27  Aligned_cols=63  Identities=32%  Similarity=0.412  Sum_probs=47.2

Q ss_pred             cccChHHHHHHHHHHHHHh-------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRS-------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~-------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .++|++++++.+...+...       ..|...|    .++||+||||||||++|++||+.+.   ..++.++++.+.
T Consensus        12 ~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~----~~vll~G~~GtGKT~la~~la~~~~---~~~~~v~~~~~~   81 (268)
T 2r62_A           12 DMAGNEEAKEEVVEIVDFLKYPERYANLGAKIP----KGVLLVGPPGTGKTLLAKAVAGEAH---VPFFSMGGSSFI   81 (268)
T ss_dssp             TSSSCTTTHHHHHHHHHHHHCHHHHHHHSCCCC----SCCCCBCSSCSSHHHHHHHHHHHHT---CCCCCCCSCTTT
T ss_pred             HhCCcHHHHHHHHHHHHHHHChHHHHHCCCCCC----ceEEEECCCCCcHHHHHHHHHHHhC---CCEEEechHHHH
Confidence            3888888888888766532       2244333    4789999999999999999999963   367777777653

>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=98.29  E-value=9.5e-07  Score=97.55  Aligned_cols=62  Identities=31%  Similarity=0.464  Sum_probs=49.5

Q ss_pred             ccChHHHHHHHHHHHHHhh-------cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSR-------VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r-------~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      |+|++++++.+...+.+.+       .|.+.|    .++||+||||||||++|++||..+   ...++.++++++.
T Consensus        18 i~G~~~~~~~l~e~v~~l~~~~~~~~~g~~~p----~gvLL~GppGtGKT~Laraia~~~---~~~f~~is~~~~~   86 (476)
T 2ce7_A           18 VGGAEEAIEELKEVVEFLKDPSKFNRIGARMP----KGILLVGPPGTGKTLLARAVAGEA---NVPFFHISGSDFV   86 (476)
T ss_dssp             CCSCHHHHHHHHHHHHHHHCTHHHHTTTCCCC----SEEEEECCTTSSHHHHHHHHHHHH---TCCEEEEEGGGTT
T ss_pred             hCCcHHHHHHHHHHHHHhhChHHHhhcCCCCC----CeEEEECCCCCCHHHHHHHHHHHc---CCCeeeCCHHHHH
Confidence            8999999998888776543       344433    579999999999999999999986   3468888887774

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=98.26  E-value=1.1e-06  Score=92.87  Aligned_cols=64  Identities=17%  Similarity=0.141  Sum_probs=51.6

Q ss_pred             HHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          619 LLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       619 ~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      .+..+...+...|+||+++++.+..++...           +++||+||||||||++|+++|+.+-   ..+++++++
T Consensus        17 ~~~~~~~~~~~~i~g~~~~~~~l~~~l~~~-----------~~vll~G~pGtGKT~la~~la~~~~---~~~~~i~~~   80 (331)
T 2r44_A           17 KIKEVIDEVGKVVVGQKYMINRLLIGICTG-----------GHILLEGVPGLAKTLSVNTLAKTMD---LDFHRIQFT   80 (331)
T ss_dssp             HHHHHHHHHTTTCCSCHHHHHHHHHHHHHT-----------CCEEEESCCCHHHHHHHHHHHHHTT---CCEEEEECC
T ss_pred             HHHHHHHHhccceeCcHHHHHHHHHHHHcC-----------CeEEEECCCCCcHHHHHHHHHHHhC---CCeEEEecC
Confidence            345677888899999999999988776542           3789999999999999999999863   346666654

>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=98.25  E-value=9.5e-07  Score=94.56  Aligned_cols=68  Identities=25%  Similarity=0.348  Sum_probs=50.3

Q ss_pred             cccChHHHHHHHHHHHHHhhcC---CCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVG---LKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~g---l~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .|+|++++++.+...+......   .....++..++||+||||||||++|++||+.+   ...++.++++++.+
T Consensus        85 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~vLl~GppGtGKT~la~aia~~~---~~~~~~i~~~~l~~  155 (357)
T 3d8b_A           85 DIAGVEFAKATIKEIVVWPMLRPDIFTGLRGPPKGILLFGPPGTGKTLIGKCIASQS---GATFFSISASSLTS  155 (357)
T ss_dssp             GSCSCHHHHHHHHHHTHHHHHCTTTSCGGGSCCSEEEEESSTTSSHHHHHHHHHHHT---TCEEEEEEGGGGCC
T ss_pred             HhCChHHHHHHHHHHHHHHhhChHhHhhccCCCceEEEECCCCCCHHHHHHHHHHHc---CCeEEEEehHHhhc
Confidence            3899999999998887653110   00011234589999999999999999999995   45788888887643

>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=98.24  E-value=7.3e-07  Score=91.10  Aligned_cols=63  Identities=16%  Similarity=0.134  Sum_probs=49.9

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .++|++.++..+...++.....   +    .++||+||||||||++|++|++.+......++.+|++.+.
T Consensus         7 ~~ig~~~~~~~~~~~~~~~~~~---~----~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~   69 (265)
T 2bjv_A            7 NLLGEANSFLEVLEQVSHLAPL---D----KPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALN   69 (265)
T ss_dssp             ---CCCHHHHHHHHHHHHHTTS---C----SCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSC
T ss_pred             cceeCCHHHHHHHHHHHHHhCC---C----CCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCC
Confidence            3789999998888777665321   1    3789999999999999999999987777789999999873

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=98.22  E-value=1.2e-06  Score=94.85  Aligned_cols=67  Identities=30%  Similarity=0.397  Sum_probs=49.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcC---CCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVG---LKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~g---l~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|...+......   ......|..++|||||||||||++|++||+.+   ...++.++++++.+
T Consensus       117 iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~vLL~GppGtGKT~la~aia~~~---~~~~~~v~~~~l~~  186 (389)
T 3vfd_A          117 IAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAES---NATFFNISAASLTS  186 (389)
T ss_dssp             SCSCHHHHHHHHHHTHHHHHCTTTSCGGGCCCSEEEEESSTTSCHHHHHHHHHHHT---TCEEEEECSCCC--
T ss_pred             hCCHHHHHHHHHHHHHHhccCHHHhcccCCCCceEEEECCCCCCHHHHHHHHHHhh---cCcEEEeeHHHhhc
Confidence            899999999998887554320   00111233589999999999999999999995   45789999988754

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=98.21  E-value=1.3e-06  Score=97.17  Aligned_cols=55  Identities=20%  Similarity=0.343  Sum_probs=47.1

Q ss_pred             HHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          618 MLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       618 ~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..+..+.+.+...|+|++++++.+..++...           +++||+||||||||++|++||+.+
T Consensus        11 ~~~~~l~~~l~~~ivGq~~~i~~l~~al~~~-----------~~VLL~GpPGtGKT~LAraLa~~l   65 (500)
T 3nbx_X           11 ERISRLSSSLEKGLYERSHAIRLCLLAALSG-----------ESVFLLGPPGIAKSLIARRLKFAF   65 (500)
T ss_dssp             HHHHHHHHHHHTTCSSCHHHHHHHHHHHHHT-----------CEEEEECCSSSSHHHHHHHGGGGB
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHHHHHHHhcC-----------CeeEeecCchHHHHHHHHHHHHHH
Confidence            4556788899999999999999887765543           389999999999999999999986

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=98.20  E-value=1.6e-06  Score=92.89  Aligned_cols=64  Identities=25%  Similarity=0.222  Sum_probs=49.0

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      +.++|++.+++.+.......+.|...+    .++||+||||||||++|+++|+.+- ....++.++.++
T Consensus        44 ~~ivG~~~~~~~l~~l~~~~~~~~~~~----~~vLl~GppGtGKT~la~~la~~l~-~~~~~~~~~~~~  107 (368)
T 3uk6_A           44 QGMVGQLAARRAAGVVLEMIREGKIAG----RAVLIAGQPGTGKTAIAMGMAQALG-PDTPFTAIAGSE  107 (368)
T ss_dssp             TTEESCHHHHHHHHHHHHHHHTTCCTT----CEEEEEESTTSSHHHHHHHHHHHHC-SSCCEEEEEGGG
T ss_pred             hhccChHHHHHHHHHHHHHHHcCCCCC----CEEEEECCCCCCHHHHHHHHHHHhc-ccCCcccccchh
Confidence            349999999999887777776654332    4899999999999999999999974 333455555444

>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=98.19  E-value=9.4e-07  Score=98.27  Aligned_cols=62  Identities=27%  Similarity=0.455  Sum_probs=49.5

Q ss_pred             cccChHHHHHHHHHHHHHh--------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRS--------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~--------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .|+|++++++.|...+.+.        +.|...|    .++|||||||||||++|++||+.+   ...++.++++++
T Consensus       205 ~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~----~~vLL~GppGtGKT~lAraia~~~---~~~fv~vn~~~l  274 (489)
T 3hu3_A          205 DIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPP----RGILLYGPPGTGKTLIARAVANET---GAFFFLINGPEI  274 (489)
T ss_dssp             GCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCC----CEEEEECSTTSSHHHHHHHHHHHC---SSEEEEEEHHHH
T ss_pred             HcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCC----CcEEEECcCCCCHHHHHHHHHHHh---CCCEEEEEchHh
Confidence            4999999999998877553        3344433    589999999999999999999995   567888886654

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=98.17  E-value=2.3e-06  Score=95.10  Aligned_cols=64  Identities=31%  Similarity=0.414  Sum_probs=49.4

Q ss_pred             cccChHHHHHHHHHHHHHhh-------cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSR-------VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r-------~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .|+|+++++..+.+.+...+       .|+..|    .++||+||||||||+||++||..+   ...++.++.+++..
T Consensus        32 dv~G~~~~k~~l~~lv~~l~~~~~~~~lg~~ip----~GvLL~GppGtGKTtLaraIa~~~---~~~~i~i~g~~~~~  102 (499)
T 2dhr_A           32 DVAGAEEAKEELKEIVEFLKNPSRFHEMGARIP----KGVLLVGPPGVGKTHLARAVAGEA---RVPFITASGSDFVE  102 (499)
T ss_dssp             SSCSCHHHHHHHHHHHHHHHCGGGTTTTSCCCC----SEEEEECSSSSSHHHHHHHHHHHT---TCCEEEEEGGGGTS
T ss_pred             HcCCcHHHHHHHHHHHHHhhchhhhhhccCCCC----ceEEEECCCCCCHHHHHHHHHHHh---CCCEEEEehhHHHH
Confidence            38999999999888776542       223222    479999999999999999999985   35688888877643

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=98.15  E-value=5.7e-07  Score=82.94  Aligned_cols=57  Identities=12%  Similarity=0.155  Sum_probs=44.2

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ++|+++++..+...++.....    .   .++||+||||||||++|++|++...    .++.+|++++
T Consensus         6 ~iG~s~~~~~l~~~~~~~~~~----~---~~vll~G~~GtGKt~lA~~i~~~~~----~~~~~~~~~~   62 (143)
T 3co5_A            6 KLGNSAAIQEMNREVEAAAKR----T---SPVFLTGEAGSPFETVARYFHKNGT----PWVSPARVEY   62 (143)
T ss_dssp             --CCCHHHHHHHHHHHHHHTC----S---SCEEEEEETTCCHHHHHGGGCCTTS----CEECCSSTTH
T ss_pred             ceeCCHHHHHHHHHHHHHhCC----C---CcEEEECCCCccHHHHHHHHHHhCC----CeEEechhhC
Confidence            789999999988887765311    1   3689999999999999999998753    7888888765

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=98.13  E-value=3.1e-06  Score=93.95  Aligned_cols=64  Identities=30%  Similarity=0.414  Sum_probs=60.8

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++++|+.|.++|+++||.||+++|||+||++++++.+..+|+++|+|.+.++..+...+
T Consensus         5 ~ft~~a~~al~~A~~~A~~~~h~~v~~eHLLlaLl~~~~~~~~~iL~~~gvd~~~l~~~l~~~l   68 (468)
T 3pxg_A            5 RFTERAQKVLALAQEEALRLGHNNIGTEHILLGLVREGEGIAAKALQALGLGSEKIQKEVESLI   68 (468)
T ss_dssp             CBCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHHHSCCSHHHHHHHHHTCCHHHHHHHHHTTS
T ss_pred             hhCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhccCcHHHHHHHHcCCCHHHHHHHHHHHh
Confidence            5999999999999999999999999999999999999999999999999999999998877665

>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=98.13  E-value=3.6e-06  Score=94.65  Aligned_cols=68  Identities=22%  Similarity=0.212  Sum_probs=52.4

Q ss_pred             cccChHHHHHHHHHHHHHhh----cCCCCCCC----CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSR----VGLKDPNR----PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r----~gl~~p~r----p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .++|++++++.+...+....    .|++.+++    +..++||+||||||||++|+++|+.+   +..++.++++.+..
T Consensus        40 dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l---~~~~i~in~s~~~~  115 (516)
T 1sxj_A           40 QVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL---GYDILEQNASDVRS  115 (516)
T ss_dssp             GCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT---TCEEEEECTTSCCC
T ss_pred             HhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHc---CCCEEEEeCCCcch
Confidence            39999999999988875432    34444432    33589999999999999999999997   45688888887644

>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=98.11  E-value=9.4e-07  Score=90.70  Aligned_cols=65  Identities=20%  Similarity=0.267  Sum_probs=43.9

Q ss_pred             hhCcccChHHHHHHHHHH----HHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          627 LKKRVIGQDEAVAAISRA----VKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       627 L~~~v~Gq~~a~~~i~~~----i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      +...++|++++++.+...    +...+..   ..++..++||+||||||||++|+++|+.+   ...++.+++++
T Consensus        31 ~~~~~i~~~~~~~~i~~~~~~l~~~l~~~---~~~~~~~vLl~G~~GtGKT~la~~ia~~~---~~~~~~i~~~~   99 (272)
T 1d2n_A           31 IMNGIIKWGDPVTRVLDDGELLVQQTKNS---DRTPLVSVLLEGPPHSGKTALAAKIAEES---NFPFIKICSPD   99 (272)
T ss_dssp             CTTCCCCCSHHHHHHHHHHHHHHHHHHHC---SSCSEEEEEEECSTTSSHHHHHHHHHHHH---TCSEEEEECGG
T ss_pred             HhcCCCCccHHHHHHHHHHHHHHHHHhcc---CCCCCeEEEEECCCCCcHHHHHHHHHHHh---CCCEEEEeCHH
Confidence            344577777777666653    2222211   12334699999999999999999999995   33577776653

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=98.09  E-value=3.5e-06  Score=89.15  Aligned_cols=63  Identities=22%  Similarity=0.270  Sum_probs=49.4

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .++|++++++.+...+...+..    ..+..++||+||||||||++|+++|+.+   ...++.++++.+.
T Consensus        30 ~iiG~~~~~~~l~~~l~~~~~~----~~~~~~vll~G~~GtGKT~la~~ia~~~---~~~~~~~~~~~~~   92 (338)
T 3pfi_A           30 GYIGQESIKKNLNVFIAAAKKR----NECLDHILFSGPAGLGKTTLANIISYEM---SANIKTTAAPMIE   92 (338)
T ss_dssp             GCCSCHHHHHHHHHHHHHHHHT----TSCCCCEEEECSTTSSHHHHHHHHHHHT---TCCEEEEEGGGCC
T ss_pred             HhCChHHHHHHHHHHHHHHHhc----CCCCCeEEEECcCCCCHHHHHHHHHHHh---CCCeEEecchhcc
Confidence            3899999999999988776532    2233589999999999999999999995   3357777776553

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.03  E-value=5.3e-06  Score=80.28  Aligned_cols=38  Identities=18%  Similarity=0.197  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHcC-CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          298 EIQRIIQILCRR-TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       298 ~i~~l~~~L~~~-~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -+..+..++..- .+++++|+||||||||++|.++++.+
T Consensus        44 f~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a~ala~~l   82 (212)
T 1tue_A           44 FLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFI   82 (212)
T ss_dssp             HHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCcccEEEEECCCCCCHHHHHHHHHHHh
Confidence            344455555442 34579999999999999999999987

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=98.02  E-value=5e-06  Score=86.81  Aligned_cols=62  Identities=24%  Similarity=0.327  Sum_probs=51.9

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++|++.++..+...+.....   .    ..++||+||||||||++|++|++........++.+|++.+
T Consensus         3 ~iig~s~~~~~~~~~~~~~a~---~----~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~   64 (304)
T 1ojl_A            3 HMIGSSPAMQHLLNEIAMVAP---S----DATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAAL   64 (304)
T ss_dssp             CCCCCSHHHHHHHHHHHHHCS---T----TSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSC
T ss_pred             CcEECCHHHHHHHHHHHHHhC---C----CCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCC
Confidence            488999999998888776531   1    1478999999999999999999997777788999999876

>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=98.01  E-value=6.6e-06  Score=83.33  Aligned_cols=59  Identities=32%  Similarity=0.406  Sum_probs=41.4

Q ss_pred             ccChHHHHHHHHHHHHHh-------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          631 VIGQDEAVAAISRAVKRS-------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~-------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      |+|+++++..+.+.+...       ..++..|    .+++|+||||||||+|+++||..+-   ...+.++.+
T Consensus        18 i~g~~~~~~~l~~l~~~~~~~~~~~~~~~~~~----~g~ll~G~~G~GKTtl~~~i~~~~~---~~~i~~~~~   83 (254)
T 1ixz_A           18 VAGAEEAKEELKEIVEFLKNPSRFHEMGARIP----KGVLLVGPPGVGKTHLARAVAGEAR---VPFITASGS   83 (254)
T ss_dssp             CCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCC----SEEEEECCTTSSHHHHHHHHHHHTT---CCEEEEEHH
T ss_pred             hCCcHHHHHHHHHHHHHHHCHHHHHHcCCCCC----CeEEEECCCCCCHHHHHHHHHHHhC---CCEEEeeHH
Confidence            777777777776655332       2344333    4699999999999999999999852   446666543

>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=98.00  E-value=4.1e-06  Score=88.90  Aligned_cols=59  Identities=29%  Similarity=0.447  Sum_probs=45.4

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC--cceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR--IHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~--~li~~d~se~  698 (710)
                      ++||+++++.+...++..+         +.++||+||||||||++|+++|+.+++...  .++.+|.+..
T Consensus        27 ~~g~~~~~~~L~~~i~~g~---------~~~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~~~   87 (340)
T 1sxj_C           27 VYGQNEVITTVRKFVDEGK---------LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDD   87 (340)
T ss_dssp             CCSCHHHHHHHHHHHHTTC---------CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSC
T ss_pred             hcCcHHHHHHHHHHHhcCC---------CceEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCccc
Confidence            8899999999988876432         125899999999999999999999987542  3444555543

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=98.00  E-value=3.7e-06  Score=80.38  Aligned_cols=61  Identities=25%  Similarity=0.342  Sum_probs=44.6

Q ss_pred             hCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC-------CCCcceeeCCCC
Q 005179          628 KKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG-------SVRIHYLFFPSP  697 (710)
Q Consensus       628 ~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg-------~~~~li~~d~se  697 (710)
                      ...++|+++.++.+...+..     .    ...++||+||||||||++|+++++.+..       ....++.++++.
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~-----~----~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (195)
T 1jbk_A           21 LDPVIGRDEEIRRTIQVLQR-----R----TKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGA   88 (195)
T ss_dssp             SCCCCSCHHHHHHHHHHHTS-----S----SSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHH
T ss_pred             ccccccchHHHHHHHHHHhc-----C----CCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEEeeHHH
Confidence            35589999988888766533     1    1247899999999999999999999854       234456666544

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.00  E-value=9.4e-06  Score=79.08  Aligned_cols=132  Identities=14%  Similarity=0.099  Sum_probs=67.2

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccC-ceEEEeehhhhhhcc------c-----cCcc--HHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS-KRIMSLDMGLLMAGA------K-----ERGE--LEARVTTLISEIQ  379 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~-~~v~~ld~~~l~~g~------~-----~~g~--~e~~l~~~~~~~~  379 (710)
                      .+++|+||+|||+++..++.....-+ +. -.+ ..++..++..+..+.      +     ..++  ....+..++. ..
T Consensus         8 ~l~tG~pGsGKT~~a~~~~~~~~~~~-~~-~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~-~~   84 (199)
T 2r2a_A            8 CLITGTPGSGKTLKMVSMMANDEMFK-PD-ENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIK-KP   84 (199)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHCGGGS-CC-TTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTT-SG
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHhhc-cc-ccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhh-cc
Confidence            58999999999999887655432000 00 012 333333332222110      0     0000  0011222211 12


Q ss_pred             hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCC
Q 005179          380 KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPS  458 (710)
Q Consensus       380 ~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps  458 (710)
                      ...+.||+|||++.+.+....+   .+ ...+...|.. -....+.+|.++.+..     .++..++.|+. .+.+..|.
T Consensus        85 ~~~~~vliIDEAq~l~~~~~~~---~e-~~rll~~l~~-~r~~~~~iil~tq~~~-----~l~~~lr~ri~~~~~l~~~~  154 (199)
T 2r2a_A           85 ENIGSIVIVDEAQDVWPARSAG---SK-IPENVQWLNT-HRHQGIDIFVLTQGPK-----LLDQNLRTLVRKHYHIASNK  154 (199)
T ss_dssp             GGTTCEEEETTGGGTSBCCCTT---CC-CCHHHHGGGG-TTTTTCEEEEEESCGG-----GBCHHHHTTEEEEEEEEECS
T ss_pred             ccCceEEEEEChhhhccCcccc---ch-hHHHHHHHHh-cCcCCeEEEEECCCHH-----HHhHHHHHHhheEEEEcCcc
Confidence            3457899999999997543211   01 1122232221 2233456666667654     68889999997 67776654

>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=97.97  E-value=5.2e-06  Score=87.05  Aligned_cols=59  Identities=34%  Similarity=0.486  Sum_probs=45.8

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFFPSP  697 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d~se  697 (710)
                      .++|++++++.+...+...+        + .++||+||||||||++|+++|+.+++..  ..++.++.++
T Consensus        26 ~~~g~~~~~~~l~~~l~~~~--------~-~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~~   86 (327)
T 1iqp_A           26 DIVGQEHIVKRLKHYVKTGS--------M-PHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASD   86 (327)
T ss_dssp             TCCSCHHHHHHHHHHHHHTC--------C-CEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTC
T ss_pred             HhhCCHHHHHHHHHHHHcCC--------C-CeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeeccc
Confidence            48999999999988776532        1 3699999999999999999999987643  2355555554

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=97.97  E-value=4.4e-06  Score=79.58  Aligned_cols=60  Identities=25%  Similarity=0.280  Sum_probs=43.8

Q ss_pred             hCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC-------CCCcceeeCCC
Q 005179          628 KKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG-------SVRIHYLFFPS  696 (710)
Q Consensus       628 ~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg-------~~~~li~~d~s  696 (710)
                      ...++|+++.++.+...+...         ...++||+||||||||++|+++|+.+..       ....++.++++
T Consensus        21 ~~~~~g~~~~~~~l~~~l~~~---------~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (187)
T 2p65_A           21 LDPVIGRDTEIRRAIQILSRR---------TKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVSLDLS   87 (187)
T ss_dssp             SCCCCSCHHHHHHHHHHHTSS---------SSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEEECHH
T ss_pred             cchhhcchHHHHHHHHHHhCC---------CCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEEEeHH
Confidence            345899999888877665321         1247899999999999999999999855       23445555544

>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=97.93  E-value=8.8e-06  Score=85.39  Aligned_cols=64  Identities=22%  Similarity=0.284  Sum_probs=48.5

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .++|++.++..+...+.....+-    ++..++||+||||||||++|+++++.+.   ..++.++++.+..
T Consensus        13 ~~ig~~~~~~~l~~~l~~~~~~~----~~~~~vll~G~~GtGKT~la~~i~~~~~---~~~~~~~~~~~~~   76 (324)
T 1hqc_A           13 EYIGQERLKQKLRVYLEAAKARK----EPLEHLLLFGPPGLGKTTLAHVIAHELG---VNLRVTSGPAIEK   76 (324)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHC----SCCCCCEEECCTTCCCHHHHHHHHHHHT---CCEEEECTTTCCS
T ss_pred             HhhCHHHHHHHHHHHHHHHHccC----CCCCcEEEECCCCCCHHHHHHHHHHHhC---CCEEEEeccccCC
Confidence            48999999999988886654211    1124789999999999999999999873   3577777776643

>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=97.93  E-value=7.5e-06  Score=86.66  Aligned_cols=49  Identities=31%  Similarity=0.509  Sum_probs=39.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ++||+.+++.+...+...+..    +.+...++|+||||||||+||++||..+
T Consensus        27 ~~g~~~~~~~l~~~i~~~~~~----~~~~~~~ll~Gp~G~GKTTLa~~ia~~l   75 (334)
T 1in4_A           27 FIGQENVKKKLSLALEAAKMR----GEVLDHVLLAGPPGLGKTTLAHIIASEL   75 (334)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHH----TCCCCCEEEESSTTSSHHHHHHHHHHHH
T ss_pred             ccCcHHHHHHHHHHHHHHHhc----CCCCCeEEEECCCCCcHHHHHHHHHHHh
Confidence            778999999998888665321    2233579999999999999999999997

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=97.91  E-value=9.2e-06  Score=79.54  Aligned_cols=62  Identities=34%  Similarity=0.469  Sum_probs=46.3

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d~se~~~  700 (710)
                      .++|++++++.+...+...+         ..++||+||||||||++|+++++.+.+..  ..++.++.+...+
T Consensus        18 ~~~g~~~~~~~l~~~l~~~~---------~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~~~~~   81 (226)
T 2chg_A           18 EVVGQDEVIQRLKGYVERKN---------IPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERG   81 (226)
T ss_dssp             GCCSCHHHHHHHHHHHHTTC---------CCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETTCTTC
T ss_pred             HHcCcHHHHHHHHHHHhCCC---------CCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccccccC
Confidence            48899999998888775421         12589999999999999999999986543  3456666665533

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=97.91  E-value=5e-06  Score=89.44  Aligned_cols=65  Identities=17%  Similarity=0.043  Sum_probs=50.8

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC--------CCcceeeCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS--------VRIHYLFFPSPF  698 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~--------~~~li~~d~se~  698 (710)
                      +.++|+++.++.+...+.....+-.     ..+++|+||||||||++|+++++.+...        ...++.++++..
T Consensus        20 ~~l~gr~~~~~~l~~~l~~~~~~~~-----~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~~~~   92 (384)
T 2qby_B           20 KEIPFREDILRDAAIAIRYFVKNEV-----KFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNCREV   92 (384)
T ss_dssp             SSCTTCHHHHHHHHHHHHHHHTTCC-----CCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEHHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCC-----CCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEECccC
Confidence            5699999999999988877654421     1489999999999999999999997443        456777776554

>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=97.91  E-value=1.1e-05  Score=84.85  Aligned_cols=58  Identities=17%  Similarity=0.107  Sum_probs=46.3

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++|+++++..+...+...        ++...+||+||||||||++|+++|+.+   ...++.++.+.+
T Consensus        27 ~ivg~~~~~~~l~~~l~~~--------~~~~~~L~~G~~G~GKT~la~~la~~l---~~~~~~i~~~~~   84 (324)
T 3u61_B           27 ECILPAFDKETFKSITSKG--------KIPHIILHSPSPGTGKTTVAKALCHDV---NADMMFVNGSDC   84 (324)
T ss_dssp             TSCCCHHHHHHHHHHHHTT--------CCCSEEEECSSTTSSHHHHHHHHHHHT---TEEEEEEETTTC
T ss_pred             HHhCcHHHHHHHHHHHHcC--------CCCeEEEeeCcCCCCHHHHHHHHHHHh---CCCEEEEccccc
Confidence            3899999999998887722        122478999999999999999999997   346778887765

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=97.90  E-value=1.3e-05  Score=82.31  Aligned_cols=59  Identities=32%  Similarity=0.406  Sum_probs=41.5

Q ss_pred             ccChHHHHHHHHHHHHHh-------hcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          631 VIGQDEAVAAISRAVKRS-------RVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~-------r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      |+|+++++..+.+.+...       ..++..|    .+++|+||||||||+|+++||..+-   ...+.++.+
T Consensus        42 i~g~~~~~~~l~~l~~~~~~~~~l~~~~~~~~----~gvll~Gp~GtGKTtl~~~i~~~~~---~~~i~~~~~  107 (278)
T 1iy2_A           42 VAGAEEAKEELKEIVEFLKNPSRFHEMGARIP----KGVLLVGPPGVGKTHLARAVAGEAR---VPFITASGS  107 (278)
T ss_dssp             SSSCHHHHHHHHHHHHHHHCHHHHHHTTCCCC----CEEEEECCTTSSHHHHHHHHHHHTT---CCEEEEEHH
T ss_pred             hCChHHHHHHHHHHHHHHHCHHHHHHcCCCCC----CeEEEECCCcChHHHHHHHHHHHcC---CCEEEecHH
Confidence            677777777766655432       2344333    3699999999999999999999863   456666544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=97.89  E-value=9.6e-06  Score=89.18  Aligned_cols=55  Identities=27%  Similarity=0.403  Sum_probs=43.4

Q ss_pred             cccChHHHH---HHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          630 RVIGQDEAV---AAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       630 ~v~Gq~~a~---~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      .++||++++   ..+...+...+.         .++||+||||||||++|++||+.+   ...++.++.+
T Consensus        27 ~ivGq~~~~~~~~~L~~~i~~~~~---------~~vLL~GppGtGKTtlAr~ia~~~---~~~f~~l~a~   84 (447)
T 3pvs_A           27 QYIGQQHLLAAGKPLPRAIEAGHL---------HSMILWGPPGTGKTTLAEVIARYA---NADVERISAV   84 (447)
T ss_dssp             TCCSCHHHHSTTSHHHHHHHHTCC---------CEEEEECSTTSSHHHHHHHHHHHT---TCEEEEEETT
T ss_pred             HhCCcHHHHhchHHHHHHHHcCCC---------cEEEEECCCCCcHHHHHHHHHHHh---CCCeEEEEec
Confidence            399999999   777777766542         389999999999999999999995   3355665543

>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=97.89  E-value=4.6e-06  Score=87.16  Aligned_cols=61  Identities=34%  Similarity=0.463  Sum_probs=46.5

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d~se~~~  700 (710)
                      ++|++++++.+...+...        ++ .++||+||||||||++|+++|+.+++..  ..++.+|.+...+
T Consensus        19 ~~g~~~~~~~l~~~l~~~--------~~-~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~~~   81 (319)
T 2chq_A           19 VVGQDEVIQRLKGYVERK--------NI-PHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNASDERG   81 (319)
T ss_dssp             SCSCHHHHHHHHTTTTTT--------CC-CCEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEETTSTTC
T ss_pred             HhCCHHHHHHHHHHHhCC--------CC-CeEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEeCccccC
Confidence            889999998887665421        11 2599999999999999999999997754  3467777776543

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=97.89  E-value=4.4e-05  Score=87.20  Aligned_cols=49  Identities=18%  Similarity=0.182  Sum_probs=40.0

Q ss_pred             hcCCCCcccCHHHHHHHHHHHHcC--CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          286 EELIDPVIGRETEIQRIIQILCRR--TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       286 ~~~l~~liGr~~~i~~l~~~L~~~--~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      |.....+|||+.++.++.+.+...  ..+-++|+|++|+|||+||..+++.
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~~~~~~~v~I~G~~GiGKTtLa~~~~~~  170 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKLKGEPGWVTIHGMAGCGKSVLAAEAVRD  170 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTSTTSCEEEEEECCTTSSHHHHHHHHHCC
T ss_pred             CCCCCeecccHHHHHHHHHHHhcccCCCceEEEEcCCCCCHHHHHHHHHhc
Confidence            345567999999999999998742  3345789999999999999998754

>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=97.87  E-value=3.4e-06  Score=88.26  Aligned_cols=60  Identities=22%  Similarity=0.303  Sum_probs=46.1

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d~se~  698 (710)
                      .++|++++++.+...++..        ++ .++||+||||||||++|+++|+.+++..  ..++.++.+..
T Consensus        22 ~~~g~~~~~~~l~~~l~~~--------~~-~~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~~~   83 (323)
T 1sxj_B           22 DIVGNKETIDRLQQIAKDG--------NM-PHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNASDD   83 (323)
T ss_dssp             GCCSCTHHHHHHHHHHHSC--------CC-CCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTTSC
T ss_pred             HHHCCHHHHHHHHHHHHcC--------CC-CeEEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCccc
Confidence            4899999999998876532        11 2499999999999999999999986543  23666776654

>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=97.85  E-value=5e-06  Score=88.30  Aligned_cols=61  Identities=30%  Similarity=0.411  Sum_probs=45.6

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC---CCcceeeCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS---VRIHYLFFPSPF  698 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~---~~~li~~d~se~  698 (710)
                      ..++|++++++.+...+...+         ..++||+||||||||++|+++|+.+.+.   ...++.++.+..
T Consensus        37 ~~i~g~~~~~~~l~~~l~~~~---------~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~~~  100 (353)
T 1sxj_D           37 DEVTAQDHAVTVLKKTLKSAN---------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDE  100 (353)
T ss_dssp             TTCCSCCTTHHHHHHHTTCTT---------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSC
T ss_pred             HHhhCCHHHHHHHHHHHhcCC---------CCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEccccc
Confidence            348999999988877654321         1359999999999999999999998642   234666776664

>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=97.83  E-value=8.9e-06  Score=84.34  Aligned_cols=74  Identities=16%  Similarity=0.324  Sum_probs=45.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEcc
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDE  390 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDE  390 (710)
                      +..++|+||||+|||+|+..++.. ....+       ..+.+.....+.  .+..+.+..+..+.+.+...+  +||||+
T Consensus       123 gsviLI~GpPGsGKTtLAlqlA~~-~G~~V-------lyIs~~~eE~v~--~~~~~le~~l~~i~~~l~~~~--LLVIDs  190 (331)
T 2vhj_A          123 SGMVIVTGKGNSGKTPLVHALGEA-LGGKD-------KYATVRFGEPLS--GYNTDFNVFVDDIARAMLQHR--VIVIDS  190 (331)
T ss_dssp             SEEEEEECSCSSSHHHHHHHHHHH-HHTTS-------CCEEEEBSCSST--TCBCCHHHHHHHHHHHHHHCS--EEEEEC
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh-CCCCE-------EEEEecchhhhh--hhhcCHHHHHHHHHHHHhhCC--EEEEec
Confidence            344699999999999999999876 21111       112221011111  112455666666666666554  999999


Q ss_pred             chhhhh
Q 005179          391 VHTLIG  396 (710)
Q Consensus       391 id~l~~  396 (710)
                      ++.+..
T Consensus       191 I~aL~~  196 (331)
T 2vhj_A          191 LKNVIG  196 (331)
T ss_dssp             CTTTC-
T ss_pred             cccccc
Confidence            999854

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=97.80  E-value=1.5e-05  Score=83.26  Aligned_cols=64  Identities=11%  Similarity=-0.012  Sum_probs=46.2

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC-------CcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV-------RIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~-------~~li~~d~se~~  699 (710)
                      +.|.++-++.|...+...-.+-..     .++++|||||||||++++++++.|....       -..+.+|+....
T Consensus        22 L~~Re~E~~~i~~~L~~~i~~~~~-----~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~   92 (318)
T 3te6_A           22 LKSQVEDFTRIFLPIYDSLMSSQN-----KLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELA   92 (318)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCC-----CEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC
T ss_pred             cCCHHHHHHHHHHHHHHHhcCCCC-----CeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccC
Confidence            556677777888777665433322     4899999999999999999999985421       235667766543

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=97.79  E-value=2.9e-05  Score=83.37  Aligned_cols=69  Identities=13%  Similarity=0.086  Sum_probs=52.9

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC-CCcceeeCCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS-VRIHYLFFPSPFNS  700 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~-~~~li~~d~se~~~  700 (710)
                      ..++|+++.++.+...+.....|-. + .+ ..++|+||||||||++++++++.+... ...++.++++....
T Consensus        17 ~~l~gr~~~~~~l~~~l~~~~~~~~-~-~~-~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~   86 (389)
T 1fnn_A           17 KRLPHREQQLQQLDILLGNWLRNPG-H-HY-PRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRN   86 (389)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTT-S-SC-CEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCS
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCCC-C-CC-CeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCC
Confidence            4589999999999888877644421 1 10 279999999999999999999998776 46678888776543

>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=97.79  E-value=7.1e-05  Score=71.52  Aligned_cols=23  Identities=39%  Similarity=0.694  Sum_probs=21.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ++.|+||+|+|||||++.|+..+
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l   24 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERL   24 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            46899999999999999999876

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=97.77  E-value=1e-05  Score=86.82  Aligned_cols=67  Identities=13%  Similarity=0.139  Sum_probs=49.8

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC------CCcceeeCCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS------VRIHYLFFPSPFNS  700 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~------~~~li~~d~se~~~  700 (710)
                      ..++|+++.++.+...+.....+-     ...+++|+||||||||++|+++++.+...      ...++.++++....
T Consensus        19 ~~~~gr~~~~~~l~~~l~~~~~~~-----~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~   91 (387)
T 2v1u_A           19 DVLPHREAELRRLAEVLAPALRGE-----KPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNARHRET   91 (387)
T ss_dssp             SCCTTCHHHHHHHHHTTGGGTSSC-----CCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETTTSCS
T ss_pred             CCCCCHHHHHHHHHHHHHHHHcCC-----CCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECCcCCC
Confidence            458999999999887765432121     12489999999999999999999997432      55678888776544

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=97.77  E-value=2e-05  Score=76.74  Aligned_cols=38  Identities=21%  Similarity=0.262  Sum_probs=31.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      .+++|+||||||||+||+++++.+......++.+++++
T Consensus        55 ~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~   92 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPE   92 (202)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHH
Confidence            48999999999999999999999876655565555543

>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=97.76  E-value=1.9e-05  Score=78.66  Aligned_cols=40  Identities=20%  Similarity=0.200  Sum_probs=33.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .+++|+||||||||++|+++|+.+......++.++++++.
T Consensus        53 ~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~   92 (242)
T 3bos_A           53 QAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHA   92 (242)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGG
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHH
Confidence            4899999999999999999999987666667777776653

>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=97.74  E-value=1.2e-05  Score=85.28  Aligned_cols=45  Identities=24%  Similarity=0.381  Sum_probs=33.8

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ++|+++++..+........         .+++||+||||||||++|+++|+.+.
T Consensus        26 i~G~~~~~~~l~~~~~~~~---------~~~vLl~G~~GtGKT~la~~la~~~~   70 (350)
T 1g8p_A           26 IVGQEDMKLALLLTAVDPG---------IGGVLVFGDRGTGKSTAVRALAALLP   70 (350)
T ss_dssp             SCSCHHHHHHHHHHHHCGG---------GCCEEEECCGGGCTTHHHHHHHHHSC
T ss_pred             ccChHHHHHHHHHHhhCCC---------CceEEEECCCCccHHHHHHHHHHhCc
Confidence            8899887776543322111         14699999999999999999999864

>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=97.72  E-value=1.2e-05  Score=85.67  Aligned_cols=51  Identities=22%  Similarity=0.371  Sum_probs=38.3

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      .++||+++++.+...+.      . .++.. ++||+||||||||++++++|+.+++...
T Consensus        15 ~~vg~~~~~~~l~~~~~------~-~~~~~-~~ll~Gp~G~GKTtl~~~la~~l~~~~~   65 (354)
T 1sxj_E           15 ALSHNEELTNFLKSLSD------Q-PRDLP-HLLLYGPNGTGKKTRCMALLESIFGPGV   65 (354)
T ss_dssp             GCCSCHHHHHHHHTTTT------C-TTCCC-CEEEECSTTSSHHHHHHTHHHHHSCTTC
T ss_pred             HhcCCHHHHHHHHHHHh------h-CCCCC-eEEEECCCCCCHHHHHHHHHHHHcCCCC
Confidence            38899998888766541      1 11222 4999999999999999999998876543

>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=97.71  E-value=3.6e-05  Score=76.23  Aligned_cols=48  Identities=35%  Similarity=0.570  Sum_probs=39.8

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .++|++++++.+...+...+.        ...++|+||||||||++|+++++.+..
T Consensus        24 ~~~g~~~~~~~l~~~l~~~~~--------~~~~ll~G~~G~GKT~l~~~~~~~~~~   71 (250)
T 1njg_A           24 DVVGQEHVLTALANGLSLGRI--------HHAYLFSGTRGVGKTSIARLLAKGLNC   71 (250)
T ss_dssp             GCCSCHHHHHHHHHHHHHTCC--------CSEEEEECSTTSCHHHHHHHHHHHHHC
T ss_pred             HHhCcHHHHHHHHHHHHcCCC--------CeEEEEECCCCCCHHHHHHHHHHHhcC
Confidence            489999999999888765321        137899999999999999999998754

>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=97.70  E-value=0.00012  Score=80.82  Aligned_cols=60  Identities=15%  Similarity=0.337  Sum_probs=40.4

Q ss_pred             hhhHHhhhhcCCCCcc-cCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          278 VDLTARASEELIDPVI-GRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       278 ~~l~~~~~~~~l~~li-Gr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+|..+++|-.|+.+- ++...+..+...+.... .+++|.|+||||||+++..++..+...
T Consensus        12 ~~~~~~~~p~~~~~Ln~~Q~~av~~~~~~i~~~~-~~~li~G~aGTGKT~ll~~~~~~l~~~   72 (459)
T 3upu_A           12 SGLVPRGSHMTFDDLTEGQKNAFNIVMKAIKEKK-HHVTINGPAGTGATTLTKFIIEALIST   72 (459)
T ss_dssp             ---------CCSSCCCHHHHHHHHHHHHHHHSSS-CEEEEECCTTSCHHHHHHHHHHHHHHT
T ss_pred             CCCccccCCCccccCCHHHHHHHHHHHHHHhcCC-CEEEEEeCCCCCHHHHHHHHHHHHHhc
Confidence            4566777888888775 56667777776666543 389999999999999999999988654

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.69  E-value=2e-05  Score=75.26  Aligned_cols=25  Identities=36%  Similarity=0.616  Sum_probs=23.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .+++|+||||||||+|+++++..+.
T Consensus        39 ~~~~l~G~~G~GKTtL~~~i~~~~~   63 (180)
T 3ec2_A           39 KGLTFVGSPGVGKTHLAVATLKAIY   63 (180)
T ss_dssp             CEEEECCSSSSSHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3789999999999999999999986

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=97.67  E-value=6.4e-05  Score=72.70  Aligned_cols=26  Identities=31%  Similarity=0.683  Sum_probs=24.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .++|||||||||||++|.+||+.+.|
T Consensus        59 n~ili~GPPGtGKTt~a~ala~~l~g   84 (212)
T 1tue_A           59 NCLVFCGPANTGKSYFGMSFIHFIQG   84 (212)
T ss_dssp             SEEEEESCGGGCHHHHHHHHHHHHTC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCC
Confidence            47999999999999999999999866

>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=97.65  E-value=4.6e-05  Score=81.44  Aligned_cols=49  Identities=35%  Similarity=0.560  Sum_probs=40.7

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .++|++++++.+...+...+.        ...+||+||||||||++|+++|+.+...
T Consensus        17 ~~vg~~~~~~~L~~~l~~~~~--------~~~~ll~G~~G~GKT~la~~la~~l~~~   65 (373)
T 1jr3_A           17 DVVGQEHVLTALANGLSLGRI--------HHAYLFSGTRGVGKTSIARLLAKGLNCE   65 (373)
T ss_dssp             TSCSCHHHHHHHHHHHHHTCC--------CSEEEEESCTTSSHHHHHHHHHHHHSCT
T ss_pred             hccCcHHHHHHHHHHHHhCCC--------CeEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            489999999999988865331        1378999999999999999999998653

>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=97.60  E-value=0.00012  Score=74.01  Aligned_cols=36  Identities=28%  Similarity=0.417  Sum_probs=28.3

Q ss_pred             HHHHHHHHcC-C-CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          300 QRIIQILCRR-T-KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       300 ~~l~~~L~~~-~-~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .-+..++... . +++++|+||||||||.++.+||..+
T Consensus        91 ~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~ala~~~  128 (267)
T 1u0j_A           91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHhCCCCCCcEEEEECCCCCCHHHHHHHHHhhh
Confidence            3455566554 3 4669999999999999999999864

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=97.58  E-value=9.6e-06  Score=92.46  Aligned_cols=84  Identities=17%  Similarity=0.230  Sum_probs=53.7

Q ss_pred             CcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhh-cCCCC-CCCCCeEEEEEcC
Q 005179          590 AVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSR-VGLKD-PNRPTAAMLFCGP  667 (710)
Q Consensus       590 ~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r-~gl~~-p~rp~~~~Lf~GP  667 (710)
                      ..++.+++..+.+.+.. +         ..+..+.+.+...|+||++++..+..++.... ....+ ..+.-.++||+||
T Consensus       266 ~~~t~~~~~~i~~~~~~-~---------~~~~~l~~~l~~~I~G~e~vk~al~~~l~~g~~~~~~~~~~r~~~~vLL~Gp  335 (595)
T 3f9v_A          266 VIISEEDEKKIKDLAKD-P---------WIRDRIISSIAPSIYGHWELKEALALALFGGVPKVLEDTRIRGDIHILIIGD  335 (595)
T ss_dssp             CCCTTSTHHHHHTTSST-T---------TGGGTHHHHTSSTTSCCHHHHHHHTTTTTCCCCEETTTTEECCSCCEEEEES
T ss_pred             CCCCHHHHHHHHHHhhC-c---------HHHHHHHHhhcchhcChHHHHHHHHHHHhCCCcccccCCCcCCCcceEEECC
Confidence            35666676665543221 1         22446777899999999998887754332110 00011 1112238999999


Q ss_pred             CCCcHHHHHHHHHHHH
Q 005179          668 TGVGKTELAKSLAACY  683 (710)
Q Consensus       668 pGtGKT~lAkaLA~~l  683 (710)
                      ||||||+||++||+.+
T Consensus       336 pGtGKT~LAr~la~~~  351 (595)
T 3f9v_A          336 PGTAKSQMLQFISRVA  351 (595)
T ss_dssp             SCCTHHHHHHSSSTTC
T ss_pred             CchHHHHHHHHHHHhC
Confidence            9999999999999986

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=97.57  E-value=6.6e-05  Score=79.37  Aligned_cols=49  Identities=14%  Similarity=0.127  Sum_probs=39.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      .-||+++++.+...++..+.        ..++||+||||||||++|+++|+.++...
T Consensus         4 ~pw~~~~~~~l~~~i~~~~~--------~~a~L~~G~~G~GKt~~a~~la~~l~~~~   52 (334)
T 1a5t_A            4 YPWLRPDFEKLVASYQAGRG--------HHALLIQALPGMGDDALIYALSRYLLCQQ   52 (334)
T ss_dssp             CGGGHHHHHHHHHHHHTTCC--------CSEEEEECCTTSCHHHHHHHHHHHHTCSS
T ss_pred             CCchHHHHHHHHHHHHcCCc--------ceeEEEECCCCchHHHHHHHHHHHHhCCC
Confidence            45788888888887764431        23799999999999999999999998654

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=97.54  E-value=1.8e-05  Score=83.16  Aligned_cols=39  Identities=18%  Similarity=0.149  Sum_probs=32.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|+||||||||++|+++++.+...+..++.++++++
T Consensus        38 ~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~~~~   76 (324)
T 1l8q_A           38 NPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF   76 (324)
T ss_dssp             SSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             CeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEHHHH
Confidence            478999999999999999999998765566777776554

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=97.54  E-value=5.7e-05  Score=86.50  Aligned_cols=57  Identities=33%  Similarity=0.503  Sum_probs=46.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ++||+.+++.+...+...           ..+||+||||||||++|++||..+.......+.++....
T Consensus        43 i~G~~~~l~~l~~~i~~g-----------~~vll~Gp~GtGKTtlar~ia~~l~~~~~~~~~~~~~~~   99 (604)
T 3k1j_A           43 VIGQEHAVEVIKTAANQK-----------RHVLLIGEPGTGKSMLGQAMAELLPTETLEDILVFPNPE   99 (604)
T ss_dssp             CCSCHHHHHHHHHHHHTT-----------CCEEEECCTTSSHHHHHHHHHHTSCCSSCEEEEEECCTT
T ss_pred             EECchhhHhhccccccCC-----------CEEEEEeCCCCCHHHHHHHHhccCCcccCCeEEEeCCcc
Confidence            999999999988877643           278999999999999999999998766545555655544

>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=97.50  E-value=0.00032  Score=86.99  Aligned_cols=51  Identities=18%  Similarity=0.157  Sum_probs=40.5

Q ss_pred             hhcCCCCcccCHHHHHHHHHHHHcC--CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          285 SEELIDPVIGRETEIQRIIQILCRR--TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       285 ~~~~l~~liGr~~~i~~l~~~L~~~--~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -|.....++||++++++|.+.|...  ...-+.|+|+.|+|||+||..+++..
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~~~~~~~v~i~G~gG~GKTtLa~~~~~~~  171 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKLNGEPGWVTIYGMAGCGKSVLAAEAVRDH  171 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTTTTSCEEEEEECSTTSSHHHHHHHHTCCH
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhccCCCCEEEEEeCCCCCHHHHHHHHhcCh
Confidence            3445667999999999999998643  23346799999999999999887653

>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=97.49  E-value=6.8e-05  Score=78.08  Aligned_cols=55  Identities=16%  Similarity=0.236  Sum_probs=39.6

Q ss_pred             ChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH--cC-CCCcceeeCCC
Q 005179          633 GQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY--FG-SVRIHYLFFPS  696 (710)
Q Consensus       633 Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l--fg-~~~~li~~d~s  696 (710)
                      ||+++++.+...++..+    .     .++|||||||||||++|+++|+..  +. ....++.++.+
T Consensus         1 g~~~~~~~L~~~i~~~~----~-----~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~   58 (305)
T 2gno_A            1 GAKDQLETLKRIIEKSE----G-----ISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPE   58 (305)
T ss_dssp             ---CHHHHHHHHHHTCS----S-----EEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCS
T ss_pred             ChHHHHHHHHHHHHCCC----C-----cEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCC
Confidence            78889999888876543    1     389999999999999999999973  21 23456777765

>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=97.49  E-value=0.00022  Score=80.65  Aligned_cols=41  Identities=29%  Similarity=0.306  Sum_probs=35.1

Q ss_pred             ccCHHHHHHHHHHHHcC---CCCCcEEEcCCCChHHHHHHHHHH
Q 005179          293 IGRETEIQRIIQILCRR---TKNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       293 iGr~~~i~~l~~~L~~~---~~~nvLL~GppG~GKT~la~~la~  333 (710)
                      +||+.+++++.+.|...   ...-+.|+|++|+|||+||+.+++
T Consensus       131 ~GR~~~~~~l~~~L~~~~~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhcccCCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            59999999999998654   234578999999999999999986

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=97.47  E-value=3e-05  Score=82.97  Aligned_cols=64  Identities=14%  Similarity=0.147  Sum_probs=45.8

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC---CCcceeeCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS---VRIHYLFFPSP  697 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~---~~~li~~d~se  697 (710)
                      ..++|+++.++.+...+.....+-     +...++++||||||||++++++++.+...   ....+.++++.
T Consensus        20 ~~~~gr~~e~~~l~~~l~~~~~~~-----~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~~   86 (386)
T 2qby_A           20 DELPHREDQIRKIASILAPLYREE-----KPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTRQ   86 (386)
T ss_dssp             SCCTTCHHHHHHHHHSSGGGGGTC-----CCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHHH
T ss_pred             CCCCChHHHHHHHHHHHHHHHcCC-----CCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECCC
Confidence            348888888888877665432221     12478999999999999999999987432   34566666543

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=97.42  E-value=0.00011  Score=76.54  Aligned_cols=37  Identities=19%  Similarity=0.203  Sum_probs=29.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc-CCCCcceeeCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF-GSVRIHYLFFPS  696 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf-g~~~~li~~d~s  696 (710)
                      .+++|+||||||||.||++||+.+. ..+...+.++++
T Consensus       153 ~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~  190 (308)
T 2qgz_A          153 KGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFP  190 (308)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHH
Confidence            4899999999999999999999987 554445444443

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.41  E-value=2.5e-05  Score=75.12  Aligned_cols=25  Identities=16%  Similarity=0.016  Sum_probs=20.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      -.+++||+|+||||++..++..+..
T Consensus         5 i~vi~G~~gsGKTT~ll~~~~~~~~   29 (184)
T 2orw_A            5 LTVITGPMYSGKTTELLSFVEIYKL   29 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3679999999999999777776643

>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=97.39  E-value=0.00014  Score=73.57  Aligned_cols=26  Identities=31%  Similarity=0.749  Sum_probs=23.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH--HcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC--YFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~--lfg  685 (710)
                      .+++||||||||||++|++||+.  ++|
T Consensus       105 n~~~l~GppgtGKt~~a~ala~~~~l~G  132 (267)
T 1u0j_A          105 NTIWLFGPATTGKTNIAEAIAHTVPFYG  132 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHSSCEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHhhhcccc
Confidence            48999999999999999999997  454

>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=97.37  E-value=7.2e-05  Score=82.19  Aligned_cols=39  Identities=21%  Similarity=0.304  Sum_probs=30.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC--CCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS--VRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~--~~~li~~d~se~  698 (710)
                      .+++||||||||||+||++||+.+...  +..++.++++++
T Consensus       131 ~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v~~~~~  171 (440)
T 2z4s_A          131 NPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKF  171 (440)
T ss_dssp             CCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEEEHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHH
Confidence            478999999999999999999998543  344566665543

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.30  E-value=0.0018  Score=63.64  Aligned_cols=30  Identities=27%  Similarity=0.204  Sum_probs=25.5

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      +.+.++++.|+|||||||++-.+|..+...
T Consensus         4 ~g~l~I~~~~kgGvGKTt~a~~la~~l~~~   33 (228)
T 2r8r_A            4 RGRLKVFLGAAPGVGKTYAMLQAAHAQLRQ   33 (228)
T ss_dssp             CCCEEEEEESSTTSSHHHHHHHHHHHHHHT
T ss_pred             CceEEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            345679999999999999999999988654

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.27  E-value=0.00059  Score=86.19  Aligned_cols=82  Identities=13%  Similarity=0.111  Sum_probs=54.2

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------hc-------cccCccHHHHHHH
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------AG-------AKERGELEARVTT  373 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------~g-------~~~~g~~e~~l~~  373 (710)
                      -..+.+++|+||||||||+||.+++......       +..+..++.....       .|       .......++.+..
T Consensus      1424 i~~g~~vll~GppGtGKT~LA~ala~ea~~~-------G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~ 1496 (2050)
T 3cmu_A         1424 LPMGRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEI 1496 (2050)
T ss_dssp             EETTSEEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHH
T ss_pred             ccCCeEEEEECCCCCCHHHHHHHHHHHHHHc-------CCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHH
Confidence            3457789999999999999999998876442       4455555544221       01       0011233444555


Q ss_pred             HHHHHHhcCCeEEEEccchhhhh
Q 005179          374 LISEIQKSGDVILFIDEVHTLIG  396 (710)
Q Consensus       374 ~~~~~~~~~~~IL~IDEid~l~~  396 (710)
                      +...++...+.+||||+++.++.
T Consensus      1497 ~~~lvr~~~~~lVVIDsi~al~p 1519 (2050)
T 3cmu_A         1497 CDALARSGAVDVIVVDSVAALTP 1519 (2050)
T ss_dssp             HHHHHHHTCCSEEEESCGGGCCC
T ss_pred             HHHHHhcCCCCEEEEcChhHhcc
Confidence            55556667889999999987764

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=97.26  E-value=0.0096  Score=67.34  Aligned_cols=50  Identities=10%  Similarity=0.047  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHH-HHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          173 ISTKRVFEAAV-EYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       173 ~~~~~vl~~A~-~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .+.+..+..+. ..+...||.|+..+.|+-...+        +   ++++.+.+.+.+....
T Consensus        72 ~R~~a~~~~~l~~~~~~~Ght~~~~~~l~~~~~~--------~---l~~~~~~~~~~~~~~~  122 (574)
T 3e1s_A           72 RRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVH--------Y---TRVTPGQARLAVETAV  122 (574)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCSCEEHHHHHHHHHH--------H---HCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCEeecHHHHHHHHHH--------H---hCCCHHHHHHHHHHHH
Confidence            36777788888 7788889999999987654432        2   3678777766665544

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=97.24  E-value=0.00018  Score=66.47  Aligned_cols=39  Identities=15%  Similarity=0.183  Sum_probs=32.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .++|+||+|+|||+|+++++..+...+...+.++.+++.
T Consensus        38 ~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~   76 (149)
T 2kjq_A           38 FIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMP   76 (149)
T ss_dssp             EEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhh
Confidence            789999999999999999999987655556777776654

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=97.20  E-value=0.0014  Score=77.76  Aligned_cols=43  Identities=26%  Similarity=0.325  Sum_probs=36.3

Q ss_pred             cccCHHHHHHHHHHHHc-CCCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          292 VIGRETEIQRIIQILCR-RTKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~-~~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+||+.++++|.+.|.. ...+-+.|+|+.|+|||+||+.+++.
T Consensus       130 ~VGRe~eLeeL~elL~~~d~~RVV~IvGmGGIGKTTLAk~Vy~d  173 (1221)
T 1vt4_I          130 NVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLS  173 (1221)
T ss_dssp             CCCCHHHHHHHHHHHHHCCSSCEEEECCSTTSSHHHHHHHHHHH
T ss_pred             CCCcHHHHHHHHHHHhccCCCeEEEEEcCCCccHHHHHHHHHHh
Confidence            49999999999998876 33345789999999999999999853

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.13  E-value=0.00044  Score=68.20  Aligned_cols=27  Identities=26%  Similarity=0.236  Sum_probs=22.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+..++|+||+|+|||++++.++..+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~l~~~~~   48 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSLHFIAKGL   48 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            345688999999999999999997664

>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=97.11  E-value=0.00069  Score=84.62  Aligned_cols=80  Identities=15%  Similarity=0.111  Sum_probs=54.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh----hhh---c---cccCcc----HHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL----LMA---G---AKERGE----LEARVTTLIS  376 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~----l~~---g---~~~~g~----~e~~l~~~~~  376 (710)
                      ++.++|+||||||||+||++++.+.....       -....++...    +..   |   .++.++    -|..+..++.
T Consensus      1082 g~~~l~~G~~g~GKT~la~~~~~~~~~~g-------~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~ 1154 (1706)
T 3cmw_A         1082 GRIVEIYGPESSGKTTLTLQVIAAAQREG-------KTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDA 1154 (1706)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHHHHHHTT-------CCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCChHHHHHHHHHHhhhcC-------CceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHH
Confidence            34489999999999999999998764432       2222232221    110   1   122233    5777877777


Q ss_pred             HHHhcCCeEEEEccchhhhhC
Q 005179          377 EIQKSGDVILFIDEVHTLIGS  397 (710)
Q Consensus       377 ~~~~~~~~IL~IDEid~l~~~  397 (710)
                      .+++..++++|+|+++.|++.
T Consensus      1155 ~ar~~~~~~i~~d~~~al~~~ 1175 (1706)
T 3cmw_A         1155 LARSGAVDVIVVDSVAALTPK 1175 (1706)
T ss_dssp             HHHHTCCSEEEESCGGGCCCH
T ss_pred             HHHhcCCeEEEeCchHhcCcc
Confidence            788888999999999998765

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=97.08  E-value=0.00025  Score=76.73  Aligned_cols=67  Identities=19%  Similarity=0.151  Sum_probs=47.9

Q ss_pred             CcccChHHHHHHHHHHH-HHhhcCCCCCCCCCeEEEE--EcCCCCcHHHHHHHHHHHHcCC------CCcceeeCCCCC
Q 005179          629 KRVIGQDEAVAAISRAV-KRSRVGLKDPNRPTAAMLF--CGPTGVGKTELAKSLAACYFGS------VRIHYLFFPSPF  698 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i-~~~r~gl~~p~rp~~~~Lf--~GPpGtGKT~lAkaLA~~lfg~------~~~li~~d~se~  698 (710)
                      ..++|.++.++.+...+ .....|...  . ...+++  +||||||||+|++++++.+-..      ....+.++++..
T Consensus        22 ~~l~gR~~el~~l~~~l~~~~~~~~~~--~-~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (412)
T 1w5s_A           22 PELRVRRGEAEALARIYLNRLLSGAGL--S-DVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNAFNA   97 (412)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCB--C-CEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEGGGC
T ss_pred             CCCCChHHHHHHHHHHHhHHHhcCCCC--C-CCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEEEEECCCC
Confidence            44889989899898888 766544211  1 147888  9999999999999999987431      334566666544

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.97  E-value=0.00065  Score=67.09  Aligned_cols=27  Identities=26%  Similarity=0.040  Sum_probs=22.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .-++++|++|+||||++..++.++...
T Consensus        13 ~i~litG~mGsGKTT~ll~~~~r~~~~   39 (223)
T 2b8t_A           13 WIEFITGPMFAGKTAELIRRLHRLEYA   39 (223)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHhc
Confidence            346788999999999999998887543

>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=96.92  E-value=0.0018  Score=61.14  Aligned_cols=24  Identities=33%  Similarity=0.364  Sum_probs=22.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|+||+||||+++.|++.+
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l   27 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            458899999999999999999987

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=96.89  E-value=0.0011  Score=68.17  Aligned_cols=33  Identities=27%  Similarity=0.297  Sum_probs=25.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      ..++|.||||+|||++|+.|++.+-+   ..+.++.
T Consensus        34 ~livl~G~sGsGKSTla~~L~~~~~~---~~~~Is~   66 (287)
T 1gvn_B           34 TAFLLGGQPGSGKTSLRSAIFEETQG---NVIVIDN   66 (287)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHTTT---CCEEECT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCC---CeEEEec
Confidence            47899999999999999999998521   3455544

>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=96.88  E-value=0.00055  Score=67.00  Aligned_cols=23  Identities=22%  Similarity=0.200  Sum_probs=20.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~  333 (710)
                      +.-++|+||||+|||+++..++.
T Consensus        20 G~~~~i~G~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           20 GVLTQVYGPYASGKTTLALQTGL   42 (220)
T ss_dssp             TSEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
Confidence            44578999999999999999987

>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=96.82  E-value=0.0008  Score=65.14  Aligned_cols=32  Identities=34%  Similarity=0.456  Sum_probs=25.0

Q ss_pred             CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          651 GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       651 gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      |...+.+|. .++|.||||+|||++|+.||+.+
T Consensus        13 ~~~~~~~~~-~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           13 GLVPRGSHM-RVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             ---CCCSCC-EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cccCCCCCe-EEEEECCCCCCHHHHHHHHHHHh
Confidence            444455554 78999999999999999999985

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=96.80  E-value=0.0015  Score=65.94  Aligned_cols=25  Identities=28%  Similarity=0.462  Sum_probs=22.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..++|.||||+|||++|+.|++.+.
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l~   57 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEFQ   57 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            4789999999999999999999863

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.74  E-value=0.00084  Score=65.00  Aligned_cols=24  Identities=33%  Similarity=0.516  Sum_probs=22.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++|+||||||||++|++||+.+
T Consensus        26 ~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           26 VRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            378999999999999999999986

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=96.64  E-value=0.00095  Score=63.55  Aligned_cols=25  Identities=36%  Similarity=0.434  Sum_probs=23.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.+++|+|+||+||||+++.|++.+
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            4578999999999999999999988

>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=96.64  E-value=0.0021  Score=63.79  Aligned_cols=26  Identities=35%  Similarity=0.414  Sum_probs=22.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-++|+||||+|||+++..++...
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~l~~~~   48 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHTLAVTC   48 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCcHHHHHHHHHHHH
Confidence            34567899999999999999999753

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.63  E-value=0.0013  Score=63.69  Aligned_cols=25  Identities=28%  Similarity=0.494  Sum_probs=23.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..+.+.||+|+|||+++++||..+.
T Consensus        26 ~~i~l~G~sGsGKSTl~~~La~~l~   50 (200)
T 3uie_A           26 CVIWVTGLSGSGKSTLACALNQMLY   50 (200)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHH
Confidence            3788999999999999999999986

>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=96.61  E-value=0.0015  Score=61.48  Aligned_cols=24  Identities=25%  Similarity=0.411  Sum_probs=21.7

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      ...++|.||||+|||++++.|+..
T Consensus         8 g~~i~l~G~~GsGKSTl~~~l~~~   31 (175)
T 1knq_A            8 HHIYVLMGVSGSGKSAVASEVAHQ   31 (175)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHh
Confidence            347899999999999999999986

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.61  E-value=0.0025  Score=63.46  Aligned_cols=28  Identities=25%  Similarity=0.386  Sum_probs=22.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      .+..++|+||||+|||+++..++..+..
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~   49 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLK   49 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3456799999999999999888776543

>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=96.59  E-value=0.019  Score=62.33  Aligned_cols=77  Identities=13%  Similarity=0.106  Sum_probs=47.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------------hc-----cccCccHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------------AG-----AKERGELEARVT  372 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------------~g-----~~~~g~~e~~l~  372 (710)
                      +.-++++|++|+||||++..||..+...       +.++..+++....             .+     .....+....+.
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~-------G~kVllv~~D~~R~aa~eqL~~~~~~~gvpv~~~~~~~dp~~i~~  172 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKR-------GYKVGVVCSDTWRPGAYHQLRQLLDRYHIEVFGNPQEKDAIKLAK  172 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTT-------TCCEEEEECCCSSTHHHHHHHHHHGGGTCEEECCTTCCCHHHHHH
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHC-------CCeEEEEeCCCcchhHHHHHHHHHHhcCCcEEecCCCCCHHHHHH
Confidence            3457899999999999999999988653       3344333321110             00     011223444455


Q ss_pred             HHHHHHHhcCCeEEEEccchhh
Q 005179          373 TLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       373 ~~~~~~~~~~~~IL~IDEid~l  394 (710)
                      ..+..+...+..+++||....+
T Consensus       173 ~al~~a~~~~~DvVIIDTaGrl  194 (443)
T 3dm5_A          173 EGVDYFKSKGVDIIIVDTAGRH  194 (443)
T ss_dssp             HHHHHHHHTTCSEEEEECCCCS
T ss_pred             HHHHHHHhCCCCEEEEECCCcc
Confidence            6667776655668999987554

>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=96.57  E-value=0.0015  Score=62.39  Aligned_cols=25  Identities=40%  Similarity=0.591  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .++|+||||||||++++.||+.++|
T Consensus        12 ~I~l~G~~GsGKSTv~~~La~~l~g   36 (184)
T 1y63_A           12 NILITGTPGTGKTSMAEMIAAELDG   36 (184)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCC
Confidence            6899999999999999999998444

>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=96.53  E-value=0.012  Score=56.48  Aligned_cols=29  Identities=34%  Similarity=0.373  Sum_probs=25.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+.++++++++|.||||+|-+++.+....
T Consensus        27 ~~g~i~v~tG~GkGKTTaA~GlalRA~g~   55 (196)
T 1g5t_A           27 ERGIIIVFTGNGKGKTTAAFGTAARAVGH   55 (196)
T ss_dssp             CCCCEEEEESSSSCHHHHHHHHHHHHHHT
T ss_pred             cCceEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            46789999999999999999999988654

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=96.49  E-value=0.0014  Score=63.39  Aligned_cols=26  Identities=27%  Similarity=0.424  Sum_probs=23.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..++|+|+||+||||+++.|++.+
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l   49 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKL   49 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHc
Confidence            35679999999999999999999988

>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=96.46  E-value=0.002  Score=61.09  Aligned_cols=26  Identities=38%  Similarity=0.532  Sum_probs=23.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.+++|+|+||+||||+++.|++.+
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            35679999999999999999999988

>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=96.45  E-value=0.0059  Score=64.97  Aligned_cols=79  Identities=15%  Similarity=0.204  Sum_probs=46.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------hcc-------ccCccHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------AGA-------KERGELEARVTTLI  375 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------~g~-------~~~g~~e~~l~~~~  375 (710)
                      .+..++|+|+||+|||+++..++..+...       +..+.+++.....       .|.       ......++.+ ..+
T Consensus        73 ~G~li~I~G~pGsGKTtlal~la~~~~~~-------g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l-~~l  144 (366)
T 1xp8_A           73 RGRITEIYGPESGGKTTLALAIVAQAQKA-------GGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQAL-EIM  144 (366)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHH-HHH
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHHHHC-------CCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHH-HHH
Confidence            34568899999999999999998877543       3344444432110       010       0012233322 333


Q ss_pred             HHH-HhcCCeEEEEccchhhhh
Q 005179          376 SEI-QKSGDVILFIDEVHTLIG  396 (710)
Q Consensus       376 ~~~-~~~~~~IL~IDEid~l~~  396 (710)
                      +.+ ......+||||.+..+..
T Consensus       145 ~~l~~~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          145 ELLVRSGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             HHHHTTTCCSEEEEECTTTCCC
T ss_pred             HHHHhcCCCCEEEEeChHHhcc
Confidence            333 335577999999999864

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=96.41  E-value=0.0016  Score=62.96  Aligned_cols=33  Identities=18%  Similarity=0.399  Sum_probs=26.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++|.||||+|||++|+.|++.+ |    ...+|...+
T Consensus        20 ~I~l~G~~GsGKSTla~~L~~~l-g----~~~i~~d~~   52 (202)
T 3t61_A           20 SIVVMGVSGSGKSSVGEAIAEAC-G----YPFIEGDAL   52 (202)
T ss_dssp             CEEEECSTTSCHHHHHHHHHHHH-T----CCEEEGGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-C----CEEEeCCcC
Confidence            68999999999999999999986 3    445555444

>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=96.40  E-value=0.008  Score=59.88  Aligned_cols=24  Identities=21%  Similarity=0.267  Sum_probs=20.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+++|+||+|+|||.++..++..+
T Consensus       109 ~~~ll~~~tG~GKT~~a~~~~~~~  132 (237)
T 2fz4_A          109 KRGCIVLPTGSGKTHVAMAAINEL  132 (237)
T ss_dssp             SEEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHHc
Confidence            459999999999999998887664

>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=96.39  E-value=0.0017  Score=61.48  Aligned_cols=23  Identities=48%  Similarity=0.687  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|+||||+|||++|+.||+.+
T Consensus        13 ~i~i~G~~GsGKst~~~~l~~~~   35 (180)
T 3iij_A           13 NILLTGTPGVGKTTLGKELASKS   35 (180)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHH
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHh
Confidence            68999999999999999999874

>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=96.37  E-value=0.0021  Score=60.02  Aligned_cols=23  Identities=26%  Similarity=0.218  Sum_probs=21.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|.|+||+||||+++.|++.+
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            47899999999999999999988

>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=96.36  E-value=0.0045  Score=66.57  Aligned_cols=62  Identities=16%  Similarity=0.166  Sum_probs=47.5

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ++|...++..+...++...    ...   ..+|++|++|||||++|++|..........++.+||+.+.
T Consensus       139 ~ig~s~~m~~l~~~i~~~a----~~~---~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~  200 (387)
T 1ny5_A          139 YVFESPKMKEILEKIKKIS----CAE---CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIP  200 (387)
T ss_dssp             CCCCSHHHHHHHHHHHHHT----TCC---SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSC
T ss_pred             hhhccHHhhHHHHHHHHhc----CCC---CCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCC
Confidence            5666666666666665532    111   2579999999999999999999987778899999999863

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.34  E-value=0.0042  Score=65.29  Aligned_cols=24  Identities=25%  Similarity=0.556  Sum_probs=22.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++|+||||+|||+++++||..+
T Consensus        25 ~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A           25 VCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHh
Confidence            378999999999999999999985

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=96.30  E-value=0.0024  Score=60.20  Aligned_cols=24  Identities=33%  Similarity=0.578  Sum_probs=22.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+++|+|+||+||||+++.|++.+
T Consensus         5 ~~i~i~G~~GsGKsTla~~La~~l   28 (175)
T 1via_A            5 KNIVFIGFMGSGKSTLARALAKDL   28 (175)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHc
Confidence            368999999999999999999988

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.30  E-value=0.0059  Score=63.51  Aligned_cols=33  Identities=30%  Similarity=0.439  Sum_probs=27.8

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      ..++|+||+|+|||+++..||+.+          +..++..|.
T Consensus         6 ~~i~i~GptGsGKTtla~~La~~l----------~~~iis~Ds   38 (323)
T 3crm_A            6 PAIFLMGPTAAGKTDLAMALADAL----------PCELISVDS   38 (323)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHS----------CEEEEEECT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc----------CCcEEeccc
Confidence            358899999999999999999988          666666663

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.28  E-value=0.0028  Score=62.29  Aligned_cols=24  Identities=21%  Similarity=0.397  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..+++.||||+||+|.|+.||+.|
T Consensus        30 kiI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           30 KVIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             EEEEEECCTTCCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHH
Confidence            478899999999999999999984

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.28  E-value=0.0026  Score=61.52  Aligned_cols=33  Identities=27%  Similarity=0.375  Sum_probs=26.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+.+.||+|+|||++++.|+..+ |    .+.+|...+
T Consensus        31 ~i~l~G~~GsGKSTl~~~L~~~~-g----~~~i~~d~~   63 (200)
T 4eun_A           31 HVVVMGVSGSGKTTIAHGVADET-G----LEFAEADAF   63 (200)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH-C----CEEEEGGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHhh-C----CeEEccccc
Confidence            68899999999999999999987 4    455554443

>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=96.27  E-value=0.0025  Score=66.09  Aligned_cols=33  Identities=21%  Similarity=0.305  Sum_probs=25.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceee
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLF  693 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~  693 (710)
                      +.++++||||||||+||.++|.. -|..-.++.+
T Consensus       124 sviLI~GpPGsGKTtLAlqlA~~-~G~~VlyIs~  156 (331)
T 2vhj_A          124 GMVIVTGKGNSGKTPLVHALGEA-LGGKDKYATV  156 (331)
T ss_dssp             EEEEEECSCSSSHHHHHHHHHHH-HHTTSCCEEE
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHh-CCCCEEEEEe
Confidence            35799999999999999999987 3333345555

>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=96.27  E-value=0.0055  Score=64.81  Aligned_cols=78  Identities=18%  Similarity=0.186  Sum_probs=45.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------hccc-------cCccHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------AGAK-------ERGELEARVTTLI  375 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------~g~~-------~~g~~e~~l~~~~  375 (710)
                      .+.-++|+||||+|||+|+..++..+...       +..+..++.....       .|..       .....++.+ .++
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~-------g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l-~~~  131 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA-------GGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQAL-EIA  131 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHH-HHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC-------CCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHH-HHH
Confidence            34568999999999999999998776543       2334444322110       0100       011233322 233


Q ss_pred             HH-HHhcCCeEEEEccchhhh
Q 005179          376 SE-IQKSGDVILFIDEVHTLI  395 (710)
Q Consensus       376 ~~-~~~~~~~IL~IDEid~l~  395 (710)
                      .. +....+.+|+||++..+.
T Consensus       132 ~~l~~~~~~~lIVIDsl~~l~  152 (349)
T 2zr9_A          132 DMLVRSGALDIIVIDSVAALV  152 (349)
T ss_dssp             HHHHTTTCCSEEEEECGGGCC
T ss_pred             HHHHhcCCCCEEEEcChHhhc
Confidence            32 334567899999999986

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.25  E-value=0.0022  Score=60.02  Aligned_cols=25  Identities=28%  Similarity=0.574  Sum_probs=22.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+++|+|++|+||||+++.|++.+
T Consensus         7 ~~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            7 MQHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             -CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             cceEEEECCCCCCHHHHHHHHHHHh
Confidence            3579999999999999999999988

>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=96.25  E-value=0.0027  Score=63.00  Aligned_cols=23  Identities=35%  Similarity=0.583  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|.||||+|||++|+.||+.|
T Consensus        18 ~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           18 RAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68999999999999999999985

>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=96.24  E-value=0.0027  Score=60.31  Aligned_cols=24  Identities=33%  Similarity=0.573  Sum_probs=22.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|+||+||||+++.|++.+
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            458999999999999999999988

>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=96.23  E-value=0.0023  Score=61.09  Aligned_cols=25  Identities=36%  Similarity=0.513  Sum_probs=22.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+.+++|+|+||+||||+++.|++.
T Consensus         9 ~~~~I~l~G~~GsGKSTv~~~La~~   33 (184)
T 1y63_A            9 KGINILITGTPGTGKTSMAEMIAAE   33 (184)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHh
Confidence            3567899999999999999999998

>3uie_A Adenylyl-sulfate kinase 1, chloroplastic; rossmann fold, transferase-transferase complex; HET: ADX ANP; 1.79A {Arabidopsis thaliana} SCOP: c.37.1.0 PDB: 4fxp_A*

Probab=96.16  E-value=0.016  Score=55.78  Aligned_cols=29  Identities=24%  Similarity=0.235  Sum_probs=24.9

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      ...+..+.|+|++|+||||+++.|+..+.
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            34556788999999999999999999884

>2iut_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- cell division, DNA translocation, KOPS, membrane; HET: DNA SAP; 2.25A {Pseudomonas aeruginosa} PDB: 2iuu_A*

Probab=96.15  E-value=0.021  Score=63.77  Aligned_cols=72  Identities=14%  Similarity=0.164  Sum_probs=45.5

Q ss_pred             eEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc---CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCH
Q 005179          384 VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG---RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQ  459 (710)
Q Consensus       384 ~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~---~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~  459 (710)
                      .+|+|||++.++...         ..++...|..+..   .-.+.+|.+|..+.   .-.++..++.-|. .|.+...+.
T Consensus       345 ivvVIDE~~~L~~~~---------~~~~~~~L~~Iar~GRa~GIhLIlaTQRPs---~d~I~~~Iran~~~RI~lrv~s~  412 (574)
T 2iut_A          345 IVVVVDEFADMMMIV---------GKKVEELIARIAQKARAAGIHLILATQRPS---VDVITGLIKANIPTRIAFQVSSK  412 (574)
T ss_dssp             EEEEESCCTTHHHHT---------CHHHHHHHHHHHHHCTTTTEEEEEEESCCC---TTTSCHHHHHTCCEEEEECCSCH
T ss_pred             EEEEEeCHHHHhhhh---------hHHHHHHHHHHHHHHhhCCeEEEEEecCcc---cccccHHHHhhhccEEEEEcCCH
Confidence            689999999886531         1233444444333   33577777766643   1135677888776 677887888


Q ss_pred             HHHHHHHH
Q 005179          460 EDAVRILL  467 (710)
Q Consensus       460 ~~~~~IL~  467 (710)
                      .+...||-
T Consensus       413 ~Dsr~ILd  420 (574)
T 2iut_A          413 IDSRTILD  420 (574)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHhcC
Confidence            87766653

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.15  E-value=0.0041  Score=59.26  Aligned_cols=28  Identities=29%  Similarity=0.321  Sum_probs=24.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      ..++|.|+||+|||++++.||..+-...
T Consensus        14 ~~i~l~G~~GsGKsT~~~~L~~~l~~~~   41 (186)
T 2yvu_A           14 IVVWLTGLPGSGKTTIATRLADLLQKEG   41 (186)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTT
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHHhcC
Confidence            3688999999999999999999975433

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.14  E-value=0.0044  Score=64.74  Aligned_cols=25  Identities=28%  Similarity=0.541  Sum_probs=22.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+||+|+|||+|+..||+.+
T Consensus        40 ~~lIvI~GPTgsGKTtLa~~LA~~l   64 (339)
T 3a8t_A           40 EKLLVLMGATGTGKSRLSIDLAAHF   64 (339)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHTTS
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHC
Confidence            3468899999999999999999987

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=96.13  E-value=0.0033  Score=58.98  Aligned_cols=25  Identities=40%  Similarity=0.634  Sum_probs=22.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|++|+||||+++.|+..+
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            3568999999999999999999887

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=96.12  E-value=0.0031  Score=58.92  Aligned_cols=24  Identities=29%  Similarity=0.497  Sum_probs=21.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++|.|+||||||++|+.||+.|
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~l   31 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLAL   31 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHh
Confidence            378999999999999999999974

>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=96.12  E-value=0.0056  Score=61.23  Aligned_cols=24  Identities=25%  Similarity=0.398  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -.++|.||||+|||++|+.|++.+
T Consensus        30 ~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           30 GRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            378999999999999999999875

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=96.11  E-value=0.0034  Score=60.09  Aligned_cols=23  Identities=22%  Similarity=0.450  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|.||||+|||++|+.||+.+
T Consensus        11 ~I~l~G~~GsGKsT~~~~La~~l   33 (196)
T 2c95_A           11 IIFVVGGPGSGKGTQCEKIVQKY   33 (196)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68999999999999999999875

>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=96.11  E-value=0.0036  Score=68.95  Aligned_cols=46  Identities=26%  Similarity=0.463  Sum_probs=34.2

Q ss_pred             ChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          633 GQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       633 Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      +|.+|+..+...+....          +.+++.||||||||+++++++..|...+.
T Consensus        29 ~Q~~av~~~~~~i~~~~----------~~~li~G~aGTGKT~ll~~~~~~l~~~~~   74 (459)
T 3upu_A           29 GQKNAFNIVMKAIKEKK----------HHVTINGPAGTGATTLTKFIIEALISTGE   74 (459)
T ss_dssp             HHHHHHHHHHHHHHSSS----------CEEEEECCTTSCHHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHhcCC----------CEEEEEeCCCCCHHHHHHHHHHHHHhcCC
Confidence            45566666655544311          37899999999999999999999876544

>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=96.10  E-value=0.0027  Score=67.37  Aligned_cols=29  Identities=14%  Similarity=0.241  Sum_probs=24.7

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..+..++|+||+|+||||++++++..+..
T Consensus       121 ~~~g~i~I~GptGSGKTTlL~~l~g~~~~  149 (356)
T 3jvv_A          121 VPRGLVLVTGPTGSGKSTTLAAMLDYLNN  149 (356)
T ss_dssp             CSSEEEEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHhcccC
Confidence            34457899999999999999999988754

>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=96.09  E-value=0.0068  Score=65.28  Aligned_cols=26  Identities=31%  Similarity=0.401  Sum_probs=21.1

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-++|+||||+|||+|+..++-..
T Consensus       177 ~Gei~~I~G~sGsGKTTLl~~la~~~  202 (400)
T 3lda_A          177 TGSITELFGEFRTGKSQLCHTLAVTC  202 (400)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEEcCCCCChHHHHHHHHHHh
Confidence            34567899999999999999876443

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=96.08  E-value=0.0029  Score=60.71  Aligned_cols=23  Identities=26%  Similarity=0.468  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -++|.||||+|||++|+.||+.+
T Consensus        14 ~I~l~G~~GsGKsT~a~~L~~~l   36 (199)
T 2bwj_A           14 IIFIIGGPGSGKGTQCEKLVEKY   36 (199)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            68999999999999999999985

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=96.08  E-value=0.0034  Score=60.66  Aligned_cols=24  Identities=25%  Similarity=0.462  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++|.||||+|||++|+.||+.+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            378999999999999999999874

>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=96.08  E-value=0.0027  Score=60.60  Aligned_cols=25  Identities=28%  Similarity=0.434  Sum_probs=22.4

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|+||+||||+++.|++.+
T Consensus         5 ~~~I~l~G~~GsGKST~~~~L~~~l   29 (193)
T 2rhm_A            5 PALIIVTGHPATGKTTLSQALATGL   29 (193)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHc
Confidence            3457899999999999999999988

>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=96.08  E-value=0.009  Score=63.15  Aligned_cols=79  Identities=14%  Similarity=0.147  Sum_probs=46.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-------cc-------ccCccHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-------GA-------KERGELEARVTTLIS  376 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-------g~-------~~~g~~e~~l~~~~~  376 (710)
                      +.-++|+||||+|||+|+..++..+...       +..+++++......       |.       ......++.+..+..
T Consensus        61 G~i~~I~GppGsGKSTLal~la~~~~~~-------gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~  133 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLALHAIAEAQKM-------GGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDE  133 (356)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHhc-------CCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHH
Confidence            4457899999999999999999887542       23344444322100       00       011223333333222


Q ss_pred             HHHhcCCeEEEEccchhhhh
Q 005179          377 EIQKSGDVILFIDEVHTLIG  396 (710)
Q Consensus       377 ~~~~~~~~IL~IDEid~l~~  396 (710)
                      .+....+.+++||.+..++.
T Consensus       134 l~~~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          134 LVRSGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             HHHTSCCSEEEEECTTTCCC
T ss_pred             HhhhcCCCeEEehHhhhhcC
Confidence            23345677999999988764

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.05  E-value=0.0028  Score=61.46  Aligned_cols=23  Identities=39%  Similarity=0.885  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|+||||+|||++++.|++.+
T Consensus        14 ~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           14 PLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            57899999999999999999986

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=96.04  E-value=0.0038  Score=62.96  Aligned_cols=32  Identities=25%  Similarity=0.327  Sum_probs=26.7

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .++|+||+|+||||+++.||..+          +..++..|.
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            36899999999999999999988          566666653

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=96.01  E-value=0.012  Score=61.41  Aligned_cols=43  Identities=19%  Similarity=0.224  Sum_probs=33.6

Q ss_pred             CCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          656 NRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       656 ~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ..+...++|+||+|+|||+++..||..+-..+...+.+|..-+
T Consensus       102 ~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D~~  144 (320)
T 1zu4_A          102 ENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAADTF  144 (320)
T ss_dssp             TTSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCS
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCc
Confidence            3444689999999999999999999998766666666665544

>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=96.00  E-value=0.011  Score=62.78  Aligned_cols=78  Identities=14%  Similarity=0.183  Sum_probs=46.5

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------hccc-------cCccHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------AGAK-------ERGELEARVTTLI  375 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------~g~~-------~~g~~e~~l~~~~  375 (710)
                      .+..++|+|+||+|||+++..++..+...       +..+..++.....       .|..       .....+. +..++
T Consensus        62 ~G~ii~I~G~pGsGKTtLal~la~~~~~~-------g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~-~~~~~  133 (356)
T 1u94_A           62 MGRIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQ-ALEIC  133 (356)
T ss_dssp             TTSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHH-HHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHC-------CCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHH-HHHHH
Confidence            45568999999999999999999877543       3344555432110       0000       0011222 33333


Q ss_pred             HHH-HhcCCeEEEEccchhhh
Q 005179          376 SEI-QKSGDVILFIDEVHTLI  395 (710)
Q Consensus       376 ~~~-~~~~~~IL~IDEid~l~  395 (710)
                      ..+ ......+|+||.+..+.
T Consensus       134 ~~l~~~~~~~lVVIDsl~~l~  154 (356)
T 1u94_A          134 DALARSGAVDVIVVDSVAALT  154 (356)
T ss_dssp             HHHHHHTCCSEEEEECGGGCC
T ss_pred             HHHHhccCCCEEEEcCHHHhc
Confidence            333 34567799999999886

>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=95.99  E-value=0.0073  Score=64.43  Aligned_cols=26  Identities=42%  Similarity=0.496  Sum_probs=23.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..++++||||+|||+++++||..+-|
T Consensus       170 ~~i~l~G~~GsGKSTl~~~l~~~~~g  195 (377)
T 1svm_A          170 RYWLFKGPIDSGKTTLAAALLELCGG  195 (377)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHCC
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhcCC
Confidence            47899999999999999999998644

>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=95.99  E-value=0.0038  Score=59.57  Aligned_cols=24  Identities=33%  Similarity=0.545  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..+.+.||||+|||++++.||..+
T Consensus        10 ~~i~l~G~~GsGKSTl~~~La~~~   33 (191)
T 1zp6_A           10 NILLLSGHPGSGKSTIAEALANLP   33 (191)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhcc
Confidence            368899999999999999999864

>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=95.98  E-value=0.004  Score=67.59  Aligned_cols=76  Identities=13%  Similarity=0.159  Sum_probs=50.1

Q ss_pred             CcCCHHHHHHHHHhhhCCChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCC
Q 005179          590 AVVGPDDIAAVASLWSGIPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTG  669 (710)
Q Consensus       590 ~~v~~~di~~~~s~~~gip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpG  669 (710)
                      ..++.+++.....-+.         +  ..+..+.+.+.. |+||++++..+.-++    .|-....|--.++|+.|+||
T Consensus       186 ~~~t~ed~~~i~~l~~---------~--~~~~~l~~sIap-I~G~e~vK~aLll~L----~GG~~k~rgdihVLL~G~PG  249 (506)
T 3f8t_A          186 VHPDPAELEEFRELAD---------K--DPLTTFARAIAP-LPGAEEVGKMLALQL----FSCVGKNSERLHVLLAGYPV  249 (506)
T ss_dssp             CCCCHHHHHHHHHHHH---------S--CHHHHHHHHHCC-STTCHHHHHHHHHHH----TTCCSSGGGCCCEEEESCHH
T ss_pred             CCCCHHHHHHHHHHHH---------H--HHHHHHHHHhcc-cCCCHHHHHHHHHHH----cCCccccCCceeEEEECCCC
Confidence            4567777655443221         1  234577888999 999999877765543    22111111112799999999


Q ss_pred             CcHHHHHHHH-HHH
Q 005179          670 VGKTELAKSL-AAC  682 (710)
Q Consensus       670 tGKT~lAkaL-A~~  682 (710)
                      | ||+|||++ ++.
T Consensus       250 t-KS~Lar~i~~~i  262 (506)
T 3f8t_A          250 V-CSEILHHVLDHL  262 (506)
T ss_dssp             H-HHHHHHHHHHHT
T ss_pred             h-HHHHHHHHHHHh
Confidence            9 99999999 665

>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=95.98  E-value=0.0044  Score=58.00  Aligned_cols=24  Identities=25%  Similarity=0.469  Sum_probs=22.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|+||+||||+++.|++.+
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            358999999999999999999988

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=95.97  E-value=0.0052  Score=59.36  Aligned_cols=25  Identities=28%  Similarity=0.523  Sum_probs=22.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ...++|+|++|+||||+++.|++.+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~l   42 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEAC   42 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999999987

>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=95.96  E-value=0.006  Score=59.89  Aligned_cols=25  Identities=36%  Similarity=0.535  Sum_probs=21.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-+.|+||+|+||||+++.++..+
T Consensus        25 G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           25 QAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            4457899999999999999998754

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=95.96  E-value=0.005  Score=59.74  Aligned_cols=23  Identities=26%  Similarity=0.345  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -+.|.|+||+|||++|+.||+.|
T Consensus        12 ~I~l~G~~GsGKST~~~~L~~~l   34 (212)
T 2wwf_A           12 FIVFEGLDRSGKSTQSKLLVEYL   34 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999975

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=95.94  E-value=0.011  Score=61.70  Aligned_cols=29  Identities=28%  Similarity=0.417  Sum_probs=24.2

Q ss_pred             CCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          655 PNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       655 p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..+|. .+.+.||+|||||++++.|+..+-
T Consensus        89 ~~~p~-iigI~GpsGSGKSTl~~~L~~ll~  117 (321)
T 3tqc_A           89 PKVPY-IIGIAGSVAVGKSTTSRVLKALLS  117 (321)
T ss_dssp             CCCCE-EEEEECCTTSSHHHHHHHHHHHHT
T ss_pred             CCCCE-EEEEECCCCCCHHHHHHHHHHHhc
Confidence            33443 788999999999999999999874

>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=95.92  E-value=0.0043  Score=59.91  Aligned_cols=25  Identities=36%  Similarity=0.493  Sum_probs=22.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|+||+||||+++.|++.+
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l   44 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKL   44 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3458899999999999999999988

>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=95.92  E-value=0.0043  Score=60.87  Aligned_cols=25  Identities=32%  Similarity=0.465  Sum_probs=22.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|+||+||||+++.|++.+
T Consensus         4 ~~~I~l~G~~GsGKsT~a~~La~~l   28 (220)
T 1aky_A            4 SIRMVLIGPPGAGKGTQAPNLQERF   28 (220)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            4568999999999999999999988

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=95.89  E-value=0.0044  Score=59.30  Aligned_cols=26  Identities=23%  Similarity=0.365  Sum_probs=23.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..++|.|+||+||||+++.|++.+
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            34568999999999999999999988

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=95.89  E-value=0.0064  Score=57.85  Aligned_cols=24  Identities=25%  Similarity=0.325  Sum_probs=22.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .++|.|+||+||||+++.|++.+.
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~   26 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILD   26 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            478999999999999999999884

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=95.89  E-value=0.0054  Score=57.73  Aligned_cols=27  Identities=22%  Similarity=0.320  Sum_probs=23.1

Q ss_pred             EEEEEcCCCCcHHHHHH------------HHHHHHcCCC
Q 005179          661 AMLFCGPTGVGKTELAK------------SLAACYFGSV  687 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAk------------aLA~~lfg~~  687 (710)
                      -+.++||+|+|||+|++            .+...+|++.
T Consensus        11 i~~l~G~nGsGKSTl~~~~~~~~~~~~~d~~~g~~~~~~   49 (171)
T 4gp7_A           11 LVVLIGSSGSGKSTFAKKHFKPTEVISSDFCRGLMSDDE   49 (171)
T ss_dssp             EEEEECCTTSCHHHHHHHHSCGGGEEEHHHHHHHHCSST
T ss_pred             EEEEECCCCCCHHHHHHHHccCCeEEccHHHHHHhcCcc
Confidence            67899999999999999            7777777654

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=95.88  E-value=0.0087  Score=57.86  Aligned_cols=37  Identities=22%  Similarity=0.145  Sum_probs=27.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      -.+.+.||+|+|||++++.|+..+-.....++.+++.
T Consensus        23 ~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d   59 (201)
T 1rz3_A           23 LVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (201)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccC
Confidence            3688999999999999999999874333334444333

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=95.88  E-value=0.0076  Score=63.10  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=35.7

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|.++.++.+...+..   |        ..++++||+|||||+|++.+++.+
T Consensus        13 ~~~gR~~el~~L~~~l~~---~--------~~v~i~G~~G~GKT~Ll~~~~~~~   55 (350)
T 2qen_A           13 DIFDREEESRKLEESLEN---Y--------PLTLLLGIRRVGKSSLLRAFLNER   55 (350)
T ss_dssp             GSCSCHHHHHHHHHHHHH---C--------SEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             hcCChHHHHHHHHHHHhc---C--------CeEEEECCCcCCHHHHHHHHHHHc
Confidence            378888888888777653   2        278999999999999999999884

>3lw7_A Adenylate kinase related protein (ADKA-like); AMP, PSI, MCSG, structural genomics, midwest center for structural genomics; HET: AMP; 2.30A {Sulfolobus solfataricus} PDB: 3h0k_A

Probab=95.85  E-value=0.0042  Score=57.91  Aligned_cols=22  Identities=27%  Similarity=0.327  Sum_probs=19.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|+|+||+||||+++.| +.+
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            4789999999999999999 665

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=95.85  E-value=0.0074  Score=66.31  Aligned_cols=28  Identities=29%  Similarity=0.343  Sum_probs=23.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      .+.-++|.|+||+|||+++..++..+..
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~  229 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVAT  229 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3455789999999999999999988754

>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=95.84  E-value=0.0043  Score=62.06  Aligned_cols=24  Identities=25%  Similarity=0.545  Sum_probs=21.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..+++.||||+|||++++.||+.+
T Consensus        28 ~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           28 LRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            378999999999999999999774

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.83  E-value=0.022  Score=58.93  Aligned_cols=33  Identities=24%  Similarity=0.189  Sum_probs=26.6

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcce
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRIHY  691 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li  691 (710)
                      ...+.|+||+|+|||++++.||..+-.+...+.
T Consensus       100 g~vi~lvG~nGsGKTTll~~Lag~l~~~~g~V~  132 (302)
T 3b9q_A          100 PAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVL  132 (302)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEE
Confidence            357889999999999999999999765444333

>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=95.83  E-value=0.011  Score=61.82  Aligned_cols=26  Identities=31%  Similarity=0.569  Sum_probs=22.5

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..++|+||||+|||+++..++..+
T Consensus       106 ~G~i~~i~G~~GsGKT~la~~la~~~  131 (324)
T 2z43_A          106 TRTMTEFFGEFGSGKTQLCHQLSVNV  131 (324)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHhHHHHHHHHHH
Confidence            45568999999999999999998765

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=95.81  E-value=0.046  Score=59.28  Aligned_cols=40  Identities=20%  Similarity=0.232  Sum_probs=32.5

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ...++|+||+|+|||+++..||..|-..+.....++...|
T Consensus       100 p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D~~  139 (443)
T 3dm5_A          100 PTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSDTW  139 (443)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCCS
T ss_pred             CeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCc
Confidence            3589999999999999999999998876666665665444

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=95.79  E-value=0.0063  Score=59.19  Aligned_cols=25  Identities=32%  Similarity=0.503  Sum_probs=22.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..+.+.||+|+|||+|++.|+..+-
T Consensus        23 ~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A           23 QLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             EEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3678999999999999999999986

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=95.79  E-value=0.014  Score=57.99  Aligned_cols=25  Identities=28%  Similarity=0.480  Sum_probs=20.8

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+.-++|+|+||+|||+++..++..
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYK   53 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            3456799999999999999887754

>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=95.77  E-value=0.0061  Score=59.21  Aligned_cols=23  Identities=17%  Similarity=0.351  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -+.|.||||+|||++|+.||+.|
T Consensus        11 ~I~l~G~~GsGKsT~~~~L~~~l   33 (215)
T 1nn5_A           11 LIVLEGVDRAGKSTQSRKLVEAL   33 (215)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999875

>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=95.76  E-value=0.015  Score=59.94  Aligned_cols=93  Identities=18%  Similarity=0.219  Sum_probs=53.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhc----cccCccHHHHHHHHHHHHHhcCCeEEEE
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAG----AKERGELEARVTTLISEIQKSGDVILFI  388 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g----~~~~g~~e~~l~~~~~~~~~~~~~IL~I  388 (710)
                      -++|+||+|+|||+|+..||+.+          +..+++.|.-.+..+    +... ..++        .... + --||
T Consensus        12 ~i~i~GptgsGKt~la~~La~~~----------~~~iis~Ds~qvY~~~~igTakp-~~~E--------~~~v-~-hhli   70 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKIL----------PVELISVDSALIYKGMDIGTAKP-NAEE--------LLAA-P-HRLL   70 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS----------CEEEEECCTTTTBTTCCTTTTCC-CHHH--------HHHS-C-EETS
T ss_pred             EEEEECCCccCHHHHHHHHHHhC----------CCcEEecccccccccccccCCCC-CHHH--------HcCC-C-EEEe
Confidence            36789999999999999999987          566777664333221    1111 1111        1111 1 2334


Q ss_pred             ccch--hhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChH
Q 005179          389 DEVH--TLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQD  433 (710)
Q Consensus       389 DEid--~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~  433 (710)
                      |.++  .....+       ....++...+....++|++.++.-.|.-
T Consensus        71 d~~~~~e~~s~~-------~f~~~a~~~i~~i~~~g~~pilVGGTgl  110 (316)
T 3foz_A           71 DIRDPSQAYSAA-------DFRRDALAEMADITAAGRIPLLVGGTML  110 (316)
T ss_dssp             SCBCTTSCCCHH-------HHHHHHHHHHHHHHHTTCEEEEEESCHH
T ss_pred             ccCCccccccHH-------HHHHHHHHHHHHHHhCCCcEEEEcCcHH
Confidence            4333  111111       3356677777788888888766666653

>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=95.75  E-value=0.015  Score=59.93  Aligned_cols=97  Identities=21%  Similarity=0.180  Sum_probs=53.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccch
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVH  392 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid  392 (710)
                      -++|.||+|+|||+|+..||+.+          +..+++.|.-.+..+.. .|.-.-..    .+.. .-+ --|||.++
T Consensus         5 ~i~i~GptgsGKt~la~~La~~~----------~~~iis~Ds~QvYr~~~-igTakp~~----~E~~-gvp-hhlid~~~   67 (322)
T 3exa_A            5 LVAIVGPTAVGKTKTSVMLAKRL----------NGEVISGDSMQVYRGMD-IGTAKITA----EEMD-GVP-HHLIDIKD   67 (322)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHTT----------TEEEEECCGGGGBTTCC-TTTTCCCH----HHHT-TCC-EESSSCBC
T ss_pred             EEEEECCCcCCHHHHHHHHHHhC----------ccceeecCcccceeeee-ecCCCCCH----HHHc-CCC-EEEeccCC
Confidence            46789999999999999999987          55666665432221111 01000000    0111 112 23444333


Q ss_pred             h--hhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChH
Q 005179          393 T--LIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQD  433 (710)
Q Consensus       393 ~--l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~  433 (710)
                      -  .+..+       ....++...+....++|++.||.-.|.-
T Consensus        68 ~~e~~s~~-------~F~~~a~~~i~~i~~~gk~pIlVGGTgl  103 (322)
T 3exa_A           68 PSESFSVA-------DFQDLATPLITEIHERGRLPFLVGGTGL  103 (322)
T ss_dssp             TTSCCCHH-------HHHHHHHHHHHHHHHTTCEEEEESCCHH
T ss_pred             hhhhccHH-------HHHHHHHHHHHHHHhCCCcEEEEcCcHH
Confidence            2  11111       3355677777777888888777666653

>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=95.75  E-value=0.0042  Score=60.69  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=21.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|+|+||+||||+++.|++.+
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            47899999999999999999887

>1kht_A Adenylate kinase; phosphotransferase, signaling protein, transferase; HET: AMP; 2.50A {Methanococcus voltae} SCOP: c.37.1.1 PDB: 3h86_B* 1ki9_A

Probab=95.71  E-value=0.0049  Score=58.64  Aligned_cols=25  Identities=20%  Similarity=0.233  Sum_probs=22.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      ..++|.|+||+||||+++.|++.+.
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            4588999999999999999999884

>1htw_A HI0065; nucleotide-binding fold, structural genomics, structure 2 function project, S2F, unknown function; HET: ADP; 1.70A {Haemophilus influenzae} SCOP: c.37.1.18 PDB: 1fl9_A

Probab=95.70  E-value=0.0098  Score=55.28  Aligned_cols=27  Identities=26%  Similarity=0.432  Sum_probs=24.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      .+.|.||.|+|||+|.|+|+..+ ++..
T Consensus        35 ~v~L~G~nGaGKTTLlr~l~g~l-~~~G   61 (158)
T 1htw_A           35 MVYLNGDLGAGKTTLTRGMLQGI-GHQG   61 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT-TCCS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC-CCCC
Confidence            68899999999999999999998 6544

>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=95.69  E-value=0.0064  Score=60.33  Aligned_cols=23  Identities=30%  Similarity=0.618  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.+.||||+|||++|+.||+.|
T Consensus        11 ~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A           11 VVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            78999999999999999999774

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=95.68  E-value=0.0061  Score=58.08  Aligned_cols=24  Identities=21%  Similarity=0.304  Sum_probs=21.9

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|.|+||+||||+++.|++.+
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~   27 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKY   27 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            457899999999999999999987

>3lxx_A GTPase IMAP family member 4; structural genomics consortium, SGC, coiled coil, GTP- binding, nucleotide-binding, immune system; HET: GDP; 2.15A {Homo sapiens}

Probab=95.68  E-value=0.015  Score=57.75  Aligned_cols=24  Identities=29%  Similarity=0.526  Sum_probs=20.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      ..+++|+|++|+|||+|+..|...
T Consensus        29 ~~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           29 QLRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEEEEECCTTSSHHHHHHHHHTS
T ss_pred             ceEEEEECCCCCCHHHHHHHHcCC
Confidence            356899999999999999998753

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=95.67  E-value=0.0054  Score=58.22  Aligned_cols=24  Identities=38%  Similarity=0.535  Sum_probs=22.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|+||+||||+++.|++.+
T Consensus         5 ~~I~l~G~~GsGKST~~~~La~~l   28 (186)
T 3cm0_A            5 QAVIFLGPPGAGKGTQASRLAQEL   28 (186)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            458999999999999999999987

>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=95.67  E-value=0.0065  Score=59.23  Aligned_cols=24  Identities=25%  Similarity=0.365  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .++|.||||+|||++++.|++.+.
T Consensus        27 ~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           27 TIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhc
Confidence            678999999999999999999876

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=95.67  E-value=0.0059  Score=59.59  Aligned_cols=23  Identities=35%  Similarity=0.518  Sum_probs=21.3

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|+|+||+||||+++.|++.+
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            37899999999999999999987

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=95.67  E-value=0.0061  Score=56.77  Aligned_cols=23  Identities=22%  Similarity=0.273  Sum_probs=21.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|+|++|+||||+++.|++.+
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

>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=95.67  E-value=0.022  Score=59.58  Aligned_cols=31  Identities=26%  Similarity=0.246  Sum_probs=25.7

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCc
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRI  689 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~  689 (710)
                      ...+.|+||+|+|||++++.||..+-.....
T Consensus       129 g~vi~lvG~nGaGKTTll~~Lag~l~~~~g~  159 (328)
T 3e70_C          129 PYVIMFVGFNGSGKTTTIAKLANWLKNHGFS  159 (328)
T ss_dssp             SEEEEEECCTTSSHHHHHHHHHHHHHHTTCC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCCE
Confidence            3578999999999999999999987554443

>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=95.64  E-value=0.0046  Score=59.41  Aligned_cols=23  Identities=39%  Similarity=0.520  Sum_probs=21.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      +++|.||||+|||+||..|++..
T Consensus        36 ~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           36 GVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             EEEEECCCTTTTHHHHHHHHTTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhC
Confidence            78999999999999999999874

>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=95.64  E-value=0.018  Score=58.05  Aligned_cols=26  Identities=35%  Similarity=0.436  Sum_probs=22.8

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..++|+|+||+||||+++.|++.+..
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~   30 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSK   30 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            45889999999999999999998643

>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=95.64  E-value=0.0067  Score=60.15  Aligned_cols=25  Identities=36%  Similarity=0.473  Sum_probs=23.0

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.+++|.|+||+||||+++.|++.+
T Consensus        16 ~~~I~l~G~~GsGKsT~a~~La~~l   40 (233)
T 1ak2_A           16 GVRAVLLGPPGAGKGTQAPKLAKNF   40 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999999988

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=95.63  E-value=0.0099  Score=65.12  Aligned_cols=27  Identities=26%  Similarity=0.254  Sum_probs=22.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +.-++|.|+||+|||+++..++..+..
T Consensus       200 G~l~ii~G~pg~GKT~lal~ia~~~a~  226 (444)
T 2q6t_A          200 GSLNIIAARPAMGKTAFALTIAQNAAL  226 (444)
T ss_dssp             TCEEEEEECTTSCHHHHHHHHHHHHHH
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            344788999999999999999988754

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=95.63  E-value=0.0059  Score=58.50  Aligned_cols=25  Identities=24%  Similarity=0.332  Sum_probs=22.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|+||+||||+++.|++.+
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            3468899999999999999999988

>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=95.62  E-value=0.011  Score=59.01  Aligned_cols=26  Identities=27%  Similarity=0.335  Sum_probs=23.1

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..++|+|+||+||||+++.|++.+
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~   53 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSH   53 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHh
Confidence            34568999999999999999999887

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=95.62  E-value=0.0076  Score=58.15  Aligned_cols=27  Identities=37%  Similarity=0.581  Sum_probs=23.3

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+..++|+|++|+||||+++.|+..+
T Consensus        27 ~~g~~i~l~G~~GsGKSTl~~~L~~~~   53 (200)
T 4eun_A           27 EPTRHVVVMGVSGSGKTTIAHGVADET   53 (200)
T ss_dssp             -CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHhh
Confidence            345678899999999999999999887

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=95.60  E-value=0.014  Score=58.77  Aligned_cols=24  Identities=33%  Similarity=0.320  Sum_probs=21.8

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|+||+||||+++.|+..+
T Consensus        33 ~~i~l~G~~GsGKSTla~~L~~~l   56 (253)
T 2p5t_B           33 IAILLGGQSGAGKTTIHRIKQKEF   56 (253)
T ss_dssp             EEEEEESCGGGTTHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhc
Confidence            457899999999999999999887

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=95.60  E-value=0.0057  Score=60.07  Aligned_cols=25  Identities=16%  Similarity=0.215  Sum_probs=23.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|.|+||+||||+++.|++.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l   29 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKY   29 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            4578999999999999999999988

>1knq_A Gluconate kinase; ALFA/beta structure, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.17 PDB: 1ko1_A 1ko4_A 1ko5_A* 1ko8_A* 1kof_A*

Probab=95.59  E-value=0.007  Score=56.84  Aligned_cols=24  Identities=38%  Similarity=0.592  Sum_probs=21.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|++|+||||+++.|+..+
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~   32 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQL   32 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHH
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhh
Confidence            457899999999999999999876

>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=95.58  E-value=0.02  Score=61.05  Aligned_cols=61  Identities=16%  Similarity=0.211  Sum_probs=44.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ++|+..++..+...+......  +     ..+|++|++||||+.+|+++...-.... .++.+|++.+.
T Consensus       131 ~ig~s~~~~~~~~~~~~~a~~--~-----~~vli~GesGtGKe~lAr~ih~~s~r~~-~fv~vnc~~~~  191 (368)
T 3dzd_A          131 FVGEHPKILEIKRLIPKIAKS--K-----APVLITGESGTGKEIVARLIHRYSGRKG-AFVDLNCASIP  191 (368)
T ss_dssp             CCCCSHHHHHHHHHHHHHHTS--C-----SCEEEECCTTSSHHHHHHHHHHHHCCCS-CEEEEESSSSC
T ss_pred             ccccchHHHHHHhhhhhhhcc--c-----hhheEEeCCCchHHHHHHHHHHhccccC-CcEEEEcccCC
Confidence            556666666666555444311  1     2689999999999999999998764444 49999999874

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.57  E-value=0.0073  Score=60.68  Aligned_cols=40  Identities=28%  Similarity=0.367  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          636 EAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       636 ~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+++.+...+.....|        ..+.|.||+|+|||++++.||+.+
T Consensus        33 ~~l~~~~~~i~~~l~g--------~~i~l~G~~GsGKSTl~~~La~~l   72 (250)
T 3nwj_A           33 QILKKKAEEVKPYLNG--------RSMYLVGMMGSGKTTVGKIMARSL   72 (250)
T ss_dssp             HHHHHHHHTTHHHHTT--------CCEEEECSTTSCHHHHHHHHHHHH
T ss_pred             hhhhhhhhhhhhhcCC--------CEEEEECCCCCCHHHHHHHHHHhc
Confidence            4555565555442212        268999999999999999999975

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=95.56  E-value=0.0058  Score=60.29  Aligned_cols=25  Identities=16%  Similarity=0.453  Sum_probs=22.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|.|+||+||||+++.|++.+
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l   31 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHF   31 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHS
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHc
Confidence            3568999999999999999999987

>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=95.56  E-value=0.0077  Score=63.21  Aligned_cols=53  Identities=11%  Similarity=0.091  Sum_probs=39.0

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++|.++.++.+.. +..            ..++++||+|+|||+|++.+++.+-.   ..+.+++..+
T Consensus        14 ~~~gR~~el~~L~~-l~~------------~~v~i~G~~G~GKT~L~~~~~~~~~~---~~~~~~~~~~   66 (357)
T 2fna_A           14 DFFDREKEIEKLKG-LRA------------PITLVLGLRRTGKSSIIKIGINELNL---PYIYLDLRKF   66 (357)
T ss_dssp             GSCCCHHHHHHHHH-TCS------------SEEEEEESTTSSHHHHHHHHHHHHTC---CEEEEEGGGG
T ss_pred             HhcChHHHHHHHHH-hcC------------CcEEEECCCCCCHHHHHHHHHHhcCC---CEEEEEchhh
Confidence            37787777777655 321            27899999999999999999998632   3566776654

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=95.56  E-value=0.0054  Score=64.05  Aligned_cols=24  Identities=38%  Similarity=0.618  Sum_probs=22.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .+++.||||||||+||..||+.+-
T Consensus        42 lIvI~GPTgsGKTtLa~~LA~~l~   65 (339)
T 3a8t_A           42 LLVLMGATGTGKSRLSIDLAAHFP   65 (339)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTTSC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHCC
Confidence            689999999999999999999853

>2qt1_A Nicotinamide riboside kinase 1; non-protein kinase, NAD+, NRK1, nicotinic acid riboside kinase activity, NAD biosynthesis; HET: NNR; 1.32A {Homo sapiens} PDB: 2qsy_A* 2qsz_A* 2qt0_A* 2p0e_A* 2qg6_A* 2ql6_A*

Probab=95.56  E-value=0.0066  Score=58.85  Aligned_cols=34  Identities=35%  Similarity=0.354  Sum_probs=25.5

Q ss_pred             cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          650 VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       650 ~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .|+-....+...+.+.||||+|||++|+.|++.+
T Consensus        12 ~~~~~~~~~~~~i~i~G~~GsGKSTl~~~L~~~~   45 (207)
T 2qt1_A           12 SGLVPRGSKTFIIGISGVTNSGKTTLAKNLQKHL   45 (207)
T ss_dssp             --CCCCSCCCEEEEEEESTTSSHHHHHHHHHTTS
T ss_pred             ccccccCCCCeEEEEECCCCCCHHHHHHHHHHhc
Confidence            3554444444578899999999999999999874

>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=95.54  E-value=0.0066  Score=58.08  Aligned_cols=24  Identities=25%  Similarity=0.414  Sum_probs=21.5

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.++|+||+|+|||||++.|....
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~   25 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhC
Confidence            468999999999999999998765

>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=95.52  E-value=0.023  Score=58.55  Aligned_cols=39  Identities=23%  Similarity=0.278  Sum_probs=29.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC-CCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG-SVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg-~~~~li~~d~se~  698 (710)
                      ..++|+||+|+|||+++..||..+-. .+.....++...+
T Consensus       106 ~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~  145 (296)
T 2px0_A          106 KYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTY  145 (296)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcc
Confidence            48899999999999999999999863 4444555554443

>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=95.51  E-value=0.0073  Score=57.41  Aligned_cols=24  Identities=25%  Similarity=0.389  Sum_probs=22.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|+||+||||+++.|++.+
T Consensus         7 ~~I~l~G~~GsGKsT~~~~L~~~l   30 (194)
T 1qf9_A            7 NVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHh
Confidence            357899999999999999999988

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=95.49  E-value=0.0067  Score=59.43  Aligned_cols=24  Identities=33%  Similarity=0.451  Sum_probs=22.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|.|+||+||||+++.|++.+
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l   29 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEY   29 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999988

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=95.48  E-value=0.0068  Score=59.48  Aligned_cols=35  Identities=17%  Similarity=0.092  Sum_probs=25.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      ..++++||||+|||+|++.++..+-......+-++
T Consensus        24 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           24 FFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            36889999999999999999976543333333333

>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=95.48  E-value=0.016  Score=60.09  Aligned_cols=33  Identities=27%  Similarity=0.348  Sum_probs=26.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCccee
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYL  692 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~  692 (710)
                      ..+.++||+|||||++++.||..+-.+......
T Consensus       103 ~vi~lvG~nGsGKTTll~~Lagll~~~~g~V~l  135 (304)
T 1rj9_A          103 RVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMF  135 (304)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEE
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEE
Confidence            478899999999999999999998665444333

>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=95.46  E-value=0.0092  Score=58.09  Aligned_cols=23  Identities=35%  Similarity=0.433  Sum_probs=21.3

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|.||||+||+|.++.|++.+
T Consensus         2 ~Iil~GpPGsGKgTqa~~La~~~   24 (206)
T 3sr0_A            2 ILVFLGPPGAGKGTQAKRLAKEK   24 (206)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            37899999999999999999988

>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=95.42  E-value=0.022  Score=58.52  Aligned_cols=26  Identities=23%  Similarity=0.424  Sum_probs=23.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..+.+.||+|+|||++|+.|+..+-.
T Consensus        32 ~ii~I~G~sGsGKSTla~~L~~~l~~   57 (290)
T 1odf_A           32 LFIFFSGPQGSGKSFTSIQIYNHLME   57 (290)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhhh
Confidence            37889999999999999999998743

>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=95.42  E-value=0.042  Score=59.54  Aligned_cols=27  Identities=33%  Similarity=0.299  Sum_probs=23.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      ..++++|++|+||||++..||..+...
T Consensus        98 ~vI~lvG~~GsGKTTt~~kLA~~l~~~  124 (433)
T 3kl4_A           98 FIIMLVGVQGSGKTTTAGKLAYFYKKR  124 (433)
T ss_dssp             EEEEECCCTTSCHHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHc
Confidence            346888999999999999999888653

>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=95.42  E-value=0.0055  Score=58.43  Aligned_cols=25  Identities=44%  Similarity=0.508  Sum_probs=21.5

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+..++|+||+|+||||+++.|+..
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~   32 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANL   32 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTC
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhc
Confidence            3456889999999999999999875

>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=95.42  E-value=0.025  Score=62.13  Aligned_cols=34  Identities=26%  Similarity=0.295  Sum_probs=26.9

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcce
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHY  691 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li  691 (710)
                      +...++|+||+|+|||++++.||..+-.....+.
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll~~~~G~V~  325 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQFEQQGKSVM  325 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHhhhcCCeEE
Confidence            3357899999999999999999998765444333

>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=95.41  E-value=0.036  Score=53.85  Aligned_cols=30  Identities=27%  Similarity=0.263  Sum_probs=25.3

Q ss_pred             HcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          307 CRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       307 ~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      ....+..++|.|++|+||||+++.|+..+.
T Consensus        21 ~~~~~~~i~~~G~~GsGKsT~~~~l~~~l~   50 (211)
T 1m7g_A           21 RNQRGLTIWLTGLSASGKSTLAVELEHQLV   50 (211)
T ss_dssp             HTSSCEEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             cCCCCCEEEEECCCCCCHHHHHHHHHHHhc
Confidence            344556788999999999999999999884

>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=95.41  E-value=0.0085  Score=61.71  Aligned_cols=24  Identities=42%  Similarity=0.544  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .++++||||+|||+||..||+.+-
T Consensus        12 ~i~i~GptgsGKt~la~~La~~~~   35 (316)
T 3foz_A           12 AIFLMGPTASGKTALAIELRKILP   35 (316)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             EEEEECCCccCHHHHHHHHHHhCC
Confidence            678999999999999999999843

>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=95.39  E-value=0.023  Score=59.89  Aligned_cols=26  Identities=23%  Similarity=0.303  Sum_probs=22.0

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-++|+||||+|||+++..++...
T Consensus       121 ~G~i~~I~G~~GsGKTtla~~la~~~  146 (343)
T 1v5w_A          121 SMAITEAFGEFRTGKTQLSHTLCVTA  146 (343)
T ss_dssp             SSEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            34457899999999999999998764

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=95.37  E-value=0.0096  Score=56.60  Aligned_cols=27  Identities=37%  Similarity=0.300  Sum_probs=23.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +..++|+|++|+||||+++.|+..+..
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~   39 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQK   39 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            445789999999999999999998843

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=95.36  E-value=0.0074  Score=58.23  Aligned_cols=24  Identities=29%  Similarity=0.379  Sum_probs=21.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+|++|+||||+++.|++.+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~   39 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDY   39 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHc
Confidence            357899999999999999999887

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=95.35  E-value=0.0081  Score=58.17  Aligned_cols=26  Identities=23%  Similarity=0.346  Sum_probs=22.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..++|+||||+||||+++.|+..+
T Consensus        11 ~~~~i~l~G~sGsGKsTl~~~L~~~~   36 (204)
T 2qor_A           11 RIPPLVVCGPSGVGKGTLIKKVLSEF   36 (204)
T ss_dssp             CCCCEEEECCTTSCHHHHHHHHHHHC
T ss_pred             cCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            34568999999999999999999876

>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=95.35  E-value=0.0075  Score=58.86  Aligned_cols=23  Identities=30%  Similarity=0.309  Sum_probs=21.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|.|+||+||||+++.|++.+
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

>3ney_A 55 kDa erythrocyte membrane protein; structural genomics consortium, SGC, 55 kDa erythrocyte MEMB protein; 2.26A {Homo sapiens} SCOP: c.37.1.0

Probab=95.34  E-value=0.01  Score=57.22  Aligned_cols=23  Identities=22%  Similarity=0.582  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.|+||+|+|||+|++.|++.+
T Consensus        21 ~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           21 TLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhhC
Confidence            67899999999999999999874

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=95.32  E-value=0.0074  Score=56.73  Aligned_cols=21  Identities=24%  Similarity=0.335  Sum_probs=19.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|.|+||+||||+++.|++
T Consensus         4 ~I~i~G~~GsGKST~a~~L~~   24 (181)
T 1ly1_A            4 IILTIGCPGSGKSTWAREFIA   24 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEecCCCCCHHHHHHHHHh
Confidence            478999999999999999998

>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=95.31  E-value=0.041  Score=62.68  Aligned_cols=27  Identities=26%  Similarity=0.476  Sum_probs=23.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ...+++.|+||||||+++..+...+..
T Consensus       164 ~~~~vi~G~pGTGKTt~l~~ll~~l~~  190 (608)
T 1w36_D          164 RRISVISGGPGTGKTTTVAKLLAALIQ  190 (608)
T ss_dssp             BSEEEEECCTTSTHHHHHHHHHHHHHH
T ss_pred             CCCEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            467899999999999999988877753

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.30  E-value=0.011  Score=59.72  Aligned_cols=29  Identities=21%  Similarity=0.282  Sum_probs=24.5

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      ...+..++|+||+|+||||+++.++..+.
T Consensus        22 i~~g~~v~i~Gp~GsGKSTll~~l~g~~~   50 (261)
T 2eyu_A           22 HRKMGLILVTGPTGSGKSTTIASMIDYIN   50 (261)
T ss_dssp             GCSSEEEEEECSTTCSHHHHHHHHHHHHH
T ss_pred             hCCCCEEEEECCCCccHHHHHHHHHHhCC
Confidence            34456789999999999999999998774

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=95.29  E-value=0.041  Score=61.69  Aligned_cols=59  Identities=20%  Similarity=0.231  Sum_probs=37.7

Q ss_pred             hhhHHhhhhcCCC-CcccCHHHHHHHHHHH--HcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          278 VDLTARASEELID-PVIGRETEIQRIIQIL--CRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       278 ~~l~~~~~~~~l~-~liGr~~~i~~l~~~L--~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      +.+.+.++.|.-. ....+.+..+.+....  ....+..+.|+|++|+||||+++.|+..+.
T Consensus       333 t~ir~~Lr~G~~~p~~f~~peV~~vLR~~~~~~~~~G~iI~LiG~sGSGKSTLar~La~~L~  394 (552)
T 3cr8_A          333 EEFQRRMRAGLKIPEWYSFPEVLAELHRQTPPRERQGFTVFFTGLSGAGKSTLARALAARLM  394 (552)
T ss_dssp             HHHHHHHTTTCCCCTTTSCHHHHHHHHHHSCCGGGSCEEEEEEESSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCccccccchhhhhhhhcccccccceEEEEECCCCChHHHHHHHHHHhhc
Confidence            3455556666543 2333444333333322  223456789999999999999999999884

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=95.28  E-value=0.013  Score=65.32  Aligned_cols=38  Identities=13%  Similarity=0.132  Sum_probs=30.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++++||+|+|||++.++|+..+-.+....+.-|-.|+
T Consensus       262 ~i~I~GptGSGKTTlL~aL~~~i~~~~giitied~~E~  299 (511)
T 2oap_1          262 SAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREI  299 (511)
T ss_dssp             CEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCCCCCCEEEEcCcccc
Confidence            68999999999999999999988655554444455554

>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=95.26  E-value=0.015  Score=60.16  Aligned_cols=39  Identities=23%  Similarity=0.324  Sum_probs=29.5

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      +...++++||+|+|||+++..||..+-..+.....++..
T Consensus       103 ~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~D  141 (306)
T 1vma_A          103 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAAD  141 (306)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEccc
Confidence            345789999999999999999999876544444444433

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=95.23  E-value=0.012  Score=59.03  Aligned_cols=25  Identities=28%  Similarity=0.404  Sum_probs=23.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|++|+||||+++.|+..+
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            5689999999999999999999988

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=95.23  E-value=0.013  Score=61.59  Aligned_cols=40  Identities=33%  Similarity=0.439  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHH----cCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          296 ETEIQRIIQILC----RRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       296 ~~~i~~l~~~L~----~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++.++..+.    .....+++|+|++|+||||+++.|+..+
T Consensus         5 ~~L~~~il~~l~~~i~~g~~~~i~l~G~~G~GKTTl~~~la~~l   48 (359)
T 2ga8_A            5 HKLADDVLQLLDNRIEDNYRVCVILVGSPGSGKSTIAEELCQII   48 (359)
T ss_dssp             HHHHHHHHHHHHHTTTTCSCEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhccCCeeEEEEECCCCCcHHHHHHHHHHHh
Confidence            334444444443    2334468999999999999999999987

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=95.22  E-value=0.012  Score=57.82  Aligned_cols=23  Identities=30%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -++|.||||+||+|.++.|++.+
T Consensus        31 iI~llGpPGsGKgTqa~~L~~~~   53 (217)
T 3umf_A           31 VIFVLGGPGSGKGTQCEKLVQKF   53 (217)
T ss_dssp             EEEEECCTTCCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            46788999999999999999988

>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=95.19  E-value=0.014  Score=57.71  Aligned_cols=25  Identities=28%  Similarity=0.433  Sum_probs=22.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      -+.|.||||+|||++++.|++.|-.
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~~   52 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLVK   52 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTT
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhc
Confidence            6789999999999999999999754

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.19  E-value=0.059  Score=56.94  Aligned_cols=34  Identities=24%  Similarity=0.177  Sum_probs=27.0

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcce
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHY  691 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li  691 (710)
                      +...++|+||+|+|||++++.||..+-.....+.
T Consensus       156 ~g~vi~lvG~nGsGKTTll~~Lag~l~~~~G~V~  189 (359)
T 2og2_A          156 KPAVIMIVGVNGGGKTTSLGKLAHRLKNEGTKVL  189 (359)
T ss_dssp             SSEEEEEECCTTSCHHHHHHHHHHHHHHTTCCEE
T ss_pred             CCeEEEEEcCCCChHHHHHHHHHhhccccCCEEE
Confidence            3357899999999999999999999765444333

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.18  E-value=0.013  Score=59.23  Aligned_cols=26  Identities=31%  Similarity=0.450  Sum_probs=23.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      +.++++||+|+|||++.++|+..+-.
T Consensus        26 ~~v~i~Gp~GsGKSTll~~l~g~~~~   51 (261)
T 2eyu_A           26 GLILVTGPTGSGKSTTIASMIDYINQ   51 (261)
T ss_dssp             EEEEEECSTTCSHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCccHHHHHHHHHHhCCC
Confidence            57899999999999999999998743

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=95.17  E-value=0.0087  Score=61.48  Aligned_cols=25  Identities=24%  Similarity=0.353  Sum_probs=21.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+||||+||||+++.|+..+
T Consensus        33 ~~livl~G~sGsGKSTla~~L~~~~   57 (287)
T 1gvn_B           33 PTAFLLGGQPGSGKTSLRSAIFEET   57 (287)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3457899999999999999999876

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=95.16  E-value=0.0089  Score=57.30  Aligned_cols=25  Identities=16%  Similarity=0.199  Sum_probs=20.7

Q ss_pred             CcEEEcCCCChHH-HHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKT-AIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT-~la~~la~~l~~  337 (710)
                      =.+++||.|+||| +|++++.+....
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~   47 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIA   47 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHc
Confidence            3578999999999 888888877654

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=95.16  E-value=0.0073  Score=57.05  Aligned_cols=25  Identities=36%  Similarity=0.344  Sum_probs=18.4

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+|+||+||||+++.|++.+
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            3458899999999999999999887

>1znw_A Guanylate kinase, GMP kinase; ATP:GMP-phosphotransferase, TR; 2.10A {Mycobacterium tuberculosis} SCOP: c.37.1.1 PDB: 1znx_A* 1zny_A* 1znz_A* 1s4q_A 1z8f_A

Probab=95.13  E-value=0.01  Score=57.67  Aligned_cols=23  Identities=26%  Similarity=0.603  Sum_probs=21.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.|.||+|+|||+|.++|+..+
T Consensus        22 i~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           22 VVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            67899999999999999999986

>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=95.09  E-value=0.012  Score=57.36  Aligned_cols=35  Identities=23%  Similarity=0.120  Sum_probs=26.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ..++++||||+|||++++.+|. -  .....+-++..+
T Consensus        21 ~~~~i~G~~GsGKTtl~~~l~~-~--~~~~v~~i~~~~   55 (220)
T 2cvh_A           21 VLTQVYGPYASGKTTLALQTGL-L--SGKKVAYVDTEG   55 (220)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHH-H--HCSEEEEEESSC
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-H--cCCcEEEEECCC
Confidence            3789999999999999999998 2  233445555443

>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=95.08  E-value=0.018  Score=59.75  Aligned_cols=38  Identities=24%  Similarity=0.192  Sum_probs=27.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc--CCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF--GSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf--g~~~~li~~d~se  697 (710)
                      ..+.+.||+|+|||+|++.|+..+-  .+......+++..
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~~~~~~G~i~vi~~d~  120 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDG  120 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHhhCCCCCeEEEEecCC
Confidence            3678999999999999999999875  3333344444443

>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=95.08  E-value=0.017  Score=61.03  Aligned_cols=26  Identities=38%  Similarity=0.547  Sum_probs=22.4

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+.|+||+|+|||+|++.++..+
T Consensus       130 ~G~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          130 TQAITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHh
Confidence            44557899999999999999998765

>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=95.08  E-value=0.013  Score=55.33  Aligned_cols=28  Identities=18%  Similarity=0.300  Sum_probs=25.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      +-.+++||+|+|||+|.+||.-.|++..
T Consensus        27 g~~~i~G~NGsGKStll~ai~~~l~~~~   54 (182)
T 3kta_A           27 GFTAIVGANGSGKSNIGDAILFVLGGLS   54 (182)
T ss_dssp             SEEEEEECTTSSHHHHHHHHHHHTTCCC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHcCCc
Confidence            4678999999999999999999988754

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.06  E-value=0.03  Score=58.28  Aligned_cols=27  Identities=26%  Similarity=0.309  Sum_probs=22.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +.-++|.|+||+|||+++..++..+..
T Consensus        68 G~l~li~G~pG~GKTtl~l~ia~~~a~   94 (315)
T 3bh0_A           68 RNFVLIAARPSMGKTAFALKQAKNMSD   94 (315)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHH
Confidence            445789999999999999999977654

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=95.06  E-value=0.015  Score=57.65  Aligned_cols=37  Identities=16%  Similarity=0.116  Sum_probs=26.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ..++++||||+|||++|..+|..+-..+...+-++..
T Consensus        24 ~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e   60 (247)
T 2dr3_A           24 NVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALE   60 (247)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            3789999999999999998887654434444444433

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=95.05  E-value=0.013  Score=57.75  Aligned_cols=23  Identities=22%  Similarity=0.369  Sum_probs=21.3

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|.|+||+||||+++.|++.+
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            37899999999999999999988

>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=95.05  E-value=0.015  Score=65.83  Aligned_cols=34  Identities=21%  Similarity=0.258  Sum_probs=26.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .++|.|+||+|||++|++||+.|+..+...+.+|
T Consensus        54 lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lD   87 (630)
T 1x6v_B           54 TVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   87 (630)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEES
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            7899999999999999999999864333344443

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=95.03  E-value=0.015  Score=73.66  Aligned_cols=39  Identities=18%  Similarity=0.135  Sum_probs=31.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++||||||||||+||.++|......+...+-++..+.
T Consensus      1428 ~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~ 1466 (2050)
T 3cmu_A         1428 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHA 1466 (2050)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccc
Confidence            489999999999999999999987665555666665554

>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=95.01  E-value=0.012  Score=62.92  Aligned_cols=30  Identities=23%  Similarity=0.303  Sum_probs=25.2

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ...+..++|+||+|+||||+++.++..+..
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~~l~~~~~~  162 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIASMIDYINQ  162 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHHHHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHHHHHHhhcCc
Confidence            345567899999999999999999988753

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.01  E-value=0.011  Score=57.94  Aligned_cols=23  Identities=43%  Similarity=0.910  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.|+||+|+|||+|++.|+..+
T Consensus        25 ~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           25 PLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            57899999999999999999976

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=94.99  E-value=0.01  Score=56.17  Aligned_cols=25  Identities=32%  Similarity=0.587  Sum_probs=21.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-++|+||+|+|||||++.|+..+
T Consensus         5 g~~i~i~GpsGsGKSTL~~~L~~~~   29 (180)
T 1kgd_A            5 RKTLVLLGAHGVGRRHIKNTLITKH   29 (180)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3457899999999999999998865

>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=94.97  E-value=0.036  Score=59.15  Aligned_cols=23  Identities=30%  Similarity=0.543  Sum_probs=21.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -++|.||+|+|||+|+..|++.+
T Consensus         4 ~i~i~GptgsGKttla~~La~~~   26 (409)
T 3eph_A            4 VIVIAGTTGVGKSQLSIQLAQKF   26 (409)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH
T ss_pred             EEEEECcchhhHHHHHHHHHHHC
Confidence            36789999999999999999988

>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=94.95  E-value=0.04  Score=57.02  Aligned_cols=26  Identities=31%  Similarity=0.360  Sum_probs=22.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      .-++|+|++|+||||++..||..+..
T Consensus       105 ~vi~ivG~~GsGKTTl~~~LA~~l~~  130 (306)
T 1vma_A          105 FVIMVVGVNGTGKTTSCGKLAKMFVD  130 (306)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCChHHHHHHHHHHHHHh
Confidence            34789999999999999999988854

>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=94.94  E-value=0.012  Score=57.66  Aligned_cols=25  Identities=40%  Similarity=0.420  Sum_probs=22.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..+.++||+|+|||+|++.|+..+.
T Consensus        26 ~~~~l~G~nGsGKSTll~~l~g~~~   50 (231)
T 4a74_A           26 AITEVFGEFGSGKTQLAHTLAVMVQ   50 (231)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHh
Confidence            4688999999999999999998643

>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=94.94  E-value=0.14  Score=48.90  Aligned_cols=25  Identities=28%  Similarity=0.271  Sum_probs=18.6

Q ss_pred             CCCcEEEcCCCChHHHHH-HHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIA-EGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la-~~la~~l  335 (710)
                      +.++++.+|+|+|||..+ ..+...+
T Consensus        38 ~~~~li~~~TGsGKT~~~~~~~~~~l   63 (207)
T 2gxq_A           38 GKDLIGQARTGTGKTLAFALPIAERL   63 (207)
T ss_dssp             TCCEEEECCTTSCHHHHHHHHHHHHC
T ss_pred             CCCEEEECCCCChHHHHHHHHHHHHH
Confidence            468999999999999764 3444444

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=94.94  E-value=0.016  Score=55.67  Aligned_cols=23  Identities=22%  Similarity=0.550  Sum_probs=21.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|.|++|+||||+++.|++.+
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l   24 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKL   24 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCccCHHHHHHHHHHhc
Confidence            37899999999999999999988

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=94.91  E-value=0.012  Score=56.79  Aligned_cols=24  Identities=29%  Similarity=0.158  Sum_probs=22.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|.|+||+||||+++.|++.+
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l   28 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWI   28 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHH
Confidence            357899999999999999999988

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=94.89  E-value=0.019  Score=56.73  Aligned_cols=38  Identities=16%  Similarity=0.138  Sum_probs=27.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH-cC-----CCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY-FG-----SVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l-fg-----~~~~li~~d~se  697 (710)
                      ..++++||||+|||+|++.+|... ..     .....+.++..+
T Consensus        25 ~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           25 SITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            378999999999999999999863 21     134456666544

>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=94.88  E-value=0.02  Score=60.48  Aligned_cols=38  Identities=18%  Similarity=0.032  Sum_probs=29.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ..++++||||||||+|+..+|..+-......+-+|..+
T Consensus        62 ~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~   99 (356)
T 3hr8_A           62 RIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEH   99 (356)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEeccc
Confidence            47899999999999999999988654444455555544

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=94.87  E-value=0.021  Score=54.26  Aligned_cols=24  Identities=33%  Similarity=0.285  Sum_probs=21.7

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++|.|++|+||||+++.|++.+..
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~   26 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQ   26 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            689999999999999999998843

>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=94.84  E-value=0.018  Score=59.98  Aligned_cols=112  Identities=15%  Similarity=0.098  Sum_probs=0.0

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccC----------------ceEEEeehhhh---------------
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS----------------KRIMSLDMGLL---------------  357 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~----------------~~v~~ld~~~l---------------  357 (710)
                      +.+..++|+|+||+|||+++..++...       .+..                ..+++++....               
T Consensus        96 ~~g~i~~i~G~~gsGKT~la~~la~~~-------~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~~~~~~~l~~~~~~~g~  168 (322)
T 2i1q_A           96 ESQSVTEFAGVFGSGKTQIMHQSCVNL-------QNPEFLFYDEEAVSKGEVAQPKAVYIDTEGTFRPERIMQMAEHAGI  168 (322)
T ss_dssp             ETTEEEEEEESTTSSHHHHHHHHHHHT-------TCGGGEECCTTTSCTTTTSSEEEEEEESSSCCCHHHHHHHHHHHTC
T ss_pred             cCCeEEEEECCCCCCHHHHHHHHHHHH-------hccccccccccccccCCCCCceEEEEECCCCCCHHHHHHHHHHcCC


Q ss_pred             ----------hhccccCccHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCCh------HhHHHhhccccc
Q 005179          358 ----------MAGAKERGELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTG------LDISNLLKPSLG  420 (710)
Q Consensus       358 ----------~~g~~~~g~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~------~~~~~~L~~~l~  420 (710)
                                +.......+....+..+...+.. .+..+|+||.+..+......+.+  ...      ..+...|+.+..
T Consensus       169 ~~~~~~~~l~~~~~~~~~~~~~~l~~l~~~~~~~~~~~lvVIDsl~~l~~~~~~~~~--~~~~r~~~~~~~~~~L~~la~  246 (322)
T 2i1q_A          169 DGQTVLDNTFVARAYNSDMQMLFAEKIEDLIQEGNNIKLVVIDSLTSTFRNEYTGRG--KLAERQQKLGRHMATLNKLAD  246 (322)
T ss_dssp             CHHHHHHTEEEEECSSHHHHHHHHHTHHHHHHTTCEEEEEEEECSSHHHHHHCCCTT--SHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHhcCEEEEeCCCHHHHHHHHHHHHHHHhhccCccEEEEECcHHHHHHHhcCCc--cHHHHHHHHHHHHHHHHHHHH


Q ss_pred             CCCeEEEEc
Q 005179          421 RGELQCIAS  429 (710)
Q Consensus       421 ~~~v~vI~a  429 (710)
                      +.++.+|.+
T Consensus       247 ~~~~~vi~~  255 (322)
T 2i1q_A          247 LFNCVVLVT  255 (322)
T ss_dssp             HTTCEEEEE
T ss_pred             HhCCEEEEE

>2ffh_A Protein (FFH); SRP54, signal recognition particle, GTPase, M domain, RNA-binding, signal sequence-binding, helix-turn-helix, protein targeting; 3.20A {Thermus aquaticus} SCOP: a.24.13.1 a.36.1.1 c.37.1.10 PDB: 2iy3_A

Probab=94.81  E-value=0.19  Score=54.31  Aligned_cols=41  Identities=29%  Similarity=0.306  Sum_probs=33.1

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +...++|+||+|+|||+++..||..+-........+|..-+
T Consensus        97 ~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D~~  137 (425)
T 2ffh_A           97 DRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQ  137 (425)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECCSS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeecccc
Confidence            34578899999999999999999998776666666666544

>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=94.80  E-value=0.016  Score=58.20  Aligned_cols=37  Identities=16%  Similarity=0.285  Sum_probs=27.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCC------CCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGS------VRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~------~~~li~~d~se~  698 (710)
                      .+.+.||+|+|||++|+.||+.| |-      ....+.+++..|
T Consensus        24 iI~I~G~~GSGKST~a~~L~~~l-g~~~~d~~~~~~~~i~~D~~   66 (252)
T 1uj2_A           24 LIGVSGGTASGKSSVCAKIVQLL-GQNEVDYRQKQVVILSQDSF   66 (252)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT-TGGGSCGGGCSEEEEEGGGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh-hhhcccccCCceEEEecCcc
Confidence            68899999999999999999974 31      122345666655

>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=94.80  E-value=0.0093  Score=57.30  Aligned_cols=25  Identities=20%  Similarity=0.108  Sum_probs=21.1

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+++||.|+||||.+..++.++...
T Consensus        11 ~v~~G~mgsGKTT~ll~~a~r~~~~   35 (191)
T 1xx6_A           11 EVIVGPMYSGKSEELIRRIRRAKIA   35 (191)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHC
Confidence            5788999999999999888887543

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=94.79  E-value=0.038  Score=53.27  Aligned_cols=42  Identities=19%  Similarity=0.155  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHcC---CCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          296 ETEIQRIIQILCRR---TKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       296 ~~~i~~l~~~L~~~---~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++.++.+.+.+...   .+.-+.|+|++|+||||+++.|+..+..
T Consensus         4 ~~~~~~l~~~~~~~~~~~~~~i~i~G~~GsGKstl~~~l~~~~~~   48 (201)
T 1rz3_A            4 RDRIDFLCKTILAIKTAGRLVLGIDGLSRSGKTTLANQLSQTLRE   48 (201)
T ss_dssp             HHHHHHHHHHHHTSCCSSSEEEEEEECTTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccCCCeEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            44566666655432   2233678999999999999999988743

>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=94.79  E-value=0.014  Score=56.25  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=20.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.|+|++|+||||+++.|+. +
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            478999999999999999998 6

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=94.77  E-value=0.014  Score=56.55  Aligned_cols=26  Identities=15%  Similarity=0.095  Sum_probs=22.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      +..++|+|++|+||||+++.|++.+.
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~   35 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLK   35 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            34578999999999999999999874

>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=94.76  E-value=0.026  Score=61.16  Aligned_cols=38  Identities=26%  Similarity=0.204  Sum_probs=29.7

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ...++|+||+|+|||+++..||..+-..+.....++..
T Consensus        97 ~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~D  134 (433)
T 3kl4_A           97 PFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAAD  134 (433)
T ss_dssp             SEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecC
Confidence            35899999999999999999999886655555444443

>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=94.75  E-value=0.014  Score=56.49  Aligned_cols=27  Identities=19%  Similarity=0.192  Sum_probs=23.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +..++|+|++|+||||+++.|++.+..
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~~   35 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALCA   35 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            456889999999999999999998743

>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=94.74  E-value=0.017  Score=56.56  Aligned_cols=24  Identities=25%  Similarity=0.369  Sum_probs=21.9

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.|+|++|+||||+++.|+..+
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            357899999999999999999887

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=94.74  E-value=0.016  Score=55.87  Aligned_cols=25  Identities=28%  Similarity=0.383  Sum_probs=21.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..+.|+||+|+|||||++.|+..+
T Consensus         4 g~~i~lvGpsGaGKSTLl~~L~~~~   28 (198)
T 1lvg_A            4 PRPVVLSGPSGAGKSTLLKKLFQEH   28 (198)
T ss_dssp             -CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            4568999999999999999998876

>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=94.73  E-value=0.03  Score=60.87  Aligned_cols=37  Identities=27%  Similarity=0.220  Sum_probs=28.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ..++|+||||+|||+++..||..+-..+.....+|+.
T Consensus       100 ~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D  136 (432)
T 2v3c_C          100 NVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAAD  136 (432)
T ss_dssp             CCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEecc
Confidence            4799999999999999999999875433444545544

>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=94.72  E-value=0.012  Score=57.32  Aligned_cols=26  Identities=31%  Similarity=0.307  Sum_probs=22.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-++|+||+|+||||+++.|+..+
T Consensus         7 ~g~~i~l~GpsGsGKsTl~~~L~~~~   32 (208)
T 3tau_A            7 RGLLIVLSGPSGVGKGTVREAVFKDP   32 (208)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHST
T ss_pred             CCcEEEEECcCCCCHHHHHHHHHhhC
Confidence            34457899999999999999998865

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=94.69  E-value=0.019  Score=57.70  Aligned_cols=22  Identities=41%  Similarity=0.674  Sum_probs=20.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .+.+.||+|+|||++++.||+.
T Consensus        29 ~I~I~G~~GsGKSTl~k~La~~   50 (252)
T 4e22_A           29 VITVDGPSGAGKGTLCKALAES   50 (252)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            6889999999999999999955

>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=94.69  E-value=0.021  Score=60.51  Aligned_cols=39  Identities=26%  Similarity=0.354  Sum_probs=28.9

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC--CCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS--VRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~--~~~li~~d~se~  698 (710)
                      +.+++.||+|+|||++.++|+..+-..  +..++.-|--++
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~  164 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEF  164 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHh
Confidence            578999999999999999999987643  333344444444

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=94.64  E-value=0.016  Score=56.26  Aligned_cols=39  Identities=23%  Similarity=0.302  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          298 EIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       298 ~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .++++.+.+..  ..+.-+.|+||+|+|||||++.|+..+.
T Consensus         7 ~~~~~~~~~~~~~~~g~~v~I~G~sGsGKSTl~~~l~~~~~   47 (208)
T 3c8u_A            7 LCQGVLERLDPRQPGRQLVALSGAPGSGKSTLSNPLAAALS   47 (208)
T ss_dssp             HHHHHHHHSCTTCCSCEEEEEECCTTSCTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCeEEEEECCCCCCHHHHHHHHHHHHh
Confidence            33444444332  2334567999999999999999999885

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=94.64  E-value=0.082  Score=50.88  Aligned_cols=25  Identities=32%  Similarity=0.272  Sum_probs=20.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.++++.+|+|+|||.++..++...
T Consensus        48 ~~~~li~~~tGsGKT~~~~~~~~~~   72 (216)
T 3b6e_A           48 GKNIIICLPTGSGKTRVAVYIAKDH   72 (216)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCHHHHHHHHHHHH
Confidence            4689999999999999887776544

>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=94.62  E-value=0.026  Score=53.12  Aligned_cols=27  Identities=33%  Similarity=0.351  Sum_probs=23.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +..++|+|++|+||||+++.|+..+..
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~   31 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVC   31 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            445789999999999999999998743

>2bbw_A Adenylate kinase 4, AK4; nucleotide kinase, nucleotide binding, human, structura genomics, structural genomics consortium, SGC, transferase; HET: GP5; 2.05A {Homo sapiens} PDB: 2ar7_A* 3ndp_A

Probab=94.59  E-value=0.017  Score=57.73  Aligned_cols=25  Identities=24%  Similarity=0.477  Sum_probs=22.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..+.|+||+|+||||+++.|++.+
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~l   51 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNF   51 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            4568999999999999999999887

>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=94.57  E-value=0.028  Score=58.85  Aligned_cols=38  Identities=29%  Similarity=0.347  Sum_probs=28.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .++++||+|+|||+|.++|+..+-.++..+..-+..++
T Consensus       173 ~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~~~e~  210 (330)
T 2pt7_A          173 NVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEI  210 (330)
T ss_dssp             CEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEESSCCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECCeecc
Confidence            78999999999999999999987665544433333343

>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=94.57  E-value=0.031  Score=60.46  Aligned_cols=32  Identities=28%  Similarity=0.255  Sum_probs=26.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcce
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHY  691 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li  691 (710)
                      +.+++.||+|+|||++.++|+..+-.....++
T Consensus       168 gii~I~GpnGSGKTTlL~allg~l~~~~g~I~  199 (418)
T 1p9r_A          168 GIILVTGPTGSGKSTTLYAGLQELNSSERNIL  199 (418)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHCCTTSCEE
T ss_pred             CeEEEECCCCCCHHHHHHHHHhhcCCCCCEEE
Confidence            56899999999999999999999866544333

>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=94.57  E-value=0.093  Score=55.44  Aligned_cols=26  Identities=27%  Similarity=0.532  Sum_probs=22.8

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..+.|+|+||+||||++..|+..+..
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~  105 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIE  105 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            45789999999999999999988754

>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=94.56  E-value=0.015  Score=60.88  Aligned_cols=26  Identities=31%  Similarity=0.405  Sum_probs=23.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.+++|+||+|+||||+++.|+..+
T Consensus       170 ~g~~v~i~G~~GsGKTTll~~l~g~~  195 (330)
T 2pt7_A          170 IGKNVIVCGGTGSGKTTYIKSIMEFI  195 (330)
T ss_dssp             HTCCEEEEESTTSCHHHHHHHGGGGS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            45689999999999999999998765

>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=94.54  E-value=0.018  Score=62.44  Aligned_cols=33  Identities=12%  Similarity=0.091  Sum_probs=26.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      -++++||||+|||++|+.|++.+     ....++..++
T Consensus       260 lIil~G~pGSGKSTla~~L~~~~-----~~~~i~~D~~  292 (416)
T 3zvl_A          260 VVVAVGFPGAGKSTFIQEHLVSA-----GYVHVNRDTL  292 (416)
T ss_dssp             EEEEESCTTSSHHHHHHHHTGGG-----TCEECCGGGS
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc-----CcEEEccchH
Confidence            78999999999999999999874     2555665554

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=94.54  E-value=0.02  Score=59.85  Aligned_cols=23  Identities=22%  Similarity=0.403  Sum_probs=21.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|.||+|+|||+++..|++.+
T Consensus         9 lI~I~GptgSGKTtla~~La~~l   31 (340)
T 3d3q_A            9 LIVIVGPTASGKTELSIEVAKKF   31 (340)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHT
T ss_pred             eEEEECCCcCcHHHHHHHHHHHc
Confidence            47899999999999999999988

>2v54_A DTMP kinase, thymidylate kinase; nucleotide biosynthesis, ATP-binding, nucleotide-binding, poxvirus, transferase; HET: TYD POP; 2.4A {Vaccinia virus copenhagen} PDB: 2w0s_A*

Probab=94.51  E-value=0.014  Score=56.08  Aligned_cols=25  Identities=20%  Similarity=0.143  Sum_probs=22.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|.|++|+||||+++.|++.+
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            4468899999999999999999876

>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=94.51  E-value=0.022  Score=54.70  Aligned_cols=23  Identities=26%  Similarity=0.309  Sum_probs=21.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.|+|++|+||||+++.|++.+
T Consensus        14 iIgltG~~GSGKSTva~~L~~~l   36 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKY   36 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhc
Confidence            47799999999999999999987

>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=94.49  E-value=0.11  Score=57.32  Aligned_cols=72  Identities=14%  Similarity=0.194  Sum_probs=43.3

Q ss_pred             eEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc---CCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCH
Q 005179          384 VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG---RGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQ  459 (710)
Q Consensus       384 ~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~---~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~  459 (710)
                      .+|+|||++.++...         ..++.+.|..+..   .-.+.+|.+|....   .-.++..++..|. .|-+...+.
T Consensus       299 ivlvIDE~~~ll~~~---------~~~~~~~l~~Lar~gRa~GI~LIlaTQrp~---~dvl~~~i~~n~~~RI~lrv~s~  366 (512)
T 2ius_A          299 IVVLVDEFADLMMTV---------GKKVEELIARLAQKARAAGIHLVLATQRPS---VDVITGLIKANIPTRIAFTVSSK  366 (512)
T ss_dssp             EEEEEETHHHHHHHH---------HHHHHHHHHHHHHHCGGGTEEEEEEESCCC---TTTSCHHHHHHCCEEEEECCSSH
T ss_pred             EEEEEeCHHHHHhhh---------hHHHHHHHHHHHHHhhhCCcEEEEEecCCc---cccccHHHHhhcCCeEEEEcCCH
Confidence            589999998886421         1233344433332   22466666665542   1135667777775 678888888


Q ss_pred             HHHHHHHH
Q 005179          460 EDAVRILL  467 (710)
Q Consensus       460 ~~~~~IL~  467 (710)
                      .+...|+.
T Consensus       367 ~dsr~ilg  374 (512)
T 2ius_A          367 IDSRTILD  374 (512)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHhcC
Confidence            88776664

>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=94.49  E-value=0.019  Score=55.39  Aligned_cols=26  Identities=31%  Similarity=0.565  Sum_probs=22.5

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-++|+||+|+|||||++.|+...
T Consensus        18 ~g~~ivl~GPSGaGKsTL~~~L~~~~   43 (197)
T 3ney_A           18 GRKTLVLIGASGVGRSHIKNALLSQN   43 (197)
T ss_dssp             SCCEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CCCEEEEECcCCCCHHHHHHHHHhhC
Confidence            44567899999999999999999775

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=94.49  E-value=0.025  Score=56.00  Aligned_cols=23  Identities=30%  Similarity=0.531  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.+.||+|+|||++++.||+.|
T Consensus        18 ~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           18 QIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             EEEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            68899999999999999999864

>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=94.45  E-value=0.062  Score=58.55  Aligned_cols=27  Identities=33%  Similarity=0.454  Sum_probs=23.1

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+..++|+|++|+|||+|+..++....
T Consensus       150 kGq~~~i~G~sGvGKTtL~~~l~~~~~  176 (473)
T 1sky_E          150 KGGKIGLFGGAGVGKTVLIQELIHNIA  176 (473)
T ss_dssp             TTCEEEEECCSSSCHHHHHHHHHHHHH
T ss_pred             cCCEEEEECCCCCCccHHHHHHHhhhh
Confidence            345689999999999999999987764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.45  E-value=0.072  Score=58.92  Aligned_cols=37  Identities=27%  Similarity=0.338  Sum_probs=26.7

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      +...++|+|+||||||+++..||..+-..+.....++
T Consensus       100 ~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd  136 (504)
T 2j37_W          100 KQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLIC  136 (504)
T ss_dssp             --EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEe
Confidence            3458999999999999999999988753333333333

>2ewv_A Twitching motility protein PILT; pilus retraction motor, ATPase, hexameric PILT, protein TRAN; HET: ADP; 2.80A {Aquifex aeolicus} PDB: 2eww_A* 2gsz_A*

Probab=94.44  E-value=0.025  Score=60.35  Aligned_cols=27  Identities=30%  Similarity=0.452  Sum_probs=24.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      +.++++||+|+|||++.++|+..+-..
T Consensus       137 ~~i~ivG~~GsGKTTll~~l~~~~~~~  163 (372)
T 2ewv_A          137 GLILVTGPTGSGKSTTIASMIDYINQT  163 (372)
T ss_dssp             EEEEEECSSSSSHHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhcCcC
Confidence            578999999999999999999987543

>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=94.42  E-value=0.019  Score=56.35  Aligned_cols=23  Identities=26%  Similarity=0.514  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -+.+.||+|+|||+|.++|+..+
T Consensus        18 ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           18 LYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhccC
Confidence            67899999999999999999985

>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=94.39  E-value=0.025  Score=59.86  Aligned_cols=38  Identities=18%  Similarity=0.158  Sum_probs=29.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ..++++||||+|||+||..+|..+-..+...+-+|..+
T Consensus        64 ~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~  101 (356)
T 1u94_A           64 RIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH  101 (356)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCC
Confidence            37899999999999999999987654444566666544

>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=94.39  E-value=0.047  Score=56.33  Aligned_cols=79  Identities=18%  Similarity=0.223  Sum_probs=45.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-------hccc-------cCccHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-------AGAK-------ERGELEARVTTLISEI  378 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-------~g~~-------~~g~~e~~l~~~~~~~  378 (710)
                      -++|+||||+|||+|+..++.......     .+..+.++|...-.       .|..       .....++..-.+++.+
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~g-----~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~l  104 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQY-----PDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQL  104 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHHC-----TTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhcC-----CCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHHH
Confidence            468999999999999888776664320     02344445432111       0000       0112333302233333


Q ss_pred             ---HhcCCeEEEEccchhhhh
Q 005179          379 ---QKSGDVILFIDEVHTLIG  396 (710)
Q Consensus       379 ---~~~~~~IL~IDEid~l~~  396 (710)
                         +...+.+|+||=|..+..
T Consensus       105 ~~i~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          105 DAIERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             HTCCTTCCEEEEEECSTTCBC
T ss_pred             HHhhccCceEEEEeccccccc
Confidence               455689999999999974

>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=94.38  E-value=0.03  Score=57.05  Aligned_cols=24  Identities=38%  Similarity=0.393  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .++++||||+|||+|++.+|..+-
T Consensus        32 i~~i~G~~GsGKTtl~~~l~~~~~   55 (279)
T 1nlf_A           32 VGALVSPGGAGKSMLALQLAAQIA   55 (279)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHh
Confidence            789999999999999999997654

>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=94.37  E-value=0.25  Score=48.75  Aligned_cols=19  Identities=21%  Similarity=0.174  Sum_probs=16.1

Q ss_pred             CCCcEEEcCCCChHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAE  329 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~  329 (710)
                      +.++++.+|+|+|||....
T Consensus        66 g~~~l~~apTGsGKT~~~~   84 (242)
T 3fe2_A           66 GLDMVGVAQTGSGKTLSYL   84 (242)
T ss_dssp             TCCEEEEECTTSCHHHHHH
T ss_pred             CCCEEEECCCcCHHHHHHH
Confidence            4689999999999997643

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.35  E-value=0.013  Score=57.80  Aligned_cols=23  Identities=30%  Similarity=0.540  Sum_probs=15.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHH-HHH
Q 005179          661 AMLFCGPTGVGKTELAKSLA-ACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA-~~l  683 (710)
                      .+.|.||+|+|||++++.|+ ..+
T Consensus        29 ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           29 ILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             EEEEECSCC----CHHHHHHC---
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCC
Confidence            57899999999999999999 764

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=94.35  E-value=0.1  Score=57.78  Aligned_cols=26  Identities=31%  Similarity=0.386  Sum_probs=23.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..++|+|++|+||||++..|+..+..
T Consensus       102 ~vI~ivG~~GvGKTTl~~kLA~~l~~  127 (504)
T 2j37_W          102 NVIMFVGLQGSGKTTTCSKLAYYYQR  127 (504)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            45789999999999999999988854

>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=94.34  E-value=0.065  Score=55.18  Aligned_cols=40  Identities=25%  Similarity=0.204  Sum_probs=31.5

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ...++++||+|+|||+++..||..+-..+.....+|...+
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~~g~~v~l~~~D~~  137 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKKKGFKVGLVGADVY  137 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHHTTCCEEEEECCCS
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEecCCC
Confidence            3478899999999999999999998655555666665544

>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=94.34  E-value=0.019  Score=54.63  Aligned_cols=22  Identities=36%  Similarity=0.542  Sum_probs=19.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~  334 (710)
                      .++|+||+|+||||+++.|+..
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~   25 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQ   25 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHhcc
Confidence            3689999999999999999863

>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=94.31  E-value=0.024  Score=58.02  Aligned_cols=21  Identities=29%  Similarity=0.499  Sum_probs=19.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAA  681 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~  681 (710)
                      .+.+.||+|+|||++|+.|++
T Consensus        77 iI~I~G~~GSGKSTva~~La~   97 (281)
T 2f6r_A           77 VLGLTGISGSGKSSVAQRLKN   97 (281)
T ss_dssp             EEEEEECTTSCHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            689999999999999999995

>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=94.31  E-value=0.025  Score=56.09  Aligned_cols=25  Identities=28%  Similarity=0.450  Sum_probs=22.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..+.|.||+|+||||+++.|++.+
T Consensus         9 ~~~i~i~G~~GsGKsTla~~la~~l   33 (233)
T 3r20_A            9 SLVVAVDGPAGTGKSSVSRGLARAL   33 (233)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHh
Confidence            3458899999999999999999988

>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=94.30  E-value=0.025  Score=54.48  Aligned_cols=23  Identities=26%  Similarity=0.354  Sum_probs=21.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.|.|++|+||||+++.|+..+
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            57899999999999999999988

>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=94.29  E-value=0.028  Score=59.38  Aligned_cols=38  Identities=21%  Similarity=0.162  Sum_probs=28.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ..++++||||+|||+||..+|..+-..+...+-++..+
T Consensus        62 ~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~   99 (349)
T 2zr9_A           62 RVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEH   99 (349)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            36899999999999999999977654444455555543

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.28  E-value=0.049  Score=59.18  Aligned_cols=42  Identities=21%  Similarity=0.312  Sum_probs=33.7

Q ss_pred             CCCeEEEEEcCCCCcHHHHHHHHHHHHcCC-CCcceeeCCCCC
Q 005179          657 RPTAAMLFCGPTGVGKTELAKSLAACYFGS-VRIHYLFFPSPF  698 (710)
Q Consensus       657 rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~-~~~li~~d~se~  698 (710)
                      ++...++|+|++|+|||+++-.||..|-.. +.....+|+..+
T Consensus        98 ~~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~~  140 (433)
T 2xxa_A           98 QPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADVY  140 (433)
T ss_dssp             SSSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCCS
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCCC
Confidence            445689999999999999999999998655 566666666655

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=94.27  E-value=0.021  Score=54.98  Aligned_cols=26  Identities=27%  Similarity=0.266  Sum_probs=22.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..+.|+||+|+||||+++.|+..+
T Consensus         5 ~g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            5 KGLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            34567899999999999999998765

>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=94.25  E-value=0.028  Score=58.03  Aligned_cols=23  Identities=35%  Similarity=0.596  Sum_probs=22.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.++||+|+|||+|++.|+..+
T Consensus       128 ~vaIvGpsGsGKSTLl~lL~gl~  150 (305)
T 2v9p_A          128 CLAFIGPPNTGKSMLCNSLIHFL  150 (305)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCcHHHHHHHHhhhc
Confidence            68899999999999999999998

>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=94.23  E-value=0.036  Score=60.01  Aligned_cols=25  Identities=16%  Similarity=0.292  Sum_probs=21.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-++|+|+||+||||+++.|++.+
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~~~~  282 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHLVSA  282 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHTGGG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhc
Confidence            4457889999999999999998766

>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=94.22  E-value=0.68  Score=46.34  Aligned_cols=18  Identities=22%  Similarity=0.272  Sum_probs=15.7

Q ss_pred             CCcEEEcCCCChHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAE  329 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~  329 (710)
                      +++++.+|+|+|||..+.
T Consensus        92 ~~~lv~a~TGsGKT~~~~  109 (262)
T 3ly5_A           92 RDLLAAAKTGSGKTLAFL  109 (262)
T ss_dssp             CCCEECCCTTSCHHHHHH
T ss_pred             CcEEEEccCCCCchHHHH
Confidence            679999999999997644

>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=94.21  E-value=0.28  Score=53.73  Aligned_cols=25  Identities=36%  Similarity=0.469  Sum_probs=21.9

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      -+.|+|++|+||||+++.|+..+..
T Consensus       295 VI~LVGpNGSGKTTLl~~LAgll~~  319 (503)
T 2yhs_A          295 VILMVGVNGVGKTTTIGKLARQFEQ  319 (503)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCcccHHHHHHHHHHHhhh
Confidence            4679999999999999999988743

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=94.19  E-value=0.023  Score=54.61  Aligned_cols=25  Identities=32%  Similarity=0.422  Sum_probs=21.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-+.|+||+|+||||+++.|+..+
T Consensus         7 g~ii~l~Gp~GsGKSTl~~~L~~~~   31 (205)
T 3tr0_A            7 ANLFIISAPSGAGKTSLVRALVKAL   31 (205)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhC
Confidence            3457899999999999999998765

>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=94.13  E-value=0.028  Score=53.97  Aligned_cols=22  Identities=23%  Similarity=0.353  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .+.+.|++|+|||++|+.||+.
T Consensus        14 iIgltG~~GSGKSTva~~L~~~   35 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNK   35 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHh
Confidence            5779999999999999999997

>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=94.13  E-value=0.032  Score=57.89  Aligned_cols=26  Identities=27%  Similarity=0.282  Sum_probs=23.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..+.+.||+|+|||||++.|+..+-.
T Consensus        91 ~ivgI~G~sGsGKSTL~~~L~gll~~  116 (312)
T 3aez_A           91 FIIGVAGSVAVGKSTTARVLQALLAR  116 (312)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCchHHHHHHHHHhhccc
Confidence            36789999999999999999998753

>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=94.09  E-value=0.044  Score=60.65  Aligned_cols=58  Identities=9%  Similarity=-0.030  Sum_probs=38.8

Q ss_pred             hhHHhhhhcCCC-CcccCHHHHHHHHHHH--HcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          279 DLTARASEELID-PVIGRETEIQRIIQIL--CRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       279 ~l~~~~~~~~l~-~liGr~~~i~~l~~~L--~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+.+.++.|..- +..-+.+..+.+.+..  ....+.+++|+|.+|+||||++++|++++.
T Consensus       360 ~IR~~Lr~G~~~P~~f~rpeV~~vLr~~~~~~~~~~~~I~l~GlsGsGKSTIa~~La~~L~  420 (511)
T 1g8f_A          360 ELRRRLRVGGEIPEWFSYPEVVKILRESNPPRPKQGFSIVLGNSLTVSREQLSIALLSTFL  420 (511)
T ss_dssp             HHHHHHHHTCCCCTTTSCHHHHHHHHHHSCCGGGCCEEEEECTTCCSCHHHHHHHHHHHHT
T ss_pred             HHHHHHhCCCCCCccccChhhHHHHHHhcccccccceEEEecccCCCCHHHHHHHHHHHHH
Confidence            344456666543 3455554544444433  123446789999999999999999999994

>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=94.07  E-value=0.022  Score=55.03  Aligned_cols=21  Identities=38%  Similarity=0.284  Sum_probs=19.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .+.|+|++|+||||+++.|+.
T Consensus         4 ~i~l~G~~GsGKST~~~~La~   24 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD   24 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHH
Confidence            367999999999999999986

>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=94.05  E-value=0.036  Score=56.88  Aligned_cols=27  Identities=15%  Similarity=0.320  Sum_probs=23.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ..++++||||+|||+|++.||..+-..
T Consensus        36 ~~~~i~G~~G~GKTTl~~~ia~~~~~~   62 (296)
T 1cr0_A           36 EVIMVTSGSGMGKSTFVRQQALQWGTA   62 (296)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHH
Confidence            378899999999999999999987644

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=94.00  E-value=0.55  Score=45.91  Aligned_cols=19  Identities=21%  Similarity=0.200  Sum_probs=16.2

Q ss_pred             CCCcEEEcCCCChHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAE  329 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~  329 (710)
                      +.++++.+|+|+|||...-
T Consensus        62 ~~~~li~a~TGsGKT~~~~   80 (236)
T 2pl3_A           62 GKDVLGAAKTGSGKTLAFL   80 (236)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCCEEEEeCCCCcHHHHHH
Confidence            4789999999999998644

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.98  E-value=0.04  Score=58.50  Aligned_cols=33  Identities=30%  Similarity=0.267  Sum_probs=26.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .++++||+|+|||+|.++|+..+-.++. .|.++
T Consensus       177 ~i~ivG~sGsGKSTll~~l~~~~~~~~g-~I~ie  209 (361)
T 2gza_A          177 VIVVAGETGSGKTTLMKALMQEIPFDQR-LITIE  209 (361)
T ss_dssp             CEEEEESSSSCHHHHHHHHHTTSCTTSC-EEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCCCCce-EEEEC
Confidence            7899999999999999999998654443 44443

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=93.97  E-value=0.038  Score=55.07  Aligned_cols=23  Identities=17%  Similarity=0.284  Sum_probs=21.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.+.||+|+||||+++.|+..+
T Consensus        27 iigI~G~~GsGKSTl~k~L~~~l   49 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIMELL   49 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            57899999999999999999986

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=93.89  E-value=0.03  Score=54.79  Aligned_cols=26  Identities=27%  Similarity=0.377  Sum_probs=22.8

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+.|+||+|+|||||++.|+..+
T Consensus        22 ~G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           22 NIYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            45668899999999999999999866

>1uj2_A Uridine-cytidine kinase 2; alpha/beta mononucleotide-binding HOLD, transferase; HET: C5P ADP; 1.80A {Homo sapiens} SCOP: c.37.1.6 PDB: 1uei_A* 1uej_A* 1udw_A 1ufq_A* 1xrj_A*

Probab=93.88  E-value=0.029  Score=56.26  Aligned_cols=24  Identities=13%  Similarity=0.138  Sum_probs=21.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.|.|++|+||||+++.|++.+
T Consensus        23 ~iI~I~G~~GSGKST~a~~L~~~l   46 (252)
T 1uj2_A           23 FLIGVSGGTASGKSSVCAKIVQLL   46 (252)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh
Confidence            347899999999999999999977

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.82  E-value=0.03  Score=54.45  Aligned_cols=39  Identities=23%  Similarity=0.222  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          297 TEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..+.+...+.......++|+|.+|+||||++..++..+
T Consensus        16 ~~~~~~~~~~~~~~~~~i~i~G~~g~GKTTl~~~l~~~~   54 (221)
T 2wsm_A           16 RLAEKNREALRESGTVAVNIMGAIGSGKTLLIERTIERI   54 (221)
T ss_dssp             HHHHHHHHHHHHHTCEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhcccCceEEEEEcCCCCCHHHHHHHHHHHh
Confidence            344444444444556678999999999999999999876

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=93.81  E-value=0.091  Score=50.95  Aligned_cols=27  Identities=26%  Similarity=0.214  Sum_probs=24.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ..++|+|++|+|||+|+..|+..++..
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~~~~~~   57 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIERIGNE   57 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhccC
Confidence            478999999999999999999987654

>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=93.81  E-value=0.046  Score=61.67  Aligned_cols=26  Identities=19%  Similarity=0.318  Sum_probs=23.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..++|.|+||+|||++|++|++.|+.
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~  422 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQ  422 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcc
Confidence            37889999999999999999999873

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=93.78  E-value=0.035  Score=51.93  Aligned_cols=35  Identities=23%  Similarity=0.243  Sum_probs=26.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH---HcCCCCcceeeC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC---YFGSVRIHYLFF  694 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~---lfg~~~~li~~d  694 (710)
                      .++||.||+|+|||++|.+|.+.   |..++...++..
T Consensus        17 ~gvli~G~SGaGKStlal~L~~rG~~lvaDD~v~i~~~   54 (181)
T 3tqf_A           17 MGVLITGEANIGKSELSLALIDRGHQLVCDDVIDLKQE   54 (181)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHTTCEEEESSEEEEEES
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHcCCeEecCCEEEEEEe
Confidence            38999999999999999999884   333444444444

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=93.74  E-value=0.037  Score=58.04  Aligned_cols=109  Identities=19%  Similarity=0.188  Sum_probs=0.0

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh-------------------------------------
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL-------------------------------------  356 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~-------------------------------------  356 (710)
                      ++|.|+||+|||+++..+|..+...       +..+..+.+..                                     
T Consensus        49 iiIaG~pG~GKTt~al~ia~~~a~~-------g~~Vl~fSlEms~~ql~~Rlls~~~~v~~~~l~~g~Ls~~e~~~l~~a  121 (338)
T 4a1f_A           49 VIIGARPSMGKTSLMMNMVLSALND-------DRGVAVFSLEMSAEQLALRALSDLTSINMHDLESGRLDDDQWENLAKC  121 (338)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHHT-------TCEEEEEESSSCHHHHHHHHHHHHHCCCHHHHHHTCCCHHHHHHHHHH
T ss_pred             EEEEeCCCCCHHHHHHHHHHHHHHc-------CCeEEEEeCCCCHHHHHHHHHHHhhCCCHHHHhcCCCCHHHHHHHHHH


Q ss_pred             --------hhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEE
Q 005179          357 --------LMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCI  427 (710)
Q Consensus       357 --------l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI  427 (710)
                              +..-....-.+......+-...... +..++|||-++.+...+. ..+....-.++...|+.+..+-++.||
T Consensus       122 ~~~l~~~~l~I~d~~~~si~~i~~~ir~l~~~~gg~~lIVIDyLqlm~~~~~-~~~r~~ei~~isr~LK~lAkel~vpVi  200 (338)
T 4a1f_A          122 FDHLSQKKLFFYDKSYVRIEQIRLQLRKLKSQHKELGIAFIDYLQLMSGSKA-TKERHEQIAEISRELKTLARELEIPII  200 (338)
T ss_dssp             HHHHHHSCEEEECCTTCCHHHHHHHHHHHHHHCTTEEEEEEEEEECCCTHHH-HHHCCCCHHHHHHHHHHHHHHHTSCEE
T ss_pred             HHHHhcCCeEEeCCCCCcHHHHHHHHHHHHHhcCCCCEEEEechHHhcCCCC-CCChHHHHHHHHHHHHHHHHHcCCeEE


Q ss_pred             Ecc
Q 005179          428 AST  430 (710)
Q Consensus       428 ~at  430 (710)
                      +.+
T Consensus       201 ~ls  203 (338)
T 4a1f_A          201 ALV  203 (338)
T ss_dssp             EEE
T ss_pred             EEE

>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=93.70  E-value=0.036  Score=57.16  Aligned_cols=39  Identities=10%  Similarity=0.245  Sum_probs=27.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC--CCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS--VRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~--~~~li~~d~se~  698 (710)
                      |.++++||||+|||+|+-.++...-..  +...+-+|..+.
T Consensus        29 GiteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s   69 (333)
T 3io5_A           29 GLLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFG   69 (333)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccch
Confidence            567999999999999988777665321  334555565443

>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=93.70  E-value=0.026  Score=54.18  Aligned_cols=25  Identities=36%  Similarity=0.430  Sum_probs=21.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..++|+||+|+|||+++..|+++.
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g   58 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRG   58 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            3458999999999999999998765

>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=93.69  E-value=0.22  Score=48.59  Aligned_cols=19  Identities=26%  Similarity=0.321  Sum_probs=16.1

Q ss_pred             CCCcEEEcCCCChHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAE  329 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~  329 (710)
                      +.++++.+|+|+|||....
T Consensus        57 ~~~~l~~apTGsGKT~~~~   75 (228)
T 3iuy_A           57 GIDLIVVAQTGTGKTLSYL   75 (228)
T ss_dssp             TCCEEEECCTTSCHHHHHH
T ss_pred             CCCEEEECCCCChHHHHHH
Confidence            5789999999999997543

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=93.68  E-value=0.14  Score=58.63  Aligned_cols=39  Identities=23%  Similarity=0.427  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          297 TEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       297 ~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      .+.+.+..+|..  +.-.||.||||||||+++-.+...+..
T Consensus       193 ~Q~~AV~~al~~--~~~~lI~GPPGTGKT~ti~~~I~~l~~  231 (646)
T 4b3f_X          193 SQKEAVLFALSQ--KELAIIHGPPGTGKTTTVVEIILQAVK  231 (646)
T ss_dssp             HHHHHHHHHHHC--SSEEEEECCTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhcC--CCceEEECCCCCCHHHHHHHHHHHHHh
Confidence            455556666653  234689999999999765555444433

>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=93.66  E-value=0.03  Score=55.00  Aligned_cols=26  Identities=23%  Similarity=0.272  Sum_probs=22.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+.|+||+|+|||||++.|+..+
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~   40 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQ   40 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccC
Confidence            34557899999999999999998876

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=93.66  E-value=0.04  Score=55.23  Aligned_cols=25  Identities=28%  Similarity=0.357  Sum_probs=22.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..+.|+||+|+||||+++.|++.+
T Consensus        27 g~~I~I~G~~GsGKSTl~k~La~~L   51 (252)
T 4e22_A           27 APVITVDGPSGAGKGTLCKALAESL   51 (252)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhc
Confidence            4467899999999999999999887

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=93.64  E-value=0.043  Score=53.38  Aligned_cols=25  Identities=32%  Similarity=0.389  Sum_probs=22.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +..+.|+|++|+||||+++.|++.+
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            3468899999999999999999987

>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=93.62  E-value=0.042  Score=61.24  Aligned_cols=23  Identities=26%  Similarity=0.424  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .++|+|+||+|||++|+.||+.|
T Consensus        37 lIvlvGlpGSGKSTia~~La~~L   59 (520)
T 2axn_A           37 VIVMVGLPARGKTYISKKLTRYL   59 (520)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999987

>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=93.56  E-value=0.094  Score=50.97  Aligned_cols=25  Identities=20%  Similarity=0.065  Sum_probs=20.6

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+++|+.|+||||.+..++.+....
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~   55 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFA   55 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHC
Confidence            3588999999999998888877543

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=93.55  E-value=0.07  Score=60.44  Aligned_cols=45  Identities=20%  Similarity=0.282  Sum_probs=34.6

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHH
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA  680 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA  680 (710)
                      ..++|.+..++.|...+....       .....++++||+|+|||+||+.++
T Consensus       124 ~~~vGR~~~l~~L~~~L~~~~-------~~~~~v~I~G~~GiGKTtLa~~~~  168 (591)
T 1z6t_A          124 VVFVTRKKLVNAIQQKLSKLK-------GEPGWVTIHGMAGCGKSVLAAEAV  168 (591)
T ss_dssp             SSCCCCHHHHHHHHHHHTTST-------TSCEEEEEECCTTSSHHHHHHHHH
T ss_pred             CeecccHHHHHHHHHHHhccc-------CCCceEEEEcCCCCCHHHHHHHHH
Confidence            348899888888877764321       112478999999999999999986

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.54  E-value=0.032  Score=55.11  Aligned_cols=24  Identities=25%  Similarity=0.256  Sum_probs=19.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      -+.|.||+|+|||++++.|++.|-
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l~   50 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRLQ   50 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
Confidence            578999999999999999999874

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=93.54  E-value=0.056  Score=52.74  Aligned_cols=35  Identities=23%  Similarity=0.265  Sum_probs=26.6

Q ss_pred             HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          301 RIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       301 ~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+...+.......++|+|.+|+|||+|+..++...
T Consensus        28 ~~r~~~~~~~~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           28 KNRKLLNKHGVVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             HHHHHHHHTTCEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHhCCCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            33333344445678999999999999999998876

>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=93.52  E-value=0.038  Score=53.85  Aligned_cols=23  Identities=30%  Similarity=0.403  Sum_probs=20.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.|+|++|+||||+++.|+. +
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-l   27 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-L   27 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-T
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-c
Confidence            3578999999999999999987 5

>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=93.51  E-value=0.062  Score=59.45  Aligned_cols=26  Identities=12%  Similarity=0.299  Sum_probs=23.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..+.|.|++|||||++|++||+.|.-
T Consensus       396 ~~I~l~GlsGsGKSTIa~~La~~L~~  421 (511)
T 1g8f_A          396 FSIVLGNSLTVSREQLSIALLSTFLQ  421 (511)
T ss_dssp             EEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             eEEEecccCCCCHHHHHHHHHHHHHH
Confidence            47899999999999999999999863

>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=93.49  E-value=0.94  Score=43.71  Aligned_cols=25  Identities=28%  Similarity=0.361  Sum_probs=18.3

Q ss_pred             CCCcEEEcCCCChHHHH-HHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAI-AEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~l-a~~la~~l  335 (710)
                      +.++++.+|+|+|||.. +-.+...+
T Consensus        51 ~~~~lv~~pTGsGKT~~~~~~~l~~l   76 (224)
T 1qde_A           51 GHDVLAQAQSGTGKTGTFSIAALQRI   76 (224)
T ss_dssp             TCCEEEECCTTSSHHHHHHHHHHHHC
T ss_pred             CCCEEEECCCCCcHHHHHHHHHHHHH
Confidence            46899999999999976 33444433

>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=93.48  E-value=0.04  Score=58.47  Aligned_cols=38  Identities=21%  Similarity=0.108  Sum_probs=27.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      ..++++||||+|||++|..+|..+-..+...+-+++..
T Consensus        75 ~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~  112 (366)
T 1xp8_A           75 RITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEH  112 (366)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             cEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCC
Confidence            36889999999999999999887643334455555443

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.48  E-value=0.051  Score=60.88  Aligned_cols=28  Identities=36%  Similarity=0.536  Sum_probs=24.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      ..+.|.||+|+|||+|+++||..+....
T Consensus       370 ~iI~LiG~sGSGKSTLar~La~~L~~~~  397 (552)
T 3cr8_A          370 FTVFFTGLSGAGKSTLARALAARLMEMG  397 (552)
T ss_dssp             EEEEEEESSCHHHHHHHHHHHHHHHTTC
T ss_pred             eEEEEECCCCChHHHHHHHHHHhhcccC
Confidence            3688999999999999999999987543

>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=93.47  E-value=0.019  Score=55.56  Aligned_cols=23  Identities=26%  Similarity=0.336  Sum_probs=21.2

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~  336 (710)
                      ++|.|++|+||||+++.|++.+.
T Consensus         3 I~i~G~~GsGKsTl~~~L~~~l~   25 (214)
T 1gtv_A            3 IAIEGVDGAGKRTLVEKLSGAFR   25 (214)
T ss_dssp             EEEEEEEEEEHHHHHHHHHHHHH
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHH
Confidence            67899999999999999999884

>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=93.47  E-value=0.072  Score=53.28  Aligned_cols=36  Identities=19%  Similarity=0.193  Sum_probs=29.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ..+++.|.+|+|||+++..||..+. .+.....+|+.
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~-~g~~v~vvd~D   50 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLE-DNYKVAYVNLD   50 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHT-TTSCEEEEECC
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHH-CCCeEEEEeCC
Confidence            4788999999999999999999998 66655555543

>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=93.42  E-value=0.053  Score=49.64  Aligned_cols=27  Identities=22%  Similarity=0.384  Sum_probs=24.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      +-.+++||+|+|||++..||.-.|||.
T Consensus        24 g~~~I~G~NGsGKStil~Ai~~~l~g~   50 (149)
T 1f2t_A           24 GINLIIGQNGSGKSSLLDAILVGLYWP   50 (149)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHCS
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHcCC
Confidence            567899999999999999999999885

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=93.42  E-value=0.048  Score=53.93  Aligned_cols=26  Identities=19%  Similarity=0.233  Sum_probs=22.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..+.|+|++|+||||+++.|+..+
T Consensus        15 ~~~~i~i~G~~gsGKst~~~~l~~~l   40 (236)
T 1q3t_A           15 KTIQIAIDGPASSGKSTVAKIIAKDF   40 (236)
T ss_dssp             CCCEEEEECSSCSSHHHHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHc
Confidence            34568899999999999999999988

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=93.37  E-value=0.044  Score=54.60  Aligned_cols=27  Identities=26%  Similarity=0.380  Sum_probs=23.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ..+.+.||+|+|||+|.|+|+..+-.+
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~p~   51 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVKPD   51 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSCCS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCCCC
Confidence            467899999999999999999886543

>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=93.34  E-value=0.095  Score=58.89  Aligned_cols=44  Identities=14%  Similarity=0.213  Sum_probs=34.3

Q ss_pred             cChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHH
Q 005179          632 IGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAA  681 (710)
Q Consensus       632 ~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~  681 (710)
                      +|.++.++.|...+....      ......+.++|++|+|||+||+.+++
T Consensus       131 ~GR~~~~~~l~~~L~~~~------~~~~~vv~I~G~gGvGKTtLA~~v~~  174 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEMC------DLDSFFLFLHGRAGSGKSVIASQALS  174 (549)
T ss_dssp             CCCHHHHHHHHHHHHHHT------TSSSEEEEEECSTTSSHHHHHHHHHH
T ss_pred             CCchHHHHHHHHHHhccc------CCCceEEEEEcCCCCCHHHHHHHHHH
Confidence            588888888887774431      11135788999999999999999996

>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=93.33  E-value=0.045  Score=60.27  Aligned_cols=24  Identities=25%  Similarity=0.346  Sum_probs=22.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .++|+|+||+|||++++.||+.++
T Consensus        41 ~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           41 LIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHh
Confidence            789999999999999999999876

>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=93.31  E-value=0.039  Score=58.75  Aligned_cols=28  Identities=25%  Similarity=0.185  Sum_probs=24.0

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.+..++|+||||+||||+++.|+...
T Consensus       166 i~~~~~i~l~G~~GsGKSTl~~~l~~~~  193 (377)
T 1svm_A          166 IPKKRYWLFKGPIDSGKTTLAAALLELC  193 (377)
T ss_dssp             CTTCCEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             cCCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3455678999999999999999999865

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=93.28  E-value=0.046  Score=61.73  Aligned_cols=29  Identities=21%  Similarity=0.217  Sum_probs=24.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      +.+++.||||||||+++++++..+-..+.
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~  233 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGL  233 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTC
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCC
Confidence            37899999999999999999988755443

>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=93.27  E-value=0.3  Score=50.19  Aligned_cols=25  Identities=32%  Similarity=0.389  Sum_probs=18.7

Q ss_pred             HHHHcCCCCCcEEEcCCCChHHHHH
Q 005179          304 QILCRRTKNNPILLGESGVGKTAIA  328 (710)
Q Consensus       304 ~~L~~~~~~nvLL~GppG~GKT~la  328 (710)
                      ..+....+.++++++|+|+|||...
T Consensus       124 ~~il~~~~~~~l~~a~TGsGKT~a~  148 (300)
T 3fmo_B          124 PLMLAEPPQNLIAQSQSGTGKTAAF  148 (300)
T ss_dssp             HHHTSSSCCCEEEECCTTSSHHHHH
T ss_pred             HHHHcCCCCeEEEECCCCCCccHHH
Confidence            3333444589999999999999753

>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=93.26  E-value=0.039  Score=53.44  Aligned_cols=26  Identities=35%  Similarity=0.454  Sum_probs=22.4

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+.|+||+|+||||+++.|+..+
T Consensus        19 ~Gei~~l~GpnGsGKSTLl~~l~gl~   44 (207)
T 1znw_A           19 VGRVVVLSGPSAVGKSTVVRCLRERI   44 (207)
T ss_dssp             CCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhC
Confidence            34557899999999999999999876

>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=93.26  E-value=0.065  Score=55.87  Aligned_cols=24  Identities=33%  Similarity=0.470  Sum_probs=21.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++++||||+|||++|..+|...
T Consensus       108 ~i~~i~G~~GsGKT~la~~la~~~  131 (324)
T 2z43_A          108 TMTEFFGEFGSGKTQLCHQLSVNV  131 (324)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCCHhHHHHHHHHHH
Confidence            378999999999999999999874

>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=93.24  E-value=0.038  Score=58.35  Aligned_cols=26  Identities=31%  Similarity=0.468  Sum_probs=22.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .+.+.||+|||||+|.|+||..+-.+
T Consensus        32 ~~~llGpsGsGKSTLLr~iaGl~~p~   57 (359)
T 3fvq_A           32 ILFIIGASGCGKTTLLRCLAGFEQPD   57 (359)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSSCCS
T ss_pred             EEEEECCCCchHHHHHHHHhcCCCCC
Confidence            57799999999999999999986443

>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=93.21  E-value=0.054  Score=53.74  Aligned_cols=26  Identities=15%  Similarity=0.249  Sum_probs=23.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      -+.|.||+|+|||++++.|++.|-..
T Consensus        29 ~i~~eG~~GsGKsT~~~~l~~~l~~~   54 (236)
T 3lv8_A           29 FIVIEGLEGAGKSTAIQVVVETLQQN   54 (236)
T ss_dssp             EEEEEESTTSCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            67899999999999999999987543

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=93.20  E-value=0.036  Score=51.97  Aligned_cols=21  Identities=33%  Similarity=0.509  Sum_probs=17.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGL  331 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~l  331 (710)
                      +.-+.|+||+|+||||+++.+
T Consensus         9 gei~~l~G~nGsGKSTl~~~~   29 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKKH   29 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHH
Confidence            344789999999999999963

>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=93.18  E-value=0.076  Score=55.88  Aligned_cols=23  Identities=30%  Similarity=0.339  Sum_probs=21.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      ..++++||||+|||++|..+|..
T Consensus       123 ~i~~I~G~~GsGKTtla~~la~~  145 (343)
T 1v5w_A          123 AITEAFGEFRTGKTQLSHTLCVT  145 (343)
T ss_dssp             EEEEEECCTTCTHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHH
Confidence            46889999999999999999987

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=93.18  E-value=0.043  Score=54.31  Aligned_cols=22  Identities=36%  Similarity=0.522  Sum_probs=19.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .++++|+||+|||++|-.+|..
T Consensus        32 l~~i~G~pG~GKT~l~l~~~~~   53 (251)
T 2zts_A           32 TVLLTGGTGTGKTTFAAQFIYK   53 (251)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHH
Confidence            6899999999999999887654

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=93.17  E-value=0.1  Score=56.66  Aligned_cols=28  Identities=21%  Similarity=0.249  Sum_probs=24.0

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      +..++++|++|+||||++..||..+...
T Consensus       100 ~~vI~ivG~~GvGKTT~a~~LA~~l~~~  127 (433)
T 2xxa_A          100 PAVVLMAGLQGAGKTTSVGKLGKFLREK  127 (433)
T ss_dssp             SEEEEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHh
Confidence            4567889999999999999999988653

>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=93.16  E-value=0.071  Score=56.38  Aligned_cols=36  Identities=17%  Similarity=0.146  Sum_probs=29.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      ..+.|+|+||+|||+++..|+..+...+.....++.
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~~  115 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLAV  115 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEec
Confidence            378999999999999999999998776655544443

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=93.15  E-value=0.038  Score=53.79  Aligned_cols=22  Identities=41%  Similarity=0.459  Sum_probs=20.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .+.+.||+|+|||+|.++|+..
T Consensus        24 ~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           24 IVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             EEEEECCTTSSTTHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6789999999999999999987

>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=93.15  E-value=0.042  Score=58.37  Aligned_cols=26  Identities=27%  Similarity=0.367  Sum_probs=23.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .-+.++||+|+|||+|++.|+..+-.
T Consensus       171 ~k~~IvG~nGsGKSTLlk~L~gl~~~  196 (365)
T 1lw7_A          171 KTVAILGGESSGKSVLVNKLAAVFNT  196 (365)
T ss_dssp             EEEEEECCTTSHHHHHHHHHHHHTTC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCC
Confidence            46889999999999999999998643

>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=93.11  E-value=0.039  Score=51.14  Aligned_cols=27  Identities=30%  Similarity=0.415  Sum_probs=23.3

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.-+.|+||.|+|||||++.|+..+
T Consensus        31 ~~Ge~v~L~G~nGaGKTTLlr~l~g~l   57 (158)
T 1htw_A           31 EKAIMVYLNGDLGAGKTTLTRGMLQGI   57 (158)
T ss_dssp             SSCEEEEEECSTTSSHHHHHHHHHHHT
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHhC
Confidence            344557899999999999999999887

>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=93.11  E-value=0.16  Score=53.78  Aligned_cols=94  Identities=17%  Similarity=0.218  Sum_probs=0.0

Q ss_pred             HHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh----------------hhhhccc
Q 005179          299 IQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG----------------LLMAGAK  362 (710)
Q Consensus       299 i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~----------------~l~~g~~  362 (710)
                      ++-+--.+.-..+..+.|+||+|+|||+|++.|++.+....     .+..++.+-++                -+.+...
T Consensus       162 iraID~~~pi~rGQr~~IvG~sG~GKTtLl~~Iar~i~~~~-----~~v~~I~~lIGER~~Ev~~~~~~~~~~vV~atad  236 (422)
T 3ice_A          162 ARVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAYNH-----PDCVLMVLLIDERPEEVTEMQRLVKGEVVASTFD  236 (422)
T ss_dssp             HHHHHHHSCCBTTCEEEEECCSSSSHHHHHHHHHHHHHHHC-----TTSEEEEEEESSCHHHHHHHHTTCSSEEEEECTT
T ss_pred             ceeeeeeeeecCCcEEEEecCCCCChhHHHHHHHHHHhhcC-----CCeeEEEEEecCChHHHHHHHHHhCeEEEEeCCC


Q ss_pred             cCccHHHHHHHHHHHHHh-----cCCeEEEEccchhhhhC
Q 005179          363 ERGELEARVTTLISEIQK-----SGDVILFIDEVHTLIGS  397 (710)
Q Consensus       363 ~~g~~e~~l~~~~~~~~~-----~~~~IL~IDEid~l~~~  397 (710)
                      .......+.....-.+.+     ...++|++|++.+++.+
T Consensus       237 ep~~~r~~~a~~alt~AEyfrd~G~dVLil~DslTR~A~A  276 (422)
T 3ice_A          237 EPASRHVQVAEMVIEKAKRLVEHKKDVIILLDSITRLARA  276 (422)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHTSCEEEEEEECHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHHhcCCCEEEEEeCchHHHHH

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=93.09  E-value=0.037  Score=54.54  Aligned_cols=34  Identities=18%  Similarity=0.094  Sum_probs=25.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .+.+.||+|+|||+|.|+|+..+-.+. .-|.++.
T Consensus        32 ~~~iiG~nGsGKSTLl~~l~Gl~~p~~-G~i~~~g   65 (224)
T 2pcj_A           32 FVSIIGASGSGKSTLLYILGLLDAPTE-GKVFLEG   65 (224)
T ss_dssp             EEEEEECTTSCHHHHHHHHTTSSCCSE-EEEEETT
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCc-eEEEECC
Confidence            577999999999999999998764432 2344443

>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=93.08  E-value=0.11  Score=53.39  Aligned_cols=27  Identities=33%  Similarity=0.340  Sum_probs=22.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +..++++|++|+||||++..||..+..
T Consensus        98 ~~vi~i~G~~G~GKTT~~~~la~~~~~  124 (297)
T 1j8m_F           98 PYVIMLVGVQGTGKTTTAGKLAYFYKK  124 (297)
T ss_dssp             SEEEEEECSSCSSTTHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            345678899999999999999988854

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=93.07  E-value=0.044  Score=52.97  Aligned_cols=24  Identities=29%  Similarity=0.320  Sum_probs=21.4

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .-+.|+||+|+||||+++.|+..+
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l~~~~   30 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQALARTL   30 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHh
Confidence            346799999999999999999877

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=93.07  E-value=0.064  Score=60.10  Aligned_cols=35  Identities=23%  Similarity=0.189  Sum_probs=27.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      ..++|.|++|+|||++|+.|++.|...+.....+|
T Consensus       373 ~~I~l~G~~GsGKSTia~~La~~L~~~G~~~~~ld  407 (546)
T 2gks_A          373 FCVWLTGLPCAGKSTIAEILATMLQARGRKVTLLD  407 (546)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEC
T ss_pred             eEEEccCCCCCCHHHHHHHHHHHhhhcCCeEEEEC
Confidence            36889999999999999999998764333334444

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.06  E-value=0.1  Score=56.93  Aligned_cols=114  Identities=17%  Similarity=0.100  Sum_probs=0.0

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh---------------------------------
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG---------------------------------  355 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~---------------------------------  355 (710)
                      ..+.-++|.|+||+|||+++..+|..+...       +.++..+.+.                                 
T Consensus       195 ~~G~liiIaG~pG~GKTtlal~ia~~~a~~-------g~~vl~fSlEms~~ql~~R~~~~~~~i~~~~l~~g~~~l~~~~  267 (444)
T 3bgw_A          195 KRRNFVLIAARPSMGKTAFALKQAKNMSDN-------DDVVNLHSLEMGKKENIKRLIVTAGSINAQKIKAARRDFASED  267 (444)
T ss_dssp             CSSCEEEEEECSSSSHHHHHHHHHHHHHHT-------TCEEEEECSSSCTTHHHHHHHHHHSCCCHHHHHHTGGGTCCSC
T ss_pred             CCCcEEEEEeCCCCChHHHHHHHHHHHHHc-------CCEEEEEECCCCHHHHHHHHHHHHcCCCHHHHhcccCCCCHHH


Q ss_pred             --------------hhhhccccCccHHHHHHHHHHHHHhcCCe--EEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc
Q 005179          356 --------------LLMAGAKERGELEARVTTLISEIQKSGDV--ILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL  419 (710)
Q Consensus       356 --------------~l~~g~~~~g~~e~~l~~~~~~~~~~~~~--IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l  419 (710)
                                    .+.......-.+.+....+-......+..  ++|||-+..+...+. .......-..+...|+.+.
T Consensus       268 ~~~l~~a~~~l~~~~l~i~d~~~~s~~~i~~~ir~l~~~~~~~~~lIVID~Lq~~~~~~~-~~~r~~~i~~i~~~Lk~lA  346 (444)
T 3bgw_A          268 WGKLSMAIGEISNSNINIFDKAGQSVNYIWSKTRQTKRKNPGKRVIVMIDYLQLLEPAKA-NDSRTNQISQISRDLKKMA  346 (444)
T ss_dssp             HHHHHHHHHHHHTSCEEEECCSSCBHHHHHHHHHHHHHHSCSSCEEEEEECSTTSBCSCS-SSCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEecHHhccCCCC-CCCHHHHHHHHHHHHHHHH


Q ss_pred             cCCCeEEEEcc
Q 005179          420 GRGELQCIAST  430 (710)
Q Consensus       420 ~~~~v~vI~at  430 (710)
                      .+-++.+|+.+
T Consensus       347 ke~~v~vi~ls  357 (444)
T 3bgw_A          347 RELDVVVIALS  357 (444)
T ss_dssp             HHHTCEEEEEE
T ss_pred             HHhCCeEEEEe

>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=93.05  E-value=0.18  Score=56.85  Aligned_cols=38  Identities=26%  Similarity=0.243  Sum_probs=28.5

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccC-ceEEEeehhh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLS-KRIMSLDMGL  356 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~-~~v~~ld~~~  356 (710)
                      ..++|+|.+|+||||+++.|++.+...       + ..++.+|...
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~-------G~~~~~~lD~D~  435 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQ-------GGRSVSLLLGDT  435 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHH-------CSSCEEEEEHHH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhccc-------CCceEEEECcHH
Confidence            457899999999999999999998431       2 4556665443

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=93.05  E-value=0.055  Score=51.73  Aligned_cols=24  Identities=29%  Similarity=0.419  Sum_probs=21.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+.|+||+|+||||+++.|+..+.
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~~   26 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVLK   26 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhcc
Confidence            478999999999999999998875

>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=93.03  E-value=0.046  Score=51.76  Aligned_cols=25  Identities=32%  Similarity=0.377  Sum_probs=21.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      ...+++|+|++|+|||+|+..+...
T Consensus        22 ~~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           22 GLPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCC
Confidence            3467999999999999999998753

>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=93.02  E-value=0.049  Score=55.59  Aligned_cols=23  Identities=35%  Similarity=0.426  Sum_probs=20.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.|+|++|+||||+++.|+ .+
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~l   98 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NL   98 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HC
Confidence            347899999999999999999 45

>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=93.00  E-value=0.049  Score=56.18  Aligned_cols=32  Identities=19%  Similarity=0.253  Sum_probs=26.4

Q ss_pred             HcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcC
Q 005179          307 CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAE  339 (710)
Q Consensus       307 ~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~  339 (710)
                      .-+.+..+.|+||+|+|||||++.|+..+ .|.
T Consensus       122 ~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~-~G~  153 (305)
T 2v9p_A          122 GIPKKNCLAFIGPPNTGKSMLCNSLIHFL-GGS  153 (305)
T ss_dssp             TCTTCSEEEEECSSSSSHHHHHHHHHHHH-TCE
T ss_pred             EecCCCEEEEECCCCCcHHHHHHHHhhhc-Cce
Confidence            34556678899999999999999999887 443

>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=92.99  E-value=0.04  Score=54.67  Aligned_cols=26  Identities=19%  Similarity=0.341  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .+.+.||+|+|||+|.++|+..+-.+
T Consensus        33 ~~~iiG~nGsGKSTLl~~l~Gl~~p~   58 (235)
T 3tif_A           33 FVSIMGPSGSGKSTMLNIIGCLDKPT   58 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCcHHHHHHHHhcCCCCC
Confidence            57899999999999999999876443

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=92.98  E-value=0.12  Score=54.65  Aligned_cols=28  Identities=29%  Similarity=0.458  Sum_probs=24.3

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -..+..++|+||+|+||||+++.|+..+
T Consensus       172 i~~G~~i~ivG~sGsGKSTll~~l~~~~  199 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTLMKALMQEI  199 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHHHHHHHTTS
T ss_pred             HhcCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            3456789999999999999999998765

>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=92.96  E-value=0.02  Score=57.71  Aligned_cols=26  Identities=15%  Similarity=0.171  Sum_probs=22.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .-+.|.|++|+|||++|+.||+.|-+
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l~~   50 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLCED   50 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCC
Confidence            36889999999999999999998633

>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=92.92  E-value=0.059  Score=56.88  Aligned_cols=24  Identities=42%  Similarity=0.473  Sum_probs=22.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..+.++||||+|||+|++.++..+
T Consensus       132 ~i~~I~G~~GsGKTTL~~~l~~~~  155 (349)
T 1pzn_A          132 AITEVFGEFGSGKTQLAHTLAVMV  155 (349)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh
Confidence            478899999999999999999886

>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=92.91  E-value=0.17  Score=52.70  Aligned_cols=28  Identities=25%  Similarity=0.275  Sum_probs=23.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      .+.-+.|+||+|+||||+++.|+..+..
T Consensus       128 ~g~vi~lvG~nGaGKTTll~~Lag~l~~  155 (328)
T 3e70_C          128 KPYVIMFVGFNGSGKTTTIAKLANWLKN  155 (328)
T ss_dssp             SSEEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHh
Confidence            3455789999999999999999988754

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=92.91  E-value=0.079  Score=54.48  Aligned_cols=39  Identities=31%  Similarity=0.329  Sum_probs=30.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      ..+.++||+|+|||+++..||..+-.........|...+
T Consensus        99 ~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~d~~  137 (295)
T 1ls1_A           99 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQ  137 (295)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecCCcc
Confidence            478899999999999999999998655555555555443

>1rif_A DAR protein, DNA helicase UVSW; bacteriophage, RECG, SF2, DNA binding protein; HET: DNA; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.23

Probab=92.89  E-value=0.69  Score=46.74  Aligned_cols=39  Identities=18%  Similarity=0.122  Sum_probs=26.1

Q ss_pred             CHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          295 RETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       295 r~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      +..+.+-+..++..   .+.+|.+|+|+|||.++-.++....
T Consensus       115 ~~~Q~~ai~~~l~~---~~~ll~~~tGsGKT~~~~~~~~~~~  153 (282)
T 1rif_A          115 HWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYYL  153 (282)
T ss_dssp             CHHHHHHHHHHHHH---SEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHhc---CCeEEEcCCCCCcHHHHHHHHHHHH
Confidence            44444444444443   4568899999999999877776543

>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=92.89  E-value=0.047  Score=58.08  Aligned_cols=33  Identities=24%  Similarity=0.387  Sum_probs=25.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .+.|+||+|||||+|.|+||..+-.+.. -|.+|
T Consensus        31 ~~~llGpsGsGKSTLLr~iaGl~~p~~G-~I~i~   63 (381)
T 3rlf_A           31 FVVFVGPSGCGKSTLLRMIAGLETITSG-DLFIG   63 (381)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEE-EEEET
T ss_pred             EEEEEcCCCchHHHHHHHHHcCCCCCCe-EEEEC
Confidence            5779999999999999999988644332 34444

>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=92.89  E-value=0.041  Score=52.38  Aligned_cols=25  Identities=28%  Similarity=0.549  Sum_probs=22.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      -+.++||+|+|||+|.+.++...|.
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~~~   55 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNEFN   55 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSCCC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCCCC
Confidence            5789999999999999999988764

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=92.88  E-value=0.089  Score=54.61  Aligned_cols=25  Identities=24%  Similarity=0.222  Sum_probs=22.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .-+++.|+||+|||++|..+|...-
T Consensus        69 ~l~li~G~pG~GKTtl~l~ia~~~a   93 (315)
T 3bh0_A           69 NFVLIAARPSMGKTAFALKQAKNMS   93 (315)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            4789999999999999999997654

---

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	710
d1qvra2	387	c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus	4e-97
d1r6bx2	268	c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, A	1e-92
d1jbka_	195	c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia col	9e-71
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	3e-35
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	3e-28
d1w5sa2	287	c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-t	2e-04
d1qvra3	315	c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus	2e-26
d1r6bx3	315	c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, A	3e-24
d1khya_	139	a.174.1.1 (A:) N-terminal domain of ClpB (heat sho	2e-16
d1khya_	139	a.174.1.1 (A:) N-terminal domain of ClpB (heat sho	5e-04
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	5e-16
d1fnna2	276	c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrob	4e-06
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	2e-14
d1qvra1	145	a.174.1.1 (A:4-148) N-terminal domain of ClpB (hea	6e-11
d1k6ka_	142	a.174.1.1 (A:) N-terminal, ClpS-binding domain of	7e-11
d1um8a_	364	c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 2	2e-10
d1g41a_	443	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	9e-10
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	2e-07
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	2e-06
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	9e-06
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	1e-05
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	0.002
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	1e-05
d1sxjd2	237	c.37.1.20 (D:26-262) Replication factor C2 {Baker'	6e-05
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	4e-05
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	4e-05
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	7e-05
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	2e-04
d1a5ta2	207	c.37.1.20 (A:1-207) delta prime subunit of DNA pol	4e-04
d1ny5a2	247	c.37.1.20 (A:138-384) Transcriptional activator si	0.001
d1sxjc2	227	c.37.1.20 (C:12-238) Replication factor C3 {Baker'	0.002
d1sxjb2	224	c.37.1.20 (B:7-230) Replication factor C4 {Baker's	0.002
d1njfa_	239	c.37.1.20 (A:) delta prime subunit of DNA polymera	0.003

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 387

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]

 Score =  303 bits (776), Expect = 4e-97
 Identities = 145/257 (56%), Positives = 187/257 (72%), Gaps = 7/257 (2%)

Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           ALEQ+ +DLT  A+E  +DPVIGR+ EI+R+IQIL RRTKNNP+L+GE GVGKTAI EGL
Sbjct: 4   ALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGL 63

Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDE 390
           A RIV+ +VP  L  KRI+SL MG L+AGAK RGE E R+  +I E+ +S G+VILFIDE
Sbjct: 64  AQRIVKGDVPEGLKGKRIVSLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDE 123

Query: 391 VHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ 450
           +HT++G+     G     +D  N+LKP+L RGEL+ I +TT DE+R + EKD AL RRFQ
Sbjct: 124 LHTVVGA-----GKAEGAVDAGNMLKPALARGELRLIGATTLDEYR-EIEKDPALERRFQ 177

Query: 451 PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLV 510
           PV + EP+ E+ + IL GL+EKYE HH  + +  AI AA  LS RYI++R LPDKAIDL+
Sbjct: 178 PVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDLI 237

Query: 511 DEAGSRAHIELFKRKKE 527
           DEA +R  + L    +E
Sbjct: 238 DEAAARLRMALESAPEE 254

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 268

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]

 Score =  287 bits (735), Expect = 1e-92
 Identities = 134/255 (52%), Positives = 184/255 (72%), Gaps = 4/255 (1%)

Query: 273 LEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLA 332
           LE F  +L   A    IDP+IGRE E++R IQ+LCRR KNNP+L+GESGVGKTAIAEGLA
Sbjct: 1   LENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLA 60

Query: 333 IRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVH 392
            RIVQ +VP  +    I SLD+G L+AG K RG+ E R   L+ ++++  + ILFIDE+H
Sbjct: 61  WRIVQGDVPEVMADCTIYSLDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIH 120

Query: 393 TLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPV 452
           T+IG+G       G  +D +NL+KP L  G+++ I STT  E    FEKD+ALARRFQ +
Sbjct: 121 TIIGAG----AASGGQVDAANLIKPLLSSGKIRVIGSTTYQEFSNIFEKDRALARRFQKI 176

Query: 453 LISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDE 512
            I+EPS E+ V+I+ GL+ KYEAHH+ ++T +A+ AAV L+ +YI+DR+LPDKAID++DE
Sbjct: 177 DITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDE 236

Query: 513 AGSRAHIELFKRKKE 527
           AG+RA +    ++K+
Sbjct: 237 AGARARLMPVSKRKK 251

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 195

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]

 Score =  226 bits (578), Expect = 9e-71
 Identities = 107/196 (54%), Positives = 144/196 (73%), Gaps = 6/196 (3%)

Query: 272 ALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGL 331
           AL+++ +DLT RA +  +DPVIGR+ EI+R IQ+L RRTKNNP+L+GE GVGKTAI EGL
Sbjct: 4   ALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGL 63

Query: 332 AIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDE 390
           A RI+  EVP  L  +R+++LDMG L+AGAK RGE E R+  +++++ K  G+VILFIDE
Sbjct: 64  AQRIINGEVPEGLKGRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDE 123

Query: 391 VHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQ 450
           +HT++G+     G     +D  N+LKP+L RGEL C+ +TT DE+R   EKD AL RRFQ
Sbjct: 124 LHTMVGA-----GKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAALERRFQ 178

Query: 451 PVLISEPSQEDAVRIL 466
            V ++EPS ED + IL
Sbjct: 179 KVFVAEPSVEDTIAIL 194

>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 =  134 bits (337), Expect = 3e-35
 Identities = 40/340 (11%), Positives = 92/340 (27%), Gaps = 44/340 (12%)

Query: 177 RVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQGE 236
           R  + A  ++ + G  F     +   +       A  V     +  +        R+   
Sbjct: 14  RAAQYAAFHTDAPGSWFDHTSGVLESVEDGTPVLAIGVESGDAIVFDK----NAQRIVAY 69

Query: 237 LAKEGREPSLAKGVRENSISGKTAALKSPGRTRASALEQFCVDLTARASEELIDPVIGRE 296
             K  +    +                       S ++     +       L+D      
Sbjct: 70  KEKSVKAEDGSV----------------------SVVQVENGFMKQGHRGWLVDLTGELV 107

Query: 297 TEIQRIIQIL-CRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG 355
                + +    R      I+ G+   GKT +   L   +   +    +     +S    
Sbjct: 108 GCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLS---- 163

Query: 356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLL 415
                     +    V  +   + +    ++ ID +  +IG+      + G      +LL
Sbjct: 164 ------GYNTDFNVFVDDIARAMLQH--RVIVIDSLKNVIGAAGGNTTSGGISRGAFDLL 215

Query: 416 KPSLGRGELQ---CIASTTQDEHRTQFEK-DKALARRFQPVLISEPSQEDAVRILLGLRE 471
                    +    IAS     +  +  +  K  +R     L+     +   ++L    E
Sbjct: 216 SDIGAMAASRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEWQVLTRTGE 275

Query: 472 KYE-AHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLV 510
             +   H  + +    +     +++    +    KAI  V
Sbjct: 276 GLQRLTHTLQTSYGEHSVLTIHTSKQSGGKQASGKAIQTV 315

>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 =  112 bits (281), Expect = 3e-28
 Identities = 32/256 (12%), Positives = 76/256 (29%), Gaps = 26/256 (10%)

Query: 290 DPVIGRETEIQRIIQILCRRTKNNP---------ILLGESGVGKTAIAEGLAIRIVQAEV 340
             +  R  E + + +I   R  +             +G  G+GKT +A+    R+ +A  
Sbjct: 16  PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAA 75

Query: 341 PVFLLSKRIM-------------SLDMGLLMAGAKERGELEARVTTLISEIQKSGD--VI 385
              L  K+               SL +       + RG     +   + +     +  ++
Sbjct: 76  KEGLTVKQAYVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLL 135

Query: 386 LFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFE-KDKA 444
           + +DE  +++ S  +   +  T L +   +    G   +  +   +     +    K   
Sbjct: 136 VILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRIGFLLVASDVRALSYMREKIPQ 195

Query: 445 LARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD 504
           +  +    L     +   +  +L  R       +  +    +     +            
Sbjct: 196 VESQIGFKLHLPAYKSRELYTILEQR-AELGLRDTVWEPRHLELISDVYGEDKGGDGSAR 254

Query: 505 KAIDLVDEAGSRAHIE 520
           +AI  +  A   A   
Sbjct: 255 RAIVALKMACEMAEAM 270

>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 = 41.7 bits (96), Expect = 2e-04
 Identities = 10/52 (19%), Positives = 17/52 (32%)

Query: 629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA 680
             +  +     A++R      +     +         G  G+GKT LAK   
Sbjct: 16  PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTV 67

>d1qvra3 c.37.1.20 (A:536-850) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]} Length = 315

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]

 Score =  108 bits (270), Expect = 2e-26
 Identities = 53/103 (51%), Positives = 68/103 (66%), Gaps = 1/103 (0%)

Query: 607 IPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCG 666
           IPV ++   ER  L+ LEE+L KRV+GQDEA+ A++ A++R+R GLKDPNRP  + LF G
Sbjct: 1   IPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLG 60

Query: 667 PTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNSVKVALSRQI 709
           PTGVGKTELAK+LAA  F       +         K A+SR I
Sbjct: 61  PTGVGKTELAKTLAATLFD-TEEAMIRIDMTEYMEKHAVSRLI 102

>d1r6bx3 c.37.1.20 (X:437-751) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]} Length = 315

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]

 Score =  101 bits (253), Expect = 3e-24
 Identities = 30/77 (38%), Positives = 47/77 (61%)

Query: 608 PVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGP 667
           P + ++  +R  L  L ++LK  V GQD+A+ A++ A+K +R GL   ++P  + LF GP
Sbjct: 1   PEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGP 60

Query: 668 TGVGKTELAKSLAACYF 684
           TGVGKTE+   L+    
Sbjct: 61  TGVGKTEVTVQLSKALG 77

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]} Length = 139

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

 Score = 74.8 bits (183), Expect = 2e-16
 Identities = 26/146 (17%), Positives = 47/146 (32%), Gaps = 10/146 (6%)

Query: 83  ERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVV 142
           +R T +   A+  +Q  A       +   HL+  L+ ++      L     +  A     
Sbjct: 1   DRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPL-----LTSAGINAG 55

Query: 143 SIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALG 202
            +    N         +G        +  S    RV     + ++ RG NFI+ E   L 
Sbjct: 56  QLRTDINQALNRLPQVEGTGGD----VQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLA 111

Query: 203 LFTVDDGSAGRVLKRLGVDVNHLAAV 228
                 G+   +LK  G    ++   
Sbjct: 112 ALE-SRGTLADILKAAGATTANITQA 136

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]} Length = 139

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

 Score = 38.6 bits (89), Expect = 5e-04
 Identities = 10/89 (11%), Positives = 32/89 (35%), Gaps = 1/89 (1%)

Query: 54  HSNYTSNNNNCNPICARKRRKIIPISSVFERFTERAVKAVIFSQREAKSLGKDMVFTQHL 113
            +   +     +   A  R   +  +    + ++  V+ +    + A+  G + + ++  
Sbjct: 49  SAGINAGQLRTDINQALNRLPQVEGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELF 108

Query: 114 LLGLIAEDRHPNGFLES-GITIDKAREAV 141
           +L  +         L++ G T     +A+
Sbjct: 109 VLAALESRGTLADILKAAGATTANITQAI 137

>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 = 76.8 bits (187), Expect = 5e-16
 Identities = 40/248 (16%), Positives = 71/248 (28%), Gaps = 24/248 (9%)

Query: 290 DPVIGRETEIQRIIQILCRRTKN------NPILLGESGVGKTAIAEGLA--------IRI 335
             +  RE ++Q++  +L    +N         LLG  G GKT     L          R 
Sbjct: 16  KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARF 75

Query: 336 VQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLI 395
           V     ++     I+      L      RG        L+ E  +  D+ +F+       
Sbjct: 76  VYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAF- 134

Query: 396 GSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLIS 455
                   +  +           LG   +  +     D      +           +  S
Sbjct: 135 ----NLAPDILSTFIRLGQEADKLGAFRIALVIVGHNDAVLNNLDPSTRGIMGKYVIRFS 190

Query: 456 EPSQEDAVRILLG-LREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD--KAIDLVDE 512
             +++    ILL   +         +  L+ I  A    A+   D    D   AID++  
Sbjct: 191 PYTKDQIFDILLDRAKAGLAEGSYSEDILQMI--ADITGAQTPLDTNRGDARLAIDILYR 248

Query: 513 AGSRAHIE 520
           +   A   
Sbjct: 249 SAYAAQQN 256

>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 = 46.7 bits (109), Expect = 4e-06
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 3/82 (3%)

Query: 629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR 688
           KR+  +++ +  +   +      L++P          G  G GKT   + L   Y     
Sbjct: 16  KRLPHREQQLQQLDILLGNW---LRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTT 72

Query: 689 IHYLFFPSPFNSVKVALSRQIC 710
             +++          A+  +I 
Sbjct: 73  ARFVYINGFIYRNFTAIIGEIA 94

>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 = 72.6 bits (177), Expect = 2e-14
 Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 5/74 (6%)

Query: 623 LEEQLKKRVIGQDEAVAAISRAVKR--SRVGLKDPNR---PTAAMLFCGPTGVGKTELAK 677
           +  +L + +IGQ +A  A++ A++    R+ L++P R       +L  GPTGVGKTE+A+
Sbjct: 8   IVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIAR 67

Query: 678 SLAACYFGSVRIHY 691
            LA           
Sbjct: 68  RLAKLANAPFIKVE 81

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]} Length = 145

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

 Score = 58.9 bits (142), Expect = 6e-11
 Identities = 20/131 (15%), Positives = 41/131 (31%), Gaps = 9/131 (6%)

Query: 83  ERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVV 142
           ER+T+ A +A+  +Q  A+ +    +   HL   L+ ++R             +  E   
Sbjct: 1   ERWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERS---------LAWRLLEKAG 51

Query: 143 SIWHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALG 202
           +   +       + A   K   +      +         A          ++A + + L 
Sbjct: 52  ADPKALKELQERELARLPKVEGAEVGQYLTSRLSGALNRAEGLMEELKDRYVAVDTLVLA 111

Query: 203 LFTVDDGSAGR 213
           L     G  G 
Sbjct: 112 LAEATPGLPGL 122

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]} Length = 142

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

 Score = 58.7 bits (141), Expect = 7e-11
 Identities = 20/137 (14%), Positives = 52/137 (37%), Gaps = 8/137 (5%)

Query: 85  FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSI 144
             +    ++  +   A+    + +  +HLLL L++            + +   R+ + + 
Sbjct: 2   LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAF 61

Query: 145 WHSTNNQDTDDAAAQGKPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLF 204
              T          +            ++S +RV + AV + +S G N +   ++ + +F
Sbjct: 62  IEQTTPVLPASEEER--------DTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIF 113

Query: 205 TVDDGSAGRVLKRLGVD 221
           +  +  A  +L++  V 
Sbjct: 114 SEQESQAAYLLRKHEVS 130

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]} Length = 364

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]

 Score = 61.0 bits (147), Expect = 2e-10
 Identities = 24/79 (30%), Positives = 34/79 (43%), Gaps = 21/79 (26%)

Query: 623 LEEQLKKRVIGQDEAVAAISRAV----KRSRV-----------------GLKDPNRPTAA 661
           L+  L   VIGQ++A    S AV    KR                     L++     + 
Sbjct: 11  LKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSN 70

Query: 662 MLFCGPTGVGKTELAKSLA 680
           +L  GPTG GKT +A++LA
Sbjct: 71  ILLIGPTGSGKTLMAQTLA 89

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]} Length = 443

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 = 59.0 bits (142), Expect = 9e-10
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 5/61 (8%)

Query: 625 EQLKKRVIGQDEAVAAISRAV----KRSRVGLKDPNRPTAA-MLFCGPTGVGKTELAKSL 679
            +L + +IGQ +A  A++ A+    +R ++     +  T   +L  GPTGVGKTE+A+ L
Sbjct: 10  SELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRL 69

Query: 680 A 680
           A
Sbjct: 70  A 70

>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 = 50.3 bits (119), Expect = 2e-07
 Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 1/48 (2%)

Query: 633 GQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLA 680
              +    ++  ++    G K    PTA  L  G  G GKT L  ++ 
Sbjct: 7   TDKQFENRLNDNLEELIQGKKAVESPTA-FLLGGQPGSGKTSLRSAIF 53

>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 = 47.6 bits (112), Expect = 2e-06
 Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 623 LEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNR-PTAAMLFCGPTGVGKTELAKSLAA 681
               +   +I   + V  +    +      K+ +R P  ++L  GP   GKT LA  +A 
Sbjct: 3   YASYIMNGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAE 62

Query: 682 CYFGSVRIH 690
                    
Sbjct: 63  ESNFPFIKI 71

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 252

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]

 Score = 45.6 bits (106), Expect = 9e-06
 Identities = 11/55 (20%), Positives = 17/55 (30%), Gaps = 8/55 (14%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG 685
           +   +E    +     + R            +L  GP G GK     +L    FG
Sbjct: 13  LSHNEELTNFLKSLSDQPRDL--------PHLLLYGPNGTGKKTRCMALLESIFG 59

>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 = 45.2 bits (107), Expect = 1e-05
 Identities = 41/189 (21%), Positives = 68/189 (35%), Gaps = 40/189 (21%)

Query: 298 EIQRIIQILCRRTK---------NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKR 348
           E++ I++ L   ++            +L+G  GVGKT +A  +A    +A VP       
Sbjct: 20  ELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVA---GEARVPFI----- 71

Query: 349 IMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTG 408
             +      +      G   ARV  L    ++    I+FIDE+  +           G G
Sbjct: 72  --TASGSDFVE--MFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRG---SGVGGG 124

Query: 409 LDISNLLKPSL--------GRGELQCIASTTQDEHRTQFEKDKALAR--RF-QPVLISEP 457
            D        L            +  +A+T + +       D AL R  RF + + I  P
Sbjct: 125 NDEREQTLNQLLVEMDGFEKDTAIVVMAATNRPD-----ILDPALLRPGRFDRQIAIDAP 179

Query: 458 SQEDAVRIL 466
             +   +IL
Sbjct: 180 DVKGREQIL 188

>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 = 37.9 bits (88), Expect = 0.002
 Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 8/62 (12%)

Query: 620 LVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSL 679
           + G EE  K+ +    E V  +    +   +G + P      +L  GP GVGKT LA+++
Sbjct: 11  VAGAEEA-KEEL---KEIVEFLKNPSRFHEMGARIPKG----VLLVGPPGVGKTHLARAV 62

Query: 680 AA 681
           A 
Sbjct: 63  AG 64

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

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]

 Score = 44.7 bits (104), Expect = 1e-05
 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 9/65 (13%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIH 690
           V  QD AV  + + +K + +           MLF GP G GKT    +L    +G   + 
Sbjct: 14  VTAQDHAVTVLKKTLKSANL---------PHMLFYGPPGTGKTSTILALTKELYGPDLMK 64

Query: 691 YLFFP 695
                
Sbjct: 65  SRILE 69

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 237

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]

 Score = 42.8 bits (99), Expect = 6e-05
 Identities = 15/117 (12%), Positives = 37/117 (31%), Gaps = 4/117 (3%)

Query: 289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKR 348
           +D V  ++  +  + + L      + +  G  G GKT+    L   +   ++    + + 
Sbjct: 11  LDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILEL 70

Query: 349 IMSLDMGL----LMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVG 401
             S + G+           R  +       +         I+ +DE  ++       
Sbjct: 71  NASDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTADAQSA 127

>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 = 43.6 bits (101), Expect = 4e-05
 Identities = 14/72 (19%), Positives = 22/72 (30%), Gaps = 8/72 (11%)

Query: 631 VIGQDEAVAAISRAVKRSRVGL--------KDPNRPTAAMLFCGPTGVGKTELAKSLAAC 682
           V G   +V  +   +               KD +    A +  GP G+GKT  A  +A  
Sbjct: 16  VCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQE 75

Query: 683 YFGSVRIHYLFF 694
               +       
Sbjct: 76  LGYDILEQNASD 87

>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 = 43.4 bits (101), Expect = 4e-05
 Identities = 13/47 (27%), Positives = 21/47 (44%), Gaps = 4/47 (8%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAK 677
            IGQ+     +   ++ ++        P   +L  GP G+GKT LA 
Sbjct: 11  YIGQERLKQKLRVYLEAAKAR----KEPLEHLLLFGPPGLGKTTLAH 53

>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 = 42.6 bits (99), Expect = 7e-05
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRI 689
            IGQ+     +S A++ +++           +L  GP G+GKT LA  +A+    ++ +
Sbjct: 11  FIGQENVKKKLSLALEAAKMR----GEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHV 65

>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 = 41.4 bits (97), Expect = 2e-04
 Identities = 41/198 (20%), Positives = 75/198 (37%), Gaps = 43/198 (21%)

Query: 292 VIGRETEIQRIIQI------------LCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAE 339
           V G +   + + ++            L  +     +++G  G GKT +A+ +A    +A+
Sbjct: 14  VAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIA---GEAK 70

Query: 340 VPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGT 399
           VP F       ++     +      G   +RV  +  + +K+   I+FIDE+  +     
Sbjct: 71  VPFF-------TISGSDFVE--MFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG 121

Query: 400 VGRGNKGTGLDISNLLKPSL--------GRGELQCIASTTQDEHRTQFEKDKALAR--RF 449
            G G    G D        +        G   +  IA+T + +       D AL R  RF
Sbjct: 122 AGLGG---GHDEREQTLNQMLVEMDGFEGNEGIIVIAATNRPD-----VLDPALLRPGRF 173

Query: 450 -QPVLISEPSQEDAVRIL 466
            + V++  P      +IL
Sbjct: 174 DRQVVVGLPDVRGREQIL 191

>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 = 40.1 bits (92), Expect = 4e-04
 Identities = 7/66 (10%), Positives = 16/66 (24%), Gaps = 8/66 (12%)

Query: 634 QDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLF 693
                  +  + +  R      +    A+L     G+G   L  +L+          +  
Sbjct: 7   LRPDFEKLVASYQAGRG----HH----ALLIQALPGMGDDALIYALSRYLLCQQPQGHKS 58

Query: 694 FPSPFN 699
                 
Sbjct: 59  CGHCRG 64

>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 = 38.7 bits (90), Expect = 0.001
 Identities = 20/104 (19%), Positives = 46/104 (44%), Gaps = 2/104 (1%)

Query: 293 IGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM 350
           +    +++ I++ + +    +   ++ GESGVGK  +A  +     +++ P   L+   +
Sbjct: 3   VFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASI 62

Query: 351 SLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTL 394
             D+        E+G     V++     + +    LF+DE+  L
Sbjct: 63  PRDIFEAELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGEL 106

>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 = 38.1 bits (87), Expect = 0.002
 Identities = 17/80 (21%), Positives = 32/80 (40%), Gaps = 9/80 (11%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIH 690
           V GQ+E +  + + V   ++           +LF GP G GKT    +LA   +G    +
Sbjct: 16  VYGQNEVITTVRKFVDEGKL---------PHLLFYGPPGTGKTSTIVALAREIYGKNYSN 66

Query: 691 YLFFPSPFNSVKVALSRQIC 710
            +   +  +   + + R   
Sbjct: 67  MVLELNASDDRGIDVVRNQI 86

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 224

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]

 Score = 37.7 bits (86), Expect = 0.002
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 9/80 (11%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIH 690
           ++G  E +  + +  K   +    P+     M+  G  G+GKT     LA    G     
Sbjct: 17  IVGNKETIDRLQQIAKDGNM----PH-----MIISGMPGIGKTTSVHCLAHELLGRSYAD 67

Query: 691 YLFFPSPFNSVKVALSRQIC 710
            +   +  +   + + R   
Sbjct: 68  GVLELNASDDRGIDVVRNQI 87

>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 = 37.8 bits (87), Expect = 0.003
 Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 8/47 (17%)

Query: 631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAK 677
           V+GQ+  + A++  +   R+     +    A LF G  GVGKT +A+
Sbjct: 14  VVGQEHVLTALANGLSLGRI----HH----AYLFSGTRGVGKTSIAR 52

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	710
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	100.0
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	100.0
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	99.88
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	99.88
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	99.87
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.84
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	99.83
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	99.81
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	99.81
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.76
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.76
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.75
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.74
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.73
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.72
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.71
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.71
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.71
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.68
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.65
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.64
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.63
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.6
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.6
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.58
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.57
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.52
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.47
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.41
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.41
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.38
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.3
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.18
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.04
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.02
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	98.99
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	98.95
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	98.93
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	98.93
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	98.85
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	98.81
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	98.78
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.77
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.77
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	98.7
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	98.62
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	98.52
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	98.5
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	98.5
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	98.48
d1khya_	139	N-terminal domain of ClpB (heat shock protein F84.	98.48
d1qvra1	145	N-terminal domain of ClpB (heat shock protein F84.	98.47
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.44
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	98.44
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	98.32
d1k6ka_	142	N-terminal, ClpS-binding domain of ClpA, an Hsp100	98.32
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	98.28
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	98.26
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	98.19
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	98.14
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.09
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	98.06
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	98.03
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.0
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	97.82
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	97.67
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	97.55
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	97.54
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.49
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.44
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	97.36
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	97.29
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.28
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	97.26
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	97.24
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.21
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.18
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.17
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.13
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.11
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.05
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.02
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	96.94
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	96.93
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	96.91
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	96.89
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	96.87
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.85
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	96.84
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	96.83
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	96.65
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	96.62
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.61
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	96.58
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.58
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	96.57
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.57
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.51
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	96.48
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.46
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	96.44
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.44
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	96.42
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	96.37
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.35
d1okkd2	207	GTPase domain of the signal recognition particle r	96.31
d2qy9a2	211	GTPase domain of the signal recognition particle r	96.29
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.29
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	96.27
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.24
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	96.23
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	96.21
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.2
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	96.2
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.2
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.2
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.19
d1tuea_	205	Replication protein E1 helicase domain {Human papi	96.18
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	96.17
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	96.17
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	96.15
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.12
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.08
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.08
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	96.06
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	96.04
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	95.98
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	95.96
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	95.95
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.93
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	95.87
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	95.87
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	95.79
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	95.77
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	95.65
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	95.63
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	95.48
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	95.38
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	95.32
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	95.26
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	95.08
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.08
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	95.07
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	95.0
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	94.94
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	94.93
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	94.92
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	94.89
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	94.83
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	94.81
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	94.66
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	94.59
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	94.55
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	94.53
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	94.48
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	94.46
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	94.41
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	94.41
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	94.4
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	94.34
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	94.14
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.12
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	94.1
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	93.98
d2fh5b1	207	Signal recognition particle receptor beta-subunit	93.9
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	93.85
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	93.82
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	93.81
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	93.79
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	93.78
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	93.76
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	93.75
d1g2912	240	Maltose transport protein MalK, N-terminal domain	93.73
d2awna2	232	Maltose transport protein MalK, N-terminal domain	93.56
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	93.55
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	93.49
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	93.46
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	93.44
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	93.32
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	93.26
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	93.23
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.14
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	93.05
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	93.02
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.02
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	93.0
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	92.96
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	92.84
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	92.8
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	92.77
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	92.71
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	92.7
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	92.64
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	92.62
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	92.58
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	92.57
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	92.56
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	92.51
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	92.44
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	92.42
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	92.41
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	92.4
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	92.29
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	92.2
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	92.13
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	92.09
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	92.08
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	92.07
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	92.03
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	92.02
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	92.01
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	91.97
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.94
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	91.92
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	91.91
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	91.88
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	91.88
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.82
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	91.73
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	91.72
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	91.7
d1nrjb_	209	Signal recognition particle receptor beta-subunit	91.69
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	91.64
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	91.58
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	91.57
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	91.55
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	91.54
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	91.53
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	91.45
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	91.45
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	91.44
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	91.43
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	91.4
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	91.39
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	91.37
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	91.36
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	91.34
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	91.34
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	91.32
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.32
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	91.32
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	91.3
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	91.29
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	91.28
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	91.28
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	91.2
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	91.2
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	91.19
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	91.16
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	91.13
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	91.12
d2awna2	232	Maltose transport protein MalK, N-terminal domain	91.04
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	91.02
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	91.0
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	91.0
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	90.9
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	90.89
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	90.88
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	90.8
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	90.8
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	90.79
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	90.75
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	90.75
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	90.74
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	90.74
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	90.72
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	90.67
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	90.66
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	90.58
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	90.53
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	90.48
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.47
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	90.42
d1g2912	240	Maltose transport protein MalK, N-terminal domain	90.42
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	90.41
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	90.41
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	90.39
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	90.36
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	90.35
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	90.35
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	90.33
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	90.26
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	90.26
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	90.23
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	90.22
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	90.17
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	90.1
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	90.1
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	90.05
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	90.05
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	90.04
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	90.02
d2dy1a2	267	Elongation factor G (EF-G), N-terminal (G) domain	90.02
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	89.99
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	89.98
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	89.87
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	89.85
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	89.84
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	89.77
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	89.57
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	89.56
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	89.54
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	89.46
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	89.41
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	89.4
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	89.31
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	89.31
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	89.29
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	89.26
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	89.23
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	89.16
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.82
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	88.79
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	88.7
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	88.5
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	88.42
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	88.39
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	88.33
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	88.28
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	88.13
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	88.12
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	88.11
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	88.05
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	88.01
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	87.97
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	87.54
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	87.53
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	87.52
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	87.48
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	87.46
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	87.33
d2afhe1	289	Nitrogenase iron protein {Azotobacter vinelandii [	87.25
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	87.22
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	87.19
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	87.11
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	87.06
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	87.04
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	87.02
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	86.95
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	86.93
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	86.92
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	86.83
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	86.81
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	86.79
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	86.69
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	86.6
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	86.58
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	86.44
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	86.35
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	86.31
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	86.11
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	85.88
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	85.87
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	85.74
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	85.48
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	85.44
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	85.39
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	85.38
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	85.34
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	85.03
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	85.01
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	84.61
d1xpua3	289	Transcription termination factor Rho, ATPase domai	84.43
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	84.32
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	84.24
d1wb1a4	179	Elongation factor SelB, N-terminal domain {Methano	84.16
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	83.71
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	83.7
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	83.52
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	83.39
d1xpua3	289	Transcription termination factor Rho, ATPase domai	82.68
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	82.29
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	82.16
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	82.02
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	81.93
d1g8fa3	122	ATP sulfurylase C-terminal domain {Baker's yeast (	81.91
d2c78a3	204	Elongation factor Tu (EF-Tu), N-terminal (G) domai	81.73
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	81.41
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	80.87
d2olra1	313	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	80.82
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	80.53

>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=100.00  E-value=8.6e-49  Score=419.65  Aligned_cols=251  Identities=58%  Similarity=0.888  Sum_probs=214.1

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ..|++||+||++.++.|++||+|||+.++++++++|+|+.++|+||+||||||||++++.||+++..+++|..+.+.+++
T Consensus         3 ~~l~~~~~~l~~~a~~g~ld~~~gr~~ei~~~~~~L~r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~   82 (387)
T d1qvra2           3 NALEQYGIDLTRLAAEGKLDPVIGRDEEIRRVIQILLRRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIV   82 (387)
T ss_dssp             SHHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHHCSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHhcCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEE
Confidence            57999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEc
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAS  429 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~a  429 (710)
                      .+|++.+++|.+++|+|+.+++.++.++... +++||||||+|.+++.|..     +++.++.++|+++|++|.+.|||+
T Consensus        83 ~ld~~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~-----~g~~d~a~~Lkp~L~rg~~~~I~~  157 (387)
T d1qvra2          83 SLQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKA-----EGAVDAGNMLKPALARGELRLIGA  157 (387)
T ss_dssp             EECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC------------------------HHHHHTTCCCEEEE
T ss_pred             EeeHhhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCC-----CCcccHHHHHHHHHhCCCcceeee
Confidence            9999999999999999999999999999776 4789999999999988754     457889999999999999999999


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDL  509 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~l  509 (710)
                      ||+++|+. ++.|++|.|||+.|.|.+|+.++...||+.+...|+.+|++.++++++..++.++.||+++|++||||+|+
T Consensus       158 tT~~ey~~-~e~d~al~rrF~~v~v~ep~~~~~~~il~~~~~~~e~~h~v~~~~~ai~~~v~ls~ryi~~r~~PdKAidl  236 (387)
T d1qvra2         158 TTLDEYRE-IEKDPALERRFQPVYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKAIDL  236 (387)
T ss_dssp             ECHHHHHH-HTTCTTTCSCCCCEEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHHHHH
T ss_pred             cCHHHHHH-hcccHHHHHhcccccCCCCcHHHHHHHHHHHHHHHHhccCCcccHHHHHHHHHhcccccccccChhhHHHH
Confidence            99999986 68899999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHhhhhhhhhhchhh
Q 005179          510 VDEAGSRAHIELFKRKKE  527 (710)
Q Consensus       510 l~~a~~~~~~~~~~~~~~  527 (710)
                      ||+||+++++....+|.+
T Consensus       237 ld~a~a~~~i~~~s~P~e  254 (387)
T d1qvra2         237 IDEAAARLRMALESAPEE  254 (387)
T ss_dssp             HHHHHHHHHHTTTTHHHH
T ss_pred             HHHHHHHHHhhccCCcHH
Confidence            999999999998888874

>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=100.00  E-value=9.7e-47  Score=382.60  Aligned_cols=244  Identities=55%  Similarity=0.884  Sum_probs=232.0

Q ss_pred             HHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          273 LEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       273 l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      |++|+.||+++++.|++++++||++++++++++|.++.++|++|+||||||||++++.+|+++..+++|..+.+++++.+
T Consensus         1 L~~~~~dlt~~a~~~~ld~~igRd~Ei~~l~~iL~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l   80 (268)
T d1r6bx2           1 LENFTTNLNQLARVGGIDPLIGREKELERAIQVLCRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSL   80 (268)
T ss_dssp             CCSSSCBHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEEC
T ss_pred             ChHHhHHHHHHHHcCCCCcccChHHHHHHHHHHHhcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEe
Confidence            46899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccCh
Q 005179          353 DMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQ  432 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~  432 (710)
                      |++.+++|.+++|+|+++++.+++++...+++||||||+|.|++.|..    .+++.++.++|+++|++|++.||++||+
T Consensus        81 ~~~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~----~g~~~d~a~~Lkp~L~rg~i~vIgatT~  156 (268)
T d1r6bx2          81 DIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAA----SGGQVDAANLIKPLLSSGKIRVIGSTTY  156 (268)
T ss_dssp             CCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCS----SSCHHHHHHHHSSCSSSCCCEEEEEECH
T ss_pred             eechHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCC----CCccccHHHHhhHHHhCCCCeEEEeCCH
Confidence            999999999999999999999999999888999999999999988765    2447899999999999999999999999


Q ss_pred             HHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHHHH
Q 005179          433 DEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLVDE  512 (710)
Q Consensus       433 ~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~  512 (710)
                      ++|.++++.|++|.+||+.|.|.+|+.++...||+.+...|+.+|++.++++++..++.++.+|++++++|+||++++|+
T Consensus       157 eey~~~~e~d~al~rrF~~I~V~Eps~e~t~~IL~~~~~~~e~~h~v~~~~~al~~~v~ls~ryi~~~~~PdKAIdllDe  236 (268)
T d1r6bx2         157 QEFSNIFEKDRALARRFQKIDITEPSIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDE  236 (268)
T ss_dssp             HHHHCCCCCTTSSGGGEEEEECCCCCHHHHHHHHHHHHHHHHHHHTCCCCHHHHHHHHHHHHHHCTTSCTTHHHHHHHHH
T ss_pred             HHHHHHHhhcHHHHhhhcccccCCCCHHHHHHHHHHhhHHHhccCCEEeChHHHHHHHHHHHhhccCCCCCcHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhhhhh
Q 005179          513 AGSRAHIE  520 (710)
Q Consensus       513 a~~~~~~~  520 (710)
                      ||+++++.
T Consensus       237 a~a~~~~~  244 (268)
T d1r6bx2         237 AGARARLM  244 (268)
T ss_dssp             HHHHHHHS
T ss_pred             HHHHHHhh
Confidence            99887764

>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=100.00  E-value=8.5e-38  Score=299.40  Aligned_cols=192  Identities=56%  Similarity=0.922  Sum_probs=178.1

Q ss_pred             hhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEE
Q 005179          271 SALEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIM  350 (710)
Q Consensus       271 ~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~  350 (710)
                      ..|++|+.||+++++.|++++++||++++++++++|+++.++|++|+||||||||++++.+|+++..+++|..+.+.+++
T Consensus         3 ~~l~~~~~dlt~~a~~g~ld~~igRd~Ei~~l~~iL~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~   82 (195)
T d1jbka_           3 QALKKYTIDLTERAEQGKLDPVIGRDEEIRRTIQVLQRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVL   82 (195)
T ss_dssp             HHHHHHEEEHHHHHHTTCSCCCCSCHHHHHHHHHHHTSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHhccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEE
Confidence            46999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeehhhhhhccccCccHHHHHHHHHHHHHhc-CCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEc
Q 005179          351 SLDMGLLMAGAKERGELEARVTTLISEIQKS-GDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIAS  429 (710)
Q Consensus       351 ~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~-~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~a  429 (710)
                      ++|++.+++|.+++|+|+++++.+++++... +++||||||+|.+++++..     .++.++.++|+++|++|++.||++
T Consensus        83 ~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~-----~g~~d~~~~Lkp~L~rg~l~~Iga  157 (195)
T d1jbka_          83 ALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKA-----DGAMDAGNMLKPALARGELHCVGA  157 (195)
T ss_dssp             EECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT-----------CCCCHHHHHHHHHTTSCCEEEE
T ss_pred             EeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCC-----CCcccHHHHHHHHHhCCCceEEec
Confidence            9999999999999999999999999998654 5799999999999987654     345678999999999999999999


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHH
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILL  467 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~  467 (710)
                      ||+++|+++++.|++|.+||+.|.|.+|+.++...||+
T Consensus       158 tT~eey~~~~e~d~aL~rrF~~I~V~Ep~~e~t~~IL~  195 (195)
T d1jbka_         158 TTLDEYRQYIEKDAALERRFQKVFVAEPSVEDTIAILR  195 (195)
T ss_dssp             ECHHHHHHHTTTCHHHHTTEEEEECCCCCHHHHHTTCC
T ss_pred             CCHHHHHHHHHcCHHHHhcCCEeecCCCCHHHHHHHhC
Confidence            99999999999999999999999999999999888763

>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=99.88  E-value=1.1e-22  Score=204.57  Aligned_cols=200  Identities=22%  Similarity=0.265  Sum_probs=144.9

Q ss_pred             CCCCcccCHHHHHHHHHHH---H---------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          288 LIDPVIGRETEIQRIIQIL---C---------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L---~---------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +|++++|.++..++|.+++   .         ...++++||+||||||||++|+++|+++          +.+++.++++
T Consensus         7 ~~~di~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~----------~~~~~~i~~~   76 (247)
T d1ixza_           7 TFKDVAGAEEAKEELKEIVEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEA----------RVPFITASGS   76 (247)
T ss_dssp             CGGGCCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHT----------TCCEEEEEHH
T ss_pred             cHHHHccHHHHHHHHHHHHHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHc----------CCCEEEEEhH
Confidence            6889999998777665543   1         1335679999999999999999999988          8899999999


Q ss_pred             hhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCC-ChHhHHHhhcccc----cCCCeEEEEcc
Q 005179          356 LLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKG-TGLDISNLLKPSL----GRGELQCIAST  430 (710)
Q Consensus       356 ~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~-~~~~~~~~L~~~l----~~~~v~vI~at  430 (710)
                      .+.  .++.|+.+..++.+|+.++...|+||||||+|.+++....+..... ....+.+.|...+    .+..+++|+||
T Consensus        77 ~l~--~~~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~vivi~tT  154 (247)
T d1ixza_          77 DFV--EMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEKDTAIVVMAAT  154 (247)
T ss_dssp             HHH--HSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCTTCCEEEEEEE
T ss_pred             Hhh--hccccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEeC
Confidence            888  4678899999999999999889999999999999876433211000 0111233333333    34678899999


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHH
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAI  507 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai  507 (710)
                      |..+     .+|+++.|  ||+ .|.|+.|+.++|.+||+.++......     .+..+..+++.+.+|..     .+..
T Consensus       155 n~~~-----~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~-----~~~~~~~la~~t~g~s~-----~di~  219 (247)
T d1ixza_         155 NRPD-----ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLA-----EDVDLALLAKRTPGFVG-----ADLE  219 (247)
T ss_dssp             SCGG-----GSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBC-----TTCCHHHHHHTCTTCCH-----HHHH
T ss_pred             CCcc-----ccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCc-----cccCHHHHHHHCCCCCH-----HHHH
Confidence            9876     78999986  997 89999999999999999877643211     22235677777766633     3445


Q ss_pred             HHHHHHH
Q 005179          508 DLVDEAG  514 (710)
Q Consensus       508 ~ll~~a~  514 (710)
                      .+++.|.
T Consensus       220 ~lv~~A~  226 (247)
T d1ixza_         220 NLLNEAA  226 (247)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            5666554

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

Probab=99.88  E-value=1.4e-22  Score=185.87  Aligned_cols=136  Identities=18%  Similarity=0.251  Sum_probs=120.2

Q ss_pred             HHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcC
Q 005179           83 ERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQG  160 (710)
Q Consensus        83 ~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~  160 (710)
                      +|||++++++|..|+.+|++++|.+|+|||||+|||.++++  ..+|..+|++++.++..+...+...|..         
T Consensus         1 ~kfT~~~~~~l~~A~~~A~~~~h~~v~~eHlL~all~~~~~~~~~iL~~~g~d~~~~~~~~~~~l~~~p~~---------   71 (139)
T d1khya_           1 DRLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQALNRLPQV---------   71 (139)
T ss_dssp             CCBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHHHHTCCHHHHHHHHHHHHTTSCCC---------
T ss_pred             CccCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCcccHHHHHHHHcCCcHHHHHHHHHHHhhccccc---------
Confidence            58999999999999999999999999999999999998876  7899999999999999999988877653         


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHH
Q 005179          161 KPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAV  230 (710)
Q Consensus       161 ~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~  230 (710)
                        .+....+++|+.+.++|+.|...|+.+|+.||+++|||+||++ +++.++++|+++||+.+.+++.+.
T Consensus        72 --~~~~~~~~~s~~~~~vl~~A~~~a~~~~d~~I~~ehlLlall~-~~~~~~~~L~~~gi~~~~l~~~i~  138 (139)
T d1khya_          72 --EGTGGDVQPSQDLVRVLNLCDKLAQKRGDNFISSELFVLAALE-SRGTLADILKAAGATTANITQAIE  138 (139)
T ss_dssp             ---------CBCHHHHHHHHHHHHHHHHHTCSSBCHHHHHHHHHT-SCHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             --cCccccccccHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHc-CCcHHHHHHHHcCCCHHHHHHHhc
Confidence              2445678999999999999999999999999999999999997 567899999999999999988653

>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=99.87  E-value=5.8e-22  Score=200.02  Aligned_cols=201  Identities=19%  Similarity=0.269  Sum_probs=149.8

Q ss_pred             cCCCCcccCHHHHHHHHHHH---H---------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          287 ELIDPVIGRETEIQRIIQIL---C---------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       287 ~~l~~liGr~~~i~~l~~~L---~---------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      -+|++++|.++..+++.+++   .         ...++++||+||||||||++|+++|.++          +.+++.+++
T Consensus         9 ~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~----------~~~~~~i~~   78 (256)
T d1lv7a_           9 TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEA----------KVPFFTISG   78 (256)
T ss_dssp             CCGGGSCSCHHHHHHTHHHHHHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHH----------TCCEEEECS
T ss_pred             CCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHc----------CCCEEEEEh
Confidence            35789999998887776643   1         2345679999999999999999999999          889999999


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCC-CChHhHHHhhcccc----cCCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNK-GTGLDISNLLKPSL----GRGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~-~~~~~~~~~L~~~l----~~~~v~vI~a  429 (710)
                      +.+.  .++.|+.+..++.+|+.++...|+||||||+|.++..+..+.... .....+.+.|...+    .+..+.+|+|
T Consensus        79 ~~l~--~~~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~~~~v~vIat  156 (256)
T d1lv7a_          79 SDFV--EMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEGNEGIIVIAA  156 (256)
T ss_dssp             CSST--TSCCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCSSSCEEEEEE
T ss_pred             HHhh--hcchhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCCCCCEEEEEe
Confidence            8887  467888899999999999999999999999999986543322111 11122333443333    3567899999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ||.++     .+|++++|  ||+ .|.|+.|+.++|.+||+....++    ++. .+..+..+++.+.+|..     .+.
T Consensus       157 Tn~~~-----~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~G~s~-----adi  221 (256)
T d1lv7a_         157 TNRPD-----VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRV----PLA-PDIDAAIIARGTPGFSG-----ADL  221 (256)
T ss_dssp             ESCTT-----TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTS----CBC-TTCCHHHHHHTCTTCCH-----HHH
T ss_pred             CCCcc-----cCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCC----CcC-cccCHHHHHHhCCCCCH-----HHH
Confidence            99886     78999997  997 89999999999999999776543    222 22335667777776633     455


Q ss_pred             HHHHHHHH
Q 005179          507 IDLVDEAG  514 (710)
Q Consensus       507 i~ll~~a~  514 (710)
                      ..++++|.
T Consensus       222 ~~l~~~A~  229 (256)
T d1lv7a_         222 ANLVNEAA  229 (256)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            56666654

>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=99.84  E-value=3.3e-21  Score=195.46  Aligned_cols=199  Identities=23%  Similarity=0.269  Sum_probs=151.3

Q ss_pred             CCCCcccCHHHHHHHHHHH----H---------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQIL----C---------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L----~---------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .|++++|.+..++++.+.+    .         ...++++||+||||||||++++++|..+          +.+++.+++
T Consensus         2 ~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~----------~~~~~~i~~   71 (258)
T d1e32a2           2 GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANET----------GAFFFLING   71 (258)
T ss_dssp             CGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHT----------TCEEEEECH
T ss_pred             ChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHh----------CCeEEEEEc
Confidence            4788999999888887753    2         1345789999999999999999999998          889999998


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhc----ccccCCCeEEEEcc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLK----PSLGRGELQCIAST  430 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~----~~l~~~~v~vI~at  430 (710)
                      +.+.  ..+.|+.+..++.+|+.+....|+||||||+|.++.....+.+  +....+.+.+.    .......+.+|+||
T Consensus        72 ~~l~--~~~~g~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~--~~~~~~~~~~~~~~~~~~~~~~vlvi~tT  147 (258)
T d1e32a2          72 PEIM--SKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHG--EVERRIVSQLLTLMDGLKQRAHVIVMAAT  147 (258)
T ss_dssp             HHHT--TSCTTHHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCC--TTHHHHHHHHHHHHHTCCCSSCEEEEEEE
T ss_pred             hhhc--ccccccHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCC--chHHHHHHHhccccccccccCCccEEEeC
Confidence            8887  4567888899999999999999999999999999865433211  22222333322    23345678999999


Q ss_pred             ChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHH
Q 005179          431 TQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAI  507 (710)
Q Consensus       431 t~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai  507 (710)
                      |..+     .+|++++|  ||+ .|.|+.|+.++|..||+.++...    .+. .+..+..+++.+.+|.+     .+..
T Consensus       148 n~~~-----~ld~al~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~----~~~-~~~~~~~la~~t~G~s~-----adl~  212 (258)
T d1e32a2         148 NRPN-----SIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNM----KLA-DDVDLEQVANETHGHVG-----ADLA  212 (258)
T ss_dssp             SCGG-----GSCGGGTSTTSSCEEEECCCCCHHHHHHHHHHTTTTS----CBC-TTCCHHHHHHHCTTCCH-----HHHH
T ss_pred             CCcc-----ccchhhhhcccccceeECCCCCHHHHHHHhhhhccCc----ccc-cccchhhhhhcccCCCH-----HHHH
Confidence            9987     78999998  997 89999999999999999876532    111 12236788888888744     4556


Q ss_pred             HHHHHHHh
Q 005179          508 DLVDEAGS  515 (710)
Q Consensus       508 ~ll~~a~~  515 (710)
                      .++.+|+.
T Consensus       213 ~lv~~A~~  220 (258)
T d1e32a2         213 ALCSEAAL  220 (258)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            67766653

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=99.83  E-value=1.4e-20  Score=173.11  Aligned_cols=138  Identities=14%  Similarity=0.208  Sum_probs=122.0

Q ss_pred             hhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCcHHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcCCCCC
Q 005179           85 FTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRHPNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQGKPFS  164 (710)
Q Consensus        85 ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~  164 (710)
                      ||.+++.+|..|+.+|++++|++|+|||||+|||.++++..++..+|++.+.++..+...+...+...        ....
T Consensus         2 ~s~~l~~~l~~A~~~A~~~~h~~i~~EHLL~aLl~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~--------~~~~   73 (142)
T d1k6ka_           2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNPSAREALEACSVDLVALRQELEAFIEQTTPVL--------PASE   73 (142)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCHHHHHHHHHTTCCHHHHHHHHHHHHHHHSCBC--------CSSC
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhchhHHHHHHHcCCchhhhHHHHHHHHHhcCCCC--------Cccc
Confidence            68899999999999999999999999999999998766688999999999999999988776654321        0123


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHH
Q 005179          165 SAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAV  230 (710)
Q Consensus       165 ~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~  230 (710)
                      ....+++|+.++++|+.|..+|+.+|+.||+++|||+||+.++++.+.++|+++||+.+++.+.+.
T Consensus        74 ~~~~~~~s~~l~~il~~A~~~a~~~~~~~i~~ehlLlall~~~~~~a~~lL~~~Gi~~~~l~~~Is  139 (142)
T d1k6ka_          74 EERDTQPTLSFQRVLQRAVFHVQSSGRNEVTGANVLVAIFSEQESQAAYLLRKHEVSRLDVVNFIS  139 (142)
T ss_dssp             SCCSCEECHHHHHHHHHHHHHHHSSSCSCBCHHHHHHHHTTCTTSHHHHHHHHTTCCHHHHHHHHH
T ss_pred             cccccccCHHHHHHHHHHHHHHHHcCCCcchHHHHHHHHHHccCcHHHHHHHHCCCCHHHHHHHHh
Confidence            456789999999999999999999999999999999999999999999999999999998877554

>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=99.81  E-value=1.4e-20  Score=191.35  Aligned_cols=202  Identities=18%  Similarity=0.278  Sum_probs=145.1

Q ss_pred             CCCCcccCHHHHHHHHHHH----H---------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          288 LIDPVIGRETEIQRIIQIL----C---------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       288 ~l~~liGr~~~i~~l~~~L----~---------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +|++++|.++..++|.+.+    .         ...+.++||+||||||||++++++|..+          +.+++.+++
T Consensus         5 ~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~----------~~~~~~~~~   74 (265)
T d1r7ra3           5 TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANEC----------QANFISIKG   74 (265)
T ss_dssp             SCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHT----------TCEEEEECH
T ss_pred             CHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHh----------CCcEEEEEH
Confidence            6888888887655555432    1         1235679999999999999999999999          889999998


Q ss_pred             hhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCC-ChHhHHHhhcccc----cCCCeEEEEc
Q 005179          355 GLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKG-TGLDISNLLKPSL----GRGELQCIAS  429 (710)
Q Consensus       355 ~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~-~~~~~~~~L~~~l----~~~~v~vI~a  429 (710)
                      +.+.  ..+.|+.+..++.+|..+....|+||||||+|.++.......++.. ....+.+.|...+    ++.++.+|+|
T Consensus        75 ~~l~--~~~~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~v~vi~t  152 (265)
T d1r7ra3          75 PELL--TMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGA  152 (265)
T ss_dssp             HHHH--TSCTTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC------CCEEEEC
T ss_pred             HHhh--hccccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCCCCCEEEEEe
Confidence            8887  4567888899999999999999999999999999764322111000 0112334444444    4567899999


Q ss_pred             cChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchH
Q 005179          430 TTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKA  506 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~a  506 (710)
                      ||..+     .+|++|.|  ||+ .|.|+.|+.++|.+||+.++.+.....++     .++.++..+.+|..     .+.
T Consensus       153 tn~~~-----~ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~-----~l~~la~~t~g~s~-----~di  217 (265)
T d1r7ra3         153 TNRPD-----IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDV-----DLEFLAKMTNGFSG-----ADL  217 (265)
T ss_dssp             CBSCT-----TTSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CC-----CCHHHHHHHCSSCC-----HHH
T ss_pred             CCCch-----hCCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhh-----hHHHHHhcCCCCCH-----HHH
Confidence            99876     78999987  897 89999999999999999766533222222     24667777777643     556


Q ss_pred             HHHHHHHHhh
Q 005179          507 IDLVDEAGSR  516 (710)
Q Consensus       507 i~ll~~a~~~  516 (710)
                      ..++++|...
T Consensus       218 ~~lv~~A~~~  227 (265)
T d1r7ra3         218 TEICQRACKL  227 (265)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            6677776543

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=99.81  E-value=7.4e-20  Score=168.33  Aligned_cols=116  Identities=16%  Similarity=0.127  Sum_probs=106.8

Q ss_pred             HHhhHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCCCc--HHHHHHCCCCHHHHHHHHHHHhhcCCCCCCchhhhcC
Q 005179           83 ERFTERAVKAVIFSQREAKSLGKDMVFTQHLLLGLIAEDRH--PNGFLESGITIDKAREAVVSIWHSTNNQDTDDAAAQG  160 (710)
Q Consensus        83 ~~ft~~a~~~l~~A~~~A~~~~~~~i~~eHLLlaLl~~~~~--~~~l~~~gv~~~~l~~~~~~~~~~~~~~~~~~~~~~~  160 (710)
                      ++||++++++|..|+++|++++|.+|+|+|||+|||.++++  ..+|..+|+|++.++..+...+.+.|..         
T Consensus         1 dkfT~~a~~~l~~A~~~A~~~~~~~i~~~HlL~all~~~~~~~~~iL~~~gvd~~~l~~~l~~~l~~~p~~---------   71 (145)
T d1qvra1           1 ERWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADPKALKELQERELARLPKV---------   71 (145)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHHTTSSCHHHHHHHHHHHHHTSCCC---------
T ss_pred             CccCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcchHHHHHHHcCCCHHHHHHHHHHHhhccccc---------
Confidence            57999999999999999999999999999999999998887  7899999999999999999999988653         


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCc
Q 005179          161 KPFSSAAKMPFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDG  209 (710)
Q Consensus       161 ~~~~~~~~~~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~  209 (710)
                        .+....+++|+.++++|+.|..+|+++|+.||+++|||+||+++.++
T Consensus        72 --~~~~~~~~~s~~l~~il~~A~~~a~~~gd~~Is~ehLllal~~~~~~  118 (145)
T d1qvra1          72 --EGAEVGQYLTSRLSGALNRAEGLMEELKDRYVAVDTLVLALAEATPG  118 (145)
T ss_dssp             --CGGGTTCEECHHHHHHHHHHHHHHHTTTCSSCCHHHHHHHHHHHSTT
T ss_pred             --CCCcccCCCCHHHHHHHHHHHHHHHHcCCccccHHHHHHHHHhcccc
Confidence              24455788999999999999999999999999999999999987764

>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=1.8e-18  Score=172.20  Aligned_cols=205  Identities=18%  Similarity=0.251  Sum_probs=150.7

Q ss_pred             HHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          273 LEQFCVDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       273 l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      ...+..+|+++++|.+|++++|+++.++.+..++......++||+||||+|||++|+.+|+++....     ....++++
T Consensus         7 ~~~~~~~w~~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtla~~iak~l~~~~-----~~~~~~e~   81 (231)
T d1iqpa2           7 VKVLEKPWVEKYRPQRLDDIVGQEHIVKRLKHYVKTGSMPHLLFAGPPGVGKTTAALALARELFGEN-----WRHNFLEL   81 (231)
T ss_dssp             HHHTTSCHHHHTCCCSTTTCCSCHHHHHHHHHHHHHTCCCEEEEESCTTSSHHHHHHHHHHHHHGGG-----HHHHEEEE
T ss_pred             hhhhhchHHHHhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHHhcc-----cCCCeeEE
Confidence            4445578999999999999999999999999999998888999999999999999999999885321     13345666


Q ss_pred             ehhhhhhccccCccHHHHHHHHHHH--HHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCeEEEE
Q 005179          353 DMGLLMAGAKERGELEARVTTLISE--IQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGELQCIA  428 (710)
Q Consensus       353 d~~~l~~g~~~~g~~e~~l~~~~~~--~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v~vI~  428 (710)
                      +.++....    ......+......  .......|+++||++.+             ....++.|+..++  ...+.+|+
T Consensus        82 n~s~~~~~----~~~~~~~~~~~~~~~~~~~~~~iilide~d~~-------------~~~~~~~ll~~l~~~~~~~~~i~  144 (231)
T d1iqpa2          82 NASDERGI----NVIREKVKEFARTKPIGGASFKIIFLDEADAL-------------TQDAQQALRRTMEMFSSNVRFIL  144 (231)
T ss_dssp             ETTCHHHH----HTTHHHHHHHHHSCCGGGCSCEEEEEETGGGS-------------CHHHHHHHHHHHHHTTTTEEEEE
T ss_pred             ecCcccch----hHHHHHHHHHHhhhhccCCCceEEeehhhhhc-------------chhHHHHHhhhcccCCcceEEEe
Confidence            55432210    0111111111111  11235789999999998             3345566666665  34567888


Q ss_pred             ccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHH
Q 005179          429 STTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID  508 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~  508 (710)
                      +++...     .+++++.+||..+.+.+|+..+...+++.++.    ..++.+++++++.+++.+.+-      .++++.
T Consensus       145 ~~n~~~-----~i~~~l~sR~~~i~~~~~~~~~~~~~l~~~~~----~e~i~i~~~~l~~I~~~~~gd------iR~ai~  209 (231)
T d1iqpa2         145 SCNYSS-----KIIEPIQSRCAIFRFRPLRDEDIAKRLRYIAE----NEGLELTEEGLQAILYIAEGD------MRRAIN  209 (231)
T ss_dssp             EESCGG-----GSCHHHHHTEEEEECCCCCHHHHHHHHHHHHH----TTTCEECHHHHHHHHHHHTTC------HHHHHH
T ss_pred             ccCChh-----hchHhHhCccccccccccchhhHHHHHHHHHH----HhCCCCCHHHHHHHHHHcCCC------HHHHHH
Confidence            887764     67899999999999999999999999988776    457889999999999887652      346777


Q ss_pred             HHHHHH
Q 005179          509 LVDEAG  514 (710)
Q Consensus       509 ll~~a~  514 (710)
                      .|+.+.
T Consensus       210 ~Lq~~~  215 (231)
T d1iqpa2         210 ILQAAA  215 (231)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            776554

>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=99.76  E-value=1e-17  Score=165.92  Aligned_cols=196  Identities=18%  Similarity=0.257  Sum_probs=146.3

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      .+|++++||..|++++|+++.++.|..++......|+||+||||+|||++|+.+++.+....     ....++.++.++.
T Consensus         3 ~pw~eKyrP~~~~d~ig~~~~~~~L~~~~~~~~~~~~ll~Gp~G~GKTt~a~~la~~l~~~~-----~~~~~~~~n~~~~   77 (224)
T d1sxjb2           3 LPWVEKYRPQVLSDIVGNKETIDRLQQIAKDGNMPHMIISGMPGIGKTTSVHCLAHELLGRS-----YADGVLELNASDD   77 (224)
T ss_dssp             CCHHHHTCCSSGGGCCSCTHHHHHHHHHHHSCCCCCEEEECSTTSSHHHHHHHHHHHHHGGG-----HHHHEEEECTTSC
T ss_pred             CchHhHhCCCCHHHhcCCHHHHHHHHHHHHcCCCCeEEEECCCCCCchhhHHHHHHHHhccc-----ccccccccccccc
Confidence            46999999999999999999999999999988888999999999999999999999985431     1234555554321


Q ss_pred             hhccccCccHHHHHHHHHHHHHh-------cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEE
Q 005179          358 MAGAKERGELEARVTTLISEIQK-------SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIA  428 (710)
Q Consensus       358 ~~g~~~~g~~e~~l~~~~~~~~~-------~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~  428 (710)
                            ++.  ..+...+.....       ....+++|||+|.+             ....++.|+..++.  ....+|.
T Consensus        78 ------~~~--~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~-------------~~~~~~~ll~~~e~~~~~~~~i~  136 (224)
T d1sxjb2          78 ------RGI--DVVRNQIKHFAQKKLHLPPGKHKIVILDEADSM-------------TAGAQQALRRTMELYSNSTRFAF  136 (224)
T ss_dssp             ------CSH--HHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGS-------------CHHHHHTTHHHHHHTTTTEEEEE
T ss_pred             ------CCc--eehhhHHHHHHHhhccCCCcceEEEEEeccccc-------------chhHHHHHhhhccccccceeeee
Confidence                  111  112222222211       23569999999999             34456777666653  3455666


Q ss_pred             ccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHH
Q 005179          429 STTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAID  508 (710)
Q Consensus       429 att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~  508 (710)
                      +++...     .+.+++++||..|.|.+|+.++...+|..++.+.    ++.+++++++.++..+.+-      +++++.
T Consensus       137 ~~~~~~-----~i~~~l~sr~~~i~~~~~~~~~i~~~l~~i~~~e----~~~i~~~~l~~I~~~s~Gd------~R~ai~  201 (224)
T d1sxjb2         137 ACNQSN-----KIIEPLQSQCAILRYSKLSDEDVLKRLLQIIKLE----DVKYTNDGLEAIIFTAEGD------MRQAIN  201 (224)
T ss_dssp             EESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHH----TCCBCHHHHHHHHHHHTTC------HHHHHH
T ss_pred             ccCchh-----hhhhHHHHHHHHhhhcccchhhhHHHHHHHHHhc----ccCCCHHHHHHHHHHcCCc------HHHHHH
Confidence            666544     6789999999999999999999999999888743    7899999999999887653      456788


Q ss_pred             HHHHHH
Q 005179          509 LVDEAG  514 (710)
Q Consensus       509 ll~~a~  514 (710)
                      .|+.++
T Consensus       202 ~Lq~~~  207 (224)
T d1sxjb2         202 NLQSTV  207 (224)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877654

>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=99.75  E-value=6.4e-19  Score=183.04  Aligned_cols=102  Identities=52%  Similarity=0.774  Sum_probs=95.9

Q ss_pred             CChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          607 IPVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       607 ip~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ||++++..++.+++.++++.|.++|+||++|++.|..++++.+.|+.+|.+|.+.|||+||||||||++|++||+.|||.
T Consensus         1 ~p~~~~~~~~~~~l~~l~~~L~~~v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~   80 (315)
T d1qvra3           1 IPVSKLLEGEREKLLRLEEELHKRVVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT   80 (315)
T ss_dssp             CHHHHTTCCHHHHHHSHHHHHHHHSCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS
T ss_pred             CCchhhhHHHHHHHHHHHHHhcCeEeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC
Confidence            67888889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcceeeCCCCCCCcchhhhccc
Q 005179          687 VRIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       687 ~~~li~~d~se~~~~~~~~~~~~  709 (710)
                      +.+++++||++| ..++++++++
T Consensus        81 ~~~~~~~~~~~~-~~~~~~~~L~  102 (315)
T d1qvra3          81 EEAMIRIDMTEY-MEKHAVSRLI  102 (315)
T ss_dssp             GGGEEEECTTTC-CSSGGGGGC-
T ss_pred             CcceEEEecccc-ccchhhhhhc
Confidence            999999999999 5667777765

>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=99.74  E-value=9.3e-18  Score=167.95  Aligned_cols=199  Identities=19%  Similarity=0.179  Sum_probs=146.8

Q ss_pred             hHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc--------------
Q 005179          280 LTARASEELIDPVIGRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL--------------  344 (710)
Q Consensus       280 l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l--------------  344 (710)
                      |.+++||.+|++++|+++.++.+..++......+ +||+||||+|||++|+.+++.+.........              
T Consensus         2 ~~~KyrP~~~~dlig~~~~~~~L~~~i~~~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~   81 (239)
T d1njfa_           2 LARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDNCREIEQG   81 (239)
T ss_dssp             HHHHTCCSSGGGSCSCHHHHHHHHHHHHTTCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHHHHHHHHT
T ss_pred             chhhhCCCCHHHccChHHHHHHHHHHHHcCCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchHHHHHHcC
Confidence            5789999999999999999999999887766555 8999999999999999999988543211100              


Q ss_pred             cCceEEEeehhhhhhccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc
Q 005179          345 LSKRIMSLDMGLLMAGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG  420 (710)
Q Consensus       345 ~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~  420 (710)
                      ....++.++.+.      .. . ...++.+++.+..    ++..|+||||+|.|             ..+.++.|+..++
T Consensus        82 ~~~~~~~~~~~~------~~-~-i~~ir~~~~~~~~~~~~~~~kviiIde~d~l-------------~~~~q~~Llk~lE  140 (239)
T d1njfa_          82 RFVDLIEIDAAS------RT-K-VEDTRDLLDNVQYAPARGRFKVYLIDEVHML-------------SRHSFNALLKTLE  140 (239)
T ss_dssp             CCTTEEEEETTC------SS-S-HHHHHHHHHSCCCSCSSSSSEEEEEETGGGS-------------CHHHHHHHHHHHH
T ss_pred             CCCeEEEecchh------cC-C-HHHHHHHHHHHHhccccCCCEEEEEECcccC-------------CHHHHHHHHHHHh
Confidence            001233333211      11 1 1224455544422    23469999999999             4567788888887


Q ss_pred             C--CCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          421 R--GELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       421 ~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      .  ....+|++|+...     .+.+++.+||..+.+++|+.++...++..++...    ++.+++++++.++..+.+   
T Consensus       141 ~~~~~~~~il~tn~~~-----~i~~~i~SRc~~i~~~~~~~~~i~~~l~~i~~~e----~~~~~~~~l~~i~~~s~G---  208 (239)
T d1njfa_         141 EPPEHVKFLLATTDPQ-----KLPVTILSRCLQFHLKALDVEQIRHQLEHILNEE----HIAHEPRALQLLARAAEG---  208 (239)
T ss_dssp             SCCTTEEEEEEESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHH----TCCBCHHHHHHHHHHTTT---
T ss_pred             cCCCCeEEEEEcCCcc-----ccChhHhhhhcccccccCcHHHhhhHHHHHHhhh----ccCCCHHHHHHHHHHcCC---
Confidence            5  5678888888765     6789999999999999999999888888777643    688999999999887654   


Q ss_pred             CCCCcchHHHHHHHHH
Q 005179          499 DRYLPDKAIDLVDEAG  514 (710)
Q Consensus       499 ~r~~p~~ai~ll~~a~  514 (710)
                         .+++++.+++.+.
T Consensus       209 ---d~R~ain~l~~~~  221 (239)
T d1njfa_         209 ---SLRDALSLTDQAI  221 (239)
T ss_dssp             ---CHHHHHHHHHHHH
T ss_pred             ---CHHHHHHHHHHHH
Confidence               3567888887765

>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=99.73  E-value=5.5e-18  Score=168.12  Aligned_cols=183  Identities=20%  Similarity=0.257  Sum_probs=135.0

Q ss_pred             hhhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          278 VDLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       278 ~~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      .+|++++||.+|++++|+++.++.|..++......++||+||||+|||++++.+++.+.....     ...++..+.+..
T Consensus         2 ~pw~ekyrP~~~~divg~~~~~~~L~~~i~~~~~~~lLl~Gp~G~GKttl~~~la~~l~~~~~-----~~~~~e~~~~~~   76 (227)
T d1sxjc2           2 LPWVEKYRPETLDEVYGQNEVITTVRKFVDEGKLPHLLFYGPPGTGKTSTIVALAREIYGKNY-----SNMVLELNASDD   76 (227)
T ss_dssp             CCHHHHTCCSSGGGCCSCHHHHHHHHHHHHTTCCCCEEEECSSSSSHHHHHHHHHHHHHTTSH-----HHHEEEECTTSC
T ss_pred             CchhhhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChhHHHHHHHHHhhcCCC-----cceeEEeccccc
Confidence            379999999999999999999999999999888889999999999999999999999843211     112333332211


Q ss_pred             hhccccCccHHHHHHHHHHHH-H-----hcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEc
Q 005179          358 MAGAKERGELEARVTTLISEI-Q-----KSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIAS  429 (710)
Q Consensus       358 ~~g~~~~g~~e~~l~~~~~~~-~-----~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~a  429 (710)
                            .+ ... ........ .     ..+..+++|||+|.+             ....++.|+..++.  ....++.+
T Consensus        77 ------~~-~~~-~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~-------------~~~~~~~Ll~~le~~~~~~~~~~~  135 (227)
T d1sxjc2          77 ------RG-IDV-VRNQIKDFASTRQIFSKGFKLIILDEADAM-------------TNAAQNALRRVIERYTKNTRFCVL  135 (227)
T ss_dssp             ------CS-HHH-HHTHHHHHHHBCCSSSCSCEEEEETTGGGS-------------CHHHHHHHHHHHHHTTTTEEEEEE
T ss_pred             ------CC-eee-eecchhhccccccccCCCeEEEEEeccccc-------------hhhHHHHHHHHhhhcccceeeccc
Confidence                  11 111 11111111 1     123459999999998             34456667766663  45666666


Q ss_pred             cChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhh
Q 005179          430 TTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       430 tt~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~  495 (710)
                      ++...     .+.+++++||..+.+.+|+.++...+|..++.    ..++.+++++++.+++.+.+
T Consensus       136 ~~~~~-----~i~~~i~sr~~~i~~~~~~~~~i~~~l~~I~~----~e~i~i~~~~l~~i~~~s~G  192 (227)
T d1sxjc2         136 ANYAH-----KLTPALLSQCTRFRFQPLPQEAIERRIANVLV----HEKLKLSPNAEKALIELSNG  192 (227)
T ss_dssp             ESCGG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHHHHH----TTTCCBCHHHHHHHHHHHTT
T ss_pred             cCcHH-----HhHHHHHHHHhhhccccccccccccccccccc----cccccCCHHHHHHHHHHcCC
Confidence            66654     68899999999999999999999888887776    45889999999999988765

>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=99.72  E-value=8e-18  Score=167.81  Aligned_cols=201  Identities=16%  Similarity=0.214  Sum_probs=139.0

Q ss_pred             hhHHhhhhcCCCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          279 DLTARASEELIDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       279 ~l~~~~~~~~l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      +|.++++|.+|++++|+++.++.+..++......+++|+||||+|||++++.+++++.....    .....+.++.+...
T Consensus         1 ~w~~ky~P~~~~diig~~~~~~~l~~~i~~~~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~----~~~~~~~~~~~~~~   76 (237)
T d1sxjd2           1 PWVEKYRPKNLDEVTAQDHAVTVLKKTLKSANLPHMLFYGPPGTGKTSTILALTKELYGPDL----MKSRILELNASDER   76 (237)
T ss_dssp             CHHHHTCCSSTTTCCSCCTTHHHHHHHTTCTTCCCEEEECSTTSSHHHHHHHHHHHHHHHHH----HTTSEEEECSSSCC
T ss_pred             CcchhhCCCCHHHccCcHHHHHHHHHHHHcCCCCeEEEECCCCCChHHHHHHHHHHHcCCcc----cccchhheeccccc
Confidence            58899999999999999999999999998888889999999999999999999999744211    12233333321111


Q ss_pred             hccccCccHHHHHHHH------------HHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc--CCCe
Q 005179          359 AGAKERGELEARVTTL------------ISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG--RGEL  424 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~------------~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~--~~~v  424 (710)
                       +..   .....++..            +.........|+||||+|.+.             ....+.+...++  ....
T Consensus        77 -~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~-------------~~~~~~l~~~~~~~~~~~  139 (237)
T d1sxjd2          77 -GIS---IVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMT-------------ADAQSALRRTMETYSGVT  139 (237)
T ss_dssp             -CHH---HHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSC-------------HHHHHHHHHHHHHTTTTE
T ss_pred             -cch---HHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccC-------------HHHHHHHhhccccccccc
Confidence             000   000011111            111112234589999999993             233444444333  3445


Q ss_pred             EEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcc
Q 005179          425 QCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPD  504 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~  504 (710)
                      .+|.+++...     .+.+++.+||..|.|.+|+.++...+|..++.    .+++.+++++++.+++.+.+      -.+
T Consensus       140 ~~i~~~~~~~-----~~~~~l~sr~~~i~f~~~~~~~~~~~L~~i~~----~e~i~i~~~~l~~ia~~s~g------d~R  204 (237)
T d1sxjd2         140 RFCLICNYVT-----RIIDPLASQCSKFRFKALDASNAIDRLRFISE----QENVKCDDGVLERILDISAG------DLR  204 (237)
T ss_dssp             EEEEEESCGG-----GSCHHHHHHSEEEECCCCCHHHHHHHHHHHHH----TTTCCCCHHHHHHHHHHTSS------CHH
T ss_pred             cccccccccc-----cccccccchhhhhccccccccccchhhhhhhh----hhcCcCCHHHHHHHHHHcCC------CHH
Confidence            5565555543     57789999999999999999999999988776    46889999999999988754      245


Q ss_pred             hHHHHHHHHHh
Q 005179          505 KAIDLVDEAGS  515 (710)
Q Consensus       505 ~ai~ll~~a~~  515 (710)
                      +++..|+.++.
T Consensus       205 ~ai~~L~~~~~  215 (237)
T d1sxjd2         205 RGITLLQSASK  215 (237)
T ss_dssp             HHHHHHHHTHH
T ss_pred             HHHHHHHHHHH
Confidence            67777776653

>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=99.71  E-value=5.4e-18  Score=176.29  Aligned_cols=98  Identities=36%  Similarity=0.538  Sum_probs=90.3

Q ss_pred             ChhhccHHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          608 PVQQITADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       608 p~~~~~~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      |+.+++.+|...+.++++.|.++|+||++|++.|..+++..+.|+.+|++|.+.|||+||||||||+|||+||+.++.  
T Consensus         1 p~~~~~~~d~~~l~~l~~~L~~~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~--   78 (315)
T d1r6bx3           1 PEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGI--   78 (315)
T ss_dssp             CCCCSSSSHHHHHHHHHHHHTTTSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTC--
T ss_pred             CcccccHhHHHHHHHHHHHhCCeecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhccC--
Confidence            566788888899999999999999999999999999999999999999999999999999999999999999999864  


Q ss_pred             CcceeeCCCCCCCcchhhhccc
Q 005179          688 RIHYLFFPSPFNSVKVALSRQI  709 (710)
Q Consensus       688 ~~li~~d~se~~~~~~~~~~~~  709 (710)
                       .++++|||+| ...++++++|
T Consensus        79 -~~i~~d~s~~-~~~~~~~~l~   98 (315)
T d1r6bx3          79 -ELLRFDMSEY-MERHTVSRLI   98 (315)
T ss_dssp             -EEEEEEGGGC-SSSSCCSSSC
T ss_pred             -CeeEeccccc-cchhhhhhhc
Confidence             7999999999 5566777765

>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=99.71  E-value=7.5e-17  Score=160.99  Aligned_cols=186  Identities=19%  Similarity=0.257  Sum_probs=132.4

Q ss_pred             hhhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          283 RASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       283 ~~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      ..||.+|++++|+++.++.+..++..     ....++||+||||||||++|+.+|+++          ++....++....
T Consensus         2 ~~RP~~~~divGqe~~~~~l~~~i~~~~~~~~~~~~~L~~GPpGtGKT~lA~~la~~~----------~~~~~~~~~~~~   71 (238)
T d1in4a2           2 FLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASEL----------QTNIHVTSGPVL   71 (238)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHHHHTCCCCCEEEESSTTSSHHHHHHHHHHHH----------TCCEEEEETTTC
T ss_pred             CCCCCcHHHcCChHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCcHHHHHHHHHhcc----------CCCcccccCccc
Confidence            36899999999999999888877642     345789999999999999999999998          666666553332


Q ss_pred             hhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc------------------
Q 005179          358 MAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL------------------  419 (710)
Q Consensus       358 ~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l------------------  419 (710)
                      .    ..    ..+..++..  ...+.++||||+|.+...             ..+.+...+                  
T Consensus        72 ~----~~----~~~~~~~~~--~~~~~~~~ide~~~~~~~-------------~~~~l~~~~~~~~~~~~~~~~~~~~~~  128 (238)
T d1in4a2          72 V----KQ----GDMAAILTS--LERGDVLFIDEIHRLNKA-------------VEELLYSAIEDFQIDIMIGKGPSAKSI  128 (238)
T ss_dssp             C----SH----HHHHHHHHH--CCTTCEEEEETGGGCCHH-------------HHHHHHHHHHTSCCCC-----------
T ss_pred             c----cH----HHHHHHHHh--hccCCchHHHHHHHhhhH-------------HHhhcccceeeeeeeeeecCccccccc
Confidence            1    11    113333332  234679999999998321             112221111                  


Q ss_pred             --cCCCeEEEEccChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          420 --GRGELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       420 --~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                        ...++++|++|+...     ..++++++||. .+.++.|+.+++..+++.+..    ..++.+++++++.++..+.+.
T Consensus       129 ~~~~~~~~~I~at~~~~-----~~~~~~~~r~~~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~l~~i~~~s~gd  199 (238)
T d1in4a2         129 RIDIQPFTLVGATTRSG-----LLSSPLRSRFGIILELDFYTVKELKEIIKRAAS----LMDVEIEDAAAEMIAKRSRGT  199 (238)
T ss_dssp             ----CCCEEEEEESCGG-----GSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHH----HTTCCBCHHHHHHHHHTSTTC
T ss_pred             ccCCCCeEEEEecCCCc-----cccccceeeeeEEEEecCCCHHHHHHHHHHhhh----hccchhhHHHHHHHHHhCCCC
Confidence              123577888888876     67899999997 679999999999999987666    447889999999998776542


Q ss_pred             hcCCCCcchHHHHHHHHHhh
Q 005179          497 ISDRYLPDKAIDLVDEAGSR  516 (710)
Q Consensus       497 i~~r~~p~~ai~ll~~a~~~  516 (710)
                            ...++.+++.+...
T Consensus       200 ------~R~ai~~l~~~~~~  213 (238)
T d1in4a2         200 ------PRIAIRLTKRVRDM  213 (238)
T ss_dssp             ------HHHHHHHHHHHHHH
T ss_pred             ------HHHHHHHHHHHHHH
Confidence                  35677777766543

>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=99.71  E-value=1.7e-20  Score=192.99  Aligned_cols=185  Identities=13%  Similarity=0.114  Sum_probs=129.0

Q ss_pred             chhHHHhhhhhHHhhhhcCCCCcccCHHHHHHHHHHHH-cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCce
Q 005179          270 ASALEQFCVDLTARASEELIDPVIGRETEIQRIIQILC-RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKR  348 (710)
Q Consensus       270 ~~~l~~~~~~l~~~~~~~~l~~liGr~~~i~~l~~~L~-~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~  348 (710)
                      ...++.+..++++.++.+..++++|+..+..++.+.+. +..++++||+||||||||.+|++||.++..        +..
T Consensus        81 ~~~~~~~~~~L~~~a~~~~~d~v~~~~~~~~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~--------~~~  152 (321)
T d1w44a_          81 VSVVQVENGFMKQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGG--------KDK  152 (321)
T ss_dssp             EEEEEEETTEEEECCSEESSCSCTTCCSBCCEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHT--------TSC
T ss_pred             cchHHHHHhHHHHHHHhcCcchhccccccchHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcC--------CCC
Confidence            34466778888888888888888888755555566664 445556677999999999999999999842        234


Q ss_pred             EEEeehhhhhhccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccc----cCCCe
Q 005179          349 IMSLDMGLLMAGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSL----GRGEL  424 (710)
Q Consensus       349 v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l----~~~~v  424 (710)
                      ++.++.+.++  .+|.|+++.+++.+|+.++.  ++||||||||.+.+.+..+.+..... ...+.|+..|    ....+
T Consensus       153 ~~~~~~~~~~--~~~~G~~e~~~~~~f~~a~~--~~ilf~DEid~~~~~r~~~~~~~~~~-r~v~~lL~e~dg~~~~~~v  227 (321)
T d1w44a_         153 YATVRFGEPL--SGYNTDFNVFVDDIARAMLQ--HRVIVIDSLKNVIGAAGGNTTSGGIS-RGAFDLLSDIGAMAASRGC  227 (321)
T ss_dssp             CEEEEBSCSS--TTCBCCHHHHHHHHHHHHHH--CSEEEEECCTTTC-----------CC-HHHHHHHHHHHHHHHHHTC
T ss_pred             eEEEEhhHhh--hcccchHHHHHHHHHHHHhh--ccEEEeehhhhhccccccCCCCCcch-hhhhhhhhhccccccCCCe
Confidence            5677777777  57999999999999999975  67999999999987764432211222 2333333322    24569


Q ss_pred             EEEEccChHHHHhhhhccHHHHc--ccc-ceEecCCCHHHHHHHHHHH
Q 005179          425 QCIASTTQDEHRTQFEKDKALAR--RFQ-PVLISEPSQEDAVRILLGL  469 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~--Rf~-~I~v~~Ps~~~~~~IL~~l  469 (710)
                      +||++||+.++.+  .+++++.+  ||. .|.++.|+.+++.+||...
T Consensus       228 ~viaatN~~~~~~--~i~~~~~r~~Rf~~~v~v~~pd~~~r~~il~~~  273 (321)
T d1w44a_         228 VVIASLNPTSNDD--KIVELVKEASRSNSTSLVISTDVDGEWQVLTRT  273 (321)
T ss_dssp             EEEEECCCCCCCH--HHHHHHHHHHHHSCSEEEEECSSTTEEEEEEEC
T ss_pred             EEEEeCCCccccc--chhhhhhccCcccceeecCCCChHHHHHHHHHh
Confidence            9999999753222  23444544  775 8999999999998888644

>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=99.68  E-value=9.2e-17  Score=160.88  Aligned_cols=180  Identities=15%  Similarity=0.157  Sum_probs=119.9

Q ss_pred             CCcccCHHHHHHHHHHHH-------c---CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh
Q 005179          290 DPVIGRETEIQRIIQILC-------R---RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~-------~---~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~  359 (710)
                      +.+||..+.+..+++...       .   ....++||+||||||||++|+++|+.+          +.+++.++.++...
T Consensus         9 ~~~i~~~~~i~~i~~~~~~~~~~~~~~~~~p~~~vLL~GppGtGKT~la~alA~~~----------~~~~~~i~~~~~~~   78 (246)
T d1d2na_           9 NGIIKWGDPVTRVLDDGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEES----------NFPFIKICSPDKMI   78 (246)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHHHHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHH----------TCSEEEEECGGGCT
T ss_pred             cCCcCcCHHHHHHHHHHHHHHHHHhccCCCCCeEEEEECcCCCCHHHHHHHHhhcc----------cccccccccccccc
Confidence            458887777766655332       1   123468999999999999999999998          78888888877665


Q ss_pred             ccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-----CCeEEEEccChHH
Q 005179          360 GAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-----GELQCIASTTQDE  434 (710)
Q Consensus       360 g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-----~~v~vI~att~~~  434 (710)
                      |.. .+.....++.+|+.+....|+||||||+|.+++....+.   .....+.+.|...+..     .+++||+|||..+
T Consensus        79 g~~-~~~~~~~i~~if~~A~~~~p~il~iDEid~l~~~~~~~~---~~~~~~~~~ll~~l~~~~~~~~~v~vi~tTn~~~  154 (246)
T d1d2na_          79 GFS-ETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGP---RFSNLVLQALLVLLKKAPPQGRKLLIIGTTSRKD  154 (246)
T ss_dssp             TCC-HHHHHHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTT---BCCHHHHHHHHHHTTCCCSTTCEEEEEEEESCHH
T ss_pred             ccc-ccchhhhhhhhhhhhhhcccceeehhhhhhHhhhccccc---chhHHHHHHHHHHhcCCCccccceeeeeccCChh
Confidence            432 223346688999999999999999999999977543321   1223344444444432     3578899999875


Q ss_pred             HHhhhhccH-HHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhh
Q 005179          435 HRTQFEKDK-ALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARY  496 (710)
Q Consensus       435 ~~~~~~~d~-aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~  496 (710)
                           .+++ .+.+||+ .|.+  |+..++.+|++.+.. .     ..+.+..+..++..+.++
T Consensus       155 -----~ld~~~~~~rF~~~i~~--P~~~~r~~il~~l~~-~-----~~~~~~~~~~i~~~~~g~  205 (246)
T d1d2na_         155 -----VLQEMEMLNAFSTTIHV--PNIATGEQLLEALEL-L-----GNFKDKERTTIAQQVKGK  205 (246)
T ss_dssp             -----HHHHTTCTTTSSEEEEC--CCEEEHHHHHHHHHH-H-----TCSCHHHHHHHHHHHTTS
T ss_pred             -----hccchhhcCccceEEec--CCchhHHHHHHHHHh-c-----cCCChHHHHHHHHHcCCC
Confidence                 3454 4677997 5666  555555566654432 1     245666666666665543

>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=99.65  E-value=7e-16  Score=153.97  Aligned_cols=185  Identities=21%  Similarity=0.206  Sum_probs=124.5

Q ss_pred             hhhcCCCCcccCHHHHHHHHHHHHc-----CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          284 ASEELIDPVIGRETEIQRIIQILCR-----RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       284 ~~~~~l~~liGr~~~i~~l~~~L~~-----~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      .||.+|+++||+++.++.+..++..     ....|+||+||||||||++|+++|+.+          ++.+..++.+...
T Consensus         3 ~RP~~~ddivGq~~~~~~L~~~i~~~~~~~~~~~~~Ll~GPpG~GKTtla~~la~~~----------~~~~~~~~~~~~~   72 (239)
T d1ixsb2           3 LRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHEL----------GVNLRVTSGPAIE   72 (239)
T ss_dssp             CCCCSGGGSCSCHHHHHHHHHHHHHHTTSSSCCCCEEEECCTTSCHHHHHHHHHHHH----------TCCEEEEETTTCC
T ss_pred             cCCCCHHHhCCHHHHHHHHHHHHHHHHhcCCCCCeEEEECCCCCCHHHHHHHHHHHh----------CCCeEeccCCccc
Confidence            4889999999999998888777643     235789999999999999999999998          5666665543321


Q ss_pred             hccccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhccc--------------------
Q 005179          359 AGAKERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPS--------------------  418 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~--------------------  418 (710)
                          ..+..    ...+... ...+.|++|||+|.+..             ..++.+...                    
T Consensus        73 ----~~~~~----~~~~~~~-~~~~~i~~iDe~~~~~~-------------~~~~~l~~~~e~~~~~~~~~~~~~~~~~~  130 (239)
T d1ixsb2          73 ----KPGDL----AAILANS-LEEGDILFIDEIHRLSR-------------QAEEHLYPAMEDFVMDIVIGQGPAARTIR  130 (239)
T ss_dssp             ----SHHHH----HHHHHTT-CCTTCEEEEETGGGCCH-------------HHHHHHHHHHHHSEEEEECSCTTCCCEEE
T ss_pred             ----cchhh----HHHHHhh-ccCCCeeeeecccccch-------------hHHHhhhhhhhhhhhhhhhccchhhhhcc
Confidence                11111    1111111 12356899999999832             122222111                    


Q ss_pred             ccCCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhc
Q 005179          419 LGRGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYIS  498 (710)
Q Consensus       419 l~~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~  498 (710)
                      .+..++++|++|+...    ....+.+.++...+.+..|+.+++..+++.++.    ..++.++++.++.++..+.+-  
T Consensus       131 ~~~~~~~~i~~~~~~~----~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~----~~~i~~~~~~l~~ia~~s~gd--  200 (239)
T d1ixsb2         131 LELPRFTLIGATTRPG----LITAPLLSRFGIVEHLEYYTPEELAQGVMRDAR----LLGVRITEEAALEIGRRSRGT--  200 (239)
T ss_dssp             EECCCCEEEEEESCCS----SCSCGGGGGCSEEEECCCCCHHHHHHHHHHHHG----GGCCCBCHHHHHHHHHHTTSS--
T ss_pred             cCCCCEEEEeeccCcc----cccchhhcccceeeEeeccChhhhhHHHHHHHH----HhCCccchHHHHHHHHHcCCC--
Confidence            1234577888777654    122344444455899999999999999887665    558899999999999887752  


Q ss_pred             CCCCcchHHHHHHHHH
Q 005179          499 DRYLPDKAIDLVDEAG  514 (710)
Q Consensus       499 ~r~~p~~ai~ll~~a~  514 (710)
                          ++.++.+++.+.
T Consensus       201 ----~R~a~~~l~~~~  212 (239)
T d1ixsb2         201 ----MRVAKRLFRRVR  212 (239)
T ss_dssp             ----HHHHHHHHHHHH
T ss_pred             ----HHHHHHHHHHHH
Confidence                345666666543

>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=99.64  E-value=3.2e-16  Score=157.55  Aligned_cols=201  Identities=12%  Similarity=0.147  Sum_probs=131.0

Q ss_pred             hHHhhhhcCCCCcccCHHHHHHHHHHHHcC-CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCc-----------
Q 005179          280 LTARASEELIDPVIGRETEIQRIIQILCRR-TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSK-----------  347 (710)
Q Consensus       280 l~~~~~~~~l~~liGr~~~i~~l~~~L~~~-~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~-----------  347 (710)
                      |+++++|.+|++++|+++..+.+..++... ...++||+||||||||++|+++++.+............           
T Consensus         1 W~eky~P~~~~diig~~~~~~~L~~~~~~~~~~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~~~~~~~~~~~   80 (252)
T d1sxje2           1 WVDKYRPKSLNALSHNEELTNFLKSLSDQPRDLPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVRQFVTASNRKL   80 (252)
T ss_dssp             CTTTTCCCSGGGCCSCHHHHHHHHTTTTCTTCCCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC----------------
T ss_pred             CCcccCCCCHHHccCcHHHHHHHHHHHHcCCCCCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccccccccccchh
Confidence            678999999999999999888888777543 34579999999999999999999987432211110000           


Q ss_pred             --------eEEEeehhhhhhccccCccHHHHHHHHHHHHH--------------hcCCeEEEEccchhhhhCCCCCCCCC
Q 005179          348 --------RIMSLDMGLLMAGAKERGELEARVTTLISEIQ--------------KSGDVILFIDEVHTLIGSGTVGRGNK  405 (710)
Q Consensus       348 --------~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~--------------~~~~~IL~IDEid~l~~~~~~~~~~~  405 (710)
                              ....+.....  +...    .......+....              .....+++|||+|.+           
T Consensus        81 ~~~~~~~~~~~~~~~~~~--~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l-----------  143 (252)
T d1sxje2          81 ELNVVSSPYHLEITPSDM--GNND----RIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSL-----------  143 (252)
T ss_dssp             --CCEECSSEEEECCC------CC----HHHHHHHHHHHTTTTC------------CCEEEEEECTTSS-----------
T ss_pred             hhhhccCCccceeeeccc--ccCC----cceeeehhhhhhhhhhhhhhhcccccCCCceEEEecccccc-----------
Confidence                    0000000000  0000    001111111111              122458999999998           


Q ss_pred             CChHhHHHhhccccc--CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCC-C
Q 005179          406 GTGLDISNLLKPSLG--RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKF-T  482 (710)
Q Consensus       406 ~~~~~~~~~L~~~l~--~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i-~  482 (710)
                        ..+.++.|+..++  ..++.+|++|+..+     .+.+++.+||..|.|++|+.++..++|..++...    ++.+ +
T Consensus       144 --~~~~~~~l~~~~e~~~~~~~~Il~tn~~~-----~i~~~l~sR~~~i~~~~~~~~~~~~~l~~i~~~e----~~~~~~  212 (252)
T d1sxje2         144 --TKDAQAALRRTMEKYSKNIRLIMVCDSMS-----PIIAPIKSQCLLIRCPAPSDSEISTILSDVVTNE----RIQLET  212 (252)
T ss_dssp             --CHHHHHHHHHHHHHSTTTEEEEEEESCSC-----SSCHHHHTTSEEEECCCCCHHHHHHHHHHHHHHH----TCEECC
T ss_pred             --ccccchhhhcccccccccccceeeecccc-----chhhhhhcchheeeecccchhhHHHHHHHHHHHc----CCCCCc
Confidence              3345566666565  35677888887765     6789999999999999999999999999887643    4544 4


Q ss_pred             HHHHHHHHHHhhhhhcCCCCcchHHHHHHHHH
Q 005179          483 LEAINAAVHLSARYISDRYLPDKAIDLVDEAG  514 (710)
Q Consensus       483 ~~~l~~l~~ls~~~i~~r~~p~~ai~ll~~a~  514 (710)
                      +++++.++..+.+-      .++++..|+.++
T Consensus       213 ~~~l~~i~~~s~Gd------~R~ai~~Lq~~~  238 (252)
T d1sxje2         213 KDILKRIAQASNGN------LRVSLLMLESMA  238 (252)
T ss_dssp             SHHHHHHHHHHTTC------HHHHHHHHTHHH
T ss_pred             HHHHHHHHHHcCCc------HHHHHHHHHHHH
Confidence            67888888776652      345666666444

>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=99.63  E-value=2.1e-15  Score=153.49  Aligned_cols=224  Identities=13%  Similarity=0.092  Sum_probs=142.6

Q ss_pred             CCcccCHHHHHHHHHHHHc-----CCCCC----cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-
Q 005179          290 DPVIGRETEIQRIIQILCR-----RTKNN----PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-  359 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~-----~~~~n----vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-  359 (710)
                      +.+.||+.+++.+..++.+     ..+.+    ++|+||||||||++++++++.+.....+.. ....+..+++..... 
T Consensus        16 ~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~-~~~~~~~~~~~~~~~~   94 (287)
T d1w5sa2          16 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEG-LTVKQAYVNAFNAPNL   94 (287)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTT-CCEEEEEEEGGGCCSH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHhhccccc-CCceeeeeccccccch
Confidence            4688999999999887632     12222    456799999999999999998854221111 123333333222210 


Q ss_pred             -------------ccccCccH-HHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCe
Q 005179          360 -------------GAKERGEL-EARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGEL  424 (710)
Q Consensus       360 -------------g~~~~g~~-e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v  424 (710)
                                   .....+.. ......+...... ....++++||+|.+......+......-..+.+.+.+.+....+
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~~~~~~~  174 (287)
T d1w5sa2          95 YTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSRDGVNRI  174 (287)
T ss_dssp             HHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCTTSCCBE
T ss_pred             hhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchhhcccce
Confidence                         01112222 2222333333332 34678889999999655322000000001123334455666778


Q ss_pred             EEEEccChHHHHh-hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCC
Q 005179          425 QCIASTTQDEHRT-QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYL  502 (710)
Q Consensus       425 ~vI~att~~~~~~-~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~  502 (710)
                      .+|+.++..++.. .....+.+.+||. .+.+++|+.++..+|++..++..  ..+..+++++++.+++++.+|...+..
T Consensus       175 ~~i~i~~~~~~~~~~~~~~~~~~~r~~~~i~f~~y~~~el~~Il~~r~~~~--~~~~~~~~~al~~ia~~~~~~~~~~gd  252 (287)
T d1w5sa2         175 GFLLVASDVRALSYMREKIPQVESQIGFKLHLPAYKSRELYTILEQRAELG--LRDTVWEPRHLELISDVYGEDKGGDGS  252 (287)
T ss_dssp             EEEEEEEETHHHHHHHHHCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHH--BCTTSCCHHHHHHHHHHHCGGGTSCCC
T ss_pred             eEEeecccHHHHHHHHhhccchhcccceeeeccCCcHHHHHHHHhhhHHHh--hccCCCCHHHHHHHHHHHhccccCCCC
Confidence            8887776655443 2345688888885 89999999999999999876533  345678999999999999999888888


Q ss_pred             cchHHHHHHHHHhh
Q 005179          503 PDKAIDLVDEAGSR  516 (710)
Q Consensus       503 p~~ai~ll~~a~~~  516 (710)
                      +++++++++.|...
T Consensus       253 ~R~ai~~l~~a~~~  266 (287)
T d1w5sa2         253 ARRAIVALKMACEM  266 (287)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            89999999988743

>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=99.60  E-value=5.3e-16  Score=156.01  Aligned_cols=182  Identities=16%  Similarity=0.216  Sum_probs=122.9

Q ss_pred             hHHhhhhcCCCCcccCHHHHHHHHHHHHc-----------------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCc
Q 005179          280 LTARASEELIDPVIGRETEIQRIIQILCR-----------------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPV  342 (710)
Q Consensus       280 l~~~~~~~~l~~liGr~~~i~~l~~~L~~-----------------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~  342 (710)
                      |+++++|.+|++++|.++.+++|..++..                 ...+++||+||||||||++|+++|+.+       
T Consensus         4 W~eky~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~-------   76 (253)
T d1sxja2           4 WTVKYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQEL-------   76 (253)
T ss_dssp             HHHHTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHT-------
T ss_pred             cccCcCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHH-------
Confidence            78899999999999999999999887742                 233579999999999999999999998       


Q ss_pred             cccCceEEEeehhhhhhccccCccHHHHHHHHH------------HH--HHhcCCeEEEEccchhhhhCCCCCCCCCCCh
Q 005179          343 FLLSKRIMSLDMGLLMAGAKERGELEARVTTLI------------SE--IQKSGDVILFIDEVHTLIGSGTVGRGNKGTG  408 (710)
Q Consensus       343 ~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~------------~~--~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~  408 (710)
                         +..++.++.+....+.    .+...+...+            ..  .......++++||++.+....          
T Consensus        77 ---~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~----------  139 (253)
T d1sxja2          77 ---GYDILEQNASDVRSKT----LLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD----------  139 (253)
T ss_dssp             ---TCEEEEECTTSCCCHH----HHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS----------
T ss_pred             ---HhhhhccccccchhhH----HHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccch----------
Confidence               6677777654432110    0000000000            00  012346789999999984331          


Q ss_pred             HhHHHhhccccc--CCCeEEEEccChHHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHH
Q 005179          409 LDISNLLKPSLG--RGELQCIASTTQDEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAI  486 (710)
Q Consensus       409 ~~~~~~L~~~l~--~~~v~vI~att~~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l  486 (710)
                      ......+.....  ...++++++++...      ....+.+|+..|.|.+|+.+++..+++.++.+    .++.++++++
T Consensus       140 ~~~~~~~~~~~~~~~~~ii~i~~~~~~~------~~~~l~~~~~~i~f~~~~~~~i~~~l~~i~~~----e~i~i~~~~l  209 (253)
T d1sxja2         140 RGGVGQLAQFCRKTSTPLILICNERNLP------KMRPFDRVCLDIQFRRPDANSIKSRLMTIAIR----EKFKLDPNVI  209 (253)
T ss_dssp             TTHHHHHHHHHHHCSSCEEEEESCTTSS------TTGGGTTTSEEEECCCCCHHHHHHHHHHHHHH----HTCCCCTTHH
T ss_pred             hhhhHHHhhhhccccccccccccccccc------ccccccceeeeeeccccchhHHHHHHHHHHHH----hCCCCCHHHH
Confidence            111222222222  23455555444432      22357788889999999999999999988764    4788999999


Q ss_pred             HHHHHHhhh
Q 005179          487 NAAVHLSAR  495 (710)
Q Consensus       487 ~~l~~ls~~  495 (710)
                      +.++..+.+
T Consensus       210 ~~i~~~s~G  218 (253)
T d1sxja2         210 DRLIQTTRG  218 (253)
T ss_dssp             HHHHHHTTT
T ss_pred             HHHHHhCCC
Confidence            999888754

>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=99.60  E-value=5.1e-14  Score=142.22  Aligned_cols=207  Identities=15%  Similarity=0.152  Sum_probs=134.7

Q ss_pred             CCcccCHHHHHHHHHHHHc------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh-----
Q 005179          290 DPVIGRETEIQRIIQILCR------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM-----  358 (710)
Q Consensus       290 ~~liGr~~~i~~l~~~L~~------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~-----  358 (710)
                      +.++||+.+++.+.++|..      ..+++++|+||||||||++++.+++.+....      +..++.+++....     
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~------~~~~~~~~~~~~~~~~~~   89 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNWLRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKT------TARFVYINGFIYRNFTAI   89 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHHHHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSC------CCEEEEEETTTCCSHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhccc------CCcEEEecchhhhhhhhh
Confidence            3479999999999998864      2346899999999999999999999984322      2333333321110     


Q ss_pred             ---------hccccCc-cHHHHHHHHHHHHHh-cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcc---cccCCCe
Q 005179          359 ---------AGAKERG-ELEARVTTLISEIQK-SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKP---SLGRGEL  424 (710)
Q Consensus       359 ---------~g~~~~g-~~e~~l~~~~~~~~~-~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~---~l~~~~v  424 (710)
                               ......+ .....+..+.+.... ....++++|+++.+...          .......+..   ......+
T Consensus        90 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~----------~~~~~~~~~~~~~~~~~~~~  159 (276)
T d1fnna2          90 IGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPD----------ILSTFIRLGQEADKLGAFRI  159 (276)
T ss_dssp             HHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHH----------HHHHHHHHTTCHHHHSSCCE
T ss_pred             hhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhh----------hhhhHHHHHhccccccccce
Confidence                     0111122 223333444444443 34677888999887321          1111222221   2235667


Q ss_pred             EEEEccChHHHHhhhhccHHHHcccc--ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCC-
Q 005179          425 QCIASTTQDEHRTQFEKDKALARRFQ--PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRY-  501 (710)
Q Consensus       425 ~vI~att~~~~~~~~~~d~aL~~Rf~--~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~-  501 (710)
                      .+|++++..++..  .+++.+.+|+.  .|.+++|+.+++.+|++......  ..+..+++++++.+++.+.++...+. 
T Consensus       160 ~~i~~~~~~~~~~--~~~~~~~~r~~~~~i~~~~~~~~e~~~il~~r~~~~--~~~~~~~~~~l~~ia~~~~~~~~~~~~  235 (276)
T d1fnna2         160 ALVIVGHNDAVLN--NLDPSTRGIMGKYVIRFSPYTKDQIFDILLDRAKAG--LAEGSYSEDILQMIADITGAQTPLDTN  235 (276)
T ss_dssp             EEEEEESSTHHHH--TSCHHHHHHHTTCEEECCCCBHHHHHHHHHHHHHHH--BCTTSSCHHHHHHHHHHHSBSSTTCTT
T ss_pred             EEeecCCchhhhh--hcchhhhhhhcchhccccchhHHHHHHHHHHHHHHh--cccccccHHHHHHHHHHhhhhhhhhhc
Confidence            8888877765332  56788888874  68999999999999999876643  34567899999999998876554433 


Q ss_pred             --CcchHHHHHHHHHhh
Q 005179          502 --LPDKAIDLVDEAGSR  516 (710)
Q Consensus       502 --~p~~ai~ll~~a~~~  516 (710)
                        .+.+++++++.|...
T Consensus       236 ~G~~R~a~~ll~~a~~~  252 (276)
T d1fnna2         236 RGDARLAIDILYRSAYA  252 (276)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence              345778888777543

>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=99.58  E-value=4.8e-16  Score=161.15  Aligned_cols=83  Identities=30%  Similarity=0.440  Sum_probs=69.9

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHH--HhhcCCCCCCC---CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVK--RSRVGLKDPNR---PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~--~~r~gl~~p~r---p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .++++.|.++|+||++|++.|+.++.  +.|.++..+.+   |.+++|||||||||||+|||+||+.++.   +++++||
T Consensus         6 ~~i~~~L~~~ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~---~~~~i~~   82 (309)
T d1ofha_           6 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANA---PFIKVEA   82 (309)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTC---CEEEEEG
T ss_pred             HHHHHHhcCcccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcccc---chhcccc
Confidence            46788899999999999999999994  36777776644   7789999999999999999999999875   8999999


Q ss_pred             CCCCCcchhhhc
Q 005179          696 SPFNSVKVALSR  707 (710)
Q Consensus       696 se~~~~~~~~~~  707 (710)
                      |+|+ ..+.|..
T Consensus        83 s~~~-~~~~~~~   93 (309)
T d1ofha_          83 TKFT-EVGYVGK   93 (309)
T ss_dssp             GGGS-SCCSGGG
T ss_pred             cccc-cceeEee
Confidence            9995 3344444

>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=99.57  E-value=4.8e-15  Score=153.50  Aligned_cols=161  Identities=23%  Similarity=0.287  Sum_probs=114.3

Q ss_pred             cccCHHHHHHHHHHHH----c----------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          292 VIGRETEIQRIIQILC----R----------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       292 liGr~~~i~~l~~~L~----~----------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      ++|+++.++.+...+.    +          ..+.++||+||||||||.||+++|+.+          +..++.++++.+
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~----------~~~~~~i~~s~~   85 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA----------NAPFIKVEATKF   85 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHH----------TCCEEEEEGGGG
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhcc----------ccchhccccccc
Confidence            8999999988876552    1          146899999999999999999999988          677889999998


Q ss_pred             hhccccCccHHHHHHHHHHHHHh-----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-----------
Q 005179          358 MAGAKERGELEARVTTLISEIQK-----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-----------  421 (710)
Q Consensus       358 ~~g~~~~g~~e~~l~~~~~~~~~-----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-----------  421 (710)
                      .....+.|..+..+..++..+..     ..++||||||||.+...+..... ......+.+.|+..++.           
T Consensus        86 ~~~~~~~~~~~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~-~~~~~gv~~~LL~~~dg~~~~~~~~~i~  164 (309)
T d1ofha_          86 TEVGYVGKEVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGA-DVSREGVQRDLLPLVEGSTVSTKHGMVK  164 (309)
T ss_dssp             SSCCSGGGSTTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSS-HHHHHHHHHHHHHHHHCCEEEETTEEEE
T ss_pred             ccceeEeeeccccccccchhhhcccccccCCceEEehhhhhhhhhccCccc-chhhhHHHHHhhHHhcCCEEecCCeEEE
Confidence            75555667777778888776533     23689999999999764332100 00011144445444432           


Q ss_pred             -CCeEEEEc----cChHHHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHH
Q 005179          422 -GELQCIAS----TTQDEHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLG  468 (710)
Q Consensus       422 -~~v~vI~a----tt~~~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~  468 (710)
                       .++.+|++    ++.+     ..++|.+.+||. .+.+.+|+.+++.+|+..
T Consensus       165 ~s~ilfi~~ga~~~~~~-----~~~~p~l~~R~~~~i~~~~~~~~~~~~Il~~  212 (309)
T d1ofha_         165 TDHILFIASGAFQVARP-----SDLIPELQGRLPIRVELTALSAADFERILTE  212 (309)
T ss_dssp             CTTCEEEEEECCSSSCG-----GGSCHHHHHTCCEEEECCCCCHHHHHHHHHS
T ss_pred             ccceeEEeccchhhcCc-----ccchhhhhhhhheeeeccCCCHHHHHHHHHH
Confidence             12445543    2222     267899999997 799999999999999753

>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=99.52  E-value=2.2e-15  Score=158.77  Aligned_cols=77  Identities=29%  Similarity=0.305  Sum_probs=66.7

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHHH---------------------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHH
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAVK---------------------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSL  679 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i~---------------------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaL  679 (710)
                      .++.+.|.++|+||++|+++|+.+++                     ....|+++|.+|+++|||+||||||||+|||+|
T Consensus         9 ~ei~~~L~~~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~L   88 (364)
T d1um8a_           9 KELKAVLDNYVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTL   88 (364)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHH
T ss_pred             HHHHHHhCCeecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHH
Confidence            46788999999999999999998883                     133466678999999999999999999999999


Q ss_pred             HHHHcCCCCcceeeCCCCCCC
Q 005179          680 AACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       680 A~~lfg~~~~li~~d~se~~~  700 (710)
                      |+.+   +.+++++|||+|+.
T Consensus        89 A~~~---~~~~ir~D~s~~~e  106 (364)
T d1um8a_          89 AKHL---DIPIAISDATSLTE  106 (364)
T ss_dssp             HHHT---TCCEEEEEGGGCC-
T ss_pred             Hhhc---ccceeehhhhhccc
Confidence            9995   55899999999987

>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=99.47  E-value=2.3e-13  Score=132.74  Aligned_cols=181  Identities=15%  Similarity=0.190  Sum_probs=117.8

Q ss_pred             CCCCcc-cCHH--HHHHHHHHHHcCC--CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc
Q 005179          288 LIDPVI-GRET--EIQRIIQILCRRT--KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK  362 (710)
Q Consensus       288 ~l~~li-Gr~~--~i~~l~~~L~~~~--~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~  362 (710)
                      +|++++ |...  ....+.++.....  .++++|+||+|+|||+|++++++.+...       +..++.++...+.... 
T Consensus         8 tFdnF~vg~~N~~a~~~~~~~~~~~~~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~-------~~~~~~~~~~~~~~~~-   79 (213)
T d1l8qa2           8 TLENFIVGEGNRLAYEVVKEALENLGSLYNPIFIYGSVGTGKTHLLQAAGNEAKKR-------GYRVIYSSADDFAQAM-   79 (213)
T ss_dssp             CSSSCCCCTTTHHHHHHHHHHHHTTTTSCSSEEEECSSSSSHHHHHHHHHHHHHHT-------TCCEEEEEHHHHHHHH-
T ss_pred             ChhhccCCCcHHHHHHHHHHHHhCcCCCCCcEEEECCCCCcHHHHHHHHHHHhccC-------ccceEEechHHHHHHH-
Confidence            566654 5432  2333344443322  2558999999999999999999998553       5567777765554211 


Q ss_pred             cCccH-HHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCCCeEEEEccChHHHHhhhhc
Q 005179          363 ERGEL-EARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRGELQCIASTTQDEHRTQFEK  441 (710)
Q Consensus       363 ~~g~~-e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~~v~vI~att~~~~~~~~~~  441 (710)
                       ...+ ......+.+....  ..+|+|||+|.+.+..       .....+.+++....+.+..++|++..++.  ..-..
T Consensus        80 -~~~~~~~~~~~~~~~~~~--~dll~iDDi~~i~~~~-------~~~~~lf~lin~~~~~~~~iiits~~~p~--~l~~~  147 (213)
T d1l8qa2          80 -VEHLKKGTINEFRNMYKS--VDLLLLDDVQFLSGKE-------RTQIEFFHIFNTLYLLEKQIILASDRHPQ--KLDGV  147 (213)
T ss_dssp             -HHHHHHTCHHHHHHHHHT--CSEEEEECGGGGTTCH-------HHHHHHHHHHHHHHHTTCEEEEEESSCGG--GCTTS
T ss_pred             -HHHHHccchhhHHHHHhh--ccchhhhhhhhhcCch-------HHHHHHHHHHHHHhhccceEEEecCCcch--hcccc
Confidence             0000 0012233333333  3489999999995432       22445677777777788777777666554  12235


Q ss_pred             cHHHHcccc---ceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHh
Q 005179          442 DKALARRFQ---PVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       442 d~aL~~Rf~---~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls  493 (710)
                      .+.|.+||.   .+.++ |+.+++.++|+..+.    ..++.+++++++++++.+
T Consensus       148 ~~dL~SRL~~g~~~~i~-p~d~~~~~iL~~~a~----~rgl~l~~~v~~yl~~~~  197 (213)
T d1l8qa2         148 SDRLVSRFEGGILVEIE-LDNKTRFKIIKEKLK----EFNLELRKEVIDYLLENT  197 (213)
T ss_dssp             CHHHHHHHHTSEEEECC-CCHHHHHHHHHHHHH----HTTCCCCHHHHHHHHHHC
T ss_pred             chHHHHHhhCceEEEEC-CCcHHHHHHHHHHHH----HcCCCCCHHHHHHHHHhc
Confidence            689999995   67775 677889999887765    568999999999998664

>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=99.41  E-value=7.1e-13  Score=128.76  Aligned_cols=179  Identities=17%  Similarity=0.194  Sum_probs=122.3

Q ss_pred             cCHHHHHHHHHHHHcCCCCC-cEEEcCCCChHHHHHHHHHHHHHhcCCCccc--------------cCceEEEeehhhhh
Q 005179          294 GRETEIQRIIQILCRRTKNN-PILLGESGVGKTAIAEGLAIRIVQAEVPVFL--------------LSKRIMSLDMGLLM  358 (710)
Q Consensus       294 Gr~~~i~~l~~~L~~~~~~n-vLL~GppG~GKT~la~~la~~l~~~~~p~~l--------------~~~~v~~ld~~~l~  358 (710)
                      ..++.++++.+.+...+..+ +||+||+|+|||++|+.+|+.+.+.......              ....++.+...   
T Consensus         6 w~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~---   82 (207)
T d1a5ta2           6 WLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPE---   82 (207)
T ss_dssp             GGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCC---
T ss_pred             ccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhh---
Confidence            35667888888888777666 8999999999999999999988543211100              01111211100   


Q ss_pred             hccccCccHHHHHHHHHHHHHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccCh
Q 005179          359 AGAKERGELEARVTTLISEIQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQ  432 (710)
Q Consensus       359 ~g~~~~g~~e~~l~~~~~~~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~  432 (710)
                       ..+ ..-....++.+.+.+..    .+..|++|||+|.+             ..+.++.|+..|+.  .++.+|.+|+.
T Consensus        83 -~~~-~~i~~~~ir~l~~~~~~~~~~~~~kviIide~d~l-------------~~~a~n~Llk~lEep~~~~~fIl~t~~  147 (207)
T d1a5ta2          83 -KGK-NTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL-------------TDAAANALLKTLEEPPAETWFFLATRE  147 (207)
T ss_dssp             -TTC-SSBCHHHHHHHHHHTTSCCTTSSCEEEEESCGGGB-------------CHHHHHHHHHHHTSCCTTEEEEEEESC
T ss_pred             -hcc-cccccchhhHHhhhhhhccccCccceEEechhhhh-------------hhhhhHHHHHHHHhhcccceeeeeecC
Confidence             000 11112335556655432    34569999999999             56688999999985  46788888777


Q ss_pred             HHHHhhhhccHHHHccccceEecCCCHHHHHHHHHHHHHHHHhhcCCCCCHHHHHHHHHHhhhhhcCCCCcchHHHHH
Q 005179          433 DEHRTQFEKDKALARRFQPVLISEPSQEDAVRILLGLREKYEAHHNCKFTLEAINAAVHLSARYISDRYLPDKAIDLV  510 (710)
Q Consensus       433 ~~~~~~~~~d~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~~~~~i~~~~l~~l~~ls~~~i~~r~~p~~ai~ll  510 (710)
                      ..     .+.+++++||..|.|.+|+.++...+|+.         .+.++++.+..++..+++      .+++|+.++
T Consensus       148 ~~-----~ll~tI~SRc~~i~~~~~~~~~~~~~L~~---------~~~~~~~~~~~i~~~s~G------s~r~al~~l  205 (207)
T d1a5ta2         148 PE-----RLLATLRSRCRLHYLAPPPEQYAVTWLSR---------EVTMSQDALLAALRLSAG------SPGAALALF  205 (207)
T ss_dssp             GG-----GSCHHHHTTSEEEECCCCCHHHHHHHHHH---------HCCCCHHHHHHHHHHTTT------CHHHHHHTT
T ss_pred             hh-----hhhhhhcceeEEEecCCCCHHHHHHHHHH---------cCCCCHHHHHHHHHHcCC------CHHHHHHHh
Confidence            64     68899999999999999999987777642         356789999998887654      245555543

>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=99.41  E-value=2.2e-12  Score=133.40  Aligned_cols=177  Identities=17%  Similarity=0.246  Sum_probs=123.7

Q ss_pred             CcccCHHHHHHHHHHHHc---------CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhcc
Q 005179          291 PVIGRETEIQRIIQILCR---------RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGA  361 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~---------~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~  361 (710)
                      .++|+++.++.+...+.+         +...+++|+||+|||||.||+.||+.+          +.+++.+|++.+....
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l----------~~~~i~~d~s~~~~~~   92 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKAL----------GIELLRFDMSEYMERH   92 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHH----------TCEEEEEEGGGCSSSS
T ss_pred             eecChHHHHHHHHHHHHHHHccCCCCCCCceEEEEECCCcchhHHHHHHHHhhc----------cCCeeEeccccccchh
Confidence            499999999999887642         112357899999999999999999988          6778889988875321


Q ss_pred             -------ccCccHHHHHH-HHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC-----------
Q 005179          362 -------KERGELEARVT-TLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG-----------  422 (710)
Q Consensus       362 -------~~~g~~e~~l~-~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~-----------  422 (710)
                             ...|....... .+...+...+..|+++||+|.+             ..++.+.|.+.++.|           
T Consensus        93 ~~~~l~g~~~gy~g~~~~~~l~~~~~~~~~~vvl~DeieKa-------------~~~V~~~lLqild~G~ltd~~Gr~vd  159 (315)
T d1r6bx3          93 TVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKA-------------HPDVFNILLQVMDNGTLTDNNGRKAD  159 (315)
T ss_dssp             CCSSSCCCCSCSHHHHHTTHHHHHHHHCSSEEEEEETGGGS-------------CHHHHHHHHHHHHHSEEEETTTEEEE
T ss_pred             hhhhhcccCCCccccccCChhhHHHHhCccchhhhcccccc-------------cchHhhhhHHhhccceecCCCCCccC
Confidence                   11122211111 1333445567789999999998             567888888777543           


Q ss_pred             --CeEEEEccChH----------------------HHHhhhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh--
Q 005179          423 --ELQCIASTTQD----------------------EHRTQFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA--  475 (710)
Q Consensus       423 --~v~vI~att~~----------------------~~~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~--  475 (710)
                        +.++|.|+|..                      ....  ...|.|.+||+ .|.+.+.+.++...|+...+..+..  
T Consensus       160 f~n~iiI~Tsnig~~~i~~~~~~~~~~~~~~~~~~~l~~--~f~pEflnRid~ii~f~~l~~~~~~~I~~~~l~~~~~~l  237 (315)
T d1r6bx3         160 FRNVVLVMTTNAGVRETERKSIGLIHQDNSTDAMEEIKK--IFTPEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQVQL  237 (315)
T ss_dssp             CTTEEEEEEECSSCC-----------------CHHHHHH--HSCHHHHTTCSEEEECCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             ccceEEEeccchhhHHHHhhhccchhhhhhHhHHHHHHH--hcCHHHHhhhhhhhcccchhhhHHHHHHHHHHHHHHHHH
Confidence              34566666621                      0111  24689999998 6788888999999888876655432  


Q ss_pred             ---hcCCCCCHHHHHHHHHH
Q 005179          476 ---HHNCKFTLEAINAAVHL  492 (710)
Q Consensus       476 ---~~~~~i~~~~l~~l~~l  492 (710)
                         ...+.+++++++.+++.
T Consensus       238 ~~~~i~l~~~~~a~~~l~~~  257 (315)
T d1r6bx3         238 DQKGVSLEVSQEARNWLAEK  257 (315)
T ss_dssp             HHTTEEEEECHHHHHHHHHH
T ss_pred             HhcCcchhhHHHHHHHHHHh
Confidence               23467899999888775

>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=99.38  E-value=3.4e-12  Score=131.71  Aligned_cols=180  Identities=21%  Similarity=0.273  Sum_probs=123.1

Q ss_pred             cccCHHHHHHHHHHHHcC--------CC-CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh---
Q 005179          292 VIGRETEIQRIIQILCRR--------TK-NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA---  359 (710)
Q Consensus       292 liGr~~~i~~l~~~L~~~--------~~-~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~---  359 (710)
                      ++|+++.++.+...+.+.        .+ .+++|+||+|||||.+|+.||+.+...       +..++.+|++.+..   
T Consensus        25 v~GQ~~ai~~v~~~i~~~~~~l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~-------~~~~~~~~~~~~~~~~~   97 (315)
T d1qvra3          25 VVGQDEAIRAVADAIRRARAGLKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDT-------EEAMIRIDMTEYMEKHA   97 (315)
T ss_dssp             SCSCHHHHHHHHHHHHHHGGGCSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSS-------GGGEEEECTTTCCSSGG
T ss_pred             EeCHHHHHHHHHHHHHHHhcCCCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCC-------CcceEEEeccccccchh
Confidence            899999999988866431        11 246888999999999999999998433       44577777765542   


Q ss_pred             -----cc--ccCccHHHHHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccCC----------
Q 005179          360 -----GA--KERGELEARVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGRG----------  422 (710)
Q Consensus       360 -----g~--~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~~----------  422 (710)
                           |.  .|.|.-+  -..+.+.+..++.+|+++||||.+             ..++++.|.++++.|          
T Consensus        98 ~~~L~g~~~gyvG~~~--~~~l~~~~~~~p~~Vvl~DEieK~-------------~~~v~~~ll~~l~~g~~~~~~gr~v  162 (315)
T d1qvra3          98 VSRLIGAPPGYVGYEE--GGQLTEAVRRRPYSVILFDEIEKA-------------HPDVFNILLQILDDGRLTDSHGRTV  162 (315)
T ss_dssp             GGGC----------------CHHHHHHHCSSEEEEESSGGGS-------------CHHHHHHHHHHHTTTEECCSSSCCE
T ss_pred             hhhhcCCCCCCcCccc--CChHHHHHHhCCCcEEEEehHhhc-------------CHHHHHHHHHHhccCceeCCCCcEe
Confidence                 11  1233211  122344556677899999999998             567888888777643          


Q ss_pred             ---CeEEEEccChHH-------------------HHh--hhhccHHHHcccc-ceEecCCCHHHHHHHHHHHHHHHHh--
Q 005179          423 ---ELQCIASTTQDE-------------------HRT--QFEKDKALARRFQ-PVLISEPSQEDAVRILLGLREKYEA--  475 (710)
Q Consensus       423 ---~v~vI~att~~~-------------------~~~--~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~l~~~~~~--  475 (710)
                         +.++|.|+|-..                   ...  .....|.|.+||+ .+.+.+.+.++..+|+.....++..  
T Consensus       163 ~~~~~i~i~tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEflnRid~Ii~F~~L~~~~~~~I~~~~l~~l~~rl  242 (315)
T d1qvra3         163 DFRNTVIILTSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLNRLDEIVVFRPLTKEQIRQIVEIQLSYLRARL  242 (315)
T ss_dssp             ECTTEEEEEECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHHTCSBCCBCCCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             cCcceEEEEecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHhcCCeeeeccchhhhhhHHHHHHHHHHHHHHH
Confidence               466888887421                   000  1125689999998 6688999999999998876555542  


Q ss_pred             ---hcCCCCCHHHHHHHHHHh
Q 005179          476 ---HHNCKFTLEAINAAVHLS  493 (710)
Q Consensus       476 ---~~~~~i~~~~l~~l~~ls  493 (710)
                         ...+.+++++++.+++.+
T Consensus       243 ~~~~i~l~i~~~~~~~L~~~~  263 (315)
T d1qvra3         243 AEKRISLELTEAAKDFLAERG  263 (315)
T ss_dssp             HTTTCEEEECHHHHHHHHHHH
T ss_pred             HhccccccccHHHHHHHHHhC
Confidence               234678999999988763

>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=99.30  E-value=1.3e-11  Score=129.59  Aligned_cols=191  Identities=25%  Similarity=0.281  Sum_probs=119.4

Q ss_pred             cccCHHHHHHHHHHHH------------------------------cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCC
Q 005179          292 VIGRETEIQRIIQILC------------------------------RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVP  341 (710)
Q Consensus       292 liGr~~~i~~l~~~L~------------------------------~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p  341 (710)
                      +||+++.++.+...+.                              ...+.|+||+||+|||||.+|++||+.+      
T Consensus        19 ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~------   92 (364)
T d1um8a_          19 VIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHL------   92 (364)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHT------
T ss_pred             ecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhc------
Confidence            8999999887765552                              2357899999999999999999999876      


Q ss_pred             ccccCceEEEeehhhhhhccccCcc-HHHHHHHHHHH----HHhcCCeEEEEccchhhhhCCCCCCC-CCCChHhHHHhh
Q 005179          342 VFLLSKRIMSLDMGLLMAGAKERGE-LEARVTTLISE----IQKSGDVILFIDEVHTLIGSGTVGRG-NKGTGLDISNLL  415 (710)
Q Consensus       342 ~~l~~~~v~~ld~~~l~~g~~~~g~-~e~~l~~~~~~----~~~~~~~IL~IDEid~l~~~~~~~~~-~~~~~~~~~~~L  415 (710)
                          +..++.+|++.+... .+.|. .+..+..++..    +.....+|+++||++...+....... ......++++.|
T Consensus        93 ----~~~~ir~D~s~~~e~-gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~~~l  167 (364)
T d1um8a_          93 ----DIPIAISDATSLTEA-GYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQAL  167 (364)
T ss_dssp             ----TCCEEEEEGGGCC---------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHH
T ss_pred             ----ccceeehhhhhcccc-hhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhccccccccccccccchHHHHhh
Confidence                667888888877632 12221 12234444432    33455779999999997643211100 011345678888


Q ss_pred             cccccCCC---------------eEEEEccCh---------------------------------------------HHH
Q 005179          416 KPSLGRGE---------------LQCIASTTQ---------------------------------------------DEH  435 (710)
Q Consensus       416 ~~~l~~~~---------------v~vI~att~---------------------------------------------~~~  435 (710)
                      ++.++.+.               .++|-+++-                                             .+.
T Consensus       168 Lqild~~~~~~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (364)
T d1um8a_         168 LKIVEGSLVNIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDL  247 (364)
T ss_dssp             HHHHHCCEEC---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHH
T ss_pred             hhhhcCceeccCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHH
Confidence            87776422               112222221                                             010


Q ss_pred             HhhhhccHHHHcccc-ceEecCCCHHHHHHHHHH----HHHHHHh---hcC--CCCCHHHHHHHHHHhh
Q 005179          436 RTQFEKDKALARRFQ-PVLISEPSQEDAVRILLG----LREKYEA---HHN--CKFTLEAINAAVHLSA  494 (710)
Q Consensus       436 ~~~~~~d~aL~~Rf~-~I~v~~Ps~~~~~~IL~~----l~~~~~~---~~~--~~i~~~~l~~l~~ls~  494 (710)
                      . .....|.|..||. .|.|.+.+.++..+|+..    +.+++..   .++  +.+++++++.+++.+-
T Consensus       248 ~-~~~f~PEf~gRi~~iv~f~~L~~~~l~~Il~~~~~~l~kq~~~~l~~~gi~L~~td~a~~~la~~g~  315 (364)
T d1um8a_         248 V-TYGLIPELIGRLPVLSTLDSISLEAMVDILQKPKNALIKQYQQLFKMDEVDLIFEEEAIKEIAQLAL  315 (364)
T ss_dssp             H-HTTCCHHHHTTCCEEEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHH
T ss_pred             h-hhhhHHHHHHHhcchhhHhhhhHHHHHHHHHHHHHHHHHHHHHHHHhCCcEEEECHHHHHHHHHhcc
Confidence            1 1125689999998 788999999999999974    4444332   234  5689999999998753

>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=99.18  E-value=2.1e-10  Score=119.50  Aligned_cols=159  Identities=19%  Similarity=0.319  Sum_probs=95.8

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcC--------------CCcc---------cc
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAE--------------VPVF---------LL  345 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~--------------~p~~---------l~  345 (710)
                      |.+++|++...+.+.-.+......|+||+||||||||++|+.++..+....              .+..         ..
T Consensus         6 f~~I~Gq~~~kral~laa~~~~~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (333)
T d1g8pa_           6 FSAIVGQEDMKLALLLTAVDPGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVEMIPDWATVLSTNVIRK   85 (333)
T ss_dssp             GGGSCSCHHHHHHHHHHHHCGGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGGGSCTTCCCSCCCEEEE
T ss_pred             hhhccCcHHHHHHHHHHHhccCCCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCccccccchhhccccCcccc
Confidence            568999997776555444433446899999999999999999998652110              0000         00


Q ss_pred             CceEEEee----hhhhhhccccCccHHHHHHH---H--HHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhc
Q 005179          346 SKRIMSLD----MGLLMAGAKERGELEARVTT---L--ISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLK  416 (710)
Q Consensus       346 ~~~v~~ld----~~~l~~g~~~~g~~e~~l~~---~--~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~  416 (710)
                      ..+++...    ...++.+.    .+...+..   .  ...+....+.|+||||++.+             ...+++.|.
T Consensus        86 ~~~~~~~~~~~~~~~l~G~~----d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~-------------~~~~~~aLl  148 (333)
T d1g8pa_          86 PTPVVDLPLGVSEDRVVGAL----DIERAISKGEKAFEPGLLARANRGYLYIDECNLL-------------EDHIVDLLL  148 (333)
T ss_dssp             CCCEEEECTTCCHHHHHCEE----CHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGS-------------CHHHHHHHH
T ss_pred             cCceeeccCCCCcccccCcc----hhhhccccCcceeeccccccccccEeecccHHHH-------------HHHHHHHHh
Confidence            11111111    11111100    00100000   0  01122234679999999998             556788888


Q ss_pred             ccccCC---------------CeEEEEccChHHHHhhhhccHHHHcccc-ceEecCC-CHHHHHHHHHH
Q 005179          417 PSLGRG---------------ELQCIASTTQDEHRTQFEKDKALARRFQ-PVLISEP-SQEDAVRILLG  468 (710)
Q Consensus       417 ~~l~~~---------------~v~vI~att~~~~~~~~~~d~aL~~Rf~-~I~v~~P-s~~~~~~IL~~  468 (710)
                      +.|+++               .+.+|+++|+.+.    .+.+++.+||. .|.+..| +.+++..++..
T Consensus       149 ~~me~~~v~i~r~g~~~~~p~~f~liaa~Np~~~----~l~~~llDRf~~~i~v~~~~~~~~~~~~~~~  213 (333)
T d1g8pa_         149 DVAQSGENVVERDGLSIRHPARFVLVGSGNPEEG----DLRPQLLDRFGLSVEVLSPRDVETRVEVIRR  213 (333)
T ss_dssp             HHHHHSEEEECCTTCCEEEECCEEEEEEECSCSC----CCCHHHHTTCSEEEECCCCCSHHHHHHHHHH
T ss_pred             hhhcCCeEEecccCceecCCCCEEEEEecCcccc----ccccchhhhhcceeeccCcchhhHHHHHHHh
Confidence            877643               4578889898762    57899999998 6777766 46666666554

>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=99.04  E-value=1e-10  Score=116.22  Aligned_cols=178  Identities=18%  Similarity=0.249  Sum_probs=110.0

Q ss_pred             CcccCHHHHHHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh--------c
Q 005179          291 PVIGRETEIQRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA--------G  360 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~--------g  360 (710)
                      ++||+++.++++.+.+.+  ....+++|+||+|||||++|++|+......       ...++.+++..+..        |
T Consensus         1 ~~v~~S~~~~~~~~~~~~~a~~~~pvlI~Ge~GtGK~~~A~~ih~~s~~~-------~~~~~~~~~~~~~~~~~~~~lfg   73 (247)
T d1ny5a2           1 EYVFESPKMKEILEKIKKISCAECPVLITGESGVGKEVVARLIHKLSDRS-------KEPFVALNVASIPRDIFEAELFG   73 (247)
T ss_dssp             CCCCCSHHHHHHHHHHHHHTTCCSCEEEECSTTSSHHHHHHHHHHHSTTT-------TSCEEEEETTTSCHHHHHHHHHC
T ss_pred             CeEecCHHHHHHHHHHHHHhCCCCCEEEECCCCcCHHHHHHHHHHhcCCc-------ccccccchhhhhhhcccHHHhcC
Confidence            478999999998887765  456789999999999999999998754222       33455555533221        1


Q ss_pred             cccCccHHH---HHHHHHHHHHhcCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC-------------CCe
Q 005179          361 AKERGELEA---RVTTLISEIQKSGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR-------------GEL  424 (710)
Q Consensus       361 ~~~~g~~e~---~l~~~~~~~~~~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~-------------~~v  424 (710)
                      . ..+.+..   ....++   ....+..|||||||.|             +.+.+..|..+++.             .++
T Consensus        74 ~-~~~~~~~~~~~~~g~l---~~a~gGtL~l~~i~~L-------------~~~~Q~~L~~~l~~~~~~~~~~~~~~~~~~  136 (247)
T d1ny5a2          74 Y-EKGAFTGAVSSKEGFF---ELADGGTLFLDEIGEL-------------SLEAQAKLLRVIESGKFYRLGGRKEIEVNV  136 (247)
T ss_dssp             B-CTTSSTTCCSCBCCHH---HHTTTSEEEEESGGGC-------------CHHHHHHHHHHHHHSEECCBTCCSBEECCC
T ss_pred             c-ccCCcCCcccccCCHH---HccCCCEEEEeChHhC-------------CHHHHHHHHHHHHhCCEEECCCCCceecCe
Confidence            0 0000000   001122   2344668999999999             44455555544432             146


Q ss_pred             EEEEccChHH--HHhhhhccHHHHccccceEecCCCH----HHHHHHHHHHHHHHHhhcC---CCCCHHHHHHHHHH
Q 005179          425 QCIASTTQDE--HRTQFEKDKALARRFQPVLISEPSQ----EDAVRILLGLREKYEAHHN---CKFTLEAINAAVHL  492 (710)
Q Consensus       425 ~vI~att~~~--~~~~~~~d~aL~~Rf~~I~v~~Ps~----~~~~~IL~~l~~~~~~~~~---~~i~~~~l~~l~~l  492 (710)
                      ++|++|+.+.  ....-..++.|..||..+.+..|+.    ++...|++.++.++....+   ..+++++++.+..+
T Consensus       137 RlI~~s~~~l~~l~~~~~f~~~L~~~l~~~~i~lPpLreR~~Di~~l~~~~l~~~~~~~~~~~~~ls~~al~~L~~~  213 (247)
T d1ny5a2         137 RILAATNRNIKELVKEGKFREDLYYRLGVIEIEIPPLRERKEDIIPLANHFLKKFSRKYAKEVEGFTKSAQELLLSY  213 (247)
T ss_dssp             EEEEEESSCHHHHHHTTSSCHHHHHHHTTEEEECCCGGGCHHHHHHHHHHHHHHHHHHTTCCCCEECHHHHHHHHHS
T ss_pred             EEEEecCCCHHHHHHcCCCcHHHHhhcCeeeecCCChhhchhhHhhhhhhhhhhhhhhcCCCCCCCCHHHHHHHHhC
Confidence            7888776532  1122235778888888666666664    5566666777776655444   34789988877543

>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=99.02  E-value=1.3e-10  Score=124.68  Aligned_cols=78  Identities=33%  Similarity=0.500  Sum_probs=60.7

Q ss_pred             HHHHHHhhCcccChHHHHHHHHHHH--HHhhcCCCCCCC---CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          621 VGLEEQLKKRVIGQDEAVAAISRAV--KRSRVGLKDPNR---PTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       621 ~~l~~~L~~~v~Gq~~a~~~i~~~i--~~~r~gl~~p~r---p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .++.+.|.++|+||++|++.++-++  .+.|..+..+.+   ..+++||+||||||||+|||.||+.+   +-+++..|+
T Consensus         6 ~~i~~~Ld~yVvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l---~VPFv~~da   82 (443)
T d1g41a_           6 REIVSELDQHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLA---NAPFIKVEA   82 (443)
T ss_dssp             HHHHHHHHTTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHT---TCCEEEEEG
T ss_pred             HHHHHHhcCcccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHh---CCCEEEeec
Confidence            3567889999999999999999888  223333333322   22599999999999999999999996   668999999


Q ss_pred             CCCCCc
Q 005179          696 SPFNSV  701 (710)
Q Consensus       696 se~~~~  701 (710)
                      +.|..+
T Consensus        83 T~fTea   88 (443)
T d1g41a_          83 TKFTEV   88 (443)
T ss_dssp             GGGC--
T ss_pred             ceeeec
Confidence            999664

>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=98.99  E-value=7.8e-10  Score=105.83  Aligned_cols=133  Identities=11%  Similarity=0.126  Sum_probs=94.6

Q ss_pred             HHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccccCccHHHHHHHHHHH
Q 005179          298 EIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAKERGELEARVTTLISE  377 (710)
Q Consensus       298 ~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~~~g~~e~~l~~~~~~  377 (710)
                      +++-+..++.+....++||+||||+|||++|..+++.+.....    ....++.+...    |. ..+  .+.++.+.+.
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~----~h~D~~~i~~~----~~-~I~--Id~IR~i~~~   70 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELPEYVEKFPP----KASDVLEIDPE----GE-NIG--IDDIRTIKDF   70 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHHHHHHTSCC----CTTTEEEECCS----SS-CBC--HHHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHHHHHhcccc----CCCCEEEEeCC----cC-CCC--HHHHHHHHHH
Confidence            3455666677778889999999999999999999987743211    12235554421    11 111  2335666666


Q ss_pred             HHh----cCCeEEEEccchhhhhCCCCCCCCCCChHhHHHhhcccccC--CCeEEEEccChHHHHhhhhccHHHHccccc
Q 005179          378 IQK----SGDVILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLGR--GELQCIASTTQDEHRTQFEKDKALARRFQP  451 (710)
Q Consensus       378 ~~~----~~~~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~~--~~v~vI~att~~~~~~~~~~d~aL~~Rf~~  451 (710)
                      +..    ++.-|++|||+|.|             ..+.++.|+..|++  ++..+|.+|+..+     .+.|++++||+.
T Consensus        71 ~~~~~~~~~~KviIId~ad~l-------------~~~aqNaLLK~LEEPp~~t~fiLit~~~~-----~ll~TI~SRC~~  132 (198)
T d2gnoa2          71 LNYSPELYTRKYVIVHDCERM-------------TQQAANAFLKALEEPPEYAVIVLNTRRWH-----YLLPTIKSRVFR  132 (198)
T ss_dssp             HTSCCSSSSSEEEEETTGGGB-------------CHHHHHHTHHHHHSCCTTEEEEEEESCGG-----GSCHHHHTTSEE
T ss_pred             HhhCcccCCCEEEEEeCcccc-------------chhhhhHHHHHHhCCCCCceeeeccCChh-----hCHHHHhcceEE
Confidence            543    23469999999999             66789999999985  4677777777765     688999999999


Q ss_pred             eEecCCCH
Q 005179          452 VLISEPSQ  459 (710)
Q Consensus       452 I~v~~Ps~  459 (710)
                      +.++.|..
T Consensus       133 i~~~~p~~  140 (198)
T d2gnoa2         133 VVVNVPKE  140 (198)
T ss_dssp             EECCCCHH
T ss_pred             EeCCCchH
Confidence            99987753

>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=98.95  E-value=3.4e-10  Score=111.72  Aligned_cols=65  Identities=23%  Similarity=0.276  Sum_probs=50.2

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      +.|+||+++++.+...+...+..-    +++.++|||||||||||++|++||+++..   ..+.++.++...
T Consensus         9 ~divGqe~~~~~l~~~i~~~~~~~----~~~~~~L~~GPpGtGKT~lA~~la~~~~~---~~~~~~~~~~~~   73 (238)
T d1in4a2           9 DEFIGQENVKKKLSLALEAAKMRG----EVLDHVLLAGPPGLGKTTLAHIIASELQT---NIHVTSGPVLVK   73 (238)
T ss_dssp             GGCCSCHHHHHHHHHHHHHHHHHT----CCCCCEEEESSTTSSHHHHHHHHHHHHTC---CEEEEETTTCCS
T ss_pred             HHcCChHHHHHHHHHHHHHHHhcC----CCCCeEEEECCCCCcHHHHHHHHHhccCC---CcccccCccccc
Confidence            349999999999999987654322    22348999999999999999999999765   456666666543

>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=98.93  E-value=2.2e-09  Score=115.03  Aligned_cols=110  Identities=25%  Similarity=0.287  Sum_probs=67.8

Q ss_pred             eEEEEccchhhhhCCCCCCCCCCChHhHHHhhccccc------------CCCeEEEEccChHHHHhhhhccHHHHcccc-
Q 005179          384 VILFIDEVHTLIGSGTVGRGNKGTGLDISNLLKPSLG------------RGELQCIASTTQDEHRTQFEKDKALARRFQ-  450 (710)
Q Consensus       384 ~IL~IDEid~l~~~~~~~~~~~~~~~~~~~~L~~~l~------------~~~v~vI~att~~~~~~~~~~d~aL~~Rf~-  450 (710)
                      .++|+||++.....+..... .......+.-+.+.++            ...+.+|+++.... .+...+-|.|..||. 
T Consensus       251 ~~~~~dei~k~~~~~~~~g~-d~~~eg~~~~ll~~~e~~~v~~~~~~~~~~~~l~i~~~~~~~-~~~~gliPEliGRlPi  328 (443)
T d1g41a_         251 GIVFIDEIDKICKKGEYSGA-DVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQV-ARPSDLIPELQGRLPI  328 (443)
T ss_dssp             CEEEEETGGGGSCCSSCSSS-HHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSS-CCGGGSCHHHHTTCCE
T ss_pred             CccccchhhhhhhcccCCCC-Ccccchhhhhhhhhccccccccccccccccchhhccccchhh-cccccchhhhccceEE
Confidence            47888888888655432110 0001112233333222            23445666544332 122356799999998 


Q ss_pred             ceEecCCCHHHHHHHHHH----HHHHHHh---hcC--CCCCHHHHHHHHHHhhh
Q 005179          451 PVLISEPSQEDAVRILLG----LREKYEA---HHN--CKFTLEAINAAVHLSAR  495 (710)
Q Consensus       451 ~I~v~~Ps~~~~~~IL~~----l~~~~~~---~~~--~~i~~~~l~~l~~ls~~  495 (710)
                      .+.+.+.+.++...||..    +..+|..   ..+  +.+++++++.+++.+-.
T Consensus       329 ~v~L~~L~~~dL~rILtEPknsLikQy~~lf~~~gv~L~ft~~al~~iA~~A~~  382 (443)
T d1g41a_         329 RVELTALSAADFERILTEPHASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFR  382 (443)
T ss_dssp             EEECCCCCHHHHHHHHHSSTTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHH
T ss_pred             EEEccCccHHHHHHHHHhhhhhHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHH
Confidence            789999999999999964    6666653   234  45799999999988764

>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=98.93  E-value=5.7e-10  Score=110.20  Aligned_cols=64  Identities=22%  Similarity=0.281  Sum_probs=50.6

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      .|+||+++++.+...+...+.+-.    +..++|||||||||||++|+++|+++.-   .+..++.+....
T Consensus        10 divGq~~~~~~L~~~i~~~~~~~~----~~~~~Ll~GPpG~GKTtla~~la~~~~~---~~~~~~~~~~~~   73 (239)
T d1ixsb2          10 EYIGQERLKQKLRVYLEAAKARKE----PLEHLLLFGPPGLGKTTLAHVIAHELGV---NLRVTSGPAIEK   73 (239)
T ss_dssp             GSCSCHHHHHHHHHHHHHHTTSSS----CCCCEEEECCTTSCHHHHHHHHHHHHTC---CEEEEETTTCCS
T ss_pred             HhCCHHHHHHHHHHHHHHHHhcCC----CCCeEEEECCCCCCHHHHHHHHHHHhCC---CeEeccCCcccc
Confidence            389999999999999887764322    3358999999999999999999999765   456666665533

>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=98.85  E-value=1.8e-09  Score=107.44  Aligned_cols=63  Identities=37%  Similarity=0.451  Sum_probs=48.9

Q ss_pred             ccChHHHHHHHHHHHHHhh-------cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSR-------VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r-------~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      |+|++++++.|.+.+.+.+       .|...|    .++|||||||||||++|++||+++   +..++.++++.+.+
T Consensus        14 i~Gl~~~k~~l~e~v~~~~~~~~~~~~g~~~~----~~iLL~GppGtGKT~la~~iA~~~---~~~~~~i~~~~l~~   83 (256)
T d1lv7a_          14 VAGCDEAKEEVAELVEYLREPSRFQKLGGKIP----KGVLMVGPPGTGKTLLAKAIAGEA---KVPFFTISGSDFVE   83 (256)
T ss_dssp             SCSCHHHHHHTHHHHHHHHCGGGC-----CCC----CEEEEECCTTSCHHHHHHHHHHHH---TCCEEEECSCSSTT
T ss_pred             HhchHHHHHHHHHHHHHHHCHHHHHHcCCCCC----CeEEeeCCCCCCccHHHHHHHHHc---CCCEEEEEhHHhhh
Confidence            8888888888877665432       344333    699999999999999999999996   45799999988754

>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=98.81  E-value=1.4e-09  Score=107.69  Aligned_cols=61  Identities=33%  Similarity=0.452  Sum_probs=47.6

Q ss_pred             ccChHHHHHHHHHHH-------HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          631 VIGQDEAVAAISRAV-------KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i-------~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      |+|++++++.|.+.+       .+.+.|...|    .++|||||||||||++|++||+++   ...++.++++.+
T Consensus        11 i~G~~~~k~~l~~~i~~l~~~~~~~~~g~~~~----~giLl~GppGtGKT~la~aia~~~---~~~~~~i~~~~l   78 (247)
T d1ixza_          11 VAGAEEAKEELKEIVEFLKNPSRFHEMGARIP----KGVLLVGPPGVGKTHLARAVAGEA---RVPFITASGSDF   78 (247)
T ss_dssp             CCSCHHHHHHHHHHHHHHHCHHHHHHTTCCCC----SEEEEECCTTSSHHHHHHHHHHHT---TCCEEEEEHHHH
T ss_pred             HccHHHHHHHHHHHHHHHHCHHHHHHcCCCCC----ceEEEecCCCCChhHHHHHHHHHc---CCCEEEEEhHHh
Confidence            777877777776655       3445566544    589999999999999999999995   457888887765

>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=98.78  E-value=3e-08  Score=99.00  Aligned_cols=178  Identities=15%  Similarity=0.187  Sum_probs=98.7

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhhccc------
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMAGAK------  362 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~g~~------  362 (710)
                      .+.++||+++++++.+.    .++.++|+||+|+|||+|++.+++.+          +.....+++........      
T Consensus        11 ~~~f~GR~~el~~l~~~----~~~~i~i~G~~G~GKTsLl~~~~~~~----------~~~~~~i~~~~~~~~~~~~~~~~   76 (283)
T d2fnaa2          11 RKDFFDREKEIEKLKGL----RAPITLVLGLRRTGKSSIIKIGINEL----------NLPYIYLDLRKFEERNYISYKDF   76 (283)
T ss_dssp             GGGSCCCHHHHHHHHHT----CSSEEEEEESTTSSHHHHHHHHHHHH----------TCCEEEEEGGGGTTCSCCCHHHH
T ss_pred             hhhCCChHHHHHHHHhc----cCCEEEEEcCCCCcHHHHHHHHHHHC----------CCCeEEEEeccccccccccHHHH
Confidence            35799999999998753    45778999999999999999998876          22222222211110000      


Q ss_pred             --------------------------------------cCccHHHHHHHHHHHHHh--cCCeEEEEccchhhhhCCCCCC
Q 005179          363 --------------------------------------ERGELEARVTTLISEIQK--SGDVILFIDEVHTLIGSGTVGR  402 (710)
Q Consensus       363 --------------------------------------~~g~~e~~l~~~~~~~~~--~~~~IL~IDEid~l~~~~~~~~  402 (710)
                                                            ........+..+++.+..  ..+.++++||++.+.....   
T Consensus        77 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~~~~~---  153 (283)
T d2fnaa2          77 LLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVKLRG---  153 (283)
T ss_dssp             HHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGGCTT---
T ss_pred             HHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhcccch---
Confidence                                                  000000112333444332  4578899999999855321   


Q ss_pred             CCCCChHhHHHhhccccc-CCCeEEEEccChHH-HHhhhh---cc-HHHHccccceEecCCCHHHHHHHHHHHHHHHHhh
Q 005179          403 GNKGTGLDISNLLKPSLG-RGELQCIASTTQDE-HRTQFE---KD-KALARRFQPVLISEPSQEDAVRILLGLREKYEAH  476 (710)
Q Consensus       403 ~~~~~~~~~~~~L~~~l~-~~~v~vI~att~~~-~~~~~~---~d-~aL~~Rf~~I~v~~Ps~~~~~~IL~~l~~~~~~~  476 (710)
                            .++...|..... ...+..|.+++... ......   .. +.+.+++..+.+.+.+.++..+++.......   
T Consensus       154 ------~~~~~~l~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~L~~l~~~e~~~~l~~~~~~~---  224 (283)
T d2fnaa2         154 ------VNLLPALAYAYDNLKRIKFIMSGSEMGLLYDYLRVEDPESPLFGRAFSTVELKPFSREEAIEFLRRGFQEA---  224 (283)
T ss_dssp             ------CCCHHHHHHHHHHCTTEEEEEEESSHHHHHHHTTTTCTTSTTTTCCCEEEEECCCCHHHHHHHHHHHHHHH---
T ss_pred             ------HHHHHHHHHHHHhhhhhhhhhccccchHHHHHHHhhhhcchhcccceeEEeeCCCCHHHHHHHHHhhhhhc---
Confidence                  122333332222 34454444433322 111111   11 2222344579999999999999988766543   


Q ss_pred             cCCCCCHHHHHHHHHHhhh
Q 005179          477 HNCKFTLEAINAAVHLSAR  495 (710)
Q Consensus       477 ~~~~i~~~~l~~l~~ls~~  495 (710)
                       ++.  .+.++.+.+.+.+
T Consensus       225 -~~~--~~~~~~i~~~~~G  240 (283)
T d2fnaa2         225 -DID--FKDYEVVYEKIGG  240 (283)
T ss_dssp             -TCC--CCCHHHHHHHHCS
T ss_pred             -CCC--HHHHHHHHHHhCC
Confidence             333  3345666666554

>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=98.77  E-value=2.3e-09  Score=107.05  Aligned_cols=63  Identities=29%  Similarity=0.463  Sum_probs=49.7

Q ss_pred             CcccChHHHHHHHHHHHH--------HhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVK--------RSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~--------~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +.|+|++++++.|...+.        +.+.|+..|    .|+|||||||||||++|+++|.+   ....++.++.+.+
T Consensus         4 ~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~----~giLL~GppGtGKT~l~~ala~~---~~~~~~~i~~~~l   74 (258)
T d1e32a2           4 DDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPP----RGILLYGPPGTGKTLIARAVANE---TGAFFFLINGPEI   74 (258)
T ss_dssp             GGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCC----CEEEEECCTTSSHHHHHHHHHHH---TTCEEEEECHHHH
T ss_pred             hhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCC----ceeEEecCCCCCchHHHHHHHHH---hCCeEEEEEchhh
Confidence            459999999998888753        345566544    68999999999999999999999   4456777776654

>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=98.77  E-value=2.4e-09  Score=107.27  Aligned_cols=60  Identities=23%  Similarity=0.283  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          636 EAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       636 ~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +..+.+...++....|.+.+..|. ++|||||||||||++|++||+.+++   .++++++++|.
T Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~P~-~ilL~GpPGtGKT~la~~la~~~~~---~~~~i~~d~~~   69 (273)
T d1gvnb_          10 QFENRLNDNLEELIQGKKAVESPT-AFLLGGQPGSGKTSLRSAIFEETQG---NVIVIDNDTFK   69 (273)
T ss_dssp             HHHHHHHHHHHHHHTTCCCCSSCE-EEEEECCTTSCTHHHHHHHHHHTTT---CCEEECTHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCCCCCE-EEEEECCCCCCHHHHHHHHHHHhhc---ceEEEecHHHH
Confidence            344556666777777888887776 7999999999999999999999865   68999988874

>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=98.70  E-value=1.4e-09  Score=107.72  Aligned_cols=68  Identities=18%  Similarity=0.199  Sum_probs=48.7

Q ss_pred             HHhhCcccChHHHHHHHHHHH----HHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          625 EQLKKRVIGQDEAVAAISRAV----KRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       625 ~~L~~~v~Gq~~a~~~i~~~i----~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      +.+...|+|+.+.++.|.+-.    ...+.+   ...|+.++|||||||||||++|++||+++   +..++.++.++.
T Consensus         5 ~~~~~~~i~~~~~i~~i~~~~~~~~~~~~~~---~~~p~~~vLL~GppGtGKT~la~alA~~~---~~~~~~i~~~~~   76 (246)
T d1d2na_           5 SYIMNGIIKWGDPVTRVLDDGELLVQQTKNS---DRTPLVSVLLEGPPHSGKTALAAKIAEES---NFPFIKICSPDK   76 (246)
T ss_dssp             TTCTTCCCCCSHHHHHHHHHHHHHHHHHHHC---SSCSEEEEEEECSTTSSHHHHHHHHHHHH---TCSEEEEECGGG
T ss_pred             HhhccCCcCcCHHHHHHHHHHHHHHHHHhcc---CCCCCeEEEEECcCCCCHHHHHHHHhhcc---cccccccccccc
Confidence            345556777767666555444    333333   33466899999999999999999999995   457888887753

>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=98.62  E-value=1.2e-08  Score=101.07  Aligned_cols=69  Identities=22%  Similarity=0.159  Sum_probs=51.1

Q ss_pred             CcccChHHHHHHHHHHHHHhhc---------CCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRV---------GLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~---------gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      +.++|++++++.|...+.....         |.. +..+..++|||||||||||++|++||+++..   .++.+++++..
T Consensus        14 ~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~-~~~~~~~lll~GPpG~GKTt~a~~la~~~~~---~~~~~~~~~~~   89 (253)
T d1sxja2          14 QQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKD-GSGVFRAAMLYGPPGIGKTTAAHLVAQELGY---DILEQNASDVR   89 (253)
T ss_dssp             GGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTT-STTSCSEEEEECSTTSSHHHHHHHHHHHTTC---EEEEECTTSCC
T ss_pred             HHhcCCHHHHHHHHHHHHhhhhcchhhhhhhccc-CCCCCceEEEECCCCCCHHHHHHHHHHHHHh---hhhccccccch
Confidence            3499999999999887743211         111 2223358999999999999999999999765   57788888765


Q ss_pred             Cc
Q 005179          700 SV  701 (710)
Q Consensus       700 ~~  701 (710)
                      +.
T Consensus        90 ~~   91 (253)
T d1sxja2          90 SK   91 (253)
T ss_dssp             CH
T ss_pred             hh
Confidence            43

>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=98.52  E-value=3.3e-08  Score=96.65  Aligned_cols=60  Identities=33%  Similarity=0.466  Sum_probs=47.4

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--CcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li~~d~se~  698 (710)
                      .|+||+++++.+...+...+         ..++|||||||||||++|+++|+++++..  ...+.+|.|+.
T Consensus        25 diig~~~~~~~l~~~i~~~~---------~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~s~~   86 (231)
T d1iqpa2          25 DIVGQEHIVKRLKHYVKTGS---------MPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNASDE   86 (231)
T ss_dssp             TCCSCHHHHHHHHHHHHHTC---------CCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETTCH
T ss_pred             HccCcHHHHHHHHHHHHcCC---------CCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEecCcc
Confidence            39999999999999886543         13799999999999999999999998742  34555665543

>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=98.50  E-value=1.6e-08  Score=98.51  Aligned_cols=61  Identities=28%  Similarity=0.436  Sum_probs=47.3

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC--cceeeCCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR--IHYLFFPSPFNS  700 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~--~li~~d~se~~~  700 (710)
                      ++||+++++.+...+...+         +.++|||||||||||++|+++|+++++...  ..+-++.++..+
T Consensus        16 ivg~~~~~~~L~~~i~~~~---------~~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~~~~~   78 (227)
T d1sxjc2          16 VYGQNEVITTVRKFVDEGK---------LPHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNASDDRG   78 (227)
T ss_dssp             CCSCHHHHHHHHHHHHTTC---------CCCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTTSCCS
T ss_pred             ccCcHHHHHHHHHHHHcCC---------CCeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEecccccCC
Confidence            9999999999988875432         126999999999999999999999988653  334455555543

>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=98.50  E-value=1.2e-08  Score=102.21  Aligned_cols=62  Identities=24%  Similarity=0.359  Sum_probs=47.1

Q ss_pred             cccChHHHHHHHHHHHHH--------hhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKR--------SRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~--------~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .|+|++++++.|.+.+.+        .+.|+..|    .++|||||||||||++|++||.++   +..++.++++.+
T Consensus         8 di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~----~giLL~Gp~GtGKT~l~~ala~~~---~~~~~~~~~~~l   77 (265)
T d1r7ra3           8 DIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS----KGVLFYGPPGCGKTLLAKAIANEC---QANFISIKGPEL   77 (265)
T ss_dssp             SCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCC----CEEEEBCCTTSSHHHHHHHHHHHT---TCEEEEECHHHH
T ss_pred             HhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCC----CeEEEECCCCCcchhHHHHHHHHh---CCcEEEEEHHHh
Confidence            378888887777766532        23455433    699999999999999999999995   457888886554

>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=98.48  E-value=5.4e-08  Score=96.87  Aligned_cols=67  Identities=16%  Similarity=0.210  Sum_probs=50.0

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC-cceeeCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR-IHYLFFPSPF  698 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~-~li~~d~se~  698 (710)
                      +.++|++..++.|...+...   +++|..+.+++||+||||||||++|++||+.+++... ..+..++..+
T Consensus        16 ~~l~~Re~ei~~l~~~l~~~---l~~~~~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~   83 (276)
T d1fnna2          16 KRLPHREQQLQQLDILLGNW---LRNPGHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIY   83 (276)
T ss_dssp             SCCTTCHHHHHHHHHHHHHH---HHSTTSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTC
T ss_pred             CCCCCHHHHHHHHHHHHHHH---HhCCCCCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecchhh
Confidence            45889999999998887643   3345556679999999999999999999999987543 2333444333

>d1khya_ a.174.1.1 (A:) N-terminal domain of ClpB (heat shock protein F84.1) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Escherichia coli [TaxId: 562]

Probab=98.48  E-value=1.5e-07  Score=84.15  Aligned_cols=64  Identities=19%  Similarity=0.301  Sum_probs=60.1

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++.+|..|...|++++|.+|+++|||+||+.++++.+..+|+++|++.+.++..+...+
T Consensus         2 kfT~~~~~~l~~A~~~A~~~~h~~v~~eHlL~all~~~~~~~~~iL~~~g~d~~~~~~~~~~~l   65 (139)
T d1khya_           2 RLTNKFQLALADAQSLALGHDNQFIEPLHLMSALLNQEGGSVSPLLTSAGINAGQLRTDINQAL   65 (139)
T ss_dssp             CBCHHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHTCTTCSHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhCcccHHHHHHHHcCCcHHHHHHHHHHHh
Confidence            4899999999999999999999999999999999999999999999999999999988776655

>d1qvra1 a.174.1.1 (A:4-148) N-terminal domain of ClpB (heat shock protein F84.1) {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal domain of ClpB (heat shock protein F84.1)
species: Thermus thermophilus [TaxId: 274]

Probab=98.47  E-value=1.4e-07  Score=85.08  Aligned_cols=64  Identities=17%  Similarity=0.200  Sum_probs=60.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhh
Q 005179          170 PFSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRL  233 (710)
Q Consensus       170 ~~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l  233 (710)
                      .||+.++++|..|...|++++|.+|+++|||+||+.++++.+..+|+++|+|.+.++..+...+
T Consensus         2 kfT~~a~~~l~~A~~~A~~~~~~~i~~~HlL~all~~~~~~~~~iL~~~gvd~~~l~~~l~~~l   65 (145)
T d1qvra1           2 RWTQAAREALAQAQVLAQRMKHQAIDLPHLWAVLLKDERSLAWRLLEKAGADPKALKELQEREL   65 (145)
T ss_dssp             CSCHHHHHHHHHHHHHHHHTTCSEECHHHHHHHHCCSSSSHHHHHHHTTSSCHHHHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHcCCcchHHHHHHHcCCCHHHHHHHHHHHh
Confidence            4899999999999999999999999999999999999999999999999999999999887766

>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=98.44  E-value=1e-07  Score=99.14  Aligned_cols=69  Identities=23%  Similarity=0.132  Sum_probs=50.1

Q ss_pred             HHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          622 GLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       622 ~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      ..-+.|+..+.|+++.+..+   ++....|.  |.+  .++|||||||||||++|++||+.+.+   .++.+|+|+..+
T Consensus       124 ~il~~l~~~~~~~~~~i~~~---l~~~~~~~--~~~--~~~~~~g~~~~gk~~~~~~~~~~~~~---~~i~in~s~~rs  192 (362)
T d1svma_         124 AGVAWLHCLLPKMDSVVYDF---LKCMVYNI--PKK--RYWLFKGPIDSGKTTLAAALLELCGG---KALNVNLPLDRL  192 (362)
T ss_dssp             HHHHHHTTTSTTHHHHHHHH---HHHHHHCC--TTC--CEEEEECSTTSSHHHHHHHHHHHHCC---EEECCSSCTTTH
T ss_pred             HHHHHHHhcccchHHHHHHH---HHHHHhCC--CCc--CeEEEECCCCCCHHHHHHHHHHHcCC---CEEEEECcchhh
Confidence            33355666677777666543   44434444  333  38999999999999999999999887   799999887643

>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=98.44  E-value=2e-08  Score=97.84  Aligned_cols=74  Identities=20%  Similarity=0.249  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHHHhhCcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC--Ccce
Q 005179          614 ADERMLLVGLEEQLKKRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV--RIHY  691 (710)
Q Consensus       614 ~~~~~~l~~l~~~L~~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~--~~li  691 (710)
                      |.+..+...+.+     ++||+++++.+...++..+    .     .++||+||||||||++|+++|+.+++..  ...+
T Consensus         5 w~eKyrP~~~~d-----~ig~~~~~~~L~~~~~~~~----~-----~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~   70 (224)
T d1sxjb2           5 WVEKYRPQVLSD-----IVGNKETIDRLQQIAKDGN----M-----PHMIISGMPGIGKTTSVHCLAHELLGRSYADGVL   70 (224)
T ss_dssp             HHHHTCCSSGGG-----CCSCTHHHHHHHHHHHSCC----C-----CCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEE
T ss_pred             hHhHhCCCCHHH-----hcCCHHHHHHHHHHHHcCC----C-----CeEEEECCCCCCchhhHHHHHHHHhccccccccc
Confidence            555444444444     9999999999988765321    1     2699999999999999999999988643  2355


Q ss_pred             eeCCCCCCCc
Q 005179          692 LFFPSPFNSV  701 (710)
Q Consensus       692 ~~d~se~~~~  701 (710)
                      -.+.++..++
T Consensus        71 ~~n~~~~~~~   80 (224)
T d1sxjb2          71 ELNASDDRGI   80 (224)
T ss_dssp             EECTTSCCSH
T ss_pred             cccccccCCc
Confidence            5666655443

>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=98.32  E-value=7e-07  Score=92.70  Aligned_cols=38  Identities=21%  Similarity=0.281  Sum_probs=32.6

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhh
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGL  356 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~  356 (710)
                      +.++.++|+||||||||++|+++|..+          +..++.++++.
T Consensus       152 ~~~~~~~~~g~~~~gk~~~~~~~~~~~----------~~~~i~in~s~  189 (362)
T d1svma_         152 PKKRYWLFKGPIDSGKTTLAAALLELC----------GGKALNVNLPL  189 (362)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHH----------CCEEECCSSCT
T ss_pred             CCcCeEEEECCCCCCHHHHHHHHHHHc----------CCCEEEEECcc
Confidence            456789999999999999999999999          77888876544

>d1k6ka_ a.174.1.1 (A:) N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Double Clp-N motif
superfamily: Double Clp-N motif
family: Double Clp-N motif
domain: N-terminal, ClpS-binding domain of ClpA, an Hsp100 chaperone
species: Escherichia coli [TaxId: 562]

Probab=98.32  E-value=5.4e-07  Score=80.71  Aligned_cols=62  Identities=21%  Similarity=0.264  Sum_probs=55.5

Q ss_pred             CCHHHHHHHHHHHHHHHHcCCCccCHHHHHHHhhhcCCchHHHHHHHhcCCHHHHHHHHHHhhh
Q 005179          171 FSISTKRVFEAAVEYSRSRGYNFIAPEHIALGLFTVDDGSAGRVLKRLGVDVNHLAAVAVSRLQ  234 (710)
Q Consensus       171 ~s~~~~~vl~~A~~~a~~~g~~~I~~ehlLlall~~~~~~a~~iL~~~gv~~~~l~~~~~~~l~  234 (710)
                      ||..++.+|..|...|++++|.||++||||+||++++  .+..++..+|++.+.++..+...+.
T Consensus         2 ~s~~l~~~l~~A~~~A~~~~h~~i~~EHLL~aLl~~~--~~~~~l~~~~~~~~~l~~~~~~~~~   63 (142)
T d1k6ka_           2 LNQELELSLNMAFARAREHRHEFMTVEHLLLALLSNP--SAREALEACSVDLVALRQELEAFIE   63 (142)
T ss_dssp             BCHHHHHHHHHHHHHHHHHTBSEECHHHHHHHHTTCH--HHHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHhch--hHHHHHHHcCCchhhhHHHHHHHHH
Confidence            7899999999999999999999999999999999744  4678999999999999887776553

>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=98.28  E-value=1.9e-07  Score=92.08  Aligned_cols=58  Identities=19%  Similarity=0.257  Sum_probs=40.0

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      ++|++++++.+...+..   +...|     ++|||||||||||++|+++|+.+++........+..
T Consensus        13 iig~~~~~~~L~~~~~~---~~~~~-----~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~   70 (252)
T d1sxje2          13 LSHNEELTNFLKSLSDQ---PRDLP-----HLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVR   70 (252)
T ss_dssp             CCSCHHHHHHHHTTTTC---TTCCC-----CEEEECSTTSSHHHHHHTHHHHHSCTTCCC------
T ss_pred             ccCcHHHHHHHHHHHHc---CCCCC-----eEEEECCCCCCHHHHHHHHHHhhcCccccccccccc
Confidence            89999888888654321   11222     699999999999999999999998766544444443

>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=98.26  E-value=1.1e-07  Score=92.75  Aligned_cols=63  Identities=29%  Similarity=0.408  Sum_probs=47.7

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC---CcceeeCCCCCCCcc
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV---RIHYLFFPSPFNSVK  702 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~---~~li~~d~se~~~~~  702 (710)
                      ++|++++++.+...++..+         +.++||+||||||||++|+++|+.+++..   ......+.+...++.
T Consensus        14 iig~~~~~~~l~~~i~~~~---------~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~   79 (237)
T d1sxjd2          14 VTAQDHAVTVLKKTLKSAN---------LPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNASDERGIS   79 (237)
T ss_dssp             CCSCCTTHHHHHHHTTCTT---------CCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECSSSCCCHH
T ss_pred             ccCcHHHHHHHHHHHHcCC---------CCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheeccccccch
Confidence            8899999988877654222         13699999999999999999999987643   345666777766553

>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=98.19  E-value=4.2e-07  Score=90.71  Aligned_cols=57  Identities=18%  Similarity=0.071  Sum_probs=41.2

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..+.|.++-++.|...+......-..|..+...++||||||||||++++++++.|+.
T Consensus        16 ~~~~~Re~e~~~l~~~l~~~~~~~~~~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~   72 (287)
T d1w5sa2          16 PELRVRRGEAEALARIYLNRLLSGAGLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSE   72 (287)
T ss_dssp             SSCSSSCHHHHHHHHHHHHHHHTSSCBCCEEEEEECTTCCSSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHcCCCCCCcceEEEeECCCCCCHHHHHHHHHHHHHh
Confidence            347777777888887765443333333344446788999999999999999999854

>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=98.14  E-value=5.4e-07  Score=91.32  Aligned_cols=41  Identities=17%  Similarity=0.051  Sum_probs=33.6

Q ss_pred             CeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCCC
Q 005179          659 TAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFNS  700 (710)
Q Consensus       659 ~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~~  700 (710)
                      -+.+|||||||||||.||++||.++- .+.+++.+++|++.+
T Consensus       123 ~g~~l~~G~pG~GKT~la~ala~~~~-~~~~~~~~~~~~~~~  163 (321)
T d1w44a_         123 SGMVIVTGKGNSGKTPLVHALGEALG-GKDKYATVRFGEPLS  163 (321)
T ss_dssp             SEEEEEECSSSSCHHHHHHHHHHHHH-TTSCCEEEEBSCSST
T ss_pred             CceEEEECCCCccHHHHHHHHHHHhc-CCCCeEEEEhhHhhh
Confidence            35677799999999999999999974 344688899998854

>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=98.09  E-value=3.9e-06  Score=83.89  Aligned_cols=45  Identities=27%  Similarity=0.283  Sum_probs=36.5

Q ss_pred             CcccCHHHHHHHHHHHHcCC---CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          291 PVIGRETEIQRIIQILCRRT---KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~---~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++||+.+++++++.|....   ..-+.|+|.+|+||||||+.+.+..
T Consensus        21 ~~~gR~~~~~~i~~~L~~~~~~~~~~v~I~GmgGiGKTtLA~~v~~~~   68 (277)
T d2a5yb3          21 TCYIREYHVDRVIKKLDEMCDLDSFFLFLHGRAGSGKSVIASQALSKS   68 (277)
T ss_dssp             CSCCCHHHHHHHHHHHHHHTTSSSEEEEEECSTTSSHHHHHHHHHHHC
T ss_pred             ceeCcHHHHHHHHHHHHhccCCCceEEEEECCCCCCHHHHHHHHHHhh
Confidence            47899999999999885421   2236799999999999999998764

>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=98.06  E-value=1.6e-06  Score=84.85  Aligned_cols=50  Identities=34%  Similarity=0.511  Sum_probs=41.3

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      .++||+++++.+...++..+        +..++|||||||||||++|+++++.+++..
T Consensus        13 dlig~~~~~~~L~~~i~~~~--------~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~   62 (239)
T d1njfa_          13 DVVGQEHVLTALANGLSLGR--------IHHAYLFSGTRGVGKTSIARLLAKGLNCET   62 (239)
T ss_dssp             GSCSCHHHHHHHHHHHHTTC--------CCSEEEEECSTTSSHHHHHHHHHHHHHCTT
T ss_pred             HccChHHHHHHHHHHHHcCC--------CCeeEEEECCCCCcHHHHHHHHHHHhcCcc
Confidence            49999999999988775432        123799999999999999999999998753

>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=98.03  E-value=9.1e-07  Score=91.19  Aligned_cols=45  Identities=24%  Similarity=0.405  Sum_probs=36.6

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .|+||++++.++..+.....         .+++||+||||||||++||++|..|
T Consensus         8 ~I~Gq~~~kral~laa~~~~---------~h~vLl~G~pG~GKT~lar~~~~iL   52 (333)
T d1g8pa_           8 AIVGQEDMKLALLLTAVDPG---------IGGVLVFGDRGTGKSTAVRALAALL   52 (333)
T ss_dssp             GSCSCHHHHHHHHHHHHCGG---------GCCEEEECCGGGCTTHHHHHHHHHS
T ss_pred             hccCcHHHHHHHHHHHhccC---------CCeEEEECCCCccHHHHHHHHHHhC
Confidence            49999999998765443211         1479999999999999999999987

>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=98.00  E-value=4.3e-06  Score=77.16  Aligned_cols=25  Identities=36%  Similarity=0.615  Sum_probs=22.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +++|+||||+|||||++.++..+..
T Consensus         2 ki~I~G~~G~GKSTLl~~i~~~l~~   26 (178)
T d1ye8a1           2 KIIITGEPGVGKTTLVKKIVERLGK   26 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGG
T ss_pred             EEEEECCCCcHHHHHHHHHHhcCCC
Confidence            3799999999999999999998743

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=97.82  E-value=8.9e-06  Score=77.52  Aligned_cols=48  Identities=15%  Similarity=0.137  Sum_probs=38.8

Q ss_pred             cChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          632 IGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       632 ~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      -|++++.+.+...+...+.        ..++||+||||+|||++|+++|+.++...
T Consensus         5 Pw~~~~~~~l~~~~~~~~l--------~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~   52 (207)
T d1a5ta2           5 PWLRPDFEKLVASYQAGRG--------HHALLIQALPGMGDDALIYALSRYLLCQQ   52 (207)
T ss_dssp             GGGHHHHHHHHHHHHTTCC--------CSEEEEECCTTSCHHHHHHHHHHHHTCSS
T ss_pred             cccHHHHHHHHHHHHcCCc--------CeEEEEECCCCCcHHHHHHHHHHhccccc
Confidence            4788888888777665442        24799999999999999999999998543

>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=97.67  E-value=1.9e-05  Score=77.91  Aligned_cols=38  Identities=18%  Similarity=0.309  Sum_probs=31.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      +.++||+||||||||++|++||..+          +..++.++.+.+.
T Consensus        32 P~~ilL~GpPGtGKT~la~~la~~~----------~~~~~~i~~d~~~   69 (273)
T d1gvnb_          32 PTAFLLGGQPGSGKTSLRSAIFEET----------QGNVIVIDNDTFK   69 (273)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHT----------TTCCEEECTHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHh----------hcceEEEecHHHH
Confidence            4469999999999999999999988          5566777766654

>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=97.55  E-value=1.9e-05  Score=71.06  Aligned_cols=25  Identities=40%  Similarity=0.634  Sum_probs=23.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.+++|+|||||||||+++.||+++
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L   26 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQL   26 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999998

>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=97.54  E-value=6.1e-05  Score=73.52  Aligned_cols=62  Identities=16%  Similarity=0.177  Sum_probs=50.9

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      .+|+..++..+...+++.-. .+      ..+|++||+|||||.+|++|...-++....++.+|++...
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~-~~------~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~   63 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISC-AE------CPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIP   63 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTT-CC------SCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSC
T ss_pred             eEecCHHHHHHHHHHHHHhC-CC------CCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhh
Confidence            57888999888887766421 11      2579999999999999999999988889999999998763

>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=97.49  E-value=2e-05  Score=73.50  Aligned_cols=35  Identities=26%  Similarity=0.395  Sum_probs=26.9

Q ss_pred             cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          650 VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       650 ~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .|....-|+. .++|+|+||+|||++|+.||+.|.-
T Consensus        11 ~~~~~~~~g~-vI~L~G~pGSGKTTiAk~La~~l~~   45 (195)
T d1x6va3          11 VGTRGGFRGC-TVWLTGLSGAGKTTVSMALEEYLVC   45 (195)
T ss_dssp             HSSSCSCCCE-EEEEESSCHHHHHHHHHHHHHHHHH
T ss_pred             HhhhcCCCCe-EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4444444443 6789999999999999999998744

>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=97.44  E-value=3.4e-05  Score=70.20  Aligned_cols=25  Identities=40%  Similarity=0.570  Sum_probs=23.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -.+++|+|+||+||||+++.|++++
T Consensus         4 ~~~I~i~G~pGsGKTTia~~La~~l   28 (173)
T d1rkba_           4 LPNILLTGTPGVGKTTLGKELASKS   28 (173)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            3579999999999999999999998

>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=97.36  E-value=6.1e-05  Score=70.11  Aligned_cols=61  Identities=25%  Similarity=0.337  Sum_probs=45.5

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCC-------CCcceeeCCCCC
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGS-------VRIHYLFFPSPF  698 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~-------~~~li~~d~se~  698 (710)
                      .-++|.++-++.+...+.+.+  .       .+.+|+||||||||.++..||..+-..       ...++.+|++.+
T Consensus        22 d~~igRd~Ei~~l~~iL~r~~--k-------~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~~~L   89 (195)
T d1jbka_          22 DPVIGRDEEIRRTIQVLQRRT--K-------NNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDMGAL   89 (195)
T ss_dssp             CCCCSCHHHHHHHHHHHTSSS--S-------CEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECHHHH
T ss_pred             CCCcCcHHHHHHHHHHHhccC--C-------CCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeHHHH
Confidence            348899998888877665432  1       378999999999999999999976542       245777775543

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=97.29  E-value=5.8e-05  Score=71.95  Aligned_cols=38  Identities=18%  Similarity=0.155  Sum_probs=30.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+++|||||||||.|+.|+++.+.......+.++++++
T Consensus        38 ~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~   75 (213)
T d1l8qa2          38 PIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDF   75 (213)
T ss_dssp             SEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             cEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHH
Confidence            47999999999999999999998766665555555443

>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=97.28  E-value=8e-05  Score=67.67  Aligned_cols=25  Identities=24%  Similarity=0.397  Sum_probs=22.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .-++|+||||||||++|+.||+.|.
T Consensus         7 ~iivl~G~~GsGKsT~a~~La~~l~   31 (171)
T d1knqa_           7 HIYVLMGVSGSGKSAVASEVAHQLH   31 (171)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhC
Confidence            4688999999999999999999873

>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=97.26  E-value=9.5e-05  Score=72.62  Aligned_cols=60  Identities=25%  Similarity=0.323  Sum_probs=44.6

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC-------CcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV-------RIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~-------~~li~~d~se~  698 (710)
                      -++|.++-++.+...+.+..  .       .+.||+||||||||.++..+|..+....       ..++.+|++.+
T Consensus        19 ~~igRd~Ei~~l~~iL~r~~--k-------~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~~~l   85 (268)
T d1r6bx2          19 PLIGREKELERAIQVLCRRR--K-------NNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDIGSL   85 (268)
T ss_dssp             CCCSCHHHHHHHHHHHTSSS--S-------CEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCCC--
T ss_pred             cccChHHHHHHHHHHHhcCc--c-------CCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeeechH
Confidence            48899998888877764332  1       3789999999999999999999765532       35777777665

>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=97.24  E-value=8e-05  Score=68.33  Aligned_cols=25  Identities=24%  Similarity=0.391  Sum_probs=23.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+|+|+|+|||||||+|++|++.+
T Consensus         7 ~K~I~i~G~~GsGKTTla~~La~~~   31 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLVNKLAAVF   31 (192)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHT
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHh
Confidence            3569999999999999999999988

>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=97.21  E-value=9e-05  Score=67.21  Aligned_cols=31  Identities=29%  Similarity=0.475  Sum_probs=27.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      |++|+|+||+||||+++.||+.+          +..++.+|
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l----------~~~~~d~d   32 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDL----------DLVFLDSD   32 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHH----------TCEEEEHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHh----------CCCEEecC
Confidence            69999999999999999999999          67766543

>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=97.18  E-value=0.00011  Score=67.21  Aligned_cols=32  Identities=22%  Similarity=0.406  Sum_probs=27.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD  353 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld  353 (710)
                      ++++|+|+||+||||+++.||+.+          ++.++..|
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~L----------g~~~id~D   34 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARAL----------GYEFVDTD   34 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHH----------TCEEEEHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHh----------CCCEEehh
Confidence            578999999999999999999999          77766543

>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=97.17  E-value=9.9e-05  Score=67.09  Aligned_cols=24  Identities=33%  Similarity=0.573  Sum_probs=22.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ++++|+|+|||||||+++.||+.+
T Consensus         2 p~IvliG~~G~GKSTig~~La~~l   25 (165)
T d2iyva1           2 PKAVLVGLPGSGKSTIGRRLAKAL   25 (165)
T ss_dssp             CSEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHh
Confidence            468999999999999999999999

>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=97.13  E-value=9.8e-05  Score=65.72  Aligned_cols=25  Identities=32%  Similarity=0.396  Sum_probs=21.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      -++++||||+|||++|+.|++...+
T Consensus         4 lIii~G~pGsGKTTla~~L~~~~~~   28 (152)
T d1ly1a_           4 IILTIGCPGSGKSTWAREFIAKNPG   28 (152)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHSTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhCCC
Confidence            5789999999999999999877544

>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=97.11  E-value=0.00015  Score=66.29  Aligned_cols=27  Identities=26%  Similarity=0.393  Sum_probs=24.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      +|++|+|||||||||+++.++..+...
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l~~~   28 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVLKSS   28 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHHHHT
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHHHHC
Confidence            589999999999999999999998654

>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=97.05  E-value=0.00011  Score=66.88  Aligned_cols=27  Identities=33%  Similarity=0.498  Sum_probs=24.4

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.+.+++|+||||+||||+++.|++.+
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            456679999999999999999999987

>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=97.02  E-value=0.00047  Score=63.83  Aligned_cols=38  Identities=18%  Similarity=0.190  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHc-CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          298 EIQRIIQILCR-RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       298 ~i~~l~~~L~~-~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -+..+..+|.. +.++.++|+|||+||||.++.+|+..+
T Consensus        39 Fl~~l~~~l~~~PKkn~i~~~GP~~TGKS~f~~sl~~~l   77 (205)
T d1tuea_          39 FLGALKSFLKGTPKKNCLVFCGPANTGKSYFGMSFIHFI   77 (205)
T ss_dssp             HHHHHHHHHHTCTTCSEEEEESCGGGCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCceEEEEECCCCccHHHHHHHHHHHh
Confidence            33445555544 445668999999999999999999887

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=96.94  E-value=0.00015  Score=66.04  Aligned_cols=36  Identities=33%  Similarity=0.333  Sum_probs=28.6

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLL  357 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l  357 (710)
                      +-++|.||||+||||+++.|++++          +.+++.++...+
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~~l----------g~~~~~~~~d~~   40 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALANLP----------GVPKVHFHSDDL   40 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCS----------SSCEEEECTTHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHh----------CCCEEEecHHHH
Confidence            447899999999999999999877          666777765443

>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=96.93  E-value=0.00026  Score=64.18  Aligned_cols=24  Identities=33%  Similarity=0.364  Sum_probs=21.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .-|+|+|+||+||||+|+.|++.+
T Consensus         4 kiI~l~G~~GsGKsTva~~L~~~l   27 (178)
T d1qhxa_           4 RMIILNGGSSAGKSGIVRCLQSVL   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHc
Confidence            347888999999999999999998

>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=96.91  E-value=0.00065  Score=65.29  Aligned_cols=81  Identities=19%  Similarity=0.233  Sum_probs=49.5

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh------------------hhhhh-c-------ccc
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM------------------GLLMA-G-------AKE  363 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~------------------~~l~~-g-------~~~  363 (710)
                      .+.-++|+|+||+|||+++..++.......       ..+..++.                  ..+.. +       ...
T Consensus        25 ~gsl~li~G~pGsGKT~l~~qia~~~~~~~-------~~~~~is~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (242)
T d1tf7a2          25 KDSIILATGATGTGKTLLVSRFVENACANK-------ERAILFAYEESRAQLLRNAYSWGMDFEEMERQNLLKIVCAYPE   97 (242)
T ss_dssp             SSCEEEEEECTTSSHHHHHHHHHHHHHTTT-------CCEEEEESSSCHHHHHHHHHTTSCCHHHHHHTTSEEECCCCGG
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc-------cccceeeccCCHHHHHHHHHHcCCChHHHhhcCceEEEEeecc
Confidence            345679999999999999999998875432       22222221                  00000 0       001


Q ss_pred             CccHHHHHHHHHHHHHhcCCeEEEEccchhhhhC
Q 005179          364 RGELEARVTTLISEIQKSGDVILFIDEVHTLIGS  397 (710)
Q Consensus       364 ~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l~~~  397 (710)
                      .......+..+...+...++.+++||.++.+...
T Consensus        98 ~~~~~~~~~~i~~~i~~~~~~~vviDs~~~~~~~  131 (242)
T d1tf7a2          98 SAGLEDHLQIIKSEINDFKPARIAIDSLSALARG  131 (242)
T ss_dssp             GSCHHHHHHHHHHHHHTTCCSEEEEECHHHHTSS
T ss_pred             hhhHHHHHHHHHHHHHhcCCceeeeecchhhhcC
Confidence            1223444555666666777889999999988643

>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=96.89  E-value=0.00046  Score=71.40  Aligned_cols=60  Identities=23%  Similarity=0.303  Sum_probs=44.2

Q ss_pred             cccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC-------CcceeeCCCCC
Q 005179          630 RVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV-------RIHYLFFPSPF  698 (710)
Q Consensus       630 ~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~-------~~li~~d~se~  698 (710)
                      -++|.++-++.+...+.+  .+.+       +.||+||||||||.++..||..+....       ..++.+|++.+
T Consensus        23 ~~~gr~~ei~~~~~~L~r--~~k~-------n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~~~l   89 (387)
T d1qvra2          23 PVIGRDEEIRRVIQILLR--RTKN-------NPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQMGSL   89 (387)
T ss_dssp             CCCSCHHHHHHHHHHHHC--SSCC-------CCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC---
T ss_pred             CCcCcHHHHHHHHHHHhc--CCCC-------CCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeHhhh
Confidence            488999988888777653  3333       349999999999999999998765543       45888888776

>d1knqa_ c.37.1.17 (A:) Gluconate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Gluconate kinase
domain: Gluconate kinase
species: Escherichia coli [TaxId: 562]

Probab=96.87  E-value=0.00029  Score=63.76  Aligned_cols=22  Identities=41%  Similarity=0.670  Sum_probs=20.8

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      ++|+|+||+||||+++.|++.+
T Consensus         9 ivl~G~~GsGKsT~a~~La~~l   30 (171)
T d1knqa_           9 YVLMGVSGSGKSAVASEVAHQL   30 (171)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6789999999999999999998

>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=96.85  E-value=0.00093  Score=62.48  Aligned_cols=24  Identities=25%  Similarity=0.300  Sum_probs=21.6

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++++|.||+||||+++.|++.+..
T Consensus         5 i~l~GlpgsGKSTla~~L~~~l~~   28 (213)
T d1bifa1           5 IVMVGLPARGKTYISKKLTRYLNF   28 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHh
Confidence            678999999999999999998843

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=96.84  E-value=0.00021  Score=65.04  Aligned_cols=26  Identities=35%  Similarity=0.385  Sum_probs=23.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ..|+|+|+||+||||+++.|++++..
T Consensus         7 ~~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           7 FTIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34789999999999999999999854

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=96.83  E-value=0.0003  Score=63.44  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=21.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -++|+||||+||||+|+.|++.+
T Consensus         4 lI~i~G~~GsGKTTva~~L~~~~   26 (176)
T d2bdta1           4 LYIITGPAGVGKSTTCKRLAAQL   26 (176)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHc
Confidence            37899999999999999999987

>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=96.65  E-value=0.0004  Score=63.62  Aligned_cols=23  Identities=35%  Similarity=0.514  Sum_probs=21.7

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|.||||+||||+++.||+.+
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            48999999999999999999998

>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=96.62  E-value=0.0006  Score=63.07  Aligned_cols=25  Identities=16%  Similarity=0.215  Sum_probs=23.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +-.++|.||||+||||+++.|++.+
T Consensus         3 Pm~I~i~GppGsGKsT~a~~La~~~   27 (189)
T d1zaka1           3 PLKVMISGAPASGKGTQCELIKTKY   27 (189)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHH
Confidence            4578999999999999999999988

>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=96.61  E-value=0.00064  Score=62.93  Aligned_cols=26  Identities=35%  Similarity=0.456  Sum_probs=23.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+-.++|+||||+||||+++.||+++
T Consensus         2 ~~~riil~G~pGSGKsT~a~~La~~~   27 (190)
T d1ak2a1           2 KGVRAVLLGPPGAGKGTQAPKLAKNF   27 (190)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CccEEEEECCCCCCHHHHHHHHHHHh
Confidence            34568899999999999999999988

>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=96.58  E-value=0.00047  Score=63.33  Aligned_cols=23  Identities=39%  Similarity=0.559  Sum_probs=21.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|.||||+||||+++.|++.+
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            58999999999999999999998

>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=96.58  E-value=0.0024  Score=59.90  Aligned_cols=76  Identities=20%  Similarity=0.170  Sum_probs=43.5

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh----------------hccccCccHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM----------------AGAKERGELEARVTTLISE  377 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~----------------~g~~~~g~~e~~l~~~~~~  377 (710)
                      ++|+||+|+||||.+-.||..+.....     ...++..|.-..-                .......++...+....+.
T Consensus        12 i~lvGptGvGKTTTiAKLA~~~~~~g~-----kV~lit~Dt~R~gA~eQL~~~a~~l~v~~~~~~~~~d~~~~l~~~~~~   86 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLARQFEQQGK-----SVMLAAGDTFRAAAVEQLQVWGQRNNIPVIAQHTGADSASVIFDAIQA   86 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTTTC-----CEEEECCCTTCHHHHHHHHHHHHHTTCCEECCSTTCCHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC-----cEEEEecccccccchhhhhhhhhhcCCcccccccCCCHHHHHHHHHHH
Confidence            578999999999988888988754321     2223333311110                0111233455555555555


Q ss_pred             HHhcCCeEEEEccchhh
Q 005179          378 IQKSGDVILFIDEVHTL  394 (710)
Q Consensus       378 ~~~~~~~IL~IDEid~l  394 (710)
                      +...+-.+++||=..+.
T Consensus        87 a~~~~~d~ilIDTaGr~  103 (211)
T d2qy9a2          87 AKARNIDVLIADTAGRL  103 (211)
T ss_dssp             HHHTTCSEEEECCCCCG
T ss_pred             HHHcCCCEEEeccCCCc
Confidence            55555568888866544

>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=96.57  E-value=0.00061  Score=66.46  Aligned_cols=42  Identities=14%  Similarity=0.182  Sum_probs=33.6

Q ss_pred             CcccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          629 KRVIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       629 ~~v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      +.++|.++.++.+...          ..   ..++++||+|||||+|++.+++.+
T Consensus        12 ~~f~GR~~el~~l~~~----------~~---~~i~i~G~~G~GKTsLl~~~~~~~   53 (283)
T d2fnaa2          12 KDFFDREKEIEKLKGL----------RA---PITLVLGLRRTGKSSIIKIGINEL   53 (283)
T ss_dssp             GGSCCCHHHHHHHHHT----------CS---SEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             hhCCChHHHHHHHHhc----------cC---CEEEEEcCCCCcHHHHHHHHHHHC
Confidence            3488888888887542          11   378999999999999999999986

>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=96.57  E-value=0.0009  Score=61.72  Aligned_cols=38  Identities=21%  Similarity=0.120  Sum_probs=28.3

Q ss_pred             CCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          657 RPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       657 rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      +|+ -+-+.||+|+|||++|+.|++.+-...-..+.+++
T Consensus        21 ~~~-iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~~   58 (198)
T d1rz3a_          21 GRL-VLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHM   58 (198)
T ss_dssp             SSE-EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEG
T ss_pred             CCE-EEEEECCCCCCHHHHHHHHHHHhccccccceeccc
Confidence            444 56799999999999999999886654444444443

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.51  E-value=0.0005  Score=62.82  Aligned_cols=23  Identities=17%  Similarity=0.320  Sum_probs=20.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .-++++|+||||||++|+.++..
T Consensus        15 ~liil~G~pGsGKST~a~~l~~~   37 (172)
T d1yj5a2          15 EVVVAVGFPGAGKSTFIQEHLVS   37 (172)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHh
Confidence            38999999999999999998765

>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=96.48  E-value=0.00053  Score=63.70  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=22.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-++|+||||+||||+++.||+.+
T Consensus         6 p~iI~i~G~pGSGKsT~a~~La~~~   30 (194)
T d1qf9a_           6 PNVVFVLGGPGSGKGTQCANIVRDF   30 (194)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHH
Confidence            3446889999999999999999988

>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=96.46  E-value=0.0011  Score=62.34  Aligned_cols=30  Identities=30%  Similarity=0.559  Sum_probs=23.1

Q ss_pred             CCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          655 PNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       655 p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |.+| -.++|+||||+|||+.+--||..+-.
T Consensus         8 ~~~p-~vi~lvGptGvGKTTTiAKLAa~~~~   37 (213)
T d1vmaa2           8 PEPP-FVIMVVGVNGTGKTTSCGKLAKMFVD   37 (213)
T ss_dssp             SSSC-EEEEEECCTTSSHHHHHHHHHHHHHH
T ss_pred             CCCC-EEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            3444 58999999999999987777766543

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=96.44  E-value=0.00062  Score=60.24  Aligned_cols=22  Identities=23%  Similarity=0.360  Sum_probs=19.2

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      ++|+|+||+||||+|+.|++..
T Consensus         5 Iii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            6889999999999999887654

>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=96.44  E-value=0.0012  Score=62.19  Aligned_cols=32  Identities=28%  Similarity=0.424  Sum_probs=20.9

Q ss_pred             CCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          652 LKDPNRPTAAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       652 l~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      +..|.+....++|+||||+|||+.+--||..+
T Consensus         5 ~~~~~k~p~vi~lvGptGvGKTTTiAKLA~~~   36 (211)
T d1j8yf2           5 KVIPDKIPYVIMLVGVQGTGKATTAGKLAYFY   36 (211)
T ss_dssp             CCSCSSSSEEEEEECSCCC----HHHHHHHHH
T ss_pred             ccCCCCCCEEEEEECCCCCCHHHHHHHHHHHH
Confidence            34466655789999999999999877777654

>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=96.42  E-value=0.00044  Score=63.89  Aligned_cols=25  Identities=36%  Similarity=0.417  Sum_probs=22.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      -|+|+|+||+||||+|+.|++.+..
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~   45 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVC   45 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHh
Confidence            4668899999999999999999843

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.37  E-value=0.0014  Score=59.67  Aligned_cols=25  Identities=16%  Similarity=0.292  Sum_probs=20.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.=++++|+||+||||+++.++...
T Consensus        14 p~liil~G~pGsGKST~a~~l~~~~   38 (172)
T d1yj5a2          14 PEVVVAVGFPGAGKSTFIQEHLVSA   38 (172)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHTGGG
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhc
Confidence            3447899999999999999886544

>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=96.35  E-value=0.0014  Score=65.97  Aligned_cols=39  Identities=23%  Similarity=0.226  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          296 ETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       296 ~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+++..++..+.+ .+.|+|++|++|+||||++++|+..+
T Consensus       152 ~~~~~~~l~~~v~-~~~nili~G~tgSGKTT~l~al~~~i  190 (323)
T d1g6oa_         152 KEQAISAIKDGIA-IGKNVIVCGGTGSGKTTYIKSIMEFI  190 (323)
T ss_dssp             HHHHHHHHHHHHH-HTCCEEEEESTTSSHHHHHHHHGGGS
T ss_pred             HHHHHHHHHHHHH-hCCCEEEEeeccccchHHHHHHhhhc
Confidence            3444444433333 35689999999999999999998766

>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=96.31  E-value=0.0025  Score=59.68  Aligned_cols=27  Identities=26%  Similarity=0.327  Sum_probs=22.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +.-++|+||+|+||||.+-.||..+..
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~   32 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQN   32 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            445688999999999988888887754

>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=96.29  E-value=0.0026  Score=59.69  Aligned_cols=32  Identities=28%  Similarity=0.309  Sum_probs=24.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcce
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHY  691 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li  691 (710)
                      ..++|+||||+|||+.+--||..+-..+.+..
T Consensus        10 ~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~   41 (211)
T d2qy9a2          10 FVILMVGVNGVGKTTTIGKLARQFEQQGKSVM   41 (211)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHHHTTTCCEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEE
Confidence            58999999999999988778877644444333

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=96.29  E-value=0.0013  Score=61.55  Aligned_cols=27  Identities=15%  Similarity=0.020  Sum_probs=24.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .++||+||||||||++|+.+|+.+...
T Consensus        16 ~~~l~~G~~g~gk~~~a~~l~~~i~~~   42 (198)
T d2gnoa2          16 ISILINGEDLSYPREVSLELPEYVEKF   42 (198)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHHHTS
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHhcc
Confidence            499999999999999999999987654

>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=96.27  E-value=0.0011  Score=60.85  Aligned_cols=23  Identities=30%  Similarity=0.518  Sum_probs=21.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|.||||+||||+++.||+.+
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

>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=96.24  E-value=0.0016  Score=58.44  Aligned_cols=26  Identities=23%  Similarity=0.211  Sum_probs=22.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+.|+|++|+|||||++.|++++...
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            46799999999999999999988654

>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=96.23  E-value=0.0012  Score=60.54  Aligned_cols=23  Identities=35%  Similarity=0.544  Sum_probs=21.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .++|.||||+||||+++.||+++
T Consensus         4 rIvl~G~pGSGKtT~a~~La~~~   26 (180)
T d1akya1           4 RMVLIGPPGAGKGTQAPNLQERF   26 (180)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            37899999999999999999988

>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=96.21  E-value=0.0013  Score=61.12  Aligned_cols=23  Identities=30%  Similarity=0.382  Sum_probs=21.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -++|.||||+||||+|+.|++.+
T Consensus        10 iI~i~GppGSGKsT~a~~La~~~   32 (196)
T d1ukza_          10 VIFVLGGPGAGKGTQCEKLVKDY   32 (196)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHHHh
Confidence            36888999999999999999988

>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=96.20  E-value=0.0051  Score=57.69  Aligned_cols=45  Identities=22%  Similarity=0.211  Sum_probs=32.7

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhh
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLM  358 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~  358 (710)
                      ...+.-++|+|.||+||||+++.|++.+....      +..++.+|...+-
T Consensus        21 ~~kg~vIwltGlsGsGKTTia~~L~~~l~~~~------~~~~~~ldgD~iR   65 (208)
T d1m7ga_          21 NQRGLTIWLTGLSASGKSTLAVELEHQLVRDR------RVHAYRLDGDNIR   65 (208)
T ss_dssp             TSSCEEEEEECSTTSSHHHHHHHHHHHHHHHH------CCCEEEECHHHHT
T ss_pred             CCCCeEEEEECCCCCCHHHHHHHHHHHHHHhc------CceEEEEcchHHH
Confidence            33445578999999999999999998874321      4566677765554

>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=96.20  E-value=0.0011  Score=61.50  Aligned_cols=25  Identities=16%  Similarity=0.381  Sum_probs=22.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .-.++|+||||+||||+++.||+.+
T Consensus         6 ~mrIiliG~PGSGKtT~a~~La~~~   30 (189)
T d2ak3a1           6 LLRAAIMGAPGSGKGTVSSRITKHF   30 (189)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHB
T ss_pred             ceeEEEECCCCCCHHHHHHHHHHHH
Confidence            3468999999999999999999987

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=96.20  E-value=0.0022  Score=60.17  Aligned_cols=24  Identities=33%  Similarity=0.414  Sum_probs=16.7

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++|+||+|+||||.+-.||..+..
T Consensus        15 i~lvGptGvGKTTTiAKLA~~~~~   38 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAGKLAYFYKK   38 (211)
T ss_dssp             EEEECSCCC----HHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            678999999999988888887754

>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=96.20  E-value=0.0013  Score=61.94  Aligned_cols=38  Identities=18%  Similarity=0.165  Sum_probs=29.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC-CCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS-VRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~-~~~li~~d~se  697 (710)
                      ..++|.|.||+|||++|++|++.|+.. ....+.+|+..
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldgD~   63 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDGDN   63 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcchH
Confidence            389999999999999999999887532 23455566443

>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=96.19  E-value=0.0045  Score=58.14  Aligned_cols=26  Identities=31%  Similarity=0.400  Sum_probs=21.4

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      -++|+||+|+||||.+-.||.++...
T Consensus        13 vi~lvGptGvGKTTTiAKLAa~~~~~   38 (213)
T d1vmaa2          13 VIMVVGVNGTGKTTSCGKLAKMFVDE   38 (213)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Confidence            36789999999999888888877543

>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=96.18  E-value=0.0014  Score=60.50  Aligned_cols=29  Identities=31%  Similarity=0.740  Sum_probs=26.0

Q ss_pred             CCCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          655 PNRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       655 p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      |.|  ..++|||||+||||++|.+|.+.|.|
T Consensus        51 PKk--n~i~~~GP~~TGKS~f~~sl~~~l~G   79 (205)
T d1tuea_          51 PKK--NCLVFCGPANTGKSYFGMSFIHFIQG   79 (205)
T ss_dssp             TTC--SEEEEESCGGGCHHHHHHHHHHHHTC
T ss_pred             CCc--eEEEEECCCCccHHHHHHHHHHHhCC
Confidence            544  48999999999999999999999977

>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=96.17  E-value=0.0012  Score=60.21  Aligned_cols=23  Identities=30%  Similarity=0.309  Sum_probs=21.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +++|.||||+||||+++.|++.+
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            47899999999999999999988

>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=96.17  E-value=0.0015  Score=60.49  Aligned_cols=22  Identities=23%  Similarity=0.410  Sum_probs=20.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      ++|.||||+||||+|+.||+.+
T Consensus         4 I~i~GppGSGKsT~a~~La~~~   25 (194)
T d1teva_           4 VFVLGGPGAGKGTQCARIVEKY   25 (194)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6899999999999999999988

>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=96.15  E-value=0.0012  Score=61.24  Aligned_cols=25  Identities=20%  Similarity=0.339  Sum_probs=22.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-++|.||||+||||+++.|++.+
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~   32 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKY   32 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHh
Confidence            3457889999999999999999987

>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=96.12  E-value=0.0045  Score=57.89  Aligned_cols=25  Identities=36%  Similarity=0.383  Sum_probs=21.4

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      ++|+||+|+||||.+-.||..+...
T Consensus        13 i~lvGp~GvGKTTTiaKLA~~~~~~   37 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAAKLALYYKGK   37 (207)
T ss_dssp             EEEECCTTTTHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            5789999999999999899888543

>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=96.08  E-value=0.0026  Score=59.64  Aligned_cols=29  Identities=38%  Similarity=0.480  Sum_probs=22.7

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      ..++|+||||+|||+.+--||..+=..+.
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g~   39 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKGR   39 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTC
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCC
Confidence            57899999999999988888876543333

>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=96.08  E-value=0.0028  Score=60.69  Aligned_cols=26  Identities=19%  Similarity=0.215  Sum_probs=21.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+..+|+||...|||++++.++....
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~   66 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIAL   66 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHH
Confidence            45689999999999999998886644

>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=96.06  E-value=0.017  Score=58.68  Aligned_cols=38  Identities=18%  Similarity=0.268  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          296 ETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       296 ~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      +.+...+..++.   .+-.+|.||||||||+++..+...+.
T Consensus       151 ~~Q~~A~~~al~---~~~~vI~G~pGTGKTt~i~~~l~~l~  188 (359)
T d1w36d1         151 NWQKVAAAVALT---RRISVISGGPGTGKTTTVAKLLAALI  188 (359)
T ss_dssp             CHHHHHHHHHHT---BSEEEEECCTTSTHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHc---CCeEEEEcCCCCCceehHHHHHHHHH
Confidence            334444554453   34678999999999998876655543

>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=96.04  E-value=0.004  Score=61.22  Aligned_cols=46  Identities=13%  Similarity=0.147  Sum_probs=35.9

Q ss_pred             ccChHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHH
Q 005179          631 VIGQDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       631 v~Gq~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      ++|.+..++.|...+.....      .....+.+||+.|+|||+||+.+.+.
T Consensus        22 ~~gR~~~~~~i~~~L~~~~~------~~~~~v~I~GmgGiGKTtLA~~v~~~   67 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEMCD------LDSFFLFLHGRAGSGKSVIASQALSK   67 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHHTT------SSSEEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eeCcHHHHHHHHHHHHhccC------CCceEEEEECCCCCCHHHHHHHHHHh
Confidence            77888888888777654321      12357889999999999999999876

>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=95.98  E-value=0.0018  Score=58.79  Aligned_cols=25  Identities=20%  Similarity=0.271  Sum_probs=22.3

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      ++|.|+||+||||+++.|++++...
T Consensus         4 I~i~G~~GsGKsT~~~~L~~~l~~~   28 (190)
T d1khta_           4 VVVTGVPGVGSTTSSQLAMDNLRKE   28 (190)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHc
Confidence            6788999999999999999998543

>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=95.96  E-value=0.0021  Score=55.72  Aligned_cols=22  Identities=18%  Similarity=0.138  Sum_probs=17.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la  332 (710)
                      ....+|.+|.|+|||.++-.++
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~   29 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY   29 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH
Confidence            3457999999999998775443

>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=95.95  E-value=0.0014  Score=56.57  Aligned_cols=26  Identities=19%  Similarity=0.080  Sum_probs=19.2

Q ss_pred             CCCCcEEEcCCCChHHHHHH-HHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAE-GLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~-~la~~l  335 (710)
                      .+.+.+|++|+|+|||..+- .+....
T Consensus         6 ~~~~~il~~~tGsGKT~~~~~~~~~~~   32 (140)
T d1yksa1           6 KGMTTVLDFHPGAGKTRRFLPQILAEC   32 (140)
T ss_dssp             TTCEEEECCCTTSSTTTTHHHHHHHHH
T ss_pred             cCCcEEEEcCCCCChhHHHHHHHHHHh
Confidence            46788999999999996653 444444

>d1sq5a_ c.37.1.6 (A:) Pantothenate kinase PanK {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Pantothenate kinase PanK
species: Escherichia coli [TaxId: 562]

Probab=95.93  E-value=0.0084  Score=59.52  Aligned_cols=34  Identities=26%  Similarity=0.387  Sum_probs=28.5

Q ss_pred             cCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          650 VGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       650 ~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .|.+.+.+|. -+.+.||+|+|||++|+.|+..|-
T Consensus        72 l~~~~~k~P~-iIGIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          72 LGTNGQRIPY-IISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             HTCC-CCCCE-EEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             hcccCCCCCE-EEEEeCCCCCCCcHHHHHHHHHHh
Confidence            4666677776 788999999999999999999973

>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=95.87  E-value=0.0036  Score=62.94  Aligned_cols=54  Identities=26%  Similarity=0.342  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCCC
Q 005179          635 DEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPFN  699 (710)
Q Consensus       635 ~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~~  699 (710)
                      ++....+..+++..           .++|++||||+|||++.++|..++-..++.++.-|..|+.
T Consensus       153 ~~~~~~l~~~v~~~-----------~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~  206 (323)
T d1g6oa_         153 EQAISAIKDGIAIG-----------KNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIV  206 (323)
T ss_dssp             HHHHHHHHHHHHHT-----------CCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCC
T ss_pred             HHHHHHHHHHHHhC-----------CCEEEEeeccccchHHHHHHhhhcccccceeeccchhhhh
Confidence            34445555555443           3789999999999999999999876666655555777763

>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=95.87  E-value=0.0025  Score=60.93  Aligned_cols=36  Identities=28%  Similarity=0.303  Sum_probs=28.8

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      ..++++||||||||++|..+|......+...+-+++
T Consensus        27 sl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~   62 (242)
T d1tf7a2          27 SIILATGATGTGKTLLVSRFVENACANKERAILFAY   62 (242)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec
Confidence            478999999999999999999997665555444443

>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=95.79  E-value=0.0022  Score=59.28  Aligned_cols=24  Identities=29%  Similarity=0.407  Sum_probs=21.9

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ++++|+||+|+|||||++.|++..
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~   24 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEH   24 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            358999999999999999999886

>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=95.77  E-value=0.0022  Score=59.05  Aligned_cols=24  Identities=25%  Similarity=0.414  Sum_probs=21.9

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ++|+|+||+|+|||+|++.|++..
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~   25 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEY   25 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhC
Confidence            468999999999999999998876

>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=95.65  E-value=0.0034  Score=58.99  Aligned_cols=22  Identities=27%  Similarity=0.450  Sum_probs=19.8

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      |.|.||||+||+|+++.|++++
T Consensus         6 I~I~GppGSGKgT~ak~La~~~   27 (225)
T d1ckea_           6 ITIDGPSGAGKGTLCKAMAEAL   27 (225)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3455999999999999999998

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=95.63  E-value=0.0044  Score=56.39  Aligned_cols=24  Identities=25%  Similarity=0.374  Sum_probs=21.6

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++|.|+||+||||+++.|++.+..
T Consensus         4 ivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           4 GIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
Confidence            568899999999999999999854

>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=95.48  E-value=0.0043  Score=58.41  Aligned_cols=22  Identities=23%  Similarity=0.303  Sum_probs=19.7

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      +.|.||||+||||+|+.||+.+
T Consensus         6 IaIdGp~GsGKgT~ak~La~~l   27 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDF   27 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            3455999999999999999998

>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=95.38  E-value=0.01  Score=54.12  Aligned_cols=23  Identities=30%  Similarity=0.380  Sum_probs=20.4

Q ss_pred             EEcCCCChHHHHHHHHHHHHHhc
Q 005179          316 LLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       316 L~GppG~GKT~la~~la~~l~~~  338 (710)
                      |.|++|+||||+|+.|+..+...
T Consensus        27 I~G~~GSGKSTla~~L~~~l~~~   49 (198)
T d1rz3a_          27 IDGLSRSGKTTLANQLSQTLREQ   49 (198)
T ss_dssp             EEECTTSSHHHHHHHHHHHHHHT
T ss_pred             EECCCCCCHHHHHHHHHHHhccc
Confidence            77999999999999999888543

>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=95.32  E-value=0.0039  Score=64.73  Aligned_cols=94  Identities=11%  Similarity=0.178  Sum_probs=55.4

Q ss_pred             CCCcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEee-hhhhh-hc------
Q 005179          289 IDPVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLD-MGLLM-AG------  360 (710)
Q Consensus       289 l~~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld-~~~l~-~g------  360 (710)
                      ++.+--.+..+..+.+++.. ...-+|++||+|+||||.+.++.+.+...       ..+++.+. ..... .+      
T Consensus       137 l~~LG~~~~~~~~l~~l~~~-~~GliLvtGpTGSGKSTTl~~~l~~~~~~-------~~~i~tiEdPiE~~~~~~~q~~v  208 (401)
T d1p9ra_         137 LHSLGMTAHNHDNFRRLIKR-PHGIILVTGPTGSGKSTTLYAGLQELNSS-------ERNILTVEDPIEFDIDGIGQTQV  208 (401)
T ss_dssp             GGGSCCCHHHHHHHHHHHTS-SSEEEEEECSTTSCHHHHHHHHHHHHCCT-------TSCEEEEESSCCSCCSSSEEEEC
T ss_pred             hhhhcccHHHHHHHHHHHhh-hhceEEEEcCCCCCccHHHHHHhhhhcCC-------CceEEEeccCcccccCCCCeeee
Confidence            34444445566666655544 45568899999999999999999887432       12233221 11110 00      


Q ss_pred             -cccCccHHHHHHHHHHHHHhcCCeEEEEccchhh
Q 005179          361 -AKERGELEARVTTLISEIQKSGDVILFIDEVHTL  394 (710)
Q Consensus       361 -~~~~g~~e~~l~~~~~~~~~~~~~IL~IDEid~l  394 (710)
                       ......    +...+..+...+|.||+|.|+-..
T Consensus       209 ~~~~~~~----~~~~l~~~lR~dPDvi~igEiRd~  239 (401)
T d1p9ra_         209 NPRVDMT----FARGLRAILRQDPDVVMVGEIRDL  239 (401)
T ss_dssp             BGGGTBC----HHHHHHHHGGGCCSEEEESCCCSH
T ss_pred             cCCcCCC----HHHHHHHHHhhcCCEEEecCcCCh
Confidence             111123    344555555678899999999654

>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=95.26  E-value=0.068  Score=51.39  Aligned_cols=42  Identities=24%  Similarity=0.279  Sum_probs=34.2

Q ss_pred             CHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          295 RETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       295 r~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      +...++.+..-+....+.+-||.|..|+|||.++-..+....
T Consensus        88 Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~  129 (264)
T d1gm5a3          88 QKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNY  129 (264)
T ss_dssp             HHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHH
Confidence            556778888888888888999999999999998876665543

>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=95.08  E-value=0.014  Score=54.85  Aligned_cols=25  Identities=24%  Similarity=0.365  Sum_probs=20.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+.-.+|+|+||+|||+++..++..
T Consensus        25 ~G~~~~I~G~~G~GKT~la~~~~~~   49 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSIQFLYN   49 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHH
Confidence            4556799999999999999776543

>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=95.08  E-value=0.052  Score=49.89  Aligned_cols=19  Identities=37%  Similarity=0.436  Sum_probs=16.6

Q ss_pred             CCCcEEEcCCCChHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAE  329 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~  329 (710)
                      +.++++.+|+|+|||+++.
T Consensus        40 ~~~~il~apTGsGKT~~a~   58 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLAE   58 (202)
T ss_dssp             CSCEEEECSSHHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHHH
Confidence            5689999999999998764

>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=95.07  E-value=0.037  Score=53.59  Aligned_cols=77  Identities=16%  Similarity=0.218  Sum_probs=47.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-------cc-------ccCccHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-------GA-------KERGELEARVTTLISE  377 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-------g~-------~~~g~~e~~l~~~~~~  377 (710)
                      .-..++||+|+|||+++..++......       +..++++|...-+.       |.       ......|+.+. +++.
T Consensus        58 ~itei~G~~~sGKT~l~l~~~~~aqk~-------g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~-~~~~  129 (268)
T d1xp8a1          58 RITEIYGPESGGKTTLALAIVAQAQKA-------GGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALE-IMEL  129 (268)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHH-HHHH
T ss_pred             eEEEEecCCccchHHHHHHHHHHHHhC-------CCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHH-HHHH
Confidence            346799999999999999888776443       34455665332110       10       01223454443 3344


Q ss_pred             H-HhcCCeEEEEccchhhhh
Q 005179          378 I-QKSGDVILFIDEVHTLIG  396 (710)
Q Consensus       378 ~-~~~~~~IL~IDEid~l~~  396 (710)
                      + +.....+++||=+..++.
T Consensus       130 l~~~~~~~liIiDSi~al~~  149 (268)
T d1xp8a1         130 LVRSGAIDVVVVDSVAALTP  149 (268)
T ss_dssp             HHTTTCCSEEEEECTTTCCC
T ss_pred             HHhcCCCcEEEEeccccccc
Confidence            3 344577999999988874

>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=95.00  E-value=0.009  Score=54.08  Aligned_cols=22  Identities=23%  Similarity=0.335  Sum_probs=19.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~  334 (710)
                      .|.|+|.+|+|||+|++.|...
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999998753

>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=94.94  E-value=0.031  Score=54.04  Aligned_cols=77  Identities=14%  Similarity=0.148  Sum_probs=43.7

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh-------cc-------ccCccHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA-------GA-------KERGELEARVTTLISE  377 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~-------g~-------~~~g~~e~~l~~~~~~  377 (710)
                      .-..|+||||+|||+++..++......       +..++++|...-..       |.       ......|+.+..+-..
T Consensus        55 ~itei~G~~gsGKTtl~l~~~~~~q~~-------g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l  127 (263)
T d1u94a1          55 RIVEIYGPESSGKTTLTLQVIAAAQRE-------GKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDAL  127 (263)
T ss_dssp             SEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHH
T ss_pred             eEEEEecCCCcHHHHHHHHHHHHHHcC-------CCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHH
Confidence            446899999999999999888776443       34455555322110       00       0112344433322222


Q ss_pred             HHhcCCeEEEEccchhhh
Q 005179          378 IQKSGDVILFIDEVHTLI  395 (710)
Q Consensus       378 ~~~~~~~IL~IDEid~l~  395 (710)
                      ++.....+++||=+..+.
T Consensus       128 ~~~~~~~liViDSi~al~  145 (263)
T d1u94a1         128 ARSGAVDVIVVDSVAALT  145 (263)
T ss_dssp             HHHTCCSEEEEECGGGCC
T ss_pred             HhcCCCCEEEEECccccc
Confidence            333556688888887664

>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=94.93  E-value=0.0082  Score=56.12  Aligned_cols=38  Identities=21%  Similarity=0.176  Sum_probs=26.4

Q ss_pred             EEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEe
Q 005179          315 ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSL  352 (710)
Q Consensus       315 LL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~l  352 (710)
                      -|.|++|+||||+++.|++.+....++.......++..
T Consensus         6 gI~G~~gSGKSTla~~L~~~l~~~~~~~~~~~~~vi~~   43 (213)
T d1uj2a_           6 GVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQ   43 (213)
T ss_dssp             EEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEG
T ss_pred             EEECCCCCCHHHHHHHHHHHhchhccccCCCceEEEec
Confidence            37799999999999999998855444333333344443

>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=94.92  E-value=0.018  Score=55.72  Aligned_cols=29  Identities=28%  Similarity=0.344  Sum_probs=24.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcC
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAE  339 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~  339 (710)
                      +.-.+|+|+||+|||+++..+|..+..+.
T Consensus        29 g~~~~i~G~~G~GKS~l~l~la~~ia~g~   57 (274)
T d1nlfa_          29 GTVGALVSPGGAGKSMLALQLAAQIAGGP   57 (274)
T ss_dssp             TSEEEEEESTTSSHHHHHHHHHHHHHTCC
T ss_pred             CcEEEEEeCCCCCHHHHHHHHHHHHHcCC
Confidence            34578999999999999999998876543

>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=94.89  E-value=0.0058  Score=55.74  Aligned_cols=23  Identities=39%  Similarity=0.524  Sum_probs=20.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -++|+||+|+||||+++.|.+..
T Consensus         4 iivl~GpsG~GK~tl~~~L~~~~   26 (182)
T d1znwa1           4 VVVLSGPSAVGKSTVVRCLRERI   26 (182)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhC
Confidence            36899999999999999998876

>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=94.83  E-value=0.048  Score=54.36  Aligned_cols=39  Identities=15%  Similarity=0.364  Sum_probs=28.1

Q ss_pred             HHHHHHHHcCCCCC--cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          300 QRIIQILCRRTKNN--PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       300 ~~l~~~L~~~~~~n--vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      .+++..+....++.  +=|+|+||+|||||+..++..+...
T Consensus        41 ~~ll~~~~~~~~~~~~IgitG~pGaGKSTLi~~l~~~~~~~   81 (327)
T d2p67a1          41 TQLLDAIMPYCGNTLRLGVTGTPGAGKSTFLEAFGMLLIRE   81 (327)
T ss_dssp             HHHHHHHGGGCSCSEEEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHhhhccCCceEEEeeCCCCCCHHHHHHHHHHHHHhc
Confidence            34454454444433  5688999999999999999887653

>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=94.81  E-value=0.039  Score=52.21  Aligned_cols=25  Identities=24%  Similarity=0.379  Sum_probs=19.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.++++++|+|+|||.++-..+...
T Consensus        58 g~~~~i~apTGsGKT~~~~~~~~~~   82 (237)
T d1gkub1          58 KESFAATAPTGVGKTSFGLAMSLFL   82 (237)
T ss_dssp             TCCEECCCCBTSCSHHHHHHHHHHH
T ss_pred             CCCEEEEecCCChHHHHHHHHHHHH
Confidence            5789999999999998765554443

>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=94.66  E-value=0.021  Score=55.44  Aligned_cols=26  Identities=19%  Similarity=0.263  Sum_probs=21.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      +.-++|.|+||+|||+++..++..+.
T Consensus        35 G~l~vi~G~~G~GKT~~~~~la~~~a   60 (277)
T d1cr2a_          35 GEVIMVTSGSGMGKSTFVRQQALQWG   60 (277)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHHHH
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHhhh
Confidence            34478899999999999999987653

>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=94.59  E-value=0.007  Score=57.42  Aligned_cols=23  Identities=26%  Similarity=0.387  Sum_probs=20.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      ..++++||||||||++|-.+|..
T Consensus        35 ~~~li~G~pGsGKT~l~lq~~~~   57 (251)
T d1szpa2          35 SITELFGEFRTGKSQLCHTLAVT   57 (251)
T ss_dssp             SEEEEEESTTSSHHHHHHHHTTT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHH
Confidence            37899999999999999888753

>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=94.55  E-value=0.026  Score=51.72  Aligned_cols=25  Identities=32%  Similarity=0.336  Sum_probs=19.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+|.|+++|.|+|||.++-.++...
T Consensus        23 ~~n~lv~~pTGsGKT~i~~~~~~~~   47 (200)
T d1wp9a1          23 ETNCLIVLPTGLGKTLIAMMIAEYR   47 (200)
T ss_dssp             GSCEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cCCeEEEeCCCCcHHHHHHHHHHHH
Confidence            3579999999999998766665543

>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=94.53  E-value=0.037  Score=55.20  Aligned_cols=56  Identities=18%  Similarity=0.270  Sum_probs=36.9

Q ss_pred             HHHHHHHHHcCCCCC--cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehhhhhh
Q 005179          299 IQRIIQILCRRTKNN--PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMGLLMA  359 (710)
Q Consensus       299 i~~l~~~L~~~~~~n--vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~~l~~  359 (710)
                      ...++..+....++.  +=|+|+||+|||||+..++..+....     ....++.+|.+.-..
T Consensus        37 ~~~~~~~~~~~~~~~~~igitG~pGaGKSTli~~l~~~~~~~g-----~~vaViavDpss~~~   94 (323)
T d2qm8a1          37 VRDLIDAVLPQTGRAIRVGITGVPGVGKSTTIDALGSLLTAAG-----HKVAVLAVDPSSTRT   94 (323)
T ss_dssp             HHHHHHHHGGGCCCSEEEEEECCTTSCHHHHHHHHHHHHHHTT-----CCEEEEEECGGGGSS
T ss_pred             HHHHHHHhhhccCCceEEeeeCCCCCCHHHHHHHHHHHHhhcC-----CceeeeecccccHHH
Confidence            344555554444444  45889999999999999998875422     144566777655543

>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=94.48  E-value=0.014  Score=52.09  Aligned_cols=24  Identities=25%  Similarity=0.320  Sum_probs=21.5

Q ss_pred             EEEcCCCChHHHHHHHHHHHHHhc
Q 005179          315 ILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       315 LL~GppG~GKT~la~~la~~l~~~  338 (710)
                      -++|.+|+|||||+..|+.++...
T Consensus         5 ~I~G~~gSGKTTli~~l~~~L~~~   28 (165)
T d1xjca_           5 QVVGYKHSGKTTLMEKWVAAAVRE   28 (165)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEeCCCCCHHHHHHHHHHHHHhC
Confidence            489999999999999999998654

>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=94.46  E-value=0.0084  Score=54.61  Aligned_cols=24  Identities=33%  Similarity=0.574  Sum_probs=21.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..++|+||+|+|||||++.|.+..
T Consensus         4 k~ivl~Gpsg~GK~tl~~~L~~~~   27 (178)
T d1kgda_           4 KTLVLLGAHGVGRRHIKNTLITKH   27 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHC
T ss_pred             CcEEEECCCCCCHHHHHHHHHHhC
Confidence            458999999999999999988764

>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=94.41  E-value=0.011  Score=56.43  Aligned_cols=24  Identities=29%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++++||||||||++|..+|...
T Consensus        38 ~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          38 AITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             EEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
Confidence            378999999999999999998753

>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=94.41  E-value=0.013  Score=55.43  Aligned_cols=79  Identities=14%  Similarity=0.167  Sum_probs=41.9

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHH--hcCCCccccCce------E-EEeehhhhhhccccCccHHHHHHHHHHHHHh-cC
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIV--QAEVPVFLLSKR------I-MSLDMGLLMAGAKERGELEARVTTLISEIQK-SG  382 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~--~~~~p~~l~~~~------v-~~ld~~~l~~g~~~~g~~e~~l~~~~~~~~~-~~  382 (710)
                      -.+|+||...|||++++.++-...  +...+.......      + ..+...+-+  ....+.|...++++-.-+.. ..
T Consensus        37 ~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~--~~~~StF~~el~~~~~il~~~~~  114 (224)
T d1ewqa2          37 LVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDL--AGGKSTFMVEMEEVALILKEATE  114 (224)
T ss_dssp             EEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC--------CCSHHHHHHHHHHHHHHHCCT
T ss_pred             EEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccc--cCCccHHHHhHHHHHHHhccCCC
Confidence            379999999999999998876543  322221111111      1 111111111  11234455555555444443 35


Q ss_pred             CeEEEEccchh
Q 005179          383 DVILFIDEVHT  393 (710)
Q Consensus       383 ~~IL~IDEid~  393 (710)
                      +.+++|||+-.
T Consensus       115 ~sLvliDE~~~  125 (224)
T d1ewqa2         115 NSLVLLDEVGR  125 (224)
T ss_dssp             TEEEEEESTTT
T ss_pred             CcEEeeccccc
Confidence            78999999854

>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=94.40  E-value=0.01  Score=54.91  Aligned_cols=24  Identities=25%  Similarity=0.356  Sum_probs=21.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++++||||+|||++|-.+|...
T Consensus        24 ~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          24 SITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHHH
Confidence            378999999999999999998764

>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=94.34  E-value=0.016  Score=55.28  Aligned_cols=24  Identities=42%  Similarity=0.473  Sum_probs=21.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..++++||||||||++|-.+|...
T Consensus        37 ~~~li~G~pGsGKT~~~lq~~~~~   60 (254)
T d1pzna2          37 AITEVFGEFGSGKTQLAHTLAVMV   60 (254)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHh
Confidence            378999999999999999888764

>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=94.14  E-value=0.038  Score=53.92  Aligned_cols=23  Identities=26%  Similarity=0.485  Sum_probs=20.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -+-+.||+|+|||+||..|...|
T Consensus        29 iIGi~G~qGSGKSTl~~~l~~~L   51 (286)
T d1odfa_          29 FIFFSGPQGSGKSFTSIQIYNHL   51 (286)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             EEEeECCCCCCHHHHHHHHHHHH
Confidence            55689999999999999888776

>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=94.12  E-value=0.0068  Score=55.81  Aligned_cols=29  Identities=24%  Similarity=0.345  Sum_probs=24.5

Q ss_pred             CCCCeEEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          656 NRPTAAMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       656 ~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      .||. -+.+.|+.|+|||++++.|++.+..
T Consensus         7 ~kp~-~I~ieG~~GsGKTTl~~~L~~~l~~   35 (197)
T d2vp4a1           7 TQPF-TVLIEGNIGSGKTTYLNHFEKYKND   35 (197)
T ss_dssp             CCCE-EEEEECSTTSCHHHHHHTTGGGTTT
T ss_pred             CCce-EEEEECCCCCCHHHHHHHHHHHhCC
Confidence            3454 6889999999999999999998754

>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=94.10  E-value=0.0098  Score=56.97  Aligned_cols=26  Identities=27%  Similarity=0.195  Sum_probs=21.8

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+.|+||+|+|||||++.|+..+
T Consensus        27 ~Ge~vaivG~sGsGKSTLl~ll~gl~   52 (242)
T d1mv5a_          27 PNSIIAFAGPSGGGKSTIFSLLERFY   52 (242)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHhh
Confidence            34557899999999999999998654

>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=93.98  E-value=0.013  Score=51.44  Aligned_cols=21  Identities=29%  Similarity=0.430  Sum_probs=18.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~  334 (710)
                      ++|+|+||||||+|++.+...
T Consensus         3 ivlvG~~~vGKSsLi~~l~~~   23 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKLG   23 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhcC
Confidence            789999999999999998754

>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=93.90  E-value=0.02  Score=53.07  Aligned_cols=23  Identities=22%  Similarity=0.258  Sum_probs=20.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~  334 (710)
                      ++|+|+|+||+|||+|+..+...
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~~   23 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLTG   23 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHHcC
Confidence            47899999999999999998753

>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=93.85  E-value=0.013  Score=54.51  Aligned_cols=24  Identities=25%  Similarity=0.310  Sum_probs=21.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .-++|+||+|+|||+|.+.|.+..
T Consensus         3 ~livi~GPSG~GK~tl~~~L~~~~   26 (205)
T d1s96a_           3 TLYIVSAPSGAGKSSLIQALLKTQ   26 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhC
Confidence            347899999999999999998875

>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=93.82  E-value=0.018  Score=54.42  Aligned_cols=29  Identities=21%  Similarity=0.234  Sum_probs=24.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      ..++++||||+|||++|-.+|..+...+.
T Consensus        35 ~l~~i~G~~G~GKT~~~l~~a~~~~~~~~   63 (258)
T d2i1qa2          35 SVTEFAGVFGSGKTQIMHQSCVNLQNPEF   63 (258)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTTCGGG
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHHHhcCC
Confidence            47899999999999999999987655433

>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=93.81  E-value=0.031  Score=57.65  Aligned_cols=41  Identities=29%  Similarity=0.292  Sum_probs=30.9

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHHHHHcCCCCc-ceeeCCCCC
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLAACYFGSVRI-HYLFFPSPF  698 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~-li~~d~se~  698 (710)
                      |.|-+||.||||.|||++..++-+.+.....+ +..=|--||
T Consensus       157 ~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~  198 (401)
T d1p9ra_         157 PHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEF  198 (401)
T ss_dssp             SSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCS
T ss_pred             hhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCccc
Confidence            34789999999999999999999988655444 344444444

>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=93.79  E-value=0.025  Score=54.86  Aligned_cols=51  Identities=22%  Similarity=0.426  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          298 EIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       298 ~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      ++..+..-+.+....=++++|.-||||||++-.||..+...       ++++..+|+.
T Consensus         7 ~~~~~~~~~~~~~~~iii~sGKGGVGKTT~a~nLA~~lA~~-------G~rVllvD~D   57 (279)
T d1ihua2           7 SLSALVDDIARNEHGLIMLMGKGGVGKTTMAAAIAVRLADM-------GFDVHLTTSD   57 (279)
T ss_dssp             CHHHHHHHHHTTSCEEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEESC
T ss_pred             cHHHHHHHhhcCCCEEEEEECCCCCCHHHHHHHHHHHHHHC-------CCcEEEEeCC
Confidence            34556666777666667888999999999999999998654       6677777754

>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=93.78  E-value=0.018  Score=50.95  Aligned_cols=24  Identities=33%  Similarity=0.505  Sum_probs=21.7

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++|.|+=|+|||++++++++.+.-
T Consensus        36 i~L~G~LGaGKTtfvr~~~~~lg~   59 (158)
T d1htwa_          36 VYLNGDLGAGKTTLTRGMLQGIGH   59 (158)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             EEEecCCCccHHHHHHHHHhhccc
Confidence            778999999999999999999843

>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=93.76  E-value=0.05  Score=50.38  Aligned_cols=38  Identities=18%  Similarity=0.254  Sum_probs=26.0

Q ss_pred             CHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          295 RETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       295 r~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ++-+.+.+..++.   ..+.+|.+|+|+|||.++-.++..+
T Consensus        72 r~yQ~eav~~~~~---~~~~ll~~~tG~GKT~~a~~~~~~~  109 (206)
T d2fz4a1          72 RDYQEKALERWLV---DKRGCIVLPTGSGKTHVAMAAINEL  109 (206)
T ss_dssp             CHHHHHHHHHHTT---TSEEEEEESSSTTHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHh---CCCcEEEeCCCCCceehHHhHHHHh
Confidence            4445444444432   3457899999999999888777665

>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=93.75  E-value=0.029  Score=49.60  Aligned_cols=28  Identities=25%  Similarity=0.407  Sum_probs=24.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      -.++|.|+=|+|||+++|.+++.| |...
T Consensus        34 ~ii~L~G~LGaGKTtfvr~~~~~l-g~~~   61 (158)
T d1htwa_          34 IMVYLNGDLGAGKTTLTRGMLQGI-GHQG   61 (158)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHT-TCCS
T ss_pred             eEEEEecCCCccHHHHHHHHHhhc-cccc
Confidence            368899999999999999999996 5443

>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=93.73  E-value=0.015  Score=55.46  Aligned_cols=26  Identities=35%  Similarity=0.473  Sum_probs=22.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      .+-+.||+|||||+|.++|+..+-.+
T Consensus        31 ~~~liG~sGaGKSTll~~i~gl~~p~   56 (240)
T d1g2912          31 FMILLGPSGCGKTTTLRMIAGLEEPS   56 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSCCS
T ss_pred             EEEEECCCCChHHHHHHHHhcCCCCC
Confidence            67899999999999999999886543

>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=93.56  E-value=0.016  Score=54.83  Aligned_cols=33  Identities=24%  Similarity=0.387  Sum_probs=25.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .+.+.||+|||||||.+.|+..+=.+.. -|.+|
T Consensus        28 i~~liGpsGsGKSTLl~~i~Gl~~p~sG-~I~i~   60 (232)
T d2awna2          28 FVVFVGPSGCGKSTLLRMIAGLETITSG-DLFIG   60 (232)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEE-EEEES
T ss_pred             EEEEECCCCChHHHHHHHHhcCCCCCCC-EEEEC
Confidence            6789999999999999999988544333 33444

>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=93.55  E-value=0.0084  Score=57.86  Aligned_cols=26  Identities=19%  Similarity=0.258  Sum_probs=21.8

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      ..+..+.|+|++|+|||||++.|+..
T Consensus        42 ~~Ge~vaivG~sGsGKSTLl~ll~gl   67 (255)
T d2hyda1          42 EKGETVAFVGMSGGGKSTLINLIPRF   67 (255)
T ss_dssp             CTTCEEEEECSTTSSHHHHHTTTTTS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHHhc
Confidence            34566899999999999999988754

>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=93.49  E-value=0.013  Score=55.03  Aligned_cols=23  Identities=26%  Similarity=0.384  Sum_probs=19.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      ..++++||||+|||++|-.+|..
T Consensus        27 ~~~~I~G~~G~GKT~la~~~~~~   49 (242)
T d1tf7a1          27 RSTLVSGTSGTGKTLFSIQFLYN   49 (242)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHH
Confidence            47899999999999999776543

>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=93.46  E-value=0.017  Score=54.84  Aligned_cols=26  Identities=27%  Similarity=0.399  Sum_probs=22.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      -+.+.||+|||||+|.|.|+..+-.+
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl~~p~   51 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGIVKPD   51 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCS
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCCC
Confidence            45589999999999999999986443

>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=93.44  E-value=0.015  Score=55.06  Aligned_cols=34  Identities=15%  Similarity=0.183  Sum_probs=26.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .+-+.||+|||||+|.+.|+..+-.+.. -|.+|.
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~gl~~p~sG-~I~~~g   66 (230)
T d1l2ta_          33 FVSIMGPSGSGKSTMLNIIGCLDKPTEG-EVYIDN   66 (230)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEE-EEEETT
T ss_pred             EEEEECCCCCCcchhhHhccCCCCCCcc-eeEECC
Confidence            6789999999999999999988644433 244443

>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=93.32  E-value=0.024  Score=51.17  Aligned_cols=23  Identities=39%  Similarity=0.560  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .++||.||+|+|||++|-.+.+.
T Consensus        15 ~gvl~~G~sG~GKStlal~l~~~   37 (176)
T d1kkma_          15 LGVLITGDSGVGKSETALELVQR   37 (176)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            48999999999999999887764

>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=93.26  E-value=0.094  Score=50.58  Aligned_cols=37  Identities=19%  Similarity=0.115  Sum_probs=26.1

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +.-..|+||+|+|||+++..++......       +..++++|.
T Consensus        60 g~i~e~~G~~~~GKT~l~l~~~~~~q~~-------g~~~vyIDt   96 (269)
T d1mo6a1          60 GRVIEIYGPESSGKTTVALHAVANAQAA-------GGVAAFIDA   96 (269)
T ss_dssp             SSEEEEECSSSSSHHHHHHHHHHHHHHT-------TCEEEEEES
T ss_pred             ceeEEEecCCCcHHHHHHHHHHHHHhcC-------CCEEEEEEC
Confidence            3446899999999999997777655332       445666663

>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=93.23  E-value=0.016  Score=54.80  Aligned_cols=28  Identities=29%  Similarity=0.396  Sum_probs=24.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      .+.+.||+|||||+|.+.|+..+-.+..
T Consensus        28 ~~~liGpsGaGKSTll~~l~Gl~~p~sG   55 (229)
T d3d31a2          28 YFVILGPTGAGKTLFLELIAGFHVPDSG   55 (229)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSCCSEE
T ss_pred             EEEEECCCCCcHHHHHHHHhcCcCCCCC
Confidence            6789999999999999999998655543

>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=93.14  E-value=0.026  Score=50.11  Aligned_cols=21  Identities=29%  Similarity=0.284  Sum_probs=18.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|++|+|||+|+..+..
T Consensus         4 ki~i~G~~~~GKTsLl~~l~~   24 (164)
T d1zd9a1           4 ELTLVGLQYSGKTTFVNVIAS   24 (164)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            478999999999999998864

>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=93.05  E-value=0.028  Score=53.03  Aligned_cols=23  Identities=22%  Similarity=0.468  Sum_probs=20.5

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~  336 (710)
                      +++.|++|+|||||++.|.+.+.
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            57899999999999999988763

>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=93.02  E-value=0.023  Score=51.33  Aligned_cols=23  Identities=35%  Similarity=0.564  Sum_probs=20.3

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .++||.||+|.|||++|-.+.+.
T Consensus        16 ~gvli~G~sG~GKS~lal~l~~~   38 (177)
T d1knxa2          16 VGVLLTGRSGIGKSECALDLINK   38 (177)
T ss_dssp             EEEEEEESSSSSHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHc
Confidence            48999999999999999888753

>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=93.02  E-value=0.021  Score=50.25  Aligned_cols=21  Identities=38%  Similarity=0.591  Sum_probs=18.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|.||||||+|++.+..
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~   27 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQV   27 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999998864

>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=93.00  E-value=0.013  Score=54.32  Aligned_cols=28  Identities=32%  Similarity=0.510  Sum_probs=23.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      .+.+.||+|+|||+|.+.|+..+-.+..
T Consensus        29 i~~l~G~NGsGKSTLl~~i~gl~~p~~G   56 (200)
T d1sgwa_          29 VVNFHGPNGIGKTTLLKTISTYLKPLKG   56 (200)
T ss_dssp             CEEEECCTTSSHHHHHHHHTTSSCCSEE
T ss_pred             EEEEECCCCChHHHHHHHHhcccccCCC
Confidence            4679999999999999999988655443

>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=92.96  E-value=0.023  Score=53.99  Aligned_cols=33  Identities=24%  Similarity=0.298  Sum_probs=25.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d  694 (710)
                      .+-+.||+|||||+|.+.|+..+-.+... |.+|
T Consensus        34 ~~~liGpsGaGKSTLl~~i~Gl~~p~sG~-I~i~   66 (239)
T d1v43a3          34 FLVLLGPSGCGKTTTLRMIAGLEEPTEGR-IYFG   66 (239)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSCCSEEE-EEET
T ss_pred             EEEEECCCCChHHHHHHHHHcCCCCCCCE-EEEc
Confidence            67899999999999999999986554432 4444

>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=92.84  E-value=0.024  Score=49.58  Aligned_cols=20  Identities=30%  Similarity=0.393  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|+||||||+|+..+..
T Consensus         3 I~liG~~nvGKSSLln~l~~   22 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKN   22 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999998765

>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=92.80  E-value=0.027  Score=53.73  Aligned_cols=34  Identities=24%  Similarity=0.362  Sum_probs=26.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      -+.++||+|+|||+|++.|+..+-.+.. -|.+|.
T Consensus        30 ~vaivG~sGsGKSTLl~ll~gl~~p~~G-~I~i~g   63 (242)
T d1mv5a_          30 IIAFAGPSGGGKSTIFSLLERFYQPTAG-EITIDG   63 (242)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSBS-CEEETT
T ss_pred             EEEEECCCCCCHHHHHHHHHHhhCCCCC-EEEECC
Confidence            5779999999999999999988654433 444443

>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=92.77  E-value=0.021  Score=54.39  Aligned_cols=24  Identities=21%  Similarity=0.263  Sum_probs=21.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      -+-+.||+|||||+|.+.|+..+=
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~Gl~~   56 (240)
T d3dhwc1          33 IYGVIGASGAGKSTLIRCVNLLER   56 (240)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCCHHHHHHHHcCCcc
Confidence            567999999999999999998743

>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=92.71  E-value=0.02  Score=55.12  Aligned_cols=37  Identities=22%  Similarity=0.281  Sum_probs=28.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+.++||+|||||+|++.|+..+-.+. .-|.+|.-+.
T Consensus        43 ~iaivG~sGsGKSTLl~ll~gl~~p~~-G~I~i~g~~i   79 (253)
T d3b60a1          43 TVALVGRSGSGKSTIASLITRFYDIDE-GHILMDGHDL   79 (253)
T ss_dssp             EEEEEECTTSSHHHHHHHHTTTTCCSE-EEEEETTEET
T ss_pred             EEEEECCCCChHHHHHHHHhcccCCCc-cEEEECCccc
Confidence            678999999999999999998865543 3455554333

>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=92.70  E-value=0.075  Score=51.29  Aligned_cols=26  Identities=27%  Similarity=0.464  Sum_probs=23.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGS  686 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~  686 (710)
                      ..++|+|||++|||+++.+|+..+ |+
T Consensus       105 n~~~l~G~~~tGKS~f~~~i~~~l-g~  130 (267)
T d1u0ja_         105 NTIWLFGPATTGKTNIAEAIAHTV-PF  130 (267)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHS-SC
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHh-cc
Confidence            488999999999999999999986 64

>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=92.64  E-value=0.024  Score=52.16  Aligned_cols=27  Identities=33%  Similarity=0.380  Sum_probs=22.4

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+.-++|+||||+|||+++..++....
T Consensus        22 ~G~v~~i~G~~GsGKT~l~l~la~~~~   48 (242)
T d1n0wa_          22 TGSITEMFGEFRTGKTQICHTLAVTCQ   48 (242)
T ss_dssp             TTSEEEEECCTTSSHHHHHHHHHHHTT
T ss_pred             CCEEEEEEeCCCCCHHHHHHHHHHHHH
Confidence            345578999999999999999987653

>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=92.62  E-value=0.026  Score=50.60  Aligned_cols=20  Identities=30%  Similarity=0.596  Sum_probs=18.0

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|++.+..
T Consensus         6 ivvvG~~~vGKTsli~r~~~   25 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTD   25 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            78999999999999998764

>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=92.58  E-value=0.019  Score=51.44  Aligned_cols=22  Identities=27%  Similarity=0.365  Sum_probs=19.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~  333 (710)
                      ..++|+|++|||||+|+..+..
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            4589999999999999998754

>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=92.57  E-value=0.018  Score=54.41  Aligned_cols=26  Identities=31%  Similarity=0.401  Sum_probs=21.1

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-++|+||||+|||+++..++...
T Consensus        33 ~G~~~li~G~pGsGKT~l~lq~~~~~   58 (251)
T d1szpa2          33 TGSITELFGEFRTGKSQLCHTLAVTC   58 (251)
T ss_dssp             SSSEEEEEESTTSSHHHHHHHHTTTT
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            34568999999999999998886543

>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=92.56  E-value=0.062  Score=50.70  Aligned_cols=46  Identities=28%  Similarity=0.378  Sum_probs=30.4

Q ss_pred             hHHHHHHHHHHHHHhhcCCCCCCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          634 QDEAVAAISRAVKRSRVGLKDPNRPTAAMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       634 q~~a~~~i~~~i~~~r~gl~~p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      |..+++.|...+...+        | ...|++|.+|+|||+++-..+...+..+.
T Consensus        60 Q~~~~~~i~~~~~~~~--------~-~~~LL~GdvGsGKT~V~~~a~~~~~~~g~  105 (233)
T d2eyqa3          60 QAQAINAVLSDMCQPL--------A-MDRLVCGDVGFGKTEVAMRAAFLAVDNHK  105 (233)
T ss_dssp             HHHHHHHHHHHHHSSS--------C-CEEEEECCCCTTTHHHHHHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHhccC--------c-cCeEEEcCCCCCcHHHHHHHHHHHHHcCC
Confidence            3445555555443332        2 37899999999999999777766555443

>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=92.51  E-value=0.035  Score=54.86  Aligned_cols=31  Identities=23%  Similarity=0.433  Sum_probs=22.5

Q ss_pred             CCCCcEEEcCCCChHHH-HHHHHHHHHHhcCC
Q 005179          310 TKNNPILLGESGVGKTA-IAEGLAIRIVQAEV  340 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~-la~~la~~l~~~~~  340 (710)
                      ...++++.|+||||||+ +++.+++.+..+..
T Consensus        23 ~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~   54 (318)
T d1pjra1          23 TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV   54 (318)
T ss_dssp             CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC
T ss_pred             CCCCEEEEecCCccHHHHHHHHHHHHHHcCCC
Confidence            35679999999999996 45666666655433

>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=92.44  E-value=0.034  Score=49.77  Aligned_cols=23  Identities=35%  Similarity=0.559  Sum_probs=20.4

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      .++||.||+|.|||++|-++.+.
T Consensus        16 ~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          16 VGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHT
T ss_pred             EEEEEEeCCCCCHHHHHHHHHHc
Confidence            48999999999999999887765

>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=92.42  E-value=0.029  Score=49.76  Aligned_cols=20  Identities=20%  Similarity=0.489  Sum_probs=18.1

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|+||||||+|+..+..
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=92.41  E-value=0.029  Score=49.90  Aligned_cols=22  Identities=32%  Similarity=0.604  Sum_probs=19.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~  334 (710)
                      .++|+|++|||||+|+..+...
T Consensus         5 Ki~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            3799999999999999988653

>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=92.40  E-value=0.029  Score=49.84  Aligned_cols=21  Identities=29%  Similarity=0.632  Sum_probs=18.7

Q ss_pred             cEEEcCCCChHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~  334 (710)
                      ++|+|++|||||+|++.+...
T Consensus         7 ivlvG~~~vGKTsli~~~~~~   27 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTEK   27 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999988753

>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=92.29  E-value=0.021  Score=54.35  Aligned_cols=23  Identities=30%  Similarity=0.498  Sum_probs=21.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+.+.||+|||||+|.+.|+..+
T Consensus        33 ~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          33 RFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTSS
T ss_pred             EEEEECCCCCcHHHHHHHHHcCc
Confidence            67899999999999999999874

>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=92.20  E-value=0.03  Score=54.87  Aligned_cols=29  Identities=24%  Similarity=0.326  Sum_probs=21.0

Q ss_pred             CCCcEEEcCCCChHHHH-HHHHHHHHHhcC
Q 005179          311 KNNPILLGESGVGKTAI-AEGLAIRIVQAE  339 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~l-a~~la~~l~~~~  339 (710)
                      ..+++|.|+||||||++ +..++..+....
T Consensus        14 ~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~   43 (306)
T d1uaaa1          14 TGPCLVLAGAGSGKTRVITNKIAHLIRGCG   43 (306)
T ss_dssp             SSEEEECCCTTSCHHHHHHHHHHHHHHHHC
T ss_pred             CCCEEEEeeCCccHHHHHHHHHHHHHHhcC
Confidence            45689999999999965 556666554433

>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=92.13  E-value=0.029  Score=49.63  Aligned_cols=21  Identities=29%  Similarity=0.404  Sum_probs=18.7

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|++|+|||+|++.+..
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~   24 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNG   24 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999998754

>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=92.09  E-value=0.033  Score=49.63  Aligned_cols=20  Identities=35%  Similarity=0.438  Sum_probs=18.3

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|+..+..
T Consensus         8 i~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999998865

>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=92.08  E-value=0.029  Score=54.05  Aligned_cols=23  Identities=17%  Similarity=0.368  Sum_probs=20.8

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      .+-++||+|||||+|+++|+..+
T Consensus        30 i~~iiG~sGsGKSTLl~~i~Gl~   52 (258)
T d1b0ua_          30 VISIIGSSGSGKSTFLRCINFLE   52 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEECCCCCcHHHHHHHHHcCc
Confidence            67799999999999999999764

>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=92.07  E-value=0.023  Score=55.53  Aligned_cols=27  Identities=30%  Similarity=0.302  Sum_probs=23.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      -+.++||+|+|||+|.++|+..+-.+.
T Consensus        64 ~vaivG~nGsGKSTLl~~i~Gl~~p~~   90 (281)
T d1r0wa_          64 MLAITGSTGSGKTSLLMLILGELEASE   90 (281)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSSCCSE
T ss_pred             EEEEECCCCChHHHHHHHHhCCCcCCC
Confidence            577999999999999999998865543

>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=92.03  E-value=0.046  Score=51.27  Aligned_cols=32  Identities=25%  Similarity=0.403  Sum_probs=23.8

Q ss_pred             HHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHH
Q 005179          299 IQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       299 i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~  333 (710)
                      ++.|...+.   +.-.+|+|++|||||||+.+|..
T Consensus        86 ~~~L~~~l~---~kt~~~~G~SGVGKSTLiN~L~~  117 (225)
T d1u0la2          86 IEELKEYLK---GKISTMAGLSGVGKSSLLNAINP  117 (225)
T ss_dssp             HHHHHHHHS---SSEEEEECSTTSSHHHHHHHHST
T ss_pred             HhhHHHHhc---CCeEEEECCCCCCHHHHHHhhcc
Confidence            444555442   34578999999999999999854

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=92.02  E-value=0.037  Score=56.10  Aligned_cols=23  Identities=30%  Similarity=0.419  Sum_probs=18.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -.++.||||||||+++..+-..+
T Consensus       165 ~~vI~G~pGTGKTt~i~~~l~~l  187 (359)
T d1w36d1         165 ISVISGGPGTGKTTTVAKLLAAL  187 (359)
T ss_dssp             EEEEECCTTSTHHHHHHHHHHHH
T ss_pred             eEEEEcCCCCCceehHHHHHHHH
Confidence            67899999999999876554443

>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=92.01  E-value=0.043  Score=52.93  Aligned_cols=23  Identities=39%  Similarity=0.443  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      ..+++||||||||++|-.||..+
T Consensus        31 ~~~i~G~~G~GKS~l~l~la~~i   53 (274)
T d1nlfa_          31 VGALVSPGGAGKSMLALQLAAQI   53 (274)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            67899999999999999998875

>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=91.97  E-value=0.048  Score=52.63  Aligned_cols=37  Identities=19%  Similarity=0.168  Sum_probs=28.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      -.+|+||||+|||++|-.++...-..+...+-+|...
T Consensus        56 itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~   92 (263)
T d1u94a1          56 IVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEH   92 (263)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSC
T ss_pred             EEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEcccc
Confidence            6889999999999999888887655555555555443

>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=91.94  E-value=0.031  Score=49.90  Aligned_cols=32  Identities=25%  Similarity=0.463  Sum_probs=23.9

Q ss_pred             HHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHH
Q 005179          301 RIIQILCRRTKNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       301 ~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~  333 (710)
                      .+..++. ...-.++|+|.||||||+|+..+..
T Consensus         6 ~~~~~~~-~k~~kI~vvG~~~~GKSsLi~rl~~   37 (177)
T d1zj6a1           6 RIWRLFN-HQEHKVIIVGLDNAGKTTILYQFSM   37 (177)
T ss_dssp             HHHHHHT-TSCEEEEEEESTTSSHHHHHHHHHT
T ss_pred             HHHHHhC-CCeEEEEEECCCCCCHHHHHHHHhc
Confidence            3444443 3445799999999999999998764

>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=91.92  E-value=0.035  Score=49.32  Aligned_cols=20  Identities=40%  Similarity=0.527  Sum_probs=18.1

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|.+|||||+|++.+..
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=91.91  E-value=0.035  Score=49.41  Aligned_cols=20  Identities=30%  Similarity=0.562  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         5 i~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999998765

>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=91.88  E-value=0.032  Score=49.94  Aligned_cols=25  Identities=28%  Similarity=0.394  Sum_probs=20.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      .-++|+|+||||||+|..+|...-|
T Consensus        14 ~kI~lvG~~~vGKTsLl~~l~~~~~   38 (186)
T d1f6ba_          14 GKLVFLGLDNAGKTTLLHMLKDDRL   38 (186)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSCC--
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            3689999999999999988865544

>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=91.88  E-value=0.03  Score=50.11  Aligned_cols=26  Identities=27%  Similarity=0.326  Sum_probs=21.3

Q ss_pred             HcCCCCCcEEEcCCCChHHHHHHHHH
Q 005179          307 CRRTKNNPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       307 ~~~~~~nvLL~GppG~GKT~la~~la  332 (710)
                      .....-.++|+|+||||||+|++.+.
T Consensus         8 ~~~k~~kIvlvG~~~vGKTSli~rl~   33 (173)
T d1e0sa_           8 FGNKEMRILMLGLDAAGKTTILYKLK   33 (173)
T ss_dssp             HTTCCEEEEEEEETTSSHHHHHHHTT
T ss_pred             hCCCeEEEEEECCCCCCHHHHHHHHh
Confidence            34445579999999999999999875

>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=91.82  E-value=0.035  Score=49.57  Aligned_cols=21  Identities=29%  Similarity=0.534  Sum_probs=18.9

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      -++|+|.+|||||+|++.+..
T Consensus         7 Ki~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           7 RLVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            389999999999999998865

>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=91.73  E-value=0.018  Score=52.33  Aligned_cols=32  Identities=13%  Similarity=0.291  Sum_probs=25.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCccee
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYL  692 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~  692 (710)
                      ..+|+||.|+|||++..||.-.|||......+
T Consensus        26 ~tvi~G~NGsGKStil~Ai~~~L~g~~~~~~~   57 (222)
T d1qhla_          26 VTTLSGGNGAGKSTTMAAFVTALIPDLTLLHF   57 (222)
T ss_dssp             HHHHHSCCSHHHHHHHHHHHHHHSCCTTTC--
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhcCCcchhhc
Confidence            34789999999999999999999987654433

>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=91.72  E-value=0.039  Score=49.19  Aligned_cols=20  Identities=40%  Similarity=0.610  Sum_probs=18.3

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|+..+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=91.70  E-value=0.037  Score=49.40  Aligned_cols=20  Identities=35%  Similarity=0.695  Sum_probs=18.4

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>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=91.69  E-value=0.035  Score=51.01  Aligned_cols=24  Identities=25%  Similarity=0.340  Sum_probs=20.6

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+.++|+|+||+|||+|+.+|...
T Consensus         3 ~p~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           3 QPSIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            356899999999999999999753

>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=91.64  E-value=0.03  Score=53.76  Aligned_cols=34  Identities=26%  Similarity=0.368  Sum_probs=25.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .+.++||+|+|||+|++.|+..+-.+.. -|.+|.
T Consensus        42 ~vaivG~sGsGKSTLl~li~gl~~p~~G-~I~i~g   75 (251)
T d1jj7a_          42 VTALVGPNGSGKSTVAALLQNLYQPTGG-QLLLDG   75 (251)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEE-EEEETT
T ss_pred             EEEEECCCCCcHHHHHHHHhcccCCCcC-EEEECC
Confidence            6789999999999999999988644332 344443

>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=91.58  E-value=0.038  Score=50.02  Aligned_cols=19  Identities=42%  Similarity=0.604  Sum_probs=17.3

Q ss_pred             cEEEcCCCChHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la  332 (710)
                      ++|+|++|||||+|++.+.
T Consensus         8 i~ivG~~~vGKTsLi~~l~   26 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYT   26 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHh
Confidence            7899999999999998775

>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=91.57  E-value=0.039  Score=48.95  Aligned_cols=20  Identities=35%  Similarity=0.602  Sum_probs=18.3

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         6 i~viG~~~vGKTsli~~l~~   25 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQ   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            79999999999999998765

>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=91.55  E-value=0.039  Score=52.31  Aligned_cols=25  Identities=36%  Similarity=0.496  Sum_probs=21.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .-++|+||||+|||+++..++....
T Consensus        37 ~~~li~G~pGsGKT~~~lq~~~~~~   61 (254)
T d1pzna2          37 AITEVFGEFGSGKTQLAHTLAVMVQ   61 (254)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHhh
Confidence            4478999999999999998887653

>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=91.54  E-value=0.032  Score=47.38  Aligned_cols=28  Identities=18%  Similarity=0.005  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHH-HHHHHHcCCCC
Q 005179          661 AMLFCGPTGVGKTELAK-SLAACYFGSVR  688 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAk-aLA~~lfg~~~  688 (710)
                      ..++++|||+|||..|- ++...+.....
T Consensus         9 ~~il~~~tGsGKT~~~~~~~~~~~~~~~~   37 (140)
T d1yksa1           9 TTVLDFHPGAGKTRRFLPQILAECARRRL   37 (140)
T ss_dssp             EEEECCCTTSSTTTTHHHHHHHHHHHTTC
T ss_pred             cEEEEcCCCCChhHHHHHHHHHHhhhcCc
Confidence            77999999999997773 55555444433

>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=91.45  E-value=0.04  Score=49.03  Aligned_cols=20  Identities=25%  Similarity=0.496  Sum_probs=17.9

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999988764

>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=91.45  E-value=0.034  Score=52.83  Aligned_cols=28  Identities=25%  Similarity=0.322  Sum_probs=24.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      .+-+.||.|+|||||.++|+..+-.+..
T Consensus        30 i~glvG~nGaGKSTLl~~l~G~~~p~~G   57 (238)
T d1vpla_          30 IFGLIGPNGAGKTTTLRIISTLIKPSSG   57 (238)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCSEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCCC
Confidence            5679999999999999999999766544

>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=91.44  E-value=0.057  Score=50.13  Aligned_cols=26  Identities=23%  Similarity=0.276  Sum_probs=22.0

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcC
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAE  339 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~  339 (710)
                      |.|.|+.|+||||+++.|++.+....
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~g   31 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAAG   31 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC
Confidence            45559999999999999999986643

>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=91.43  E-value=0.043  Score=49.15  Aligned_cols=20  Identities=35%  Similarity=0.694  Sum_probs=18.1

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|++.+..
T Consensus         7 i~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998754

>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=91.40  E-value=0.041  Score=49.26  Aligned_cols=21  Identities=29%  Similarity=0.542  Sum_probs=18.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|++|||||+|++.+..
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999988764

>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=91.39  E-value=0.027  Score=53.65  Aligned_cols=34  Identities=24%  Similarity=0.294  Sum_probs=26.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .+.++||+|+|||+|++.|+..+-.+. .-|.+|.
T Consensus        31 ~vaIvG~sGsGKSTLl~ll~gl~~p~~-G~I~i~g   64 (241)
T d2pmka1          31 VIGIVGRSGSGKSTLTKLIQRFYIPEN-GQVLIDG   64 (241)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSE-EEEEETT
T ss_pred             EEEEECCCCCCHHHHHHHHHhcCCCCC-CEEEECC
Confidence            578999999999999999999864433 3455554

>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=91.37  E-value=0.05  Score=53.15  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=18.0

Q ss_pred             eEEEEEcCCCCcHHHH-HHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTEL-AKSLAACY  683 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~l-AkaLA~~l  683 (710)
                      +.+|..||||||||++ +..++..+
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll   39 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLI   39 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHH
Confidence            4689999999999975 44455544

>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=91.36  E-value=0.044  Score=48.37  Aligned_cols=20  Identities=35%  Similarity=0.592  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998864

>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=91.34  E-value=0.037  Score=52.25  Aligned_cols=25  Identities=20%  Similarity=0.296  Sum_probs=20.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+..+-|+||+|+|||||++.++..
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~gl   54 (230)
T d1l2ta_          30 EGEFVSIMGPSGSGKSTMLNIIGCL   54 (230)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCCcchhhHhccCC
Confidence            4556889999999999999988753

>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=91.34  E-value=0.056  Score=48.21  Aligned_cols=27  Identities=37%  Similarity=0.588  Sum_probs=21.3

Q ss_pred             CCCCCCeEEEEEcCCCCcHHHHHHHHHH
Q 005179          654 DPNRPTAAMLFCGPTGVGKTELAKSLAA  681 (710)
Q Consensus       654 ~p~rp~~~~Lf~GPpGtGKT~lAkaLA~  681 (710)
                      .|.+.+ -++++|+||||||+|...+..
T Consensus        12 ~~~~~~-kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          12 APDQEV-RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             CCSSCE-EEEEEESTTSSHHHHHHHHCC
T ss_pred             CCCCEE-EEEEECCCCCCHHHHHHHHhc
Confidence            344544 689999999999999987743

>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=91.32  E-value=0.043  Score=48.47  Aligned_cols=20  Identities=35%  Similarity=0.599  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|.+|||||+|++.+..
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=91.32  E-value=0.045  Score=48.57  Aligned_cols=21  Identities=38%  Similarity=0.580  Sum_probs=18.6

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|.+|||||+|++.+..
T Consensus         6 Ki~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           6 KVCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            378999999999999998764

>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=91.30  E-value=0.043  Score=48.61  Aligned_cols=20  Identities=35%  Similarity=0.640  Sum_probs=18.1

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|++.+..
T Consensus         5 i~vvG~~~vGKTSli~~l~~   24 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVE   24 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=91.29  E-value=0.043  Score=48.65  Aligned_cols=21  Identities=24%  Similarity=0.370  Sum_probs=18.7

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|++|||||+|++.+..
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            489999999999999998764

>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=91.28  E-value=0.046  Score=48.50  Aligned_cols=21  Identities=33%  Similarity=0.619  Sum_probs=18.7

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|.+|||||+|++.+..
T Consensus         5 KivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           5 KLVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            389999999999999998764

>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=91.28  E-value=0.066  Score=51.68  Aligned_cols=23  Identities=17%  Similarity=0.450  Sum_probs=20.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -+++.|+||+|||+++..+|..+
T Consensus        37 l~vi~G~~G~GKT~~~~~la~~~   59 (277)
T d1cr2a_          37 VIMVTSGSGMGKSTFVRQQALQW   59 (277)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHhh
Confidence            68999999999999999999653

>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=91.20  E-value=0.057  Score=49.91  Aligned_cols=27  Identities=22%  Similarity=0.243  Sum_probs=23.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHhcC
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQAE  339 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~~~  339 (710)
                      -|+|.|+.|+||||+++.|++.+....
T Consensus         4 fIviEG~dGsGKsT~~~~L~~~L~~~g   30 (210)
T d4tmka_           4 YIVIEGLEGAGKTTARNVVVETLEQLG   30 (210)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhCC
Confidence            367889999999999999999986543

>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=91.20  E-value=0.045  Score=56.66  Aligned_cols=37  Identities=27%  Similarity=0.275  Sum_probs=31.0

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      .+++++|+||+|||.+.+.+...+...+..++.+|..
T Consensus        51 ~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~k   87 (433)
T d1e9ra_          51 RHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN   87 (433)
T ss_dssp             GCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEET
T ss_pred             ceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4899999999999999988887777777778888743

>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=91.19  E-value=0.043  Score=51.96  Aligned_cols=23  Identities=35%  Similarity=0.475  Sum_probs=19.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l  335 (710)
                      -+.|+||+|+||||+++.|+..+
T Consensus        26 ~~~liGpnGaGKSTll~~i~Gl~   48 (240)
T d2onka1          26 YCVLLGPTGAGKSVFLELIAGIV   48 (240)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSS
T ss_pred             EEEEECCCCChHHHHHHHHHcCC
Confidence            35689999999999999998654

>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=91.16  E-value=0.063  Score=49.31  Aligned_cols=25  Identities=28%  Similarity=0.339  Sum_probs=22.0

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      |.|.|..|+||||+++.|++.+...
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~   27 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAA   27 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
Confidence            5678999999999999999998654

>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=91.13  E-value=0.042  Score=50.71  Aligned_cols=26  Identities=23%  Similarity=0.408  Sum_probs=21.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+.|+||.|+|||||++.++..+
T Consensus        26 ~Gei~~l~G~NGsGKSTLl~~i~gl~   51 (200)
T d1sgwa_          26 KGNVVNFHGPNGIGKTTLLKTISTYL   51 (200)
T ss_dssp             TTCCEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhccc
Confidence            34557799999999999999997654

>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=91.12  E-value=0.048  Score=48.67  Aligned_cols=20  Identities=45%  Similarity=0.712  Sum_probs=18.0

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999998764

>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=91.04  E-value=0.048  Score=51.46  Aligned_cols=26  Identities=23%  Similarity=0.294  Sum_probs=21.4

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||+|+|||||++.++..+
T Consensus        25 ~Gei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          25 EGEFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            44557899999999999999987543

>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=91.02  E-value=0.052  Score=48.34  Aligned_cols=22  Identities=18%  Similarity=0.339  Sum_probs=19.6

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      -++|+|.||||||+|...+...
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            6899999999999999988653

>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=91.00  E-value=0.052  Score=49.31  Aligned_cols=17  Identities=35%  Similarity=0.573  Sum_probs=15.3

Q ss_pred             EEcCCCChHHHHHHHHH
Q 005179          316 LLGESGVGKTAIAEGLA  332 (710)
Q Consensus       316 L~GppG~GKT~la~~la  332 (710)
                      |+|++|+||||+|+.|.
T Consensus         8 itG~~gSGKstva~~l~   24 (191)
T d1uf9a_           8 ITGNIGSGKSTVAALLR   24 (191)
T ss_dssp             EEECTTSCHHHHHHHHH
T ss_pred             EECCCCCCHHHHHHHHH
Confidence            66999999999999884

>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=91.00  E-value=0.047  Score=48.58  Aligned_cols=20  Identities=25%  Similarity=0.517  Sum_probs=18.3

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      |.|+|+||+|||+|+++|..
T Consensus         3 V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           3 VLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            68999999999999999864

>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=90.90  E-value=0.051  Score=49.02  Aligned_cols=20  Identities=45%  Similarity=0.720  Sum_probs=18.0

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|.+|||||+|+..+..
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=90.89  E-value=0.065  Score=48.78  Aligned_cols=23  Identities=26%  Similarity=0.452  Sum_probs=20.1

Q ss_pred             CCeEEEEEcCCCCcHHHHHHHHH
Q 005179          658 PTAAMLFCGPTGVGKTELAKSLA  680 (710)
Q Consensus       658 p~~~~Lf~GPpGtGKT~lAkaLA  680 (710)
                      ++..++++|+||+|||+|..+|.
T Consensus        22 ~~~~I~lvG~~n~GKSTLin~L~   44 (195)
T d1svia_          22 GLPEIALAGRSNVGKSSFINSLI   44 (195)
T ss_dssp             CCCEEEEEEBTTSSHHHHHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHHHHhc
Confidence            33469999999999999999996

>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=90.88  E-value=0.049  Score=48.80  Aligned_cols=20  Identities=20%  Similarity=0.335  Sum_probs=17.8

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         5 ivvvG~~~vGKTsLi~~~~~   24 (177)
T d1kmqa_           5 LVIVGDGACGKTCLLIVNSK   24 (177)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987764

>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=90.80  E-value=0.06  Score=53.06  Aligned_cols=26  Identities=23%  Similarity=0.318  Sum_probs=19.1

Q ss_pred             eEEEEEcCCCCcHHHHH-HHHHHHHcC
Q 005179          660 AAMLFCGPTGVGKTELA-KSLAACYFG  685 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lA-kaLA~~lfg  685 (710)
                      |.+|..||||||||+++ ..+|..+..
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll~~   51 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLMAE   51 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHHHT
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHHHc
Confidence            46899999999999755 445665543

>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=90.80  E-value=0.046  Score=49.08  Aligned_cols=21  Identities=33%  Similarity=0.414  Sum_probs=18.9

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .|+|+|+||+|||||+.+|..
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~   22 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTG   22 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            378999999999999999864

>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=90.79  E-value=0.048  Score=51.86  Aligned_cols=37  Identities=19%  Similarity=0.261  Sum_probs=27.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .+-|.||+|+|||||.++|+..+-.+.. -|.+|.-+.
T Consensus        34 i~~liGpnGaGKSTl~~~i~Gl~~p~~G-~I~~~G~~i   70 (240)
T d1ji0a_          34 IVTLIGANGAGKTTTLSAIAGLVRAQKG-KIIFNGQDI   70 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSEE-EEEETTEEC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCCcc-EEEeccccc
Confidence            6779999999999999999988644433 455554443

>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=90.75  E-value=0.046  Score=48.78  Aligned_cols=20  Identities=40%  Similarity=0.574  Sum_probs=17.9

Q ss_pred             CcEEEcCCCChHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la  332 (710)
                      .++++|++|||||+|++.+.
T Consensus        18 kI~vvG~~~vGKSsLi~~l~   37 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLA   37 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48999999999999998774

>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=90.75  E-value=0.054  Score=48.83  Aligned_cols=21  Identities=24%  Similarity=0.479  Sum_probs=18.7

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|.+|||||+|++.+..
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            379999999999999998865

>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=90.74  E-value=0.055  Score=48.34  Aligned_cols=20  Identities=40%  Similarity=0.730  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999988765

>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=90.74  E-value=0.13  Score=49.83  Aligned_cols=22  Identities=18%  Similarity=0.336  Sum_probs=18.9

Q ss_pred             EEcCCCChHHHHHHHHHHHHHh
Q 005179          316 LLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       316 L~GppG~GKT~la~~la~~l~~  337 (710)
                      |.|++|+||||++..|...+..
T Consensus        32 i~G~qGSGKSTl~~~l~~~L~~   53 (286)
T d1odfa_          32 FSGPQGSGKSFTSIQIYNHLME   53 (286)
T ss_dssp             EECCTTSSHHHHHHHHHHHHHH
T ss_pred             eECCCCCCHHHHHHHHHHHHHH
Confidence            5699999999999999887744

>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=90.72  E-value=0.052  Score=48.43  Aligned_cols=20  Identities=20%  Similarity=0.502  Sum_probs=18.0

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|.+|||||+|++.+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998754

>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=90.67  E-value=0.05  Score=51.45  Aligned_cols=25  Identities=24%  Similarity=0.295  Sum_probs=21.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      +.-++|+|+||+|||+++..++...
T Consensus        37 G~~~~i~G~~GsGKT~lalq~~~~~   61 (258)
T d1v5wa_          37 MAITEAFGEFRTGKTQLSHTLCVTA   61 (258)
T ss_dssp             SEEEEEECCTTCTHHHHHHHHHHHT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
Confidence            3457899999999999999998765

>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=90.66  E-value=0.057  Score=47.97  Aligned_cols=20  Identities=40%  Similarity=0.617  Sum_probs=17.9

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         6 i~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998754

>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=90.58  E-value=0.055  Score=48.09  Aligned_cols=20  Identities=45%  Similarity=0.647  Sum_probs=17.9

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         4 i~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCcCHHHHHHHHhC
Confidence            78999999999999998754

>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=90.53  E-value=0.059  Score=47.88  Aligned_cols=20  Identities=35%  Similarity=0.632  Sum_probs=18.1

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=90.48  E-value=0.06  Score=47.84  Aligned_cols=20  Identities=40%  Similarity=0.622  Sum_probs=18.0

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|++.+..
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998754

>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=90.42  E-value=0.055  Score=47.40  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=18.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++|+|+||+|||+|+.+|..
T Consensus         3 kI~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           3 KVVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEEESTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999998874

>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=90.42  E-value=0.054  Score=51.36  Aligned_cols=26  Identities=38%  Similarity=0.322  Sum_probs=21.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||+|+||||+++.++..+
T Consensus        28 ~Ge~~~liG~sGaGKSTll~~i~gl~   53 (240)
T d1g2912          28 DGEFMILLGPSGCGKTTTLRMIAGLE   53 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCC
Confidence            34567899999999999999997544

>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=90.41  E-value=0.047  Score=49.15  Aligned_cols=23  Identities=35%  Similarity=0.465  Sum_probs=19.9

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~  333 (710)
                      +..++|.|++|+|||+++-.+.+
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~   36 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQ   36 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHH
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHH
Confidence            45689999999999999987765

>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=90.41  E-value=0.058  Score=48.59  Aligned_cols=20  Identities=35%  Similarity=0.506  Sum_probs=18.1

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         5 ivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999997765

>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=90.39  E-value=0.097  Score=50.79  Aligned_cols=37  Identities=32%  Similarity=0.530  Sum_probs=29.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      ++-+++.|.-||||||++-++|..+...       +.++.-+|+
T Consensus         8 p~~i~~sGKGGVGKTTvaa~lA~~lA~~-------G~rVLlvD~   44 (296)
T d1ihua1           8 PPYLFFTGKGGVGKTSISCATAIRLAEQ-------GKRVLLVST   44 (296)
T ss_dssp             CSEEEEECSTTSSHHHHHHHHHHHHHHT-------TCCEEEEEC
T ss_pred             CeEEEEECCCcChHHHHHHHHHHHHHHC-------CCCEEEEeC
Confidence            4456788999999999999999999764       566666654

>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=90.36  E-value=0.047  Score=52.34  Aligned_cols=27  Identities=30%  Similarity=0.361  Sum_probs=22.5

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+..+-|+||+|+|||||++.|+..+
T Consensus        39 ~~Ge~iaivG~sGsGKSTLl~ll~gl~   65 (253)
T d3b60a1          39 PAGKTVALVGRSGSGKSTIASLITRFY   65 (253)
T ss_dssp             CTTCEEEEEECTTSSHHHHHHHHTTTT
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhccc
Confidence            345668999999999999999987654

>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=90.35  E-value=0.062  Score=48.13  Aligned_cols=20  Identities=35%  Similarity=0.620  Sum_probs=18.3

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|++.+..
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=90.35  E-value=0.054  Score=52.95  Aligned_cols=17  Identities=35%  Similarity=0.364  Sum_probs=15.0

Q ss_pred             CCCCcEEEcCCCChHHH
Q 005179          310 TKNNPILLGESGVGKTA  326 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~  326 (710)
                      .++++|+.+|+|+|||+
T Consensus         8 ~~~~~lv~~~TGsGKT~   24 (305)
T d2bmfa2           8 KKRLTIMDLHPGAGKTK   24 (305)
T ss_dssp             TTCEEEECCCTTSSTTT
T ss_pred             cCCcEEEEECCCCCHHH
Confidence            46778999999999995

>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=90.33  E-value=0.17  Score=47.48  Aligned_cols=43  Identities=23%  Similarity=0.434  Sum_probs=34.9

Q ss_pred             cCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          294 GRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       294 Gr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .+...++.+.+.+....+.+.||+|..|+|||.++-..+....
T Consensus        59 ~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~  101 (233)
T d2eyqa3          59 DQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAV  101 (233)
T ss_dssp             HHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHH
Confidence            3556777888888888888999999999999998876665553

>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=90.26  E-value=0.062  Score=50.87  Aligned_cols=26  Identities=35%  Similarity=0.312  Sum_probs=21.7

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||+|+||||+++.++..+
T Consensus        31 ~Ge~~~liGpsGaGKSTLl~~i~Gl~   56 (239)
T d1v43a3          31 DGEFLVLLGPSGCGKTTTLRMIAGLE   56 (239)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHHcCC
Confidence            44567899999999999999987654

>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=90.26  E-value=0.06  Score=48.04  Aligned_cols=20  Identities=45%  Similarity=0.698  Sum_probs=17.9

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|++.+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999988753

>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=90.23  E-value=0.049  Score=51.64  Aligned_cols=26  Identities=19%  Similarity=0.279  Sum_probs=21.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||+|+|||||++.|+..+
T Consensus        30 ~Ge~~~iiG~sGsGKSTLl~~i~Gl~   55 (240)
T d3dhwc1          30 AGQIYGVIGASGAGKSTLIRCVNLLE   55 (240)
T ss_dssp             SSCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCc
Confidence            34557899999999999999987543

>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=90.22  E-value=0.11  Score=47.55  Aligned_cols=34  Identities=26%  Similarity=0.329  Sum_probs=23.1

Q ss_pred             EEEEEcCCCCcHHHHHH-HHHHHHcCCCCcceeeC
Q 005179          661 AMLFCGPTGVGKTELAK-SLAACYFGSVRIHYLFF  694 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAk-aLA~~lfg~~~~li~~d  694 (710)
                      .+++++|||+|||++|- ++...+......++.+.
T Consensus        42 ~~il~apTGsGKT~~a~l~i~~~~~~~~~vl~l~P   76 (202)
T d2p6ra3          42 NLLLAMPTAAGKTLLAEMAMVREAIKGGKSLYVVP   76 (202)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CEEEEcCCCCchhHHHHHHHHHHhhccCcceeecc
Confidence            67999999999999873 34444444444444443

>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=90.17  E-value=0.068  Score=47.46  Aligned_cols=27  Identities=22%  Similarity=0.413  Sum_probs=22.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      =++++|.+|||||+|...+..--|...
T Consensus         8 Ki~vvG~~~vGKTsLi~~l~~~~f~~~   34 (170)
T d1r2qa_           8 KLVLLGESAVGKSSLVLRFVKGQFHEF   34 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHSCCCTT
T ss_pred             EEEEECCCCcCHHHHHHHHHhCCCCcc
Confidence            468999999999999999987655543

>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=90.10  E-value=0.05  Score=51.72  Aligned_cols=26  Identities=19%  Similarity=0.236  Sum_probs=22.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+..+.|+||+|+|||||++.|...+
T Consensus        28 ~Ge~vaIvG~sGsGKSTLl~ll~gl~   53 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKSTLTKLIQRFY   53 (241)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcC
Confidence            45668899999999999999998654

>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=90.10  E-value=0.055  Score=51.81  Aligned_cols=27  Identities=30%  Similarity=0.386  Sum_probs=22.5

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+..+.|+||+|+|||||++.|...+
T Consensus        38 ~~Ge~vaivG~sGsGKSTLl~li~gl~   64 (251)
T d1jj7a_          38 RPGEVTALVGPNGSGKSTVAALLQNLY   64 (251)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             cCCCEEEEECCCCCcHHHHHHHHhccc
Confidence            345668999999999999999987654

>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=90.05  E-value=0.056  Score=50.81  Aligned_cols=26  Identities=31%  Similarity=0.331  Sum_probs=21.6

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||+|+||||+++.|+..+
T Consensus        25 ~Ge~~~liGpsGaGKSTll~~l~Gl~   50 (229)
T d3d31a2          25 SGEYFVILGPTGAGKTLFLELIAGFH   50 (229)
T ss_dssp             TTCEEEEECCCTHHHHHHHHHHHTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcCc
Confidence            34557899999999999999998644

>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=90.05  E-value=0.063  Score=50.35  Aligned_cols=27  Identities=22%  Similarity=0.304  Sum_probs=22.7

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +.-++|+|+||+|||+++..+|..+..
T Consensus        34 G~l~~i~G~~G~GKT~~~l~~a~~~~~   60 (258)
T d2i1qa2          34 QSVTEFAGVFGSGKTQIMHQSCVNLQN   60 (258)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHHTTC
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHh
Confidence            445789999999999999999877643

>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=90.04  E-value=0.12  Score=48.53  Aligned_cols=33  Identities=27%  Similarity=0.359  Sum_probs=23.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCC-Ccceee
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSV-RIHYLF  693 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~-~~li~~  693 (710)
                      .+++.+|||+|||+++-..+..+...+ ..++.+
T Consensus        60 ~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~   93 (237)
T d1gkub1          60 SFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIF   93 (237)
T ss_dssp             CEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEE
T ss_pred             CEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEe
Confidence            689999999999998776665544333 344433

>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=90.02  E-value=0.064  Score=48.50  Aligned_cols=20  Identities=30%  Similarity=0.494  Sum_probs=17.9

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|.+|||||+|++.+..
T Consensus        12 i~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            78999999999999988754

>d2dy1a2 c.37.1.8 (A:8-274) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus, EF-G-2 [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: Elongation factor G (EF-G), N-terminal (G) domain
species: Thermus thermophilus, EF-G-2 [TaxId: 274]

Probab=90.02  E-value=0.1  Score=50.28  Aligned_cols=23  Identities=35%  Similarity=0.622  Sum_probs=20.5

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~  334 (710)
                      +|+.|+|..|+|||||+.+|...
T Consensus         3 RNv~iiGh~~~GKTtL~e~ll~~   25 (267)
T d2dy1a2           3 RTVALVGHAGSGKTTLTEALLYK   25 (267)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCcHHHHHHHHHHH
Confidence            58899999999999999999654

>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=89.99  E-value=0.033  Score=50.84  Aligned_cols=22  Identities=23%  Similarity=0.286  Sum_probs=19.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      |.|.|+.|+||||+++.|++.+
T Consensus        12 I~ieG~~GsGKTTl~~~L~~~l   33 (197)
T d2vp4a1          12 VLIEGNIGSGKTTYLNHFEKYK   33 (197)
T ss_dssp             EEEECSTTSCHHHHHHTTGGGT
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            6778999999999999999876

>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=89.98  E-value=0.046  Score=51.86  Aligned_cols=27  Identities=30%  Similarity=0.228  Sum_probs=22.4

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.-+-|+||+|+||||+++.|+..+
T Consensus        29 ~~Ge~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          29 ENGERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CCCCEEEEECCCCCcHHHHHHHHHcCc
Confidence            345668899999999999999998643

>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=89.87  E-value=0.063  Score=51.46  Aligned_cols=34  Identities=24%  Similarity=0.335  Sum_probs=25.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      .+-|.||+|+|||+|.++|+..+=.+. .-|.++.
T Consensus        32 i~~liG~nGaGKSTLl~~i~Gl~~p~~-G~I~~~g   65 (254)
T d1g6ha_          32 VTLIIGPNGSGKSTLINVITGFLKADE-GRVYFEN   65 (254)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCSE-EEEEETT
T ss_pred             EEEEECCCCCcHHHHHHHHHCCCcCCC-cEEEECC
Confidence            578999999999999999998853332 2344443

>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=89.85  E-value=0.084  Score=46.83  Aligned_cols=24  Identities=33%  Similarity=0.469  Sum_probs=20.7

Q ss_pred             EEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          662 MLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       662 ~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ++++|++|||||.|.+.+..-=|.
T Consensus         9 i~vvG~~~vGKTsli~~~~~~~~~   32 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKDGAFL   32 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHHSCCC
T ss_pred             EEEECCCCcCHHHHHHHHHhCCCC
Confidence            789999999999999988775553

>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=89.84  E-value=0.073  Score=47.32  Aligned_cols=20  Identities=30%  Similarity=0.589  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         7 i~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998865

>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=89.77  E-value=0.069  Score=48.50  Aligned_cols=20  Identities=25%  Similarity=0.489  Sum_probs=17.8

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         6 vvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987754

>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=89.57  E-value=0.11  Score=50.20  Aligned_cols=38  Identities=18%  Similarity=0.154  Sum_probs=27.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      .-..|+||||+|||++|-.++...-..+...+-+|.-.
T Consensus        61 ~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~   98 (269)
T d1mo6a1          61 RVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEH   98 (269)
T ss_dssp             SEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSC
T ss_pred             eeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCc
Confidence            36789999999999999777776544455455555444

>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=89.56  E-value=0.073  Score=48.49  Aligned_cols=20  Identities=35%  Similarity=0.599  Sum_probs=18.2

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|++|||||+|+..+..
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            78999999999999998864

>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=89.54  E-value=0.75  Score=41.86  Aligned_cols=16  Identities=31%  Similarity=0.461  Sum_probs=14.3

Q ss_pred             CCCcEEEcCCCChHHH
Q 005179          311 KNNPILLGESGVGKTA  326 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~  326 (710)
                      ++++++.+|+|+|||.
T Consensus        38 g~dvi~~a~tGsGKTl   53 (206)
T d1s2ma1          38 GRDILARAKNGTGKTA   53 (206)
T ss_dssp             TCCEEEECCTTSCHHH
T ss_pred             CCCEEEecCCcchhhh
Confidence            4689999999999994

>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=89.46  E-value=0.18  Score=49.56  Aligned_cols=22  Identities=27%  Similarity=0.348  Sum_probs=19.5

Q ss_pred             EEEcCCCChHHHHHHHHHHHHH
Q 005179          315 ILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       315 LL~GppG~GKT~la~~la~~l~  336 (710)
                      -|.|++|+||||+++.|...+.
T Consensus        84 GIaG~sgSGKSTla~~L~~lL~  105 (308)
T d1sq5a_          84 SIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEeCCCCCCCcHHHHHHHHHHh
Confidence            3669999999999999998884

>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=89.41  E-value=0.044  Score=52.55  Aligned_cols=34  Identities=24%  Similarity=0.276  Sum_probs=26.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      -+.++||+|+|||+|++.|+..+-.+ ..-|.+|.
T Consensus        46 ~vaivG~sGsGKSTLl~ll~gl~~p~-~G~I~i~g   79 (255)
T d2hyda1          46 TVAFVGMSGGGKSTLINLIPRFYDVT-SGQILIDG   79 (255)
T ss_dssp             EEEEECSTTSSHHHHHTTTTTSSCCS-EEEEEETT
T ss_pred             EEEEECCCCCcHHHHHHHHHhcCCcc-ccccccCC
Confidence            67899999999999999999865443 33455543

>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=89.40  E-value=0.073  Score=51.79  Aligned_cols=27  Identities=19%  Similarity=0.240  Sum_probs=22.5

Q ss_pred             CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          309 RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       309 ~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+.-+.|+||+|+|||||++.|+..+
T Consensus        60 ~~Ge~vaivG~nGsGKSTLl~~i~Gl~   86 (281)
T d1r0wa_          60 EKGEMLAITGSTGSGKTSLLMLILGEL   86 (281)
T ss_dssp             CTTCEEEEEESTTSSHHHHHHHHHTSS
T ss_pred             cCCCEEEEECCCCChHHHHHHHHhCCC
Confidence            345567899999999999999998654

>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=89.31  E-value=0.067  Score=48.67  Aligned_cols=21  Identities=33%  Similarity=0.439  Sum_probs=19.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .+.|+|+||+|||||+++|..
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            489999999999999999973

>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=89.31  E-value=0.053  Score=48.81  Aligned_cols=25  Identities=32%  Similarity=0.434  Sum_probs=20.5

Q ss_pred             cCCCCCcEEEcCCCChHHHHHHHHH
Q 005179          308 RRTKNNPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       308 ~~~~~nvLL~GppG~GKT~la~~la  332 (710)
                      ....-.++|+|++|||||+|++.+.
T Consensus        14 ~~k~~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          14 SNKELRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             CSSCEEEEEEEETTSSHHHHHHHTC
T ss_pred             CCceEEEEEECCCCCCHHHHHHHHh
Confidence            3444568999999999999998764

>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=89.29  E-value=0.051  Score=48.89  Aligned_cols=23  Identities=35%  Similarity=0.436  Sum_probs=19.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~  333 (710)
                      +..+||.|++|+|||+++-.+..
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~   37 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLIN   37 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH
Confidence            45689999999999999988764

>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=89.26  E-value=0.063  Score=47.96  Aligned_cols=24  Identities=33%  Similarity=0.502  Sum_probs=20.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      +..+||.|++|+|||+++-.+.++
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~   38 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR   38 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc
Confidence            456899999999999999777654

>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=89.16  E-value=0.051  Score=48.55  Aligned_cols=20  Identities=40%  Similarity=0.650  Sum_probs=8.5

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++|+|.+|||||+|++.+..
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998764

>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=88.82  E-value=0.084  Score=47.90  Aligned_cols=26  Identities=31%  Similarity=0.616  Sum_probs=20.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCC
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVP  341 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p  341 (710)
                      ++|+|.+|||||+|++.+  .......|
T Consensus         5 ivllG~~~vGKTsll~r~--~f~~~~~p   30 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQM--RIIHGQDP   30 (200)
T ss_dssp             EEEECSTTSSHHHHHHHH--HHHHSCCC
T ss_pred             EEEECCCCCCHHHHHHHH--hcCCCCCC
Confidence            789999999999999998  34444444

>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=88.79  E-value=0.084  Score=46.98  Aligned_cols=21  Identities=24%  Similarity=0.333  Sum_probs=19.0

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      +|.|+|.||+|||+|+++|..
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999974

>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=88.70  E-value=0.059  Score=48.01  Aligned_cols=20  Identities=30%  Similarity=0.557  Sum_probs=17.4

Q ss_pred             cEEEcCCCChHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~  333 (710)
                      ++++|++|||||+|+..+..
T Consensus         6 i~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC-
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999987754

>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=88.50  E-value=0.081  Score=49.91  Aligned_cols=35  Identities=26%  Similarity=0.412  Sum_probs=26.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSP  697 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se  697 (710)
                      .+-+.||+|+|||+|.++|+.. .. ...-|.++.-.
T Consensus        27 i~~iiG~nGaGKSTLl~~l~Gl-~~-~~G~I~~~g~~   61 (231)
T d1l7vc_          27 ILHLVGPNGAGKSTLLARMAGM-TS-GKGSIQFAGQP   61 (231)
T ss_dssp             EEECBCCTTSSHHHHHHHHHTS-CC-CSSEEEESSSB
T ss_pred             EEEEECCCCCcHHHHHHHHhCC-CC-CceEEEECCEE
Confidence            5779999999999999999984 33 33446666543

>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=88.42  E-value=0.079  Score=47.57  Aligned_cols=21  Identities=33%  Similarity=0.485  Sum_probs=18.5

Q ss_pred             eEEEEEcCCCCcHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLA  680 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA  680 (710)
                      --++|+|+||||||+|...+.
T Consensus        18 ~KI~lvG~~~vGKTsLi~~l~   38 (182)
T d1moza_          18 LRILILGLDGAGKTTILYRLQ   38 (182)
T ss_dssp             EEEEEEEETTSSHHHHHHHTC
T ss_pred             EEEEEECCCCCCHHHHHHHHh
Confidence            368999999999999998764

>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=88.39  E-value=1.8  Score=39.75  Aligned_cols=16  Identities=44%  Similarity=0.551  Sum_probs=14.7

Q ss_pred             CCCcEEEcCCCChHHH
Q 005179          311 KNNPILLGESGVGKTA  326 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~  326 (710)
                      ++++++..|+|+|||.
T Consensus        54 g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          54 GRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             TCCEEEECCTTSSHHH
T ss_pred             CCCeEEEcCcchhhhh
Confidence            6799999999999995

>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=88.33  E-value=0.12  Score=47.10  Aligned_cols=24  Identities=38%  Similarity=0.483  Sum_probs=19.7

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF  684 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf  684 (710)
                      ..|+++|||+|||.++-.++..++
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~~   48 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYRL   48 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHH
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHHH
Confidence            468999999999998887776554

>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=88.28  E-value=0.12  Score=47.58  Aligned_cols=19  Identities=37%  Similarity=0.578  Sum_probs=16.5

Q ss_pred             cEEEcCCCChHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la  332 (710)
                      +-|+|.+|+||||+++.+.
T Consensus         6 IgitG~igSGKStv~~~l~   24 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA   24 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH
T ss_pred             EEEECCCcCCHHHHHHHHH
Confidence            3489999999999999875

>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=88.13  E-value=0.13  Score=49.49  Aligned_cols=36  Identities=22%  Similarity=0.130  Sum_probs=27.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPS  696 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~s  696 (710)
                      -..||||||||||++|-.++...-..+...+-+|..
T Consensus        59 itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE   94 (268)
T d1xp8a1          59 ITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAE   94 (268)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESS
T ss_pred             EEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECC
Confidence            678999999999999999888765444445555544

>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=88.12  E-value=0.082  Score=47.35  Aligned_cols=22  Identities=18%  Similarity=0.330  Sum_probs=19.3

Q ss_pred             CCcEEEcCCCChHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~  333 (710)
                      .+|.|+|.||+|||||+++|..
T Consensus         2 ~~VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           2 ADVGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             CSEEEECCGGGCHHHHHHHHCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3688999999999999999853

>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=88.11  E-value=0.15  Score=48.99  Aligned_cols=25  Identities=28%  Similarity=0.316  Sum_probs=20.2

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      ..||.|-+|+|||++|-..+.....
T Consensus       106 ~rLL~GdvGSGKT~Va~~a~~~~~~  130 (264)
T d1gm5a3         106 NRLLQGDVGSGKTVVAQLAILDNYE  130 (264)
T ss_dssp             CCEEECCSSSSHHHHHHHHHHHHHH
T ss_pred             eeeeeccccccccHHHHHHHHHHHh
Confidence            5699999999999999776655433

>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=88.05  E-value=0.093  Score=50.32  Aligned_cols=25  Identities=20%  Similarity=0.357  Sum_probs=20.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .+.-+-|+||+|+|||||++.|+..
T Consensus        27 ~GEi~~iiG~sGsGKSTLl~~i~Gl   51 (258)
T d1b0ua_          27 AGDVISIIGSSGSGKSTFLRCINFL   51 (258)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHTTS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHcC
Confidence            4455789999999999999999753

>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=88.01  E-value=0.16  Score=48.83  Aligned_cols=36  Identities=28%  Similarity=0.394  Sum_probs=27.3

Q ss_pred             HHHHHHHHc--CCCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          300 QRIIQILCR--RTKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       300 ~~l~~~L~~--~~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      ..+..+|.+  +..+-++|+||+++|||+++.+|...+
T Consensus        91 ~~l~~~L~~~~~k~n~~~l~G~~~tGKS~f~~~i~~~l  128 (267)
T d1u0ja_          91 SVFLGWATKKFGKRNTIWLFGPATTGKTNIAEAIAHTV  128 (267)
T ss_dssp             HHHHHHHTTCSTTCCEEEEECSTTSSHHHHHHHHHHHS
T ss_pred             HHHHHHHcCCCCccEEEEEEcCCCCCHHHHHHHHHHHh
Confidence            344555643  334567899999999999999999877

>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=87.97  E-value=0.088  Score=46.83  Aligned_cols=22  Identities=27%  Similarity=0.351  Sum_probs=19.3

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAAC  682 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~  682 (710)
                      -++++|+||||||+|...+...
T Consensus        14 kIvlvG~~~vGKTSli~rl~~~   35 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKLG   35 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999987643

>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=87.54  E-value=0.12  Score=47.53  Aligned_cols=18  Identities=44%  Similarity=0.486  Sum_probs=15.9

Q ss_pred             EEEcCCCChHHHHHHHHH
Q 005179          315 ILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       315 LL~GppG~GKT~la~~la  332 (710)
                      -|+|++|+||||+++.+.
T Consensus         6 gITG~igSGKStv~~~l~   23 (205)
T d1jjva_           6 GLTGGIGSGKTTIANLFT   23 (205)
T ss_dssp             EEECSTTSCHHHHHHHHH
T ss_pred             EEECCCCCCHHHHHHHHH
Confidence            379999999999998775

>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=87.53  E-value=0.14  Score=47.78  Aligned_cols=20  Identities=30%  Similarity=0.552  Sum_probs=18.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLA  680 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA  680 (710)
                      ...|.|+||||||+|..+|.
T Consensus        97 t~~~~G~SGVGKSTLiN~L~  116 (225)
T d1u0la2          97 ISTMAGLSGVGKSSLLNAIN  116 (225)
T ss_dssp             EEEEECSTTSSHHHHHHHHS
T ss_pred             eEEEECCCCCCHHHHHHhhc
Confidence            66899999999999998884

>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=87.52  E-value=0.1  Score=46.89  Aligned_cols=21  Identities=24%  Similarity=0.321  Sum_probs=18.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .|-|+|+|++|||+|+.+|..
T Consensus         3 ~VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           3 DVGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             CEEEESSTTSSHHHHHHHSEE
T ss_pred             eEEEECCCCCCHHHHHHHHhC
Confidence            578999999999999998853

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=87.48  E-value=1.8  Score=39.23  Aligned_cols=22  Identities=27%  Similarity=0.182  Sum_probs=17.5

Q ss_pred             CCCcEEEcCCCChHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la  332 (710)
                      +.++++..|+|+|||...-...
T Consensus        42 ~~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1          42 EYNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             CSEEEEECCSSSSHHHHHHHHH
T ss_pred             CCCeeeechhcccccceeeccc
Confidence            4589999999999998665443

>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=87.46  E-value=0.16  Score=48.59  Aligned_cols=24  Identities=21%  Similarity=0.441  Sum_probs=20.8

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .-+++|+|.+|+|||+++..|...
T Consensus        32 ~l~I~LvG~tg~GKSSliN~ilg~   55 (257)
T d1h65a_          32 SLTILVMGKGGVGKSSTVNSIIGE   55 (257)
T ss_dssp             EEEEEEEESTTSSHHHHHHHHHTS
T ss_pred             CcEEEEECCCCCcHHHHHHHHhCC
Confidence            457999999999999999998743

>d1cp2a_ c.37.1.10 (A:) Nitrogenase iron protein {Clostridium pasteurianum [TaxId: 1501]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Clostridium pasteurianum [TaxId: 1501]

Probab=87.33  E-value=0.2  Score=47.93  Aligned_cols=35  Identities=23%  Similarity=0.435  Sum_probs=28.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      |.++|.-||||||++-.||..+...       |+++.-+|+.
T Consensus         4 Iai~gKGGvGKTT~a~nLA~~LA~~-------G~rVllID~D   38 (269)
T d1cp2a_           4 VAIYGKGGIGKSTTTQNLTSGLHAM-------GKTIMVVGCD   38 (269)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHTT-------TCCEEEEEEC
T ss_pred             EEEECCCcCCHHHHHHHHHHHHHhC-------CCcEEEEecC
Confidence            5578999999999999999999653       6777777753

>d2afhe1 c.37.1.10 (E:1-289) Nitrogenase iron protein {Azotobacter vinelandii [TaxId: 354]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Nitrogenase iron protein
species: Azotobacter vinelandii [TaxId: 354]

Probab=87.25  E-value=0.2  Score=48.54  Aligned_cols=35  Identities=20%  Similarity=0.481  Sum_probs=28.8

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeehh
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDMG  355 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~~  355 (710)
                      +.++|.-||||||++-.||..+...       |+++.-+|+.
T Consensus         5 IaisgKGGVGKTT~a~NLA~~LA~~-------G~rVLlID~D   39 (289)
T d2afhe1           5 CAIYGKGGIGKSTTTQNLVAALAEM-------GKKVMIVGCD   39 (289)
T ss_dssp             EEEEECTTSSHHHHHHHHHHHHHHT-------TCCEEEEEEC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC-------CCCEEEEecC
Confidence            5679999999999999999988653       6778777763

>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=87.22  E-value=0.16  Score=50.33  Aligned_cols=36  Identities=17%  Similarity=0.195  Sum_probs=28.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCC--cceeeCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVR--IHYLFFPS  696 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~--~li~~d~s  696 (710)
                      .+-+.||||+|||+|..+|+..+-+.+.  ..+.+|.|
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDps   93 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPS   93 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCc
Confidence            6789999999999999999998876543  34555543

>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=87.19  E-value=0.63  Score=42.70  Aligned_cols=18  Identities=28%  Similarity=0.438  Sum_probs=15.6

Q ss_pred             CCCCcEEEcCCCChHHHH
Q 005179          310 TKNNPILLGESGVGKTAI  327 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~l  327 (710)
                      .+.++++..|+|+|||..
T Consensus        46 ~g~dvl~~a~TGsGKT~a   63 (212)
T d1qdea_          46 EGHDVLAQAQSGTGKTGT   63 (212)
T ss_dssp             TTCCEEEECCTTSSHHHH
T ss_pred             cCCCEEeecccccchhhh
Confidence            367899999999999964

>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=87.11  E-value=0.5  Score=42.87  Aligned_cols=21  Identities=14%  Similarity=0.116  Sum_probs=17.3

Q ss_pred             CCCcEEEcCCCChHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGL  331 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~l  331 (710)
                      ++|+++.-|+|+|||.+....
T Consensus        40 g~~vlv~apTGsGKT~~~~~~   60 (206)
T d1oywa2          40 GRDCLVVMPTGGGKSLCYQIP   60 (206)
T ss_dssp             TCCEEEECSCHHHHHHHHHHH
T ss_pred             CCCEEEEcCCCCCCcchhhhh
Confidence            468999999999999876433

>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=87.06  E-value=0.067  Score=50.27  Aligned_cols=23  Identities=26%  Similarity=0.622  Sum_probs=19.0

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~  334 (710)
                      .-.+|+|++|||||||+.+|...
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~  120 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPE  120 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC-
T ss_pred             ceEEEECCCCccHHHHHHhhccH
Confidence            44689999999999999998643

>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=87.04  E-value=0.55  Score=42.77  Aligned_cols=17  Identities=24%  Similarity=0.321  Sum_probs=15.0

Q ss_pred             CCCcEEEcCCCChHHHH
Q 005179          311 KNNPILLGESGVGKTAI  327 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~l  327 (710)
                      +.++++..|+|+|||..
T Consensus        38 G~dvii~a~TGSGKTla   54 (209)
T d1q0ua_          38 GESMVGQSQTGTGKTHA   54 (209)
T ss_dssp             TCCEEEECCSSHHHHHH
T ss_pred             CCCeEeeccccccccee
Confidence            56899999999999963

>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=87.02  E-value=0.062  Score=48.53  Aligned_cols=22  Identities=23%  Similarity=0.450  Sum_probs=19.6

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      .+|+||.|+|||+++.+|.-.+
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L   48 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTAL   48 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            4688999999999999998766

>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=86.95  E-value=0.12  Score=46.61  Aligned_cols=33  Identities=30%  Similarity=0.263  Sum_probs=25.6

Q ss_pred             CCCCCeEEEEEcCCCCcHHHHHHHHHHHHcCCC
Q 005179          655 PNRPTAAMLFCGPTGVGKTELAKSLAACYFGSV  687 (710)
Q Consensus       655 p~rp~~~~Lf~GPpGtGKT~lAkaLA~~lfg~~  687 (710)
                      |++++--++++|.+|||||.|...+..--|..+
T Consensus         5 ~~~~~~Ki~lvG~~~vGKTsLi~r~~~~~f~~~   37 (185)
T d2atxa1           5 PGALMLKCVVVGDGAVGKTCLLMSYANDAFPEE   37 (185)
T ss_dssp             CEEEEEEEEEEECTTSSHHHHHHHHHHSSCCCS
T ss_pred             CCCcEEEEEEECCCCCCHHHHHHHHhhCCCCCc
Confidence            444444688999999999999998887655544

>d2bcjq2 c.37.1.8 (Q:38-66,Q:184-354) Transducin (alpha subunit) {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.93  E-value=0.14  Score=46.25  Aligned_cols=22  Identities=27%  Similarity=0.463  Sum_probs=19.2

Q ss_pred             CcEEEcCCCChHHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~  334 (710)
                      .++|.|.+|||||+|+..+...
T Consensus         4 Kiv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           4 KLLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3799999999999999988544

>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=86.92  E-value=0.48  Score=43.35  Aligned_cols=17  Identities=18%  Similarity=0.407  Sum_probs=15.0

Q ss_pred             CCCCcEEEcCCCChHHH
Q 005179          310 TKNNPILLGESGVGKTA  326 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~  326 (710)
                      .+.++++..|+|+|||.
T Consensus        39 ~g~dvl~~a~TGsGKTl   55 (206)
T d1veca_          39 SGRDILARAKNGTGKSG   55 (206)
T ss_dssp             TTCCEEEECCSSSTTHH
T ss_pred             cCCCEEeeccCcccccc
Confidence            35789999999999995

>d1rifa_ c.37.1.23 (A:) DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: DNA helicase UvsW
domain: DNA helicase UvsW
species: Bacteriophage T4 [TaxId: 10665]

Probab=86.83  E-value=1.5  Score=41.97  Aligned_cols=43  Identities=16%  Similarity=0.094  Sum_probs=32.6

Q ss_pred             CcccCHHHHHHHHHHHHcCCCCCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          291 PVIGRETEIQRIIQILCRRTKNNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       291 ~liGr~~~i~~l~~~L~~~~~~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      ++.-|+-+.+.+..++..   ++.++.-|.|+|||.++-.++..+.
T Consensus       111 ~~~~rdyQ~~av~~~l~~---~~~il~~pTGsGKT~i~~~i~~~~~  153 (282)
T d1rifa_         111 RIEPHWYQKDAVFEGLVN---RRRILNLPTSAGRSLIQALLARYYL  153 (282)
T ss_dssp             ECCCCHHHHHHHHHHHHH---SEEEECCCTTSCHHHHHHHHHHHHH
T ss_pred             ccccchHHHHHHHHHHhc---CCceeEEEcccCccHHHHHHHHHhh
Confidence            345577787777777764   3468888999999998888876653

>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=86.81  E-value=0.22  Score=51.19  Aligned_cols=37  Identities=22%  Similarity=0.363  Sum_probs=28.4

Q ss_pred             CCCcEEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          311 KNNPILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      ..|++++|++|+|||+++..+...+...       +..++.+|.
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            4689999999999999988777666432       556666664

>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=86.79  E-value=0.059  Score=50.68  Aligned_cols=23  Identities=17%  Similarity=0.115  Sum_probs=20.9

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~  336 (710)
                      |.|.|+-|+||||+++.|++.+.
T Consensus         5 I~ieG~dGsGKST~~~~L~~~l~   27 (241)
T d1p5zb_           5 ISIEGNIAAGKSTFVNILKQLCE   27 (241)
T ss_dssp             EEEECSTTSSHHHHHTTTGGGCT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHh
Confidence            67899999999999999998873

>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=86.69  E-value=1.4  Score=40.46  Aligned_cols=17  Identities=41%  Similarity=0.476  Sum_probs=15.1

Q ss_pred             CCCcEEEcCCCChHHHH
Q 005179          311 KNNPILLGESGVGKTAI  327 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~l  327 (710)
                      +.++++..|+|+|||..
T Consensus        49 g~dvl~~a~TGsGKTla   65 (218)
T d2g9na1          49 GYDVIAQAQSGTGKTAT   65 (218)
T ss_dssp             TCCEEEECCTTSSHHHH
T ss_pred             CCCEEEEcccchhhhhh
Confidence            57899999999999964

>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=86.60  E-value=0.057  Score=47.21  Aligned_cols=21  Identities=24%  Similarity=0.494  Sum_probs=19.1

Q ss_pred             cEEEcCCCChHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~  334 (710)
                      +.|+|.||+|||+|+.+|...
T Consensus         3 I~liG~~n~GKSSLin~l~g~   23 (160)
T d1xzpa2           3 MVIVGKPNVGKSTLLNRLLNE   23 (160)
T ss_dssp             EEEECCHHHHTCHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999754

>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=86.58  E-value=0.16  Score=45.38  Aligned_cols=21  Identities=19%  Similarity=0.346  Sum_probs=18.5

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .++++|++|||||+|+..+..
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~   27 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLT   27 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            478999999999999997764

>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=86.44  E-value=0.15  Score=45.60  Aligned_cols=21  Identities=19%  Similarity=0.423  Sum_probs=18.9

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      .+.|+|.+|+|||+|+.+|..
T Consensus        10 kV~iiG~~~~GKSTLin~l~~   30 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILN   30 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHC
Confidence            478999999999999999864

>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=86.35  E-value=0.64  Score=45.72  Aligned_cols=36  Identities=25%  Similarity=0.267  Sum_probs=27.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHc--CCCCcceeeCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYF--GSVRIHYLFFPS  696 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lf--g~~~~li~~d~s  696 (710)
                      .+=+.||||+|||+|.-.|+..+-  |-.-..+.+|.|
T Consensus        53 ~igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDps   90 (323)
T d2qm8a1          53 RVGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPS   90 (323)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGG
T ss_pred             EEeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeecccc
Confidence            577999999999999999998754  333355666644

>d1azta2 c.37.1.8 (A:35-65,A:202-391) Transducin (alpha subunit) {Cow (Bos taurus) [TaxId: 9913]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Transducin (alpha subunit)
species: Cow (Bos taurus) [TaxId: 9913]

Probab=86.31  E-value=0.14  Score=47.60  Aligned_cols=20  Identities=30%  Similarity=0.541  Sum_probs=18.1

Q ss_pred             CcEEEcCCCChHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la  332 (710)
                      -+||.|++|+|||+|++.+.
T Consensus         8 KilllG~~~vGKTsll~~~~   27 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMR   27 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHh
Confidence            48999999999999999874

>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=86.11  E-value=0.086  Score=47.01  Aligned_cols=22  Identities=23%  Similarity=0.300  Sum_probs=19.2

Q ss_pred             CCCcEEEcCCCChHHHHHHHHH
Q 005179          311 KNNPILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       311 ~~nvLL~GppG~GKT~la~~la  332 (710)
                      ...|.|+|.|++|||+|+++|.
T Consensus        16 ~~~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          16 GIEVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHh
Confidence            3458999999999999999884

>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=85.88  E-value=0.13  Score=48.50  Aligned_cols=24  Identities=29%  Similarity=0.313  Sum_probs=20.1

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .-+-|+||.|+|||||.+.|+..+
T Consensus        29 ei~glvG~nGaGKSTLl~~l~G~~   52 (238)
T d1vpla_          29 EIFGLIGPNGAGKTTTLRIISTLI   52 (238)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCC
Confidence            345699999999999999987654

>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=85.87  E-value=0.14  Score=43.50  Aligned_cols=21  Identities=24%  Similarity=0.327  Sum_probs=17.2

Q ss_pred             eEEEEEcCCCCcHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLA  680 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA  680 (710)
                      ...++.+|||+|||+++-.+.
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~   29 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAY   29 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHH
T ss_pred             CEEEEEeCCCCCHHHHHHHHH
Confidence            478999999999999875443

>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=85.74  E-value=0.16  Score=47.61  Aligned_cols=25  Identities=20%  Similarity=0.230  Sum_probs=21.8

Q ss_pred             CcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          313 NPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      =++|-|+-|+||||+++.|++.+..
T Consensus         4 ~IviEG~~GsGKST~~~~L~~~l~~   28 (241)
T d2ocpa1           4 RLSIEGNIAVGKSTFVKLLTKTYPE   28 (241)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHCTT
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhh
Confidence            3678899999999999999998843

>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=85.48  E-value=0.14  Score=48.37  Aligned_cols=26  Identities=27%  Similarity=0.368  Sum_probs=21.4

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||.|+||||+++.|+-.+
T Consensus        31 ~Gei~~liGpnGaGKSTl~~~i~Gl~   56 (240)
T d1ji0a_          31 RGQIVTLIGANGAGKTTTLSAIAGLV   56 (240)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhCCC
Confidence            34557799999999999999987544

>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=85.44  E-value=0.3  Score=44.59  Aligned_cols=35  Identities=23%  Similarity=0.190  Sum_probs=28.3

Q ss_pred             CcEEEcC-CCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          313 NPILLGE-SGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       313 nvLL~Gp-pG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      .++++|- +||||||++-.||..+.+.       |.++..+|.
T Consensus         3 ~~~i~gt~~GVGKTtvs~~La~aLa~~-------G~rVl~id~   38 (224)
T d1byia_           3 RYFVTGTDTEVGKTVASCALLQAAKAA-------GYRTAGYKP   38 (224)
T ss_dssp             EEEEEESSTTSCHHHHHHHHHHHHHHT-------TCCEEEECS
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHHHC-------CCeEEEECc
Confidence            4688998 5999999999999999664       666766663

>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=85.39  E-value=0.2  Score=46.39  Aligned_cols=25  Identities=20%  Similarity=0.174  Sum_probs=21.8

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIRIV  336 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~l~  336 (710)
                      .=|.|.|+-|+||||+++.|++.+.
T Consensus         4 k~I~iEG~DGsGKST~~~~L~~~L~   28 (214)
T d1tmka_           4 KLILIEGLDRTGKTTQCNILYKKLQ   28 (214)
T ss_dssp             CEEEEEESTTSSHHHHHHHHHHHTT
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHH
Confidence            3467889999999999999999883

>d1puia_ c.37.1.8 (A:) Probable GTPase EngB {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Probable GTPase EngB
species: Escherichia coli [TaxId: 562]

Probab=85.38  E-value=0.16  Score=45.16  Aligned_cols=21  Identities=24%  Similarity=0.490  Sum_probs=18.6

Q ss_pred             eEEEEEcCCCCcHHHHHHHHH
Q 005179          660 AAMLFCGPTGVGKTELAKSLA  680 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA  680 (710)
                      .-+.|+|+|++|||+|..+|.
T Consensus        17 ~~I~lvG~~NvGKSSL~n~L~   37 (188)
T d1puia_          17 IEVAFAGRSNAGKSSALNTLT   37 (188)
T ss_dssp             EEEEEEECTTSSHHHHHTTTC
T ss_pred             CEEEEECCCCCCHHHHHHHHh
Confidence            379999999999999998873

>d1svsa1 c.37.1.8 (A:32-60,A:182-347) Transducin (alpha subunit) {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: Transducin (alpha subunit)
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=85.34  E-value=0.17  Score=45.26  Aligned_cols=19  Identities=32%  Similarity=0.567  Sum_probs=17.2

Q ss_pred             cEEEcCCCChHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLA  332 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la  332 (710)
                      ++|+|..|||||+|++.+.
T Consensus         5 ivllG~~~vGKTsl~~r~~   23 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMK   23 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            7999999999999998764

>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=84.61  E-value=0.2  Score=48.55  Aligned_cols=25  Identities=16%  Similarity=0.275  Sum_probs=18.6

Q ss_pred             cEEEcCCCChHHHHHHHHHHHHHhc
Q 005179          314 PILLGESGVGKTAIAEGLAIRIVQA  338 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l~~~  338 (710)
                      +-+.|++|+||||++++|.+.+...
T Consensus         7 IgIaG~SGSGKTTva~~l~~i~~~~   31 (288)
T d1a7ja_           7 ISVTGSSGAGTSTVKHTFDQIFRRE   31 (288)
T ss_dssp             EEEESCC---CCTHHHHHHHHHHHH
T ss_pred             EEEECCCCCcHHHHHHHHHHHHhhc
Confidence            4578999999999999999988554

>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=84.43  E-value=0.27  Score=47.58  Aligned_cols=23  Identities=30%  Similarity=0.407  Sum_probs=21.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY  683 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l  683 (710)
                      -.++.||+|||||+|+..+++..
T Consensus        45 r~~I~g~~g~GKT~l~~~i~~~~   67 (289)
T d1xpua3          45 RGLIVAPPKAGKTMLLQNIAQSI   67 (289)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHH
T ss_pred             eeeEeCCCCCCHHHHHHHHHHHH
Confidence            68999999999999999999865

>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=84.32  E-value=0.26  Score=45.23  Aligned_cols=33  Identities=21%  Similarity=0.096  Sum_probs=24.5

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~  695 (710)
                      ..++.+|||+|||.+|-.++..+-  ...+|....
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~~--~~~Liv~p~  119 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINELS--TPTLIVVPT  119 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSC--SCEEEEESS
T ss_pred             CcEEEeCCCCCceehHHhHHHHhc--CceeEEEcc
Confidence            457889999999999998888752  345555543

>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=84.24  E-value=0.16  Score=47.84  Aligned_cols=24  Identities=25%  Similarity=0.360  Sum_probs=20.3

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~  333 (710)
                      .+.-+-|+||.|+|||||.+.++.
T Consensus        24 ~Gei~~iiG~nGaGKSTLl~~l~G   47 (231)
T d1l7vc_          24 AGEILHLVGPNGAGKSTLLARMAG   47 (231)
T ss_dssp             TTCEEECBCCTTSSHHHHHHHHHT
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhC
Confidence            445577999999999999998875

>d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: G proteins
domain: Elongation factor SelB, N-terminal domain
species: Methanococcus maripaludis [TaxId: 39152]

Probab=84.16  E-value=0.36  Score=42.99  Aligned_cols=21  Identities=29%  Similarity=0.346  Sum_probs=19.1

Q ss_pred             CcEEEcCCCChHHHHHHHHHH
Q 005179          313 NPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       313 nvLL~GppG~GKT~la~~la~  333 (710)
                      |+-|+|.|++|||||+.+|..
T Consensus         7 nIaiiG~~naGKSTL~n~L~~   27 (179)
T d1wb1a4           7 NLGIFGHIDHGKTTLSKVLTE   27 (179)
T ss_dssp             EEEEEECTTSSHHHHHHHHHT
T ss_pred             EEEEEeCCCCcHHHHHHHHHH
Confidence            688999999999999999874

>d1j3ba1 c.91.1.1 (A:212-529) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Thermus thermophilus [TaxId: 274]

Probab=83.71  E-value=0.21  Score=48.87  Aligned_cols=29  Identities=28%  Similarity=0.405  Sum_probs=21.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCCc
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVRI  689 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~  689 (710)
                      ..||+|.+|||||+|.-.=-+.|-|+++.
T Consensus        16 valffGLSGTGKTTLs~~~~r~ligDDe~   44 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTDPERPLIGDDEH   44 (318)
T ss_dssp             EEEEEECTTSCHHHHTCBTTBCEEESSEE
T ss_pred             EEEEEccCCCCccccccCCCceEEcCcce
Confidence            67999999999999975544445665543

>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=83.70  E-value=0.14  Score=48.05  Aligned_cols=21  Identities=33%  Similarity=0.756  Sum_probs=18.1

Q ss_pred             EEEEEcCCCCcHHHHHHHHHH
Q 005179          661 AMLFCGPTGVGKTELAKSLAA  681 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~  681 (710)
                      ..+|.|++||||++|..+|..
T Consensus        99 ~~vl~G~SGVGKSSLiN~L~~  119 (231)
T d1t9ha2          99 TTVFAGQSGVGKSSLLNAISP  119 (231)
T ss_dssp             EEEEEESHHHHHHHHHHHHCC
T ss_pred             eEEEECCCCccHHHHHHhhcc
Confidence            567999999999999988753

>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=83.52  E-value=0.2  Score=47.83  Aligned_cols=26  Identities=15%  Similarity=0.387  Sum_probs=21.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l  335 (710)
                      .+.-+-|+||.|+|||||++.|+-.+
T Consensus        29 ~Gei~~liG~nGaGKSTLl~~i~Gl~   54 (254)
T d1g6ha_          29 KGDVTLIIGPNGSGKSTLINVITGFL   54 (254)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHCCC
Confidence            34457799999999999999987544

>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=83.39  E-value=0.42  Score=45.66  Aligned_cols=39  Identities=26%  Similarity=0.254  Sum_probs=33.1

Q ss_pred             eEEEEEcCCCCcHHHHHHHHHHHHcCCCCcceeeCCCCC
Q 005179          660 AAMLFCGPTGVGKTELAKSLAACYFGSVRIHYLFFPSPF  698 (710)
Q Consensus       660 ~~~Lf~GPpGtGKT~lAkaLA~~lfg~~~~li~~d~se~  698 (710)
                      .-+.|.|--|||||++|-.||..|-..+...+.+|....
T Consensus        21 ~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~Dp~   59 (279)
T d1ihua2          21 GLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSDPA   59 (279)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESCCC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCCCC
Confidence            477899999999999999998888777778888887754

>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=82.68  E-value=0.39  Score=46.36  Aligned_cols=37  Identities=16%  Similarity=0.335  Sum_probs=28.5

Q ss_pred             HHHHHHHc-CCCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          301 RIIQILCR-RTKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       301 ~l~~~L~~-~~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      +++..+.. .++...+|.|++|||||+|+..+++....
T Consensus        32 r~ID~l~PigrGQr~~I~g~~g~GKT~l~~~i~~~~~~   69 (289)
T d1xpua3          32 RVLDLASPIGRGQRGLIVAPPKAGKTMLLQNIAQSIAY   69 (289)
T ss_dssp             HHHHHHSCCBTTCEEEEEECSSSSHHHHHHHHHHHHHH
T ss_pred             eeeeecccccCCCeeeEeCCCCCCHHHHHHHHHHHHhh
Confidence            45555543 45667999999999999999999987643

>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=82.29  E-value=0.3  Score=45.71  Aligned_cols=22  Identities=23%  Similarity=0.194  Sum_probs=19.5

Q ss_pred             cEEEcCCCChHHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIRI  335 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~l  335 (710)
                      +-|+|+.|+||||+|+.|+...
T Consensus         4 IgiTG~igSGKsTva~~l~e~~   25 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNY   25 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHhC
Confidence            4689999999999999998765

>d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Cell division regulator MinD
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=82.16  E-value=0.55  Score=43.24  Aligned_cols=33  Identities=27%  Similarity=0.517  Sum_probs=26.1

Q ss_pred             EEEcCCCChHHHHHHHHHHHHHhcCCCccccCceEEEeeh
Q 005179          315 ILLGESGVGKTAIAEGLAIRIVQAEVPVFLLSKRIMSLDM  354 (710)
Q Consensus       315 LL~GppG~GKT~la~~la~~l~~~~~p~~l~~~~v~~ld~  354 (710)
                      +..|..|+||||++..||..+.+.       +.++..+|+
T Consensus         6 v~s~KGGvGKTtia~nlA~~la~~-------g~~VlliD~   38 (232)
T d1hyqa_           6 VASGKGGTGKTTITANLGVALAQL-------GHDVTIVDA   38 (232)
T ss_dssp             EEESSSCSCHHHHHHHHHHHHHHT-------TCCEEEEEC
T ss_pred             EECCCCCChHHHHHHHHHHHHHhC-------CCCEEEEeC
Confidence            445889999999999999998653       556766664

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal 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: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=82.02  E-value=0.8  Score=37.81  Aligned_cols=28  Identities=14%  Similarity=0.102  Sum_probs=23.9

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHHHHHh
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAIRIVQ  337 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~~l~~  337 (710)
                      ++-.++|.|-+|+||+++|++|...+.+
T Consensus         5 qgf~i~~tg~~~~gk~~ia~al~~~l~q   32 (122)
T d1g8fa3           5 QGFSIVLGNSLTVSREQLSIALLSTFLQ   32 (122)
T ss_dssp             CCEEEEECTTCCSCHHHHHHHHHHHHTT
T ss_pred             cceEEEEeCCCCCCHHHHHHHHHHHHHH
Confidence            3456889999999999999999888855

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=81.93  E-value=0.21  Score=48.53  Aligned_cols=25  Identities=20%  Similarity=0.445  Sum_probs=20.9

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFG  685 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg  685 (710)
                      -.+|+||.|+|||.+-.||+-.|.+
T Consensus        26 lnvlvG~NgsGKS~iL~Ai~~~lg~   50 (308)
T d1e69a_          26 VTAIVGPNGSGKSNIIDAIKWVFGE   50 (308)
T ss_dssp             EEEEECCTTTCSTHHHHHHHHTSCC
T ss_pred             eEEEECCCCCcHHHHHHHHHHHhCC
Confidence            4589999999999999999765433

>d1g8fa3 c.37.1.15 (A:390-511) ATP sulfurylase C-terminal 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: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=81.91  E-value=0.63  Score=38.47  Aligned_cols=35  Identities=20%  Similarity=0.379  Sum_probs=28.0

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHH--cCCCCcceeeCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACY--FGSVRIHYLFFP  695 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~l--fg~~~~li~~d~  695 (710)
                      .++|.|-+|.||.++|+||-..|  |+.++...-+|-
T Consensus         8 ~i~~tg~~~~gk~~ia~al~~~l~q~~G~R~vtll~~   44 (122)
T d1g8fa3           8 SIVLGNSLTVSREQLSIALLSTFLQFGGGRYYKIFEH   44 (122)
T ss_dssp             EEEECTTCCSCHHHHHHHHHHHHTTSCSCCCEEECCC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHHHHhcCCcceEEecC
Confidence            78999999999999999998887  444555555554

>d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) 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: Elongation factor Tu (EF-Tu), N-terminal (G) domain
species: Thermus thermophilus [TaxId: 274]

Probab=81.73  E-value=0.67  Score=42.27  Aligned_cols=23  Identities=26%  Similarity=0.286  Sum_probs=20.2

Q ss_pred             CCcEEEcCCCChHHHHHHHHHHH
Q 005179          312 NNPILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       312 ~nvLL~GppG~GKT~la~~la~~  334 (710)
                      -|+.++|-++.|||||+.+|...
T Consensus         4 ini~iiGhvd~GKSTL~~~Ll~~   26 (204)
T d2c78a3           4 VNVGTIGHVDHGKTTLTAALTYV   26 (204)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHH
T ss_pred             eEEEEEeCCCCcHHHHHHHHHHH
Confidence            37899999999999999999654

>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=81.41  E-value=1.6  Score=36.96  Aligned_cols=19  Identities=32%  Similarity=0.335  Sum_probs=14.7

Q ss_pred             EEEcCCCChHHH-HHHHHHH
Q 005179          315 ILLGESGVGKTA-IAEGLAI  333 (710)
Q Consensus       315 LL~GppG~GKT~-la~~la~  333 (710)
                      +++||=.+|||+ |++.+-+
T Consensus         6 ~i~GpMfsGKTteLi~~~~~   25 (139)
T d2b8ta1           6 FITGPMFAGKTAELIRRLHR   25 (139)
T ss_dssp             EEECSTTSCHHHHHHHHHHH
T ss_pred             EEEccccCHHHHHHHHHHHH
Confidence            689999999998 5555443

>d1e69a_ c.37.1.12 (A:) Smc head domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Thermotoga maritima [TaxId: 2336]

Probab=80.87  E-value=0.24  Score=48.20  Aligned_cols=21  Identities=24%  Similarity=0.517  Sum_probs=18.5

Q ss_pred             cEEEcCCCChHHHHHHHHHHH
Q 005179          314 PILLGESGVGKTAIAEGLAIR  334 (710)
Q Consensus       314 vLL~GppG~GKT~la~~la~~  334 (710)
                      -+|+||.|+|||++.+||.-.
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~   47 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWV   47 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHT
T ss_pred             EEEECCCCCcHHHHHHHHHHH
Confidence            389999999999999999653

>d2olra1 c.91.1.1 (A:228-540) Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase) {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: PEP carboxykinase-like
superfamily: PEP carboxykinase-like
family: PEP carboxykinase C-terminal domain
domain: Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
species: Escherichia coli [TaxId: 562]

Probab=80.82  E-value=0.34  Score=47.07  Aligned_cols=28  Identities=29%  Similarity=0.451  Sum_probs=20.4

Q ss_pred             EEEEEcCCCCcHHHHHHHHHHHHcCCCC
Q 005179          661 AMLFCGPTGVGKTELAKSLAACYFGSVR  688 (710)
Q Consensus       661 ~~Lf~GPpGtGKT~lAkaLA~~lfg~~~  688 (710)
                      ..||+|.+|||||+|..-=-+.|-|++.
T Consensus        16 ~alfFGLSGTGKTTLs~d~~r~ligDDe   43 (313)
T d2olra1          16 VAVFFGLSGTGKTTLSTDPKRRLIGDDE   43 (313)
T ss_dssp             EEEEECSTTSSHHHHHCCTTSEEEESSC
T ss_pred             EEEEEccCCCCcccceeCCCCceecCce
Confidence            6799999999999998543334555543

>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=80.53  E-value=0.43  Score=48.57  Aligned_cols=24  Identities=29%  Similarity=0.378  Sum_probs=21.2

Q ss_pred             CCCCcEEEcCCCChHHHHHHHHHH
Q 005179          310 TKNNPILLGESGVGKTAIAEGLAI  333 (710)
Q Consensus       310 ~~~nvLL~GppG~GKT~la~~la~  333 (710)
                      .+-+|.|+|.||+|||+|+.+|..
T Consensus        55 ~~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          55 SVLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhC
Confidence            456799999999999999999863