Citrus Sinensis ID: 011664

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480
Protein Sequence
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFDLAAAENHS
Secondary Structure (PSIPRED)
cHHHHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHHHHHccccEEEEEEEccccccccHHHHHHHHHHHHccccccccccccccccccccEEEEccccccEEEEEccEEEEEEEcccccccEEEEEEEccccccHHHHHHHHHHHHHHHHHHHHHHcccEEEEEEcccccccccccEEcccccccccccccccHHHHHHHHHHHHHHHHcHHHHHHHccccccEEEEEccccccHHHHHHHHHHHcccEEEEEEccccccHHHHHHHHHHccccEEEEEEcccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccccEEEEEcccccHHHHHHHHHHHccccccccHHHHHHHHHccccccHHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccEEEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHcccEEEEEEEccccccccHHHHHHHHHHHHccccHHHHHHHEEccccccccEEEEEccccEEEEEEccEEEEEEEcccccccEEEEEEEcHHcHHHHHHHHHHHHHHHHHHHHHHHHcEEEEEEcccccccccccccEEEcccccccHHHHcccHHHHHHHHHHHHHHHHcHHHHHHHHHHHHccEEEEccccccHHHHHHHHHHHccccEEEEEEcEccccHHHHHHHHHccccEEEEEEEccccccccccEEEEHHHHHHHccHHHccccccEEEEEEcccHHcccHHHcccccccEEEEEccccHHHHHHHHHHHccccccccHHHHHHHHHHHccccHHHHHHHHHcccccHHHHHHHHHHHHHHHHHHHHHHccccccHccccccccccccccccccccccccHHHHHHHHcHEEEcccccccccccccccccc
Coil and Loop (DISEMBL)
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHvhqffkvpefnegmqeNQLYRKVYAYLNSltsiedsdftnlftgkksndivlgldpnqliqdnflgaplswanqddsATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRndrdgccgrwrsvpfthpstfdtiSMETDLKNRVKSDLESFLKAKHYYHRLGRVWkrsyllygpsgtgksSFAAAMASFMSydvydvdlsrvaddaDLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNskdhvdqallrpgridvhihfplcdfssfktlassylglkdhklfpQVEEIfqngsslspaeIGELMIANRNSPSRALKSVITALQtdgegrgaanagrrldksgskkstdadsgehggvfsreNTVKEFRKLYGLLtlknsrksqsFDLAAAENHS
Flexible Loop (DISEMBL)
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHihavsdeleqkkkrdLRLFVNlrndrdgccgrwrsvpfthpstfdtismeTDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALqtdgegrgaanagrrldksgskkstdadsgehggvfsrentvKEFRKLYGLltlknsrksqsfdlaaaenhs
Low Complexity Region (SEG)
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKssfaaamasfmsYDVYDVDLSRVADDADlkslllqttsksVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEgrgaanagrrLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFDLAAAENHS
Disordered region (IsUnstruct)
***AIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQ*************************************************************************VKEFRKLYGLLTL******************
Disordered Region (DISOPRED)
***AIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTS**********************DPNQLIQDNFLGAPLSWANQDD*****TLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCC********THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDR***************NFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT***************************************RENTVKEFRKLYGLLT*******************
Disordered Region (DISEMBL)
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTD******************************GVFSRENTVKEFRKLYGLLTLKNSRKSQS**********
Disordered Region (DISPRO)
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEG********************************ENTVKEFRKLYGLLTLK*****************
Transmembrane Helix (TMHMM)
iiiiHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiHHHHHHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
SSSSSSSSSSSSSSiiHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
SSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MMRAIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFDLAAAENHS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	480	2.2.26 [Sep-21-2011]
Q9P6Q3	449	Probable mitochondrial ch	yes	no	0.452	0.483	0.296	9e-24
P32839	456	Mitochondrial chaperone B	yes	no	0.454	0.478	0.300	7e-21
Q54HY8	421	Probable mitochondrial ch	no	no	0.472	0.539	0.302	1e-20
Q9Y276	419	Mitochondrial chaperone B	yes	no	0.456	0.522	0.286	3e-20
Q9CZP5	418	Mitochondrial chaperone B	yes	no	0.462	0.531	0.286	3e-20
Q7ZV60	420	Mitochondrial chaperone B	yes	no	0.422	0.483	0.291	4e-20
Q5E9H5	419	Mitochondrial chaperone B	yes	no	0.462	0.529	0.278	1e-19
Q7ZTL7	419	Mitochondrial chaperone B	N/A	no	0.360	0.412	0.310	2e-18
Q54DY9	458	Probable mitochondrial ch	no	no	0.458	0.480	0.266	2e-18
Q2SF13	619	ATP-dependent zinc metall	yes	no	0.329	0.255	0.284	3e-11

>sp|Q9P6Q3|BCS1_SCHPO Probable mitochondrial chaperone bcs1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=SPAC644.07 PE=2 SV=1

 Score =  112 bits (279), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 123/236 (52%), Gaps = 19/236 (8%)

Query: 178 WRSVPFTHPST---FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
           W+  PF HP +     ++ +E+++K  +  D+  FL+   +Y   G  ++R YLLYGP G
Sbjct: 195 WK--PFGHPRSKRMLSSVVLESNVKKMITDDVHDFLRNSQWYDTRGIPYRRGYLLYGPPG 252

Query: 235 TGKSSFAAAMASFMSYDVYDVDLSRVA-DDADLKSLLLQTTSKSVILIEDLDRFLVEKP- 292
           +GK+SF  A+A  + YD+  ++L+     D  L  LL     K+V+L+ED+D     +  
Sbjct: 253 SGKTSFLYALAGELDYDICVLNLAEKGLTDDRLNHLLSNVPPKAVVLLEDVDSAFQGRER 312

Query: 293 -------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFP 345
                  A V+ SG+LN +DGV +S   +ER++  T N  + +D AL+RPGR+DV  +  
Sbjct: 313 SGEVGFHANVTFSGLLNALDGVTSS---DERIIFMTTNHPEKLDPALVRPGRVDVKAYLG 369

Query: 346 LCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRAL 401
                  + + + + G          + +    +S+  A +  L + N++SP+ A+
Sbjct: 370 NATPEQVREMFTRFYGHSPEMADDLSDIVCPKNTSM--ASLQGLFVMNKSSPADAV 423

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P32839|BCS1_YEAST Mitochondrial chaperone BCS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=BCS1 PE=1 SV=2

 Score =  102 bits (254), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 125/243 (51%), Gaps = 25/243 (10%)

Query: 178 WRSVPFTHPST---FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
           WR   F  P       ++ +++ +K  +  D+  F+K   +Y   G  ++R YLLYGP G
Sbjct: 213 WRK--FGQPKAKRMLPSVILDSGIKEGILDDVYDFMKNGKWYSDRGIPYRRGYLLYGPPG 270

Query: 235 TGKSSFAAAMASFMSYDVYDVDLSR--VADDADLKSLLLQTTSKSVILIEDLDRFLVEKP 292
           +GK+SF  A+A  + Y++  ++LS   + DD  L  L+     +S++L+ED+D    ++ 
Sbjct: 271 SGKTSFIQALAGELDYNICILNLSENNLTDDR-LNHLMNNMPERSILLLEDIDAAFNKRS 329

Query: 293 --------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHF 344
                   ++V+ SG+LN +DGV +S   EE +   T N  + +D A++RPGRID  +  
Sbjct: 330 QTGEQGFHSSVTFSGLLNALDGVTSS---EETITFMTTNHPEKLDAAIMRPGRIDYKVFV 386

Query: 345 P-LCDFSSFKTLASSYLGLKD--HKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRAL 401
                +   K     Y G  D   K    V+E+     ++S A++  L + N+++P  AL
Sbjct: 387 GNATPYQVEKMFMKFYPGETDICKKFVNSVKEL---DITVSTAQLQGLFVMNKDAPHDAL 443

Query: 402 KSV 404
           K V
Sbjct: 444 KMV 446

Essential for the expression of the Rieske iron-sulfur protein.

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

>sp|Q54HY8|BCS1A_DICDI Probable mitochondrial chaperone BCS1-A OS=Dictyostelium discoideum GN=bcs1la PE=3 SV=1

 Score =  101 bits (252), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 125/251 (49%), Gaps = 24/251 (9%)

Query: 172 DGCCGRWRSVPFTHPSTFDTIS---METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYL 228
           +G  G W    F +P +  ++S   +  DLK+++  D++SF+  + +Y   G  ++R YL
Sbjct: 168 NGGNGNWER--FGNPRSIRSLSSVILADDLKSKLIEDIKSFITNESWYRNRGIPYRRGYL 225

Query: 229 LYGPSGTGKSSFAAAMASFMSYDVYDVDL-SRVADDADLKSLLLQTTSKSVILIEDLDRF 287
           LYG  G GKSS   A+A  ++ D+  V L S+  DD  +  LL     KS++LIED+D  
Sbjct: 226 LYGEPGNGKSSLINAIAGELNLDICIVSLSSKDIDDKQINHLLNNAPPKSILLIEDIDAA 285

Query: 288 L-------------VEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLR 334
                              +++ SG+LN +DGV      E R++  T N  + +D AL+R
Sbjct: 286 FKSHRDNVDSNNNNSNNNNSLTYSGLLNALDGV---ASQEGRILFMTTNKIELLDSALIR 342

Query: 335 PGRIDVHIHFPLCDFSSFKTLASSYLGL-KDHKLFPQVEEIFQNGSSLSPAEIGELMIAN 393
            GRID+ I       S    L + +  L  D++L  +  E   +   LS ++I   ++  
Sbjct: 343 EGRIDLKIKVSNATKSQAAQLFTHFYNLPTDNQLAIRFSENLHD-HQLSMSQIQGFLLKY 401

Query: 394 RNSPSRALKSV 404
            NSP +A++ V
Sbjct: 402 INSPEKAIEEV 412

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9Y276|BCS1_HUMAN Mitochondrial chaperone BCS1 OS=Homo sapiens GN=BCS1L PE=1 SV=1

 Score =  100 bits (248), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 117/241 (48%), Gaps = 22/241 (9%)

Query: 178 WRSVPFTHPS---TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
           WR  PF +P      +++ ++  L +R+  D++ F+    +Y   G  ++R YLLYGP G
Sbjct: 176 WR--PFGYPRRRRPLNSVVLQQGLADRIVRDVQEFIDNPKWYTDRGIPYRRGYLLYGPPG 233

Query: 235 TGKSSFAAAMASFMSYDV-YDVDLSRVADDADLKSLLLQTTSKSVILIEDLD-RFL---- 288
            GKSSF  A+A  + + +           D  L  LL     +S++L+ED+D  FL    
Sbjct: 234 CGKSSFITALAGELEHSICLLSLTDSSLSDDRLNHLLSVAPQQSLVLLEDVDAAFLSRDL 293

Query: 289 -VEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVH 341
            VE P        ++ SG+LN +DGV ++   E R++  T N  D +D AL+RPGR+D+ 
Sbjct: 294 AVENPVKYQGLGRLTFSGLLNALDGVAST---EARIVFMTTNHVDRLDPALIRPGRVDLK 350

Query: 342 IHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIANRNSPSRA 400
            +   C       +   +   +   L     E + +  + +SPA++    +  +N P  A
Sbjct: 351 EYVGYCSHWQLTQMFQRFYPGQAPSLAENFAEHVLRATNQISPAQVQGYFMLYKNDPVGA 410

Query: 401 L 401
           +
Sbjct: 411 I 411

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Homo sapiens (taxid: 9606)

>sp|Q9CZP5|BCS1_MOUSE Mitochondrial chaperone BCS1 OS=Mus musculus GN=Bcs1l PE=1 SV=1

 Score =  100 bits (248), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 118/244 (48%), Gaps = 22/244 (9%)

Query: 178 WRSVPFTHPS---TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
           WR+  F +P      D++ ++  L +R+  D+  F+    +Y   G  ++R YLLYGP G
Sbjct: 176 WRT--FGYPRRRRPLDSVVLQQGLADRIVKDIREFIDNPKWYIDRGIPYRRGYLLYGPPG 233

Query: 235 TGKSSFAAAMASFMSYDV-YDVDLSRVADDADLKSLLLQTTSKSVILIEDLD-RFL---- 288
            GKSSF  A+A  + + +           D  L  LL     +S++L+ED+D  FL    
Sbjct: 234 CGKSSFITALAGELEHSICLLSLTDSSLSDDRLNHLLSVAPQQSLVLLEDVDAAFLSRDL 293

Query: 289 -VEKP------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVH 341
            VE P        ++ SG+LN +DGV ++   E R++  T N  D +D AL+RPGR+D+ 
Sbjct: 294 AVENPIKYQGLGRLTFSGLLNALDGVAST---EARIVFMTTNYIDRLDPALIRPGRVDLK 350

Query: 342 IHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIANRNSPSRA 400
            +   C       +   +   +   L     E + +  S +SPA++    +  +N P  A
Sbjct: 351 EYVGYCSHWQLTQMFQRFYPGQAPSLAENFAEHVLKATSEISPAQVQGYFMLYKNDPMGA 410

Query: 401 LKSV 404
           + ++
Sbjct: 411 VHNI 414

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Mus musculus (taxid: 10090)

>sp|Q7ZV60|BCS1_DANRE Mitochondrial chaperone BCS1 OS=Danio rerio GN=bcs1l PE=2 SV=2

 Score = 99.8 bits (247), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 115/237 (48%), Gaps = 34/237 (14%)

Query: 191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY 250
           ++ +E+ +  R+  D++ F+    +Y   G  ++R YLLYGP G GKSSF  A+A  + Y
Sbjct: 190 SVVLESGVAERIVDDVKEFIGNPKWYTDRGIPYRRGYLLYGPPGCGKSSFITALAGELGY 249

Query: 251 DVYDVDLS-RVADDADLKSLLLQTTSKSVILIEDLDRFLV-------EKPAA------VS 296
            +  + LS R   D  L  LL     +S+IL+ED+D   V       E P A      ++
Sbjct: 250 SICLMSLSDRSLSDDRLNHLLSVAPQQSIILLEDVDAAFVSRELLPTENPLAYQGMGRLT 309

Query: 297 LSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLA 356
            SG+LN +DGV +S   E R++  T N  + +D AL+RPGR+D+  +   C       + 
Sbjct: 310 FSGLLNALDGVASS---EARIVFMTTNFIERLDPALVRPGRVDLKQYVGHCSHWQLTQMF 366

Query: 357 SSYLGLKDHKLFPQ---------VEEIFQNGSSLSPAEIGELMIANRNSPSRALKSV 404
                    + +PQ          E+     + LS A++    +  +  P+ A+K++
Sbjct: 367 --------RRFYPQESAAEADHFSEQALAAHTDLSAAQVQGHFMLYKTDPAGAIKNI 415

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Danio rerio (taxid: 7955)

>sp|Q5E9H5|BCS1_BOVIN Mitochondrial chaperone BCS1 OS=Bos taurus GN=BCS1L PE=2 SV=1

 Score = 98.2 bits (243), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 117/244 (47%), Gaps = 22/244 (9%)

Query: 178 WRSVPFTHPS---TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
           WR  PF +P      +++ +E  +  R+  D+  F+    +Y   G  ++R YLLYGP G
Sbjct: 176 WR--PFGYPRRRRPLNSVVLEQGVTERIVRDIREFIDNPKWYIDRGIPYRRGYLLYGPPG 233

Query: 235 TGKSSFAAAMASFMSYDV-YDVDLSRVADDADLKSLLLQTTSKSVILIEDLD-RFLVEKP 292
            GKSSF  A+A  + + +           D  L  LL     +S++L+ED+D  FL    
Sbjct: 234 CGKSSFITALAGELQHSICLLSLTDSSLSDDRLNHLLSVAPQQSLVLLEDVDAAFLSRDL 293

Query: 293 AA-----------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVH 341
           AA           ++ SG+LN +DGV ++   E R++  T N  D +D AL+RPGR+D+ 
Sbjct: 294 AAENPIKYQGLGRLTFSGLLNALDGVAST---EARIVFMTTNHIDRLDPALIRPGRVDMK 350

Query: 342 IHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIANRNSPSRA 400
            +   C       +   +   +   L     + + Q  + +SPA++    +  +N P+ A
Sbjct: 351 EYVGHCSRWQLTQMFQRFYPGQATSLAENFADRVLQATTQISPAQVQGYFMLYKNDPAGA 410

Query: 401 LKSV 404
           +++ 
Sbjct: 411 IQNA 414

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III. Plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex.

Bos taurus (taxid: 9913)

>sp|Q7ZTL7|BCS1_XENLA Mitochondrial chaperone BCS1 OS=Xenopus laevis GN=bcs1l PE=2 SV=1

 Score = 94.4 bits (233), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 59/190 (31%), Positives = 93/190 (48%), Gaps = 17/190 (8%)

Query: 172 DGCCGRWRSVPFTHPS-TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLY 230
           +     WR   F        ++ +E  +  ++  D++ F++   +Y   G  ++R YLLY
Sbjct: 170 NAVGAEWRQFGFPRRRRPLSSVVLEQGISEKIVQDVKGFIENPKWYSDRGIPYRRGYLLY 229

Query: 231 GPSGTGKSSFAAAMASFMSYDV-YDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLV 289
           GP G GKSSF  A+A  + Y +           D  L  LL     +S+IL+ED+D   V
Sbjct: 230 GPPGCGKSSFITALAGELEYSICLMSLSDSSLSDDRLNHLLSVAPQQSIILLEDVDAAFV 289

Query: 290 ------EKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGR 337
                 + P A      ++ SG+LN +DGV ++   E R++  T N  D +D AL+RPGR
Sbjct: 290 SRDLNKQNPTAYQGMGRLTFSGLLNALDGVAST---EARIVFMTTNHIDRLDPALIRPGR 346

Query: 338 IDVHIHFPLC 347
           +DV  +   C
Sbjct: 347 VDVKQYVGHC 356

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Xenopus laevis (taxid: 8355)

>sp|Q54DY9|BCS1B_DICDI Probable mitochondrial chaperone BCS1-B OS=Dictyostelium discoideum GN=bcsl1b PE=3 SV=1

 Score = 94.0 bits (232), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/266 (26%), Positives = 118/266 (44%), Gaps = 46/266 (17%)

Query: 178 WRSVPFTHPS---TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
           WR   F HP       ++ ++      +  D++ FL    +Y+  G  ++R YLLYGP G
Sbjct: 194 WRR--FGHPRRKRPISSVILDKGKSELIIQDVKKFLNNSDWYNDRGIPYRRGYLLYGPPG 251

Query: 235 TGKSSFAAAMASFMSYDVYDVDLS-RVADDADLKSLLLQTTSKSVILIEDLDRFL----- 288
           TGKSSF  A+A  +   +  ++L+ +   D  L  LL     +S+IL+ED+D  +     
Sbjct: 252 TGKSSFITALAGELQLSICILNLAGKSVSDTSLNQLLATAPQRSIILLEDIDSAIQTGNH 311

Query: 289 --------VEKP----------------------AAVSLSGVLNFMDGVLNSCCFEERVM 318
                      P                      +A++ SG+LN +DGV  S   E R++
Sbjct: 312 DLSAKSNSANAPSISSGGLQYQGYYGNPSVSSGGSALTFSGLLNALDGVAAS---EGRIL 368

Query: 319 VFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNG 378
             T N  + +D+ L+RPGR+D+ I   LC     + +   +    D  L  Q  E  +N 
Sbjct: 369 FMTTNHLEKLDKVLIRPGRVDLQIEIGLCSSYQMEQMFLKFYP-TDFDLAKQFVEKLEN- 426

Query: 379 SSLSPAEIGELMIANRNSPSRALKSV 404
              SPA++    +   N+   A+ ++
Sbjct: 427 YKFSPAQLQAYFMTYSNNSIEAINNL 452

Chaperone necessary for the assembly of mitochondrial respiratory chain complex III.

Dictyostelium discoideum (taxid: 44689)

>sp|Q2SF13|FTSH_HAHCH ATP-dependent zinc metalloprotease FtsH OS=Hahella chejuensis (strain KCTC 2396) GN=ftsH PE=3 SV=1

 Score = 70.5 bits (171), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 87/179 (48%), Gaps = 21/179 (11%)

Query: 187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS 246
           +TFD ++ +T+ K  V+ +L  +L+    +HR+G +  R  LL GP GTGK+  A A+A 
Sbjct: 173 TTFDEVAGQTNAKREVQ-ELVEYLRDPDRFHRVGALAPRGVLLMGPPGTGKTLLARALAG 231

Query: 247 FMSYDVYDVDLSRVAD------DADLKSL--LLQTTSKSVILIEDLDRFLVEKPAAV--- 295
               + Y +  S   +       + ++ L  + +  S S+I I++LD     + A     
Sbjct: 232 EAGVNFYPMSASEFIEVFVGVGASRVRQLFKIAKENSPSIIFIDELDSVGRTRGAGYGGG 291

Query: 296 ------SLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCD 348
                 +L+ +L  MDG       +  +++   N  D +D AL+RPGR D H+   L D
Sbjct: 292 HDEREQTLNQILAEMDGF---AGHDAVIVLAATNRPDVLDPALMRPGRFDRHVTLDLPD 347

Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins.

Hahella chejuensis (strain KCTC 2396) (taxid: 349521)

EC: 3

EC: .

EC: 4

EC: .

EC: 2

EC: 4

EC: .

EC: -

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	480
224130620	488	predicted protein [Populus trichocarpa]	0.931	0.915	0.736	0.0
224064334	488	predicted protein [Populus trichocarpa]	0.929	0.913	0.729	0.0
255585257	480	ATP binding protein, putative [Ricinus c	0.935	0.935	0.733	0.0
449432020	481	PREDICTED: ATP-dependent zinc metallopro	0.975	0.972	0.669	0.0
449477963	481	PREDICTED: LOW QUALITY PROTEIN: ATP-depe	0.975	0.972	0.665	1e-180
30690453	491	P-loop containing nucleoside triphosphat	0.972	0.951	0.658	1e-179
356504187	462	PREDICTED: probable mitochondrial chaper	0.929	0.965	0.668	1e-178
356571258	452	PREDICTED: mitochondrial chaperone BCS1-	0.904	0.960	0.682	1e-176
225453553	462	PREDICTED: uncharacterized protein LOC10	0.943	0.980	0.665	1e-172
4415942	459	hypothetical protein [Arabidopsis thalia	0.918	0.960	0.665	1e-170

>gi|224130620|ref|XP_002320886.1| predicted protein [Populus trichocarpa] gi|222861659|gb|EEE99201.1| predicted protein [Populus trichocarpa]

 Score =  696 bits (1795), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 335/455 (73%), Positives = 390/455 (85%), Gaps = 8/455 (1%)

Query: 24  KTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTN 83
           KTGLI++ KKWWR IEDC HV+QFFKVPEFNE MQENQLY KV  YL+SL S+EDSD+TN
Sbjct: 27  KTGLIYITKKWWRSIEDCFHVYQFFKVPEFNESMQENQLYHKVSIYLSSLASMEDSDYTN 86

Query: 84  LFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQD--DSATARTLVLKLRKADRRRILRP 141
           LF GKKSNDI+L LDPNQ+I D FLGA +SW N D  D+   RTLVLK+R+AD+RRILRP
Sbjct: 87  LFAGKKSNDIILHLDPNQVIDDYFLGARVSWINDDKSDTTCCRTLVLKVRRADKRRILRP 146

Query: 142 YLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNR 201
           YLQHIH  SDE+EQKKK  L+L++N+ +       RWRSVPF HPSTFDTI M++DLKN+
Sbjct: 147 YLQHIHITSDEVEQKKK-GLKLYINIGSHEQN--RRWRSVPFNHPSTFDTIVMDSDLKNK 203

Query: 202 VKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA 261
           +KSDLESFLK K YYHRLGR WKRSYLLYGPSGTGKSSF AAMA+F+ YDVY +DLSRV 
Sbjct: 204 LKSDLESFLKTKQYYHRLGRAWKRSYLLYGPSGTGKSSFVAAMANFIGYDVYGIDLSRVL 263

Query: 262 DDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFT 321
           DD+DLK+LLLQTTSKSVILIEDLDRFL++K   VSLSGVLNFMDG+LN+CC EER+MVFT
Sbjct: 264 DDSDLKTLLLQTTSKSVILIEDLDRFLMDKSTGVSLSGVLNFMDGILNACCAEERIMVFT 323

Query: 322 MNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSL 381
           MN KDHVD A+LRPGRIDVHIHFPLCDF++FKTLA+SYLG+KDHKLFPQVEEIF  G+SL
Sbjct: 324 MNGKDHVDPAILRPGRIDVHIHFPLCDFAAFKTLANSYLGVKDHKLFPQVEEIFLTGASL 383

Query: 382 SPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHG 441
           SPAEIGELM+ANRNSPSRALKSVITALQTDG+GRG+ N  R+   + S+KST+ DSGEH 
Sbjct: 384 SPAEIGELMLANRNSPSRALKSVITALQTDGDGRGSLNIRRQWTDNSSRKSTE-DSGEHS 442

Query: 442 GVFSRE--NTVKEFRKLYGLLTLKNSRKSQSFDLA 474
           GVFS+E  + +K+FRKLYGLL  K+++ S+SFD+ 
Sbjct: 443 GVFSKEGVHAMKDFRKLYGLLRFKSNKTSESFDMT 477

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224064334|ref|XP_002301424.1| predicted protein [Populus trichocarpa] gi|222843150|gb|EEE80697.1| predicted protein [Populus trichocarpa]

 Score =  686 bits (1770), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 331/454 (72%), Positives = 389/454 (85%), Gaps = 8/454 (1%)

Query: 23  FKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFT 82
           FKTGLI++ KKWWR IEDC HV+QFFKVPEFNE MQ+N LY +V  YL+S+ SIEDSDF 
Sbjct: 26  FKTGLIYITKKWWRSIEDCFHVYQFFKVPEFNENMQKNHLYCEVSIYLSSIASIEDSDFI 85

Query: 83  NLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQD--DSATARTLVLKLRKADRRRILR 140
           NLFTGKK +DIVL LDPNQ+I D FLGA +SW N++  D+   RT VLK+R+AD+R+ILR
Sbjct: 86  NLFTGKKPHDIVLHLDPNQVIDDYFLGARVSWINEEKNDTNRCRTFVLKIRRADKRKILR 145

Query: 141 PYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKN 200
           PYLQHIH  SDELEQKKK D++L++N+  D      +WRSVPF HPSTFDTI+ME+DLKN
Sbjct: 146 PYLQHIHITSDELEQKKK-DVKLYINI--DSHEQSRQWRSVPFKHPSTFDTIAMESDLKN 202

Query: 201 RVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV 260
           ++KSDLESFLKAKHYYHRLGR WKRSYLLYGPSGTGKSSF AA+A+F+ YDVYD+DLSRV
Sbjct: 203 KLKSDLESFLKAKHYYHRLGRAWKRSYLLYGPSGTGKSSFVAAIANFLGYDVYDIDLSRV 262

Query: 261 ADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF 320
            DD+D+K LLLQTT KSVILIEDLDRFL++K   VSLSG+LNFMDGVLNSCC +ER+MV+
Sbjct: 263 LDDSDMKMLLLQTTCKSVILIEDLDRFLMDKSTRVSLSGILNFMDGVLNSCCADERIMVY 322

Query: 321 TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSS 380
           TMN KDHVD A+LRPGRIDVHIHFPLCDFS+FKTLA++YLG+KDHKLFPQVEE FQ G+S
Sbjct: 323 TMNCKDHVDPAILRPGRIDVHIHFPLCDFSAFKTLANNYLGVKDHKLFPQVEEFFQTGAS 382

Query: 381 LSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEH 440
           LSPAEIGELMIANRNSPSRALKSV+TALQTDG+GRG+ N  R+   + S+KST+ DSGE 
Sbjct: 383 LSPAEIGELMIANRNSPSRALKSVVTALQTDGDGRGSLNIRRQWTDNSSRKSTE-DSGEQ 441

Query: 441 GGVFSRE--NTVKEFRKLYGLLTLKNSRKSQSFD 472
            GVFS+E  N +K+ RKLYGLL LK+ + S+SFD
Sbjct: 442 SGVFSKEGVNAMKDIRKLYGLLRLKSRKNSESFD 475

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585257|ref|XP_002533329.1| ATP binding protein, putative [Ricinus communis] gi|223526834|gb|EEF29050.1| ATP binding protein, putative [Ricinus communis]

 Score =  677 bits (1748), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 336/458 (73%), Positives = 394/458 (86%), Gaps = 9/458 (1%)

Query: 23  FKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFT 82
            KTGLIF+ KK WR  E+  HV+QFFKVPEFNE MQ+NQL+RKV  YLNSL+SIEDSDFT
Sbjct: 26  IKTGLIFLTKKLWRICEEWFHVYQFFKVPEFNESMQDNQLHRKVSVYLNSLSSIEDSDFT 85

Query: 83  NLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPY 142
           NLFTGKKSN+I+L LDPNQ+I D FLG  +SW N+ +S   RTLVLK+RK+D+RRILRPY
Sbjct: 86  NLFTGKKSNEIILRLDPNQVIDDYFLGTRISWINEVNSGATRTLVLKIRKSDKRRILRPY 145

Query: 143 LQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRV 202
           LQHIH VSDELEQK  R+L+L++N  +      GRWR VPFTHPSTF+TI+ME+DLK ++
Sbjct: 146 LQHIHTVSDELEQK--RELKLYMNNHHQN----GRWRFVPFTHPSTFETIAMESDLKTKL 199

Query: 203 KSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD 262
           KSDLESFLKAK YYHRLGRVWKRSYLLYGPSGTGKSSF AAMA+F+SYDVYD+DLS+V D
Sbjct: 200 KSDLESFLKAKQYYHRLGRVWKRSYLLYGPSGTGKSSFVAAMANFLSYDVYDIDLSKVLD 259

Query: 263 DADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM 322
           D+ LK LLLQTT+KSVIL+EDLDRFL++K   VSLSGVLNFMDG+LNSCC EER+MVFTM
Sbjct: 260 DSHLKLLLLQTTTKSVILVEDLDRFLMDKSTDVSLSGVLNFMDGILNSCCAEERIMVFTM 319

Query: 323 NSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLS 382
           NSKDH+D A+LRPGRIDVHIHFP CDFS+FK+LA+SYLG+K+HKLFPQVEEIFQ G+SLS
Sbjct: 320 NSKDHIDPAILRPGRIDVHIHFPTCDFSAFKSLANSYLGVKEHKLFPQVEEIFQAGASLS 379

Query: 383 PAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKS-TDADSGEHG 441
           PAEIGELMIANRNSPSRALKSVITALQT+G+ RG+ N GRRL +SGSK S  + +SGE+ 
Sbjct: 380 PAEIGELMIANRNSPSRALKSVITALQTEGDCRGSVNIGRRLVESGSKGSFVEVESGENS 439

Query: 442 GVFSRE--NTVKEFRKLYGLLTLKNSRKSQSFDLAAAE 477
           G+FSRE  N +K+ RKLYGLL L+++RK QS DL   +
Sbjct: 440 GIFSRESVNAIKDIRKLYGLLRLRSNRKEQSLDLTMGQ 477

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449432020|ref|XP_004133798.1| PREDICTED: ATP-dependent zinc metalloprotease FtsH-like [Cucumis sativus]

 Score =  645 bits (1665), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 318/475 (66%), Positives = 388/475 (81%), Gaps = 7/475 (1%)

Query: 9   LVIG-CLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVY 67
           + IG C  +++R+LLF+TGLIF+ KKWW  +EDC HV+Q F++PEFNE  Q N LYRKV 
Sbjct: 11  IFIGICFSWLLRILLFRTGLIFLVKKWWANLEDCFHVYQSFRIPEFNETSQHNHLYRKVS 70

Query: 68  AYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLV 127
           AYL SL+S+EDSDFTNL TG K NDI+L LD NQ +QDNFLGA + W N+   +  R  V
Sbjct: 71  AYLTSLSSLEDSDFTNLITGNKPNDIILRLDSNQTVQDNFLGAKVFWTNEQKGS--RNFV 128

Query: 128 LKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPS 187
           L++RKAD+RRILRPYLQHIH ++ +  +++K DL+LF+N + + +    RW+S+ F HPS
Sbjct: 129 LRIRKADKRRILRPYLQHIHTLTADENEQRKGDLKLFMNSKPN-NHSDTRWKSIQFKHPS 187

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           TFD+I+METDLK +VKSDLESFLK+K YYHRLGRVWKRSYLLYGPSGTGKSSF AAMA+F
Sbjct: 188 TFDSIAMETDLKEKVKSDLESFLKSKQYYHRLGRVWKRSYLLYGPSGTGKSSFVAAMANF 247

Query: 248 MSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV 307
           +SYDVYD+DL +V+DD+DLK LLLQTTSKSVI++EDLDRFL+EK +A+SLS +LNFMDG+
Sbjct: 248 LSYDVYDIDLFKVSDDSDLKFLLLQTTSKSVIVVEDLDRFLIEKSSALSLSALLNFMDGI 307

Query: 308 LNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL 367
           L SCC EERVMVFT+N K+ V+ A+LRPGRIDVHIHFPLCDFS+FK LA +YLG+KDHKL
Sbjct: 308 LTSCCAEERVMVFTVNCKEQVEPAILRPGRIDVHIHFPLCDFSAFKNLAINYLGVKDHKL 367

Query: 368 FPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKS 427
           FPQVEEIFQ G+SLSPAEI ELMIANRNSPSRA+KSVI+ALQTDG+ R  +N GRRL   
Sbjct: 368 FPQVEEIFQTGASLSPAEISELMIANRNSPSRAIKSVISALQTDGDRRRVSNIGRRLSDC 427

Query: 428 GSKKSTDADSGEHGGVFSRENTV--KEFRKLYGLLTLKNSRKSQSFDLAAAENHS 480
           GS+KS  A+S E GGV   ENT   KEFRKLYG L +K+++ SQSFD +     S
Sbjct: 428 GSRKSV-AESIESGGVVCSENTQTGKEFRKLYGFLRMKSNKISQSFDSSPIRKES 481

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449477963|ref|XP_004155177.1| PREDICTED: LOW QUALITY PROTEIN: ATP-dependent zinc metalloprotease FtsH-like [Cucumis sativus]

 Score =  639 bits (1648), Expect = e-180,   Method: Compositional matrix adjust.
 Identities = 316/475 (66%), Positives = 386/475 (81%), Gaps = 7/475 (1%)

Query: 9   LVIG-CLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVY 67
           + IG C  +++R+LLF+TGLIF+ KKWW  +EDC HV+Q F++PEFNE  Q N LYRKV 
Sbjct: 11  IFIGICFSWLLRILLFRTGLIFLVKKWWANLEDCFHVYQSFRIPEFNETSQHNHLYRKVS 70

Query: 68  AYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLV 127
           AYL SL+S+EDSDFTNL TG K NDI+L LD NQ +QD FLGA + W N+   +  R  V
Sbjct: 71  AYLTSLSSLEDSDFTNLITGNKPNDIILRLDSNQTVQDXFLGAKVFWTNEQKGS--RNFV 128

Query: 128 LKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPS 187
           L++RKAD+RRILRPYLQHIH ++ +  +++K DL+L +N + + +    RW+S+ F HPS
Sbjct: 129 LRIRKADKRRILRPYLQHIHTLTADENEQRKGDLKLXMNSKPN-NHSDTRWKSIQFKHPS 187

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           TFD+I+METDLK +VKSDLESFLK+K YYHRLGRVWKRSYLLYGPSGTGKSSF AAMA+F
Sbjct: 188 TFDSIAMETDLKXKVKSDLESFLKSKQYYHRLGRVWKRSYLLYGPSGTGKSSFVAAMANF 247

Query: 248 MSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV 307
           +SYDVYD+DL +V+DD+DLK LLLQTTSKSVI++EDLDRFL+EK +A+SLS +LNFMDG+
Sbjct: 248 LSYDVYDIDLFKVSDDSDLKFLLLQTTSKSVIVVEDLDRFLIEKSSALSLSALLNFMDGI 307

Query: 308 LNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL 367
           L SCC EERVMVFT+N K+ V+ A+LRPGRIDVHIHFPLCDFS+FK LA +YLG+KDHKL
Sbjct: 308 LTSCCAEERVMVFTVNCKEQVEPAILRPGRIDVHIHFPLCDFSAFKNLAINYLGVKDHKL 367

Query: 368 FPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKS 427
           FPQVEEIFQ G+SLSPAEI ELMIANRNSPSRA+KSVI+ALQTDG+ R  +N GRRL   
Sbjct: 368 FPQVEEIFQTGASLSPAEISELMIANRNSPSRAIKSVISALQTDGDRRRVSNIGRRLSDC 427

Query: 428 GSKKSTDADSGEHGGVFSRENTV--KEFRKLYGLLTLKNSRKSQSFDLAAAENHS 480
           GS+KS  A+S E GGV   ENT   KEFRKLYG L +K+++ SQSFD +     S
Sbjct: 428 GSRKSV-AESIESGGVVCSENTQTGKEFRKLYGFLRMKSNKISQSFDSSPIRKES 481

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30690453|ref|NP_182185.2| P-loop containing nucleoside triphosphate hydrolase-like protein [Arabidopsis thaliana] gi|330255636|gb|AEC10730.1| P-loop containing nucleoside triphosphate hydrolase-like protein [Arabidopsis thaliana]

 Score =  633 bits (1632), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 318/483 (65%), Positives = 383/483 (79%), Gaps = 16/483 (3%)

Query: 4   AIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLY 63
           + ++LLV    LF++R+LLFKTGLI++ K W R I D  HV+QF+KVPEFN+ +QEN LY
Sbjct: 7   SFLLLLVSTFALFLVRILLFKTGLIYMVKLWRRKIIDWFHVYQFYKVPEFNDNVQENHLY 66

Query: 64  RKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATA 123
           +KVY YLNSL+SIE+SDFTNLFTGKKSN+I+L LD NQ++ D FLGA + W N +D   A
Sbjct: 67  QKVYMYLNSLSSIENSDFTNLFTGKKSNEIILRLDRNQVVGDEFLGARVCWINGEDEDGA 126

Query: 124 RTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLR-----NDRDGCCGRW 178
           R  VLK+RKAD+RRIL  YLQHIH VSDELEQ+   +L+LF+N+      N +    GRW
Sbjct: 127 RNFVLKIRKADKRRILGSYLQHIHTVSDELEQRNT-ELKLFINVGIDDHLNKKKKKNGRW 185

Query: 179 RSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKS 238
           RS+PF HP TFD I+METDLKN+VKSDLESFLK K YY+RLGRVWKRSYLLYGPSGTGKS
Sbjct: 186 RSIPFDHPCTFDNIAMETDLKNKVKSDLESFLKGKQYYNRLGRVWKRSYLLYGPSGTGKS 245

Query: 239 SFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLS 298
           SF AAMA+F+ YDVYD+DLS+V DD+DLK LLLQT  KSVI+IEDLDR L  K  AV+LS
Sbjct: 246 SFVAAMANFLDYDVYDIDLSKVVDDSDLKMLLLQTRGKSVIVIEDLDRHLSTKSTAVNLS 305

Query: 299 GVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASS 358
           G+LNF D +L+SC  +ER+MVFTM  K+ +D A+LRPGR+DVHIHFPLCDF++FKTLA++
Sbjct: 306 GILNFTDSILSSCTADERIMVFTMTGKEQIDPAMLRPGRVDVHIHFPLCDFTAFKTLANN 365

Query: 359 YLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAA 418
           YLG+K+HKLF QVE IFQNG+SLSPAEIGELMIANRNSP+RALK VI ALQTDG+ RG  
Sbjct: 366 YLGVKEHKLFSQVEGIFQNGASLSPAEIGELMIANRNSPTRALKHVINALQTDGDRRG-- 423

Query: 419 NAGRR-LDKSGSKKSTDADSGE------HGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF 471
             GRR L ++GS+KST  D  +       GG       VKEFRKLYGLL +K+SRKS SF
Sbjct: 424 -TGRRLLLENGSRKSTSEDVSDDMSGSLCGGGGGSSPAVKEFRKLYGLLRIKSSRKSGSF 482

Query: 472 DLA 474
           D+A
Sbjct: 483 DVA 485

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356504187|ref|XP_003520880.1| PREDICTED: probable mitochondrial chaperone BCS1-B-like [Glycine max]

 Score =  629 bits (1623), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 313/468 (66%), Positives = 369/468 (78%), Gaps = 22/468 (4%)

Query: 5   IIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYR 64
           +I+      +L      LF+TG    AKK WR IED  HV+QFFKVPE N+  Q N LYR
Sbjct: 1   MILFSFTSIVLIAFGATLFQTGH---AKKLWRRIEDWFHVYQFFKVPELNDTTQHNHLYR 57

Query: 65  KVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATAR 124
           KV  YL+SL SIEDSDF NL TGKK NDIVL L PNQ I+D+FLGA L W NQ       
Sbjct: 58  KVSLYLHSLPSIEDSDFANLITGKKQNDIVLCLGPNQTIEDHFLGATLFWFNQ-----TG 112

Query: 125 TLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFT 184
           T +LK+RK D+RRILRPYLQHIHAV+DE++Q+ KRDL LF+N+ +D      RWRSVPFT
Sbjct: 113 TFLLKIRKVDKRRILRPYLQHIHAVADEIDQRGKRDLLLFMNIADD----FRRWRSVPFT 168

Query: 185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAM 244
           HPSTFDT++ME DLK++VKSDLESFL+AK YYHRLGRVWKRS+LLYGPSGTGKSSF AAM
Sbjct: 169 HPSTFDTVAMEPDLKSKVKSDLESFLRAKQYYHRLGRVWKRSFLLYGPSGTGKSSFVAAM 228

Query: 245 ASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFM 304
           A+F+SYDVYD+DL +++ D+DLKSLLLQTT KSV++IEDLDRFL EK A +S SG+LNFM
Sbjct: 229 ANFLSYDVYDIDLCKISSDSDLKSLLLQTTPKSVVVIEDLDRFLAEKTARISASGILNFM 288

Query: 305 DGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKD 364
           D +L SCC EERVMVFTMN+K+HVD  LLRPGR+DVHIHFPLCDFS+FKTLASSYLG+K+
Sbjct: 289 DALLTSCCAEERVMVFTMNTKEHVDPNLLRPGRVDVHIHFPLCDFSAFKTLASSYLGVKE 348

Query: 365 HKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRL 424
           HKLFPQV+EIFQNG+SLSPAEIGELMIANRNSPSRA+KSVITALQTDG+GRG    GR  
Sbjct: 349 HKLFPQVQEIFQNGASLSPAEIGELMIANRNSPSRAIKSVITALQTDGDGRGCGLIGR-- 406

Query: 425 DKSGSKKSTDADSGEHGGVFSRE--NTVKEFRKLYGLLTLKNSRKSQS 470
                 ++ D +  E  GV   E  +TVK+ RKLYG  + + +R+S S
Sbjct: 407 ------QTEDDEMDEPDGVVCGETFHTVKDLRKLYGFFSFRVTRRSSS 448

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356571258|ref|XP_003553796.1| PREDICTED: mitochondrial chaperone BCS1-like [Glycine max]

 Score =  625 bits (1613), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 311/456 (68%), Positives = 363/456 (79%), Gaps = 22/456 (4%)

Query: 20  VLLFKTGLIFVA---KKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSI 76
           + +F + L+ +A   KK W  IED  HV+QFFKVPE NE  Q N LYRKV  YL+SL SI
Sbjct: 3   LFIFLSTLVLIAVRAKKLWIAIEDWFHVYQFFKVPELNETTQHNHLYRKVSLYLHSLPSI 62

Query: 77  EDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRR 136
           EDS F NL TGKK NDIVL L PNQ IQD+FLGA L W NQ       T VLK+RK D+R
Sbjct: 63  EDSVFANLITGKKQNDIVLCLGPNQTIQDHFLGATLFWFNQ-----TGTFVLKIRKVDKR 117

Query: 137 RILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMET 196
           RILRPYLQHIHAV+DE++Q+ KRDLRLF+N  +D     GRWRSVPFTHPSTFDTI+ME 
Sbjct: 118 RILRPYLQHIHAVADEIDQQGKRDLRLFINSAHD----FGRWRSVPFTHPSTFDTIAMEP 173

Query: 197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD 256
           DLK +VKSDLESFL+AK YYHRLGRVWKRS+LLYGPSGTGKSSF AAMA+F+SYDVY++D
Sbjct: 174 DLKTKVKSDLESFLRAKQYYHRLGRVWKRSFLLYGPSGTGKSSFVAAMANFLSYDVYEID 233

Query: 257 LSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEER 316
           L ++ +D+DLKSLLLQ+T KSV++IEDLDRFL +K A +S SG+LNFMDG+L SCC EER
Sbjct: 234 LCKIPNDSDLKSLLLQSTPKSVVVIEDLDRFLADKTARISASGILNFMDGLLTSCCAEER 293

Query: 317 VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQ 376
           VMVFTMN+K+HVD  LLRPGR+DVHIHFPLCDFS+FKTLASSYLG+K+HKLFPQV+EIFQ
Sbjct: 294 VMVFTMNTKEHVDPNLLRPGRVDVHIHFPLCDFSAFKTLASSYLGVKEHKLFPQVQEIFQ 353

Query: 377 NGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTDAD 436
           NG+SLSPAEIGELMIANRNSPSRA+KSVITALQTDG+GRG    GR+ D        D +
Sbjct: 354 NGASLSPAEIGELMIANRNSPSRAIKSVITALQTDGDGRGCGLIGRQTD--------DDE 405

Query: 437 SGEHGGVFSRE--NTVKEFRKLYGLLTLKNSRKSQS 470
             E  GV   E  +TVK+ RKLY     + +R+S S
Sbjct: 406 MDEPDGVVCGEGLHTVKDLRKLYDFFRFRVTRRSSS 441

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453553|ref|XP_002262724.1| PREDICTED: uncharacterized protein LOC100255828 [Vitis vinifera]

 Score =  612 bits (1578), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 310/466 (66%), Positives = 375/466 (80%), Gaps = 13/466 (2%)

Query: 16  FMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTS 75
           + I VL    GL+ VA K W  + D    +Q FKVPEFNE MQ+N LYRKV  Y+NSL +
Sbjct: 5   YPIWVLALVLGLVAVALKKWSRVGDWFQAYQLFKVPEFNENMQDNYLYRKVSVYINSLVA 64

Query: 76  IEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADR 135
           +EDSDFTNLF+GKK+N+IVL LDPNQ + D FLGA +SW N   + + RT VLK+RK D+
Sbjct: 65  LEDSDFTNLFSGKKANEIVLALDPNQTVHDTFLGARVSWTNAH-ANSCRTFVLKIRKKDK 123

Query: 136 RRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCCGRWRSVPFTHPSTFDTISME 195
           RRILRPYLQHIH+V DE EQ+K R++ L++N      G  GRWRSVPF+HPST +TI+M+
Sbjct: 124 RRILRPYLQHIHSVFDEFEQRK-REVSLYMN------GADGRWRSVPFSHPSTLETIAMD 176

Query: 196 TDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV 255
           +DLKNRVKSDLESFLK+K YYHRLGRVWKRS+LLYGPSGTGKSSF AAMA F+ YDVYDV
Sbjct: 177 SDLKNRVKSDLESFLKSKQYYHRLGRVWKRSFLLYGPSGTGKSSFVAAMAKFLCYDVYDV 236

Query: 256 DLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEE 315
           DLSRV+DD+DLK LLLQT +KSVI++EDLDRF+V+K   +S SGVLNFMDG+LNSCC +E
Sbjct: 237 DLSRVSDDSDLKLLLLQTRNKSVIVVEDLDRFVVDKTTTLSFSGVLNFMDGLLNSCCGDE 296

Query: 316 RVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIF 375
           RVMVFTMN+KDH+D A+LRPGR+D+HI+FPLCDF++FKTLA+SYLG+KDHKLFPQ+EEIF
Sbjct: 297 RVMVFTMNTKDHIDPAMLRPGRVDLHIYFPLCDFNAFKTLANSYLGVKDHKLFPQLEEIF 356

Query: 376 QNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRR-LDKSGSKKSTD 434
           Q+G++LSPAEIGE+MI NR+SPSRALKSVITALQ +G+ R  A  G+R  DK        
Sbjct: 357 QSGATLSPAEIGEIMIVNRSSPSRALKSVITALQINGDSRSPAKIGQRSADKPPRPVEEA 416

Query: 435 ADSGEHGGVFSRE--NTVKEFRKLYGLLTLKNSRKSQSFDLAAAEN 478
            D G  GG   RE  +TV+EFRKLYG L LK+SRKS SFDL + +N
Sbjct: 417 GDQG--GGFLCRESVHTVREFRKLYGFLRLKSSRKSGSFDLDSNQN 460

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|4415942|gb|AAD20172.1| hypothetical protein [Arabidopsis thaliana] gi|18700084|gb|AAL77654.1| At2g46620/F13A10.15 [Arabidopsis thaliana] gi|23506091|gb|AAN28905.1| At2g46620/F13A10.15 [Arabidopsis thaliana]

 Score =  604 bits (1557), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 304/457 (66%), Positives = 362/457 (79%), Gaps = 16/457 (3%)

Query: 30  VAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKK 89
           + K W R I D  HV+QF+KVPEFN+ +QEN LY+KVY YLNSL+SIE+SDFTNLFTGKK
Sbjct: 1   MVKLWRRKIIDWFHVYQFYKVPEFNDNVQENHLYQKVYMYLNSLSSIENSDFTNLFTGKK 60

Query: 90  SNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHAV 149
           SN+I+L LD NQ++ D FLGA + W N +D   AR  VLK+RKAD+RRIL  YLQHIH V
Sbjct: 61  SNEIILRLDRNQVVGDEFLGARVCWINGEDEDGARNFVLKIRKADKRRILGSYLQHIHTV 120

Query: 150 SDELEQKKKRDLRLFVNLR-----NDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKS 204
           SDELEQ+   +L+LF+N+      N +    GRWRS+PF HP TFD I+METDLKN+VKS
Sbjct: 121 SDELEQRNT-ELKLFINVGIDDHLNKKKKKNGRWRSIPFDHPCTFDNIAMETDLKNKVKS 179

Query: 205 DLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA 264
           DLESFLK K YY+RLGRVWKRSYLLYGPSGTGKSSF AAMA+F+ YDVYD+DLS+V DD+
Sbjct: 180 DLESFLKGKQYYNRLGRVWKRSYLLYGPSGTGKSSFVAAMANFLDYDVYDIDLSKVVDDS 239

Query: 265 DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS 324
           DLK LLLQT  KSVI+IEDLDR L  K  AV+LSG+LNF D +L+SC  +ER+MVFTM  
Sbjct: 240 DLKMLLLQTRGKSVIVIEDLDRHLSTKSTAVNLSGILNFTDSILSSCTADERIMVFTMTG 299

Query: 325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPA 384
           K+ +D A+LRPGR+DVHIHFPLCDF++FKTLA++YLG+K+HKLF QVE IFQNG+SLSPA
Sbjct: 300 KEQIDPAMLRPGRVDVHIHFPLCDFTAFKTLANNYLGVKEHKLFSQVEGIFQNGASLSPA 359

Query: 385 EIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRR-LDKSGSKKSTDADSGE---- 439
           EIGELMIANRNSP+RALK VI ALQTDG+ RG    GRR L ++GS+KST  D  +    
Sbjct: 360 EIGELMIANRNSPTRALKHVINALQTDGDRRG---TGRRLLLENGSRKSTSEDVSDDMSG 416

Query: 440 --HGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFDLA 474
              GG       VKEFRKLYGLL +K+SRKS SFD+A
Sbjct: 417 SLCGGGGGSSPAVKEFRKLYGLLRIKSSRKSGSFDVA 453

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	480
TAIR|locus:2039981	491	AT2G46620 [Arabidopsis thalian	0.975	0.953	0.618	1.5e-152
TAIR|locus:2174502	520	AT5G57480 [Arabidopsis thalian	0.568	0.525	0.316	1.6e-57
TAIR|locus:505006520	506	AT4G25835 [Arabidopsis thalian	0.568	0.539	0.309	1.1e-56
TAIR|locus:2095512	500	AT3G28580 [Arabidopsis thalian	0.477	0.458	0.329	4.8e-56
TAIR|locus:2098648	510	AT3G28540 [Arabidopsis thalian	0.516	0.486	0.315	2e-55
TAIR|locus:2178067	514	AATP1 "AAA-ATPase 1" [Arabidop	0.470	0.439	0.318	9.5e-53
TAIR|locus:2128916	519	AT4G30250 [Arabidopsis thalian	0.543	0.502	0.302	1.1e-51
TAIR|locus:2098658	530	AT3G28510 [Arabidopsis thalian	0.489	0.443	0.309	1e-50
TAIR|locus:1005716649	495	AT2G18193 [Arabidopsis thalian	0.727	0.705	0.333	1.7e-50
TAIR|locus:2098638	478	AT3G28520 [Arabidopsis thalian	0.489	0.491	0.302	9.8e-50

TAIR|locus:2039981 AT2G46620 [Arabidopsis thaliana (taxid:3702)]

 Score = 1488 (528.9 bits), Expect = 1.5e-152, P = 1.5e-152
 Identities = 298/482 (61%), Positives = 360/482 (74%)

Query:     4 AIIVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLY 63
             + ++LLV    LF++R+LLFKTGLI++ K W R I D  HV+QF+KVPEFN+ +QEN LY
Sbjct:     7 SFLLLLVSTFALFLVRILLFKTGLIYMVKLWRRKIIDWFHVYQFYKVPEFNDNVQENHLY 66

Query:    64 RKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATA 123
             +KVY YLNSL+SIE+SDFTNLFTGKKSN+I+L LD NQ++ D FLGA + W N +D   A
Sbjct:    67 QKVYMYLNSLSSIENSDFTNLFTGKKSNEIILRLDRNQVVGDEFLGARVCWINGEDEDGA 126

Query:   124 RTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLR-----NDRDGCCGRW 178
             R  VLK+RKAD+RRIL  YLQHIH VSDELEQ+   +L+LF+N+      N +    GRW
Sbjct:   127 RNFVLKIRKADKRRILGSYLQHIHTVSDELEQRNT-ELKLFINVGIDDHLNKKKKKNGRW 185

Query:   179 RSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKX 238
             RS+PF HP TFD I+METDLKN+VKSDLESFLK K YY+RLGRVWKRSYLLYGPSGTGK 
Sbjct:   186 RSIPFDHPCTFDNIAMETDLKNKVKSDLESFLKGKQYYNRLGRVWKRSYLLYGPSGTGKS 245

Query:   239 XXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXXVILIEDLDRFLVEKPAAVSLS 298
                        YDVYD+DLS+V DD+D            VI+IEDLDR L  K  AV+LS
Sbjct:   246 SFVAAMANFLDYDVYDIDLSKVVDDSDLKMLLLQTRGKSVIVIEDLDRHLSTKSTAVNLS 305

Query:   299 GVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASS 358
             G+LNF D +L+SC  +ER+MVFTM  K+ +D A+LRPGR+DVHIHFPLCDF++FKTLA++
Sbjct:   306 GILNFTDSILSSCTADERIMVFTMTGKEQIDPAMLRPGRVDVHIHFPLCDFTAFKTLANN 365

Query:   359 YLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEXXXXX 418
             YLG+K+HKLF QVE IFQNG+SLSPAEIGELMIANRNSP+RALK VI ALQTDG+     
Sbjct:   366 YLGVKEHKLFSQVEGIFQNGASLSPAEIGELMIANRNSPTRALKHVINALQTDGDRRGTG 425

Query:   419 XXXXXLDKSGSKKSTDAD-----SGEH-GGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD 472
                  L ++GS+KST  D     SG   GG       VKEFRKLYGLL +K+SRKS SFD
Sbjct:   426 RRL--LLENGSRKSTSEDVSDDMSGSLCGGGGGSSPAVKEFRKLYGLLRIKSSRKSGSFD 483

Query:   473 LA 474
             +A
Sbjct:   484 VA 485

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0009693 "ethylene biosynthetic process" evidence=RCA

TAIR|locus:2174502 AT5G57480 [Arabidopsis thaliana (taxid:3702)]

 Score = 377 (137.8 bits), Expect = 1.6e-57, Sum P(2) = 1.6e-57
 Identities = 92/291 (31%), Positives = 145/291 (49%)

Query:    10 VIGCLLFMIRVL--LFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVY 67
             ++G L F   ++  +F   L F   K++  I      + +F + E  +G+  N+LY  V 
Sbjct:    11 LLGVLAFCQSLMQSIFPPELRFAFLKFFNRIFHVFSSYCYFDITEI-DGVNTNELYNAVQ 69

Query:    68 AYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWAN---QDDSAT-- 122
              YL+S  SI  +  + L     S+ I  GL  N  I D F G  + W +   Q  + T  
Sbjct:    70 LYLSSSVSIAGNRLS-LTRAVNSSSITFGLSNNDSIVDTFNGVTVLWEHVVTQRQTQTFA 128

Query:   123 -------ARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCC 175
                     R   L+++K D+  IL  YL +I   ++E+ ++K +D  L+ N R       
Sbjct:   129 WRPLPEEKRGFTLRIKKKDKTLILNSYLDYIMERANEI-RRKNQDRLLYTNSRGGSLDSR 187

Query:   176 GR-WRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
             G  W SVPF HPSTF+T++M+   K ++  DL+ F + + +Y + GR WKR YLLYGP G
Sbjct:   188 GHPWESVPFKHPSTFETLAMDPRKKQQIMDDLKDFAEGQVFYQKTGRAWKRGYLLYGPPG 247

Query:   235 TGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXXVILIEDLD 285
             TGK            YD+YD++L+ V  +++            +I+IED+D
Sbjct:   248 TGKSSMIAAMANYLGYDIYDLELTEVHSNSELRKLLMKTSSKSIIVIEDID 298

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0009407 "toxin catabolic process" evidence=RCA

GO:0010583 "response to cyclopentenone" evidence=RCA

TAIR|locus:505006520 AT4G25835 [Arabidopsis thaliana (taxid:3702)]

 Score = 364 (133.2 bits), Expect = 1.1e-56, Sum P(2) = 1.1e-56
 Identities = 90/291 (30%), Positives = 140/291 (48%)

Query:    10 VIGCLLFMIRVL--LFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVY 67
             ++G L F   ++  +F   L F   K +           +F + E  +G+  N+LY  V 
Sbjct:    11 LLGVLAFCQSLMNSVFPPELRFAISKLFNKFFKLFSTFCYFDITEI-DGVNTNELYNAVQ 69

Query:    68 AYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWAN---QDDSAT-- 122
              YL+S  SI  +  + L     S+ +  GL  N  I D F    + W +   Q  + T  
Sbjct:    70 LYLSSSVSIAGNRLS-LTRAVNSSSVTFGLSNNDSIVDTFNSVTVVWEHIVTQRQTQTFA 128

Query:   123 -------ARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLFVNLRNDRDGCC 175
                     R   L+++K D+  IL  YL +I   ++E+ ++  +D  L+ N R       
Sbjct:   129 WRPMPEEKRGFTLRIKKKDKNLILDSYLDYIMEKANEI-RRLNQDRLLYTNSRGGSLDSR 187

Query:   176 GR-WRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSG 234
             G  W SVPF HPSTFDT++M+   K ++  DL+ F + + +Y R GR WKR YLLYGP G
Sbjct:   188 GLPWESVPFKHPSTFDTLAMDPVKKQQIMEDLKDFAECQSFYERTGRAWKRGYLLYGPPG 247

Query:   235 TGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXXVILIEDLD 285
             TGK            YD+YD++L+ V  +++            +I+IED+D
Sbjct:   248 TGKSSMIAAMANYLRYDIYDLELTEVKSNSELRKLLMKTSSKSIIVIEDID 298

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2095512 AT3G28580 [Arabidopsis thaliana (taxid:3702)]

 Score = 366 (133.9 bits), Expect = 4.8e-56, Sum P(2) = 4.8e-56
 Identities = 80/243 (32%), Positives = 124/243 (51%)

Query:    55 EGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSW 114
             E  + ++ Y  + +YL+  +S          T K S  IVL +D  + I D+F G  + W
Sbjct:    61 EHFKRSEAYLGIQSYLSKDSSARAKKL-KANTTKGSKSIVLSMDDKEEITDDFEGIRVWW 119

Query:   115 ANQDDSATARTL------------VLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLR 162
              ++ + AT ++             +L+  + DR  I+  YL+H+      +EQK  R+ +
Sbjct:   120 QSKKEGATRQSFSFYPEANEKRYYMLRFHRRDREVIIERYLEHVMREGKTIEQKN-RERK 178

Query:   163 LFVNLRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRV 222
             L+ N      G   +W  V F HP+TFDT++ME + K  +KSDL  F K+K YY ++G+ 
Sbjct:   179 LYSNTPGQSHGNNSKWSHVTFEHPATFDTLAMEENKKEEIKSDLIKFSKSKDYYKKIGKA 238

Query:   223 WKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXXVILIE 282
             WKR YLL+GP GTGK            YDVYD++L+ V D+              +I+IE
Sbjct:   239 WKRGYLLFGPPGTGKSTMIAAMANFLEYDVYDLELTTVKDNTHLRRLLIETSAKSIIVIE 298

Query:   283 DLD 285
             D+D
Sbjct:   299 DID 301

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0009737 "response to abscisic acid stimulus" evidence=IEP;RCA

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0009723 "response to ethylene stimulus" evidence=RCA

TAIR|locus:2098648 AT3G28540 [Arabidopsis thaliana (taxid:3702)]

 Score = 373 (136.4 bits), Expect = 2.0e-55, Sum P(2) = 2.0e-55
 Identities = 83/263 (31%), Positives = 139/263 (52%)

Query:    33 KWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSND 92
             K +  + + +H+ +F +  E ++G++++Q Y  +  YL+S ++   +        K S  
Sbjct:    43 KMFGLVSNSVHI-KFTEYTE-DKGLKKSQAYDLIRNYLSSKSTAR-AQRLKANESKNSKS 99

Query:    93 IVLGLDPNQLIQDNFLGAPLSWA-------NQDDSATARTLVLKLRKADRRRILRPYLQH 145
             +VL LD ++ ++D F G  + W+       +Q DS+  R L L      R  I   YL H
Sbjct:   100 LVLSLDNHEAVEDVFQGVKVVWSLSVWKSNDQADSSEKRYLTLSFHNRYREMITTTYLDH 159

Query:   146 IHAVSDELEQKKKRDLRLFVNLRNDRDGCC---GRWRSVPFTHPSTFDTISMETDLKNRV 202
             +     E+  K  R+ +L+ N  + +D      GRW +VPF HP+TF+T++M+ + K  +
Sbjct:   160 VLREGKEIGLKN-RERKLYTN-NSSQDYSAWREGRWSNVPFDHPATFETLAMDLEKKEGM 217

Query:   203 KSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVAD 262
             K DL  F K K YY ++G+ WKR YLL+GP GTGK            YDVYD++L+ V D
Sbjct:   218 KKDLIKFTKGKDYYRKVGKPWKRGYLLFGPPGTGKSTMISAMANFLEYDVYDLELTTVKD 277

Query:   263 DADXXXXXXXXXXXXVILIEDLD 285
             +++            +++IED+D
Sbjct:   278 NSELKKLMLDTKGKSIVVIEDID 300

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2178067 AATP1 "AAA-ATPase 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 342 (125.4 bits), Expect = 9.5e-53, Sum P(2) = 9.5e-53
 Identities = 79/248 (31%), Positives = 124/248 (50%)

Query:    55 EGMQENQLYRKVYAYLNSLTSIEDSDFT-NLFTGKKSNDIVLGLDPNQLIQDNFLGAPLS 113
             E  + + +Y  + +YL+  +S      T N   G KS  I+L +D ++ I D F G  + 
Sbjct:    62 ERFKRSDVYDAIQSYLSKDSSSRAKKLTANTIKGNKS--IILSMDDHEEITDEFQGVKVW 119

Query:   114 WANQDDSATARTL------------VLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDL 161
             W ++   + +R +            +LK  + DR  I + YL H+ +    +E K  R+ 
Sbjct:   120 WQSKKHQSESRAISFYPKADESRFYMLKFHRRDREVITKKYLNHVISEGKTIEVKN-RER 178

Query:   162 RLFVNLRNDRDGCCG----RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYH 217
             +L+ N  N      G    +W  V F HP+TFDT++ME   K  +K+DL  F  +K YY 
Sbjct:   179 KLYSN--NPSQNWSGYKQTKWSHVTFEHPATFDTLAMEYKKKEEIKNDLIKFSNSKDYYK 236

Query:   218 RLGRVWKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXX 277
             ++G+ WKR YLL+GP GTGK            YDVYD++L+ V D+ +            
Sbjct:   237 KIGKAWKRGYLLFGPPGTGKSTMIAAMANLLEYDVYDLELTTVKDNTELRRLLIETSGKS 296

Query:   278 VILIEDLD 285
             +I+IED+D
Sbjct:   297 IIVIEDID 304

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

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

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0010154 "fruit development" evidence=IMP

GO:0010431 "seed maturation" evidence=IMP

GO:0001666 "response to hypoxia" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2128916 AT4G30250 [Arabidopsis thaliana (taxid:3702)]

 Score = 327 (120.2 bits), Expect = 1.1e-51, Sum P(2) = 1.1e-51
 Identities = 84/278 (30%), Positives = 132/278 (47%)

Query:    54 NEGMQENQLYRKVYAYLN-SLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPL 112
             NE     QLY      +N +++S  ++   +L     S+ +  GL  N  I D F G  +
Sbjct:    62 NELYNAVQLYLSSSVTVNDAVSSSNNNTRLSLTRVPNSSSVTFGLSNNDRITDVFNGVTI 121

Query:   113 SWAN-----QDDSATARTL-------VLKLRKADRRRILRPYLQHIHAVSDELEQKKKRD 160
              W +     Q  S + R +        L++ K D+  +L  YL +I   S+E+ ++ +  
Sbjct:   122 LWEHVVVQRQVQSFSWRPMPEEKRGFTLQINKRDKALVLDSYLDYIVGKSEEIRRRNEER 181

Query:   161 LRLFVNLRN-DRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRL 219
             L L+ N R    D     W SV F HPSTFDT++M+ + K R+  DL  F   + +Y + 
Sbjct:   182 L-LYTNSRGVSLDARSHPWDSVRFKHPSTFDTLAMDPEKKKRIMEDLREFANGQGFYQKT 240

Query:   220 GRVWKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXXVI 279
             GR WKR YLLYGP GTGK            YD+YD++L+ V ++++            +I
Sbjct:   241 GRAWKRGYLLYGPPGTGKSSLIAAMANYLGYDIYDLELTEVQNNSELRKLLMKTSSKSII 300

Query:   280 LIEDLDRF--LVEKPAAVSLSGVLNFMDGVLNSCCFEE 315
             +IED+D    L ++      +G   +  G+ N    EE
Sbjct:   301 VIEDIDCSISLTKRGKNKKKNGSYEYDPGLTNGSGLEE 338

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

TAIR|locus:2098658 AT3G28510 [Arabidopsis thaliana (taxid:3702)]

 Score = 329 (120.9 bits), Expect = 1.0e-50, Sum P(2) = 1.0e-50
 Identities = 78/252 (30%), Positives = 123/252 (48%)

Query:    49 KVPEF-NEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQDNF 107
             K  E+ +EG++ +Q Y  +  YL S ++          T K S  +V  +D ++ I+D F
Sbjct:    55 KFTEYTDEGLKRSQAYDSIRNYLASKSTALAKRLKANET-KNSKSLVFSMDDHEEIEDEF 113

Query:   108 LGAPLSW-AN-----------QDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQ 155
              G  + W +N           Q  S   R   L   +  R  I+  YL H+      +  
Sbjct:   114 EGVKVKWYSNVKVIQPQSNYGQRSSEERRHFTLSFHRRHRGMIIETYLDHVLREGKAIGL 173

Query:   156 KKKRDLRLFVNLRNDR--DGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAK 213
                R+ +L+ N  +        G+W +VPF HP+TF+T++M+ + K  +K DL  F K K
Sbjct:   174 MN-RERKLYTNNSSQEWYPWRSGKWSNVPFHHPATFETLAMDPEKKEGIKKDLIKFSKGK 232

Query:   214 HYYHRLGRVWKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXX 273
              YY ++G+ WKR YLL+GP GTGK            YDVYD++L+ V D+++        
Sbjct:   233 DYYKKVGKPWKRGYLLFGPPGTGKSTMIAAIANFLDYDVYDLELTTVKDNSELKKLLLDT 292

Query:   274 XXXXVILIEDLD 285
                 +I+IED+D
Sbjct:   293 TSKSIIVIEDID 304

GO:0000166 "nucleotide binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0001666 "response to hypoxia" evidence=RCA

GO:0009862 "systemic acquired resistance, salicylic acid mediated signaling pathway" evidence=RCA

GO:0010310 "regulation of hydrogen peroxide metabolic process" evidence=RCA

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:1005716649 AT2G18193 [Arabidopsis thaliana (taxid:3702)]

 Score = 525 (189.9 bits), Expect = 1.7e-50, P = 1.7e-50
 Identities = 127/381 (33%), Positives = 205/381 (53%)

Query:    54 NEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGK--KSNDIVLGLDPNQLIQDNFLGAP 111
             N G+  NQ++     YL S    E      L  GK  K     + ++  + I D F  + 
Sbjct:    66 NFGLNRNQVFDAAEMYLRSKIGPETE---RLRVGKIPKQKHFTISIERGEEILDTFEESE 122

Query:   112 LSWA-----NQDDSATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKKRDLRLF-- 164
             + W+     N+      R   L   K  R ++L  YL H+ A S+E++ +  R ++L+  
Sbjct:   123 VKWSYVQSENEKGDKVKRYYELTFEKKLRDKVLNSYLTHVVAESEEIK-RNLRVVKLYSR 181

Query:   165 -VNLRNDRDGCCG-RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRV 222
              V   +D DG  G  W  +   HPSTFDT++M+ + K ++  DLE FLK K +Y R+G+ 
Sbjct:   182 DVYASDDDDGMAGGNWGCINLEHPSTFDTLAMDPNAKKKIIDDLERFLKRKEFYKRVGKA 241

Query:   223 WKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXXXXXVILIE 282
             WKR YLLYGP GTGK            +DV+D++LS + D+ +            +++IE
Sbjct:   242 WKRGYLLYGPPGTGKSSLIAAMANYLKFDVFDLELSSIYDNGELKRVLLSTTNRSILVIE 301

Query:   283 DLD--RFLVEKPAA----------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ 330
             D+D    + ++ A           V+LSG+LNF+DG+ +S   +ER++VFT N K+ +D 
Sbjct:   302 DIDCNAEVRDREAENQEDEQIKGKVTLSGILNFIDGLWSSFG-DERIIVFTTNHKERLDP 360

Query:   331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK--DHKLFPQVEEIFQNGSSLSPAEIGE 388
             ALLRPGR+DVHI+   C    F+TL S+YLGL   +H L  ++E +  + + ++PAE+ E
Sbjct:   361 ALLRPGRMDVHINMSYCTGLGFRTLVSNYLGLDGLNHPLCEEIEALVDS-TEVTPAELAE 419

Query:   389 LMIANRNSPSRALKSVITALQ 409
              ++ + ++    L+ VI+ ++
Sbjct:   420 ELMQDDDTDV-VLRGVISFVE 439

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005783 "endoplasmic reticulum" evidence=IDA

TAIR|locus:2098638 AT3G28520 [Arabidopsis thaliana (taxid:3702)]

 Score = 330 (121.2 bits), Expect = 9.8e-50, Sum P(2) = 9.8e-50
 Identities = 76/251 (30%), Positives = 125/251 (49%)

Query:    47 FFKVPEFN-EGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPNQLIQD 105
             + + PE+  EG+ +++ Y ++  YL+S+++            + S  +VL LD ++ +  
Sbjct:    43 YIRFPEYTGEGLSKSRAYDEIGNYLSSISTARAKRL-KAKESENSKSLVLCLDDDEAVVV 101

Query:   106 NFLGAPLSWAN----QDD---SATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQKKK 158
              F G  + W++    ++D   S   R L L      R  I   Y+ H+     E+  K  
Sbjct:   102 VFQGVNVVWSSTVVDKEDKHNSKEGRYLTLTFENHHRDIITNTYIDHVLREGKEIALKN- 160

Query:   159 RDLRLFVNLRNDRDGCC----GRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKH 214
             R+ +L+ N  ND         G W +VPF H ++F+T+ M+ D K  +K DL  F K K 
Sbjct:   161 RERKLYTN--NDSSSYSSWWEGLWSNVPFNHHASFETLGMDLDKKEEIKKDLIKFTKGKD 218

Query:   215 YYHRLGRVWKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLSRVADDADXXXXXXXXX 274
             YY ++ + WKR YLL+GP GTGK            YDVYD++L+ V D+A+         
Sbjct:   219 YYRKVAKPWKRGYLLFGPPGTGKSTMISAIANFLEYDVYDLELTTVKDNAELKKLMLDTK 278

Query:   275 XXXVILIEDLD 285
                +++IED+D
Sbjct:   279 GKSIVVIEDID 289

GO:0000166 "nucleotide binding" evidence=IEA

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

GO:0005886 "plasma membrane" evidence=ISM

GO:0016887 "ATPase activity" evidence=ISS

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

GO:0005739 "mitochondrion" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: eugene3.00140479 hypothetical protein (489 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	480
pfam00004	131	pfam00004, AAA, ATPase family associated with vari	1e-16
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	2e-12
pfam14363	100	pfam14363, AAA_assoc, Domain associated at C-termi	7e-11
cd00009	151	cd00009, AAA, The AAA+ (ATPases Associated with a	3e-09
COG0465	596	COG0465, HflB, ATP-dependent Zn proteases [Posttra	7e-09
PTZ00454	398	PTZ00454, PTZ00454, 26S protease regulatory subuni	3e-08
CHL00176	638	CHL00176, ftsH, cell division protein; Validated	1e-07
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	1e-06
COG1222	406	COG1222, RPT1, ATP-dependent 26S proteasome regula	1e-06
TIGR01243	733	TIGR01243, CDC48, AAA family ATPase, CDC48 subfami	2e-06
TIGR01241	495	TIGR01241, FtsH_fam, ATP-dependent metalloprotease	2e-06
smart00382	148	smart00382, AAA, ATPases associated with a variety	2e-06
PTZ00361	438	PTZ00361, PTZ00361, 26 proteosome regulatory subun	4e-06
TIGR01242	364	TIGR01242, 26Sp45, 26S proteasome subunit P45 fami	2e-05
PRK10733	644	PRK10733, hflB, ATP-dependent metalloprotease; Rev	4e-05
COG0464	494	COG0464, SpoVK, ATPases of the AAA+ class [Posttra	5e-04
PRK04195	482	PRK04195, PRK04195, replication factor C large sub	5e-04
PRK03992	389	PRK03992, PRK03992, proteasome-activating nucleoti	0.001

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

 Score = 76.1 bits (188), Expect = 1e-16
 Identities = 39/135 (28%), Positives = 63/135 (46%), Gaps = 19/135 (14%)

Query: 227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------DADLKSLL--LQTTSKSV 278
            LLYGP GTGK++ A A+A  +     ++  S +        +  L+ L    +  +  V
Sbjct: 1   LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCV 60

Query: 279 ILIEDLDRFL------VEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM-NSKDHVDQA 331
           I I+++D          +  +   ++ +L  +DG  +S     +V+V    N  D +D A
Sbjct: 61  IFIDEIDALAGSRGSGGDSESRRVVNQLLTELDGFTSS---LSKVIVIAATNRPDKLDPA 117

Query: 332 LLRPGRIDVHIHFPL 346
           LLR GR D  I FPL
Sbjct: 118 LLR-GRFDRIIEFPL 131

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

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

 Score = 69.1 bits (169), Expect = 2e-12
 Identities = 64/237 (27%), Positives = 95/237 (40%), Gaps = 40/237 (16%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           T D I    + K  +K  +E+ LK    + +LG    +  LLYGP GTGK+  A A+A  
Sbjct: 240 TLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALE 299

Query: 248 MSYDVYDVDLS---------------RVADDADLKSLLLQTTSKSVILIEDLDRFLVEKP 292
                  V  S                + + A          + S+I I+++D     + 
Sbjct: 300 SRSRFISVKGSELLSKWVGESEKNIRELFEKARKL-------APSIIFIDEIDSLASGRG 352

Query: 293 AAVSLSG------VLNFMDGVLNSCCFEERVMVFTM-NSKDHVDQALLRPGRIDVHIHFP 345
            +   SG      +L  +DG+  +    E V+V    N  D +D ALLRPGR D  I+ P
Sbjct: 353 PSEDGSGRRVVGQLLTELDGIEKA----EGVLVIAATNRPDDLDPALLRPGRFDRLIYVP 408

Query: 346 LCDFSSFKTLASSYLGLKDHKLFPQV--EEIFQNGSSLSPAEIGEL-----MIANRN 395
           L D      +   +L  K   L   V  EE+ +     S A+I  L     + A R 
Sbjct: 409 LPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALRE 465

Length = 494

>gnl|CDD|222710 pfam14363, AAA_assoc, Domain associated at C-terminal with AAA

 Score = 58.4 bits (142), Expect = 7e-11
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 4/89 (4%)

Query: 29  FVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGK 88
           +++    R        +    + E+ +G   NQLY    AYL++  S   +        K
Sbjct: 9   YLSSLLRRLFGSRFSPYLTIVIDEY-DGFSRNQLYDAAEAYLSTKISP-SARRLKASKAK 66

Query: 89  KSN--DIVLGLDPNQLIQDNFLGAPLSWA 115
           KS    +VL LD  + + D F G  + W 
Sbjct: 67  KSKNSSLVLSLDDGEEVTDVFEGVKVWWT 95

This domain is found in association with the AAA family, pfam00004. Length = 100

>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 = 55.2 bits (133), Expect = 3e-09
 Identities = 29/138 (21%), Positives = 52/138 (37%), Gaps = 20/138 (14%)

Query: 224 KRSYLLYGPSGTGKSSFAAAMA---SFMSYDVYDVDLSRVADDADLKSL----------- 269
            ++ LLYGP GTGK++ A A+A            ++ S + +   +  L           
Sbjct: 19  PKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFE 78

Query: 270 LLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM-NSKDHV 328
           L +     V+ I+++D            + +L  ++ + +     E V V    N     
Sbjct: 79  LAEKAKPGVLFIDEIDSLSRGA-----QNALLRVLETLNDLRIDRENVRVIGATNRPLLG 133

Query: 329 DQALLRPGRIDVHIHFPL 346
           D       R+D+ I  PL
Sbjct: 134 DLDRALYDRLDIRIVIPL 151

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. Length = 151

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

 Score = 57.7 bits (140), Expect = 7e-09
 Identities = 54/174 (31%), Positives = 68/174 (39%), Gaps = 42/174 (24%)

Query: 204 SDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-------FMSYDVYD-- 254
           S+L  FLK    Y  LG    +  LL GP GTGK+  A A+A         +S   +   
Sbjct: 163 SELVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM 222

Query: 255 ---VDLSRVADDADLKSLLLQT--TSKSVILIEDLDRFLVEKPAAVSLSG-------VLN 302
              V  SRV D      L  Q    +  +I I+++D   V +     L G        LN
Sbjct: 223 FVGVGASRVRD------LFEQAKKNAPCIIFIDEID--AVGRQRGAGLGGGNDEREQTLN 274

Query: 303 ----FMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDVHIHFPLCDF 349
                MDG      F     V  +   N  D +D ALLRPGR D  I   L D 
Sbjct: 275 QLLVEMDG------FGGNEGVIVIAATNRPDVLDPALLRPGRFDRQILVELPDI 322

Length = 596

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

 Score = 55.2 bits (133), Expect = 3e-08
 Identities = 53/174 (30%), Positives = 75/174 (43%), Gaps = 34/174 (19%)

Query: 199 KNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS 258
           K  ++  +E  L     Y ++G    R  LLYGP GTGK+  A A+A   +     V   
Sbjct: 154 KQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRV--- 210

Query: 259 RVADDADLKSL------------LLQTTSKSVILIEDLD-----RFLVEKPAAVSLSGVL 301
            V  +   K L            L +  + S+I I+++D     RF  +  A   +  +L
Sbjct: 211 -VGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRIL 269

Query: 302 ----NFMDGVLNSCCFEERVMV---FTMNSKDHVDQALLRPGRIDVHIHFPLCD 348
               N MDG      F++   V      N  D +D ALLRPGR+D  I FPL D
Sbjct: 270 LELLNQMDG------FDQTTNVKVIMATNRADTLDPALLRPGRLDRKIEFPLPD 317

Length = 398

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

 Score = 53.5 bits (129), Expect = 1e-07
 Identities = 53/193 (27%), Positives = 80/193 (41%), Gaps = 49/193 (25%)

Query: 188 TFDTIS-METDLKNRVKSDLE---SFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAA 243
           TF  I+ +E       K + E   SFLK    +  +G    +  LL GP GTGK+  A A
Sbjct: 181 TFRDIAGIEE-----AKEEFEEVVSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKA 235

Query: 244 MA-------------SFMSYDVYDVDLSRVADDADLKSLLLQTTSKS--VILIEDLDRFL 288
           +A              F+   V  V  +RV D      L  +    S  ++ I+++D   
Sbjct: 236 IAGEAEVPFFSISGSEFVEMFV-GVGAARVRD------LFKKAKENSPCIVFIDEIDAVG 288

Query: 289 VEKPAAV---------SLSGVLNFMDGVLNSCCFEER---VMVFTMNSKDHVDQALLRPG 336
            ++ A +         +L+ +L  MDG      F+     +++   N  D +D ALLRPG
Sbjct: 289 RQRGAGIGGGNDEREQTLNQLLTEMDG------FKGNKGVIVIAATNRVDILDAALLRPG 342

Query: 337 RIDVHIHFPLCDF 349
           R D  I   L D 
Sbjct: 343 RFDRQITVSLPDR 355

Length = 638

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

 Score = 50.7 bits (121), Expect = 1e-06
 Identities = 41/172 (23%), Positives = 80/172 (46%), Gaps = 23/172 (13%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           T++ I    + K +++  +E  +K    +  LG    +  LLYGP GTGK+  A A+A+ 
Sbjct: 176 TYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANE 235

Query: 248 MSYDVYDVD----LSRVADDAD--LKSLL--LQTTSKSVILIEDLDRFLVEKPAAVS--- 296
                  ++    +S+   +++  L+ +    +  + S+I I+++D    ++        
Sbjct: 236 AGAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVE 295

Query: 297 ---LSGVLNFMDGVLNSCCFEER---VMVFTMNSKDHVDQALLRPGRIDVHI 342
              ++ +L  MDG+      + R   +++   N  D +D AL RPGR D  I
Sbjct: 296 KRVVAQLLTLMDGL------KGRGRVIVIGATNRPDALDPALRRPGRFDREI 341

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

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

 Score = 50.3 bits (121), Expect = 1e-06
 Identities = 48/163 (29%), Positives = 65/163 (39%), Gaps = 66/163 (40%)

Query: 228 LLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQ--------------- 272
           LLYGP GTGK+  A A+A+       D    RV       S L+Q               
Sbjct: 189 LLYGPPGTGKTLLAKAVANQT-----DATFIRVV-----GSELVQKYIGEGARLVRELFE 238

Query: 273 ---TTSKSVILIEDLD------------------RFLVEKPAAVSLSGVLNFMDGVLNSC 311
                + S+I I+++D                  R ++E         +LN +DG     
Sbjct: 239 LAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLE---------LLNQLDG----- 284

Query: 312 CFEER----VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFS 350
            F+ R    V++ T N  D +D ALLRPGR D  I FPL D  
Sbjct: 285 -FDPRGNVKVIMAT-NRPDILDPALLRPGRFDRKIEFPLPDEE 325

Length = 406

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

 Score = 49.9 bits (119), Expect = 2e-06
 Identities = 44/184 (23%), Positives = 84/184 (45%), Gaps = 23/184 (12%)

Query: 181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSF 240
           VP      +  I    ++K  ++  +E  LK    + ++G    +  LL+GP GTGK+  
Sbjct: 447 VPNVR---WSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLL 503

Query: 241 AAAMAS-----FMSYDVYDVDLSRVADDAD--LKSLL--LQTTSKSVILIEDLDRFLVEK 291
           A A+A+     F++    ++ LS+   +++  ++ +    +  + ++I  +++D     +
Sbjct: 504 AKAVATESGANFIAVRGPEI-LSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPAR 562

Query: 292 PAAVS-------LSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHF 344
            A          ++ +L  MDG+         V++   N  D +D ALLRPGR D  I  
Sbjct: 563 GARFDTSVTDRIVNQLLTEMDGIQEL---SNVVVIAATNRPDILDPALLRPGRFDRLILV 619

Query: 345 PLCD 348
           P  D
Sbjct: 620 PPPD 623

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

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

 Score = 50.0 bits (120), Expect = 2e-06
 Identities = 50/170 (29%), Positives = 68/170 (40%), Gaps = 40/170 (23%)

Query: 208 SFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA-----SFMSYDVYD-------V 255
            FLK    + +LG    +  LL GP GTGK+  A A+A      F S    D       V
Sbjct: 72  DFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGV 131

Query: 256 DLSRVADDADLKSLLLQTTSK---SVILIEDLDRFLVEKPAAVS---------LSGVLNF 303
             SRV D       L +   K    +I I+++D    ++ A +          L+ +L  
Sbjct: 132 GASRVRD-------LFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVE 184

Query: 304 MDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDVHIHFPLCDFS 350
           MDG      F     V  +   N  D +D ALLRPGR D  +   L D  
Sbjct: 185 MDG------FGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIK 228

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

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

 Score = 47.4 bits (112), Expect = 2e-06
 Identities = 29/150 (19%), Positives = 56/150 (37%), Gaps = 28/150 (18%)

Query: 224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLKSL----------- 269
               L+ GP G+GK++ A A+A  +      V  +D   + ++   + L           
Sbjct: 2   GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASG 61

Query: 270 -----------LLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVM 318
                      L +     V++++++   L  +  A+ L      +  +L S   +   +
Sbjct: 62  SGELRLRLALALARKLKPDVLILDEITSLLDAEQEALLLLLEELRLLLLLKS--EKNLTV 119

Query: 319 VFTMNSKDHVDQALLRPGRIDVHIHFPLCD 348
           + T N +  +  ALLR  R D  I   L  
Sbjct: 120 ILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. Length = 148

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

 Score = 48.6 bits (116), Expect = 4e-06
 Identities = 48/177 (27%), Positives = 76/177 (42%), Gaps = 46/177 (25%)

Query: 202 VKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV------ 255
           +K  +E  L     Y  +G    +  +LYGP GTGK+  A A+A+  S     V      
Sbjct: 195 IKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELI 254

Query: 256 ------------DLSRVADDADLKSLLLQTTSKSVILIEDLD-----RFLV----EKPAA 294
                       +L RVA++           + S++ I+++D     R+      EK   
Sbjct: 255 QKYLGDGPKLVRELFRVAEE----------NAPSIVFIDEIDAIGTKRYDATSGGEKEIQ 304

Query: 295 VSLSGVLNFMDGVLNSCCFEERV---MVFTMNSKDHVDQALLRPGRIDVHIHFPLCD 348
            ++  +LN +DG      F+ R    ++   N  + +D AL+RPGRID  I FP  D
Sbjct: 305 RTMLELLNQLDG------FDSRGDVKVIMATNRIESLDPALIRPGRIDRKIEFPNPD 355

Length = 438

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

 Score = 46.3 bits (110), Expect = 2e-05
 Identities = 50/171 (29%), Positives = 77/171 (45%), Gaps = 32/171 (18%)

Query: 202 VKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA-----SFMSYDVYDVD 256
           ++  +E  LK    +  +G    +  LLYGP GTGK+  A A+A     +F+   V   +
Sbjct: 134 IREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIR--VVGSE 191

Query: 257 LSR--VADDADLKSLLLQTT---SKSVILIEDLDRFLVEKPAAVSLSG----------VL 301
           L R  + + A L   + +     + S+I I+++D  +  K      SG          +L
Sbjct: 192 LVRKYIGEGARLVREIFELAKEKAPSIIFIDEIDA-IAAKRTDSGTSGDREVQRTLMQLL 250

Query: 302 NFMDGVLNSCCFEER---VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF 349
             +DG      F+ R    ++   N  D +D ALLRPGR D  I  PL DF
Sbjct: 251 AELDG------FDPRGNVKVIAATNRPDILDPALLRPGRFDRIIEVPLPDF 295

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

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

 Score = 45.8 bits (108), Expect = 4e-05
 Identities = 49/186 (26%), Positives = 83/186 (44%), Gaps = 35/186 (18%)

Query: 187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS 246
           +TF  ++   + K  V ++L  +L+    + +LG    +  L+ GP GTGK+  A A+A 
Sbjct: 149 TTFADVAGCDEAKEEV-AELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG 207

Query: 247 -----FMSYDVYD-------VDLSRVADDADLKSLLLQTTSKS---VILIEDLDRFLVEK 291
                F +    D       V  SRV D       + +   K+   +I I+++D    ++
Sbjct: 208 EAKVPFFTISGSDFVEMFVGVGASRVRD-------MFEQAKKAAPCIIFIDEIDAVGRQR 260

Query: 292 PAAV---------SLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHI 342
            A +         +L+ +L  MDG   +   E  +++   N  D +D ALLRPGR D  +
Sbjct: 261 GAGLGGGHDEREQTLNQMLVEMDGFEGN---EGIIVIAATNRPDVLDPALLRPGRFDRQV 317

Query: 343 HFPLCD 348
              L D
Sbjct: 318 VVGLPD 323

Length = 644

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

 Score = 42.1 bits (99), Expect = 5e-04
 Identities = 35/134 (26%), Positives = 60/134 (44%), Gaps = 17/134 (12%)

Query: 228 LLYGPSGTGKSSFAAAMAS----FMSYDV-YDVDLSRVADDADLKSLL--LQTTSKSVIL 280
           LL+GP GTGK+  A A+A+    F+S +    +       +  L+ L    +  + S+I 
Sbjct: 22  LLHGPPGTGKTLLARALANEGAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIF 81

Query: 281 IEDLDRFLVEKPAAVSLSG------VLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLR 334
           I+++D    ++ +            +L  MDG+       + +++   N  D +D A  R
Sbjct: 82  IDEIDALAPKRSSDQGEVERRVVAQLLALMDGL----KRGQVIVIGATNRPDGLDPAKRR 137

Query: 335 PGRIDVHIHFPLCD 348
           PGR D  I   L D
Sbjct: 138 PGRFDREIEVNLPD 151

Length = 494

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

 Score = 42.2 bits (100), Expect = 5e-04
 Identities = 30/106 (28%), Positives = 49/106 (46%), Gaps = 18/106 (16%)

Query: 186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA 245
           P T   +      K +++  +ES+LK K          K++ LLYGP G GK+S A A+A
Sbjct: 10  PKTLSDVVGNEKAKEQLREWIESWLKGKP---------KKALLLYGPPGVGKTSLAHALA 60

Query: 246 SFMSYDVYDV---------DLSRVADDADLKSLLLQTTSKSVILIE 282
           +   ++V ++          + RVA +A     L     K ++L E
Sbjct: 61  NDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARRKLILLDE 106

Length = 482

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

 Score = 41.0 bits (97), Expect = 0.001
 Identities = 46/161 (28%), Positives = 64/161 (39%), Gaps = 64/161 (39%)

Query: 228 LLYGPSGTGKSSFAAAM-----ASFMSYDVYDVDLSRVA----------DDADLKSLLLQ 272
           LLYGP GTGK+  A A+     A+F+          RV           + A L   L +
Sbjct: 169 LLYGPPGTGKTLLAKAVAHETNATFI----------RVVGSELVQKFIGEGARLVRELFE 218

Query: 273 TTSK---SVILIEDLDRFLVEKPAAV-------SLSG----------VLNFMDGVLNSCC 312
              +   S+I I+++D        A+         SG          +L  MDG      
Sbjct: 219 LAREKAPSIIFIDEID--------AIAAKRTDSGTSGDREVQRTLMQLLAEMDG------ 264

Query: 313 FEER----VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF 349
           F+ R    ++  T N  D +D A+LRPGR D  I  PL D 
Sbjct: 265 FDPRGNVKIIAAT-NRIDILDPAILRPGRFDRIIEVPLPDE 304

Length = 389

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	480
KOG0743	457	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG1222	406	RPT1 ATP-dependent 26S proteasome regulatory subun	100.0
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	100.0
KOG0734	752	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0733	802	consensus Nuclear AAA ATPase (VCP subfamily) [Post	100.0
KOG0736	953	consensus Peroxisome assembly factor 2 containing	100.0
KOG0726	440	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0727	408	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0731	774	consensus AAA+-type ATPase containing the peptidas	100.0
KOG0728	404	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00454	398	26S protease regulatory subunit 6B-like protein; P	100.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	100.0
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	100.0
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	100.0
COG0465	596	HflB ATP-dependent Zn proteases [Posttranslational	100.0
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	100.0
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	100.0
PRK03992	389	proteasome-activating nucleotidase; Provisional	100.0
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	100.0
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	100.0
PTZ00361	438	26 proteosome regulatory subunit 4-like protein; P	100.0
TIGR01241	495	FtsH_fam ATP-dependent metalloprotease FtsH. HflB(	100.0
CHL00195	489	ycf46 Ycf46; Provisional	100.0
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	100.0
TIGR03689	512	pup_AAA proteasome ATPase. In the Actinobacteria,	100.0
CHL00176	638	ftsH cell division protein; Validated	100.0
TIGR01242	364	26Sp45 26S proteasome subunit P45 family. Many pro	99.98
CHL00206	2281	ycf2 Ycf2; Provisional	99.97
KOG0651	388	consensus 26S proteasome regulatory complex, ATPas	99.97
PRK10733	644	hflB ATP-dependent metalloprotease; Reviewed	99.97
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.97
KOG0730	693	consensus AAA+-type ATPase [Posttranslational modi	99.97
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	99.96
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	99.96
PLN00020	413	ribulose bisphosphate carboxylase/oxygenase activa	99.96
PF14363	98	AAA_assoc: Domain associated at C-terminal with AA	99.86
PF05496	233	RuvB_N: Holliday junction DNA helicase ruvB N-term	99.83
PF00004	132	AAA: ATPase family associated with various cellula	99.82
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	99.81
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	99.8
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	99.8
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	99.78
CHL00181	287	cbbX CbbX; Provisional	99.78
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	99.77
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	99.76
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	99.74
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	99.74
COG2255	332	RuvB Holliday junction resolvasome, helicase subun	99.72
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	99.7
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	99.68
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	99.68
PF05673	249	DUF815: Protein of unknown function (DUF815); Inte	99.68
PRK04195	482	replication factor C large subunit; Provisional	99.68
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	99.67
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	99.67
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	99.66
PRK06893	229	DNA replication initiation factor; Validated	99.66
COG2256	436	MGS1 ATPase related to the helicase subunit of the	99.65
KOG0736	953	consensus Peroxisome assembly factor 2 containing	99.65
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	99.65
PHA02544	316	44 clamp loader, small subunit; Provisional	99.65
PLN03025	319	replication factor C subunit; Provisional	99.63
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	99.63
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	99.63
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	99.62
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	99.61
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	99.61
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	99.61
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.6
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	99.6
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	99.6
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	99.6
PRK13342	413	recombination factor protein RarA; Reviewed	99.6
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	99.6
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	99.59
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	99.58
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	99.58
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	99.58
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	99.58
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	99.57
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	99.57
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	99.57
COG0464	494	SpoVK ATPases of the AAA+ class [Posttranslational	99.57
PRK07940	394	DNA polymerase III subunit delta'; Validated	99.57
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	99.57
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	99.57
PRK08727	233	hypothetical protein; Validated	99.57
PRK00149	450	dnaA chromosomal replication initiation protein; R	99.57
PRK08903	227	DnaA regulatory inactivator Hda; Validated	99.56
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	99.56
TIGR02902	531	spore_lonB ATP-dependent protease LonB. Members of	99.56
PRK08084	235	DNA replication initiation factor; Provisional	99.56
PRK12402	337	replication factor C small subunit 2; Reviewed	99.56
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	99.55
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.55
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	99.55
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	99.54
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	99.54
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	99.53
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	99.53
PRK14086	617	dnaA chromosomal replication initiation protein; P	99.53
PRK05642	234	DNA replication initiation factor; Validated	99.53
PRK05342	412	clpX ATP-dependent protease ATP-binding subunit Cl	99.53
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	99.53
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	99.52
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	99.52
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.51
PRK10865	857	protein disaggregation chaperone; Provisional	99.51
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	99.51
PRK14088	440	dnaA chromosomal replication initiation protein; P	99.51
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	99.5
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	99.49
PRK00440	319	rfc replication factor C small subunit; Reviewed	99.49
TIGR00382	413	clpX endopeptidase Clp ATP-binding regulatory subu	99.48
PRK12422	445	chromosomal replication initiation protein; Provis	99.47
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	99.47
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	99.47
PRK13341	725	recombination factor protein RarA/unknown domain f	99.46
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	99.46
PRK06620	214	hypothetical protein; Validated	99.45
PRK00411	394	cdc6 cell division control protein 6; Reviewed	99.44
PRK05201	443	hslU ATP-dependent protease ATP-binding subunit Hs	99.44
TIGR00390	441	hslU ATP-dependent protease HslVU, ATPase subunit.	99.44
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.43
CHL00095	821	clpC Clp protease ATP binding subunit	99.42
COG2607	287	Predicted ATPase (AAA+ superfamily) [General funct	99.42
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	99.41
PRK14087	450	dnaA chromosomal replication initiation protein; P	99.4
COG2812	515	DnaX DNA polymerase III, gamma/tau subunits [DNA r	99.37
PRK09112	351	DNA polymerase III subunit delta'; Validated	99.37
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	99.36
TIGR02903	615	spore_lon_C ATP-dependent protease, Lon family. Me	99.36
PRK07471	365	DNA polymerase III subunit delta'; Validated	99.35
PTZ00112	1164	origin recognition complex 1 protein; Provisional	99.35
KOG2028	554	consensus ATPase related to the helicase subunit o	99.34
PRK09087	226	hypothetical protein; Validated	99.33
PRK13407	334	bchI magnesium chelatase subunit I; Provisional	99.31
PRK05564	313	DNA polymerase III subunit delta'; Validated	99.3
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	99.3
PRK10865	857	protein disaggregation chaperone; Provisional	99.28
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	99.28
KOG1969	877	consensus DNA replication checkpoint protein CHL12	99.28
COG0714	329	MoxR-like ATPases [General function prediction onl	99.27
PF07728	139	AAA_5: AAA domain (dynein-related subfamily); Inte	99.27
TIGR01650	327	PD_CobS cobaltochelatase, CobS subunit. This model	99.26
PHA02244	383	ATPase-like protein	99.25
CHL00081	350	chlI Mg-protoporyphyrin IX chelatase	99.23
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	99.22
CHL00095	821	clpC Clp protease ATP binding subunit	99.22
COG0593	408	DnaA ATPase involved in DNA replication initiation	99.21
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	99.19
PRK07952	244	DNA replication protein DnaC; Validated	99.19
TIGR02030	337	BchI-ChlI magnesium chelatase ATPase subunit I. Th	99.19
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	99.19
PRK08116	268	hypothetical protein; Validated	99.16
PRK11608	326	pspF phage shock protein operon transcriptional ac	99.14
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	99.12
PRK08058	329	DNA polymerase III subunit delta'; Validated	99.12
TIGR01817	534	nifA Nif-specific regulatory protein. This model r	99.12
smart00382	148	AAA ATPases associated with a variety of cellular	99.12
PRK07399	314	DNA polymerase III subunit delta'; Validated	99.11
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	99.1
PRK05707	328	DNA polymerase III subunit delta'; Validated	99.07
PRK13531	498	regulatory ATPase RavA; Provisional	99.07
smart00763	361	AAA_PrkA PrkA AAA domain. This is a family of PrkA	99.07
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	99.07
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	99.06
PF07724	171	AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR	99.06
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	99.06
PRK08181	269	transposase; Validated	99.05
PRK12377	248	putative replication protein; Provisional	99.03
PF07726	131	AAA_3: ATPase family associated with various cellu	99.02
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	99.01
PRK15429	686	formate hydrogenlyase transcriptional activator Fh	99.0
TIGR02329	526	propionate_PrpR propionate catabolism operon regul	99.0
COG3829	560	RocR Transcriptional regulator containing PAS, AAA	99.0
PRK05022	509	anaerobic nitric oxide reductase transcription reg	98.99
TIGR02442	633	Cob-chelat-sub cobaltochelatase subunit. A number	98.99
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	98.99
PRK08939	306	primosomal protein DnaI; Reviewed	98.98
PRK15424	538	propionate catabolism operon regulatory protein Pr	98.96
PRK04132	846	replication factor C small subunit; Provisional	98.95
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	98.94
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	98.93
PF06068	398	TIP49: TIP49 C-terminus; InterPro: IPR010339 This	98.93
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	98.92
PRK06835	329	DNA replication protein DnaC; Validated	98.92
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	98.91
smart00350	509	MCM minichromosome maintenance proteins.	98.91
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	98.9
PRK06526	254	transposase; Provisional	98.88
COG1224	450	TIP49 DNA helicase TIP49, TBP-interacting protein	98.87
PF00158	168	Sigma54_activat: Sigma-54 interaction domain; Inte	98.87
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	98.86
PRK06964	342	DNA polymerase III subunit delta'; Validated	98.85
COG1221	403	PspF Transcriptional regulators containing an AAA-	98.84
COG1484	254	DnaC DNA replication protein [DNA replication, rec	98.84
PRK08769	319	DNA polymerase III subunit delta'; Validated	98.83
PRK06921	266	hypothetical protein; Provisional	98.83
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	98.82
COG0542	786	clpA ATP-binding subunits of Clp protease and DnaK	98.8
PRK07993	334	DNA polymerase III subunit delta'; Validated	98.79
PRK06871	325	DNA polymerase III subunit delta'; Validated	98.75
COG1220	444	HslU ATP-dependent protease HslVU (ClpYQ), ATPase	98.74
TIGR02031	589	BchD-ChlD magnesium chelatase ATPase subunit D. Th	98.73
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	98.73
COG2204	464	AtoC Response regulator containing CheY-like recei	98.72
KOG0745	564	consensus Putative ATP-dependent Clp-type protease	98.71
PF14532	138	Sigma54_activ_2: Sigma-54 interaction domain; PDB:	98.71
TIGR00368	499	Mg chelatase-related protein. The N-terminal end m	98.71
PRK09183	259	transposase/IS protein; Provisional	98.7
PRK08699	325	DNA polymerase III subunit delta'; Validated	98.69
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	98.69
PRK06090	319	DNA polymerase III subunit delta'; Validated	98.69
PF13173	128	AAA_14: AAA domain	98.67
PF03215	519	Rad17: Rad17 cell cycle checkpoint protein	98.66
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	98.66
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	98.65
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	98.63
PF00910	107	RNA_helicase: RNA helicase; InterPro: IPR000605 He	98.61
PRK15115	444	response regulator GlrR; Provisional	98.58
KOG1942	456	consensus DNA helicase, TBP-interacting protein [R	98.54
KOG0990	360	consensus Replication factor C, subunit RFC5 [Repl	98.53
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	98.52
COG1239	423	ChlI Mg-chelatase subunit ChlI [Coenzyme metabolis	98.5
PRK10365	441	transcriptional regulatory protein ZraR; Provision	98.47
PRK09862	506	putative ATP-dependent protease; Provisional	98.47
KOG1514	767	consensus Origin recognition complex, subunit 1, a	98.44
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	98.43
KOG2035	351	consensus Replication factor C, subunit RFC3 [Cell	98.43
PTZ00111	915	DNA replication licensing factor MCM4; Provisional	98.41
TIGR00764	608	lon_rel lon-related putative ATP-dependent proteas	98.4
PF05729	166	NACHT: NACHT domain	98.39
PRK07132	299	DNA polymerase III subunit delta'; Validated	98.38
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	98.38
PF12774	231	AAA_6: Hydrolytic ATP binding site of dynein motor	98.35
COG0606	490	Predicted ATPase with chaperone activity [Posttran	98.34
COG3604	550	FhlA Transcriptional regulator containing GAF, AAA	98.33
PHA00729	226	NTP-binding motif containing protein	98.32
PHA02624	647	large T antigen; Provisional	98.32
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	98.32
PLN03210	1153	Resistant to P. syringae 6; Provisional	98.27
KOG2227	529	consensus Pre-initiation complex, subunit CDC6, AA	98.26
KOG1968	871	consensus Replication factor C, subunit RFC1 (larg	98.24
PRK05917	290	DNA polymerase III subunit delta'; Validated	98.22
KOG1970	634	consensus Checkpoint RAD17-RFC complex, RAD17/RAD2	98.22
PF00931	287	NB-ARC: NB-ARC domain; InterPro: IPR002182 This is	98.22
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	98.21
PRK07276	290	DNA polymerase III subunit delta'; Validated	98.16
PF05707	193	Zot: Zonular occludens toxin (Zot); InterPro: IPR0	98.14
KOG0478	804	consensus DNA replication licensing factor, MCM4 c	98.07
PHA02774	613	E1; Provisional	98.04
PRK05818	261	DNA polymerase III subunit delta'; Validated	98.03
TIGR02237	209	recomb_radB DNA repair and recombination protein R	98.01
PF13207	121	AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6	97.9
PRK13406	584	bchD magnesium chelatase subunit D; Provisional	97.9
PRK15455	644	PrkA family serine protein kinase; Provisional	97.89
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	97.88
KOG2680	454	consensus DNA helicase TIP49, TBP-interacting prot	97.85
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	97.84
PF00493	331	MCM: MCM2/3/5 family This family extends the MCM d	97.84
KOG0480	764	consensus DNA replication licensing factor, MCM6 c	97.83
PRK00131	175	aroK shikimate kinase; Reviewed	97.8
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.78
COG5245	3164	DYN1 Dynein, heavy chain [Cytoskeleton]	97.77
cd01394	218	radB RadB. The archaeal protein radB shares simila	97.73
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	97.73
PRK07261	171	topology modulation protein; Provisional	97.72
PRK08118	167	topology modulation protein; Reviewed	97.68
PRK08533	230	flagellar accessory protein FlaH; Reviewed	97.67
COG3283	511	TyrR Transcriptional regulator of aromatic amino a	97.66
COG1485	367	Predicted ATPase [General function prediction only	97.65
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	97.64
PRK06067	234	flagellar accessory protein FlaH; Validated	97.63
COG1116	248	TauB ABC-type nitrate/sulfonate/bicarbonate transp	97.62
) 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	97.61
TIGR01618	220	phage_P_loop phage nucleotide-binding protein. Thi	97.6
COG1241	682	MCM2 Predicted ATPase involved in replication cont	97.59
COG3267	269	ExeA Type II secretory pathway, component ExeA (pr	97.58
PF13671	143	AAA_33: AAA domain; PDB: 1LTQ_A 2IA5_K 1RC8_A 1LY1	97.57
PRK13947	171	shikimate kinase; Provisional	97.55
cd00464	154	SK Shikimate kinase (SK) is the fifth enzyme in th	97.55
PRK09361	225	radB DNA repair and recombination protein RadB; Pr	97.55
COG5271	4600	MDN1 AAA ATPase containing von Willebrand factor t	97.54
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	97.53
PRK03839	180	putative kinase; Provisional	97.52
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	97.5
PRK05973	237	replicative DNA helicase; Provisional	97.49
cd00983	325	recA RecA is a bacterial enzyme which has roles in	97.48
PF10443	431	RNA12: RNA12 protein; InterPro: IPR018850 Mitochon	97.47
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	97.47
COG1618	179	Predicted nucleotide kinase [Nucleotide transport	97.46
PRK00625	173	shikimate kinase; Provisional	97.46
PRK13949	169	shikimate kinase; Provisional	97.46
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	97.45
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	97.45
PRK05800	170	cobU adenosylcobinamide kinase/adenosylcobinamide-	97.44
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	97.43
PRK13765	637	ATP-dependent protease Lon; Provisional	97.42
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	97.41
PF14516	331	AAA_35: AAA-like domain	97.41
cd01123	235	Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of r	97.4
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	97.4
PRK11823	446	DNA repair protein RadA; Provisional	97.4
COG0703	172	AroK Shikimate kinase [Amino acid transport and me	97.39
PF05272	198	VirE: Virulence-associated protein E; InterPro: IP	97.39
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	97.38
cd02021	150	GntK Gluconate kinase (GntK) catalyzes the phospho	97.37
cd00544	169	CobU Adenosylcobinamide kinase / adenosylcobinamid	97.36
PRK14532	188	adenylate kinase; Provisional	97.36
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	97.35
TIGR01359	183	UMP_CMP_kin_fam UMP-CMP kinase family. This subfam	97.35
PRK13948	182	shikimate kinase; Provisional	97.34
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	97.33
PRK14531	183	adenylate kinase; Provisional	97.32
PRK06217	183	hypothetical protein; Validated	97.32
TIGR01313	163	therm_gnt_kin carbohydrate kinase, thermoresistant	97.31
PRK00771	437	signal recognition particle protein Srp54; Provisi	97.3
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	97.3
cd02020	147	CMPK Cytidine monophosphate kinase (CMPK) catalyze	97.3
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	97.3
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	97.3
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	97.28
PF07693	325	KAP_NTPase: KAP family P-loop domain; InterPro: IP	97.28
PRK04841	903	transcriptional regulator MalT; Provisional	97.27
cd01428	194	ADK Adenylate kinase (ADK) catalyzes the reversibl	97.26
KOG3347	176	consensus Predicted nucleotide kinase/nuclear prot	97.24
PRK05057	172	aroK shikimate kinase I; Reviewed	97.23
PRK13946	184	shikimate kinase; Provisional	97.23
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	97.22
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	97.22
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	97.19
PRK03731	171	aroL shikimate kinase II; Reviewed	97.19
PRK06762	166	hypothetical protein; Provisional	97.19
PRK08233	182	hypothetical protein; Provisional	97.18
COG4650	531	RtcR Sigma54-dependent transcription regulator con	97.17
PRK13764	602	ATPase; Provisional	97.17
cd03216	163	ABC_Carb_Monos_I This family represents the domain	97.17
PF13191	185	AAA_16: AAA ATPase domain; PDB: 2V1U_A.	97.16
PRK14530	215	adenylate kinase; Provisional	97.16
cd00227	175	CPT Chloramphenicol (Cm) phosphotransferase (CPT).	97.15
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	97.14
TIGR01613	304	primase_Cterm phage/plasmid primase, P4 family, C-	97.13
PRK09354	349	recA recombinase A; Provisional	97.13
COG4619	223	ABC-type uncharacterized transport system, ATPase	97.11
COG1102	179	Cmk Cytidylate kinase [Nucleotide transport and me	97.1
PRK06547	172	hypothetical protein; Provisional	97.09
PRK04296	190	thymidine kinase; Provisional	97.09
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	97.09
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	97.08
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	97.08
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	97.07
TIGR01360	188	aden_kin_iso1 adenylate kinase, isozyme 1 subfamil	97.07
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	97.07
PRK02496	184	adk adenylate kinase; Provisional	97.05
PF13245	76	AAA_19: Part of AAA domain	97.05
KOG1051	898	consensus Chaperone HSP104 and related ATP-depende	97.04
KOG2383	467	consensus Predicted ATPase [General function predi	97.03
COG3854	308	SpoIIIAA ncharacterized protein conserved in bacte	97.02
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	97.02
PRK14528	186	adenylate kinase; Provisional	97.01
cd03246	173	ABCC_Protease_Secretion This family represents the	97.01
PLN02200	234	adenylate kinase family protein	97.0
KOG0477	854	consensus DNA replication licensing factor, MCM2 c	97.0
PTZ00088	229	adenylate kinase 1; Provisional	97.0
PF06431	417	Polyoma_lg_T_C: Polyomavirus large T antigen C-ter	96.98
TIGR01351	210	adk adenylate kinases. Adenylate kinase (EC 2.7.4.	96.98
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	96.97
cd02019	69	NK Nucleoside/nucleotide kinase (NK) is a protein	96.96
PF08298	358	AAA_PrkA: PrkA AAA domain; InterPro: IPR013153 Thi	96.95
PRK06696	223	uridine kinase; Validated	96.95
PRK13695	174	putative NTPase; Provisional	96.94
COG3284	606	AcoR Transcriptional activator of acetoin/glycerol	96.94
PRK10416	318	signal recognition particle-docking protein FtsY;	96.94
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	96.94
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	96.93
PRK00279	215	adk adenylate kinase; Reviewed	96.93
PF13238	129	AAA_18: AAA domain; PDB: 3IIK_A 3IIJ_A 3IIL_A 1RKB	96.92
PRK04040	188	adenylate kinase; Provisional	96.91
COG1936	180	Predicted nucleotide kinase (related to CMP and AM	96.9
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	96.9
PRK14974	336	cell division protein FtsY; Provisional	96.9
PRK06581	263	DNA polymerase III subunit delta'; Validated	96.89
PRK04182	180	cytidylate kinase; Provisional	96.87
COG1855	604	ATPase (PilT family) [General function prediction	96.86
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	96.86
PHA00350	399	putative assembly protein	96.85
PRK14527	191	adenylate kinase; Provisional	96.84
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	96.83
PRK01184	184	hypothetical protein; Provisional	96.82
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	96.8
PF00406	151	ADK: Adenylate kinase; InterPro: IPR000850 Adenyla	96.79
TIGR02173	171	cyt_kin_arch cytidylate kinase, putative. Proteins	96.78
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	96.78
PF10236	309	DAP3: Mitochondrial ribosomal death-associated pro	96.78
PLN03187	344	meiotic recombination protein DMC1 homolog; Provis	96.78
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	96.78
PHA02530	300	pseT polynucleotide kinase; Provisional	96.78
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	96.77
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	96.77
PTZ00035	337	Rad51 protein; Provisional	96.76
PRK13833	323	conjugal transfer protein TrbB; Provisional	96.76
PF13521	163	AAA_28: AAA domain; PDB: 1LW7_A.	96.75
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	96.74
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	96.74
TIGR02533	486	type_II_gspE general secretory pathway protein E.	96.72
COG0563	178	Adk Adenylate kinase and related kinases [Nucleoti	96.72
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	96.72
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	96.71
PRK14526	211	adenylate kinase; Provisional	96.7
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	96.7
TIGR00235	207	udk uridine kinase. Model contains a number of lon	96.7
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.7
PRK10078	186	ribose 1,5-bisphosphokinase; Provisional	96.69
TIGR00150	133	HI0065_YjeE ATPase, YjeE family. Members of this f	96.68
KOG0482	721	consensus DNA replication licensing factor, MCM7 c	96.67
cd02027	149	APSK Adenosine 5'-phosphosulfate kinase (APSK) cat	96.67
cd01128	249	rho_factor Transcription termination factor rho is	96.65
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	96.64
smart00487	201	DEXDc DEAD-like helicases superfamily.	96.63
PF02367	123	UPF0079: Uncharacterised P-loop hydrolase UPF0079;	96.63
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.62
PLN02199	303	shikimate kinase	96.62
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	96.6
PRK09376	416	rho transcription termination factor Rho; Provisio	96.6
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	96.59
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	96.58
PF01745	233	IPT: Isopentenyl transferase; InterPro: IPR002648	96.58
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	96.57
COG4178	604	ABC-type uncharacterized transport system, permeas	96.56
PF13479	213	AAA_24: AAA domain	96.55
COG1136	226	SalX ABC-type antimicrobial peptide transport syst	96.54
COG1126	240	GlnQ ABC-type polar amino acid transport system, A	96.54
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	96.53
TIGR03574	249	selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Mem	96.53
PLN02674	244	adenylate kinase	96.53
PRK10436	462	hypothetical protein; Provisional	96.51
PRK12339	197	2-phosphoglycerate kinase; Provisional	96.51
PF08433	270	KTI12: Chromatin associated protein KTI12 ; InterP	96.49
KOG3354	191	consensus Gluconate kinase [Carbohydrate transport	96.49
PRK05541	176	adenylylsulfate kinase; Provisional	96.47
PF09336	62	Vps4_C: Vps4 C terminal oligomerisation domain; In	96.45
PF02456	369	Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR	96.44
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	96.44
TIGR02236	310	recomb_radA DNA repair and recombination protein R	96.43
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	96.42
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	96.42
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	96.42
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	96.41
cd02022	179	DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.2	96.39
PRK00889	175	adenylylsulfate kinase; Provisional	96.38
PRK09519	790	recA DNA recombination protein RecA; Reviewed	96.37
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	96.37
PF06414	199	Zeta_toxin: Zeta toxin; InterPro: IPR010488 This e	96.35
PRK05480	209	uridine/cytidine kinase; Provisional	96.35
TIGR02322	179	phosphon_PhnN phosphonate metabolism protein/1,5-b	96.34
TIGR00064	272	ftsY signal recognition particle-docking protein F	96.34
PRK14529	223	adenylate kinase; Provisional	96.33
PRK09825	176	idnK D-gluconate kinase; Provisional	96.33
PRK12338	319	hypothetical protein; Provisional	96.32
PF12780	268	AAA_8: P-loop containing dynein motor region D4; I	96.3
TIGR00767	415	rho transcription termination factor Rho. Members	96.28
PRK09302	509	circadian clock protein KaiC; Reviewed	96.27
PLN02459	261	probable adenylate kinase	96.26
PRK04301	317	radA DNA repair and recombination protein RadA; Va	96.26
PTZ00202	550	tuzin; Provisional	96.24
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	96.24
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	96.23
PRK04220	301	2-phosphoglycerate kinase; Provisional	96.23
PLN02165	334	adenylate isopentenyltransferase	96.23
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	96.22
PRK04328	249	hypothetical protein; Provisional	96.22
cd02028	179	UMPK_like Uridine monophosphate kinase_like (UMPK_	96.21
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	96.21
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	96.2
cd02024	187	NRK1 Nicotinamide riboside kinase (NRK) is an enzy	96.19
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	96.19
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	96.19
TIGR03263	180	guanyl_kin guanylate kinase. Members of this famil	96.18
PRK10646	153	ADP-binding protein; Provisional	96.18
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	96.17
PRK12337	475	2-phosphoglycerate kinase; Provisional	96.17
PRK12608	380	transcription termination factor Rho; Provisional	96.16
COG4133	209	CcmA ABC-type transport system involved in cytochr	96.15
cd02023	198	UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.	96.15
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	96.14
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	96.14
PF01583	156	APS_kinase: Adenylylsulphate kinase; InterPro: IPR	96.14
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	96.13
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	96.13
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	96.13
PLN03186	342	DNA repair protein RAD51 homolog; Provisional	96.13
PRK00300	205	gmk guanylate kinase; Provisional	96.13
PF03266	168	NTPase_1: NTPase; InterPro: IPR004948 This entry r	96.12
cd00071	137	GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.	96.12

>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=1.4e-79  Score=625.53  Aligned_cols=404  Identities=39%  Similarity=0.683  Sum_probs=371.1

Q ss_pred             HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhhhccceEEEEeecCCCCCcchHHHHHHHHhccccCCccccccccc
Q 011664            6 IVLLVIGCLLFMIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLF   85 (480)
Q Consensus         6 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~i~e~~~~~~~~~~~~~~~~yl~~~~~~~~~~~~~~~   85 (480)
                      +.++.++++...+. .++|..++.|+-.+.++|..+|++|+++.++|+.+ +.+||+|.+++.||+++++..+.++ ++.
T Consensus         9 s~~~~~~~~~~~~~-~~~p~~~~~y~~~~~~~l~g~~s~~~~~~~~e~~g-~~~n~~~~aie~yl~~k~~~~~~rl-~~~   85 (457)
T KOG0743|consen    9 SLLGSLMFIKSMLQ-DIIPPSINPYFISALRGLFGVFSSYALIRIGEQDG-VFRNQLYVAIEVYLSSKSSAIAKRL-TQN   85 (457)
T ss_pred             HHHHHHHHHHHHHH-HhcchhHHHHHHHHHHHhhccCcccEEEEeehhcc-chHHHHHHHHHHhhhccchhhhhhh-hhh
Confidence            56666678888887 89999999999999999999999999999999866 8999999999999999998877765 466


Q ss_pred             cCCCCCceEEecCCCCceeecccceeEEEEeccC----------CCCcceEEEEEeccchhhhhhhhHHHHHHHHHHHHH
Q 011664           86 TGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDD----------SATARTLVLKLRKADRRRILRPYLQHIHAVSDELEQ  155 (480)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~d~f~g~~~~w~~~~~----------~~~~~~~~l~~~~~~~~~~l~~~l~~~~~~~~~~~~  155 (480)
                      ...+++++++.+++|++|.|+|+|++++|.+...          ..+.|+|+|+|++++++.|+.+||+|+.+.+++|.+
T Consensus        86 ~~~~s~~~~l~~~~~~~i~d~f~gv~~~w~~~~~~~~~~~~~~~~~~~r~~~L~f~k~~~e~V~~syl~~v~~~~k~I~~  165 (457)
T KOG0743|consen   86 LSKNSKSLVLGLDDNEEISDEFEGVPVKWRHFVDYNEKWIFVEREREKRYFELTFHKKPRELVTLSYLPYVVSKAKEILE  165 (457)
T ss_pred             hccccccceEEecCCcEEEEEEeceEEEEEEEEEecCcccccccCCcceEEEEEecCccHHHhHHhHHHHHHHHHHHHHH
Confidence            7788889999999999999999999999988753          456799999999999999999999999999999999


Q ss_pred             hhhhhhhhhhhccCCCCC--CCCcceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccC
Q 011664          156 KKKRDLRLFVNLRNDRDG--CCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPS  233 (480)
Q Consensus       156 ~~~~~~~~~~~~~~~~~~--~~~~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPp  233 (480)
                      + ++++++|++.++..++  .++.|++++++||++|++|++++++|+.|++++..|++++++|++.|++|+|||||||||
T Consensus       166 ~-~r~~kl~t~~~~~~~~~~~~~~W~~v~f~HpstF~TlaMd~~~K~~I~~Dl~~F~k~k~~YkrvGkawKRGYLLYGPP  244 (457)
T KOG0743|consen  166 E-NRELKLYTNSGKTVIYTAKGGEWRSVGFPHPSTFETLAMDPDLKERIIDDLDDFIKGKDFYKRVGKAWKRGYLLYGPP  244 (457)
T ss_pred             H-HHHHHHhhcCCCcccccccCCcceecCCCCCCCccccccChhHHHHHHHHHHHHHhcchHHHhcCcchhccceeeCCC
Confidence            7 9999999998654444  367899999999999999999999999999999999999999999999999999999999


Q ss_pred             CCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCc-------------ccccchhhh
Q 011664          234 GTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEK-------------PAAVSLSGV  300 (480)
Q Consensus       234 GTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~-------------~~~~~ls~l  300 (480)
                      |||||++++|||+++++++|.++++++..+++|++++..+.+.|||+|+||||-+.-+             .+.+++|+|
T Consensus       245 GTGKSS~IaAmAn~L~ydIydLeLt~v~~n~dLr~LL~~t~~kSIivIEDIDcs~~l~~~~~~~~~~~~~~~~~VTlSGL  324 (457)
T KOG0743|consen  245 GTGKSSFIAAMANYLNYDIYDLELTEVKLDSDLRHLLLATPNKSILLIEDIDCSFDLRERRKKKKENFEGDLSRVTLSGL  324 (457)
T ss_pred             CCCHHHHHHHHHhhcCCceEEeeeccccCcHHHHHHHHhCCCCcEEEEeecccccccccccccccccccCCcceeehHHh
Confidence            9999999999999999999999999999999999999999999999999999986411             133789999


Q ss_pred             hhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccC-CCCCchhHHHHHHhCC
Q 011664          301 LNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK-DHKLFPQVEEIFQNGS  379 (480)
Q Consensus       301 L~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~-~~~l~~~i~~l~~~~~  379 (480)
                      ||++||+|+ +|++++|||||||+++.|||||+||||||+||+|++|++++++.++++||+.. +|.++++++.+...+ 
T Consensus       325 LNfiDGlwS-scg~ERIivFTTNh~EkLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~l~~~~-  402 (457)
T KOG0743|consen  325 LNFLDGLWS-SCGDERIIVFTTNHKEKLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDEIERLIEET-  402 (457)
T ss_pred             hhhhccccc-cCCCceEEEEecCChhhcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHHHhhcC-
Confidence            999999999 89999999999999999999999999999999999999999999999999987 499999999976654 


Q ss_pred             CCCHHHHHHHHHHhhhcHHHHHHHHHHHHHhcCCCC
Q 011664          380 SLSPAEIGELMIANRNSPSRALKSVITALQTDGEGR  415 (480)
Q Consensus       380 g~s~adI~~ll~~a~~~~~~al~~~i~~~~~~~~~~  415 (480)
                      .+|||||++.++..+.++..+++.+++.++.+....
T Consensus       403 ~~tPA~V~e~lm~~~~dad~~lk~Lv~~l~~~~~~~  438 (457)
T KOG0743|consen  403 EVTPAQVAEELMKNKNDADVALKGLVEALESKKEKR  438 (457)
T ss_pred             ccCHHHHHHHHhhccccHHHHHHHHHHHHHhhhhhh
Confidence            999999999998887789999999999999885444

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

Probab=100.00  E-value=2.8e-49  Score=391.95  Aligned_cols=215  Identities=23%  Similarity=0.275  Sum_probs=195.1

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +...|.+|+++|+|+++++++|+|.++.|+++|+.|..+|+.+|+|+|||||||||||+||+|+|++.++.|+.+..|++
T Consensus       142 v~e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSEl  221 (406)
T COG1222         142 VEEKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSEL  221 (406)
T ss_pred             eccCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHHcCCCCCCceEeeCCCCCcHHHHHHHHHhccCceEEEeccHHH
Confidence            34457799999999999999999999999999999999999999999999999999999999999999999999999876


Q ss_pred             C----C--hHHHHHHH--HhhcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecC
Q 011664          261 A----D--DADLKSLL--LQTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       261 ~----~--~~~l~~l~--~~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      .    +  ..-++.+|  ++.++||||||||||+++..|.+         ++++-+||++|||+..   .+++-||+|||
T Consensus       222 VqKYiGEGaRlVRelF~lArekaPsIIFiDEIDAIg~kR~d~~t~gDrEVQRTmleLL~qlDGFD~---~~nvKVI~ATN  298 (406)
T COG1222         222 VQKYIGEGARLVRELFELAREKAPSIIFIDEIDAIGAKRFDSGTSGDREVQRTMLELLNQLDGFDP---RGNVKVIMATN  298 (406)
T ss_pred             HHHHhccchHHHHHHHHHHhhcCCeEEEEechhhhhcccccCCCCchHHHHHHHHHHHHhccCCCC---CCCeEEEEecC
Confidence            5    3  34478888  56679999999999999875532         4678999999999988   67888999999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHH
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPS  398 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~  398 (480)
                      +++.|||||+||||||+.|+||+|+.++|.+|++.|....+..-+.+++.|+..++|+|||||+++|..|.+.+.
T Consensus       299 R~D~LDPALLRPGR~DRkIEfplPd~~gR~~Il~IHtrkM~l~~dvd~e~la~~~~g~sGAdlkaictEAGm~Ai  373 (406)
T COG1222         299 RPDILDPALLRPGRFDRKIEFPLPDEEGRAEILKIHTRKMNLADDVDLELLARLTEGFSGADLKAICTEAGMFAI  373 (406)
T ss_pred             CccccChhhcCCCcccceeecCCCCHHHHHHHHHHHhhhccCccCcCHHHHHHhcCCCchHHHHHHHHHHhHHHH
Confidence            999999999999999999999999999999999999988777777788999999999999999999998876554

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

Probab=100.00  E-value=8.5e-47  Score=365.12  Aligned_cols=280  Identities=20%  Similarity=0.269  Sum_probs=245.9

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc-
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV-  260 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~-  260 (480)
                      -..|.+.|+||+|++.+|+.|++.+..+++.|++|..-..|| +|+|||||||||||.||+|+|.+.+..|+.|+.|++ 
T Consensus       125 ~EKPNVkWsDVAGLE~AKeALKEAVILPIKFPqlFtGkR~Pw-rgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLv  203 (439)
T KOG0739|consen  125 REKPNVKWSDVAGLEGAKEALKEAVILPIKFPQLFTGKRKPW-RGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV  203 (439)
T ss_pred             ccCCCCchhhhccchhHHHHHHhheeecccchhhhcCCCCcc-eeEEEeCCCCCcHHHHHHHHHhhcCCceEEeehHHHH
Confidence            345778999999999999999999999999999999866666 599999999999999999999999999999997765 


Q ss_pred             ---CChHH--HHHHH--HhhcCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          261 ---ADDAD--LKSLL--LQTTSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       261 ---~~~~~--l~~l~--~~~~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                         +++++  ++.+|  ++.+.|+||||||||++|+.++.+      +...+||.+|.|+..+  .++++|+++||-||.
T Consensus       204 SKWmGESEkLVknLFemARe~kPSIIFiDEiDslcg~r~enEseasRRIKTEfLVQMqGVG~d--~~gvLVLgATNiPw~  281 (439)
T KOG0739|consen  204 SKWMGESEKLVKNLFEMARENKPSIIFIDEIDSLCGSRSENESEASRRIKTEFLVQMQGVGND--NDGVLVLGATNIPWV  281 (439)
T ss_pred             HHHhccHHHHHHHHHHHHHhcCCcEEEeehhhhhccCCCCCchHHHHHHHHHHHHhhhccccC--CCceEEEecCCCchh
Confidence               45544  67777  466799999999999999877544      4578999999999874  678888899999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch-hHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHH
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP-QVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT  406 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~-~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~  406 (480)
                      ||.|++|  ||+++|++|+|+..+|..+++.+++...+.+.+ ++.+|+..|+|||++||.-+++.+-+.|+|.++...+
T Consensus       282 LDsAIRR--RFekRIYIPLPe~~AR~~MF~lhlG~tp~~LT~~d~~eL~~kTeGySGsDisivVrDalmePvRkvqsAth  359 (439)
T KOG0739|consen  282 LDSAIRR--RFEKRIYIPLPEAHARARMFKLHLGDTPHVLTEQDFKELARKTEGYSGSDISIVVRDALMEPVRKVQSATH  359 (439)
T ss_pred             HHHHHHH--HhhcceeccCCcHHHhhhhheeccCCCccccchhhHHHHHhhcCCCCcCceEEEehhhhhhhHHHhhhhhh
Confidence            9999999  999999999999999999999999999988875 7899999999999999999999999999999999999


Q ss_pred             HHHhcCCCCcccccccccccCCCCCCCCCCC----CCCCCccccCCcHHHHHHhhcccccCcccCCcCcc
Q 011664          407 ALQTDGEGRGAANAGRRLDKSGSKKSTDADS----GEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD  472 (480)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~  472 (480)
                      +.+..+.. ........+.+|.++++++-+.    .+.+++.+++|||.||.++     ++++||+|+.|
T Consensus       360 Fk~v~~~s-~~~~~~~lltpcspgd~ga~em~w~dv~~dkl~eP~vt~~D~~k~-----l~~tkPTvn~~  423 (439)
T KOG0739|consen  360 FKKVSGPS-NPSEVDDLLTPCSPGDPGAIEMSWMDVPADKLLEPPVTMRDFLKS-----LSRTKPTVNED  423 (439)
T ss_pred             hhccCCCC-ChhhhccccCCCCCCCcchhhhhhccCCHhhccCCCccHHHHHHH-----HhhcCCCCCHH
Confidence            98877544 3344677889999999876332    2566789999999999999     99999999954

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

Probab=100.00  E-value=9e-46  Score=389.91  Aligned_cols=247  Identities=26%  Similarity=0.341  Sum_probs=216.3

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC----
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS----  258 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s----  258 (480)
                      ..++++|+||+|++++|+++++.+.+++++|+.|.++|+.+++|||||||||||||++|+|+|++++.+|+.+...    
T Consensus       427 e~p~v~W~dIGGlE~lK~elq~~V~~p~~~pe~F~r~Gi~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~s  506 (693)
T KOG0730|consen  427 EMPNVSWDDIGGLEELKRELQQAVEWPLKHPEKFARFGISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFS  506 (693)
T ss_pred             cCCCCChhhccCHHHHHHHHHHHHhhhhhchHHHHHhcCCCCceEEEECCCCcchHHHHHHHhhhhcCCeeeccCHHHHH
Confidence            3467999999999999999999999999999999999999999999999999999999999999999999999755    


Q ss_pred             CcCCh--HHHHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          259 RVADD--ADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       259 ~~~~~--~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      .+.++  ..++.+|.++  .+|||||+||||+++..|+++      +.+++||++|||+..   ..+++||++||+|+.|
T Consensus       507 k~vGeSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R~g~~~~v~~RVlsqLLtEmDG~e~---~k~V~ViAATNRpd~I  583 (693)
T KOG0730|consen  507 KYVGESERAIREVFRKARQVAPCIIFFDEIDALAGSRGGSSSGVTDRVLSQLLTEMDGLEA---LKNVLVIAATNRPDMI  583 (693)
T ss_pred             HhcCchHHHHHHHHHHHhhcCCeEEehhhHHhHhhccCCCccchHHHHHHHHHHHcccccc---cCcEEEEeccCChhhc
Confidence            45554  4599999665  579999999999999887533      558999999999987   5789999999999999


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHH
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITAL  408 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~  408 (480)
                      |+||+||||||+.|++|+||.++|.+|++.+++..+..-+.++++|++.|+|||||||.++|+.|   +..|+++.++  
T Consensus       584 D~ALlRPGRlD~iiyVplPD~~aR~~Ilk~~~kkmp~~~~vdl~~La~~T~g~SGAel~~lCq~A---~~~a~~e~i~--  658 (693)
T KOG0730|consen  584 DPALLRPGRLDRIIYVPLPDLEARLEILKQCAKKMPFSEDVDLEELAQATEGYSGAEIVAVCQEA---ALLALRESIE--  658 (693)
T ss_pred             CHHHcCCcccceeEeecCccHHHHHHHHHHHHhcCCCCccccHHHHHHHhccCChHHHHHHHHHH---HHHHHHHhcc--
Confidence            99999999999999999999999999999999887776667889999999999999999999865   3445554433  


Q ss_pred             HhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcc-cccccc
Q 011664          409 QTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD-LAAAEN  478 (480)
Q Consensus       409 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~-~~~~~~  478 (480)
                                                          ...++.+||+++     ++..+||++.. .+.||+
T Consensus       659 ------------------------------------a~~i~~~hf~~a-----l~~~r~s~~~~~~~~Ye~  688 (693)
T KOG0730|consen  659 ------------------------------------ATEITWQHFEEA-----LKAVRPSLTSELLEKYED  688 (693)
T ss_pred             ------------------------------------cccccHHHHHHH-----HHhhcccCCHHHHHHHHH
Confidence                                                145678999999     99999999954 444443

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

Probab=100.00  E-value=1e-44  Score=377.13  Aligned_cols=259  Identities=19%  Similarity=0.284  Sum_probs=215.4

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC----C
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS----R  259 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s----~  259 (480)
                      -|.++|+||+++++++.++...+..++++|+.|+.+|+..|.|+|||||||||||.||+|+|++.|.+|+.|...    .
T Consensus       505 VPdVtW~dIGaL~~vR~eL~~aI~~PiK~pd~~k~lGi~~PsGvLL~GPPGCGKTLlAKAVANEag~NFisVKGPELlNk  584 (802)
T KOG0733|consen  505 VPDVTWDDIGALEEVRLELNMAILAPIKRPDLFKALGIDAPSGVLLCGPPGCGKTLLAKAVANEAGANFISVKGPELLNK  584 (802)
T ss_pred             cCCCChhhcccHHHHHHHHHHHHhhhccCHHHHHHhCCCCCCceEEeCCCCccHHHHHHHHhhhccCceEeecCHHHHHH
Confidence            367899999999999999999999999999999999999999999999999999999999999999999999855    4


Q ss_pred             cCChHH--HHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          260 VADDAD--LKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       260 ~~~~~~--l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                      ++++++  ++++|.++  ..||||||||+|++++.|+..      +.+++||..|||+..   ..++.||+|||+|+.+|
T Consensus       585 YVGESErAVR~vFqRAR~saPCVIFFDEiDaL~p~R~~~~s~~s~RvvNqLLtElDGl~~---R~gV~viaATNRPDiID  661 (802)
T KOG0733|consen  585 YVGESERAVRQVFQRARASAPCVIFFDEIDALVPRRSDEGSSVSSRVVNQLLTELDGLEE---RRGVYVIAATNRPDIID  661 (802)
T ss_pred             HhhhHHHHHHHHHHHhhcCCCeEEEecchhhcCcccCCCCchhHHHHHHHHHHHhccccc---ccceEEEeecCCCcccc
Confidence            556555  89999655  689999999999999977643      558999999999987   57899999999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch--hHHHHHHhCC--CCCHHHHHHHHHHhhhcHHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP--QVEEIFQNGS--SLSPAEIGELMIANRNSPSRALKSVI  405 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~--~i~~l~~~~~--g~s~adI~~ll~~a~~~~~~al~~~i  405 (480)
                      ||++||||||+.+++++|+.++|..|++...+....++..  ++++|+..+.  |||||||..+|+++   ...||+.-+
T Consensus       662 pAiLRPGRlDk~LyV~lPn~~eR~~ILK~~tkn~k~pl~~dVdl~eia~~~~c~gftGADLaaLvreA---si~AL~~~~  738 (802)
T KOG0733|consen  662 PAILRPGRLDKLLYVGLPNAEERVAILKTITKNTKPPLSSDVDLDEIARNTKCEGFTGADLAALVREA---SILALRESL  738 (802)
T ss_pred             hhhcCCCccCceeeecCCCHHHHHHHHHHHhccCCCCCCcccCHHHHhhcccccCCchhhHHHHHHHH---HHHHHHHHH
Confidence            9999999999999999999999999999999865555554  5689998776  99999999999755   455666555


Q ss_pred             HHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC-ccccccc
Q 011664          406 TALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS-FDLAAAE  477 (480)
Q Consensus       406 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~-~~~~~~~  477 (480)
                      ......                      .++.  ...+..--+|+.||+.|     +++++|||+ .|-..|+
T Consensus       739 ~~~~~~----------------------~~~~--~~~~~~~~~t~~hF~eA-----~~~i~pSv~~~dr~~Yd  782 (802)
T KOG0733|consen  739 FEIDSS----------------------EDDV--TVRSSTIIVTYKHFEEA-----FQRIRPSVSERDRKKYD  782 (802)
T ss_pred             hhcccc----------------------Cccc--ceeeeeeeecHHHHHHH-----HHhcCCCccHHHHHHHH
Confidence            422111                      0011  00011123789999999     999999999 4544444

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

Probab=100.00  E-value=1.8e-44  Score=359.53  Aligned_cols=262  Identities=23%  Similarity=0.287  Sum_probs=212.4

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC---
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR---  259 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~---  259 (480)
                      -++.+.|+||+|++++|+-|+|++..++.-|++|+.+..||+ |+|++||||||||+||+|+|.+++..|+.|+.+.   
T Consensus       205 ~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~F~GirrPWk-gvLm~GPPGTGKTlLAKAvATEc~tTFFNVSsstltS  283 (491)
T KOG0738|consen  205 RNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEFFKGIRRPWK-GVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTS  283 (491)
T ss_pred             cCCCcChHhhcchHHHHHHHHHHHhhhhhhHHHHhhcccccc-eeeeeCCCCCcHHHHHHHHHHhhcCeEEEechhhhhh
Confidence            345689999999999999999999999999999999988886 9999999999999999999999999999999765   


Q ss_pred             -cCChHH--HHHHH--HhhcCCcEEEEecccccccCcccc-------cchhhhhhhcccccccccCCceE-EEEecCCCc
Q 011664          260 -VADDAD--LKSLL--LQTTSKSVILIEDLDRFLVEKPAA-------VSLSGVLNFMDGVLNSCCFEERV-MVFTMNSKD  326 (480)
Q Consensus       260 -~~~~~~--l~~l~--~~~~~~sII~IDEiD~l~~~~~~~-------~~ls~lL~~ldg~~~~~~~~~~i-vI~tTN~~~  326 (480)
                       +.++++  ++-+|  ++..+|++|||||||++++.|++.       +..++||.+|||+.....+..+| |+++||.||
T Consensus       284 KwRGeSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG~~~t~e~~k~VmVLAATN~PW  363 (491)
T KOG0738|consen  284 KWRGESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDGVQGTLENSKVVMVLAATNFPW  363 (491)
T ss_pred             hhccchHHHHHHHHHHHHHhCCceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhccccccccceeEEEEeccCCCc
Confidence             445554  55555  455799999999999999877643       45799999999998743333444 455899999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHH
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT  406 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~  406 (480)
                      +||+||+|  ||+++|++|+|+.++|..+++..|+.....-..+++.|++.++||||+||.++|+.+.+.+   +++.+.
T Consensus       364 diDEAlrR--RlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~~~lae~~eGySGaDI~nvCreAsm~~---mRR~i~  438 (491)
T KOG0738|consen  364 DIDEALRR--RLEKRIYIPLPDAEARSALIKILLRSVELDDPVNLEDLAERSEGYSGADITNVCREASMMA---MRRKIA  438 (491)
T ss_pred             chHHHHHH--HHhhheeeeCCCHHHHHHHHHHhhccccCCCCccHHHHHHHhcCCChHHHHHHHHHHHHHH---HHHHHh
Confidence            99999999  9999999999999999999999997665555567889999999999999999998765544   444433


Q ss_pred             HHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC-cccccccc
Q 011664          407 ALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS-FDLAAAEN  478 (480)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~-~~~~~~~~  478 (480)
                      -+.....        ..+              ..+.+. .|++++||++|     +++++|||+ .|+..+||
T Consensus       439 g~~~~ei--------~~l--------------akE~~~-~pv~~~Dfe~A-----l~~v~pSvs~~d~~k~ek  483 (491)
T KOG0738|consen  439 GLTPREI--------RQL--------------AKEEPK-MPVTNEDFEEA-----LRKVRPSVSAADLEKYEK  483 (491)
T ss_pred             cCCcHHh--------hhh--------------hhhccc-cccchhhHHHH-----HHHcCcCCCHHHHHHHHH
Confidence            2221100        000              011111 67999999999     999999999 78887776

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

Probab=100.00  E-value=2.4e-42  Score=354.70  Aligned_cols=204  Identities=25%  Similarity=0.351  Sum_probs=186.7

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC----
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA----  261 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~----  261 (480)
                      .++|+|+-|.+++|+++.| +..|++.|..|.++|...|+||||.||||||||+||+|+|++.+.+|++...+++.    
T Consensus       300 nv~F~dVkG~DEAK~ELeE-iVefLkdP~kftrLGGKLPKGVLLvGPPGTGKTlLARAvAGEA~VPFF~~sGSEFdEm~V  378 (752)
T KOG0734|consen  300 NVTFEDVKGVDEAKQELEE-IVEFLKDPTKFTRLGGKLPKGVLLVGPPGTGKTLLARAVAGEAGVPFFYASGSEFDEMFV  378 (752)
T ss_pred             ccccccccChHHHHHHHHH-HHHHhcCcHHhhhccCcCCCceEEeCCCCCchhHHHHHhhcccCCCeEeccccchhhhhh
Confidence            5789999999999999986 66799999999999999999999999999999999999999999999999988764    


Q ss_pred             --ChHHHHHHHHh--hcCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccCccc
Q 011664          262 --DDADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQA  331 (480)
Q Consensus       262 --~~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~a  331 (480)
                        +...+|.+|.+  ..+||||||||||++.+.|..      .+++++||..|||+..   ++++|||++||.|+.||+|
T Consensus       379 GvGArRVRdLF~aAk~~APcIIFIDEiDavG~kR~~~~~~y~kqTlNQLLvEmDGF~q---NeGiIvigATNfpe~LD~A  455 (752)
T KOG0734|consen  379 GVGARRVRDLFAAAKARAPCIIFIDEIDAVGGKRNPSDQHYAKQTLNQLLVEMDGFKQ---NEGIIVIGATNFPEALDKA  455 (752)
T ss_pred             cccHHHHHHHHHHHHhcCCeEEEEechhhhcccCCccHHHHHHHHHHHHHHHhcCcCc---CCceEEEeccCChhhhhHH
Confidence              46779999965  468999999999999987643      3679999999999987   7899999999999999999


Q ss_pred             ccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          332 LLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       332 LlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      |.||||||++|.+|.||...|.+|++.|+....+.-+.|..-||.-|.|||||||++++.++
T Consensus       456 L~RPGRFD~~v~Vp~PDv~GR~eIL~~yl~ki~~~~~VD~~iiARGT~GFsGAdLaNlVNqA  517 (752)
T KOG0734|consen  456 LTRPGRFDRHVTVPLPDVRGRTEILKLYLSKIPLDEDVDPKIIARGTPGFSGADLANLVNQA  517 (752)
T ss_pred             hcCCCccceeEecCCCCcccHHHHHHHHHhcCCcccCCCHhHhccCCCCCchHHHHHHHHHH
Confidence            99999999999999999999999999999877766666778899999999999999999765

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

Probab=100.00  E-value=3.3e-41  Score=351.01  Aligned_cols=219  Identities=18%  Similarity=0.220  Sum_probs=194.7

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC----
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA----  261 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~----  261 (480)
                      .++|++|+|.+....++.+.+.. +++|+.|..+|..|+||+|||||||||||+||+|+|++++.+|+.|+..++.    
T Consensus       186 nv~f~diGG~d~~~~el~~li~~-i~~Pe~~~~lGv~PprGvLlHGPPGCGKT~lA~AiAgel~vPf~~isApeivSGvS  264 (802)
T KOG0733|consen  186 NVSFSDIGGLDKTLAELCELIIH-IKHPEVFSSLGVRPPRGVLLHGPPGCGKTSLANAIAGELGVPFLSISAPEIVSGVS  264 (802)
T ss_pred             CcchhhccChHHHHHHHHHHHHH-hcCchhHhhcCCCCCCceeeeCCCCccHHHHHHHHhhhcCCceEeecchhhhcccC
Confidence            57899999999999999988777 9999999999999999999999999999999999999999999999987654    


Q ss_pred             C--hHHHHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhccccccccc-CCceEEEEecCCCccCcc
Q 011664          262 D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCC-FEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       262 ~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~-~~~~ivI~tTN~~~~LD~  330 (480)
                      +  +..++++|.++  ..|||+||||||++.+.|...      +.+++||+.||++..... +..++||+|||+|+.|||
T Consensus       265 GESEkkiRelF~~A~~~aPcivFiDeIDAI~pkRe~aqreMErRiVaQLlt~mD~l~~~~~~g~~VlVIgATnRPDslDp  344 (802)
T KOG0733|consen  265 GESEKKIRELFDQAKSNAPCIVFIDEIDAITPKREEAQREMERRIVAQLLTSMDELSNEKTKGDPVLVIGATNRPDSLDP  344 (802)
T ss_pred             cccHHHHHHHHHHHhccCCeEEEeecccccccchhhHHHHHHHHHHHHHHHhhhcccccccCCCCeEEEecCCCCcccCH
Confidence            3  56699999766  589999999999999987643      568999999999976422 467889999999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITAL  408 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~  408 (480)
                      ||+|+||||+.|.+..|+..+|.+|++..+....+...-++++||..|.||.|||+..+|..|   +..|++++...-
T Consensus       345 aLRRaGRFdrEI~l~vP~e~aR~~IL~~~~~~lrl~g~~d~~qlA~lTPGfVGADL~AL~~~A---a~vAikR~ld~~  419 (802)
T KOG0733|consen  345 ALRRAGRFDREICLGVPSETAREEILRIICRGLRLSGDFDFKQLAKLTPGFVGADLMALCREA---AFVAIKRILDQS  419 (802)
T ss_pred             HHhccccccceeeecCCchHHHHHHHHHHHhhCCCCCCcCHHHHHhcCCCccchhHHHHHHHH---HHHHHHHHhhcc
Confidence            999999999999999999999999999999877777777889999999999999999999765   456677765533

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

Probab=100.00  E-value=5.7e-41  Score=356.56  Aligned_cols=264  Identities=22%  Similarity=0.284  Sum_probs=214.7

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      .|.-|.++|+||+|.+++|.+|.+-+..|+++|+.|.. |...+.|||||||||||||.+|+|+|.++..+|+.|...++
T Consensus       663 APKIPnV~WdDVGGLeevK~eIldTIqlPL~hpeLfss-glrkRSGILLYGPPGTGKTLlAKAVATEcsL~FlSVKGPEL  741 (953)
T KOG0736|consen  663 APKIPNVSWDDVGGLEEVKTEILDTIQLPLKHPELFSS-GLRKRSGILLYGPPGTGKTLLAKAVATECSLNFLSVKGPEL  741 (953)
T ss_pred             CCCCCccchhcccCHHHHHHHHHHHhcCcccChhhhhc-cccccceeEEECCCCCchHHHHHHHHhhceeeEEeecCHHH
Confidence            46678899999999999999999999999999999875 77777899999999999999999999999999999997665


Q ss_pred             C------ChHHHHHHHHhh--cCCcEEEEecccccccCcccc--------cchhhhhhhcccccccccCCceEEEEecCC
Q 011664          261 A------DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA--------VSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       261 ~------~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~--------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      .      +++++|++|.++  .+|||||+||+|+++++|+.+        +.+||||.+|||+.. .....++||+|||+
T Consensus       742 LNMYVGqSE~NVR~VFerAR~A~PCVIFFDELDSlAP~RG~sGDSGGVMDRVVSQLLAELDgls~-~~s~~VFViGATNR  820 (953)
T KOG0736|consen  742 LNMYVGQSEENVREVFERARSAAPCVIFFDELDSLAPNRGRSGDSGGVMDRVVSQLLAELDGLSD-SSSQDVFVIGATNR  820 (953)
T ss_pred             HHHHhcchHHHHHHHHHHhhccCCeEEEeccccccCccCCCCCCccccHHHHHHHHHHHhhcccC-CCCCceEEEecCCC
Confidence            3      467799999766  589999999999999987643        458999999999986 35678889999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCH-HHHHHHHHHHhccCCCCCchhHHHHHHhC-CCCCHHHHHHHHHHhhhcHHHHHH
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDF-SSFKTLASSYLGLKDHKLFPQVEEIFQNG-SSLSPAEIGELMIANRNSPSRALK  402 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~-~~r~~il~~~l~~~~~~l~~~i~~l~~~~-~g~s~adI~~ll~~a~~~~~~al~  402 (480)
                      |+-|||||+||||||+-++++.++. +.+..+++........+-+.++.++|+.. ..|||||+=.+|..|+.+   |++
T Consensus       821 PDLLDpALLRPGRFDKLvyvG~~~d~esk~~vL~AlTrkFkLdedVdL~eiAk~cp~~~TGADlYsLCSdA~l~---Aik  897 (953)
T KOG0736|consen  821 PDLLDPALLRPGRFDKLVYVGPNEDAESKLRVLEALTRKFKLDEDVDLVEIAKKCPPNMTGADLYSLCSDAMLA---AIK  897 (953)
T ss_pred             ccccChhhcCCCccceeEEecCCccHHHHHHHHHHHHHHccCCCCcCHHHHHhhCCcCCchhHHHHHHHHHHHH---HHH
Confidence            9999999999999999999999865 55778888887766666566778888765 599999999999877654   455


Q ss_pred             HHHHHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC-ccccccc
Q 011664          403 SVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS-FDLAAAE  477 (480)
Q Consensus       403 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~-~~~~~~~  477 (480)
                      +.+..++...           .         .++.+++   ..--|+|+||.|+     +++-+||+| .++-.||
T Consensus       898 R~i~~ie~g~-----------~---------~~~e~~~---~~v~V~~eDflks-----~~~l~PSvS~~EL~~ye  945 (953)
T KOG0736|consen  898 RTIHDIESGT-----------I---------SEEEQES---SSVRVTMEDFLKS-----AKRLQPSVSEQELLRYE  945 (953)
T ss_pred             HHHHHhhhcc-----------c---------cccccCC---ceEEEEHHHHHHH-----HHhcCCcccHHHHHHHH
Confidence            5555544320           0         0001111   1244899999999     999999999 4554444

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

Probab=100.00  E-value=1.1e-39  Score=314.94  Aligned_cols=214  Identities=24%  Similarity=0.313  Sum_probs=187.9

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +...|.-++.||+|.+.+.++|++.++.++.+|++|...|+.+|+|++|||+||||||.||+|+||...+.|+.+-.|++
T Consensus       176 ~eKaP~Ety~diGGle~QiQEiKEsvELPLthPE~YeemGikpPKGVIlyG~PGTGKTLLAKAVANqTSATFlRvvGseL  255 (440)
T KOG0726|consen  176 VEKAPQETYADIGGLESQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGEPGTGKTLLAKAVANQTSATFLRVVGSEL  255 (440)
T ss_pred             cccCchhhhcccccHHHHHHHHHHhhcCCCCCHHHHHHcCCCCCCeeEEeCCCCCchhHHHHHHhcccchhhhhhhhHHH
Confidence            34456679999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             C------ChHHHHHHH--HhhcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecC
Q 011664          261 A------DDADLKSLL--LQTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       261 ~------~~~~l~~l~--~~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      .      +..-++++|  +..++|||+||||||++...|.+         ++++-+|||++||+.+   .+.+-||+|||
T Consensus       256 iQkylGdGpklvRqlF~vA~e~apSIvFiDEIdAiGtKRyds~SggerEiQrtmLELLNQldGFds---rgDvKvimATn  332 (440)
T KOG0726|consen  256 IQKYLGDGPKLVRELFRVAEEHAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDS---RGDVKVIMATN  332 (440)
T ss_pred             HHHHhccchHHHHHHHHHHHhcCCceEEeehhhhhccccccCCCccHHHHHHHHHHHHHhccCccc---cCCeEEEEecc
Confidence            4      234578888  45679999999999999875532         3567899999999988   57788999999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcH
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSP  397 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~  397 (480)
                      +.+.|||||+||||+|+.|+||.||...++.|+..+.......-+..++.+....+.+|+|||.++|..+..-+
T Consensus       333 rie~LDPaLiRPGrIDrKIef~~pDe~TkkkIf~IHTs~Mtl~~dVnle~li~~kddlSGAdIkAictEaGllA  406 (440)
T KOG0726|consen  333 RIETLDPALIRPGRIDRKIEFPLPDEKTKKKIFQIHTSRMTLAEDVNLEELIMTKDDLSGADIKAICTEAGLLA  406 (440)
T ss_pred             cccccCHhhcCCCccccccccCCCchhhhceeEEEeecccchhccccHHHHhhcccccccccHHHHHHHHhHHH
Confidence            99999999999999999999999999999999998877665555567788888778999999999998765433

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

Probab=100.00  E-value=5.4e-39  Score=305.06  Aligned_cols=214  Identities=25%  Similarity=0.331  Sum_probs=190.8

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-  261 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-  261 (480)
                      ..+.+++.||+|.+-+|++|++.++.++.+.++|+++|+.+|+|+|||||||||||+|++|+|+...+.|+.+..|++. 
T Consensus       148 ekpdvsy~diggld~qkqeireavelplt~~~ly~qigidpprgvllygppg~gktml~kava~~t~a~firvvgsefvq  227 (408)
T KOG0727|consen  148 EKPDVSYADIGGLDVQKQEIREAVELPLTHADLYKQIGIDPPRGVLLYGPPGTGKTMLAKAVANHTTAAFIRVVGSEFVQ  227 (408)
T ss_pred             CCCCccccccccchhhHHHHHHHHhccchHHHHHHHhCCCCCcceEEeCCCCCcHHHHHHHHhhccchheeeeccHHHHH
Confidence            4567899999999999999999999999999999999999999999999999999999999999999999999988765 


Q ss_pred             -----ChHHHHHHH--HhhcCCcEEEEecccccccCcc---------cccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          262 -----DDADLKSLL--LQTTSKSVILIEDLDRFLVEKP---------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       262 -----~~~~l~~l~--~~~~~~sII~IDEiD~l~~~~~---------~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                           +..-++.+|  ++.++|+||||||||++...+-         -++.+-+|||+|||+..   ..++-+|++||+.
T Consensus       228 kylgegprmvrdvfrlakenapsiifideidaiatkrfdaqtgadrevqril~ellnqmdgfdq---~~nvkvimatnra  304 (408)
T KOG0727|consen  228 KYLGEGPRMVRDVFRLAKENAPSIIFIDEIDAIATKRFDAQTGADREVQRILIELLNQMDGFDQ---TTNVKVIMATNRA  304 (408)
T ss_pred             HHhccCcHHHHHHHHHHhccCCcEEEeehhhhHhhhhccccccccHHHHHHHHHHHHhccCcCc---ccceEEEEecCcc
Confidence                 234467776  5668999999999999986542         23568899999999987   5778899999999


Q ss_pred             ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHH
Q 011664          326 DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSR  399 (480)
Q Consensus       326 ~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~  399 (480)
                      +.|||||+||||+|+.|+||+|+..+++-++.......+..-..+++.+..+.+..|+|||..+|+.+.+.+++
T Consensus       305 dtldpallrpgrldrkiefplpdrrqkrlvf~titskm~ls~~vdle~~v~rpdkis~adi~aicqeagm~avr  378 (408)
T KOG0727|consen  305 DTLDPALLRPGRLDRKIEFPLPDRRQKRLVFSTITSKMNLSDEVDLEDLVARPDKISGADINAICQEAGMLAVR  378 (408)
T ss_pred             cccCHhhcCCccccccccCCCCchhhhhhhHHhhhhcccCCcccCHHHHhcCccccchhhHHHHHHHHhHHHHH
Confidence            99999999999999999999999999999999988877776677889999999999999999999987665544

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

Probab=100.00  E-value=2.6e-38  Score=342.32  Aligned_cols=212  Identities=24%  Similarity=0.332  Sum_probs=188.7

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC--
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA--  261 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~--  261 (480)
                      +..++|+|++|.+++|++|.| +..|+++|+.|.++|...|+|+||+||||||||+||+|+|.|.|.+|+.++.+++.  
T Consensus       305 ~t~V~FkDVAG~deAK~El~E-~V~fLKNP~~Y~~lGAKiPkGvLL~GPPGTGKTLLAKAiAGEAgVPF~svSGSEFvE~  383 (774)
T KOG0731|consen  305 NTGVKFKDVAGVDEAKEELME-FVKFLKNPEQYQELGAKIPKGVLLVGPPGTGKTLLAKAIAGEAGVPFFSVSGSEFVEM  383 (774)
T ss_pred             CCCCccccccCcHHHHHHHHH-HHHHhcCHHHHHHcCCcCcCceEEECCCCCcHHHHHHHHhcccCCceeeechHHHHHH
Confidence            345899999999999999997 55799999999999999999999999999999999999999999999999999865  


Q ss_pred             ----ChHHHHHHHHhh--cCCcEEEEecccccccCccc----------ccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          262 ----DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPA----------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       262 ----~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~----------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                          +.+.++.+|..+  ..||||||||||++...+.+          ..+++|||..|||+..   ..++|++++||+|
T Consensus       384 ~~g~~asrvr~lf~~ar~~aP~iifideida~~~~r~G~~~~~~~~e~e~tlnQll~emDgf~~---~~~vi~~a~tnr~  460 (774)
T KOG0731|consen  384 FVGVGASRVRDLFPLARKNAPSIIFIDEIDAVGRKRGGKGTGGGQDEREQTLNQLLVEMDGFET---SKGVIVLAATNRP  460 (774)
T ss_pred             hcccchHHHHHHHHHhhccCCeEEEecccccccccccccccCCCChHHHHHHHHHHHHhcCCcC---CCcEEEEeccCCc
Confidence                477899999654  68999999999999876631          2579999999999987   5789999999999


Q ss_pred             ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCC-CchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHH
Q 011664          326 DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHK-LFPQVEEIFQNGSSLSPAEIGELMIANRNSPSR  399 (480)
Q Consensus       326 ~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~-l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~  399 (480)
                      +.||+||+||||||++|.++.|+...|.+|++.|+...+.. -..++..++..|.|||||||+++|.++.-.+.+
T Consensus       461 d~ld~allrpGRfdr~i~i~~p~~~~r~~i~~~h~~~~~~~~e~~dl~~~a~~t~gf~gadl~n~~neaa~~a~r  535 (774)
T KOG0731|consen  461 DILDPALLRPGRFDRQIQIDLPDVKGRASILKVHLRKKKLDDEDVDLSKLASLTPGFSGADLANLCNEAALLAAR  535 (774)
T ss_pred             cccCHHhcCCCccccceeccCCchhhhHHHHHHHhhccCCCcchhhHHHHHhcCCCCcHHHHHhhhhHHHHHHHH
Confidence            99999999999999999999999999999999999877664 234666799999999999999999887655554

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

Probab=100.00  E-value=2.2e-38  Score=300.56  Aligned_cols=211  Identities=23%  Similarity=0.293  Sum_probs=188.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      |.++++-++|++.+.++|++.++.+.++|++|..+|++.|+|+|||||||||||.||+|+|.+..+.|+.++.+++.   
T Consensus       142 PDStYeMiGgLd~QIkeIkEVIeLPvKHPELF~aLGIaQPKGvlLygppgtGktLlaraVahht~c~firvsgselvqk~  221 (404)
T KOG0728|consen  142 PDSTYEMIGGLDKQIKEIKEVIELPVKHPELFEALGIAQPKGVLLYGPPGTGKTLLARAVAHHTDCTFIRVSGSELVQKY  221 (404)
T ss_pred             CccHHHHhccHHHHHHHHHHHHhccccCHHHHHhcCCCCCcceEEecCCCCchhHHHHHHHhhcceEEEEechHHHHHHH
Confidence            56789999999999999999999999999999999999999999999999999999999999999999999988764   


Q ss_pred             -C--hHHHHHHH--HhhcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          262 -D--DADLKSLL--LQTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       262 -~--~~~l~~l~--~~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                       +  ..-++++|  ++.++|+|||+||||++.+.+..         ++++-+|||++||+..   ..++-+|++||+.+-
T Consensus       222 igegsrmvrelfvmarehapsiifmdeidsigs~r~e~~~ggdsevqrtmlellnqldgfea---tknikvimatnridi  298 (404)
T KOG0728|consen  222 IGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSSRVESGSGGDSEVQRTMLELLNQLDGFEA---TKNIKVIMATNRIDI  298 (404)
T ss_pred             hhhhHHHHHHHHHHHHhcCCceEeeecccccccccccCCCCccHHHHHHHHHHHHhcccccc---ccceEEEEecccccc
Confidence             2  23377777  56689999999999999875421         3567889999999988   678889999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHH
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPS  398 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~  398 (480)
                      |||||+||||+|+.|+||+|+.++|..|++.+....+..-..++..+|+...|.|+|++...|..+.+.+.
T Consensus       299 ld~allrpgridrkiefp~p~e~ar~~ilkihsrkmnl~rgi~l~kiaekm~gasgaevk~vcteagm~al  369 (404)
T KOG0728|consen  299 LDPALLRPGRIDRKIEFPPPNEEARLDILKIHSRKMNLTRGINLRKIAEKMPGASGAEVKGVCTEAGMYAL  369 (404)
T ss_pred             ccHhhcCCCcccccccCCCCCHHHHHHHHHHhhhhhchhcccCHHHHHHhCCCCccchhhhhhhhhhHHHH
Confidence            99999999999999999999999999999998876666556678999999999999999999988766543

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

Probab=100.00  E-value=9.3e-37  Score=317.45  Aligned_cols=210  Identities=25%  Similarity=0.333  Sum_probs=183.5

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-  261 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-  261 (480)
                      ..+.++|++|+|.+.+|++|.+.+..++.+++.|..+|.++++|+|||||||||||++|+++|++++.+++.+..+.+. 
T Consensus       138 ~~p~v~~~digGl~~~k~~l~~~v~~pl~~~~~~~~~Gl~~pkgvLL~GppGTGKT~LAkalA~~l~~~fi~i~~s~l~~  217 (398)
T PTZ00454        138 EKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQ  217 (398)
T ss_pred             CCCCCCHHHcCCHHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHHH
Confidence            3567899999999999999999999999999999999999999999999999999999999999999999999876542 


Q ss_pred             ---C--hHHHHHHHH--hhcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          262 ---D--DADLKSLLL--QTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       262 ---~--~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                         +  ...++.+|.  ...+|+||||||||.++..+.+         ...+.++++.||++..   ..+++||+|||++
T Consensus       218 k~~ge~~~~lr~lf~~A~~~~P~ILfIDEID~i~~~r~~~~~~~d~~~~r~l~~LL~~ld~~~~---~~~v~VI~aTN~~  294 (398)
T PTZ00454        218 KYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGADREVQRILLELLNQMDGFDQ---TTNVKVIMATNRA  294 (398)
T ss_pred             HhcchhHHHHHHHHHHHHhcCCeEEEEECHhhhccccccccCCccHHHHHHHHHHHHHhhccCC---CCCEEEEEecCCc
Confidence               2  334667764  4468999999999999865421         1357789999999876   4678899999999


Q ss_pred             ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          326 DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       326 ~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      +.||||++||||||..|+|++|+.++|..|++.++...+.....+++.++..+.||||+||.++|..+..
T Consensus       295 d~LDpAllR~GRfd~~I~~~~P~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA~~  364 (398)
T PTZ00454        295 DTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGM  364 (398)
T ss_pred             hhCCHHHcCCCcccEEEEeCCcCHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999987666556678899999999999999999987654

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=100.00  E-value=9.8e-37  Score=341.27  Aligned_cols=260  Identities=22%  Similarity=0.304  Sum_probs=211.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc----
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV----  260 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~----  260 (480)
                      +.++|++|+|++++|+.|.+.+..++++++.|.++|..+++|+|||||||||||++|+++|++++.+|+.++.+++    
T Consensus       448 ~~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g~~~~~giLL~GppGtGKT~lakalA~e~~~~fi~v~~~~l~~~~  527 (733)
T TIGR01243       448 PNVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKW  527 (733)
T ss_pred             cccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhcCCCEEEEehHHHhhcc
Confidence            4679999999999999999999999999999999999999999999999999999999999999999999997654    


Q ss_pred             CC--hHHHHHHHHh--hcCCcEEEEecccccccCcccc-------cchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          261 AD--DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA-------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       261 ~~--~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~-------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                      .+  +..++.+|..  ...||||||||||.+++.++..       ..+++||..|||+..   ..+++||+|||+|+.||
T Consensus       528 vGese~~i~~~f~~A~~~~p~iifiDEid~l~~~r~~~~~~~~~~~~~~~lL~~ldg~~~---~~~v~vI~aTn~~~~ld  604 (733)
T TIGR01243       528 VGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARFDTSVTDRIVNQLLTEMDGIQE---LSNVVVIAATNRPDILD  604 (733)
T ss_pred             cCcHHHHHHHHHHHHHhcCCEEEEEEChhhhhccCCCCCCccHHHHHHHHHHHHhhcccC---CCCEEEEEeCCChhhCC
Confidence            33  4458888854  4689999999999998765422       346889999999876   56789999999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQ  409 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~  409 (480)
                      +|++||||||++|++|+|+.++|.+|++.++...+.....+++.|+..+.|||++||..+|+.+..   .++++.+....
T Consensus       605 ~allRpgRfd~~i~v~~Pd~~~R~~i~~~~~~~~~~~~~~~l~~la~~t~g~sgadi~~~~~~A~~---~a~~~~~~~~~  681 (733)
T TIGR01243       605 PALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAM---AALRESIGSPA  681 (733)
T ss_pred             HhhcCCCccceEEEeCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHH---HHHHHHhhhcc
Confidence            999999999999999999999999999999876665555678999999999999999999976543   34444332211


Q ss_pred             hcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc-cccccc
Q 011664          410 TDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF-DLAAAE  477 (480)
Q Consensus       410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~-~~~~~~  477 (480)
                      ..           .+.. .     ..+     .....+++++||.++     +++++||++. +...||
T Consensus       682 ~~-----------~~~~-~-----~~~-----~~~~~~i~~~~f~~a-----l~~~~ps~~~~~~~~~~  723 (733)
T TIGR01243       682 KE-----------KLEV-G-----EEE-----FLKDLKVEMRHFLEA-----LKKVKPSVSKEDMLRYE  723 (733)
T ss_pred             ch-----------hhhc-c-----ccc-----ccccCcccHHHHHHH-----HHHcCCCCCHHHHHHHH
Confidence            00           0000 0     000     112257999999999     8999999995 334444

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

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

Probab=100.00  E-value=3.4e-36  Score=323.24  Aligned_cols=238  Identities=27%  Similarity=0.365  Sum_probs=208.5

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-  261 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-  261 (480)
                      ..+.++|++++|++++|+.+++.+..++.+++.|.+.|+.+++|+|||||||||||+||+|+|++++.+|+.++.+++. 
T Consensus       235 ~~~~v~~~diggl~~~k~~l~e~v~~~~~~~e~~~~~~~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~s  314 (494)
T COG0464         235 EDEDVTLDDIGGLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLS  314 (494)
T ss_pred             CCCCcceehhhcHHHHHHHHHHHHHhHhhChHHHHhcCCCCCCeeEEECCCCCCHHHHHHHHHhhCCCeEEEeeCHHHhc
Confidence            4466899999999999999999999999999999999999999999999999999999999999999999999977554 


Q ss_pred             ---C--hHHHHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          262 ---D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       262 ---~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                         +  +..++.+|..+  .+||||||||+|++++.++..      +.++++|.+|||+..   ..+++||+|||+|+.+
T Consensus       315 k~vGesek~ir~~F~~A~~~~p~iiFiDEiDs~~~~r~~~~~~~~~r~~~~lL~~~d~~e~---~~~v~vi~aTN~p~~l  391 (494)
T COG0464         315 KWVGESEKNIRELFEKARKLAPSIIFIDEIDSLASGRGPSEDGSGRRVVGQLLTELDGIEK---AEGVLVIAATNRPDDL  391 (494)
T ss_pred             cccchHHHHHHHHHHHHHcCCCcEEEEEchhhhhccCCCCCchHHHHHHHHHHHHhcCCCc---cCceEEEecCCCcccc
Confidence               3  45689999655  589999999999999877643      578999999999987   6778899999999999


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc--hhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHH
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF--PQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT  406 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~--~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~  406 (480)
                      |+|++||||||..|++|+||.++|.+|++.++......+.  .+++.+++.+.|||++||..+|+.+...+.+...    
T Consensus       392 d~a~lR~gRfd~~i~v~~pd~~~r~~i~~~~~~~~~~~~~~~~~~~~l~~~t~~~sgadi~~i~~ea~~~~~~~~~----  467 (494)
T COG0464         392 DPALLRPGRFDRLIYVPLPDLEERLEIFKIHLRDKKPPLAEDVDLEELAEITEGYSGADIAALVREAALEALREAR----  467 (494)
T ss_pred             CHhhcccCccceEeecCCCCHHHHHHHHHHHhcccCCcchhhhhHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHhc----
Confidence            9999999999999999999999999999999986555433  4567899999999999999999876554332211    


Q ss_pred             HHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC
Q 011664          407 ALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS  470 (480)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~  470 (480)
                                                            ..+++++||.++     +++++||++
T Consensus       468 --------------------------------------~~~~~~~~~~~a-----~~~~~p~~~  488 (494)
T COG0464         468 --------------------------------------RREVTLDDFLDA-----LKKIKPSVT  488 (494)
T ss_pred             --------------------------------------cCCccHHHHHHH-----HHhcCCCCC
Confidence                                                  267899999999     889999988

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

Probab=100.00  E-value=1.3e-36  Score=303.37  Aligned_cols=263  Identities=19%  Similarity=0.276  Sum_probs=203.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      -.++|+||+|++++|+.+++.+..++++|++|..-+ ..+++|+|||||||||||++|+|+|.+.|.+|+.|+++.+.+ 
T Consensus        87 I~v~f~DIggLe~v~~~L~e~VilPlr~pelF~~g~Ll~p~kGiLL~GPpG~GKTmlAKA~Akeaga~fInv~~s~lt~K  166 (386)
T KOG0737|consen   87 IGVSFDDIGGLEEVKDALQELVILPLRRPELFAKGKLLRPPKGILLYGPPGTGKTMLAKAIAKEAGANFINVSVSNLTSK  166 (386)
T ss_pred             ceeehhhccchHHHHHHHHHHHhhcccchhhhcccccccCCccceecCCCCchHHHHHHHHHHHcCCCcceeeccccchh
Confidence            347899999999999999999999999999997433 457889999999999999999999999999999999986654 


Q ss_pred             ---hHH--HHHHH--HhhcCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          263 ---DAD--LKSLL--LQTTSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       263 ---~~~--l~~l~--~~~~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                         +++  ++.+|  +..-+||||||||+|+++..|.+.      ...++|...+||+.+. ....++|.+|||+|.+||
T Consensus       167 WfgE~eKlv~AvFslAsKl~P~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM~~WDGl~s~-~~~rVlVlgATNRP~DlD  245 (386)
T KOG0737|consen  167 WFGEAQKLVKAVFSLASKLQPSIIFIDEVDSFLGQRRSTDHEATAMMKNEFMALWDGLSSK-DSERVLVLGATNRPFDLD  245 (386)
T ss_pred             hHHHHHHHHHHHHhhhhhcCcceeehhhHHHHHhhcccchHHHHHHHHHHHHHHhccccCC-CCceEEEEeCCCCCccHH
Confidence               333  55666  344589999999999998766432      3468899999999883 222355566999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQ  409 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~  409 (480)
                      .|++|  ||..+++++.|+.++|.+|++.+|...+..-..++.+++..|.||||+||.++|..+...|   ++.++..- 
T Consensus       246 eAiiR--R~p~rf~V~lP~~~qR~kILkviLk~e~~e~~vD~~~iA~~t~GySGSDLkelC~~Aa~~~---ire~~~~~-  319 (386)
T KOG0737|consen  246 EAIIR--RLPRRFHVGLPDAEQRRKILKVILKKEKLEDDVDLDEIAQMTEGYSGSDLKELCRLAALRP---IRELLVSE-  319 (386)
T ss_pred             HHHHH--hCcceeeeCCCchhhHHHHHHHHhcccccCcccCHHHHHHhcCCCcHHHHHHHHHHHhHhH---HHHHHHhc-
Confidence            99999  9999999999999999999999999888877778999999999999999999998765544   45554432 


Q ss_pred             hcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC
Q 011664          410 TDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS  470 (480)
Q Consensus       410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~  470 (480)
                      ..  .   ........+..+.+.      ...+...|+++++||.++     ...+-+|+.
T Consensus       320 ~~--~---~d~d~~~~d~~~~~~------~~~~~~~r~l~~eDf~~a-----~~~v~~~~~  364 (386)
T KOG0737|consen  320 TG--L---LDLDKAIADLKPTQA------AASSCLLRPLEQEDFPKA-----INRVSASVA  364 (386)
T ss_pred             cc--c---hhhhhhhhhccCCcc------cccccccCcccHHHHHHH-----HHhhhhHHH
Confidence            10  0   000000111111111      022345699999999999     555555544

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

Probab=100.00  E-value=1.8e-36  Score=323.10  Aligned_cols=207  Identities=26%  Similarity=0.349  Sum_probs=187.8

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC--
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA--  261 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~--  261 (480)
                      ...++|.|++|.+++|+++.| +..|++.|..|..+|...|+|+||+||||||||+||+|+|.+.+.+|+.++.|++.  
T Consensus       144 ~~~v~F~DVAG~dEakeel~E-iVdfLk~p~ky~~lGakiPkGvlLvGpPGTGKTLLAkAvAgEA~VPFf~iSGS~FVem  222 (596)
T COG0465         144 QVKVTFADVAGVDEAKEELSE-LVDFLKNPKKYQALGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM  222 (596)
T ss_pred             ccCcChhhhcCcHHHHHHHHH-HHHHHhCchhhHhcccccccceeEecCCCCCcHHHHHHHhcccCCCceeccchhhhhh
Confidence            355899999999999999996 56799999999999999999999999999999999999999999999999999865  


Q ss_pred             ----ChHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          262 ----DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       262 ----~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                          +.+.+|.+|.++  ++||||||||||++...|+.         .+++++||.+|||+..   +++++++++||+|+
T Consensus       223 fVGvGAsRVRdLF~qAkk~aP~IIFIDEiDAvGr~Rg~g~GggnderEQTLNQlLvEmDGF~~---~~gviviaaTNRpd  299 (596)
T COG0465         223 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGG---NEGVIVIAATNRPD  299 (596)
T ss_pred             hcCCCcHHHHHHHHHhhccCCCeEEEehhhhcccccCCCCCCCchHHHHHHHHHHhhhccCCC---CCceEEEecCCCcc
Confidence                578899999766  47999999999999876632         2689999999999986   68899999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      -|||||+||||||++|.++.||...|++|++.++.......+.++..++..|.|+|+||+.+++..+.
T Consensus       300 VlD~ALlRpgRFDRqI~V~~PDi~gRe~IlkvH~~~~~l~~~Vdl~~iAr~tpGfsGAdL~nl~NEAa  367 (596)
T COG0465         300 VLDPALLRPGRFDRQILVELPDIKGREQILKVHAKNKPLAEDVDLKKIARGTPGFSGADLANLLNEAA  367 (596)
T ss_pred             cchHhhcCCCCcceeeecCCcchhhHHHHHHHHhhcCCCCCcCCHHHHhhhCCCcccchHhhhHHHHH
Confidence            99999999999999999999999999999999988777776677888999999999999999997653

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

Probab=100.00  E-value=1.9e-36  Score=288.84  Aligned_cols=214  Identities=19%  Similarity=0.236  Sum_probs=188.8

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +...|.-+++||+|.+.+.+++.+.+..++.+++.|.++|+.+|+|+|+|||||||||.+|+|.|...+..|..+....+
T Consensus       162 vDekPtE~YsDiGGldkQIqELvEAiVLpmth~ekF~~lgi~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQL  241 (424)
T KOG0652|consen  162 VDEKPTEQYSDIGGLDKQIQELVEAIVLPMTHKEKFENLGIRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQL  241 (424)
T ss_pred             eccCCcccccccccHHHHHHHHHHHhccccccHHHHHhcCCCCCCceEeeCCCCCcHHHHHHHHHHhccchHHHhcchHH
Confidence            44556679999999999999999999999999999999999999999999999999999999999999999988876654


Q ss_pred             C----C--hHHHHHHH--HhhcCCcEEEEecccccccCcc---------cccchhhhhhhcccccccccCCceEEEEecC
Q 011664          261 A----D--DADLKSLL--LQTTSKSVILIEDLDRFLVEKP---------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       261 ~----~--~~~l~~l~--~~~~~~sII~IDEiD~l~~~~~---------~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      .    +  ..-++..|  ++...|+||||||+|++...+.         -++++-+|||++||+.+   .+.+-||++||
T Consensus       242 VQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDAIGtKRfDSek~GDREVQRTMLELLNQLDGFss---~~~vKviAATN  318 (424)
T KOG0652|consen  242 VQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFSS---DDRVKVIAATN  318 (424)
T ss_pred             HhhhhcchHHHHHHHHHHhhccCCeEEEEechhhhccccccccccccHHHHHHHHHHHHhhcCCCC---ccceEEEeecc
Confidence            3    2  33467766  4567899999999999986543         34678899999999988   57778999999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcH
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSP  397 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~  397 (480)
                      +.+-|||||+|.||+|+.|+||.|+.++|..|++.+....+..-+.++++|+..|++|.+|+...+|..+.+.+
T Consensus       319 RvDiLDPALlRSGRLDRKIEfP~Pne~aRarIlQIHsRKMnv~~DvNfeELaRsTddFNGAQcKAVcVEAGMiA  392 (424)
T KOG0652|consen  319 RVDILDPALLRSGRLDRKIEFPHPNEEARARILQIHSRKMNVSDDVNFEELARSTDDFNGAQCKAVCVEAGMIA  392 (424)
T ss_pred             cccccCHHHhhcccccccccCCCCChHHHHHHHHHhhhhcCCCCCCCHHHHhhcccccCchhheeeehhhhHHH
Confidence            99999999999999999999999999999999999988777777778899999999999999999998765543

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

Probab=100.00  E-value=8.3e-36  Score=314.74  Aligned_cols=216  Identities=19%  Similarity=0.274  Sum_probs=192.2

Q ss_pred             cceeCCCCCC--CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          177 RWRSVPFTHP--STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       177 ~w~~v~~~~~--~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      +.+++.+..+  ..|++|+|+.++|+.+.+.+++|.+.|..|...+++.+.|+|||||||||||.||.|+|...+.+|+.
T Consensus       652 aLR~ik~~k~tgi~w~digg~~~~k~~l~~~i~~P~kyp~if~~~plr~~~giLLyGppGcGKT~la~a~a~~~~~~fis  731 (952)
T KOG0735|consen  652 ALRGIKLVKSTGIRWEDIGGLFEAKKVLEEVIEWPSKYPQIFANCPLRLRTGILLYGPPGCGKTLLASAIASNSNLRFIS  731 (952)
T ss_pred             HhhhccccccCCCCceecccHHHHHHHHHHHHhccccchHHHhhCCcccccceEEECCCCCcHHHHHHHHHhhCCeeEEE
Confidence            3455555444  57999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EeCCCcC------ChHHHHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEE
Q 011664          255 VDLSRVA------DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVF  320 (480)
Q Consensus       255 i~~s~~~------~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~  320 (480)
                      +...++.      ++..+|.+|.++  ..|||+|+||+|+++++|+..      +.+++||.+|||...   -.++.|++
T Consensus       732 vKGPElL~KyIGaSEq~vR~lF~rA~~a~PCiLFFDEfdSiAPkRGhDsTGVTDRVVNQlLTelDG~Eg---l~GV~i~a  808 (952)
T KOG0735|consen  732 VKGPELLSKYIGASEQNVRDLFERAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTELDGAEG---LDGVYILA  808 (952)
T ss_pred             ecCHHHHHHHhcccHHHHHHHHHHhhccCCeEEEeccccccCcccCCCCCCchHHHHHHHHHhhccccc---cceEEEEE
Confidence            9876543      367799999655  589999999999999988754      448999999999987   68899999


Q ss_pred             ecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          321 TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       321 tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      +|.+|+.|||||+||||+|+.++.|.|+..+|.+|++.........-..+++.+|..|+|||+||++.++-.|..
T Consensus       809 aTsRpdliDpALLRpGRlD~~v~C~~P~~~eRl~il~~ls~s~~~~~~vdl~~~a~~T~g~tgADlq~ll~~A~l  883 (952)
T KOG0735|consen  809 ATSRPDLIDPALLRPGRLDKLVYCPLPDEPERLEILQVLSNSLLKDTDVDLECLAQKTDGFTGADLQSLLYNAQL  883 (952)
T ss_pred             ecCCccccCHhhcCCCccceeeeCCCCCcHHHHHHHHHHhhccCCccccchHHHhhhcCCCchhhHHHHHHHHHH
Confidence            999999999999999999999999999999999999988765555666788999999999999999999976644

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=100.00  E-value=3.5e-35  Score=306.07  Aligned_cols=212  Identities=24%  Similarity=0.263  Sum_probs=183.7

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +...+..+|++|+|.+++++++.+.+..++.+++.|..+|..+++|+|||||||||||++|+++|++++.+++.++++.+
T Consensus       122 ~~~~p~~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g~~~p~gvLL~GppGtGKT~lAkaia~~~~~~~i~v~~~~l  201 (389)
T PRK03992        122 VIESPNVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSEL  201 (389)
T ss_pred             ecCCCCCCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCceEEECCCCCChHHHHHHHHHHhCCCEEEeehHHH
Confidence            34456789999999999999999999999999999999999999999999999999999999999999999999998776


Q ss_pred             CC------hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecC
Q 011664          261 AD------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       261 ~~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      ..      ...++.+|..  ..+|+||||||+|.++..+..         ...+.++++.+|++..   ..+.+||+|||
T Consensus       202 ~~~~~g~~~~~i~~~f~~a~~~~p~IlfiDEiD~l~~~r~~~~~~~~~~~~~~l~~lL~~ld~~~~---~~~v~VI~aTn  278 (389)
T PRK03992        202 VQKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAEMDGFDP---RGNVKIIAATN  278 (389)
T ss_pred             hHhhccchHHHHHHHHHHHHhcCCeEEEEechhhhhcccccCCCCccHHHHHHHHHHHHhccccCC---CCCEEEEEecC
Confidence            32      3446667754  457999999999999865432         1346778888998765   46788999999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      +++.+|+|++||||||..|+||+|+.++|.+|++.++.........++..++..+.|||++||..+|..+..
T Consensus       279 ~~~~ld~allRpgRfd~~I~v~~P~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA~~  350 (389)
T PRK03992        279 RIDILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGM  350 (389)
T ss_pred             ChhhCCHHHcCCccCceEEEECCCCHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999876655555678999999999999999999987654

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

Probab=100.00  E-value=5.4e-35  Score=278.85  Aligned_cols=198  Identities=18%  Similarity=0.292  Sum_probs=176.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh-
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD-  263 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~-  263 (480)
                      +..+|||++|++++|+..+ .+..++.+|+.|..+   .|+++|+|||||||||++|+|+|++...+++.+..+++.++ 
T Consensus       116 ~~it~ddViGqEeAK~kcr-li~~yLenPe~Fg~W---APknVLFyGppGTGKTm~Akalane~kvp~l~vkat~liGeh  191 (368)
T COG1223         116 SDITLDDVIGQEEAKRKCR-LIMEYLENPERFGDW---APKNVLFYGPPGTGKTMMAKALANEAKVPLLLVKATELIGEH  191 (368)
T ss_pred             ccccHhhhhchHHHHHHHH-HHHHHhhChHHhccc---CcceeEEECCCCccHHHHHHHHhcccCCceEEechHHHHHHH
Confidence            4579999999999999986 677899999988665   48899999999999999999999999999999998887652 


Q ss_pred             -----HHHHHHHHhh--cCCcEEEEecccccccCccc-------ccchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          264 -----ADLKSLLLQT--TSKSVILIEDLDRFLVEKPA-------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       264 -----~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~-------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                           ..+++++.++  .+|||+||||+|+++-++.-       ...++.||..|||+..   +++++.|++||+|+.||
T Consensus       192 VGdgar~Ihely~rA~~~aPcivFiDE~DAiaLdRryQelRGDVsEiVNALLTelDgi~e---neGVvtIaaTN~p~~LD  268 (368)
T COG1223         192 VGDGARRIHELYERARKAAPCIVFIDELDAIALDRRYQELRGDVSEIVNALLTELDGIKE---NEGVVTIAATNRPELLD  268 (368)
T ss_pred             hhhHHHHHHHHHHHHHhcCCeEEEehhhhhhhhhhhHHHhcccHHHHHHHHHHhccCccc---CCceEEEeecCChhhcC
Confidence                 4478888554  68999999999999876543       2457889999999987   79999999999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      ||+++  ||+..|+|.+|+.++|..|++.|.+..+.++..+++.+++.+.|+|+.||.+-+.
T Consensus       269 ~aiRs--RFEeEIEF~LP~~eEr~~ile~y~k~~Plpv~~~~~~~~~~t~g~SgRdikekvl  328 (368)
T COG1223         269 PAIRS--RFEEEIEFKLPNDEERLEILEYYAKKFPLPVDADLRYLAAKTKGMSGRDIKEKVL  328 (368)
T ss_pred             HHHHh--hhhheeeeeCCChHHHHHHHHHHHHhCCCccccCHHHHHHHhCCCCchhHHHHHH
Confidence            99999  9999999999999999999999999999999889999999999999999987553

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

Probab=100.00  E-value=2.1e-35  Score=282.39  Aligned_cols=224  Identities=22%  Similarity=0.230  Sum_probs=194.1

Q ss_pred             eCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC
Q 011664          180 SVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR  259 (480)
Q Consensus       180 ~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~  259 (480)
                      .|...+.+|++|++|-.++.+.+++.++.++.+|+.|-++|+.+|+|+|||||||||||.+|+|+|+..++.|+.+-.|+
T Consensus       167 ~veekpdvty~dvggckeqieklrevve~pll~perfv~lgidppkgvllygppgtgktl~aravanrtdacfirvigse  246 (435)
T KOG0729|consen  167 QVEEKPDVTYSDVGGCKEQIEKLREVVELPLLHPERFVNLGIDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSE  246 (435)
T ss_pred             EeecCCCcccccccchHHHHHHHHHHHhccccCHHHHhhcCCCCCCceEEeCCCCCchhHHHHHHhcccCceEEeehhHH
Confidence            45566789999999999999999999999999999999999999999999999999999999999999999999998887


Q ss_pred             cC----C--hHHHHHHHH--hhcCCcEEEEecccccccCcc---------cccchhhhhhhcccccccccCCceEEEEec
Q 011664          260 VA----D--DADLKSLLL--QTTSKSVILIEDLDRFLVEKP---------AAVSLSGVLNFMDGVLNSCCFEERVMVFTM  322 (480)
Q Consensus       260 ~~----~--~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~---------~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT  322 (480)
                      +.    +  ..-++++|.  +....||||+||||++.+.+-         -++++-+|++++||+..   ..++-|+++|
T Consensus       247 lvqkyvgegarmvrelf~martkkaciiffdeidaiggarfddg~ggdnevqrtmleli~qldgfdp---rgnikvlmat  323 (435)
T KOG0729|consen  247 LVQKYVGEGARMVRELFEMARTKKACIIFFDEIDAIGGARFDDGAGGDNEVQRTMLELINQLDGFDP---RGNIKVLMAT  323 (435)
T ss_pred             HHHHHhhhhHHHHHHHHHHhcccceEEEEeeccccccCccccCCCCCcHHHHHHHHHHHHhccCCCC---CCCeEEEeec
Confidence            64    2  334788885  445679999999999987442         23678899999999987   5677788999


Q ss_pred             CCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHH
Q 011664          323 NSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALK  402 (480)
Q Consensus       323 N~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~  402 (480)
                      |+|+.|||||+||||+|+.++|.+|+.+.|..|++.+.......-+..++-|+....+-|+|+|..+|..+.+.+.++-+
T Consensus       324 nrpdtldpallrpgrldrkvef~lpdlegrt~i~kihaksmsverdir~ellarlcpnstgaeirsvcteagmfairarr  403 (435)
T KOG0729|consen  324 NRPDTLDPALLRPGRLDRKVEFGLPDLEGRTHIFKIHAKSMSVERDIRFELLARLCPNSTGAEIRSVCTEAGMFAIRARR  403 (435)
T ss_pred             CCCCCcCHhhcCCcccccceeccCCcccccceeEEEeccccccccchhHHHHHhhCCCCcchHHHHHHHHhhHHHHHHHh
Confidence            99999999999999999999999999999999999887655555455567788888899999999999998888877766


Q ss_pred             HHHH
Q 011664          403 SVIT  406 (480)
Q Consensus       403 ~~i~  406 (480)
                      ++..
T Consensus       404 k~at  407 (435)
T KOG0729|consen  404 KVAT  407 (435)
T ss_pred             hhhh
Confidence            6543

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

Probab=100.00  E-value=1.4e-34  Score=303.37  Aligned_cols=211  Identities=23%  Similarity=0.291  Sum_probs=182.6

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...++.+|++|+|.++++++|.+.+..++.+++.|..+|..+++|+|||||||||||++|+++|++++.+++.+..+++.
T Consensus       175 ~~~p~~~~~DIgGl~~qi~~l~e~v~lpl~~p~~~~~~gi~~p~gVLL~GPPGTGKT~LAraIA~el~~~fi~V~~seL~  254 (438)
T PTZ00361        175 DKAPLESYADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELI  254 (438)
T ss_pred             ccCCCCCHHHhcCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCcEEEEECCCCCCHHHHHHHHHHhhCCCEEEEecchhh
Confidence            34467899999999999999999999999999999999999999999999999999999999999999999999877653


Q ss_pred             C------hHHHHHHHH--hhcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 D------DADLKSLLL--QTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ~------~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      +      ...++.+|.  ....|+||||||||.++..+..         ...+.++|+.|||+..   ..++.||+|||+
T Consensus       255 ~k~~Ge~~~~vr~lF~~A~~~~P~ILfIDEID~l~~kR~~~~sgg~~e~qr~ll~LL~~Ldg~~~---~~~V~VI~ATNr  331 (438)
T PTZ00361        255 QKYLGDGPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEKEIQRTMLELLNQLDGFDS---RGDVKVIMATNR  331 (438)
T ss_pred             hhhcchHHHHHHHHHHHHHhCCCcEEeHHHHHHHhccCCCCCCcccHHHHHHHHHHHHHHhhhcc---cCCeEEEEecCC
Confidence            2      233666664  3468999999999999865432         2346789999999865   467889999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      ++.||+|++||||||.+|+|++|+.++|.+|++.++.........+++.++..+.|||++||..+|..|..
T Consensus       332 ~d~LDpaLlRpGRfd~~I~~~~Pd~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA~~  402 (438)
T PTZ00361        332 IESLDPALIRPGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGL  402 (438)
T ss_pred             hHHhhHHhccCCeeEEEEEeCCCCHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999876655555578899999999999999999976544

>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH

Probab=100.00  E-value=8.6e-34  Score=304.56  Aligned_cols=206  Identities=23%  Similarity=0.337  Sum_probs=180.3

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC--
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA--  261 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~--  261 (480)
                      .+.++|++|+|.+++|+++.+.+. ++++++.|...|..+++|+|||||||||||++|+++|++++.+++.++++++.  
T Consensus        49 ~~~~~~~di~g~~~~k~~l~~~~~-~l~~~~~~~~~g~~~~~giLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~~  127 (495)
T TIGR01241        49 KPKVTFKDVAGIDEAKEELMEIVD-FLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM  127 (495)
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHH-HHHCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCeeeccHHHHHHH
Confidence            467899999999999999997554 68999999999999999999999999999999999999999999999987653  


Q ss_pred             ----ChHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          262 ----DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       262 ----~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                          +...++.+|..+  .+||||||||||.++..+..         ...+++||+.||++.+   ..+++||+|||+|+
T Consensus       128 ~~g~~~~~l~~~f~~a~~~~p~Il~iDEid~l~~~r~~~~~~~~~~~~~~~~~lL~~~d~~~~---~~~v~vI~aTn~~~  204 (495)
T TIGR01241       128 FVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGNDEREQTLNQLLVEMDGFGT---NTGVIVIAATNRPD  204 (495)
T ss_pred             HhcccHHHHHHHHHHHHhcCCCEEEEechhhhhhccccCcCCccHHHHHHHHHHHhhhccccC---CCCeEEEEecCChh
Confidence                345688888654  57999999999999865432         2457889999999876   56788999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .||||++||||||.+|++++|+.++|.+|++.++.........++..++..+.|||++||..+|..+
T Consensus       205 ~ld~al~r~gRfd~~i~i~~Pd~~~R~~il~~~l~~~~~~~~~~l~~la~~t~G~sgadl~~l~~eA  271 (495)
T TIGR01241       205 VLDPALLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEA  271 (495)
T ss_pred             hcCHHHhcCCcceEEEEcCCCCHHHHHHHHHHHHhcCCCCcchhHHHHHHhCCCCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999766555456788999999999999999999765

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

>CHL00195 ycf46 Ycf46; Provisional

Probab=100.00  E-value=1.4e-33  Score=299.67  Aligned_cols=202  Identities=21%  Similarity=0.257  Sum_probs=166.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      +..+|++|+|.+.+|+.+.+....|..   .+...|.++++|+|||||||||||++|+++|++++.+++.++++.+.   
T Consensus       223 ~~~~~~dvgGl~~lK~~l~~~~~~~~~---~~~~~gl~~pkGILL~GPpGTGKTllAkaiA~e~~~~~~~l~~~~l~~~~  299 (489)
T CHL00195        223 VNEKISDIGGLDNLKDWLKKRSTSFSK---QASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGI  299 (489)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHhhH---HHHhcCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEEEhHHhcccc
Confidence            457899999999999999876655533   34567899999999999999999999999999999999999986543   


Q ss_pred             -C--hHHHHHHHH--hhcCCcEEEEecccccccCccc-------ccchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          262 -D--DADLKSLLL--QTTSKSVILIEDLDRFLVEKPA-------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       262 -~--~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~~-------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                       +  +..++++|.  +..+||||||||||.++..+..       ...++.|++.|+..     ...++||+|||+++.||
T Consensus       300 vGese~~l~~~f~~A~~~~P~IL~IDEID~~~~~~~~~~d~~~~~rvl~~lL~~l~~~-----~~~V~vIaTTN~~~~Ld  374 (489)
T CHL00195        300 VGESESRMRQMIRIAEALSPCILWIDEIDKAFSNSESKGDSGTTNRVLATFITWLSEK-----KSPVFVVATANNIDLLP  374 (489)
T ss_pred             cChHHHHHHHHHHHHHhcCCcEEEehhhhhhhccccCCCCchHHHHHHHHHHHHHhcC-----CCceEEEEecCChhhCC
Confidence             3  455888885  4568999999999998764321       13356677777642     34678899999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCC--chhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL--FPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l--~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      ||++||||||..|+++.|+.++|.+|++.++.......  ..+++.|+..+.||||+||.++|..+.
T Consensus       375 ~allR~GRFD~~i~v~lP~~~eR~~Il~~~l~~~~~~~~~~~dl~~La~~T~GfSGAdI~~lv~eA~  441 (489)
T CHL00195        375 LEILRKGRFDEIFFLDLPSLEEREKIFKIHLQKFRPKSWKKYDIKKLSKLSNKFSGAEIEQSIIEAM  441 (489)
T ss_pred             HHHhCCCcCCeEEEeCCcCHHHHHHHHHHHHhhcCCCcccccCHHHHHhhcCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999998654322  457889999999999999999987653

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

Probab=100.00  E-value=1.2e-33  Score=290.84  Aligned_cols=247  Identities=22%  Similarity=0.277  Sum_probs=210.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      .++.|++++|++.+|+.+.+.+..++.++..|..+.- +.+|+||.||||||||+|++|||.|+++.|+.++.+++.   
T Consensus       148 ~~v~~~di~gl~~~k~~l~e~vi~p~lr~d~F~glr~-p~rglLLfGPpgtGKtmL~~aiAsE~~atff~iSassLtsK~  226 (428)
T KOG0740|consen  148 RNVGWDDIAGLEDAKQSLKEAVILPLLRPDLFLGLRE-PVRGLLLFGPPGTGKTMLAKAIATESGATFFNISASSLTSKY  226 (428)
T ss_pred             CcccccCCcchhhHHHHhhhhhhhcccchHhhhcccc-ccchhheecCCCCchHHHHHHHHhhhcceEeeccHHHhhhhc
Confidence            5588999999999999999999999999999988754 567999999999999999999999999999999987654   


Q ss_pred             -ChH--HHHHHH--HhhcCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          262 -DDA--DLKSLL--LQTTSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       262 -~~~--~l~~l~--~~~~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                       ++.  .++.+|  ++..+|+||||||||.++..+..+      +...++|.++++..+ ...+.++||+|||.||.+|.
T Consensus       227 ~Ge~eK~vralf~vAr~~qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~~s-~~~drvlvigaTN~P~e~De  305 (428)
T KOG0740|consen  227 VGESEKLVRALFKVARSLQPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGKNS-APDDRVLVIGATNRPWELDE  305 (428)
T ss_pred             cChHHHHHHHHHHHHHhcCCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccccC-CCCCeEEEEecCCCchHHHH
Confidence             443  477777  566799999999999999876433      457899999999987 55566777889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc-hhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHH--HHH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF-PQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSV--ITA  407 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~-~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~--i~~  407 (480)
                      |++|  ||.+++++|+|+.++|..++.+++...++.+. .+++.|++.|+|||++||.++|+.+.+.+.+.+...  ++.
T Consensus       306 a~~R--rf~kr~yiplPd~etr~~~~~~ll~~~~~~l~~~d~~~l~~~Tegysgsdi~~l~kea~~~p~r~~~~~~~~~~  383 (428)
T KOG0740|consen  306 AARR--RFVKRLYIPLPDYETRSLLWKQLLKEQPNGLSDLDISLLAKVTEGYSGSDITALCKEAAMGPLRELGGTTDLEF  383 (428)
T ss_pred             HHHH--HhhceeeecCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHhcCcccccHHHHHHHhhcCchhhcccchhhhh
Confidence            9999  99999999999999999999999988766665 588999999999999999999999988887766643  111


Q ss_pred             HHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcc
Q 011664          408 LQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD  472 (480)
Q Consensus       408 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~  472 (480)
                      .                                ..-..|++++.||+.+     ++.++|++|..
T Consensus       384 ~--------------------------------~~~~~r~i~~~df~~a-----~~~i~~~~s~~  411 (428)
T KOG0740|consen  384 I--------------------------------DADKIRPITYPDFKNA-----FKNIKPSVSLE  411 (428)
T ss_pred             c--------------------------------chhccCCCCcchHHHH-----HHhhccccCcc
Confidence            1                                0112388999999999     99999999943

>TIGR03689 pup_AAA proteasome ATPase

Probab=100.00  E-value=2.3e-32  Score=290.31  Aligned_cols=202  Identities=19%  Similarity=0.322  Sum_probs=167.2

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc----------EE
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD----------VY  253 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~----------~~  253 (480)
                      .++++|++|+|++++++.|++.+..++.+++.|...|+++++|+|||||||||||++|+++|++++.+          |+
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            35789999999999999999999999999999999999999999999999999999999999998654          34


Q ss_pred             EEeCCCc----CC--hHHHHHHHHhh------cCCcEEEEecccccccCcccc-------cchhhhhhhcccccccccCC
Q 011664          254 DVDLSRV----AD--DADLKSLLLQT------TSKSVILIEDLDRFLVEKPAA-------VSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       254 ~i~~s~~----~~--~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~-------~~ls~lL~~ldg~~~~~~~~  314 (480)
                      .+..+++    .+  +..++.+|..+      ..|+||||||+|+++..++..       ..+++||++|||+.+   .+
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 NIKGPELLNKYVGETERQIRLIFQRAREKASDGRPVIVFFDEMDSIFRTRGSGVSSDVETTVVPQLLSELDGVES---LD  332 (512)
T ss_pred             eccchhhcccccchHHHHHHHHHHHHHHHhhcCCCceEEEehhhhhhcccCCCccchHHHHHHHHHHHHhccccc---CC
Confidence            4443332    22  33466666443      269999999999998765432       346899999999976   46


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      +++||+|||+++.|||||+||||||.+|+|++|+.++|++|++.|+... .++..+   + ....|++++++..++..+
T Consensus       333 ~ViVI~ATN~~d~LDpALlRpGRfD~~I~~~~Pd~e~r~~Il~~~l~~~-l~l~~~---l-~~~~g~~~a~~~al~~~a  406 (512)
T TIGR03689       333 NVIVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFSKYLTDS-LPLDAD---L-AEFDGDREATAAALIQRA  406 (512)
T ss_pred             ceEEEeccCChhhCCHhhcCccccceEEEeCCCCHHHHHHHHHHHhhcc-CCchHH---H-HHhcCCCHHHHHHHHHHH
Confidence            7899999999999999999999999999999999999999999998642 233222   2 345799999999998764

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.

>CHL00176 ftsH cell division protein; Validated

Probab=100.00  E-value=3.6e-32  Score=297.12  Aligned_cols=207  Identities=25%  Similarity=0.325  Sum_probs=179.1

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-  261 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-  261 (480)
                      .....+|++++|.+++|+++.+. ..+++.++.|..+|..+++|+||+||||||||++|+++|++++.+++.++++++. 
T Consensus       176 ~~~~~~f~dv~G~~~~k~~l~ei-v~~lk~~~~~~~~g~~~p~gVLL~GPpGTGKT~LAralA~e~~~p~i~is~s~f~~  254 (638)
T CHL00176        176 ADTGITFRDIAGIEEAKEEFEEV-VSFLKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVE  254 (638)
T ss_pred             cCCCCCHHhccChHHHHHHHHHH-HHHHhCHHHHhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeeeccHHHHHH
Confidence            34568999999999999999764 5678999999999999999999999999999999999999999999999988754 


Q ss_pred             -----ChHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          262 -----DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       262 -----~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                           +...++.+|..+  ..||||||||||+++..++.         ..++++||+.|||+..   ..+++||+|||++
T Consensus       255 ~~~g~~~~~vr~lF~~A~~~~P~ILfIDEID~l~~~r~~~~~~~~~e~~~~L~~LL~~~dg~~~---~~~ViVIaaTN~~  331 (638)
T CHL00176        255 MFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIGGGNDEREQTLNQLLTEMDGFKG---NKGVIVIAATNRV  331 (638)
T ss_pred             HhhhhhHHHHHHHHHHHhcCCCcEEEEecchhhhhcccCCCCCCcHHHHHHHHHHHhhhccccC---CCCeeEEEecCch
Confidence                 234577778654  57999999999999754421         2457889999999876   5678899999999


Q ss_pred             ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          326 DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       326 ~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      +.+|+||+||||||.+|++++|+.++|.+|++.++.........++..++..+.|||++||.++|..+
T Consensus       332 ~~LD~ALlRpGRFd~~I~v~lPd~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneA  399 (638)
T CHL00176        332 DILDAALLRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEA  399 (638)
T ss_pred             HhhhhhhhccccCceEEEECCCCHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999999875544455678999999999999999999765

>TIGR01242 26Sp45 26S proteasome subunit P45 family

Probab=99.98  E-value=8e-32  Score=278.80  Aligned_cols=212  Identities=22%  Similarity=0.261  Sum_probs=179.2

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...+..+|++|+|.++++++|.+.+..++.+++.|..+|..+++|+|||||||||||++|+++|++++.+++.+..+.+.
T Consensus       114 ~~~p~~~~~di~Gl~~~~~~l~~~i~~~~~~~~~~~~~g~~~p~gvLL~GppGtGKT~lakaia~~l~~~~~~v~~~~l~  193 (364)
T TIGR01242       114 EERPNVSYEDIGGLEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV  193 (364)
T ss_pred             ccCCCCCHHHhCChHHHHHHHHHHHHHHhcCHHHHHhcCCCCCceEEEECCCCCCHHHHHHHHHHhCCCCEEecchHHHH
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999998765543


Q ss_pred             C------hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 D------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      .      ...++.+|..  ...|+||||||+|.++..+..         ...+.++++.+|++..   ..++.||+|||+
T Consensus       194 ~~~~g~~~~~i~~~f~~a~~~~p~il~iDEiD~l~~~~~~~~~~~~~~~~~~l~~ll~~ld~~~~---~~~v~vI~ttn~  270 (364)
T TIGR01242       194 RKYIGEGARLVREIFELAKEKAPSIIFIDEIDAIAAKRTDSGTSGDREVQRTLMQLLAELDGFDP---RGNVKVIAATNR  270 (364)
T ss_pred             HHhhhHHHHHHHHHHHHHHhcCCcEEEhhhhhhhccccccCCCCccHHHHHHHHHHHHHhhCCCC---CCCEEEEEecCC
Confidence            2      2235556643  457999999999998754321         2346778888888755   457889999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhc
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNS  396 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~  396 (480)
                      ++.+|++++||||||..|+|+.|+.++|.+|++.++.........+++.++..+.|||++||..+|..+...
T Consensus       271 ~~~ld~al~r~grfd~~i~v~~P~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~~A~~~  342 (364)
T TIGR01242       271 PDILDPALLRPGRFDRIIEVPLPDFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMF  342 (364)
T ss_pred             hhhCChhhcCcccCceEEEeCCcCHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999998665544445788999999999999999999866543

Many proteins may score above the trusted cutoff because an internal

>CHL00206 ycf2 Ycf2; Provisional

Probab=99.97  E-value=4.7e-32  Score=311.17  Aligned_cols=187  Identities=16%  Similarity=0.162  Sum_probs=153.2

Q ss_pred             hhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh----------------------------
Q 011664          212 AKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD----------------------------  263 (480)
Q Consensus       212 ~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~----------------------------  263 (480)
                      ++..+.++|..+++|+||+||||||||.||+|+|++++++|+.++++++.+.                            
T Consensus      1618 ~kP~slrLGl~pPKGILLiGPPGTGKTlLAKALA~es~VPFIsISgs~fl~~~~~~~~~d~i~iges~~~~~~~~~~~~~ 1697 (2281)
T CHL00206       1618 GKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDDSDDIDDSDDIDRDL 1697 (2281)
T ss_pred             CcCHHHHcCCCCCCceEEECCCCCCHHHHHHHHHHhcCCceEEEEHHHHhhccccccccccccccccccccccccccccc
Confidence            3456678899999999999999999999999999999999999998765420                            


Q ss_pred             ---------------------HHHHHHH--HhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEE
Q 011664          264 ---------------------ADLKSLL--LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF  320 (480)
Q Consensus       264 ---------------------~~l~~l~--~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~  320 (480)
                                           ..++.+|  ++..+||||+|||||+++.......++++|++.|||....+...+++||+
T Consensus      1698 ~~e~~e~~n~~~~~m~~~e~~~rIr~lFelARk~SPCIIFIDEIDaL~~~ds~~ltL~qLLneLDg~~~~~s~~~VIVIA 1777 (2281)
T CHL00206       1698 DTELLTMMNALTMDMMPKIDRFYITLQFELAKAMSPCIIWIPNIHDLNVNESNYLSLGLLVNSLSRDCERCSTRNILVIA 1777 (2281)
T ss_pred             chhhhhhcchhhhhhhhhhhHHHHHHHHHHHHHCCCeEEEEEchhhcCCCccceehHHHHHHHhccccccCCCCCEEEEE
Confidence                                 1145566  44578999999999999876555566899999999875423356789999


Q ss_pred             ecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc---hhHHHHHHhCCCCCHHHHHHHHHHhhhcH
Q 011664          321 TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF---PQVEEIFQNGSSLSPAEIGELMIANRNSP  397 (480)
Q Consensus       321 tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~---~~i~~l~~~~~g~s~adI~~ll~~a~~~~  397 (480)
                      |||+|+.|||||+||||||++|+++.|+..+|++++...+...+..+.   .+++.+|..|.|||||||+++|.+|...+
T Consensus      1778 ATNRPD~LDPALLRPGRFDR~I~Ir~Pd~p~R~kiL~ILl~tkg~~L~~~~vdl~~LA~~T~GfSGADLanLvNEAaliA 1857 (2281)
T CHL00206       1778 STHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTNEALSIS 1857 (2281)
T ss_pred             eCCCcccCCHhHcCCCCCCeEEEeCCCCchhHHHHHHHHHhhcCCCCCcccccHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999988765433333333   35789999999999999999998876544


Q ss_pred             H
Q 011664          398 S  398 (480)
Q Consensus       398 ~  398 (480)
                      .
T Consensus      1858 i 1858 (2281)
T CHL00206       1858 I 1858 (2281)
T ss_pred             H
Confidence            4

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

Probab=99.97  E-value=4.7e-32  Score=264.36  Aligned_cols=208  Identities=22%  Similarity=0.305  Sum_probs=177.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--  262 (480)
                      ...+|+.++|+-++..++++.++.++..|..|.++|+.+|.|++||||||||||.+|+++|..+|++|+.+..+.+.+  
T Consensus       127 ~~~s~~~~ggl~~qirelre~ielpl~np~lf~rvgIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~lv~ky  206 (388)
T KOG0651|consen  127 RNISFENVGGLFYQIRELREVIELPLTNPELFLRVGIKPPKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKY  206 (388)
T ss_pred             cccCHHHhCChHHHHHHHHhheEeeccCchhccccCCCCCceeEEeCCCCCchhHHHHHHHHhcCCceEEeeHhhhhhhh
Confidence            346899999999999999999999999999999999999999999999999999999999999999999999887764  


Q ss_pred             --hH--HHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          263 --DA--DLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       263 --~~--~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                        ++  -+++.|..+  ..|||||+||||+.++.+.+         +.++-+|+++|||+..   ...+-+|+|||+|+.
T Consensus       207 iGEsaRlIRemf~yA~~~~pciifmdeiDAigGRr~se~Ts~dreiqrTLMeLlnqmdgfd~---l~rVk~ImatNrpdt  283 (388)
T KOG0651|consen  207 IGESARLIRDMFRYAREVIPCIIFMDEIDAIGGRRFSEGTSSDREIQRTLMELLNQMDGFDT---LHRVKTIMATNRPDT  283 (388)
T ss_pred             cccHHHHHHHHHHHHhhhCceEEeehhhhhhccEEeccccchhHHHHHHHHHHHHhhccchh---cccccEEEecCCccc
Confidence              32  367777544  57999999999999875533         2568889999999987   567779999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |||||+||||+|+.+++|.|+...|..|++.+-......-.-+.+.+.+-.+||.++|+.+.|..+..
T Consensus       284 LdpaLlRpGRldrk~~iPlpne~~r~~I~Kih~~~i~~~Geid~eaivK~~d~f~gad~rn~~tEag~  351 (388)
T KOG0651|consen  284 LDPALLRPGRLDRKVEIPLPNEQARLGILKIHVQPIDFHGEIDDEAILKLVDGFNGADLRNVCTEAGM  351 (388)
T ss_pred             cchhhcCCccccceeccCCcchhhceeeEeeccccccccccccHHHHHHHHhccChHHHhhhcccccc
Confidence            99999999999999999999999999987766543322212235677777899999999998876543

>PRK10733 hflB ATP-dependent metalloprotease; Reviewed

Probab=99.97  E-value=2.2e-30  Score=285.32  Aligned_cols=207  Identities=23%  Similarity=0.322  Sum_probs=178.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      ...+|+++.|.+..++.+.+.+. ++..+..|..++...++|+||+||||||||++++++|++++.+|+.++++++.   
T Consensus       147 ~~~~~~di~g~~~~~~~l~~i~~-~~~~~~~~~~~~~~~~~gill~G~~G~GKt~~~~~~a~~~~~~f~~is~~~~~~~~  225 (644)
T PRK10733        147 IKTTFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMF  225 (644)
T ss_pred             hhCcHHHHcCHHHHHHHHHHHHH-HhhCHHHHHhcCCCCCCcEEEECCCCCCHHHHHHHHHHHcCCCEEEEehHHhHHhh
Confidence            45789999999999999987654 57778888888888899999999999999999999999999999999987643   


Q ss_pred             ---ChHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          262 ---DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       262 ---~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                         +...++.+|..+  .+||||||||||.++..++.         ...+++||..|||+.+   ..++++|+|||+|+.
T Consensus       226 ~g~~~~~~~~~f~~a~~~~P~IifIDEiD~l~~~r~~~~~g~~~~~~~~ln~lL~~mdg~~~---~~~vivIaaTN~p~~  302 (644)
T PRK10733        226 VGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG---NEGIIVIAATNRPDV  302 (644)
T ss_pred             hcccHHHHHHHHHHHHhcCCcEEEehhHhhhhhccCCCCCCCchHHHHHHHHHHHhhhcccC---CCCeeEEEecCChhh
Confidence               245577777544  58999999999999865532         2467899999999876   577899999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      ||+|++||||||++|++++|+.++|.+|++.++...+.....++..++..+.|||++||.++|+.+..
T Consensus       303 lD~Al~RpgRfdr~i~v~~Pd~~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~  370 (644)
T PRK10733        303 LDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAAL  370 (644)
T ss_pred             cCHHHhCCcccceEEEcCCCCHHHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999987665555677889999999999999999987644

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.97  E-value=1.5e-29  Score=283.50  Aligned_cols=207  Identities=21%  Similarity=0.309  Sum_probs=179.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      +..+|++|+|.+++++.|.+.+..++.+++.|..+|..+++|+|||||||||||++++++|++++.+++.++++.+.   
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~gi~~~~giLL~GppGtGKT~laraia~~~~~~~i~i~~~~i~~~~  252 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKY  252 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCceEEEECCCCCChHHHHHHHHHHhCCeEEEEecHHHhccc
Confidence            56899999999999999999999999999999999999999999999999999999999999999999999876543   


Q ss_pred             -C--hHHHHHHHHhh--cCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          262 -D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       262 -~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                       +  +..++.+|..+  ..|+||||||||.+++.+..      ...+++|++.||++..   ...++||+|||+++.||+
T Consensus       253 ~g~~~~~l~~lf~~a~~~~p~il~iDEid~l~~~r~~~~~~~~~~~~~~Ll~~ld~l~~---~~~vivI~atn~~~~ld~  329 (733)
T TIGR01243       253 YGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKG---RGRVIVIGATNRPDALDP  329 (733)
T ss_pred             ccHHHHHHHHHHHHHHhcCCcEEEeehhhhhcccccCCcchHHHHHHHHHHHHhhcccc---CCCEEEEeecCChhhcCH
Confidence             2  34577777543  57899999999999876543      2356789999999866   456788889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      +++|||||+..|+++.|+.++|.+|++.+.......-..+++.+++.+.||+++|+..++..+.
T Consensus       330 al~r~gRfd~~i~i~~P~~~~R~~Il~~~~~~~~l~~d~~l~~la~~t~G~~gadl~~l~~~a~  393 (733)
T TIGR01243       330 ALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAA  393 (733)
T ss_pred             HHhCchhccEEEEeCCcCHHHHHHHHHHHhcCCCCccccCHHHHHHhCCCCCHHHHHHHHHHHH
Confidence            9999999999999999999999999998876554444556889999999999999999987653

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.

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

Probab=99.97  E-value=6.7e-30  Score=270.12  Aligned_cols=207  Identities=19%  Similarity=0.255  Sum_probs=186.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      ++.+ ++++|.......+.+.+..++..+..|...|.++++|+|+|||||||||.+++|+|++.++.++.++.+++.   
T Consensus       180 ~~~~-~~~gg~~~~~~~i~e~v~~pl~~~~~~~s~g~~~prg~Ll~gppg~Gkt~l~~aVa~e~~a~~~~i~~peli~k~  258 (693)
T KOG0730|consen  180 PEVG-DDIGGLKRQLSVIRELVELPLRHPALFKSIGIKPPRGLLLYGPPGTGKTFLVRAVANEYGAFLFLINGPELISKF  258 (693)
T ss_pred             cccc-cccchhHHHHHHHHHHHHhhhcchhhhhhcCCCCCCCccccCCCCCChHHHHHHHHHHhCceeEecccHHHHHhc
Confidence            6777 899999999999999999999999999999999999999999999999999999999999999999987654   


Q ss_pred             ---ChHHHHHHHHhh--cC-CcEEEEecccccccCccc-----ccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          262 ---DDADLKSLLLQT--TS-KSVILIEDLDRFLVEKPA-----AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       262 ---~~~~l~~l~~~~--~~-~sII~IDEiD~l~~~~~~-----~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                         +++.+++.|+++  .+ |++|||||+|.+++++..     .+..++++..|||..+   ..++|+++|||+|+.|||
T Consensus       259 ~gEte~~LR~~f~~a~k~~~psii~IdEld~l~p~r~~~~~~e~Rv~sqlltL~dg~~~---~~~vivl~atnrp~sld~  335 (693)
T KOG0730|consen  259 PGETESNLRKAFAEALKFQVPSIIFIDELDALCPKREGADDVESRVVSQLLTLLDGLKP---DAKVIVLAATNRPDSLDP  335 (693)
T ss_pred             ccchHHHHHHHHHHHhccCCCeeEeHHhHhhhCCcccccchHHHHHHHHHHHHHhhCcC---cCcEEEEEecCCccccCh
Confidence               366799999765  35 999999999999986543     3557899999999986   577888999999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhc
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNS  396 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~  396 (480)
                      +++| ||||..+++..|+..+|..|++.+....++.-..++..++..+.||+++|+..+|..+...
T Consensus       336 alRR-gRfd~ev~IgiP~~~~RldIl~~l~k~~~~~~~~~l~~iA~~thGyvGaDL~~l~~ea~~~  400 (693)
T KOG0730|consen  336 ALRR-GRFDREVEIGIPGSDGRLDILRVLTKKMNLLSDVDLEDIAVSTHGYVGADLAALCREASLQ  400 (693)
T ss_pred             hhhc-CCCcceeeecCCCchhHHHHHHHHHHhcCCcchhhHHHHHHHccchhHHHHHHHHHHHHHH
Confidence            9999 9999999999999999999999999887777557889999999999999999999876543

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

Probab=99.96  E-value=3.1e-29  Score=278.20  Aligned_cols=208  Identities=23%  Similarity=0.312  Sum_probs=179.2

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-----cEEEEe--
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-----DVYDVD--  256 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-----~~~~i~--  256 (480)
                      ...++|++|+|+++++..+++-+..++.+|+.|..+++.+|+|+|+|||||||||++|+|+|..+..     .|+.-+  
T Consensus       259 ~~~v~fd~vggl~~~i~~LKEmVl~PLlyPE~f~~~~itpPrgvL~~GppGTGkTl~araLa~~~s~~~~kisffmrkga  338 (1080)
T KOG0732|consen  259 DSSVGFDSVGGLENYINQLKEMVLLPLLYPEFFDNFNITPPRGVLFHGPPGTGKTLMARALAAACSRGNRKISFFMRKGA  338 (1080)
T ss_pred             hcccCccccccHHHHHHHHHHHHHhHhhhhhHhhhcccCCCcceeecCCCCCchhHHHHhhhhhhcccccccchhhhcCc
Confidence            3457899999999999999999999999999999999999999999999999999999999998732     344333  


Q ss_pred             --CCCcCCh--HHHHHHHHh--hcCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCC
Q 011664          257 --LSRVADD--ADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       257 --~s~~~~~--~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                        ++.+.++  .+++-+|.+  ...|+|||+||||-+++-+++.      ..++.||..|||+.+   .+.+++|+|||+
T Consensus       339 D~lskwvgEaERqlrllFeeA~k~qPSIIffdeIdGlapvrSskqEqih~SIvSTLLaLmdGlds---RgqVvvigATnR  415 (1080)
T KOG0732|consen  339 DCLSKWVGEAERQLRLLFEEAQKTQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDS---RGQVVVIGATNR  415 (1080)
T ss_pred             hhhccccCcHHHHHHHHHHHHhccCceEEeccccccccccccchHHHhhhhHHHHHHHhccCCCC---CCceEEEcccCC
Confidence              4556654  458888854  4689999999999998876443      457889999999988   577888999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      |+.+||||+||||||+.++||+|+.++|.+|+..+......++... ...|++.+.||-+|||+.+|..|.
T Consensus       416 pda~dpaLRRPgrfdref~f~lp~~~ar~~Il~Ihtrkw~~~i~~~l~~~la~~t~gy~gaDlkaLCTeAa  486 (1080)
T KOG0732|consen  416 PDAIDPALRRPGRFDREFYFPLPDVDARAKILDIHTRKWEPPISRELLLWLAEETSGYGGADLKALCTEAA  486 (1080)
T ss_pred             ccccchhhcCCcccceeEeeeCCchHHHHHHHHHhccCCCCCCCHHHHHHHHHhccccchHHHHHHHHHHh
Confidence            9999999999999999999999999999999999887766665554 478999999999999999998654

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

Probab=99.96  E-value=7.7e-30  Score=262.56  Aligned_cols=251  Identities=19%  Similarity=0.280  Sum_probs=186.9

Q ss_pred             CCCCcccc--ccChHHHHH-HHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEE-EEe----
Q 011664          185 HPSTFDTI--SMETDLKNR-VKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVY-DVD----  256 (480)
Q Consensus       185 ~~~~~~~i--~g~~~~k~~-l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~-~i~----  256 (480)
                      |.-.|+++  +|++.--.. .+.+...-+-.|+.-+++|++..+|+|||||||||||.+|+.|...+++.=. .++    
T Consensus       214 Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~HVKGiLLyGPPGTGKTLiARqIGkMLNArePKIVNGPeI  293 (744)
T KOG0741|consen  214 PDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKHVKGILLYGPPGTGKTLIARQIGKMLNAREPKIVNGPEI  293 (744)
T ss_pred             CCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccceeeEEEECCCCCChhHHHHHHHHHhcCCCCcccCcHHH
Confidence            34467775  555433332 2333333344688889999999999999999999999999999999876432 233    


Q ss_pred             CCCcCC--hHHHHHHHHhh----------cCCcEEEEecccccccCcccc--------cchhhhhhhcccccccccCCce
Q 011664          257 LSRVAD--DADLKSLLLQT----------TSKSVILIEDLDRFLVEKPAA--------VSLSGVLNFMDGVLNSCCFEER  316 (480)
Q Consensus       257 ~s~~~~--~~~l~~l~~~~----------~~~sII~IDEiD~l~~~~~~~--------~~ls~lL~~ldg~~~~~~~~~~  316 (480)
                      ++++.+  ++++|.+|+.+          ..-.||++||||++|..|++.        ..+++||.-|||+..   -+++
T Consensus       294 L~KYVGeSE~NvR~LFaDAEeE~r~~g~~SgLHIIIFDEiDAICKqRGS~~g~TGVhD~VVNQLLsKmDGVeq---LNNI  370 (744)
T KOG0741|consen  294 LNKYVGESEENVRKLFADAEEEQRRLGANSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKMDGVEQ---LNNI  370 (744)
T ss_pred             HHHhhcccHHHHHHHHHhHHHHHHhhCccCCceEEEehhhHHHHHhcCCCCCCCCccHHHHHHHHHhcccHHh---hhcE
Confidence            334444  56799999654          133799999999999876543        348999999999988   6889


Q ss_pred             EEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccC--CC--CCchhHHHHHHhCCCCCHHHHHHHHHH
Q 011664          317 VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK--DH--KLFPQVEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       317 ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~--~~--~l~~~i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      +||+-||+++.+|+||+|||||+.++++.+||++.|.+|++.+....  ..  .-+.++++||..|.+||||+|..+++.
T Consensus       371 LVIGMTNR~DlIDEALLRPGRlEVqmEIsLPDE~gRlQIl~IHT~rMre~~~l~~dVdl~elA~lTKNfSGAEleglVks  450 (744)
T KOG0741|consen  371 LVIGMTNRKDLIDEALLRPGRLEVQMEISLPDEKGRLQILKIHTKRMRENNKLSADVDLKELAALTKNFSGAELEGLVKS  450 (744)
T ss_pred             EEEeccCchhhHHHHhcCCCceEEEEEEeCCCccCceEEEEhhhhhhhhcCCCCCCcCHHHHHHHhcCCchhHHHHHHHH
Confidence            99999999999999999999999999999999999999999887642  22  234467899999999999999999987


Q ss_pred             hhhcHHHHHHHHHHHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc
Q 011664          393 NRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF  471 (480)
Q Consensus       393 a~~~~~~al~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~  471 (480)
                      |...   |+.+.++.-                         .++...+.....-.|++.||..|     +..++|+...
T Consensus       451 A~S~---A~nR~vk~~-------------------------~~~~~~~~~~e~lkV~r~DFl~a-----L~dVkPAFG~  496 (744)
T KOG0741|consen  451 AQSF---AMNRHVKAG-------------------------GKVEVDPVAIENLKVTRGDFLNA-----LEDVKPAFGI  496 (744)
T ss_pred             HHHH---HHHhhhccC-------------------------cceecCchhhhheeecHHHHHHH-----HHhcCcccCC
Confidence            6543   344333211                         00001122222356899999999     7889998764

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

Probab=99.96  E-value=5.5e-28  Score=243.92  Aligned_cols=192  Identities=13%  Similarity=0.078  Sum_probs=142.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      ...+|+++.|.=.+-....+.+...+ .+.+....|+.+|++++||||||||||++|+++|+++|.+++.++.+++.   
T Consensus       110 ~~~~f~~~~g~~~~~p~f~dk~~~hi-~kn~l~~~~ik~PlgllL~GPPGcGKTllAraiA~elg~~~i~vsa~eL~sk~  188 (413)
T PLN00020        110 RTRSFDNLVGGYYIAPAFMDKVAVHI-AKNFLALPNIKVPLILGIWGGKGQGKSFQCELVFKKMGIEPIVMSAGELESEN  188 (413)
T ss_pred             hhcchhhhcCccccCHHHHHHHHHHH-HhhhhhccCCCCCeEEEeeCCCCCCHHHHHHHHHHHcCCCeEEEEHHHhhcCc
Confidence            44577777333333333333222221 12233446889999999999999999999999999999999999977654   


Q ss_pred             -C--hHHHHHHHHhhc-------CCcEEEEecccccccCcccc------cc-hhhhhhhcccc--------c-ccccCCc
Q 011664          262 -D--DADLKSLLLQTT-------SKSVILIEDLDRFLVEKPAA------VS-LSGVLNFMDGV--------L-NSCCFEE  315 (480)
Q Consensus       262 -~--~~~l~~l~~~~~-------~~sII~IDEiD~l~~~~~~~------~~-ls~lL~~ldg~--------~-~~~~~~~  315 (480)
                       +  +..++++|..+.       +||||||||||++++.+++.      +. ..+|++.||+.        | .......
T Consensus       189 vGEsEk~IR~~F~~A~~~a~~~~aPcVLFIDEIDA~~g~r~~~~~tv~~qiV~~tLLnl~D~p~~v~l~G~w~~~~~~~~  268 (413)
T PLN00020        189 AGEPGKLIRQRYREAADIIKKKGKMSCLFINDLDAGAGRFGTTQYTVNNQMVNGTLMNIADNPTNVSLGGDWREKEEIPR  268 (413)
T ss_pred             CCcHHHHHHHHHHHHHHHhhccCCCeEEEEehhhhcCCCCCCCCcchHHHHHHHHHHHHhcCCccccccccccccccCCC
Confidence             3  455899996543       69999999999999876422      12 36889998863        3 1112456


Q ss_pred             eEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCC
Q 011664          316 RVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSS  380 (480)
Q Consensus       316 ~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g  380 (480)
                      ++||+|||+|+.|||||+||||||+.+  ..|+.++|..|++.+++..+.. ..++..|+..+.|
T Consensus       269 V~VIaTTNrpd~LDpALlRpGRfDk~i--~lPd~e~R~eIL~~~~r~~~l~-~~dv~~Lv~~f~g  330 (413)
T PLN00020        269 VPIIVTGNDFSTLYAPLIRDGRMEKFY--WAPTREDRIGVVHGIFRDDGVS-REDVVKLVDTFPG  330 (413)
T ss_pred             ceEEEeCCCcccCCHhHcCCCCCCcee--CCCCHHHHHHHHHHHhccCCCC-HHHHHHHHHcCCC
Confidence            788899999999999999999999865  5899999999999999876554 4677888876654

>PF14363 AAA_assoc: Domain associated at C-terminal with AAA

Probab=99.86  E-value=1e-21  Score=165.84  Aligned_cols=96  Identities=26%  Similarity=0.373  Sum_probs=89.0

Q ss_pred             hhHHHHHHHHHHHHHHHhh-hhccceEEEEeecCCCCCcchHHHHHHHHhccccCCccccccccccCCCCCceEEecCCC
Q 011664           22 LFKTGLIFVAKKWWRFIED-CLHVHQFFKVPEFNEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFTGKKSNDIVLGLDPN  100 (480)
Q Consensus        22 ~~~~~l~~~~~~~~~~l~~-~~~~~~~~~i~e~~~~~~~~~~~~~~~~yl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  100 (480)
                      |+|++|++++.++++++.. +|+||++++|+|+. |+++|++|+||++||+++++.+++++ ++..++++++++++|++|
T Consensus         1 ~~P~~lr~~~~~~~~~~~~~~~s~~~ti~I~E~~-g~~~N~ly~a~~~YL~s~~s~~a~rL-~~~~~~~~~~~~l~l~~~   78 (98)
T PF14363_consen    1 LLPHELRSYLRSLLRRLFSSRFSPYLTIVIPEFD-GLSRNELYDAAQAYLSSKISPSARRL-KASKSKNSKNLVLSLDDG   78 (98)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCCcEEEEEEeCC-CccccHHHHHHHHHHhhccCccccee-eecccCCCCceEEecCCC
Confidence            6899999999999988665 99999999999997 68999999999999999999999776 688899999999999999


Q ss_pred             CceeecccceeEEEEeccC
Q 011664          101 QLIQDNFLGAPLSWANQDD  119 (480)
Q Consensus       101 ~~~~d~f~g~~~~w~~~~~  119 (480)
                      ++|.|+|+|+++||.+.+.
T Consensus        79 e~V~D~F~Gv~v~W~~~~~   97 (98)
T PF14363_consen   79 EEVVDVFEGVKVWWSSVCT   97 (98)
T ss_pred             CEEEEEECCEEEEEEEEcc
Confidence            9999999999999998764

>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=99.83  E-value=1.4e-19  Score=172.51  Aligned_cols=195  Identities=15%  Similarity=0.206  Sum_probs=131.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA  264 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~  264 (480)
                      .|.+|++++|++++++.+.-.+.....+.        ....++|||||||+||||||+.||++++.++...+...+....
T Consensus        19 RP~~L~efiGQ~~l~~~l~i~i~aa~~r~--------~~l~h~lf~GPPG~GKTTLA~IIA~e~~~~~~~~sg~~i~k~~   90 (233)
T PF05496_consen   19 RPKSLDEFIGQEHLKGNLKILIRAAKKRG--------EALDHMLFYGPPGLGKTTLARIIANELGVNFKITSGPAIEKAG   90 (233)
T ss_dssp             S-SSCCCS-S-HHHHHHHHHHHHHHHCTT--------S---EEEEESSTTSSHHHHHHHHHHHCT--EEEEECCC--SCH
T ss_pred             CCCCHHHccCcHHHHhhhHHHHHHHHhcC--------CCcceEEEECCCccchhHHHHHHHhccCCCeEeccchhhhhHH
Confidence            67899999999999998775554432221        1234799999999999999999999999999999988777778


Q ss_pred             HHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccc----ccC---------CceEEEEecCCCccCccc
Q 011664          265 DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS----CCF---------EERVMVFTMNSKDHVDQA  331 (480)
Q Consensus       265 ~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~----~~~---------~~~ivI~tTN~~~~LD~a  331 (480)
                      ++..++.....+.|||||||+.+-.     ....-|+..|+...-.    .+.         ..--+|+||++...|.++
T Consensus        91 dl~~il~~l~~~~ILFIDEIHRlnk-----~~qe~LlpamEd~~idiiiG~g~~ar~~~~~l~~FTligATTr~g~ls~p  165 (233)
T PF05496_consen   91 DLAAILTNLKEGDILFIDEIHRLNK-----AQQEILLPAMEDGKIDIIIGKGPNARSIRINLPPFTLIGATTRAGLLSSP  165 (233)
T ss_dssp             HHHHHHHT--TT-EEEECTCCC--H-----HHHHHHHHHHHCSEEEEEBSSSSS-BEEEEE----EEEEEESSGCCTSHC
T ss_pred             HHHHHHHhcCCCcEEEEechhhccH-----HHHHHHHHHhccCeEEEEeccccccceeeccCCCceEeeeeccccccchh
Confidence            8888888888899999999998832     1223344444321100    111         123578899999999999


Q ss_pred             ccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          332 LLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       332 LlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |+.  ||.....+.+++.++..+|+.+.....+.++.++. .++|.+. .-||.--..+++..++
T Consensus       166 Lrd--RFgi~~~l~~Y~~~el~~Iv~r~a~~l~i~i~~~~~~~Ia~rs-rGtPRiAnrll~rvrD  227 (233)
T PF05496_consen  166 LRD--RFGIVLRLEFYSEEELAKIVKRSARILNIEIDEDAAEEIARRS-RGTPRIANRLLRRVRD  227 (233)
T ss_dssp             CCT--TSSEEEE----THHHHHHHHHHCCHCTT-EE-HHHHHHHHHCT-TTSHHHHHHHHHHHCC
T ss_pred             HHh--hcceecchhcCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHhc-CCChHHHHHHHHHHHH
Confidence            999  99999999999999999999988877777777655 4666655 6678776777766543

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.

>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=99.82  E-value=2.3e-20  Score=163.65  Aligned_cols=117  Identities=29%  Similarity=0.581  Sum_probs=96.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------hHHHHHHHHhh--cC-CcEEEEecccccccCcc-----
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------DADLKSLLLQT--TS-KSVILIEDLDRFLVEKP-----  292 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------~~~l~~l~~~~--~~-~sII~IDEiD~l~~~~~-----  292 (480)
                      +||+||||||||++|+++|+.++.+++.++++.+.+      ...+...|.++  .. |+||+|||+|.+.+...     
T Consensus         1 ill~G~~G~GKT~l~~~la~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~vl~iDe~d~l~~~~~~~~~~   80 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLARALAQYLGFPFIEIDGSELISSYAGDSEQKIRDFFKKAKKSAKPCVLFIDEIDKLFPKSQPSSSS   80 (132)
T ss_dssp             EEEESSTTSSHHHHHHHHHHHTTSEEEEEETTHHHTSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGTSHHCSTSSSH
T ss_pred             CEEECcCCCCeeHHHHHHHhhcccccccccccccccccccccccccccccccccccccceeeeeccchhccccccccccc
Confidence            689999999999999999999999999999987652      34467777554  34 89999999999987651     


Q ss_pred             -cccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCC
Q 011664          293 -AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       293 -~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~  346 (480)
                       ....+..|++.++.....  ...+++|+|||.++.++++++| |||+.+|++|+
T Consensus        81 ~~~~~~~~L~~~l~~~~~~--~~~~~vI~ttn~~~~i~~~l~~-~rf~~~i~~~~  132 (132)
T PF00004_consen   81 FEQRLLNQLLSLLDNPSSK--NSRVIVIATTNSPDKIDPALLR-SRFDRRIEFPL  132 (132)
T ss_dssp             HHHHHHHHHHHHHHTTTTT--SSSEEEEEEESSGGGSCHHHHS-TTSEEEEEE-S
T ss_pred             ccccccceeeecccccccc--cccceeEEeeCChhhCCHhHHh-CCCcEEEEcCC
Confidence             123467888999887762  3568899999999999999998 89999999984

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 ....

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.81  E-value=1.2e-19  Score=183.03  Aligned_cols=195  Identities=25%  Similarity=0.330  Sum_probs=143.6

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC---
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD---  262 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~---  262 (480)
                      ...|++|+..+.+++.|.+....--+.+     ....+-|++|+|||||||||++|+-+|...|.+.-.....++..   
T Consensus       351 k~pl~~ViL~psLe~Rie~lA~aTaNTK-----~h~apfRNilfyGPPGTGKTm~ArelAr~SGlDYA~mTGGDVAPlG~  425 (630)
T KOG0742|consen  351 KDPLEGVILHPSLEKRIEDLAIATANTK-----KHQAPFRNILFYGPPGTGKTMFARELARHSGLDYAIMTGGDVAPLGA  425 (630)
T ss_pred             CCCcCCeecCHHHHHHHHHHHHHhcccc-----cccchhhheeeeCCCCCCchHHHHHHHhhcCCceehhcCCCccccch
Confidence            3459999999999999876544332221     22335578999999999999999999999999988877766542   


Q ss_pred             --hHHHHHHHH--hh-cCCcEEEEecccccccCcccc-------cchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          263 --DADLKSLLL--QT-TSKSVILIEDLDRFLVEKPAA-------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       263 --~~~l~~l~~--~~-~~~sII~IDEiD~l~~~~~~~-------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                        -..+.++|.  +. ...-+|||||.|+++..+...       ..++.||-- -|-.    ....++|++||+|.++|.
T Consensus       426 qaVTkiH~lFDWakkS~rGLllFIDEADAFLceRnktymSEaqRsaLNAlLfR-TGdq----SrdivLvlAtNrpgdlDs  500 (630)
T KOG0742|consen  426 QAVTKIHKLFDWAKKSRRGLLLFIDEADAFLCERNKTYMSEAQRSALNALLFR-TGDQ----SRDIVLVLATNRPGDLDS  500 (630)
T ss_pred             HHHHHHHHHHHHHhhcccceEEEehhhHHHHHHhchhhhcHHHHHHHHHHHHH-hccc----ccceEEEeccCCccchhH
Confidence              334677774  22 345688999999998766533       123444322 2322    356778889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccC-------CC---------------CCc-----hhHHHHHHhCCCCCH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK-------DH---------------KLF-----PQVEEIFQNGSSLSP  383 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~-------~~---------------~l~-----~~i~~l~~~~~g~s~  383 (480)
                      |+-.  |+|..|+||+|..++|..|+..|+...       +.               .+.     .-+.+.+..|.||||
T Consensus       501 AV~D--Ride~veFpLPGeEERfkll~lYlnkyi~~~~~~~~~~~~~~lfkk~sQ~i~l~~~~t~~~~~EaAkkTeGfSG  578 (630)
T KOG0742|consen  501 AVND--RIDEVVEFPLPGEEERFKLLNLYLNKYILKPATSGKPGKWSHLFKKESQRIKLAGFDTGRKCSEAAKKTEGFSG  578 (630)
T ss_pred             HHHh--hhhheeecCCCChHHHHHHHHHHHHHHhcCcCCCCCCchhhHHHhhhhheeeeccchHHHHHHHHHHhccCCcH
Confidence            9999  999999999999999999999988531       10               011     123567788999999


Q ss_pred             HHHHHHHHH
Q 011664          384 AEIGELMIA  392 (480)
Q Consensus       384 adI~~ll~~  392 (480)
                      .+|..|+..
T Consensus       579 REiakLva~  587 (630)
T KOG0742|consen  579 REIAKLVAS  587 (630)
T ss_pred             HHHHHHHHH
Confidence            999998754

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=99.80  E-value=5.2e-19  Score=177.20  Aligned_cols=172  Identities=17%  Similarity=0.246  Sum_probs=127.0

Q ss_pred             cc-ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC---CceEEEEccCCCcHHHHHHHHHHcCC-------CcEEEEeC
Q 011664          189 FD-TISMETDLKNRVKSDLESFLKAKHYYHRLGRVW---KRSYLLYGPSGTGKSSFAAAMASFMS-------YDVYDVDL  257 (480)
Q Consensus       189 ~~-~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~---~rgiLL~GPpGTGKT~La~aiA~~l~-------~~~~~i~~  257 (480)
                      ++ +++|++++|+.|.+.+.. +..++.+.+.|...   ..++||+||||||||++|+++|..+.       .+++.+++
T Consensus        20 l~~~l~Gl~~vk~~i~e~~~~-~~~~~~r~~~g~~~~~~~~~vll~G~pGTGKT~lA~~ia~~l~~~g~~~~~~~v~v~~   98 (284)
T TIGR02880        20 LDRELIGLKPVKTRIREIAAL-LLVERLRQRLGLASAAPTLHMSFTGNPGTGKTTVALRMAQILHRLGYVRKGHLVSVTR   98 (284)
T ss_pred             HHHhccCHHHHHHHHHHHHHH-HHHHHHHHHhCCCcCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCcccceEEEecH
Confidence            44 689999999999987666 66777778888764   34899999999999999999998663       26888886


Q ss_pred             CCcCC------hHHHHHHHHhhcCCcEEEEecccccccCcc----cccchhhhhhhcccccccccCCceEEEEecCC--C
Q 011664          258 SRVAD------DADLKSLLLQTTSKSVILIEDLDRFLVEKP----AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS--K  325 (480)
Q Consensus       258 s~~~~------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~----~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~--~  325 (480)
                      +++.+      ...++.+|.++ .+++|||||++.+...+.    +......|++.|+.-     ..+.+||++++.  .
T Consensus        99 ~~l~~~~~g~~~~~~~~~~~~a-~~gvL~iDEi~~L~~~~~~~~~~~~~~~~Ll~~le~~-----~~~~~vI~a~~~~~~  172 (284)
T TIGR02880        99 DDLVGQYIGHTAPKTKEILKRA-MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENQ-----RDDLVVILAGYKDRM  172 (284)
T ss_pred             HHHhHhhcccchHHHHHHHHHc-cCcEEEEechhhhccCCCccchHHHHHHHHHHHHhcC-----CCCEEEEEeCCcHHH
Confidence            55432      23355566654 458999999998853321    223456778888642     245666776543  2


Q ss_pred             cc---CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          326 DH---VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       326 ~~---LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      +.   ++|+|.+  ||+..|+||.++.+++..|++.++......+.+
T Consensus       173 ~~~~~~np~L~s--R~~~~i~fp~l~~edl~~I~~~~l~~~~~~l~~  217 (284)
T TIGR02880       173 DSFFESNPGFSS--RVAHHVDFPDYSEAELLVIAGLMLKEQQYRFSA  217 (284)
T ss_pred             HHHHhhCHHHHh--hCCcEEEeCCcCHHHHHHHHHHHHHHhccccCH
Confidence            32   4899999  999999999999999999999999765544443

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.

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=99.80  E-value=2.1e-18  Score=170.71  Aligned_cols=175  Identities=14%  Similarity=0.190  Sum_probs=124.9

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC---CceEEEEccCCCcHHHHHHHHHHcC-------CCcEEEEeC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVW---KRSYLLYGPSGTGKSSFAAAMASFM-------SYDVYDVDL  257 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~---~rgiLL~GPpGTGKT~La~aiA~~l-------~~~~~~i~~  257 (480)
                      .+++++|++++|+.|.+.+...... ....+.|...   ..+++|+||||||||++|+++|+.+       ..+++.+++
T Consensus         4 ~l~~~~Gl~~vk~~i~~~~~~~~~~-~~~~~~g~~~~~~~~~vll~GppGtGKTtlA~~ia~~l~~~~~~~~~~~v~~~~   82 (261)
T TIGR02881         4 ELSRMVGLDEVKALIKEIYAWIQIN-EKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARILGKLFKEMNVLSKGHLIEVER   82 (261)
T ss_pred             HHHHhcChHHHHHHHHHHHHHHHHH-HHHHHcCCCCCCCcceEEEEcCCCCCHHHHHHHHHHHHHhcCcccCCceEEecH
Confidence            3678999999999999877665444 3344456543   3468999999999999999999864       235777776


Q ss_pred             CCcCC------hHHHHHHHHhhcCCcEEEEecccccccCccc---ccchhhhhhhcccccccccCCceEEEEecCCC---
Q 011664          258 SRVAD------DADLKSLLLQTTSKSVILIEDLDRFLVEKPA---AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK---  325 (480)
Q Consensus       258 s~~~~------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~---~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~---  325 (480)
                      +++.+      ...++.+|.++ .++||||||+|.+......   ...+..|+..|+...     ...++|++++..   
T Consensus        83 ~~l~~~~~g~~~~~~~~~~~~a-~~~VL~IDE~~~L~~~~~~~~~~~~i~~Ll~~~e~~~-----~~~~vila~~~~~~~  156 (261)
T TIGR02881        83 ADLVGEYIGHTAQKTREVIKKA-LGGVLFIDEAYSLARGGEKDFGKEAIDTLVKGMEDNR-----NEFVLILAGYSDEMD  156 (261)
T ss_pred             HHhhhhhccchHHHHHHHHHhc-cCCEEEEechhhhccCCccchHHHHHHHHHHHHhccC-----CCEEEEecCCcchhH
Confidence            65543      23456666554 4689999999998642221   234566777776532     334555554322   


Q ss_pred             --ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          326 --DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       326 --~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                        ..++|+|++  ||+.+|+||.++.+++.+|++.++...+..+.++.
T Consensus       157 ~~~~~~p~L~s--Rf~~~i~f~~~~~~el~~Il~~~~~~~~~~l~~~a  202 (261)
T TIGR02881       157 YFLSLNPGLRS--RFPISIDFPDYTVEELMEIAERMVKEREYKLTEEA  202 (261)
T ss_pred             HHHhcChHHHh--ccceEEEECCCCHHHHHHHHHHHHHHcCCccCHHH
Confidence              236899999  99999999999999999999999987666666554

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.

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=99.78  E-value=2.9e-18  Score=175.25  Aligned_cols=193  Identities=16%  Similarity=0.206  Sum_probs=145.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA  264 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~  264 (480)
                      .|.+|++++|.++.++.+...+......       + ..+.++|||||||||||++|+++|++++.++..++.+.+....
T Consensus        20 rP~~~~~~vG~~~~~~~l~~~l~~~~~~-------~-~~~~~~ll~GppG~GKT~la~~ia~~l~~~~~~~~~~~~~~~~   91 (328)
T PRK00080         20 RPKSLDEFIGQEKVKENLKIFIEAAKKR-------G-EALDHVLLYGPPGLGKTTLANIIANEMGVNIRITSGPALEKPG   91 (328)
T ss_pred             CcCCHHHhcCcHHHHHHHHHHHHHHHhc-------C-CCCCcEEEECCCCccHHHHHHHHHHHhCCCeEEEecccccChH
Confidence            5779999999999999988766543221       1 2456899999999999999999999999998888777666666


Q ss_pred             HHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccc-----cc--------ccCCceEEEEecCCCccCccc
Q 011664          265 DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----NS--------CCFEERVMVFTMNSKDHVDQA  331 (480)
Q Consensus       265 ~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----~~--------~~~~~~ivI~tTN~~~~LD~a  331 (480)
                      .+..++.....++||||||||.+....     ...+.+.|+...     ..        .......+|++||.+..++++
T Consensus        92 ~l~~~l~~l~~~~vl~IDEi~~l~~~~-----~e~l~~~~e~~~~~~~l~~~~~~~~~~~~l~~~~li~at~~~~~l~~~  166 (328)
T PRK00080         92 DLAAILTNLEEGDVLFIDEIHRLSPVV-----EEILYPAMEDFRLDIMIGKGPAARSIRLDLPPFTLIGATTRAGLLTSP  166 (328)
T ss_pred             HHHHHHHhcccCCEEEEecHhhcchHH-----HHHHHHHHHhcceeeeeccCccccceeecCCCceEEeecCCcccCCHH
Confidence            777777777788999999999884321     112333333211     00        001235678899999999999


Q ss_pred             ccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHHh
Q 011664          332 LLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       332 LlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      |++  ||...+.+++|+.+++.++++...+..+..+.++. +.++... +-+|..+..++...
T Consensus       167 L~s--Rf~~~~~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~-~G~pR~a~~~l~~~  226 (328)
T PRK00080        167 LRD--RFGIVQRLEFYTVEELEKIVKRSARILGVEIDEEGALEIARRS-RGTPRIANRLLRRV  226 (328)
T ss_pred             HHH--hcCeeeecCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHc-CCCchHHHHHHHHH
Confidence            999  99999999999999999999999887777776654 5676666 45667677666543

>CHL00181 cbbX CbbX; Provisional

Probab=99.78  E-value=2.9e-18  Score=171.99  Aligned_cols=172  Identities=19%  Similarity=0.273  Sum_probs=125.2

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCc---eEEEEccCCCcHHHHHHHHHHcCC-------CcEEEEeCCC
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKR---SYLLYGPSGTGKSSFAAAMASFMS-------YDVYDVDLSR  259 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~r---giLL~GPpGTGKT~La~aiA~~l~-------~~~~~i~~s~  259 (480)
                      ++++|++++|++|.+.+.. +..++.+...|...+.   ++||+||||||||++|+++|..+.       .+++.++.+.
T Consensus        23 ~~l~Gl~~vK~~i~e~~~~-~~~~~~~~~~g~~~~~~~~~ill~G~pGtGKT~lAr~la~~~~~~g~~~~~~~~~v~~~~  101 (287)
T CHL00181         23 EELVGLAPVKTRIREIAAL-LLIDRLRKNLGLTSSNPGLHMSFTGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDD  101 (287)
T ss_pred             HhcCCcHHHHHHHHHHHHH-HHHHHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHHcCCCCCCceEEecHHH
Confidence            4799999999999987655 5556777778876542   489999999999999999998652       2578887654


Q ss_pred             cCC------hHHHHHHHHhhcCCcEEEEecccccccCcc----cccchhhhhhhcccccccccCCceEEEEecCCC--c-
Q 011664          260 VAD------DADLKSLLLQTTSKSVILIEDLDRFLVEKP----AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK--D-  326 (480)
Q Consensus       260 ~~~------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~----~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~--~-  326 (480)
                      +.+      ......++.++ .++||||||+|.+...+.    +......|+..|+..     ..+.+||++++..  + 
T Consensus       102 l~~~~~g~~~~~~~~~l~~a-~ggVLfIDE~~~l~~~~~~~~~~~e~~~~L~~~me~~-----~~~~~vI~ag~~~~~~~  175 (287)
T CHL00181        102 LVGQYIGHTAPKTKEVLKKA-MGGVLFIDEAYYLYKPDNERDYGSEAIEILLQVMENQ-----RDDLVVIFAGYKDRMDK  175 (287)
T ss_pred             HHHHHhccchHHHHHHHHHc-cCCEEEEEccchhccCCCccchHHHHHHHHHHHHhcC-----CCCEEEEEeCCcHHHHH
Confidence            432      22344555554 568999999999864321    223456677777643     2346677776532  1 


Q ss_pred             --cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          327 --HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       327 --~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                        .++|+|++  ||+.+|+|++++.+++.+|+..++...+..+.++
T Consensus       176 ~~~~np~L~s--R~~~~i~F~~~t~~el~~I~~~~l~~~~~~l~~~  219 (287)
T CHL00181        176 FYESNPGLSS--RIANHVDFPDYTPEELLQIAKIMLEEQQYQLTPE  219 (287)
T ss_pred             HHhcCHHHHH--hCCceEEcCCcCHHHHHHHHHHHHHHhcCCCChh
Confidence              34699999  9999999999999999999999998766555543

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=99.77  E-value=8e-18  Score=169.77  Aligned_cols=189  Identities=16%  Similarity=0.223  Sum_probs=138.4

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLK  267 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~  267 (480)
                      +|++++|.+++++.+...+......+        ..+.+++||||||||||++|+++|++++.++..+..+.......+.
T Consensus         2 ~~~~~iG~~~~~~~l~~~l~~~~~~~--------~~~~~~ll~Gp~G~GKT~la~~ia~~~~~~~~~~~~~~~~~~~~l~   73 (305)
T TIGR00635         2 LLAEFIGQEKVKEQLQLFIEAAKMRQ--------EALDHLLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDLA   73 (305)
T ss_pred             CHHHHcCHHHHHHHHHHHHHHHHhcC--------CCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeccchhcCchhHH
Confidence            69999999999999887665443221        2345799999999999999999999999988877766555555666


Q ss_pred             HHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccc-------------ccCCceEEEEecCCCccCcccccC
Q 011664          268 SLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS-------------CCFEERVMVFTMNSKDHVDQALLR  334 (480)
Q Consensus       268 ~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~-------------~~~~~~ivI~tTN~~~~LD~aLlr  334 (480)
                      ..+.....+.+|||||+|.+.+..     ...|++.|+.....             ......++|++||++..+++++++
T Consensus        74 ~~l~~~~~~~vl~iDEi~~l~~~~-----~e~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~li~~t~~~~~l~~~l~s  148 (305)
T TIGR00635        74 AILTNLEEGDVLFIDEIHRLSPAV-----EELLYPAMEDFRLDIVIGKGPSARSVRLDLPPFTLVGATTRAGMLTSPLRD  148 (305)
T ss_pred             HHHHhcccCCEEEEehHhhhCHHH-----HHHhhHHHhhhheeeeeccCccccceeecCCCeEEEEecCCccccCHHHHh
Confidence            666666788999999999885321     22344443321100             011236788899999999999999


Q ss_pred             CCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHH
Q 011664          335 PGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       335 pGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~  392 (480)
                        ||...+.+++|+.++..++++..++..+..+.++. +.++....| .|..+..++..
T Consensus       149 --R~~~~~~l~~l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G-~pR~~~~ll~~  204 (305)
T TIGR00635       149 --RFGIILRLEFYTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRG-TPRIANRLLRR  204 (305)
T ss_pred             --hcceEEEeCCCCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCC-CcchHHHHHHH
Confidence              99999999999999999999988876666666554 567666544 45555555543

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.

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=99.76  E-value=1.6e-17  Score=178.12  Aligned_cols=204  Identities=21%  Similarity=0.276  Sum_probs=153.8

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCC-ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWK-RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKS  268 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~-rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~  268 (480)
                      .+=.|++++|++|.|.+.--...++        .+ .-++|+||||+|||+|+++||..+|..|+.++++.+.++++++-
T Consensus       323 ~dHYGLekVKeRIlEyLAV~~l~~~--------~kGpILcLVGPPGVGKTSLgkSIA~al~RkfvR~sLGGvrDEAEIRG  394 (782)
T COG0466         323 KDHYGLEKVKERILEYLAVQKLTKK--------LKGPILCLVGPPGVGKTSLGKSIAKALGRKFVRISLGGVRDEAEIRG  394 (782)
T ss_pred             ccccCchhHHHHHHHHHHHHHHhcc--------CCCcEEEEECCCCCCchhHHHHHHHHhCCCEEEEecCccccHHHhcc
Confidence            3568999999999987754322211        12 24678999999999999999999999999999999998887643


Q ss_pred             H---------------HHhh-cCCcEEEEecccccccCcccccchhhhhhhccccccc----------ccCCceEEEEec
Q 011664          269 L---------------LLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS----------CCFEERVMVFTM  322 (480)
Q Consensus       269 l---------------~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~----------~~~~~~ivI~tT  322 (480)
                      .               +.++ ....+++|||||.+..+-. ...-+.||..+|.-.+.          ..-.+++||+|.
T Consensus       395 HRRTYIGamPGrIiQ~mkka~~~NPv~LLDEIDKm~ss~r-GDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTA  473 (782)
T COG0466         395 HRRTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDKMGSSFR-GDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATA  473 (782)
T ss_pred             ccccccccCChHHHHHHHHhCCcCCeEEeechhhccCCCC-CChHHHHHhhcCHhhcCchhhccccCccchhheEEEeec
Confidence            1               2222 2446999999999976533 33458899888855442          112468899999


Q ss_pred             CCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHH--HHHhCCCCCHHHHHHHHHH-hhhcHHH
Q 011664          323 NSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEE--IFQNGSSLSPAEIGELMIA-NRNSPSR  399 (480)
Q Consensus       323 N~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~--l~~~~~g~s~adI~~ll~~-a~~~~~~  399 (480)
                      |..+.++.+|+.  ||+ +|+++-++.++..+|+++||=..      .+++  |-...-.++.+-|..+++. +|++.+|
T Consensus       474 Nsl~tIP~PLlD--RME-iI~lsgYt~~EKl~IAk~~LiPk------~~~~~gL~~~el~i~d~ai~~iI~~YTREAGVR  544 (782)
T COG0466         474 NSLDTIPAPLLD--RME-VIRLSGYTEDEKLEIAKRHLIPK------QLKEHGLKKGELTITDEAIKDIIRYYTREAGVR  544 (782)
T ss_pred             CccccCChHHhc--cee-eeeecCCChHHHHHHHHHhcchH------HHHHcCCCccceeecHHHHHHHHHHHhHhhhhh
Confidence            999999999999  996 99999999999999999998422      1111  1111235777778887766 6788999


Q ss_pred             HHHHHHHHHHhc
Q 011664          400 ALKSVITALQTD  411 (480)
Q Consensus       400 al~~~i~~~~~~  411 (480)
                      .|++.+..+.++
T Consensus       545 ~LeR~i~ki~RK  556 (782)
T COG0466         545 NLEREIAKICRK  556 (782)
T ss_pred             HHHHHHHHHHHH
Confidence            999999988877

>TIGR00763 lon ATP-dependent protease La

Probab=99.74  E-value=1.7e-17  Score=187.18  Aligned_cols=206  Identities=20%  Similarity=0.235  Sum_probs=137.5

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH------
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA------  264 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~------  264 (480)
                      ++.|++++|+.|.+.+......       +......+||+||||||||++|+++|+.++.+++.++++.+.+.+      
T Consensus       321 ~~~G~~~~k~~i~~~~~~~~~~-------~~~~~~~lll~GppG~GKT~lAk~iA~~l~~~~~~i~~~~~~~~~~i~g~~  393 (775)
T TIGR00763       321 DHYGLKKVKERILEYLAVQKLR-------GKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHR  393 (775)
T ss_pred             hcCChHHHHHHHHHHHHHHHhh-------cCCCCceEEEECCCCCCHHHHHHHHHHHhcCCeEEEeCCCcccHHHHcCCC
Confidence            5889999999998866544322       112233799999999999999999999999999999876543322      


Q ss_pred             ---------HHHHHHHhh-cCCcEEEEecccccccCcccccchhhhhhhccccccc----------ccCCceEEEEecCC
Q 011664          265 ---------DLKSLLLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS----------CCFEERVMVFTMNS  324 (480)
Q Consensus       265 ---------~l~~l~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~----------~~~~~~ivI~tTN~  324 (480)
                               .+.+.|..+ ..+.||||||||.+..+.. ....+.|+..||.....          ....+.++|+|||.
T Consensus       394 ~~~~g~~~g~i~~~l~~~~~~~~villDEidk~~~~~~-~~~~~aLl~~ld~~~~~~f~d~~~~~~~d~s~v~~I~TtN~  472 (775)
T TIGR00763       394 RTYVGAMPGRIIQGLKKAKTKNPLFLLDEIDKIGSSFR-GDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANS  472 (775)
T ss_pred             CceeCCCCchHHHHHHHhCcCCCEEEEechhhcCCccC-CCHHHHHHHhcCHHhcCccccccCCceeccCCEEEEEecCC
Confidence                     234445433 2445999999999975432 22346677777631110          11246788999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHH-hhhcHHHHHHH
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIA-NRNSPSRALKS  403 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~-a~~~~~~al~~  403 (480)
                      ++.++++|++  ||+ .|+|+.|+.+++.+|+++|+......    ...+....-.+++..+..++.. .++..+|.|++
T Consensus       473 ~~~i~~~L~~--R~~-vi~~~~~~~~e~~~I~~~~l~~~~~~----~~~l~~~~~~~~~~~l~~i~~~~~~e~g~R~l~r  545 (775)
T TIGR00763       473 IDTIPRPLLD--RME-VIELSGYTEEEKLEIAKKYLIPKALE----DHGLKPDELKITDEALLLLIKYYTREAGVRNLER  545 (775)
T ss_pred             chhCCHHHhC--Cee-EEecCCCCHHHHHHHHHHHHHHHHHH----HcCCCcceEEECHHHHHHHHHhcChhcCChHHHH
Confidence            9999999999  996 79999999999999999987321000    0000011124566666666553 33445566666


Q ss_pred             HHHHHHhc
Q 011664          404 VITALQTD  411 (480)
Q Consensus       404 ~i~~~~~~  411 (480)
                      .++.+.++
T Consensus       546 ~i~~~~~~  553 (775)
T TIGR00763       546 QIEKICRK  553 (775)
T ss_pred             HHHHHHHH
Confidence            66655544

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.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=99.74  E-value=2.2e-18  Score=169.68  Aligned_cols=169  Identities=19%  Similarity=0.306  Sum_probs=130.4

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhh-CCCCCceEEEEccCCCcHHHHHHHHHHcCCC---------cEEEEeC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRL-GRVWKRSYLLYGPSGTGKSSFAAAMASFMSY---------DVYDVDL  257 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~-g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~---------~~~~i~~  257 (480)
                      -|+.++-+.++|+++.......+...+.--.. =+.|.|-+||+||||||||+|++|+|+.+..         .++.+++
T Consensus       140 lWEsLiyds~lK~~ll~Ya~s~l~fsek~vntnlIt~NRliLlhGPPGTGKTSLCKaLaQkLSIR~~~~y~~~~liEins  219 (423)
T KOG0744|consen  140 LWESLIYDSNLKERLLSYAASALLFSEKKVNTNLITWNRLILLHGPPGTGKTSLCKALAQKLSIRTNDRYYKGQLIEINS  219 (423)
T ss_pred             hHHHHhhcccHHHHHHHHHHHHHHHHhcCCCCceeeeeeEEEEeCCCCCChhHHHHHHHHhheeeecCccccceEEEEeh
Confidence            47888999999999998776665544332221 2568899999999999999999999998743         4667775


Q ss_pred             CC----cCChH--HHHHHHHhhc-----CC--cEEEEecccccccCccc----------ccchhhhhhhcccccccccCC
Q 011664          258 SR----VADDA--DLKSLLLQTT-----SK--SVILIEDLDRFLVEKPA----------AVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       258 s~----~~~~~--~l~~l~~~~~-----~~--sII~IDEiD~l~~~~~~----------~~~ls~lL~~ldg~~~~~~~~  314 (480)
                      .+    |.+++  .+.++|.+..     ..  -.++|||++++...|.+          -+.++.+|.+||.+..   ..
T Consensus       220 hsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lVfvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~---~~  296 (423)
T KOG0744|consen  220 HSLFSKWFSESGKLVAKMFQKIQELVEDRGNLVFVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKR---YP  296 (423)
T ss_pred             hHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEEEEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhcc---CC
Confidence            44    44443  3566665432     23  34579999998764421          1458899999999987   57


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ++++.+|+|-.+.||.|+..  |-|-+.++++|+.+++.+|++..+.
T Consensus       297 NvliL~TSNl~~siD~AfVD--RADi~~yVG~Pt~~ai~~Ilkscie  341 (423)
T KOG0744|consen  297 NVLILATSNLTDSIDVAFVD--RADIVFYVGPPTAEAIYEILKSCIE  341 (423)
T ss_pred             CEEEEeccchHHHHHHHhhh--HhhheeecCCccHHHHHHHHHHHHH
Confidence            88888899999999999999  9999999999999999999987653

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

Probab=99.72  E-value=1.3e-16  Score=155.24  Aligned_cols=194  Identities=14%  Similarity=0.212  Sum_probs=147.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA  264 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~  264 (480)
                      +|.+|++.+|++++|+.+.-.+...-.+.        ...-.+|||||||.||||||+.||+++|.++-..+...+....
T Consensus        21 RP~~l~efiGQ~~vk~~L~ifI~AAk~r~--------e~lDHvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~g   92 (332)
T COG2255          21 RPKTLDEFIGQEKVKEQLQIFIKAAKKRG--------EALDHVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKPG   92 (332)
T ss_pred             CcccHHHhcChHHHHHHHHHHHHHHHhcC--------CCcCeEEeeCCCCCcHHHHHHHHHHHhcCCeEecccccccChh
Confidence            68899999999999988875555443222        2345799999999999999999999999999999998888899


Q ss_pred             HHHHHHHhhcCCcEEEEecccccccCcccccchhh-hhhhccccccc----cc---------CCceEEEEecCCCccCcc
Q 011664          265 DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSG-VLNFMDGVLNS----CC---------FEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       265 ~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~-lL~~ldg~~~~----~~---------~~~~ivI~tTN~~~~LD~  330 (480)
                      ++..++......+|+|||||+.+.+.      ..+ |.-.|+.+.-+    ..         -..--+|+||.+...|..
T Consensus        93 DlaaiLt~Le~~DVLFIDEIHrl~~~------vEE~LYpaMEDf~lDI~IG~gp~Arsv~ldLppFTLIGATTr~G~lt~  166 (332)
T COG2255          93 DLAAILTNLEEGDVLFIDEIHRLSPA------VEEVLYPAMEDFRLDIIIGKGPAARSIRLDLPPFTLIGATTRAGMLTN  166 (332)
T ss_pred             hHHHHHhcCCcCCeEEEehhhhcChh------HHHHhhhhhhheeEEEEEccCCccceEeccCCCeeEeeeccccccccc
Confidence            99999999999999999999998532      122 22333321100    00         112347889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      .|+.  ||....++.+++.++..+|+++.....+..+.++- .++|.+. .-||.--..++++.++
T Consensus       167 PLrd--RFGi~~rlefY~~~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rS-RGTPRIAnRLLrRVRD  229 (332)
T COG2255         167 PLRD--RFGIIQRLEFYTVEELEEIVKRSAKILGIEIDEEAALEIARRS-RGTPRIANRLLRRVRD  229 (332)
T ss_pred             hhHH--hcCCeeeeecCCHHHHHHHHHHHHHHhCCCCChHHHHHHHHhc-cCCcHHHHHHHHHHHH
Confidence            9999  99999999999999999999998877777776654 5666665 5566555555554443

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=99.70  E-value=2.5e-16  Score=168.19  Aligned_cols=204  Identities=22%  Similarity=0.297  Sum_probs=147.4

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHH--
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLK--  267 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~--  267 (480)
                      +|=.|++++|++|.|.+.--    ++   .|-.-.+-++|+||||+|||+++++||..+|..|+.+++..+.+.++++  
T Consensus       411 eDHYgm~dVKeRILEfiAV~----kL---rgs~qGkIlCf~GPPGVGKTSI~kSIA~ALnRkFfRfSvGG~tDvAeIkGH  483 (906)
T KOG2004|consen  411 EDHYGMEDVKERILEFIAVG----KL---RGSVQGKILCFVGPPGVGKTSIAKSIARALNRKFFRFSVGGMTDVAEIKGH  483 (906)
T ss_pred             ccccchHHHHHHHHHHHHHH----hh---cccCCCcEEEEeCCCCCCcccHHHHHHHHhCCceEEEeccccccHHhhccc
Confidence            46789999999999866421    11   1111223467889999999999999999999999999998887766553  


Q ss_pred             -------------HHHHhh-cCCcEEEEecccccccCcccccchhhhhhhccccccc----------ccCCceEEEEecC
Q 011664          268 -------------SLLLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS----------CCFEERVMVFTMN  323 (480)
Q Consensus       268 -------------~l~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~----------~~~~~~ivI~tTN  323 (480)
                                   +.+.+. ....+++|||||.+...- ....-+.||..||.-.+.          ..-..+++|+|.|
T Consensus       484 RRTYVGAMPGkiIq~LK~v~t~NPliLiDEvDKlG~g~-qGDPasALLElLDPEQNanFlDHYLdVp~DLSkVLFicTAN  562 (906)
T KOG2004|consen  484 RRTYVGAMPGKIIQCLKKVKTENPLILIDEVDKLGSGH-QGDPASALLELLDPEQNANFLDHYLDVPVDLSKVLFICTAN  562 (906)
T ss_pred             ceeeeccCChHHHHHHHhhCCCCceEEeehhhhhCCCC-CCChHHHHHHhcChhhccchhhhccccccchhheEEEEecc
Confidence                         222222 245699999999997322 234457888888754431          1124688999999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccC---CCCCchhHHHHHHhCCCCCHHHHHHHHHH-hhhcHHH
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK---DHKLFPQVEEIFQNGSSLSPAEIGELMIA-NRNSPSR  399 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~---~~~l~~~i~~l~~~~~g~s~adI~~ll~~-a~~~~~~  399 (480)
                      ..+.|+++|+.  ||+ .|+++-+..++...|+++||-..   .+.+.+       ....++.+.+..++.. ++++.+|
T Consensus       563 ~idtIP~pLlD--RME-vIelsGYv~eEKv~IA~~yLip~a~~~~gl~~-------e~v~is~~al~~lI~~YcrEaGVR  632 (906)
T KOG2004|consen  563 VIDTIPPPLLD--RME-VIELSGYVAEEKVKIAERYLIPQALKDCGLKP-------EQVKISDDALLALIERYCREAGVR  632 (906)
T ss_pred             ccccCChhhhh--hhh-eeeccCccHHHHHHHHHHhhhhHHHHHcCCCH-------HhcCccHHHHHHHHHHHHHHHhHH
Confidence            99999999999  996 89999999999999999998432   122221       1235555666666654 6788888


Q ss_pred             HHHHHHHHHHhc
Q 011664          400 ALKSVITALQTD  411 (480)
Q Consensus       400 al~~~i~~~~~~  411 (480)
                      .|++-++.+.++
T Consensus       633 nLqk~iekI~Rk  644 (906)
T KOG2004|consen  633 NLQKQIEKICRK  644 (906)
T ss_pred             HHHHHHHHHHHH
Confidence            888888877655

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

Probab=99.68  E-value=6.2e-16  Score=164.99  Aligned_cols=192  Identities=15%  Similarity=0.175  Sum_probs=143.2

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC----CcEEEEeCCCcCChH-
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS----YDVYDVDLSRVADDA-  264 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~----~~~~~i~~s~~~~~~-  264 (480)
                      .+++-.+..|++..+....+           ...+..+||+||+|||||.|++++++++.    +++..++|+.+.+.+ 
T Consensus       408 ~d~i~~~s~kke~~n~~~sp-----------v~~~~~Ill~G~~GsGKT~L~kal~~~~~k~~~~hv~~v~Cs~l~~~~~  476 (952)
T KOG0735|consen  408 HDFIQVPSYKKENANQELSP-----------VFRHGNILLNGPKGSGKTNLVKALFDYYSKDLIAHVEIVSCSTLDGSSL  476 (952)
T ss_pred             Cceeecchhhhhhhhhhccc-----------ccccccEEEeCCCCCCHhHHHHHHHHHhccccceEEEEEechhccchhH
Confidence            56666677777666533333           23455899999999999999999999874    467788998887643 


Q ss_pred             -H----HHHHHHhh--cCCcEEEEecccccccCcccc--------cchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          265 -D----LKSLLLQT--TSKSVILIEDLDRFLVEKPAA--------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       265 -~----l~~l~~~~--~~~sII~IDEiD~l~~~~~~~--------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                       .    +...|.++  .+|+||++||+|++++..+.+        ..+..+++++-.... ..+..+.+|+|.+....|.
T Consensus       477 e~iQk~l~~vfse~~~~~PSiIvLDdld~l~~~s~~e~~q~~~~~~rla~flnqvi~~y~-~~~~~ia~Iat~qe~qtl~  555 (952)
T KOG0735|consen  477 EKIQKFLNNVFSEALWYAPSIIVLDDLDCLASASSNENGQDGVVSERLAAFLNQVIKIYL-KRNRKIAVIATGQELQTLN  555 (952)
T ss_pred             HHHHHHHHHHHHHHHhhCCcEEEEcchhhhhccCcccCCcchHHHHHHHHHHHHHHHHHH-ccCcEEEEEEechhhhhcC
Confidence             2    34445443  699999999999998733222        225566766543333 2233456788889999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCC-CCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKD-HKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~-~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      |-|.+|++|+.++.+|.|+..+|.+|+...+.... .....+++-++..|+||.+-|+..++.++
T Consensus       556 ~~L~s~~~Fq~~~~L~ap~~~~R~~IL~~~~s~~~~~~~~~dLd~ls~~TEGy~~~DL~ifVeRa  620 (952)
T KOG0735|consen  556 PLLVSPLLFQIVIALPAPAVTRRKEILTTIFSKNLSDITMDDLDFLSVKTEGYLATDLVIFVERA  620 (952)
T ss_pred             hhhcCccceEEEEecCCcchhHHHHHHHHHHHhhhhhhhhHHHHHHHHhcCCccchhHHHHHHHH
Confidence            99999999999999999999999999999886543 23445677789999999999999887644

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.68  E-value=8.8e-16  Score=163.56  Aligned_cols=160  Identities=16%  Similarity=0.267  Sum_probs=119.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++.+++.|...+.    ..        ..+.++|||||||||||++|+++|+.+++              
T Consensus         9 RP~~~~divGq~~i~~~L~~~i~----~~--------~l~~~~Lf~GPpGtGKTTlA~~lA~~l~~~~~~~~~pc~~c~~   76 (472)
T PRK14962          9 RPKTFSEVVGQDHVKKLIINALK----KN--------SISHAYIFAGPRGTGKTTVARILAKSLNCENRKGVEPCNECRA   76 (472)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHH----cC--------CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCCCcccHH
Confidence            68899999999998777665333    21        24557999999999999999999998764              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+.-.+-..++.+....      ....||+|||+|.+.     ......|+..++..     +.
T Consensus        77 c~~i~~g~~~dv~el~aa~~~gid~iR~i~~~~~~~p~~~~~kVvIIDE~h~Lt-----~~a~~~LLk~LE~p-----~~  146 (472)
T PRK14962         77 CRSIDEGTFMDVIELDAASNRGIDEIRKIRDAVGYRPMEGKYKVYIIDEVHMLT-----KEAFNALLKTLEEP-----PS  146 (472)
T ss_pred             HHHHhcCCCCccEEEeCcccCCHHHHHHHHHHHhhChhcCCeEEEEEEChHHhH-----HHHHHHHHHHHHhC-----CC
Confidence                      56777765444555666654332      245799999999884     22346677777642     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      ..++|++|+.+..+++++++  |+. .++|.+++.++...+++..+...+..+.+
T Consensus       147 ~vv~Ilattn~~kl~~~L~S--R~~-vv~f~~l~~~el~~~L~~i~~~egi~i~~  198 (472)
T PRK14962        147 HVVFVLATTNLEKVPPTIIS--RCQ-VIEFRNISDELIIKRLQEVAEAEGIEIDR  198 (472)
T ss_pred             cEEEEEEeCChHhhhHHHhc--CcE-EEEECCccHHHHHHHHHHHHHHcCCCCCH
Confidence            56777777788899999999  885 89999999999888888887655555543

>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function

Probab=99.68  E-value=1.6e-15  Score=146.58  Aligned_cols=201  Identities=18%  Similarity=0.254  Sum_probs=155.7

Q ss_pred             CCcceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCc
Q 011664          175 CGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYD  251 (480)
Q Consensus       175 ~~~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~  251 (480)
                      .+....|+...++.+++++|.+.+|+.|.+....|+.+.         +...+||||++|||||++++|+.++.   |..
T Consensus        12 ~~~l~~i~~~~~~~l~~L~Gie~Qk~~l~~Nt~~Fl~G~---------pannvLL~G~rGtGKSSlVkall~~y~~~GLR   82 (249)
T PF05673_consen   12 SGYLEPIKHPDPIRLDDLIGIERQKEALIENTEQFLQGL---------PANNVLLWGARGTGKSSLVKALLNEYADQGLR   82 (249)
T ss_pred             CCcEEecCCCCCCCHHHhcCHHHHHHHHHHHHHHHHcCC---------CCcceEEecCCCCCHHHHHHHHHHHHhhcCce
Confidence            345778888889999999999999999999998887652         45689999999999999999999866   778


Q ss_pred             EEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc-
Q 011664          252 VYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ-  330 (480)
Q Consensus       252 ~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~-  330 (480)
                      ++.++-.++..-..+...+.....+-|||+||+-  +  .........|-..|||-.. ..+++++|.+|+|+..-+.+ 
T Consensus        83 lIev~k~~L~~l~~l~~~l~~~~~kFIlf~DDLs--F--e~~d~~yk~LKs~LeGgle-~~P~NvliyATSNRRHLv~E~  157 (249)
T PF05673_consen   83 LIEVSKEDLGDLPELLDLLRDRPYKFILFCDDLS--F--EEGDTEYKALKSVLEGGLE-ARPDNVLIYATSNRRHLVPES  157 (249)
T ss_pred             EEEECHHHhccHHHHHHHHhcCCCCEEEEecCCC--C--CCCcHHHHHHHHHhcCccc-cCCCcEEEEEecchhhccchh
Confidence            8888887887777777888877889999999965  2  2223345677788888766 55788889999996422211 


Q ss_pred             ----------------------cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch-hHH----HHHHhCCCCCH
Q 011664          331 ----------------------ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP-QVE----EIFQNGSSLSP  383 (480)
Q Consensus       331 ----------------------aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~-~i~----~l~~~~~g~s~  383 (480)
                                            +|-.  ||...|.|..|+.++..+|++.|++..+..+.. ++.    ..+....|.||
T Consensus       158 ~~d~~~~~~~eih~~d~~eEklSLsD--RFGL~l~F~~~~q~~YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~RSG  235 (249)
T PF05673_consen  158 FSDREDIQDDEIHPSDTIEEKLSLSD--RFGLWLSFYPPDQEEYLAIVRHYAERYGLELDEEELRQEALQWALRRGGRSG  235 (249)
T ss_pred             hhhccCCCccccCcchHHHHHHhHHH--hCCcEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCCCH
Confidence                                  2334  999999999999999999999999887777763 332    23344456777


Q ss_pred             HHHHHHHH
Q 011664          384 AEIGELMI  391 (480)
Q Consensus       384 adI~~ll~  391 (480)
                      .--.+.+.
T Consensus       236 RtA~QF~~  243 (249)
T PF05673_consen  236 RTARQFID  243 (249)
T ss_pred             HHHHHHHH
Confidence            65555543

>PRK04195 replication factor C large subunit; Provisional

Probab=99.68  E-value=1e-15  Score=164.27  Aligned_cols=177  Identities=20%  Similarity=0.303  Sum_probs=132.5

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ..-.|.+|++|+|++++++.+.+.+..+.+        |. +++++|||||||||||++|+++|++++.+++.++.++..
T Consensus         6 eKyrP~~l~dlvg~~~~~~~l~~~l~~~~~--------g~-~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r   76 (482)
T PRK04195          6 EKYRPKTLSDVVGNEKAKEQLREWIESWLK--------GK-PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQR   76 (482)
T ss_pred             hhcCCCCHHHhcCCHHHHHHHHHHHHHHhc--------CC-CCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEcccccc
Confidence            445789999999999999999988876652        22 367899999999999999999999999999999998876


Q ss_pred             ChHHHHHHHHhh--------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc-cc
Q 011664          262 DDADLKSLLLQT--------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ-AL  332 (480)
Q Consensus       262 ~~~~l~~l~~~~--------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~-aL  332 (480)
                      ....+..+....        ..+.||+|||+|.+... ........|++.++.       ....+|+++|.+..+++ .|
T Consensus        77 ~~~~i~~~i~~~~~~~sl~~~~~kvIiIDEaD~L~~~-~d~~~~~aL~~~l~~-------~~~~iIli~n~~~~~~~k~L  148 (482)
T PRK04195         77 TADVIERVAGEAATSGSLFGARRKLILLDEVDGIHGN-EDRGGARAILELIKK-------AKQPIILTANDPYDPSLREL  148 (482)
T ss_pred             cHHHHHHHHHHhhccCcccCCCCeEEEEecCcccccc-cchhHHHHHHHHHHc-------CCCCEEEeccCccccchhhH
Confidence            655555554322        25789999999998642 222345667776652       22346778898888887 56


Q ss_pred             cCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhC
Q 011664          333 LRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNG  378 (480)
Q Consensus       333 lrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~  378 (480)
                      ++  |+ ..|.|+.|+.++...+++..+...+..+.+++ +.|++.+
T Consensus       149 rs--r~-~~I~f~~~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s  192 (482)
T PRK04195        149 RN--AC-LMIEFKRLSTRSIVPVLKRICRKEGIECDDEALKEIAERS  192 (482)
T ss_pred             hc--cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            55  55 68999999999999999998876666555433 4555443

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.67  E-value=1.1e-15  Score=161.32  Aligned_cols=161  Identities=16%  Similarity=0.317  Sum_probs=119.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++.+.+.|...+..           | ..+..+||+||||||||++|+++|+.+++              
T Consensus        13 RP~~f~dvVGQe~iv~~L~~~i~~-----------~-ri~ha~Lf~GP~GtGKTTlAriLAk~Lnce~~~~~~pCg~C~s   80 (484)
T PRK14956         13 RPQFFRDVIHQDLAIGALQNALKS-----------G-KIGHAYIFFGPRGVGKTTIARILAKRLNCENPIGNEPCNECTS   80 (484)
T ss_pred             CCCCHHHHhChHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHhcCcccccCccccCCCcH
Confidence            688999999999999887765431           1 13456999999999999999999998865              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++...-.+-..++.+....      ....|+||||+|.+.     ....+.||..|+.-     ..
T Consensus        81 C~~i~~g~~~dviEIdaas~~gVd~IReL~e~l~~~p~~g~~KV~IIDEah~Ls-----~~A~NALLKtLEEP-----p~  150 (484)
T PRK14956         81 CLEITKGISSDVLEIDAASNRGIENIRELRDNVKFAPMGGKYKVYIIDEVHMLT-----DQSFNALLKTLEEP-----PA  150 (484)
T ss_pred             HHHHHccCCccceeechhhcccHHHHHHHHHHHHhhhhcCCCEEEEEechhhcC-----HHHHHHHHHHhhcC-----CC
Confidence                      35555554333344555554322      245699999999883     23467778777532     45


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                      ..++|++|+.+..|.+++++  |+. ++.|..++.++....++..+...+..+.++
T Consensus       151 ~viFILaTte~~kI~~TI~S--RCq-~~~f~~ls~~~i~~~L~~i~~~Egi~~e~e  203 (484)
T PRK14956        151 HIVFILATTEFHKIPETILS--RCQ-DFIFKKVPLSVLQDYSEKLCKIENVQYDQE  203 (484)
T ss_pred             ceEEEeecCChhhccHHHHh--hhh-eeeecCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence            67888899999999999999  994 789999998888888888877666555443

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=99.67  E-value=1.6e-15  Score=165.86  Aligned_cols=161  Identities=15%  Similarity=0.292  Sum_probs=123.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|...+.            +...+..|||+||+|||||++++++|+.+++              
T Consensus        11 RPqtFdEVIGQe~Vv~~L~~aL~------------~gRL~HAyLFtGPpGvGKTTlAriLAKaLnCe~~~~~~PCG~C~s   78 (830)
T PRK07003         11 RPKDFASLVGQEHVVRALTHALD------------GGRLHHAYLFTGTRGVGKTTLSRIFAKALNCETGVTSQPCGVCRA   78 (830)
T ss_pred             CCCcHHHHcCcHHHHHHHHHHHh------------cCCCCeEEEEECCCCCCHHHHHHHHHHHhcCccCCCCCCCcccHH
Confidence            57899999999999998876543            1124567999999999999999999998754              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.++-.+-.+++.++...      ....|+||||+|.+.     ....+.||..|+.-     ..
T Consensus        79 Cr~I~~G~h~DviEIDAas~rgVDdIReLIe~a~~~P~~gr~KVIIIDEah~LT-----~~A~NALLKtLEEP-----P~  148 (830)
T PRK07003         79 CREIDEGRFVDYVEMDAASNRGVDEMAALLERAVYAPVDARFKVYMIDEVHMLT-----NHAFNAMLKTLEEP-----PP  148 (830)
T ss_pred             HHHHhcCCCceEEEecccccccHHHHHHHHHHHHhccccCCceEEEEeChhhCC-----HHHHHHHHHHHHhc-----CC
Confidence                      45666655444455667666542      245799999999883     23457788877542     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                      ..+||++||.+..|.+.+++  |+ .++.|..++.++....++..++.++..+.++
T Consensus       149 ~v~FILaTtd~~KIp~TIrS--RC-q~f~Fk~Ls~eeIv~~L~~Il~~EgI~id~e  201 (830)
T PRK07003        149 HVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPAGHIVSHLERILGEERIAFEPQ  201 (830)
T ss_pred             CeEEEEEECChhhccchhhh--he-EEEecCCcCHHHHHHHHHHHHHHcCCCCCHH
Confidence            67889999999999999999  99 5999999999999988988887666655543

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=8.2e-16  Score=166.12  Aligned_cols=181  Identities=15%  Similarity=0.216  Sum_probs=133.8

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|...+..           | ..+..+||+||+|||||++|+++|+.+++              
T Consensus        11 RPqtFddVIGQe~vv~~L~~al~~-----------g-RLpHA~LFtGP~GvGKTTLAriLAkaLnC~~p~~~~g~~~~PC   78 (700)
T PRK12323         11 RPRDFTTLVGQEHVVRALTHALEQ-----------Q-RLHHAYLFTGTRGVGKTTLSRILAKSLNCTGADGEGGITAQPC   78 (700)
T ss_pred             CCCcHHHHcCcHHHHHHHHHHHHh-----------C-CCceEEEEECCCCCCHHHHHHHHHHHhcCCCccccccCCCCCC
Confidence            688999999999999988765541           1 24568999999999999999999998865              


Q ss_pred             ---------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccc
Q 011664          251 ---------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN  309 (480)
Q Consensus       251 ---------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~  309 (480)
                                     +++.++.++-.+-.+++.++...      ....|+||||+|.+.     ....+.||..|+.-  
T Consensus        79 G~C~sC~~I~aG~hpDviEIdAas~~gVDdIReLie~~~~~P~~gr~KViIIDEah~Ls-----~~AaNALLKTLEEP--  151 (700)
T PRK12323         79 GQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDKAVYAPTAGRFKVYMIDEVHMLT-----NHAFNAMLKTLEEP--  151 (700)
T ss_pred             cccHHHHHHHcCCCCcceEecccccCCHHHHHHHHHHHHhchhcCCceEEEEEChHhcC-----HHHHHHHHHhhccC--
Confidence                           45666655444555677766432      245799999999883     23457788877542  


Q ss_pred             cccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHH
Q 011664          310 SCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       310 ~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~  388 (480)
                         ....+||++||.+..|.+.+++  |+ .++.|..++.++..+.++.++...+....++. +.|+.. .+-++.+..+
T Consensus       152 ---P~~v~FILaTtep~kLlpTIrS--RC-q~f~f~~ls~eei~~~L~~Il~~Egi~~d~eAL~~IA~~-A~Gs~RdALs  224 (700)
T PRK12323        152 ---PEHVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPGHIVSHLDAILGEEGIAHEVNALRLLAQA-AQGSMRDALS  224 (700)
T ss_pred             ---CCCceEEEEeCChHhhhhHHHH--HH-HhcccCCCChHHHHHHHHHHHHHcCCCCCHHHHHHHHHH-cCCCHHHHHH
Confidence               4567889999999999999999  99 59999999999998888888876666655443 344443 3555555555


Q ss_pred             HHH
Q 011664          389 LMI  391 (480)
Q Consensus       389 ll~  391 (480)
                      ++.
T Consensus       225 LLd  227 (700)
T PRK12323        225 LTD  227 (700)
T ss_pred             HHH
Confidence            443

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.66  E-value=2.5e-15  Score=155.80  Aligned_cols=181  Identities=15%  Similarity=0.231  Sum_probs=127.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++|+|++.+++.+...+..           | ..+..+||+||||||||++|+++|+.+.+              
T Consensus        11 rP~~~~~iiGq~~~~~~l~~~~~~-----------~-~~~h~~L~~Gp~G~GKTtla~~la~~l~c~~~~~~~pc~~c~~   78 (363)
T PRK14961         11 RPQYFRDIIGQKHIVTAISNGLSL-----------G-RIHHAWLLSGTRGVGKTTIARLLAKSLNCQNGITSNPCRKCII   78 (363)
T ss_pred             CCCchhhccChHHHHHHHHHHHHc-----------C-CCCeEEEEecCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHH
Confidence            578999999999999887754431           1 24567999999999999999999998753              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+.-..-..++.++...      ....|++|||+|.+.     ....+.||..++..     +.
T Consensus        79 c~~~~~~~~~d~~~~~~~~~~~v~~ir~i~~~~~~~p~~~~~kviIIDEa~~l~-----~~a~naLLk~lEe~-----~~  148 (363)
T PRK14961         79 CKEIEKGLCLDLIEIDAASRTKVEEMREILDNIYYSPSKSRFKVYLIDEVHMLS-----RHSFNALLKTLEEP-----PQ  148 (363)
T ss_pred             HHHHhcCCCCceEEecccccCCHHHHHHHHHHHhcCcccCCceEEEEEChhhcC-----HHHHHHHHHHHhcC-----CC
Confidence                      34445443323334466655432      234699999999873     22345677777542     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~  391 (480)
                      ...+|++|+.++.+.+++++  |+ ..++|++++.++...++...+...+..+.++. +.++..+ +-++.++.+++.
T Consensus       149 ~~~fIl~t~~~~~l~~tI~S--Rc-~~~~~~~l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s-~G~~R~al~~l~  222 (363)
T PRK14961        149 HIKFILATTDVEKIPKTILS--RC-LQFKLKIISEEKIFNFLKYILIKESIDTDEYALKLIAYHA-HGSMRDALNLLE  222 (363)
T ss_pred             CeEEEEEcCChHhhhHHHHh--hc-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHHH
Confidence            56677888888899999998  88 58999999999999999888776665555543 4455444 445555555443

>PRK06893 DNA replication initiation factor; Validated

Probab=99.66  E-value=1.3e-15  Score=148.05  Aligned_cols=173  Identities=10%  Similarity=0.147  Sum_probs=111.3

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      ++..++.+||+.++.++..  ....+..      .+..   .....++||||||||||+|++|+|+++   +....++++
T Consensus         7 ~~~~~~~~fd~f~~~~~~~--~~~~~~~------~~~~---~~~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~   75 (229)
T PRK06893          7 IHQIDDETLDNFYADNNLL--LLDSLRK------NFID---LQQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPL   75 (229)
T ss_pred             CCCCCcccccccccCChHH--HHHHHHH------Hhhc---cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeH
Confidence            4455778999998766422  1111111      1111   123358999999999999999999976   456666666


Q ss_pred             CCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC-CCccCc---cccc
Q 011664          258 SRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKDHVD---QALL  333 (480)
Q Consensus       258 s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~~LD---~aLl  333 (480)
                      +...  ......+....+..+|+|||++.+.+......   .+++.++....   .+..++|+|+| .|..++   |+|.
T Consensus        76 ~~~~--~~~~~~~~~~~~~dlLilDDi~~~~~~~~~~~---~l~~l~n~~~~---~~~~illits~~~p~~l~~~~~~L~  147 (229)
T PRK06893         76 SKSQ--YFSPAVLENLEQQDLVCLDDLQAVIGNEEWEL---AIFDLFNRIKE---QGKTLLLISADCSPHALSIKLPDLA  147 (229)
T ss_pred             HHhh--hhhHHHHhhcccCCEEEEeChhhhcCChHHHH---HHHHHHHHHHH---cCCcEEEEeCCCChHHccccchhHH
Confidence            4321  11223444556778999999998865443333   34444444333   23455565554 566654   8999


Q ss_pred             CCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHH
Q 011664          334 RPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVE  372 (480)
Q Consensus       334 rpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~  372 (480)
                      +..+.+..+.++.|+.+++.+++++.+...+..+.+++-
T Consensus       148 sRl~~g~~~~l~~pd~e~~~~iL~~~a~~~~l~l~~~v~  186 (229)
T PRK06893        148 SRLTWGEIYQLNDLTDEQKIIVLQRNAYQRGIELSDEVA  186 (229)
T ss_pred             HHHhcCCeeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHH
Confidence            933335789999999999999999888766666666553

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

Probab=99.65  E-value=2.6e-15  Score=152.49  Aligned_cols=150  Identities=20%  Similarity=0.326  Sum_probs=109.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA  264 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~  264 (480)
                      +|.++++++|++.+...-. -+...+..         ..-.+.+|||||||||||+|+.||+..+.+|..++... .+-.
T Consensus        19 RP~~lde~vGQ~HLlg~~~-~lrr~v~~---------~~l~SmIl~GPPG~GKTTlA~liA~~~~~~f~~~sAv~-~gvk   87 (436)
T COG2256          19 RPKSLDEVVGQEHLLGEGK-PLRRAVEA---------GHLHSMILWGPPGTGKTTLARLIAGTTNAAFEALSAVT-SGVK   87 (436)
T ss_pred             CCCCHHHhcChHhhhCCCc-hHHHHHhc---------CCCceeEEECCCCCCHHHHHHHHHHhhCCceEEecccc-ccHH
Confidence            6889999999987664311 11122221         12347999999999999999999999999999998642 3466


Q ss_pred             HHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEe-c-CCCccCcccccCCC
Q 011664          265 DLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFT-M-NSKDHVDQALLRPG  336 (480)
Q Consensus       265 ~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~t-T-N~~~~LD~aLlrpG  336 (480)
                      +++.++.++      ....|||||||+.+-  +.   ....||-.|+       .+.+++|+| | |.--.|.+||++  
T Consensus        88 dlr~i~e~a~~~~~~gr~tiLflDEIHRfn--K~---QQD~lLp~vE-------~G~iilIGATTENPsF~ln~ALlS--  153 (436)
T COG2256          88 DLREIIEEARKNRLLGRRTILFLDEIHRFN--KA---QQDALLPHVE-------NGTIILIGATTENPSFELNPALLS--  153 (436)
T ss_pred             HHHHHHHHHHHHHhcCCceEEEEehhhhcC--hh---hhhhhhhhhc-------CCeEEEEeccCCCCCeeecHHHhh--
Confidence            788887554      246899999999883  22   2234555552       345667764 4 555789999999  


Q ss_pred             ceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          337 RIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       337 Rfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                      |. ++.++.+.+.++..+++++-+
T Consensus       154 R~-~vf~lk~L~~~di~~~l~ra~  176 (436)
T COG2256         154 RA-RVFELKPLSSEDIKKLLKRAL  176 (436)
T ss_pred             hh-heeeeecCCHHHHHHHHHHHH
Confidence            88 588999999999999888844

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

Probab=99.65  E-value=1.3e-15  Score=163.79  Aligned_cols=168  Identities=17%  Similarity=0.249  Sum_probs=131.3

Q ss_pred             CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------hHHHHHHHHhh--cCCcEEEEecccccccCcc
Q 011664          221 RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------DADLKSLLLQT--TSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       221 ~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~  292 (480)
                      +...-.+||+|+||||||++++++|.++|.+++.++|.++..      +..+...|.++  .+|+|||+-++|.+..+..
T Consensus       428 ~~~~~~vLLhG~~g~GK~t~V~~vas~lg~h~~evdc~el~~~s~~~~etkl~~~f~~a~~~~pavifl~~~dvl~id~d  507 (953)
T KOG0736|consen  428 LTLNPSVLLHGPPGSGKTTVVRAVASELGLHLLEVDCYELVAESASHTETKLQAIFSRARRCSPAVLFLRNLDVLGIDQD  507 (953)
T ss_pred             cccceEEEEeCCCCCChHHHHHHHHHHhCCceEeccHHHHhhcccchhHHHHHHHHHHHhhcCceEEEEeccceeeecCC
Confidence            334457999999999999999999999999999999987764      44566777544  5899999999998875544


Q ss_pred             cccc------hhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCC
Q 011664          293 AAVS------LSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHK  366 (480)
Q Consensus       293 ~~~~------ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~  366 (480)
                      +...      +..++. .|....  .....++|+||+..+.+++.+++  -|-..|.+|.|+.++|.+|++.|+......
T Consensus       508 gged~rl~~~i~~~ls-~e~~~~--~~~~~ivv~t~~s~~~lp~~i~~--~f~~ei~~~~lse~qRl~iLq~y~~~~~~n  582 (953)
T KOG0736|consen  508 GGEDARLLKVIRHLLS-NEDFKF--SCPPVIVVATTSSIEDLPADIQS--LFLHEIEVPALSEEQRLEILQWYLNHLPLN  582 (953)
T ss_pred             CchhHHHHHHHHHHHh-cccccC--CCCceEEEEeccccccCCHHHHH--hhhhhccCCCCCHHHHHHHHHHHHhccccc
Confidence            3321      112222 233332  25678899999999999999998  888899999999999999999998755443


Q ss_pred             CchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          367 LFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       367 l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      -......++..+.|||.+|+..++...
T Consensus       583 ~~v~~k~~a~~t~gfs~~~L~~l~~~~  609 (953)
T KOG0736|consen  583 QDVNLKQLARKTSGFSFGDLEALVAHS  609 (953)
T ss_pred             hHHHHHHHHHhcCCCCHHHHHHHhcCc
Confidence            334557899999999999999998543

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.65  E-value=2.3e-15  Score=162.95  Aligned_cols=180  Identities=17%  Similarity=0.264  Sum_probs=131.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|...+.    .       | ..+..|||+||||||||++|+++|+.+++              
T Consensus        10 RPktFddVIGQe~vv~~L~~aI~----~-------g-rl~HAyLF~GPpGvGKTTlAriLAK~LnC~~~~~~~pCg~C~s   77 (702)
T PRK14960         10 RPRNFNELVGQNHVSRALSSALE----R-------G-RLHHAYLFTGTRGVGKTTIARILAKCLNCETGVTSTPCEVCAT   77 (702)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHH----c-------C-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCcCCCCCCCccCHH
Confidence            57899999999999888876554    1       2 23568999999999999999999998865              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.++-.+-.+++.++...      ....|++|||+|.+..     ...+.|+..|+..     .+
T Consensus        78 C~~I~~g~hpDviEIDAAs~~~VddIReli~~~~y~P~~gk~KV~IIDEVh~LS~-----~A~NALLKtLEEP-----P~  147 (702)
T PRK14960         78 CKAVNEGRFIDLIEIDAASRTKVEDTRELLDNVPYAPTQGRFKVYLIDEVHMLST-----HSFNALLKTLEEP-----PE  147 (702)
T ss_pred             HHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhhhhcCCcEEEEEechHhcCH-----HHHHHHHHHHhcC-----CC
Confidence                      56666665444555677766433      2457999999998832     3456777777642     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ...+|++|+.+..+.+.+++  |+ .+++|..++.++....+...+...+....++. ..++... +-+..++.+++
T Consensus       148 ~v~FILaTtd~~kIp~TIlS--RC-q~feFkpLs~eEI~k~L~~Il~kEgI~id~eAL~~IA~~S-~GdLRdALnLL  220 (702)
T PRK14960        148 HVKFLFATTDPQKLPITVIS--RC-LQFTLRPLAVDEITKHLGAILEKEQIAADQDAIWQIAESA-QGSLRDALSLT  220 (702)
T ss_pred             CcEEEEEECChHhhhHHHHH--hh-heeeccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            56788888888899899988  88 58999999999998888888877666655443 3444443 33555544443

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=99.65  E-value=5.2e-15  Score=150.02  Aligned_cols=154  Identities=21%  Similarity=0.232  Sum_probs=113.1

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ..-.|.+|++++|++++++.++..+.    .       | ..+..+||+||||+|||++++++|++++.+++.++++. .
T Consensus        13 ~kyrP~~~~~~~~~~~~~~~l~~~~~----~-------~-~~~~~lll~G~~G~GKT~la~~l~~~~~~~~~~i~~~~-~   79 (316)
T PHA02544         13 QKYRPSTIDECILPAADKETFKSIVK----K-------G-RIPNMLLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSD-C   79 (316)
T ss_pred             eccCCCcHHHhcCcHHHHHHHHHHHh----c-------C-CCCeEEEeeCcCCCCHHHHHHHHHHHhCccceEeccCc-c
Confidence            34578999999999999998876553    1       2 23557778999999999999999999999999999887 2


Q ss_pred             ChHHHHHHH---H-hh---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccC
Q 011664          262 DDADLKSLL---L-QT---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLR  334 (480)
Q Consensus       262 ~~~~l~~l~---~-~~---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlr  334 (480)
                      ....++..+   . ..   ..+.||+|||+|.+...    .....|...++..     ..+..+|+|||.+..+++++++
T Consensus        80 ~~~~i~~~l~~~~~~~~~~~~~~vliiDe~d~l~~~----~~~~~L~~~le~~-----~~~~~~Ilt~n~~~~l~~~l~s  150 (316)
T PHA02544         80 RIDFVRNRLTRFASTVSLTGGGKVIIIDEFDRLGLA----DAQRHLRSFMEAY-----SKNCSFIITANNKNGIIEPLRS  150 (316)
T ss_pred             cHHHHHHHHHHHHHhhcccCCCeEEEEECcccccCH----HHHHHHHHHHHhc-----CCCceEEEEcCChhhchHHHHh
Confidence            222232222   1 11   35789999999987321    1223344445443     2356788899999999999999


Q ss_pred             CCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          335 PGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       335 pGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                        |+. .+.++.|+.+++..+++.++
T Consensus       151 --R~~-~i~~~~p~~~~~~~il~~~~  173 (316)
T PHA02544        151 --RCR-VIDFGVPTKEEQIEMMKQMI  173 (316)
T ss_pred             --hce-EEEeCCCCHHHHHHHHHHHH
Confidence              995 78999999999988776643

>PLN03025 replication factor C subunit; Provisional

Probab=99.63  E-value=3.6e-15  Score=151.87  Aligned_cols=162  Identities=15%  Similarity=0.193  Sum_probs=115.9

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEe
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVD  256 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~  256 (480)
                      ...+|.+|++++|++++.+.|...+.    .       + .. ..+|||||||||||++|+++|+++.     ..++.++
T Consensus         5 ~kyrP~~l~~~~g~~~~~~~L~~~~~----~-------~-~~-~~lll~Gp~G~GKTtla~~la~~l~~~~~~~~~~eln   71 (319)
T PLN03025          5 EKYRPTKLDDIVGNEDAVSRLQVIAR----D-------G-NM-PNLILSGPPGTGKTTSILALAHELLGPNYKEAVLELN   71 (319)
T ss_pred             hhcCCCCHHHhcCcHHHHHHHHHHHh----c-------C-CC-ceEEEECCCCCCHHHHHHHHHHHHhcccCccceeeec
Confidence            34578999999999998887765332    1       1 12 2599999999999999999999872     2466677


Q ss_pred             CCCcCChHHHHHHH---Hhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          257 LSRVADDADLKSLL---LQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       257 ~s~~~~~~~l~~l~---~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      .++..+-..++..+   .+.      ..+.|++|||+|.+..     .....|+..|+...     ....+|++||.+..
T Consensus        72 ~sd~~~~~~vr~~i~~~~~~~~~~~~~~~kviiiDE~d~lt~-----~aq~aL~~~lE~~~-----~~t~~il~~n~~~~  141 (319)
T PLN03025         72 ASDDRGIDVVRNKIKMFAQKKVTLPPGRHKIVILDEADSMTS-----GAQQALRRTMEIYS-----NTTRFALACNTSSK  141 (319)
T ss_pred             ccccccHHHHHHHHHHHHhccccCCCCCeEEEEEechhhcCH-----HHHHHHHHHHhccc-----CCceEEEEeCCccc
Confidence            66655544455443   222      2357999999999842     22355666665322     33457788898889


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      +.++|++  |+ ..++|+.|+.++....++..+..++..+.+
T Consensus       142 i~~~L~S--Rc-~~i~f~~l~~~~l~~~L~~i~~~egi~i~~  180 (319)
T PLN03025        142 IIEPIQS--RC-AIVRFSRLSDQEILGRLMKVVEAEKVPYVP  180 (319)
T ss_pred             cchhHHH--hh-hcccCCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            9999999  87 489999999999988888877665554443

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=99.63  E-value=7.5e-15  Score=157.28  Aligned_cols=181  Identities=14%  Similarity=0.226  Sum_probs=130.2

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-------------  250 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------  250 (480)
                      -+|.+|++++|++.+.+.+...+..           | ..+.++||+||||||||++|+++|+.+++             
T Consensus        15 yRP~~f~dliGq~~vv~~L~~ai~~-----------~-ri~~a~Lf~Gp~G~GKTT~ArilAk~Lnc~~~~~~~~~~~~C   82 (507)
T PRK06645         15 YRPSNFAELQGQEVLVKVLSYTILN-----------D-RLAGGYLLTGIRGVGKTTSARIIAKAVNCSALITENTTIKTC   82 (507)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHHhcCccccccCcCcCCC
Confidence            3689999999999999877754321           1 23568999999999999999999998754             


Q ss_pred             ---------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccc
Q 011664          251 ---------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN  309 (480)
Q Consensus       251 ---------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~  309 (480)
                                     +++.++..+-.+-.+++.++...      ....|++|||+|.+.     ....+.|+..|+.-  
T Consensus        83 ~~C~~C~~i~~~~h~Dv~eidaas~~~vd~Ir~iie~a~~~P~~~~~KVvIIDEa~~Ls-----~~a~naLLk~LEep--  155 (507)
T PRK06645         83 EQCTNCISFNNHNHPDIIEIDAASKTSVDDIRRIIESAEYKPLQGKHKIFIIDEVHMLS-----KGAFNALLKTLEEP--  155 (507)
T ss_pred             CCChHHHHHhcCCCCcEEEeeccCCCCHHHHHHHHHHHHhccccCCcEEEEEEChhhcC-----HHHHHHHHHHHhhc--
Confidence                           34455554434456677776543      245799999999873     23456777777532  


Q ss_pred             cccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHH
Q 011664          310 SCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       310 ~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~  388 (480)
                         ....++|++|+.++.+.+++++  |+ .+++|..++.++...+++..+...+....++. +.++..+ +-+..++.+
T Consensus       156 ---p~~~vfI~aTte~~kI~~tI~S--Rc-~~~ef~~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s-~GslR~al~  228 (507)
T PRK06645        156 ---PPHIIFIFATTEVQKIPATIIS--RC-QRYDLRRLSFEEIFKLLEYITKQENLKTDIEALRIIAYKS-EGSARDAVS  228 (507)
T ss_pred             ---CCCEEEEEEeCChHHhhHHHHh--cc-eEEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHH
Confidence               4567788888888999999998  88 58999999999999999998877766555443 3444443 334444444


Q ss_pred             HH
Q 011664          389 LM  390 (480)
Q Consensus       389 ll  390 (480)
                      ++
T Consensus       229 ~L  230 (507)
T PRK06645        229 IL  230 (507)
T ss_pred             HH
Confidence            43

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.63  E-value=6.1e-15  Score=156.99  Aligned_cols=180  Identities=16%  Similarity=0.201  Sum_probs=134.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------------  248 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------------  248 (480)
                      .|.+|++|+|++.+++.+...+..           | ..+.++||+||||||||++|+++|+.+                
T Consensus         8 RP~~f~dliGQe~vv~~L~~a~~~-----------~-ri~ha~Lf~Gp~G~GKTT~ArilAk~LnC~~~~~~~pCg~C~~   75 (491)
T PRK14964          8 RPSSFKDLVGQDVLVRILRNAFTL-----------N-KIPQSILLVGASGVGKTTCARIISLCLNCSNGPTSDPCGTCHN   75 (491)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCceEEEECCCCccHHHHHHHHHHHHcCcCCCCCCCccccHH
Confidence            578999999999988877644321           2 246689999999999999999999854                


Q ss_pred             --------CCcEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          249 --------SYDVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       249 --------~~~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                              +.+++.++.++-.+-.+++.++...      ....|++|||+|.+.     ....+.|+..|+.-     .+
T Consensus        76 C~~i~~~~~~Dv~eidaas~~~vddIR~Iie~~~~~P~~~~~KVvIIDEah~Ls-----~~A~NaLLK~LEeP-----p~  145 (491)
T PRK14964         76 CISIKNSNHPDVIEIDAASNTSVDDIKVILENSCYLPISSKFKVYIIDEVHMLS-----NSAFNALLKTLEEP-----AP  145 (491)
T ss_pred             HHHHhccCCCCEEEEecccCCCHHHHHHHHHHHHhccccCCceEEEEeChHhCC-----HHHHHHHHHHHhCC-----CC
Confidence                    2357788877666667787776543      245799999999873     23457788887643     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.+..+.+.+++  |+ ..++|..++.++....+...+...+..+.++. +.++... +-+..++.+++
T Consensus       146 ~v~fIlatte~~Kl~~tI~S--Rc-~~~~f~~l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s-~GslR~alslL  218 (491)
T PRK14964        146 HVKFILATTEVKKIPVTIIS--RC-QRFDLQKIPTDKLVEHLVDIAKKENIEHDEESLKLIAENS-SGSMRNALFLL  218 (491)
T ss_pred             CeEEEEEeCChHHHHHHHHH--hh-eeeecccccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            67788888888899999999  88 57999999999999999988887777666544 3444443 44555554444

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.62  E-value=6.1e-15  Score=158.63  Aligned_cols=160  Identities=16%  Similarity=0.277  Sum_probs=121.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|...+..           + ..+..+||+||||||||++|+++|+.+++              
T Consensus        11 RP~~f~divGq~~v~~~L~~~~~~-----------~-~l~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~   78 (509)
T PRK14958         11 RPRCFQEVIGQAPVVRALSNALDQ-----------Q-YLHHAYLFTGTRGVGKTTISRILAKCLNCEKGVSANPCNDCEN   78 (509)
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHh-----------C-CCCeeEEEECCCCCCHHHHHHHHHHHhcCCCCCCcccCCCCHH
Confidence            578999999999999988865532           1 23557999999999999999999998854              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.++-.+-.+++.++...      ....|++|||+|.+..     ...+.||..|+..     ++
T Consensus        79 C~~i~~g~~~d~~eidaas~~~v~~iR~l~~~~~~~p~~~~~kV~iIDE~~~ls~-----~a~naLLk~LEep-----p~  148 (509)
T PRK14958         79 CREIDEGRFPDLFEVDAASRTKVEDTRELLDNIPYAPTKGRFKVYLIDEVHMLSG-----HSFNALLKTLEEP-----PS  148 (509)
T ss_pred             HHHHhcCCCceEEEEcccccCCHHHHHHHHHHHhhccccCCcEEEEEEChHhcCH-----HHHHHHHHHHhcc-----CC
Confidence                      26777765555556677766432      2347999999998842     3456788777643     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      ..++|++|+.+..+.+.+++  |+ ..++|..++.++....++..+...+....+
T Consensus       149 ~~~fIlattd~~kl~~tI~S--Rc-~~~~f~~l~~~~i~~~l~~il~~egi~~~~  200 (509)
T PRK14958        149 HVKFILATTDHHKLPVTVLS--RC-LQFHLAQLPPLQIAAHCQHLLKEENVEFEN  200 (509)
T ss_pred             CeEEEEEECChHhchHHHHH--Hh-hhhhcCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            57788888889999888998  88 588999999888877777777766655543

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=99.61  E-value=1.4e-14  Score=149.01  Aligned_cols=180  Identities=19%  Similarity=0.324  Sum_probs=128.0

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------------  249 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------------  249 (480)
                      +|.+|++++|++++++.+.+.+..           | ..+..+|||||||+|||++|+++|+.+.               
T Consensus         9 rp~~~~~iig~~~~~~~l~~~~~~-----------~-~~~~~~Ll~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~   76 (355)
T TIGR02397         9 RPQTFEDVIGQEHIVQTLKNAIKN-----------G-RIAHAYLFSGPRGTGKTSIARIFAKALNCQNGPDGEPCNECES   76 (355)
T ss_pred             CCCcHhhccCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHH
Confidence            678999999999999988875532           2 2456899999999999999999998763               


Q ss_pred             ---------CcEEEEeCCCcCChHHHHHHHHhhc------CCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          250 ---------YDVYDVDLSRVADDADLKSLLLQTT------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       250 ---------~~~~~i~~s~~~~~~~l~~l~~~~~------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                               .+++.++.....+...++.++....      .+.|++|||+|.+.     ....+.|+..++..     ..
T Consensus        77 c~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~vviidea~~l~-----~~~~~~Ll~~le~~-----~~  146 (355)
T TIGR02397        77 CKEINSGSSLDVIEIDAASNNGVDDIREILDNVKYAPSSGKYKVYIIDEVHMLS-----KSAFNALLKTLEEP-----PE  146 (355)
T ss_pred             HHHHhcCCCCCEEEeeccccCCHHHHHHHHHHHhcCcccCCceEEEEeChhhcC-----HHHHHHHHHHHhCC-----cc
Confidence                     2355555543333344666664432      34699999999873     23456777777542     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++||.++.+.+++++  |+ ..+++++|+.++...++..++...+..+.++. ..++... +-++..+.+.+
T Consensus       147 ~~~lIl~~~~~~~l~~~l~s--r~-~~~~~~~~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~-~g~~~~a~~~l  219 (355)
T TIGR02397       147 HVVFILATTEPHKIPATILS--RC-QRFDFKRIPLEDIVERLKKILDKEGIKIEDEALELIARAA-DGSLRDALSLL  219 (355)
T ss_pred             ceeEEEEeCCHHHHHHHHHh--he-eEEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCChHHHHHHH
Confidence            56778888889999999998  88 47899999999999999988877666665443 3444443 33454444443

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.

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=99.61  E-value=1.2e-14  Score=163.32  Aligned_cols=234  Identities=18%  Similarity=0.223  Sum_probs=151.1

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHH----
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADL----  266 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l----  266 (480)
                      +..|++++|+.|.+.+......       +......++|+||||||||++++++|+.++.+++.++++.+.+...+    
T Consensus       323 ~~~g~~~vK~~i~~~l~~~~~~-------~~~~g~~i~l~GppG~GKTtl~~~ia~~l~~~~~~i~~~~~~d~~~i~g~~  395 (784)
T PRK10787        323 DHYGLERVKDRILEYLAVQSRV-------NKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHR  395 (784)
T ss_pred             hccCHHHHHHHHHHHHHHHHhc-------ccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEEcCCCCCHHHhccch
Confidence            4899999999998877644322       11123468999999999999999999999999999998876654433    


Q ss_pred             -----------HHHHHhhc-CCcEEEEecccccccCcccccchhhhhhhccccccc----------ccCCceEEEEecCC
Q 011664          267 -----------KSLLLQTT-SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS----------CCFEERVMVFTMNS  324 (480)
Q Consensus       267 -----------~~l~~~~~-~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~----------~~~~~~ivI~tTN~  324 (480)
                                 .+.+.... ...||+|||||.+..... ....+.|+..+|.-.+.          ..-+++++|+|+|.
T Consensus       396 ~~~~g~~~G~~~~~l~~~~~~~~villDEidk~~~~~~-g~~~~aLlevld~~~~~~~~d~~~~~~~dls~v~~i~TaN~  474 (784)
T PRK10787        396 RTYIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDMR-GDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNS  474 (784)
T ss_pred             hccCCCCCcHHHHHHHhcCCCCCEEEEEChhhcccccC-CCHHHHHHHHhccccEEEEecccccccccCCceEEEEcCCC
Confidence                       22233322 346999999999875422 23457788888742110          12357788899998


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHH--HhCCCCCHHHHHHHHHH-hhhcHHHHH
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIF--QNGSSLSPAEIGELMIA-NRNSPSRAL  401 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~--~~~~g~s~adI~~ll~~-a~~~~~~al  401 (480)
                      . .|+|||+.  ||+ .|.++.++.++..+|+++|+...      ..++..  ...-.++.+-+..++.. .+...+|.+
T Consensus       475 ~-~i~~aLl~--R~~-ii~~~~~t~eek~~Ia~~~L~~k------~~~~~~l~~~~l~i~~~ai~~ii~~yt~e~GaR~L  544 (784)
T PRK10787        475 M-NIPAPLLD--RME-VIRLSGYTEDEKLNIAKRHLLPK------QIERNALKKGELTVDDSAIIGIIRYYTREAGVRSL  544 (784)
T ss_pred             C-CCCHHHhc--cee-eeecCCCCHHHHHHHHHHhhhHH------HHHHhCCCCCeEEECHHHHHHHHHhCCcccCCcHH
Confidence            7 59999999  996 79999999999999999998421      111110  01123455555555433 224445666


Q ss_pred             HHHHHHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccC
Q 011664          402 KSVITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLK  463 (480)
Q Consensus       402 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~  463 (480)
                      ++.++.+.++.-       .+.+ ..             +....-.|+.+++++.+|.-++.
T Consensus       545 eR~I~~i~r~~l-------~~~~-~~-------------~~~~~v~v~~~~~~~~lg~~~~~  585 (784)
T PRK10787        545 EREISKLCRKAV-------KQLL-LD-------------KSLKHIEINGDNLHDYLGVQRFD  585 (784)
T ss_pred             HHHHHHHHHHHH-------HHHH-hc-------------CCCceeeecHHHHHHHhCCCccc
Confidence            666655443300       0000 00             00112458889999998876653

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=99.61  E-value=1.7e-14  Score=157.08  Aligned_cols=180  Identities=14%  Similarity=0.263  Sum_probs=131.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------------  249 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------------  249 (480)
                      .|.+|++++|++.+++.+...+..            ...+..||||||+|||||++|+.+|+.+.               
T Consensus        11 rP~~f~~viGq~~v~~~L~~~i~~------------~~~~hayLf~Gp~GtGKTt~Ak~lAkal~c~~~~~~~pC~~C~~   78 (559)
T PRK05563         11 RPQTFEDVVGQEHITKTLKNAIKQ------------GKISHAYLFSGPRGTGKTSAAKIFAKAVNCLNPPDGEPCNECEI   78 (559)
T ss_pred             CCCcHHhccCcHHHHHHHHHHHHc------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccHH
Confidence            578999999999999888876542            12456899999999999999999998764               


Q ss_pred             ---------CcEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          250 ---------YDVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       250 ---------~~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                               .+++.++.++-.+-..++.+....      ....|++|||+|.+.     ....+.||..++..     +.
T Consensus        79 C~~i~~g~~~dv~eidaas~~~vd~ir~i~~~v~~~p~~~~~kViIIDE~~~Lt-----~~a~naLLKtLEep-----p~  148 (559)
T PRK05563         79 CKAITNGSLMDVIEIDAASNNGVDEIRDIRDKVKYAPSEAKYKVYIIDEVHMLS-----TGAFNALLKTLEEP-----PA  148 (559)
T ss_pred             HHHHhcCCCCCeEEeeccccCCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC-----HHHHHHHHHHhcCC-----CC
Confidence                     356677765544555677666543      245799999999883     23456788877643     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.+..+.+.+++  |+. .+.|+.|+.++....++..+...+..+.++. ..++... +-+..+..+++
T Consensus       149 ~~ifIlatt~~~ki~~tI~S--Rc~-~~~f~~~~~~ei~~~L~~i~~~egi~i~~~al~~ia~~s-~G~~R~al~~L  221 (559)
T PRK05563        149 HVIFILATTEPHKIPATILS--RCQ-RFDFKRISVEDIVERLKYILDKEGIEYEDEALRLIARAA-EGGMRDALSIL  221 (559)
T ss_pred             CeEEEEEeCChhhCcHHHHh--Hhe-EEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            67888888889999999998  885 7899999999988888888876666665443 3444433 33444444433

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

Probab=99.60  E-value=2.6e-15  Score=168.66  Aligned_cols=155  Identities=18%  Similarity=0.253  Sum_probs=113.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|..+++++|.++..+.+.+.+.             ...+.+++|+||||||||++++++|..+          +..++.
T Consensus       177 r~~~l~~~igr~~ei~~~~~~L~-------------~~~~~n~lL~G~pG~GKT~l~~~la~~~~~~~~p~~l~~~~~~~  243 (731)
T TIGR02639       177 KNGKIDPLIGREDELERTIQVLC-------------RRKKNNPLLVGEPGVGKTAIAEGLALRIAEGKVPENLKNAKIYS  243 (731)
T ss_pred             hcCCCCcccCcHHHHHHHHHHHh-------------cCCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCeEEE
Confidence            45678999999888876664432             1235689999999999999999999976          778999


Q ss_pred             EeCCCcCC--------hHHHHHHHHhh--cCCcEEEEecccccccCccc---ccchhhhhhhcccccccccCCceEEEEe
Q 011664          255 VDLSRVAD--------DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---AVSLSGVLNFMDGVLNSCCFEERVMVFT  321 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---~~~ls~lL~~ldg~~~~~~~~~~ivI~t  321 (480)
                      ++++.+..        +..++.++...  ..++||||||||.+.+....   ......+|.   ....   .+...+|++
T Consensus       244 ~~~~~l~a~~~~~g~~e~~l~~i~~~~~~~~~~ILfiDEih~l~~~g~~~~~~~~~~~~L~---~~l~---~g~i~~Iga  317 (731)
T TIGR02639       244 LDMGSLLAGTKYRGDFEERLKAVVSEIEKEPNAILFIDEIHTIVGAGATSGGSMDASNLLK---PALS---SGKLRCIGS  317 (731)
T ss_pred             ecHHHHhhhccccchHHHHHHHHHHHHhccCCeEEEEecHHHHhccCCCCCccHHHHHHHH---HHHh---CCCeEEEEe
Confidence            99766542        24577888654  45899999999999864321   122233332   1112   356778888


Q ss_pred             cCCC-----ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          322 MNSK-----DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       322 TN~~-----~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ||..     ..+|+||.|  ||+ .|+++.|+.+++.+|++....
T Consensus       318 Tt~~e~~~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~  359 (731)
T TIGR02639       318 TTYEEYKNHFEKDRALSR--RFQ-KIDVGEPSIEETVKILKGLKE  359 (731)
T ss_pred             cCHHHHHHHhhhhHHHHH--hCc-eEEeCCCCHHHHHHHHHHHHH
Confidence            8753     357999999  997 799999999999999986553

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.60  E-value=2.4e-14  Score=153.73  Aligned_cols=160  Identities=19%  Similarity=0.340  Sum_probs=119.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++|+|++.+++.|...+..           + ..+..+|||||||||||++|+++|+.+.+              
T Consensus         9 RP~~~~dvvGq~~v~~~L~~~i~~-----------~-~l~ha~Lf~GppGtGKTTlA~~lA~~l~c~~~~~~~cg~C~sc   76 (504)
T PRK14963          9 RPITFDEVVGQEHVKEVLLAALRQ-----------G-RLGHAYLFSGPRGVGKTTTARLIAMAVNCSGEDPKPCGECESC   76 (504)
T ss_pred             CCCCHHHhcChHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHHhccCCCCCCCCcChhh
Confidence            588999999999998888765542           1 24556899999999999999999998743              


Q ss_pred             ---------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCc
Q 011664          251 ---------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEE  315 (480)
Q Consensus       251 ---------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~  315 (480)
                               +++.++.+.-.+-..++.+....      ..+.||+|||+|.+.     ...++.|+..|+.-     ...
T Consensus        77 ~~i~~~~h~dv~el~~~~~~~vd~iR~l~~~~~~~p~~~~~kVVIIDEad~ls-----~~a~naLLk~LEep-----~~~  146 (504)
T PRK14963         77 LAVRRGAHPDVLEIDAASNNSVEDVRDLREKVLLAPLRGGRKVYILDEAHMMS-----KSAFNALLKTLEEP-----PEH  146 (504)
T ss_pred             HHHhcCCCCceEEecccccCCHHHHHHHHHHHhhccccCCCeEEEEECccccC-----HHHHHHHHHHHHhC-----CCC
Confidence                     25666655433444455543221      356799999999762     23456777777542     345


Q ss_pred             eEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          316 RVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       316 ~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      .++|++||.+..+.+++.+  |+. +++|+.++.++....++..+...+....+
T Consensus       147 t~~Il~t~~~~kl~~~I~S--Rc~-~~~f~~ls~~el~~~L~~i~~~egi~i~~  197 (504)
T PRK14963        147 VIFILATTEPEKMPPTILS--RTQ-HFRFRRLTEEEIAGKLRRLLEAEGREAEP  197 (504)
T ss_pred             EEEEEEcCChhhCChHHhc--ceE-EEEecCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            6788888999999999998  885 89999999999999998888766655544

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=1.1e-14  Score=158.91  Aligned_cols=180  Identities=15%  Similarity=0.249  Sum_probs=130.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|...+..            ...+.+|||+||||||||++|+++|+.+++              
T Consensus        11 RP~tFddIIGQe~vv~~L~~ai~~------------~rl~Ha~Lf~GP~GvGKTTlAriLAk~LnC~~~~~~~pCg~C~s   78 (709)
T PRK08691         11 RPKTFADLVGQEHVVKALQNALDE------------GRLHHAYLLTGTRGVGKTTIARILAKSLNCENAQHGEPCGVCQS   78 (709)
T ss_pred             CCCCHHHHcCcHHHHHHHHHHHHc------------CCCCeEEEEECCCCCcHHHHHHHHHHHhcccCCCCCCCCcccHH
Confidence            578999999999999988876542            124568999999999999999999998653              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++...-.+-..++.++...      ....|+||||+|.+.     ....+.||..|+..     .+
T Consensus        79 Cr~i~~g~~~DvlEidaAs~~gVd~IRelle~a~~~P~~gk~KVIIIDEad~Ls-----~~A~NALLKtLEEP-----p~  148 (709)
T PRK08691         79 CTQIDAGRYVDLLEIDAASNTGIDNIREVLENAQYAPTAGKYKVYIIDEVHMLS-----KSAFNAMLKTLEEP-----PE  148 (709)
T ss_pred             HHHHhccCccceEEEeccccCCHHHHHHHHHHHHhhhhhCCcEEEEEECccccC-----HHHHHHHHHHHHhC-----CC
Confidence                      23455544444455677776432      245799999999773     23456788887643     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++||.+..+.+.+++  |+ ..+.|+.++.++....+...+...+..+.++. ..|+... +-+..++.+++
T Consensus       149 ~v~fILaTtd~~kL~~TIrS--RC-~~f~f~~Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A-~GslRdAlnLL  221 (709)
T PRK08691        149 HVKFILATTDPHKVPVTVLS--RC-LQFVLRNMTAQQVADHLAHVLDSEKIAYEPPALQLLGRAA-AGSMRDALSLL  221 (709)
T ss_pred             CcEEEEEeCCccccchHHHH--HH-hhhhcCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHh-CCCHHHHHHHH
Confidence            56788888999999999987  98 58899999999999999988887776665543 3444333 45555555554

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.60  E-value=1.7e-14  Score=160.40  Aligned_cols=180  Identities=17%  Similarity=0.237  Sum_probs=126.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc-------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD-------------  251 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~-------------  251 (480)
                      +|.+|++|+|++.+++.|+..+.    .       | ..+..|||+||||||||++|+++|+.+++.             
T Consensus        11 RP~tFddIIGQe~Iv~~LknaI~----~-------~-rl~HAyLFtGPpGtGKTTLARiLAk~Lnce~~~~~~pCg~C~s   78 (944)
T PRK14949         11 RPATFEQMVGQSHVLHALTNALT----Q-------Q-RLHHAYLFTGTRGVGKTSLARLFAKGLNCEQGVTATPCGVCSS   78 (944)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHH----h-------C-CCCeEEEEECCCCCCHHHHHHHHHHhccCccCCCCCCCCCchH
Confidence            57899999999999988775443    1       1 245678999999999999999999988653             


Q ss_pred             -----------EEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          252 -----------VYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       252 -----------~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                 ++.++..+-.+-..++.+....      ....|+||||+|.+.     ....+.||..|+.-     ..
T Consensus        79 C~~i~~g~~~DviEidAas~~kVDdIReLie~v~~~P~~gk~KViIIDEAh~LT-----~eAqNALLKtLEEP-----P~  148 (944)
T PRK14949         79 CVEIAQGRFVDLIEVDAASRTKVDDTRELLDNVQYRPSRGRFKVYLIDEVHMLS-----RSSFNALLKTLEEP-----PE  148 (944)
T ss_pred             HHHHhcCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCcEEEEEechHhcC-----HHHHHHHHHHHhcc-----CC
Confidence                       2333333223334456555322      235799999999883     34567788888642     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.+..|.+.+++  |+ .++.|..++.++....++..+...+..+.++. ..|+... +-++.++..+|
T Consensus       149 ~vrFILaTTe~~kLl~TIlS--RC-q~f~fkpLs~eEI~~~L~~il~~EgI~~edeAL~lIA~~S-~Gd~R~ALnLL  221 (944)
T PRK14949        149 HVKFLLATTDPQKLPVTVLS--RC-LQFNLKSLTQDEIGTQLNHILTQEQLPFEAEALTLLAKAA-NGSMRDALSLT  221 (944)
T ss_pred             CeEEEEECCCchhchHHHHH--hh-eEEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            56677778888889999999  88 68999999999988888888776555555433 3444433 44455554444

>PRK13342 recombination factor protein RarA; Reviewed

Probab=99.60  E-value=1.4e-14  Score=152.62  Aligned_cols=150  Identities=21%  Similarity=0.321  Sum_probs=110.2

Q ss_pred             CCCCCccccccChHHHHH---HHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          184 THPSTFDTISMETDLKNR---VKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~---l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      -+|.+|++++|++.+...   +...+.    .       +  ...+++|+||||||||++|+++|+.++.+++.++.+..
T Consensus         6 ~RP~~l~d~vGq~~~v~~~~~L~~~i~----~-------~--~~~~ilL~GppGtGKTtLA~~ia~~~~~~~~~l~a~~~   72 (413)
T PRK13342          6 MRPKTLDEVVGQEHLLGPGKPLRRMIE----A-------G--RLSSMILWGPPGTGKTTLARIIAGATDAPFEALSAVTS   72 (413)
T ss_pred             hCCCCHHHhcCcHHHhCcchHHHHHHH----c-------C--CCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEecccc
Confidence            367899999999988655   544332    1       1  23479999999999999999999999999999987643


Q ss_pred             CChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEec--CCCccCcccc
Q 011664          261 ADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM--NSKDHVDQAL  332 (480)
Q Consensus       261 ~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT--N~~~~LD~aL  332 (480)
                       +...++.++...      ..+.||||||+|.+..     .....|+..++.       ...++|++|  |....++++|
T Consensus        73 -~~~~ir~ii~~~~~~~~~g~~~vL~IDEi~~l~~-----~~q~~LL~~le~-------~~iilI~att~n~~~~l~~aL  139 (413)
T PRK13342         73 -GVKDLREVIEEARQRRSAGRRTILFIDEIHRFNK-----AQQDALLPHVED-------GTITLIGATTENPSFEVNPAL  139 (413)
T ss_pred             -cHHHHHHHHHHHHHhhhcCCceEEEEechhhhCH-----HHHHHHHHHhhc-------CcEEEEEeCCCChhhhccHHH
Confidence             344555555433      2678999999998742     223456665532       234556544  3456899999


Q ss_pred             cCCCceeEEEEcCCCCHHHHHHHHHHHhcc
Q 011664          333 LRPGRIDVHIHFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       333 lrpGRfd~~I~~~~p~~~~r~~il~~~l~~  362 (480)
                      ++  |+ ..+.|++++.++...+++..+..
T Consensus       140 ~S--R~-~~~~~~~ls~e~i~~lL~~~l~~  166 (413)
T PRK13342        140 LS--RA-QVFELKPLSEEDIEQLLKRALED  166 (413)
T ss_pred             hc--cc-eeeEeCCCCHHHHHHHHHHHHHH
Confidence            99  98 68999999999999999887754

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=99.60  E-value=2e-14  Score=157.29  Aligned_cols=160  Identities=19%  Similarity=0.322  Sum_probs=120.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|...+..           | ..+..|||+||||||||++|+++|+.+++              
T Consensus        11 RP~~f~divGQe~vv~~L~~~l~~-----------~-rl~hAyLf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~~   78 (647)
T PRK07994         11 RPQTFAEVVGQEHVLTALANALDL-----------G-RLHHAYLFSGTRGVGKTTIARLLAKGLNCETGITATPCGECDN   78 (647)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHhhhhccCCCCCCCCCCHH
Confidence            578999999999999887755431           1 24567999999999999999999998865              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.++-.+-.+++.+....      ....|++|||+|.+.     ....+.||..|+.-     .+
T Consensus        79 C~~i~~g~~~D~ieidaas~~~VddiR~li~~~~~~p~~g~~KV~IIDEah~Ls-----~~a~NALLKtLEEP-----p~  148 (647)
T PRK07994         79 CREIEQGRFVDLIEIDAASRTKVEDTRELLDNVQYAPARGRFKVYLIDEVHMLS-----RHSFNALLKTLEEP-----PE  148 (647)
T ss_pred             HHHHHcCCCCCceeecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEechHhCC-----HHHHHHHHHHHHcC-----CC
Confidence                      34555554333445566665432      245799999999883     34567788887642     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      ..++|++|+.+..|.+.+++  |+ ..++|..++.++....+...+...+....+
T Consensus       149 ~v~FIL~Tt~~~kLl~TI~S--RC-~~~~f~~Ls~~ei~~~L~~il~~e~i~~e~  200 (647)
T PRK07994        149 HVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRQQLEHILQAEQIPFEP  200 (647)
T ss_pred             CeEEEEecCCccccchHHHh--hh-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            56788888889999999999  97 799999999999988888887655555443

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=99.59  E-value=1.2e-14  Score=139.85  Aligned_cols=186  Identities=14%  Similarity=0.171  Sum_probs=112.0

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      +...+.+|++.+..  ..+...+.+..++.         ...+++++|+||||||||++|+++++++   +.++++++++
T Consensus         7 ~~~~~~~~~~~~~~--~~~~~~~~l~~~~~---------~~~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~   75 (226)
T TIGR03420         7 GLPDDPTFDNFYAG--GNAELLAALRQLAA---------GKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLA   75 (226)
T ss_pred             CCCCchhhcCcCcC--CcHHHHHHHHHHHh---------cCCCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHH
Confidence            34455678888732  22233333333322         1235689999999999999999999876   5678889887


Q ss_pred             CcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC-CCccCc---ccccC
Q 011664          259 RVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKDHVD---QALLR  334 (480)
Q Consensus       259 ~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~~LD---~aLlr  334 (480)
                      .+...  ....+.......+|+|||+|.+......   ...+...++....   .+. .+|+|++ .+..++   +.|.+
T Consensus        76 ~~~~~--~~~~~~~~~~~~lLvIDdi~~l~~~~~~---~~~L~~~l~~~~~---~~~-~iIits~~~~~~~~~~~~~L~~  146 (226)
T TIGR03420        76 ELAQA--DPEVLEGLEQADLVCLDDVEAIAGQPEW---QEALFHLYNRVRE---AGG-RLLIAGRAAPAQLPLRLPDLRT  146 (226)
T ss_pred             HHHHh--HHHHHhhcccCCEEEEeChhhhcCChHH---HHHHHHHHHHHHH---cCC-eEEEECCCChHHCCcccHHHHH
Confidence            66432  1233443445679999999987432211   2344444444332   223 3455554 444432   67777


Q ss_pred             CCce--eEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          335 PGRI--DVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       335 pGRf--d~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                        |+  ..+|.+|+|+.+++..+++.++...+..+.++. +.|+.. -+-++.++.+++
T Consensus       147 --r~~~~~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~-~~gn~r~L~~~l  202 (226)
T TIGR03420       147 --RLAWGLVFQLPPLSDEEKIAALQSRAARRGLQLPDEVADYLLRH-GSRDMGSLMALL  202 (226)
T ss_pred             --HHhcCeeEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh-ccCCHHHHHHHH
Confidence              76  478999999999999999887654444444433 333332 233444444443

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.

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=3.4e-14  Score=154.43  Aligned_cols=162  Identities=19%  Similarity=0.328  Sum_probs=121.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|+..+..           | ..+..|||+||+|||||++|+++|+.+.+              
T Consensus         8 RP~~f~eivGq~~i~~~L~~~i~~-----------~-r~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pCg~C~~   75 (584)
T PRK14952          8 RPATFAEVVGQEHVTEPLSSALDA-----------G-RINHAYLFSGPRGCGKTSSARILARSLNCAQGPTATPCGVCES   75 (584)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhccccCCCCCcccccHH
Confidence            588999999999999988765541           2 24557999999999999999999987653              


Q ss_pred             ------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          251 ------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       251 ------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                                  +++.++.+...+-.+++.+....      ....|++|||+|.+.     ....+.||..|+..     
T Consensus        76 C~~i~~~~~~~~dvieidaas~~gvd~iRel~~~~~~~P~~~~~KVvIIDEah~Lt-----~~A~NALLK~LEEp-----  145 (584)
T PRK14952         76 CVALAPNGPGSIDVVELDAASHGGVDDTRELRDRAFYAPAQSRYRIFIVDEAHMVT-----TAGFNALLKIVEEP-----  145 (584)
T ss_pred             HHHhhcccCCCceEEEeccccccCHHHHHHHHHHHHhhhhcCCceEEEEECCCcCC-----HHHHHHHHHHHhcC-----
Confidence                        35556554444445555554322      245799999999883     23457788887643     


Q ss_pred             CCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          313 FEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       313 ~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                      ....++|++|+.+..|.+++++  |+ .+++|..++.++....+..++...+..+.++.
T Consensus       146 p~~~~fIL~tte~~kll~TI~S--Rc-~~~~F~~l~~~~i~~~L~~i~~~egi~i~~~a  201 (584)
T PRK14952        146 PEHLIFIFATTEPEKVLPTIRS--RT-HHYPFRLLPPRTMRALIARICEQEGVVVDDAV  201 (584)
T ss_pred             CCCeEEEEEeCChHhhHHHHHH--hc-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            4567888888888999999999  86 58999999999988888888877776665544

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=99.58  E-value=1.4e-14  Score=152.21  Aligned_cols=193  Identities=14%  Similarity=0.209  Sum_probs=125.6

Q ss_pred             CCCCCCCccc-cccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEE
Q 011664          182 PFTHPSTFDT-ISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDV  255 (480)
Q Consensus       182 ~~~~~~~~~~-i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i  255 (480)
                      ++.+..+|++ ++|.....  ....+..+...+      +. ...+++||||||||||+|++|+++++     +..++++
T Consensus       102 ~l~~~~tfd~fi~g~~n~~--a~~~~~~~~~~~------~~-~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi  172 (405)
T TIGR00362       102 PLNPKYTFDNFVVGKSNRL--AHAAALAVAENP------GK-AYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYV  172 (405)
T ss_pred             CCCCCCcccccccCCcHHH--HHHHHHHHHhCc------Cc-cCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEE
Confidence            4556678999 55654422  222233332221      21 23479999999999999999999987     5778888


Q ss_pred             eCCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc-
Q 011664          256 DLSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH-  327 (480)
Q Consensus       256 ~~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~-  327 (480)
                      ++.++...       ..+..+........+|+|||+|.+.+...   +..+|+..++.+..   .+..+||.++..|.. 
T Consensus       173 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~~---~~~~l~~~~n~~~~---~~~~iiits~~~p~~l  246 (405)
T TIGR00362       173 SSEKFTNDFVNALRNNKMEEFKEKYRSVDLLLIDDIQFLAGKER---TQEEFFHTFNALHE---NGKQIVLTSDRPPKEL  246 (405)
T ss_pred             EHHHHHHHHHHHHHcCCHHHHHHHHHhCCEEEEehhhhhcCCHH---HHHHHHHHHHHHHH---CCCCEEEecCCCHHHH
Confidence            87654321       01112222334578999999998864332   23456666655544   233444444445654 


Q ss_pred             --CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHH
Q 011664          328 --VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       328 --LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~  392 (480)
                        +++.|++  ||.  ..++++.|+.++|..|++..+...+..+.+++ +.|+... .-+..++...+..
T Consensus       247 ~~l~~~l~S--Rl~~g~~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~-~~~~r~l~~~l~~  313 (405)
T TIGR00362       247 PGLEERLRS--RFEWGLVVDIEPPDLETRLAILQKKAEEEGLELPDEVLEFIAKNI-RSNVRELEGALNR  313 (405)
T ss_pred             hhhhhhhhh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-CCCHHHHHHHHHH
Confidence              5688998  996  58999999999999999999988777777765 4556544 5566666665543

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).

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=99.58  E-value=3e-14  Score=154.10  Aligned_cols=180  Identities=16%  Similarity=0.255  Sum_probs=127.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++.+++.+...+..           | ..++++||+||||||||++|+++|+.+.+              
T Consensus        11 RP~~F~dIIGQe~iv~~L~~aI~~-----------~-rl~hA~Lf~GP~GvGKTTlA~~lAk~L~C~~~~~~~~Cg~C~s   78 (605)
T PRK05896         11 RPHNFKQIIGQELIKKILVNAILN-----------N-KLTHAYIFSGPRGIGKTSIAKIFAKAINCLNPKDGDCCNSCSV   78 (605)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccHH
Confidence            688999999999999888764431           1 23568999999999999999999997642              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+...+-.+++.+....      ....|++|||+|.+..     ...+.|+..|+..     +.
T Consensus        79 Cr~i~~~~h~DiieIdaas~igVd~IReIi~~~~~~P~~~~~KVIIIDEad~Lt~-----~A~NaLLKtLEEP-----p~  148 (605)
T PRK05896         79 CESINTNQSVDIVELDAASNNGVDEIRNIIDNINYLPTTFKYKVYIIDEAHMLST-----SAWNALLKTLEEP-----PK  148 (605)
T ss_pred             HHHHHcCCCCceEEeccccccCHHHHHHHHHHHHhchhhCCcEEEEEechHhCCH-----HHHHHHHHHHHhC-----CC
Confidence                      45556654434445566665432      2346999999998732     2346777777642     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.+..|.+++++  |+. .++|+.++.++....+...+...+....++. ..++..+ +-++.++..++
T Consensus       149 ~tvfIL~Tt~~~KLl~TI~S--Rcq-~ieF~~Ls~~eL~~~L~~il~kegi~Is~eal~~La~lS-~GdlR~AlnlL  221 (605)
T PRK05896        149 HVVFIFATTEFQKIPLTIIS--RCQ-RYNFKKLNNSELQELLKSIAKKEKIKIEDNAIDKIADLA-DGSLRDGLSIL  221 (605)
T ss_pred             cEEEEEECCChHhhhHHHHh--hhh-hcccCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCcHHHHHHHH
Confidence            67788888889999999999  885 8999999999988888887766655554433 3444433 33444443333

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.58  E-value=3.9e-14  Score=154.62  Aligned_cols=180  Identities=16%  Similarity=0.235  Sum_probs=128.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++.+++.|...+..            ...+..|||+||+|||||++|+++|+.+++              
T Consensus        11 RP~~f~dviGQe~vv~~L~~~l~~------------~rl~ha~Lf~Gp~GvGKTtlAr~lAk~LnC~~~~~~~~~~~~pC   78 (618)
T PRK14951         11 RPRSFSEMVGQEHVVQALTNALTQ------------QRLHHAYLFTGTRGVGKTTVSRILAKSLNCQGPDGQGGITATPC   78 (618)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCCCcccccCCCCCCC
Confidence            578999999999988877764431            123557999999999999999999998764              


Q ss_pred             ---------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccc
Q 011664          251 ---------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN  309 (480)
Q Consensus       251 ---------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~  309 (480)
                                     +++.++..+-.+-.+++.++...      ....|++|||+|.+.     ....+.||..|+.-  
T Consensus        79 g~C~~C~~i~~g~h~D~~eldaas~~~Vd~iReli~~~~~~p~~g~~KV~IIDEvh~Ls-----~~a~NaLLKtLEEP--  151 (618)
T PRK14951         79 GVCQACRDIDSGRFVDYTELDAASNRGVDEVQQLLEQAVYKPVQGRFKVFMIDEVHMLT-----NTAFNAMLKTLEEP--  151 (618)
T ss_pred             CccHHHHHHHcCCCCceeecCcccccCHHHHHHHHHHHHhCcccCCceEEEEEChhhCC-----HHHHHHHHHhcccC--
Confidence                           34555544434445677776542      134699999999884     23356677777542  


Q ss_pred             cccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHH
Q 011664          310 SCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       310 ~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~  388 (480)
                         .+..++|++|+.+..+.+.+++  |+ .+++|..++.++....++..+...+....++. ..|+... +-+..++.+
T Consensus       152 ---P~~~~fIL~Ttd~~kil~TIlS--Rc-~~~~f~~Ls~eei~~~L~~i~~~egi~ie~~AL~~La~~s-~GslR~al~  224 (618)
T PRK14951        152 ---PEYLKFVLATTDPQKVPVTVLS--RC-LQFNLRPMAPETVLEHLTQVLAAENVPAEPQALRLLARAA-RGSMRDALS  224 (618)
T ss_pred             ---CCCeEEEEEECCchhhhHHHHH--hc-eeeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHH
Confidence               3456788888888889888998  88 69999999999988888888877766665543 3444433 334544444


Q ss_pred             HH
Q 011664          389 LM  390 (480)
Q Consensus       389 ll  390 (480)
                      ++
T Consensus       225 lL  226 (618)
T PRK14951        225 LT  226 (618)
T ss_pred             HH
Confidence            43

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=6.8e-14  Score=145.10  Aligned_cols=167  Identities=17%  Similarity=0.314  Sum_probs=119.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC------------cE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY------------DV  252 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~------------~~  252 (480)
                      +|.+|++++|++.+++.+...+..           | ..+.++|||||||+|||++|+++|+.+..            ++
T Consensus        12 rP~~~~~iig~~~~~~~l~~~i~~-----------~-~~~~~~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~~~~~~~   79 (367)
T PRK14970         12 RPQTFDDVVGQSHITNTLLNAIEN-----------N-HLAQALLFCGPRGVGKTTCARILARKINQPGYDDPNEDFSFNI   79 (367)
T ss_pred             CCCcHHhcCCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCcce
Confidence            688999999999998887765542           2 24568999999999999999999998743            23


Q ss_pred             EEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          253 YDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       253 ~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                      +.++.....+...++.++...      ..+.||+|||+|.+..     ...+.|+..++..     ....++|++|+.+.
T Consensus        80 ~~l~~~~~~~~~~i~~l~~~~~~~p~~~~~kiviIDE~~~l~~-----~~~~~ll~~le~~-----~~~~~~Il~~~~~~  149 (367)
T PRK14970         80 FELDAASNNSVDDIRNLIDQVRIPPQTGKYKIYIIDEVHMLSS-----AAFNAFLKTLEEP-----PAHAIFILATTEKH  149 (367)
T ss_pred             EEeccccCCCHHHHHHHHHHHhhccccCCcEEEEEeChhhcCH-----HHHHHHHHHHhCC-----CCceEEEEEeCCcc
Confidence            333333333345666666532      2457999999997742     2356677777542     33467777888889


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHH
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQ  376 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~  376 (480)
                      .+.+++.+  |+. .++++.|+.++...++...+...+..+.++. +.++.
T Consensus       150 kl~~~l~s--r~~-~v~~~~~~~~~l~~~l~~~~~~~g~~i~~~al~~l~~  197 (367)
T PRK14970        150 KIIPTILS--RCQ-IFDFKRITIKDIKEHLAGIAVKEGIKFEDDALHIIAQ  197 (367)
T ss_pred             cCCHHHHh--cce-eEecCCccHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            99999998  774 7899999999988888887776666555443 33443

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=2.5e-14  Score=154.67  Aligned_cols=180  Identities=14%  Similarity=0.245  Sum_probs=127.8

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.+...+..            ...+..|||+||||||||++|+++|+.+++              
T Consensus        11 rP~~f~divGq~~v~~~L~~~i~~------------~~~~ha~Lf~Gp~G~GKTt~A~~lAk~l~c~~~~~~~pcg~C~~   78 (527)
T PRK14969         11 RPKSFSELVGQEHVVRALTNALEQ------------QRLHHAYLFTGTRGVGKTTLARILAKSLNCETGVTATPCGVCSA   78 (527)
T ss_pred             CCCcHHHhcCcHHHHHHHHHHHHc------------CCCCEEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCCCHH
Confidence            478999999999999987765542            124567999999999999999999998854              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+.-.+-..++.++...      ....|++|||+|.+.     ....+.||..|+..     .+
T Consensus        79 C~~i~~~~~~d~~ei~~~~~~~vd~ir~l~~~~~~~p~~~~~kVvIIDEad~ls-----~~a~naLLK~LEep-----p~  148 (527)
T PRK14969         79 CLEIDSGRFVDLIEVDAASNTQVDAMRELLDNAQYAPTRGRFKVYIIDEVHMLS-----KSAFNAMLKTLEEP-----PE  148 (527)
T ss_pred             HHHHhcCCCCceeEeeccccCCHHHHHHHHHHHhhCcccCCceEEEEcCcccCC-----HHHHHHHHHHHhCC-----CC
Confidence                      34555554333445577666433      234799999999883     23456788887653     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.+..+.+.+++  |+ ..++|..++.++....+...+...+....++. ..++... +-++.++.+++
T Consensus       149 ~~~fIL~t~d~~kil~tI~S--Rc-~~~~f~~l~~~~i~~~L~~il~~egi~~~~~al~~la~~s-~Gslr~al~ll  221 (527)
T PRK14969        149 HVKFILATTDPQKIPVTVLS--RC-LQFNLKQMPPPLIVSHLQHILEQENIPFDATALQLLARAA-AGSMRDALSLL  221 (527)
T ss_pred             CEEEEEEeCChhhCchhHHH--HH-HHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            56788888888888888888  88 58999999999988888888766665554432 3444433 44444444443

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=4.3e-14  Score=155.57  Aligned_cols=180  Identities=16%  Similarity=0.273  Sum_probs=127.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc-------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD-------------  251 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~-------------  251 (480)
                      +|.+|++|+|++.+++.+...+..            ...+..||||||||||||++|+++|+.+.+.             
T Consensus        13 RP~~f~dIiGQe~~v~~L~~aI~~------------~rl~HAYLF~GP~GtGKTt~AriLAk~LnC~~~~~~~~pC~~C~   80 (725)
T PRK07133         13 RPKTFDDIVGQDHIVQTLKNIIKS------------NKISHAYLFSGPRGTGKTSVAKIFANALNCSHKTDLLEPCQECI   80 (725)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc------------CCCCeEEEEECCCCCcHHHHHHHHHHHhcccccCCCCCchhHHH
Confidence            688999999999999888876642            1245689999999999999999999877442             


Q ss_pred             --------EEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceE
Q 011664          252 --------VYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERV  317 (480)
Q Consensus       252 --------~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~i  317 (480)
                              ++.++...-.+-..++.+....      ....|++|||+|.+..     ...+.||..|+..     +...+
T Consensus        81 ~~~~~~~Dvieidaasn~~vd~IReLie~~~~~P~~g~~KV~IIDEa~~LT~-----~A~NALLKtLEEP-----P~~ti  150 (725)
T PRK07133         81 ENVNNSLDIIEMDAASNNGVDEIRELIENVKNLPTQSKYKIYIIDEVHMLSK-----SAFNALLKTLEEP-----PKHVI  150 (725)
T ss_pred             HhhcCCCcEEEEeccccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhCCH-----HHHHHHHHHhhcC-----CCceE
Confidence                    2333332222344566665433      2457999999998742     3456788877643     34677


Q ss_pred             EEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHH
Q 011664          318 MVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       318 vI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll  390 (480)
                      +|++|+.++.|.+++++  |+. +++|.+++.++....+...+...+.....+ +..++... +-+..++..++
T Consensus       151 fILaTte~~KLl~TI~S--Rcq-~ieF~~L~~eeI~~~L~~il~kegI~id~eAl~~LA~lS-~GslR~AlslL  220 (725)
T PRK07133        151 FILATTEVHKIPLTILS--RVQ-RFNFRRISEDEIVSRLEFILEKENISYEKNALKLIAKLS-SGSLRDALSIA  220 (725)
T ss_pred             EEEEcCChhhhhHHHHh--hce-eEEccCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            88888899999999999  985 899999999998888888776665555443 33444433 44444444433

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

Probab=99.57  E-value=4.7e-14  Score=151.92  Aligned_cols=179  Identities=23%  Similarity=0.311  Sum_probs=143.9

Q ss_pred             HhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC----C--hHHHHHHHH--hhcCCcEEEE
Q 011664          210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA----D--DADLKSLLL--QTTSKSVILI  281 (480)
Q Consensus       210 l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~----~--~~~l~~l~~--~~~~~sII~I  281 (480)
                      +..+..+...+..++++++++||||||||++++++|++ +..+..++.....    +  +..++.+|.  ....|+++++
T Consensus         4 ~~~~~~~~~~~~~~~~~v~~~g~~~~~~t~~~~~~a~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~ii~~   82 (494)
T COG0464           4 LKEPELFKKLGIEPPKGVLLHGPPGTGKTLLARALANE-GAEFLSINGPEILSKYVGESELRLRELFEEAEKLAPSIIFI   82 (494)
T ss_pred             ccCHHHHHHhCCCCCCCceeeCCCCCchhHHHHHHHhc-cCcccccCcchhhhhhhhHHHHHHHHHHHHHHHhCCCeEee
Confidence            44567788899999999999999999999999999999 5555555544332    3  334556664  3457899999


Q ss_pred             ecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHH
Q 011664          282 EDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTL  355 (480)
Q Consensus       282 DEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~i  355 (480)
                      ||+|.+.+.+..      ....++++..||++..   .. .+++..||.+..+|+++++||||+..+.++.|+...+.++
T Consensus        83 d~~~~~~~~~~~~~~~~~~~v~~~l~~~~d~~~~---~~-v~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~ei  158 (494)
T COG0464          83 DEIDALAPKRSSDQGEVERRVVAQLLALMDGLKR---GQ-VIVIGATNRPDGLDPAKRRPGRFDREIEVNLPDEAGRLEI  158 (494)
T ss_pred             chhhhcccCccccccchhhHHHHHHHHhcccccC---Cc-eEEEeecCCccccChhHhCccccceeeecCCCCHHHHHHH
Confidence            999999887665      2347889999999872   55 7777799999999999999999999999999999999888


Q ss_pred             HHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          356 ASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       356 l~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      +.............+...++..+.|++++++..++..+
T Consensus       159 ~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~l~~~~  196 (494)
T COG0464         159 LQIHTRLMFLGPPGTGKTLAARTVGKSGADLGALAKEA  196 (494)
T ss_pred             HHHHHhcCCCcccccHHHHHHhcCCccHHHHHHHHHHH
Confidence            88776544433345778999999999999999998654

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=99.57  E-value=4.3e-14  Score=147.48  Aligned_cols=178  Identities=15%  Similarity=0.167  Sum_probs=123.2

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc----------------
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD----------------  251 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~----------------  251 (480)
                      .|++|+|++.+++.|+..+.....   .+...+...+.++||+||||+|||++|+++|+.+.+.                
T Consensus         3 ~f~~IiGq~~~~~~L~~~i~~~~~---~~~~~~~~l~ha~Lf~Gp~G~GKt~lA~~lA~~l~c~~~~~~~Cg~C~~C~~~   79 (394)
T PRK07940          3 VWDDLVGQEAVVAELRAAARAARA---DVAAAGSGMTHAWLFTGPPGSGRSVAARAFAAALQCTDPDEPGCGECRACRTV   79 (394)
T ss_pred             hhhhccChHHHHHHHHHHHHhccc---cccccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHH
Confidence            589999999999999988775433   2333455567899999999999999999999876432                


Q ss_pred             -------EEEEeCCC-cCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceE
Q 011664          252 -------VYDVDLSR-VADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERV  317 (480)
Q Consensus       252 -------~~~i~~s~-~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~i  317 (480)
                             ++.+.... ..+-.+++.++...      ....|++|||+|.+..     ...+.||..|+.-     ..+.+
T Consensus        80 ~~~~hpD~~~i~~~~~~i~i~~iR~l~~~~~~~p~~~~~kViiIDead~m~~-----~aanaLLk~LEep-----~~~~~  149 (394)
T PRK07940         80 LAGTHPDVRVVAPEGLSIGVDEVRELVTIAARRPSTGRWRIVVIEDADRLTE-----RAANALLKAVEEP-----PPRTV  149 (394)
T ss_pred             hcCCCCCEEEeccccccCCHHHHHHHHHHHHhCcccCCcEEEEEechhhcCH-----HHHHHHHHHhhcC-----CCCCe
Confidence                   33333321 23345577766543      2346999999999842     2346688887642     34566


Q ss_pred             EEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHH
Q 011664          318 MVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAE  385 (480)
Q Consensus       318 vI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~ad  385 (480)
                      +|++|+.++.|.|++++  |+ ..++|+.|+.++..+.+....+   .. .+....++....|..+..
T Consensus       150 fIL~a~~~~~llpTIrS--Rc-~~i~f~~~~~~~i~~~L~~~~~---~~-~~~a~~la~~s~G~~~~A  210 (394)
T PRK07940        150 WLLCAPSPEDVLPTIRS--RC-RHVALRTPSVEAVAEVLVRRDG---VD-PETARRAARASQGHIGRA  210 (394)
T ss_pred             EEEEECChHHChHHHHh--hC-eEEECCCCCHHHHHHHHHHhcC---CC-HHHHHHHHHHcCCCHHHH
Confidence            77777779999999999  98 5999999999988777753322   11 233445665665554433

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=99.57  E-value=4.2e-14  Score=159.15  Aligned_cols=162  Identities=20%  Similarity=0.316  Sum_probs=120.8

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-------------  250 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------  250 (480)
                      .+|.+|++|+|++.+++.|+..+..           | ..+..|||+||+|||||++|+++|+.+.+             
T Consensus         9 yRP~~f~eiiGqe~v~~~L~~~i~~-----------~-ri~Ha~Lf~Gp~G~GKTt~A~~lAr~L~C~~~~~~~pCg~C~   76 (824)
T PRK07764          9 YRPATFAEVIGQEHVTEPLSTALDS-----------G-RINHAYLFSGPRGCGKTSSARILARSLNCVEGPTSTPCGECD   76 (824)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHh-----------C-CCCceEEEECCCCCCHHHHHHHHHHHhCcccCCCCCCCcccH
Confidence            3688999999999999887765531           1 23457999999999999999999998853             


Q ss_pred             -------------cEEEEeCCCcCChHHHHHHHHh------hcCCcEEEEecccccccCcccccchhhhhhhcccccccc
Q 011664          251 -------------DVYDVDLSRVADDADLKSLLLQ------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSC  311 (480)
Q Consensus       251 -------------~~~~i~~s~~~~~~~l~~l~~~------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~  311 (480)
                                   +++.++.....+-.+++.+...      .....|+||||+|.+.     ....+.||+.|+..    
T Consensus        77 sC~~~~~g~~~~~dv~eidaas~~~Vd~iR~l~~~~~~~p~~~~~KV~IIDEad~lt-----~~a~NaLLK~LEEp----  147 (824)
T PRK07764         77 SCVALAPGGPGSLDVTEIDAASHGGVDDARELRERAFFAPAESRYKIFIIDEAHMVT-----PQGFNALLKIVEEP----  147 (824)
T ss_pred             HHHHHHcCCCCCCcEEEecccccCCHHHHHHHHHHHHhchhcCCceEEEEechhhcC-----HHHHHHHHHHHhCC----
Confidence                         3455554443344555554322      1355799999999984     23456788888653    


Q ss_pred             cCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          312 CFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       312 ~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                       ....+||++|+.++.|-+.|++  |+ .+++|..++.++...++...+...+..+..+
T Consensus       148 -P~~~~fIl~tt~~~kLl~TIrS--Rc-~~v~F~~l~~~~l~~~L~~il~~EGv~id~e  202 (824)
T PRK07764        148 -PEHLKFIFATTEPDKVIGTIRS--RT-HHYPFRLVPPEVMRGYLERICAQEGVPVEPG  202 (824)
T ss_pred             -CCCeEEEEEeCChhhhhHHHHh--he-eEEEeeCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence             3467888888888889999998  88 5899999999999888888887666655443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.57  E-value=5.3e-14  Score=151.74  Aligned_cols=161  Identities=17%  Similarity=0.285  Sum_probs=118.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++.+++.+...+..           | ..+..+||+||||||||++|+++|+.+.+              
T Consensus        11 RP~~f~diiGq~~~v~~L~~~i~~-----------~-rl~ha~Lf~Gp~GvGKTTlAr~lAk~L~c~~~~~~~pCg~C~s   78 (546)
T PRK14957         11 RPQSFAEVAGQQHALNSLVHALET-----------Q-KVHHAYLFTGTRGVGKTTLGRLLAKCLNCKTGVTAEPCNKCEN   78 (546)
T ss_pred             CcCcHHHhcCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHH
Confidence            578999999999999887755431           1 23557999999999999999999997753              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++...-.+-.+++.++...      ....|++|||+|.+.     ....+.||..|+..     ++
T Consensus        79 C~~i~~~~~~dlieidaas~~gvd~ir~ii~~~~~~p~~g~~kViIIDEa~~ls-----~~a~naLLK~LEep-----p~  148 (546)
T PRK14957         79 CVAINNNSFIDLIEIDAASRTGVEETKEILDNIQYMPSQGRYKVYLIDEVHMLS-----KQSFNALLKTLEEP-----PE  148 (546)
T ss_pred             HHHHhcCCCCceEEeecccccCHHHHHHHHHHHHhhhhcCCcEEEEEechhhcc-----HHHHHHHHHHHhcC-----CC
Confidence                      45556654434444555555332      245799999999873     23456788887643     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                      ..++|++|+.+..+.+++++  |+ ..++|..++.++....+...+...+....++
T Consensus       149 ~v~fIL~Ttd~~kil~tI~S--Rc-~~~~f~~Ls~~eI~~~L~~il~~egi~~e~~  201 (546)
T PRK14957        149 YVKFILATTDYHKIPVTILS--RC-IQLHLKHISQADIKDQLKIILAKENINSDEQ  201 (546)
T ss_pred             CceEEEEECChhhhhhhHHH--he-eeEEeCCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence            56777777778888888988  88 6999999999998888888776665555443

>PRK08727 hypothetical protein; Validated

Probab=99.57  E-value=3.8e-14  Score=138.15  Aligned_cols=173  Identities=18%  Similarity=0.243  Sum_probs=112.2

Q ss_pred             CCCCCCCCccccccChH-HHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          181 VPFTHPSTFDTISMETD-LKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~-~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      ++.....+|++.++.+. ....+.    ....        | .+...++||||+|||||+|++|+++++   +....+++
T Consensus        10 ~~~~~~~~f~~f~~~~~n~~~~~~----~~~~--------~-~~~~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~   76 (233)
T PRK08727         10 LRYPSDQRFDSYIAAPDGLLAQLQ----ALAA--------G-QSSDWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLP   76 (233)
T ss_pred             CCCCCcCChhhccCCcHHHHHHHH----HHHh--------c-cCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEe
Confidence            44556678999765554 222211    1111        1 133469999999999999999998764   66777777


Q ss_pred             CCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEec-CCCccC---cccc
Q 011664          257 LSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM-NSKDHV---DQAL  332 (480)
Q Consensus       257 ~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT-N~~~~L---D~aL  332 (480)
                      +.+..  ..+...+....+..+|+|||++.+.........+..+++.   ...    .+.-+|+|+ +.|..+   +|+|
T Consensus        77 ~~~~~--~~~~~~~~~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n~---~~~----~~~~vI~ts~~~p~~l~~~~~dL  147 (233)
T PRK08727         77 LQAAA--GRLRDALEALEGRSLVALDGLESIAGQREDEVALFDFHNR---ARA----AGITLLYTARQMPDGLALVLPDL  147 (233)
T ss_pred             HHHhh--hhHHHHHHHHhcCCEEEEeCcccccCChHHHHHHHHHHHH---HHH----cCCeEEEECCCChhhhhhhhHHH
Confidence            65533  2344555666778899999999886544433333334433   322    223355554 467665   7999


Q ss_pred             cCCCce--eEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHh
Q 011664          333 LRPGRI--DVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQN  377 (480)
Q Consensus       333 lrpGRf--d~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~  377 (480)
                      .+  ||  ..++.++.|+.+++.++++......+..+.+++ +.|++.
T Consensus       148 ~S--Rl~~~~~~~l~~~~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~  193 (233)
T PRK08727        148 RS--RLAQCIRIGLPVLDDVARAAVLRERAQRRGLALDEAAIDWLLTH  193 (233)
T ss_pred             HH--HHhcCceEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHh
Confidence            99  97  478999999999999999987765555555544 344443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=99.57  E-value=1.6e-14  Score=153.91  Aligned_cols=193  Identities=15%  Similarity=0.240  Sum_probs=125.6

Q ss_pred             CCCCCCCCcccc-ccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEE
Q 011664          181 VPFTHPSTFDTI-SMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYD  254 (480)
Q Consensus       181 v~~~~~~~~~~i-~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~  254 (480)
                      .++.+..+|++. .|... .. ....+..+...+      |.. .++++||||||||||+|++|+|+++     +..+++
T Consensus       113 ~~l~~~~tfd~fv~g~~n-~~-a~~~~~~~~~~~------~~~-~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~y  183 (450)
T PRK00149        113 SPLNPKYTFDNFVVGKSN-RL-AHAAALAVAENP------GKA-YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVY  183 (450)
T ss_pred             cCCCCCCcccccccCCCc-HH-HHHHHHHHHhCc------Ccc-CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEE
Confidence            355667799995 45433 22 122222232221      222 2479999999999999999999987     566888


Q ss_pred             EeCCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          255 VDLSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       255 i~~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      +++.++..+       .....+........+|+|||+|.+.....   +..+|+..++.+..   .+..+||.++..|..
T Consensus       184 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~~---~~~~l~~~~n~l~~---~~~~iiits~~~p~~  257 (450)
T PRK00149        184 VTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGKER---TQEEFFHTFNALHE---AGKQIVLTSDRPPKE  257 (450)
T ss_pred             EEHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCCHH---HHHHHHHHHHHHHH---CCCcEEEECCCCHHH
Confidence            887665321       11122333445788999999998864332   33456666665544   233444544455555


Q ss_pred             ---CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHH
Q 011664          328 ---VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       328 ---LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~  391 (480)
                         ++++|++  ||.  ..++++.|+.++|.+|++..+...+..+.+++ +.|+... +-+..++..++.
T Consensus       258 l~~l~~~l~S--Rl~~gl~v~i~~pd~~~r~~il~~~~~~~~~~l~~e~l~~ia~~~-~~~~R~l~~~l~  324 (450)
T PRK00149        258 LPGLEERLRS--RFEWGLTVDIEPPDLETRIAILKKKAEEEGIDLPDEVLEFIAKNI-TSNVRELEGALN  324 (450)
T ss_pred             HHHHHHHHHh--HhcCCeeEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHcCc-CCCHHHHHHHHH
Confidence               6789998  996  68999999999999999999887777777766 4454443 555666655544

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=99.56  E-value=5e-14  Score=136.30  Aligned_cols=162  Identities=14%  Similarity=0.179  Sum_probs=102.8

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      ++...+.+||+..+..+  +.+...+..+..        +....++++|+||||||||+||+++++++   +.+++.+++
T Consensus         9 ~~~~~~~~~d~f~~~~~--~~~~~~l~~~~~--------~~~~~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~   78 (227)
T PRK08903          9 LGPPPPPTFDNFVAGEN--AELVARLRELAA--------GPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDA   78 (227)
T ss_pred             CCCCChhhhcccccCCc--HHHHHHHHHHHh--------ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeh
Confidence            45567788999763321  122222322221        22345689999999999999999999865   678888887


Q ss_pred             CCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC---ccCcccccC
Q 011664          258 SRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK---DHVDQALLR  334 (480)
Q Consensus       258 s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~---~~LD~aLlr  334 (480)
                      ......      +.......+|+|||+|.+..  .   ....|+..++....   ....++|+|++.+   ..+.+.|++
T Consensus        79 ~~~~~~------~~~~~~~~~liiDdi~~l~~--~---~~~~L~~~~~~~~~---~~~~~vl~~~~~~~~~~~l~~~L~s  144 (227)
T PRK08903         79 ASPLLA------FDFDPEAELYAVDDVERLDD--A---QQIALFNLFNRVRA---HGQGALLVAGPAAPLALPLREDLRT  144 (227)
T ss_pred             HHhHHH------HhhcccCCEEEEeChhhcCc--h---HHHHHHHHHHHHHH---cCCcEEEEeCCCCHHhCCCCHHHHH
Confidence            654321      23334678999999998732  1   22445555554433   2333456655532   235677777


Q ss_pred             CCce--eEEEEcCCCCHHHHHHHHHHHhccCCCCCc
Q 011664          335 PGRI--DVHIHFPLCDFSSFKTLASSYLGLKDHKLF  368 (480)
Q Consensus       335 pGRf--d~~I~~~~p~~~~r~~il~~~l~~~~~~l~  368 (480)
                        ||  ...+++|+|+.+++..++..+....+..+.
T Consensus       145 --r~~~~~~i~l~pl~~~~~~~~l~~~~~~~~v~l~  178 (227)
T PRK08903        145 --RLGWGLVYELKPLSDADKIAALKAAAAERGLQLA  178 (227)
T ss_pred             --HHhcCeEEEecCCCHHHHHHHHHHHHHHcCCCCC
Confidence              77  479999999999888888766544443333

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.56  E-value=8e-14  Score=149.25  Aligned_cols=180  Identities=14%  Similarity=0.242  Sum_probs=126.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++.+.+.+...+..            ...+..||||||||+|||++|+++|..+.+              
T Consensus        11 RP~~f~diiGq~~i~~~L~~~i~~------------~~i~hayLf~Gp~G~GKTtlAr~lAk~L~c~~~~~~~pc~~c~n   78 (486)
T PRK14953         11 RPKFFKEVIGQEIVVRILKNAVKL------------QRVSHAYIFAGPRGTGKTTIARILAKVLNCLNPQEGEPCGKCEN   78 (486)
T ss_pred             CCCcHHHccChHHHHHHHHHHHHc------------CCCCeEEEEECCCCCCHHHHHHHHHHHhcCcCCCCCCCCCccHH
Confidence            678999999999999888765531            124567999999999999999999998753              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+.-.+-..++.+....      ..+.|++|||+|.+.     ....+.|+..++..     ..
T Consensus        79 c~~i~~g~~~d~~eidaas~~gvd~ir~I~~~~~~~P~~~~~KVvIIDEad~Lt-----~~a~naLLk~LEep-----p~  148 (486)
T PRK14953         79 CVEIDKGSFPDLIEIDAASNRGIDDIRALRDAVSYTPIKGKYKVYIIDEAHMLT-----KEAFNALLKTLEEP-----PP  148 (486)
T ss_pred             HHHHhcCCCCcEEEEeCccCCCHHHHHHHHHHHHhCcccCCeeEEEEEChhhcC-----HHHHHHHHHHHhcC-----CC
Confidence                      34455554434444455554322      245799999999873     22346677777543     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.++.+.+++.+  |+. .+.|++++.++....+..++...+....++. +.++..+ +-+..++.+++
T Consensus       149 ~~v~Il~tt~~~kl~~tI~S--Rc~-~i~f~~ls~~el~~~L~~i~k~egi~id~~al~~La~~s-~G~lr~al~~L  221 (486)
T PRK14953        149 RTIFILCTTEYDKIPPTILS--RCQ-RFIFSKPTKEQIKEYLKRICNEEKIEYEEKALDLLAQAS-EGGMRDAASLL  221 (486)
T ss_pred             CeEEEEEECCHHHHHHHHHH--hce-EEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            56777778888889999998  885 7999999999999999988877666665543 3444443 33444443333

>TIGR02902 spore_lonB ATP-dependent protease LonB

Probab=99.56  E-value=3.5e-14  Score=153.90  Aligned_cols=188  Identities=19%  Similarity=0.246  Sum_probs=126.1

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEE
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVY  253 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~  253 (480)
                      .+|.+|++++|.+...+.++..+.            + +.+.++||+||||||||++|+++++++          +.+|+
T Consensus        59 ~rp~~f~~iiGqs~~i~~l~~al~------------~-~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~s~~~~~~~fi  125 (531)
T TIGR02902        59 TRPKSFDEIIGQEEGIKALKAALC------------G-PNPQHVIIYGPPGVGKTAAARLVLEEAKKNPASPFKEGAAFV  125 (531)
T ss_pred             hCcCCHHHeeCcHHHHHHHHHHHh------------C-CCCceEEEECCCCCCHHHHHHHHHHHhhhccCCCcCCCCCEE
Confidence            477899999999998888774321            1 234589999999999999999998642          36789


Q ss_pred             EEeCCCc-CChHHHH-HH--------------H------------HhhcCCcEEEEecccccccCcccccchhhhhhhcc
Q 011664          254 DVDLSRV-ADDADLK-SL--------------L------------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD  305 (480)
Q Consensus       254 ~i~~s~~-~~~~~l~-~l--------------~------------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld  305 (480)
                      .++++.. .++..+. .+              |            .......+|||||||.+..     ...+.|+..|+
T Consensus       126 ~id~~~~~~~~~~~~~~li~~~~~p~~~~~~~~g~~g~~~~~~G~l~~a~gG~L~IdEI~~L~~-----~~q~~LL~~Le  200 (531)
T TIGR02902       126 EIDATTARFDERGIADPLIGSVHDPIYQGAGPLGIAGIPQPKPGAVTRAHGGVLFIDEIGELHP-----VQMNKLLKVLE  200 (531)
T ss_pred             EEccccccCCccccchhhcCCcccchhccccccccCCcccccCchhhccCCcEEEEechhhCCH-----HHHHHHHHHHH
Confidence            9998642 1111110 00              0            0122457999999998843     23344554442


Q ss_pred             cc--------c----------------ccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          306 GV--------L----------------NSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       306 g~--------~----------------~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      .-        .                .....+-++|++|||.|+.++|++++  |+. .|.|+.++.++...|++..+.
T Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~rlI~ATt~~p~~L~paLrs--R~~-~I~f~pL~~eei~~Il~~~a~  277 (531)
T TIGR02902       201 DRKVFLDSAYYNSENPNIPSHIHDIFQNGLPADFRLIGATTRNPEEIPPALRS--RCV-EIFFRPLLDEEIKEIAKNAAE  277 (531)
T ss_pred             hCeeeeccccccccCcccccchhhhcccCcccceEEEEEecCCcccCChHHhh--hhh-eeeCCCCCHHHHHHHHHHHHH
Confidence            10        0                00011235666688899999999999  985 789999999999999999988


Q ss_pred             cCCCCCchhHH-HHHHhCCCCCHHHHHHHHHHhh
Q 011664          362 LKDHKLFPQVE-EIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       362 ~~~~~l~~~i~-~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      ..+..+.++.- .+...+  .++.++.++++.+.
T Consensus       278 k~~i~is~~al~~I~~y~--~n~Rel~nll~~Aa  309 (531)
T TIGR02902       278 KIGINLEKHALELIVKYA--SNGREAVNIVQLAA  309 (531)
T ss_pred             HcCCCcCHHHHHHHHHhh--hhHHHHHHHHHHHH
Confidence            77766666553 333322  36777777776543

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.

>PRK08084 DNA replication initiation factor; Provisional

Probab=99.56  E-value=4.2e-14  Score=138.05  Aligned_cols=168  Identities=15%  Similarity=0.136  Sum_probs=104.9

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      +.+..+||+.+-..+  +.....+..+...         +....++||||||||||+|++++|+++   |..+.++++..
T Consensus        15 ~~~~~~fd~f~~~~n--~~a~~~l~~~~~~---------~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~   83 (235)
T PRK08084         15 LPDDETFASFYPGDN--DSLLAALQNALRQ---------EHSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDK   83 (235)
T ss_pred             CCCcCCccccccCcc--HHHHHHHHHHHhC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHH
Confidence            445668988762222  1123333333211         123479999999999999999999865   45566776654


Q ss_pred             cCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCc-eEEEEecCCCcc---CcccccCC
Q 011664          260 VADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEE-RVMVFTMNSKDH---VDQALLRP  335 (480)
Q Consensus       260 ~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~-~ivI~tTN~~~~---LD~aLlrp  335 (480)
                      ...  ....++....+..+|+|||++.+.........+..+++.+   ..   .+. .+++.+++.|..   +.|+|++ 
T Consensus        84 ~~~--~~~~~~~~~~~~dlliiDdi~~~~~~~~~~~~lf~l~n~~---~e---~g~~~li~ts~~~p~~l~~~~~~L~S-  154 (235)
T PRK08084         84 RAW--FVPEVLEGMEQLSLVCIDNIECIAGDELWEMAIFDLYNRI---LE---SGRTRLLITGDRPPRQLNLGLPDLAS-  154 (235)
T ss_pred             Hhh--hhHHHHHHhhhCCEEEEeChhhhcCCHHHHHHHHHHHHHH---HH---cCCCeEEEeCCCChHHcCcccHHHHH-
Confidence            221  1122222233447999999998865443333344444433   22   222 455555566655   5799999 


Q ss_pred             Ccee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          336 GRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       336 GRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                       |+.  .++.+..|+.+++.++++......+..+.+++
T Consensus       155 -Rl~~g~~~~l~~~~~~~~~~~l~~~a~~~~~~l~~~v  191 (235)
T PRK08084        155 -RLDWGQIYKLQPLSDEEKLQALQLRARLRGFELPEDV  191 (235)
T ss_pred             -HHhCCceeeecCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence             986  89999999999999999886655555555544

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=99.56  E-value=1.1e-13  Score=141.20  Aligned_cols=162  Identities=12%  Similarity=0.198  Sum_probs=110.6

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEeC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVDL  257 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~~  257 (480)
                      ...|.+|++++|.+++++.+...+.    .       +.  ..++|||||||||||++|+++|+++.     .++..+++
T Consensus         8 ky~P~~~~~~~g~~~~~~~L~~~~~----~-------~~--~~~lll~Gp~GtGKT~la~~~~~~l~~~~~~~~~~~i~~   74 (337)
T PRK12402          8 KYRPALLEDILGQDEVVERLSRAVD----S-------PN--LPHLLVQGPPGSGKTAAVRALARELYGDPWENNFTEFNV   74 (337)
T ss_pred             hhCCCcHHHhcCCHHHHHHHHHHHh----C-------CC--CceEEEECCCCCCHHHHHHHHHHHhcCcccccceEEech
Confidence            3478899999999998888776443    1       11  12699999999999999999999874     34677777


Q ss_pred             CCcCCh--------------------------HHHHHHHHhh-------cCCcEEEEecccccccCcccccchhhhhhhc
Q 011664          258 SRVADD--------------------------ADLKSLLLQT-------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFM  304 (480)
Q Consensus       258 s~~~~~--------------------------~~l~~l~~~~-------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~l  304 (480)
                      +++...                          ..++.+....       ..+.+|+|||+|.+..     .....|...+
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlilDe~~~l~~-----~~~~~L~~~l  149 (337)
T PRK12402         75 ADFFDQGKKYLVEDPRFAHFLGTDKRIRSSKIDNFKHVLKEYASYRPLSADYKTILLDNAEALRE-----DAQQALRRIM  149 (337)
T ss_pred             hhhhhcchhhhhcCcchhhhhhhhhhhccchHHHHHHHHHHHHhcCCCCCCCcEEEEeCcccCCH-----HHHHHHHHHH
Confidence            653210                          1122222111       2457999999998732     1223455555


Q ss_pred             ccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          305 DGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       305 dg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                      +...     ....+|++|+.+..+.++|.+  |+ ..+++++|+.++...+++..+...+..+.++
T Consensus       150 e~~~-----~~~~~Il~~~~~~~~~~~L~s--r~-~~v~~~~~~~~~~~~~l~~~~~~~~~~~~~~  207 (337)
T PRK12402        150 EQYS-----RTCRFIIATRQPSKLIPPIRS--RC-LPLFFRAPTDDELVDVLESIAEAEGVDYDDD  207 (337)
T ss_pred             Hhcc-----CCCeEEEEeCChhhCchhhcC--Cc-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHH
Confidence            4332     234466677777788888888  76 5799999999999999998887666655543

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.55  E-value=8.2e-14  Score=151.37  Aligned_cols=162  Identities=17%  Similarity=0.262  Sum_probs=118.0

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc-------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD-------------  251 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~-------------  251 (480)
                      .|.+|++|+|++.+++.|...+..           | ..+..|||+||||||||++|+++|+.+.+.             
T Consensus        11 RP~sf~dIiGQe~v~~~L~~ai~~-----------~-ri~ha~Lf~GPpG~GKTtiArilAk~L~C~~~~~~~pCg~C~s   78 (624)
T PRK14959         11 RPQTFAEVAGQETVKAILSRAAQE-----------N-RVAPAYLFSGTRGVGKTTIARIFAKALNCETAPTGEPCNTCEQ   78 (624)
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHhccccCCCCCCCCcccHH
Confidence            688999999999998887765531           1 224589999999999999999999988642             


Q ss_pred             -----------EEEEeCCCcCChHHHHHHHHh------hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          252 -----------VYDVDLSRVADDADLKSLLLQ------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       252 -----------~~~i~~s~~~~~~~l~~l~~~------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                 ++.++...-.+-..++.+...      .....||||||+|.+.     ....+.|+..|+.-     ..
T Consensus        79 C~~i~~g~hpDv~eId~a~~~~Id~iR~L~~~~~~~p~~g~~kVIIIDEad~Lt-----~~a~naLLk~LEEP-----~~  148 (624)
T PRK14959         79 CRKVTQGMHVDVVEIDGASNRGIDDAKRLKEAIGYAPMEGRYKVFIIDEAHMLT-----REAFNALLKTLEEP-----PA  148 (624)
T ss_pred             HHHHhcCCCCceEEEecccccCHHHHHHHHHHHHhhhhcCCceEEEEEChHhCC-----HHHHHHHHHHhhcc-----CC
Confidence                       555654332333444443321      1245799999999883     23357778777542     24


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                      ..++|++||.+..+.+.+++  |+. +++|+.++.++...++...+...+..+..+.
T Consensus       149 ~~ifILaTt~~~kll~TI~S--Rcq-~i~F~pLs~~eL~~~L~~il~~egi~id~ea  202 (624)
T PRK14959        149 RVTFVLATTEPHKFPVTIVS--RCQ-HFTFTRLSEAGLEAHLTKVLGREGVDYDPAA  202 (624)
T ss_pred             CEEEEEecCChhhhhHHHHh--hhh-ccccCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            57788889989999989998  884 7899999999998888887766665555443

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

Probab=99.55  E-value=1.9e-14  Score=160.75  Aligned_cols=155  Identities=19%  Similarity=0.273  Sum_probs=110.9

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDL  257 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~  257 (480)
                      .++.++|.++..+.+.+.+..             ..+.++||+||||||||++|+++|..+          +..++.+++
T Consensus       184 ~~~~liGR~~ei~~~i~iL~r-------------~~~~n~LLvGppGvGKT~lae~la~~i~~~~vP~~l~~~~~~~l~~  250 (758)
T PRK11034        184 GIDPLIGREKELERAIQVLCR-------------RRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI  250 (758)
T ss_pred             CCCcCcCCCHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhcCCCchhcCCeEEeccH
Confidence            467788888777777764432             134578999999999999999999764          566777765


Q ss_pred             CCcC------C--hHHHHHHHHh--hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc-
Q 011664          258 SRVA------D--DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD-  326 (480)
Q Consensus       258 s~~~------~--~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~-  326 (480)
                      +.+.      +  +..++.++..  ...++||||||||.+++.+........+.|.+..+..   .....+|++||.++ 
T Consensus       251 ~~llaG~~~~Ge~e~rl~~l~~~l~~~~~~ILfIDEIh~L~g~g~~~~g~~d~~nlLkp~L~---~g~i~vIgATt~~E~  327 (758)
T PRK11034        251 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS---SGKIRVIGSTTYQEF  327 (758)
T ss_pred             HHHhcccchhhhHHHHHHHHHHHHHhcCCCEEEeccHHHHhccCCCCCcHHHHHHHHHHHHh---CCCeEEEecCChHHH
Confidence            5433      1  2335566543  3468899999999998655322222334444444444   45677888888764 


Q ss_pred             ----cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          327 ----HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       327 ----~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                          ..|+||.|  ||+ .|+++.|+.+++..|++.+..
T Consensus       328 ~~~~~~D~AL~r--RFq-~I~v~ePs~~~~~~IL~~~~~  363 (758)
T PRK11034        328 SNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKP  363 (758)
T ss_pred             HHHhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHH
Confidence                57999999  996 799999999999999987654

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.55  E-value=7e-14  Score=152.83  Aligned_cols=161  Identities=15%  Similarity=0.298  Sum_probs=121.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++|+|++.+++.|...+..           | ..+..||||||||||||++|+++|+.+.+              
T Consensus        11 RP~~f~~iiGq~~v~~~L~~~i~~-----------~-~~~hayLf~Gp~G~GKtt~A~~lak~l~c~~~~~~~~c~~c~~   78 (576)
T PRK14965         11 RPQTFSDLTGQEHVSRTLQNAIDT-----------G-RVAHAFLFTGARGVGKTSTARILAKALNCEQGLTAEPCNVCPP   78 (576)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHhhcCCCCCCCCCCCccHH
Confidence            578999999999999888865542           1 24668999999999999999999998753              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++..+-.+-.+++.+....      ....|++|||+|.+.     ....+.|+..|+.-     .+
T Consensus        79 c~~i~~g~~~d~~eid~~s~~~v~~ir~l~~~~~~~p~~~~~KVvIIdev~~Lt-----~~a~naLLk~LEep-----p~  148 (576)
T PRK14965         79 CVEITEGRSVDVFEIDGASNTGVDDIRELRENVKYLPSRSRYKIFIIDEVHMLS-----TNAFNALLKTLEEP-----PP  148 (576)
T ss_pred             HHHHhcCCCCCeeeeeccCccCHHHHHHHHHHHHhccccCCceEEEEEChhhCC-----HHHHHHHHHHHHcC-----CC
Confidence                      25556554444445666665432      234699999999884     23457788888643     35


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ  370 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~  370 (480)
                      ..++|++||.+..|.+.+++  |+. +++|..++.++....+..++...+..+..+
T Consensus       149 ~~~fIl~t~~~~kl~~tI~S--Rc~-~~~f~~l~~~~i~~~L~~i~~~egi~i~~~  201 (576)
T PRK14965        149 HVKFIFATTEPHKVPITILS--RCQ-RFDFRRIPLQKIVDRLRYIADQEGISISDA  201 (576)
T ss_pred             CeEEEEEeCChhhhhHHHHH--hhh-hhhcCCCCHHHHHHHHHHHHHHhCCCCCHH
Confidence            67888888999999999999  884 899999999888888888777666555443

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=99.54  E-value=2.8e-14  Score=140.39  Aligned_cols=164  Identities=17%  Similarity=0.240  Sum_probs=118.5

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC------cEEEE
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY------DVYDV  255 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~------~~~~i  255 (480)
                      ....|.+|++++|++.+.+.++..+..             .--..+|||||||||||+.|+++|+++..      .+...
T Consensus        28 eKYrPkt~de~~gQe~vV~~L~~a~~~-------------~~lp~~LFyGPpGTGKTStalafar~L~~~~~~~~rvl~l   94 (346)
T KOG0989|consen   28 EKYRPKTFDELAGQEHVVQVLKNALLR-------------RILPHYLFYGPPGTGKTSTALAFARALNCEQLFPCRVLEL   94 (346)
T ss_pred             HHhCCCcHHhhcchHHHHHHHHHHHhh-------------cCCceEEeeCCCCCcHhHHHHHHHHHhcCccccccchhhh
Confidence            455789999999999999999876653             01126999999999999999999999865      24445


Q ss_pred             eCCCcCChHHHHHH---HHhh------------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEE
Q 011664          256 DLSRVADDADLKSL---LLQT------------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF  320 (480)
Q Consensus       256 ~~s~~~~~~~l~~l---~~~~------------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~  320 (480)
                      +.|...+-+-++.-   |++.            ....||+|||.|.+.     ....+.|...|+...     ....+|+
T Consensus        95 naSderGisvvr~Kik~fakl~~~~~~~~~~~~~~fKiiIlDEcdsmt-----sdaq~aLrr~mE~~s-----~~trFiL  164 (346)
T KOG0989|consen   95 NASDERGISVVREKIKNFAKLTVLLKRSDGYPCPPFKIIILDECDSMT-----SDAQAALRRTMEDFS-----RTTRFIL  164 (346)
T ss_pred             cccccccccchhhhhcCHHHHhhccccccCCCCCcceEEEEechhhhh-----HHHHHHHHHHHhccc-----cceEEEE
Confidence            55554443222211   2211            123799999999884     345577888888742     4577888


Q ss_pred             ecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          321 TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       321 tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                      .||..+.|.+.+.+  |+. .+.|+....+.-...++.+...++.+.+++.
T Consensus       165 Icnylsrii~pi~S--RC~-KfrFk~L~d~~iv~rL~~Ia~~E~v~~d~~a  212 (346)
T KOG0989|consen  165 ICNYLSRIIRPLVS--RCQ-KFRFKKLKDEDIVDRLEKIASKEGVDIDDDA  212 (346)
T ss_pred             EcCChhhCChHHHh--hHH-HhcCCCcchHHHHHHHHHHHHHhCCCCCHHH
Confidence            99999999999999  996 6777777776666667777776776666543

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=1.5e-13  Score=146.18  Aligned_cols=169  Identities=15%  Similarity=0.213  Sum_probs=120.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++|+|++.+++.+...+..            ...+..+|||||||+|||++|+++|+.+.+              
T Consensus        12 RP~~~~diiGq~~~v~~L~~~i~~------------~~i~ha~Lf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~c~~c~   79 (451)
T PRK06305         12 RPQTFSEILGQDAVVAVLKNALRF------------NRAAHAYLFSGIRGTGKTTLARIFAKALNCQNPTEDQEPCNQCA   79 (451)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc------------CCCceEEEEEcCCCCCHHHHHHHHHHHhcCCCcccCCCCCcccH
Confidence            578999999999998877765531            124568999999999999999999997643              


Q ss_pred             -----------cEEEEeCCCcCChHHHHHHHH------hhcCCcEEEEecccccccCcccccchhhhhhhcccccccccC
Q 011664          251 -----------DVYDVDLSRVADDADLKSLLL------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCF  313 (480)
Q Consensus       251 -----------~~~~i~~s~~~~~~~l~~l~~------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~  313 (480)
                                 +++.++.....+-..++.+..      ....+.|++|||+|.+..     ...+.|+..|+.-     .
T Consensus        80 ~C~~i~~~~~~d~~~i~g~~~~gid~ir~i~~~l~~~~~~~~~kvvIIdead~lt~-----~~~n~LLk~lEep-----~  149 (451)
T PRK06305         80 SCKEISSGTSLDVLEIDGASHRGIEDIRQINETVLFTPSKSRYKIYIIDEVHMLTK-----EAFNSLLKTLEEP-----P  149 (451)
T ss_pred             HHHHHhcCCCCceEEeeccccCCHHHHHHHHHHHHhhhhcCCCEEEEEecHHhhCH-----HHHHHHHHHhhcC-----C
Confidence                       344555433333344444321      124678999999998842     2346677777642     3


Q ss_pred             CceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhC
Q 011664          314 EERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNG  378 (480)
Q Consensus       314 ~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~  378 (480)
                      +..++|++||.+..|.+++++  |+. .++|+.++.++....+...+...+.....+. +.|+...
T Consensus       150 ~~~~~Il~t~~~~kl~~tI~s--Rc~-~v~f~~l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s  212 (451)
T PRK06305        150 QHVKFFLATTEIHKIPGTILS--RCQ-KMHLKRIPEETIIDKLALIAKQEGIETSREALLPIARAA  212 (451)
T ss_pred             CCceEEEEeCChHhcchHHHH--hce-EEeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence            456788888888999999999  885 7999999999988888887766555555433 3444433

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=99.54  E-value=1.5e-13  Score=149.28  Aligned_cols=180  Identities=18%  Similarity=0.270  Sum_probs=127.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.++..+..           | ..+..||||||||+|||++|+++|+.+.+              
T Consensus        11 RP~~f~diiGqe~iv~~L~~~i~~-----------~-~i~hayLf~Gp~G~GKTt~Ar~lAk~L~c~~~~~~~pC~~C~~   78 (563)
T PRK06647         11 RPRDFNSLEGQDFVVETLKHSIES-----------N-KIANAYIFSGPRGVGKTSSARAFARCLNCVNGPTPMPCGECSS   78 (563)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHhhccccCCCCCCCccchH
Confidence            578999999999999988765541           1 24567999999999999999999998754              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++...-.+-.+++.+....      ....|++|||+|.+.     ....+.||..++..     +.
T Consensus        79 C~~i~~~~~~dv~~idgas~~~vddIr~l~e~~~~~p~~~~~KVvIIDEa~~Ls-----~~a~naLLK~LEep-----p~  148 (563)
T PRK06647         79 CKSIDNDNSLDVIEIDGASNTSVQDVRQIKEEIMFPPASSRYRVYIIDEVHMLS-----NSAFNALLKTIEEP-----PP  148 (563)
T ss_pred             HHHHHcCCCCCeEEecCcccCCHHHHHHHHHHHHhchhcCCCEEEEEEChhhcC-----HHHHHHHHHhhccC-----CC
Confidence                      34444433222334566554322      345799999999883     23456788777642     45


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ..++|++|+.+..|.+++++  |+. .++|..++.++....++..+...+..+.++. ..|+... +-+..++..++
T Consensus       149 ~~vfI~~tte~~kL~~tI~S--Rc~-~~~f~~l~~~el~~~L~~i~~~egi~id~eAl~lLa~~s-~GdlR~alslL  221 (563)
T PRK06647        149 YIVFIFATTEVHKLPATIKS--RCQ-HFNFRLLSLEKIYNMLKKVCLEDQIKYEDEALKWIAYKS-TGSVRDAYTLF  221 (563)
T ss_pred             CEEEEEecCChHHhHHHHHH--hce-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            67888888888999999999  885 7899999999998888888766666655544 3344433 33555444444

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=99.53  E-value=2.1e-13  Score=146.47  Aligned_cols=180  Identities=18%  Similarity=0.276  Sum_probs=129.0

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------------  249 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------------  249 (480)
                      +|.+|++|+|++.+++.+...+.    .       | ..+..||||||||+|||++|+++|+.+.               
T Consensus         9 RP~~fdeiiGqe~v~~~L~~~I~----~-------g-rl~hayLf~Gp~G~GKTt~Ar~LAk~L~c~~~~~~~pC~~C~~   76 (535)
T PRK08451          9 RPKHFDELIGQESVSKTLSLALD----N-------N-RLAHAYLFSGLRGSGKTSSARIFARALVCEQGPSSTPCDTCIQ   76 (535)
T ss_pred             CCCCHHHccCcHHHHHHHHHHHH----c-------C-CCCeeEEEECCCCCcHHHHHHHHHHHhcCCCCCCCCCCcccHH
Confidence            67899999999999988886553    1       2 2466899999999999999999998763               


Q ss_pred             ---------CcEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          250 ---------YDVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       250 ---------~~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                               .+++.++.+.-.+-..++.+....      ....|++|||+|.+.     ....+.||..|+..     +.
T Consensus        77 C~~~~~~~h~dv~eldaas~~gId~IRelie~~~~~P~~~~~KVvIIDEad~Lt-----~~A~NALLK~LEEp-----p~  146 (535)
T PRK08451         77 CQSALENRHIDIIEMDAASNRGIDDIRELIEQTKYKPSMARFKIFIIDEVHMLT-----KEAFNALLKTLEEP-----PS  146 (535)
T ss_pred             HHHHhhcCCCeEEEeccccccCHHHHHHHHHHHhhCcccCCeEEEEEECcccCC-----HHHHHHHHHHHhhc-----CC
Confidence                     235555544333445677766432      234699999999883     34456788877653     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ...+|++|+.+..|.+++++  |+ .+++|.+++.++....+...+...+....++. +.++... +-+..++..++
T Consensus       147 ~t~FIL~ttd~~kL~~tI~S--Rc-~~~~F~~Ls~~ei~~~L~~Il~~EGi~i~~~Al~~Ia~~s-~GdlR~alnlL  219 (535)
T PRK08451        147 YVKFILATTDPLKLPATILS--RT-QHFRFKQIPQNSIISHLKTILEKEGVSYEPEALEILARSG-NGSLRDTLTLL  219 (535)
T ss_pred             ceEEEEEECChhhCchHHHh--hc-eeEEcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCcHHHHHHHH
Confidence            56677788888999999999  87 58999999999988888888877666655443 3444333 44555555544

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.53  E-value=7.8e-14  Score=146.27  Aligned_cols=178  Identities=13%  Similarity=0.242  Sum_probs=121.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++|+|++.+++.|...+..           | ..+..+|||||||||||++|+++|+.+.+              
T Consensus        11 RP~~~~eiiGq~~~~~~L~~~~~~-----------~-~~~ha~lf~Gp~G~GKtt~A~~~a~~l~c~~~~~~~~~~~~~~   78 (397)
T PRK14955         11 RPKKFADITAQEHITRTIQNSLRM-----------G-RVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDADYLQEVT   78 (397)
T ss_pred             CCCcHhhccChHHHHHHHHHHHHh-----------C-CcceeEEEECCCCCCHHHHHHHHHHHhcCCCCcCcccccccCC
Confidence            688999999999999887654431           2 24567999999999999999999998854              


Q ss_pred             ------------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhccc
Q 011664          251 ------------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG  306 (480)
Q Consensus       251 ------------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg  306 (480)
                                        +++.++.....+-.+++.+....      ....|++|||+|.+..     ...+.|+..++.
T Consensus        79 ~~c~~c~~c~~~~~~~~~n~~~~~~~~~~~id~Ir~l~~~~~~~p~~~~~kvvIIdea~~l~~-----~~~~~LLk~LEe  153 (397)
T PRK14955         79 EPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRLLRENVRYGPQKGRYRVYIIDEVHMLSI-----AAFNAFLKTLEE  153 (397)
T ss_pred             CCCCCCHHHHHHhcCCCCCeEeecccccCCHHHHHHHHHHHhhchhcCCeEEEEEeChhhCCH-----HHHHHHHHHHhc
Confidence                              23334333333334566554333      2457999999998842     234567777753


Q ss_pred             ccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHH
Q 011664          307 VLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAE  385 (480)
Q Consensus       307 ~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~ad  385 (480)
                      .     .+..++|++|+.+..+-+++.+  |+. .++|+.++.++....+...+...+..+.++. +.++..+ |-+...
T Consensus       154 p-----~~~t~~Il~t~~~~kl~~tl~s--R~~-~v~f~~l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s-~g~lr~  224 (397)
T PRK14955        154 P-----PPHAIFIFATTELHKIPATIAS--RCQ-RFNFKRIPLEEIQQQLQGICEAEGISVDADALQLIGRKA-QGSMRD  224 (397)
T ss_pred             C-----CCCeEEEEEeCChHHhHHHHHH--HHH-HhhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHH
Confidence            2     3456777777778888889988  875 8999999999888888887766555555443 3343333 334443


Q ss_pred             HHH
Q 011664          386 IGE  388 (480)
Q Consensus       386 I~~  388 (480)
                      +.+
T Consensus       225 a~~  227 (397)
T PRK14955        225 AQS  227 (397)
T ss_pred             HHH
Confidence            333

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=99.53  E-value=4.6e-14  Score=152.76  Aligned_cols=158  Identities=14%  Similarity=0.201  Sum_probs=110.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCcc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~  292 (480)
                      ..++|||++|||||+|++|||+++     +..++++++.++..+       ..+..+..+..+..+|+||||+.+.....
T Consensus       315 NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gke~  394 (617)
T PRK14086        315 NPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDKES  394 (617)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCCHH
Confidence            469999999999999999999976     578889987665421       11112223345689999999998865443


Q ss_pred             cccchhhhhhhcccccccccCCceEEEEecCC-C---ccCcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCC
Q 011664          293 AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS-K---DHVDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHK  366 (480)
Q Consensus       293 ~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~-~---~~LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~  366 (480)
                      ..   .+|++.++.+..   .+.. ||+|+|. |   ..+++.|++  ||.  ..+++..|+.+.|.+|++..+...+..
T Consensus       395 tq---eeLF~l~N~l~e---~gk~-IIITSd~~P~eL~~l~~rL~S--Rf~~GLvv~I~~PD~EtR~aIL~kka~~r~l~  465 (617)
T PRK14086        395 TQ---EEFFHTFNTLHN---ANKQ-IVLSSDRPPKQLVTLEDRLRN--RFEWGLITDVQPPELETRIAILRKKAVQEQLN  465 (617)
T ss_pred             HH---HHHHHHHHHHHh---cCCC-EEEecCCChHhhhhccHHHHh--hhhcCceEEcCCCCHHHHHHHHHHHHHhcCCC
Confidence            33   445555554443   2333 4556664 3   346889999  885  888999999999999999999888888


Q ss_pred             CchhHH-HHHHhCCCCCHHHHHHHHHH
Q 011664          367 LFPQVE-EIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       367 l~~~i~-~l~~~~~g~s~adI~~ll~~  392 (480)
                      +.+++- .|+.+. .-+..+|..++.+
T Consensus       466 l~~eVi~yLa~r~-~rnvR~LegaL~r  491 (617)
T PRK14086        466 APPEVLEFIASRI-SRNIRELEGALIR  491 (617)
T ss_pred             CCHHHHHHHHHhc-cCCHHHHHHHHHH
Confidence            887764 454443 4456666655543

>PRK05642 DNA replication initiation factor; Validated

Probab=99.53  E-value=1.3e-13  Score=134.55  Aligned_cols=173  Identities=14%  Similarity=0.131  Sum_probs=109.1

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      ++..+..+||+.+....  ....+.+..+....      +....++++||||+|||||+|++|+++++   +..+++++.
T Consensus        10 ~~~~~~~tfdnF~~~~~--~~a~~~~~~~~~~~------~~~~~~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~   81 (234)
T PRK05642         10 VRLRDDATFANYYPGAN--AAALGYVERLCEAD------AGWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPL   81 (234)
T ss_pred             CCCCCcccccccCcCCh--HHHHHHHHHHhhcc------ccCCCCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeH
Confidence            44556678999863332  33333343332211      11123679999999999999999999754   678888887


Q ss_pred             CCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC---cccccC
Q 011664          258 SRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV---DQALLR  334 (480)
Q Consensus       258 s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L---D~aLlr  334 (480)
                      .++...  ...++....+..+|+|||++.+.+.....   .+|++.++....   .+..+++.++..|..+   .|+|++
T Consensus        82 ~~~~~~--~~~~~~~~~~~d~LiiDDi~~~~~~~~~~---~~Lf~l~n~~~~---~g~~ilits~~~p~~l~~~~~~L~S  153 (234)
T PRK05642         82 AELLDR--GPELLDNLEQYELVCLDDLDVIAGKADWE---EALFHLFNRLRD---SGRRLLLAASKSPRELPIKLPDLKS  153 (234)
T ss_pred             HHHHhh--hHHHHHhhhhCCEEEEechhhhcCChHHH---HHHHHHHHHHHh---cCCEEEEeCCCCHHHcCccCccHHH
Confidence            665432  12233333455799999999875443333   345555544433   2344545454455433   689999


Q ss_pred             CCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          335 PGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       335 pGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                        ||.  ..+.+..|+.+++..+++......+..+.+++
T Consensus       154 --Rl~~gl~~~l~~~~~e~~~~il~~ka~~~~~~l~~ev  190 (234)
T PRK05642        154 --RLTLALVFQMRGLSDEDKLRALQLRASRRGLHLTDEV  190 (234)
T ss_pred             --HHhcCeeeecCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence              984  78899999999999999876554444444443

>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional

Probab=99.53  E-value=1.7e-13  Score=143.73  Aligned_cols=217  Identities=17%  Similarity=0.258  Sum_probs=133.8

Q ss_pred             Ccc-ccccChHHHHHHHHHHHHHHhhhhHHhhh--C-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          188 TFD-TISMETDLKNRVKSDLESFLKAKHYYHRL--G-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       188 ~~~-~i~g~~~~k~~l~e~l~~~l~~~~~~~~~--g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      .++ .|+|++++|+.+...+....++-..-...  . .....++||+||||||||++|+++|..++.+|+.++++.+.. 
T Consensus        68 ~L~~~ViGq~~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~~~iLl~Gp~GtGKT~lAr~lA~~l~~pf~~id~~~l~~~  147 (412)
T PRK05342         68 HLDQYVIGQERAKKVLSVAVYNHYKRLRHGDKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEA  147 (412)
T ss_pred             HHhhHeeChHHHHHHHHHHHHHHHHhhhcccccccccccCCceEEEEcCCCCCHHHHHHHHHHHhCCCceecchhhcccC
Confidence            344 38999999999987776544332111000  1 124568999999999999999999999999999999876542 


Q ss_pred             -------hHHHHHHHH------hhcCCcEEEEecccccccCccc---------ccchhhhhhhccccccc--------cc
Q 011664          263 -------DADLKSLLL------QTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNS--------CC  312 (480)
Q Consensus       263 -------~~~l~~l~~------~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~--------~~  312 (480)
                             +..+..++.      +...++||||||||.+.....+         ......||..|||-...        ..
T Consensus       148 gyvG~d~e~~l~~l~~~~~~~~~~a~~gIi~iDEIdkl~~~~~~~~~~~d~s~~~vQ~~LL~~Leg~~~~v~~~gg~~~~  227 (412)
T PRK05342        148 GYVGEDVENILLKLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHP  227 (412)
T ss_pred             CcccchHHHHHHHHHHhccccHHHcCCcEEEEechhhhccccCCCCcCCCcccHHHHHHHHHHHhcCeEEeCCCCCcCcC
Confidence                   122333332      2246899999999999754211         12467899999864210        11


Q ss_pred             CCceEEEEecCCCc----------------------------------------------------cCcccccCCCceeE
Q 011664          313 FEERVMVFTMNSKD----------------------------------------------------HVDQALLRPGRIDV  340 (480)
Q Consensus       313 ~~~~ivI~tTN~~~----------------------------------------------------~LD~aLlrpGRfd~  340 (480)
                      ....++|.|+|-..                                                    -+.|+++  ||+|.
T Consensus       228 ~~~~~~i~t~nilfi~~Gaf~g~~~~~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~dL~~~gf~PEfl--gRld~  305 (412)
T PRK05342        228 QQEFIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKEKRTEGELLKQVEPEDLIKFGLIPEFI--GRLPV  305 (412)
T ss_pred             CCCeEEeccCCceeeecccccCcHHHHHHHHhhcccCCccccccccccchhHHHHHhcCHHHHHHHhhhHHHh--CCCCe
Confidence            12235566665410                                                    0233444  59999


Q ss_pred             EEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhC---CCCCHHHHHHHHHHh--hhcHHHHHHHHHHHHHh
Q 011664          341 HIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNG---SSLSPAEIGELMIAN--RNSPSRALKSVITALQT  410 (480)
Q Consensus       341 ~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~---~g~s~adI~~ll~~a--~~~~~~al~~~i~~~~~  410 (480)
                      .+.|...+.+...+|+...+.    .+..++..+.+..   -.++.+-+..+...+  +....|.|+++++..-.
T Consensus       306 iv~f~~L~~~~L~~Il~~~~~----~l~~q~~~~l~~~~i~L~~t~~al~~Ia~~~~~~~~GAR~Lrriie~~l~  376 (412)
T PRK05342        306 VATLEELDEEALVRILTEPKN----ALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILL  376 (412)
T ss_pred             eeecCCCCHHHHHHHHHHHHH----HHHHHHHHHHHhCCcEEEECHHHHHHHHHhCCCCCCCCchHHHHHHHHhH
Confidence            999999999999888874321    0112222222211   146666666666652  23445666666665543

>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=99.53  E-value=5.6e-14  Score=135.75  Aligned_cols=158  Identities=13%  Similarity=0.209  Sum_probs=103.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCcc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~  292 (480)
                      ..++||||+|+|||+|++|+++++     +..++++++.++..+       ..+..+........+|+|||++.+.... 
T Consensus        35 ~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~~~~~~~~~~~DlL~iDDi~~l~~~~-  113 (219)
T PF00308_consen   35 NPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRDGEIEEFKDRLRSADLLIIDDIQFLAGKQ-  113 (219)
T ss_dssp             SEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSHHHHHHHHCTSSEEEEETGGGGTTHH-
T ss_pred             CceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHcccchhhhhhhhcCCEEEEecchhhcCch-
Confidence            368999999999999999999864     567889987655321       2233444556688999999999986433 


Q ss_pred             cccchhhhhhhcccccccccCCceEEEEecCCCcc---CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCC
Q 011664          293 AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH---VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKL  367 (480)
Q Consensus       293 ~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~---LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l  367 (480)
                        .+..+|+..++.+..   .++.+|+.+...|..   +++.|.+  ||.  ..+.+..|+.+.|.++++......+..+
T Consensus       114 --~~q~~lf~l~n~~~~---~~k~li~ts~~~P~~l~~~~~~L~S--Rl~~Gl~~~l~~pd~~~r~~il~~~a~~~~~~l  186 (219)
T PF00308_consen  114 --RTQEELFHLFNRLIE---SGKQLILTSDRPPSELSGLLPDLRS--RLSWGLVVELQPPDDEDRRRILQKKAKERGIEL  186 (219)
T ss_dssp             --HHHHHHHHHHHHHHH---TTSEEEEEESS-TTTTTTS-HHHHH--HHHCSEEEEE----HHHHHHHHHHHHHHTT--S
T ss_pred             --HHHHHHHHHHHHHHh---hCCeEEEEeCCCCccccccChhhhh--hHhhcchhhcCCCCHHHHHHHHHHHHHHhCCCC
Confidence              234555555555544   345555555556655   4678888  886  7999999999999999999998888888


Q ss_pred             chhHHH-HHHhCCCCCHHHHHHHHH
Q 011664          368 FPQVEE-IFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       368 ~~~i~~-l~~~~~g~s~adI~~ll~  391 (480)
                      .+++-+ |+... .-+..+|..++.
T Consensus       187 ~~~v~~~l~~~~-~~~~r~L~~~l~  210 (219)
T PF00308_consen  187 PEEVIEYLARRF-RRDVRELEGALN  210 (219)
T ss_dssp             -HHHHHHHHHHT-TSSHHHHHHHHH
T ss_pred             cHHHHHHHHHhh-cCCHHHHHHHHH
Confidence            777644 44433 445555555543

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.

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=99.52  E-value=1.8e-13  Score=141.42  Aligned_cols=159  Identities=13%  Similarity=0.154  Sum_probs=109.2

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------CcEEEEeCC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------YDVYDVDLS  258 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------~~~~~i~~s  258 (480)
                      ..+++.|.++..+.|...+...+.+         ..+.+++++||||||||++++++++++.         ..++++++.
T Consensus        13 ~p~~l~gRe~e~~~l~~~l~~~~~~---------~~~~~i~I~G~~GtGKT~l~~~~~~~l~~~~~~~~~~~~~v~in~~   83 (365)
T TIGR02928        13 VPDRIVHRDEQIEELAKALRPILRG---------SRPSNVFIYGKTGTGKTAVTKYVMKELEEAAEDRDVRVVTVYVNCQ   83 (365)
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhccCCceEEEEEECC
Confidence            4468899999999998877655432         1345799999999999999999998653         567888876


Q ss_pred             CcCChHH--------------------------HHHHHH---hhcCCcEEEEecccccccCcccccchhhhhhhcccccc
Q 011664          259 RVADDAD--------------------------LKSLLL---QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN  309 (480)
Q Consensus       259 ~~~~~~~--------------------------l~~l~~---~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~  309 (480)
                      ...+...                          +..++.   ....+.||+|||+|.+...  .+..+.+|+...+... 
T Consensus        84 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlvIDE~d~L~~~--~~~~L~~l~~~~~~~~-  160 (365)
T TIGR02928        84 ILDTLYQVLVELANQLRGSGEEVPTTGLSTSEVFRRLYKELNERGDSLIIVLDEIDYLVGD--DDDLLYQLSRARSNGD-  160 (365)
T ss_pred             CCCCHHHHHHHHHHHHhhcCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEECchhhhccC--CcHHHHhHhccccccC-
Confidence            5443211                          111111   2235679999999999722  2223344443311111 


Q ss_pred             cccCCceEEEEecCCCc---cCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhc
Q 011664          310 SCCFEERVMVFTMNSKD---HVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       310 ~~~~~~~ivI~tTN~~~---~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~  361 (480)
                       .......+|+++|.++   .+++++.+  ||. ..|+|++++.++..+|++..+.
T Consensus       161 -~~~~~v~lI~i~n~~~~~~~l~~~~~s--~~~~~~i~f~p~~~~e~~~il~~r~~  213 (365)
T TIGR02928       161 -LDNAKVGVIGISNDLKFRENLDPRVKS--SLCEEEIIFPPYDAEELRDILENRAE  213 (365)
T ss_pred             -CCCCeEEEEEEECCcchHhhcCHHHhc--cCCcceeeeCCCCHHHHHHHHHHHHH
Confidence             1124567788888775   58888888  775 6899999999999999998875

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.

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=99.52  E-value=2.7e-13  Score=148.15  Aligned_cols=181  Identities=15%  Similarity=0.257  Sum_probs=129.1

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD------------  251 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~------------  251 (480)
                      ..|.+|++|+|++.+++.|...+..           | ..+.++||+||+|+|||++|+++|+.+.+.            
T Consensus        18 yRP~~f~dliGq~~~v~~L~~~~~~-----------g-ri~ha~L~~Gp~GvGKTt~Ar~lAk~L~c~~~~~~~~~~~~~   85 (598)
T PRK09111         18 YRPQTFDDLIGQEAMVRTLTNAFET-----------G-RIAQAFMLTGVRGVGKTTTARILARALNYEGPDGDGGPTIDL   85 (598)
T ss_pred             hCCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHhhCcCCccccCCCcccc
Confidence            3688999999999999888765431           2 245689999999999999999999987543            


Q ss_pred             -----------------EEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhccccc
Q 011664          252 -----------------VYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL  308 (480)
Q Consensus       252 -----------------~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~  308 (480)
                                       ++.++..+-.+-.+++.++...      ....|++|||+|.+.     ....+.||..|+.. 
T Consensus        86 cg~c~~C~~i~~g~h~Dv~e~~a~s~~gvd~IReIie~~~~~P~~a~~KVvIIDEad~Ls-----~~a~naLLKtLEeP-  159 (598)
T PRK09111         86 CGVGEHCQAIMEGRHVDVLEMDAASHTGVDDIREIIESVRYRPVSARYKVYIIDEVHMLS-----TAAFNALLKTLEEP-  159 (598)
T ss_pred             CcccHHHHHHhcCCCCceEEecccccCCHHHHHHHHHHHHhchhcCCcEEEEEEChHhCC-----HHHHHHHHHHHHhC-
Confidence                             2333333333445677765433      245799999999883     23457778777543 


Q ss_pred             ccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHH
Q 011664          309 NSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIG  387 (480)
Q Consensus       309 ~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~  387 (480)
                          .+..++|++|+.++.+.+.+++  |+ ..++|..++.++....+...+...+....++. +.++... +-+..++.
T Consensus       160 ----p~~~~fIl~tte~~kll~tI~S--Rc-q~~~f~~l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a-~Gdlr~al  231 (598)
T PRK09111        160 ----PPHVKFIFATTEIRKVPVTVLS--RC-QRFDLRRIEADVLAAHLSRIAAKEGVEVEDEALALIARAA-EGSVRDGL  231 (598)
T ss_pred             ----CCCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHH
Confidence                3457788888888888888998  88 48999999999999999988877766666443 3333333 44555544


Q ss_pred             HHH
Q 011664          388 ELM  390 (480)
Q Consensus       388 ~ll  390 (480)
                      +++
T Consensus       232 ~~L  234 (598)
T PRK09111        232 SLL  234 (598)
T ss_pred             HHH
Confidence            444

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.51  E-value=9.8e-14  Score=157.53  Aligned_cols=157  Identities=16%  Similarity=0.176  Sum_probs=111.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|-+++.++|.++....+.+.+..             ..+.+++|+||||||||++|+.+|..+          +.+++.
T Consensus       182 r~~~ld~~iGr~~ei~~~i~~l~r-------------~~~~n~lLvG~pGvGKTal~~~La~~i~~~~v~~~l~~~~i~~  248 (852)
T TIGR03345       182 REGKIDPVLGRDDEIRQMIDILLR-------------RRQNNPILTGEAGVGKTAVVEGLALRIAAGDVPPALRNVRLLS  248 (852)
T ss_pred             cCCCCCcccCCHHHHHHHHHHHhc-------------CCcCceeEECCCCCCHHHHHHHHHHHHhhCCCCccccCCeEEE
Confidence            466899999999876555543321             234589999999999999999999865          356888


Q ss_pred             EeCCCcC------C--hHHHHHHHHhh---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC
Q 011664          255 VDLSRVA------D--DADLKSLLLQT---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       255 i~~s~~~------~--~~~l~~l~~~~---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      ++++.+.      +  +..++.++...   ..++|||||||+.+.+.++.... ...-|.|.....   .+...+|+||+
T Consensus       249 l~l~~l~ag~~~~ge~e~~lk~ii~e~~~~~~~~ILfIDEih~l~~~g~~~~~-~d~~n~Lkp~l~---~G~l~~IgaTT  324 (852)
T TIGR03345       249 LDLGLLQAGASVKGEFENRLKSVIDEVKASPQPIILFIDEAHTLIGAGGQAGQ-GDAANLLKPALA---RGELRTIAATT  324 (852)
T ss_pred             eehhhhhcccccchHHHHHHHHHHHHHHhcCCCeEEEEeChHHhccCCCcccc-ccHHHHhhHHhh---CCCeEEEEecC
Confidence            8877654      2  24577777644   35799999999999864432111 111223333323   45677888777


Q ss_pred             CC-----ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          324 SK-----DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       324 ~~-----~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ..     -.+|+||.|  ||. .|.++.|+.++...|++.+..
T Consensus       325 ~~e~~~~~~~d~AL~r--Rf~-~i~v~eps~~~~~~iL~~~~~  364 (852)
T TIGR03345       325 WAEYKKYFEKDPALTR--RFQ-VVKVEEPDEETAIRMLRGLAP  364 (852)
T ss_pred             HHHHhhhhhccHHHHH--hCe-EEEeCCCCHHHHHHHHHHHHH
Confidence            53     348999999  996 899999999999999765543

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.

>PRK10865 protein disaggregation chaperone; Provisional

Probab=99.51  E-value=1.2e-13  Score=157.06  Aligned_cols=155  Identities=17%  Similarity=0.221  Sum_probs=113.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .+-.++.++|.+...+.+.+.+..             ..+.+++|+||||||||++|+++|..+          +.+++.
T Consensus       173 r~~~l~~vigr~~ei~~~i~iL~r-------------~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~vp~~l~~~~~~~  239 (857)
T PRK10865        173 EQGKLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA  239 (857)
T ss_pred             hcCCCCcCCCCHHHHHHHHHHHhc-------------CCcCceEEECCCCCCHHHHHHHHHHHhhcCCCchhhCCCEEEE
Confidence            356789999998866655544321             235579999999999999999999987          788999


Q ss_pred             EeCCCcCC--------hHHHHHHHHh---hcCCcEEEEecccccccCccccc--chhhhhhhcccccccccCCceEEEEe
Q 011664          255 VDLSRVAD--------DADLKSLLLQ---TTSKSVILIEDLDRFLVEKPAAV--SLSGVLNFMDGVLNSCCFEERVMVFT  321 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~~---~~~~sII~IDEiD~l~~~~~~~~--~ls~lL~~ldg~~~~~~~~~~ivI~t  321 (480)
                      ++++.+..        +..++.+|..   ...++||||||+|.+.+...+..  ..+.+|   .....   .+...+|+|
T Consensus       240 l~l~~l~ag~~~~g~~e~~lk~~~~~~~~~~~~~ILfIDEih~l~~~~~~~~~~d~~~~l---kp~l~---~g~l~~Iga  313 (857)
T PRK10865        240 LDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNML---KPALA---RGELHCVGA  313 (857)
T ss_pred             EehhhhhhccchhhhhHHHHHHHHHHHHHcCCCeEEEEecHHHhccCCCCccchhHHHHh---cchhh---cCCCeEEEc
Confidence            98876542        2346777754   24689999999999986543222  223333   22223   456778888


Q ss_pred             cCCCc-----cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          322 MNSKD-----HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       322 TN~~~-----~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      |+..+     .+|+||.|  ||+ .|.++.|+.+++..|++.+..
T Consensus       314 Tt~~e~r~~~~~d~al~r--Rf~-~i~v~eP~~~~~~~iL~~l~~  355 (857)
T PRK10865        314 TTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAILRGLKE  355 (857)
T ss_pred             CCCHHHHHHhhhcHHHHh--hCC-EEEeCCCCHHHHHHHHHHHhh
Confidence            87665     48999999  997 689999999999999987654

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.51  E-value=3.4e-13  Score=147.61  Aligned_cols=169  Identities=13%  Similarity=0.254  Sum_probs=119.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++|+|++.+++.|+..+.            ....+.+|||+||||||||++|+++|+.+.+              
T Consensus        11 RP~~f~eivGQe~i~~~L~~~i~------------~~ri~ha~Lf~Gp~GvGKttlA~~lAk~L~c~~~~~~~~~~~~~~   78 (620)
T PRK14954         11 RPSKFADITAQEHITHTIQNSLR------------MDRVGHGYIFSGLRGVGKTTAARVFAKAVNCQRMIDDPVYLQEVT   78 (620)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHH------------cCCCCeeEEEECCCCCCHHHHHHHHHHHhCCCCcCCccccccccC
Confidence            57899999999999998775432            1235668999999999999999999998855              


Q ss_pred             ------------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhccc
Q 011664          251 ------------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG  306 (480)
Q Consensus       251 ------------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg  306 (480)
                                        +++.++.....+-.+++.+....      ....|++|||+|.+..     ...+.||..|+.
T Consensus        79 ~~Cg~C~sC~~~~~g~~~n~~~~d~~s~~~vd~Ir~l~e~~~~~P~~~~~KVvIIdEad~Lt~-----~a~naLLK~LEe  153 (620)
T PRK14954         79 EPCGECESCRDFDAGTSLNISEFDAASNNSVDDIRQLRENVRYGPQKGRYRVYIIDEVHMLST-----AAFNAFLKTLEE  153 (620)
T ss_pred             CCCccCHHHHHHhccCCCCeEEecccccCCHHHHHHHHHHHHhhhhcCCCEEEEEeChhhcCH-----HHHHHHHHHHhC
Confidence                              23333333333345566655333      2457999999998842     235678877764


Q ss_pred             ccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhC
Q 011664          307 VLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNG  378 (480)
Q Consensus       307 ~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~  378 (480)
                      .     .+..++|++|+.+..|-+++.+  |. ..++|..++.++....+...+...+..+.++. +.|+..+
T Consensus       154 P-----p~~tv~IL~t~~~~kLl~TI~S--Rc-~~vef~~l~~~ei~~~L~~i~~~egi~I~~eal~~La~~s  218 (620)
T PRK14954        154 P-----PPHAIFIFATTELHKIPATIAS--RC-QRFNFKRIPLDEIQSQLQMICRAEGIQIDADALQLIARKA  218 (620)
T ss_pred             C-----CCCeEEEEEeCChhhhhHHHHh--hc-eEEecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHh
Confidence            3     3456777777778899999998  77 58999999999988888877766565555443 3444443

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=99.51  E-value=1.2e-13  Score=146.52  Aligned_cols=191  Identities=14%  Similarity=0.225  Sum_probs=121.1

Q ss_pred             CCCCCCCccccc-cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEE
Q 011664          182 PFTHPSTFDTIS-METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDV  255 (480)
Q Consensus       182 ~~~~~~~~~~i~-g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i  255 (480)
                      ++.+..||++.+ |.... .. ...+..+...+      |  +..+++||||||||||+|++|+|+++     +..++++
T Consensus        97 ~l~~~~tFdnFv~g~~n~-~a-~~~~~~~~~~~------~--~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi  166 (440)
T PRK14088         97 PLNPDYTFENFVVGPGNS-FA-YHAALEVAKNP------G--RYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYI  166 (440)
T ss_pred             CCCCCCcccccccCCchH-HH-HHHHHHHHhCc------C--CCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEE
Confidence            556778999976 54332 22 22222232221      2  23469999999999999999999975     4678888


Q ss_pred             eCCCcCCh-------HHHHHHHHhh-cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          256 DLSRVADD-------ADLKSLLLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       256 ~~s~~~~~-------~~l~~l~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      ++.++..+       ..+....... .++.+|+|||++.+.+....   ..+++..++.+..   ....+|+.+.+.|..
T Consensus       167 ~~~~f~~~~~~~~~~~~~~~f~~~~~~~~dvLlIDDi~~l~~~~~~---q~elf~~~n~l~~---~~k~iIitsd~~p~~  240 (440)
T PRK14088        167 TSEKFLNDLVDSMKEGKLNEFREKYRKKVDVLLIDDVQFLIGKTGV---QTELFHTFNELHD---SGKQIVICSDREPQK  240 (440)
T ss_pred             EHHHHHHHHHHHHhcccHHHHHHHHHhcCCEEEEechhhhcCcHHH---HHHHHHHHHHHHH---cCCeEEEECCCCHHH
Confidence            87654321       1111222222 26889999999988643322   2345555555444   233444444456655


Q ss_pred             ---CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhHH-HHHHhCCCCCHHHHHHHHH
Q 011664          328 ---VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVE-EIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       328 ---LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~-~l~~~~~g~s~adI~~ll~  391 (480)
                         +++.+++  ||.  ..+.+.+|+.+.|.+|++..+...+..+.+++- .|+... .-+..++..++.
T Consensus       241 l~~l~~rL~S--R~~~gl~v~i~~pd~e~r~~IL~~~~~~~~~~l~~ev~~~Ia~~~-~~~~R~L~g~l~  307 (440)
T PRK14088        241 LSEFQDRLVS--RFQMGLVAKLEPPDEETRKKIARKMLEIEHGELPEEVLNFVAENV-DDNLRRLRGAII  307 (440)
T ss_pred             HHHHHHHHhh--HHhcCceEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHhcc-ccCHHHHHHHHH
Confidence               5678888  885  788999999999999999998877777777664 454443 345555555443

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.50  E-value=5e-13  Score=146.86  Aligned_cols=169  Identities=19%  Similarity=0.307  Sum_probs=121.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++++|++.+++.|...+..           | ....++||+||||||||++|+++|+.+.+              
T Consensus        11 RP~~f~~liGq~~i~~~L~~~l~~-----------~-rl~~a~Lf~Gp~G~GKttlA~~lAk~L~c~~~~~~~~~~Cg~C   78 (620)
T PRK14948         11 RPQRFDELVGQEAIATTLKNALIS-----------N-RIAPAYLFTGPRGTGKTSSARILAKSLNCLNSDKPTPEPCGKC   78 (620)
T ss_pred             CCCcHhhccChHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCChHHHHHHHHHHhcCCCcCCCCCCCCccc
Confidence            678999999999999988765542           1 12347999999999999999999998755              


Q ss_pred             ------------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          251 ------------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       251 ------------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                                  +++.++.....+-..++.++...      ....|++|||+|.+.     ....+.||..|+.-     
T Consensus        79 ~~C~~i~~g~h~D~~ei~~~~~~~vd~IReii~~a~~~p~~~~~KViIIDEad~Lt-----~~a~naLLK~LEeP-----  148 (620)
T PRK14948         79 ELCRAIAAGNALDVIEIDAASNTGVDNIRELIERAQFAPVQARWKVYVIDECHMLS-----TAAFNALLKTLEEP-----  148 (620)
T ss_pred             HHHHHHhcCCCccEEEEeccccCCHHHHHHHHHHHhhChhcCCceEEEEECccccC-----HHHHHHHHHHHhcC-----
Confidence                        34455544333445677776443      234799999999883     23457788888742     


Q ss_pred             CCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhC
Q 011664          313 FEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNG  378 (480)
Q Consensus       313 ~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~  378 (480)
                      ....++|++|+.+..+-+++++  |+ ..++|+.++.++....+...+...+..+..+ +..++...
T Consensus       149 p~~tvfIL~t~~~~~llpTIrS--Rc-~~~~f~~l~~~ei~~~L~~ia~kegi~is~~al~~La~~s  212 (620)
T PRK14948        149 PPRVVFVLATTDPQRVLPTIIS--RC-QRFDFRRIPLEAMVQHLSEIAEKESIEIEPEALTLVAQRS  212 (620)
T ss_pred             CcCeEEEEEeCChhhhhHHHHh--he-eEEEecCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHc
Confidence            3457788888889999999998  88 4789999988887777777666555555433 33444433

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.49  E-value=5.8e-13  Score=146.09  Aligned_cols=180  Identities=17%  Similarity=0.302  Sum_probs=124.8

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++|+|++.+++.|+..+..           | ..+..+|||||||+|||++|+++|+.+.+              
T Consensus        11 RP~~~~eiiGq~~~~~~L~~~i~~-----------~-~i~~a~Lf~Gp~G~GKTtlA~~lA~~l~c~~~~~~~~~c~~c~   78 (585)
T PRK14950         11 RSQTFAELVGQEHVVQTLRNAIAE-----------G-RVAHAYLFTGPRGVGKTSTARILAKAVNCTTNDPKGRPCGTCE   78 (585)
T ss_pred             CCCCHHHhcCCHHHHHHHHHHHHh-----------C-CCceEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCCccCH
Confidence            688999999999999988765542           1 23457899999999999999999987643              


Q ss_pred             -----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccC
Q 011664          251 -----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCF  313 (480)
Q Consensus       251 -----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~  313 (480)
                                 +++.++.+...+-.+++.+....      ....||+|||+|.+.     ....+.||..|+..     .
T Consensus        79 ~c~~i~~~~~~d~~~i~~~~~~~vd~ir~ii~~~~~~p~~~~~kVvIIDEa~~L~-----~~a~naLLk~LEep-----p  148 (585)
T PRK14950         79 MCRAIAEGSAVDVIEMDAASHTSVDDAREIIERVQFRPALARYKVYIIDEVHMLS-----TAAFNALLKTLEEP-----P  148 (585)
T ss_pred             HHHHHhcCCCCeEEEEeccccCCHHHHHHHHHHHhhCcccCCeEEEEEeChHhCC-----HHHHHHHHHHHhcC-----C
Confidence                       23444544334444555554322      245799999999873     23456777777643     3


Q ss_pred             CceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          314 EERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       314 ~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ...++|++|+.++.+.+.+++  |+. +++|+.++..+...++...+...+..+.++. ..++... +-++.++.+.+
T Consensus       149 ~~tv~Il~t~~~~kll~tI~S--R~~-~i~f~~l~~~el~~~L~~~a~~egl~i~~eal~~La~~s-~Gdlr~al~~L  222 (585)
T PRK14950        149 PHAIFILATTEVHKVPATILS--RCQ-RFDFHRHSVADMAAHLRKIAAAEGINLEPGALEAIARAA-TGSMRDAENLL  222 (585)
T ss_pred             CCeEEEEEeCChhhhhHHHHh--ccc-eeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            456777778888888888888  874 7899999999988888888776666555443 3444333 33554444433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=99.49  E-value=6.7e-13  Score=134.19  Aligned_cols=170  Identities=16%  Similarity=0.214  Sum_probs=115.5

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEe
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVD  256 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~  256 (480)
                      ....|.+|++++|.+++++.+...+.    .       +.  ..+++||||||||||++++++++++.     .+++.++
T Consensus         9 ~kyrP~~~~~~~g~~~~~~~l~~~i~----~-------~~--~~~~ll~G~~G~GKt~~~~~l~~~l~~~~~~~~~i~~~   75 (319)
T PRK00440          9 EKYRPRTLDEIVGQEEIVERLKSYVK----E-------KN--MPHLLFAGPPGTGKTTAALALARELYGEDWRENFLELN   75 (319)
T ss_pred             hhhCCCcHHHhcCcHHHHHHHHHHHh----C-------CC--CCeEEEECCCCCCHHHHHHHHHHHHcCCccccceEEec
Confidence            55678999999999998888876553    1       11  12589999999999999999999873     3455555


Q ss_pred             CCCcCChHHHHHHH---Hhh-----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          257 LSRVADDADLKSLL---LQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       257 ~s~~~~~~~l~~l~---~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      .+...+...++..+   ...     ..+.+|+|||+|.+..     .....|+..++...     ....+|+++|.+..+
T Consensus        76 ~~~~~~~~~~~~~i~~~~~~~~~~~~~~~vviiDe~~~l~~-----~~~~~L~~~le~~~-----~~~~lIl~~~~~~~l  145 (319)
T PRK00440         76 ASDERGIDVIRNKIKEFARTAPVGGAPFKIIFLDEADNLTS-----DAQQALRRTMEMYS-----QNTRFILSCNYSSKI  145 (319)
T ss_pred             cccccchHHHHHHHHHHHhcCCCCCCCceEEEEeCcccCCH-----HHHHHHHHHHhcCC-----CCCeEEEEeCCcccc
Confidence            44433322222222   111     2356999999998842     12345666665432     235677788888888


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHh
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQN  377 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~  377 (480)
                      .+++.+  |+. .++|++++.++...+++.++...+..+.++ ++.++..
T Consensus       146 ~~~l~s--r~~-~~~~~~l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~  192 (319)
T PRK00440        146 IDPIQS--RCA-VFRFSPLKKEAVAERLRYIAENEGIEITDDALEAIYYV  192 (319)
T ss_pred             chhHHH--Hhh-eeeeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            888888  875 699999999999999998887666555443 2344443

>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX)

Probab=99.48  E-value=4.7e-13  Score=139.94  Aligned_cols=214  Identities=18%  Similarity=0.267  Sum_probs=132.6

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhh----hCCC-CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC----
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHR----LGRV-WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA----  261 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~----~g~~-~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~----  261 (480)
                      .|+|++++|+.+...+....++-.....    .+.. .+.++||+||||||||++|+++|..++.+|..++++.+.    
T Consensus        78 ~ViGQe~A~~~l~~av~~h~~~~~~~~~~~~~~~~~~~~~~iLL~GP~GsGKT~lAraLA~~l~~pf~~~da~~L~~~gy  157 (413)
T TIGR00382        78 YVIGQEQAKKVLSVAVYNHYKRLNFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGY  157 (413)
T ss_pred             eecCHHHHHHHHHHHHHHHHhhhccccccccccccccCCceEEEECCCCcCHHHHHHHHHHhcCCCeEEechhhcccccc
Confidence            3699999999998777544333211000    0111 245899999999999999999999999999988876643    


Q ss_pred             -Ch---HHHHHHHH------hhcCCcEEEEecccccccCccc---------ccchhhhhhhccccccc--------ccCC
Q 011664          262 -DD---ADLKSLLL------QTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNS--------CCFE  314 (480)
Q Consensus       262 -~~---~~l~~l~~------~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~--------~~~~  314 (480)
                       +.   ..+..++.      ....++||||||||.+.....+         ....+.||..|+|....        ....
T Consensus       158 vG~d~e~~L~~~~~~~~~~l~~a~~gIV~lDEIdkl~~~~~~~s~~~dvsg~~vq~~LL~iLeG~~~~v~~~~gr~~~~~  237 (413)
T TIGR00382       158 VGEDVENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQ  237 (413)
T ss_pred             ccccHHHHHHHHHHhCcccHHhcccceEEecccchhchhhccccccccccchhHHHHHHHHhhccceecccCCCccccCC
Confidence             21   12333332      2346789999999998763221         13567799999876421        1123


Q ss_pred             ceEEEEecCCCc--------------------------------------------------cCcccccCCCceeEEEEc
Q 011664          315 ERVMVFTMNSKD--------------------------------------------------HVDQALLRPGRIDVHIHF  344 (480)
Q Consensus       315 ~~ivI~tTN~~~--------------------------------------------------~LD~aLlrpGRfd~~I~~  344 (480)
                      +.++|+|+|-..                                                  .+.|+++  ||+|.++.|
T Consensus       238 ~~i~i~TsNilfi~~Gaf~g~~~i~~~r~~~~~~gf~~~~~~~~~~~~~~~~~~~~~dl~~~g~~PEfl--gRld~Iv~f  315 (413)
T TIGR00382       238 EFIQIDTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFI--GRLPVIATL  315 (413)
T ss_pred             CeEEEEcCCceeeecccccChHHHHHHHhhhccccccccccccchhhHHHHHHHHHHHHHHHhhHHHHh--CCCCeEeec
Confidence            457788887510                                                  0224444  499999999


Q ss_pred             CCCCHHHHHHHHHHHhccCCCCCchhHHHHHHh---CCCCCHHHHHHHHHHh--hhcHHHHHHHHHHHHHh
Q 011664          345 PLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQN---GSSLSPAEIGELMIAN--RNSPSRALKSVITALQT  410 (480)
Q Consensus       345 ~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~---~~g~s~adI~~ll~~a--~~~~~~al~~~i~~~~~  410 (480)
                      .+.+.++..+|+..-+.    .+..++..+...   .-.++++-+..+...+  .....|.++.+++..-.
T Consensus       316 ~pL~~~~L~~Il~~~~n----~l~kq~~~~l~~~gi~L~~t~~a~~~Ia~~~~~~~~GAR~Lr~iie~~l~  382 (413)
T TIGR00382       316 EKLDEEALIAILTKPKN----ALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLL  382 (413)
T ss_pred             CCCCHHHHHHHHHHHHH----HHHHHHHHHhccCCeEEEECHHHHHHHHHhCCCCCCCchHHHHHHHHhhH
Confidence            99999998888765321    011122222211   1245666666666553  23445677777665544

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.

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=99.47  E-value=3.5e-13  Score=142.95  Aligned_cols=145  Identities=12%  Similarity=0.254  Sum_probs=100.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCcccc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAA  294 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~  294 (480)
                      ++++||||||+|||+|++|+|+++   +..+++++...+...       .....+-.......+|+|||++.+.+....+
T Consensus       142 npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~~f~~~~~~~dvLiIDDiq~l~~k~~~q  221 (445)
T PRK12422        142 NPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQRFRQFYRNVDALFIEDIEVFSGKGATQ  221 (445)
T ss_pred             ceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHHHHHHHcccCCEEEEcchhhhcCChhhH
Confidence            579999999999999999999976   678888886544221       1111111223567899999999886433333


Q ss_pred             cchhhhhhhcccccccccCCceEEEEecC-CCc---cCcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCc
Q 011664          295 VSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKD---HVDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLF  368 (480)
Q Consensus       295 ~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~---~LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~  368 (480)
                         .+|+..++.+..    .+..+|+|+| .|.   .++++|++  ||.  ..+.+++|+.+.+.+|++..+...+..+.
T Consensus       222 ---eelf~l~N~l~~----~~k~IIlts~~~p~~l~~l~~rL~S--R~~~Gl~~~l~~pd~e~r~~iL~~k~~~~~~~l~  292 (445)
T PRK12422        222 ---EEFFHTFNSLHT----EGKLIVISSTCAPQDLKAMEERLIS--RFEWGIAIPLHPLTKEGLRSFLERKAEALSIRIE  292 (445)
T ss_pred             ---HHHHHHHHHHHH----CCCcEEEecCCCHHHHhhhHHHHHh--hhcCCeEEecCCCCHHHHHHHHHHHHHHcCCCCC
Confidence               344444443333    2234555555 454   46799999  996  89999999999999999999887777777


Q ss_pred             hhHHH-HHHhC
Q 011664          369 PQVEE-IFQNG  378 (480)
Q Consensus       369 ~~i~~-l~~~~  378 (480)
                      +++-+ |+...
T Consensus       293 ~evl~~la~~~  303 (445)
T PRK12422        293 ETALDFLIEAL  303 (445)
T ss_pred             HHHHHHHHHhc
Confidence            76644 55543

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=99.47  E-value=1.2e-12  Score=143.94  Aligned_cols=178  Identities=16%  Similarity=0.302  Sum_probs=129.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------------  249 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------------  249 (480)
                      .|.+|++|+|++.+++.|...+..           | ..+..||||||+|+|||++|+++|+.+.               
T Consensus        12 RP~~f~~viGq~~~~~~L~~~i~~-----------~-~l~hayLf~Gp~G~GKtt~A~~lAk~l~c~~~~~~~~~Cg~C~   79 (614)
T PRK14971         12 RPSTFESVVGQEALTTTLKNAIAT-----------N-KLAHAYLFCGPRGVGKTTCARIFAKTINCQNLTADGEACNECE   79 (614)
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHc-----------C-CCCeeEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCCCcch
Confidence            678999999999999988765541           1 2466899999999999999999999764               


Q ss_pred             ----------CcEEEEeCCCcCChHHHHHHHHhhc------CCcEEEEecccccccCcccccchhhhhhhcccccccccC
Q 011664          250 ----------YDVYDVDLSRVADDADLKSLLLQTT------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCF  313 (480)
Q Consensus       250 ----------~~~~~i~~s~~~~~~~l~~l~~~~~------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~  313 (480)
                                .+++.++.++..+-..++.++.+..      ...|++|||+|.+.     ....+.|+..|+..     .
T Consensus        80 sC~~~~~~~~~n~~~ld~~~~~~vd~Ir~li~~~~~~P~~~~~KVvIIdea~~Ls-----~~a~naLLK~LEep-----p  149 (614)
T PRK14971         80 SCVAFNEQRSYNIHELDAASNNSVDDIRNLIEQVRIPPQIGKYKIYIIDEVHMLS-----QAAFNAFLKTLEEP-----P  149 (614)
T ss_pred             HHHHHhcCCCCceEEecccccCCHHHHHHHHHHHhhCcccCCcEEEEEECcccCC-----HHHHHHHHHHHhCC-----C
Confidence                      3556666654444456777664432      34699999999883     23456788887653     3


Q ss_pred             CceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHH
Q 011664          314 EERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       314 ~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~  388 (480)
                      +..++|++|+.+..|-++|++  |+. .++|..++.++....+...+...+.....+ ++.|+... |-+..++.+
T Consensus       150 ~~tifIL~tt~~~kIl~tI~S--Rc~-iv~f~~ls~~ei~~~L~~ia~~egi~i~~~al~~La~~s-~gdlr~al~  221 (614)
T PRK14971        150 SYAIFILATTEKHKILPTILS--RCQ-IFDFNRIQVADIVNHLQYVASKEGITAEPEALNVIAQKA-DGGMRDALS  221 (614)
T ss_pred             CCeEEEEEeCCchhchHHHHh--hhh-eeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHH
Confidence            456788888888899999999  884 799999999998888888877666665554 34444443 444444433

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

Probab=99.47  E-value=5.8e-13  Score=148.96  Aligned_cols=160  Identities=16%  Similarity=0.292  Sum_probs=114.4

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLL  270 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~  270 (480)
                      .|+|++++++.|.+.+.....+-.   . ...+..++||+||||||||.+|+++|..++.+++.++++++.....+..++
T Consensus       459 ~ViGQ~~ai~~l~~~i~~~~~gl~---~-~~kp~~~~Lf~GP~GvGKT~lAk~LA~~l~~~~i~id~se~~~~~~~~~Li  534 (758)
T PRK11034        459 LVFGQDKAIEALTEAIKMSRAGLG---H-EHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSRLI  534 (758)
T ss_pred             eEeCcHHHHHHHHHHHHHHhcccc---C-CCCCcceEEEECCCCCCHHHHHHHHHHHhCCCcEEeechhhcccccHHHHc
Confidence            479999999999888765422100   0 012334799999999999999999999999999999998875432222222


Q ss_pred             ------------------HhhcCCcEEEEecccccccCcccccchhhhhhhcc-ccccc-----ccCCceEEEEecCCC-
Q 011664          271 ------------------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-GVLNS-----CCFEERVMVFTMNSK-  325 (480)
Q Consensus       271 ------------------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-g~~~~-----~~~~~~ivI~tTN~~-  325 (480)
                                        .+..+.+||||||||.+.     ....+.|++.|| |....     ....+.+||+|||.- 
T Consensus       535 G~~~gyvg~~~~g~L~~~v~~~p~sVlllDEieka~-----~~v~~~LLq~ld~G~ltd~~g~~vd~rn~iiI~TsN~g~  609 (758)
T PRK11034        535 GAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAH-----PDVFNLLLQVMDNGTLTDNNGRKADFRNVVLVMTTNAGV  609 (758)
T ss_pred             CCCCCcccccccchHHHHHHhCCCcEEEeccHhhhh-----HHHHHHHHHHHhcCeeecCCCceecCCCcEEEEeCCcCH
Confidence                              122356999999999884     234567777776 32211     112467899999922 


Q ss_pred             ------------------------ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          326 ------------------------DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       326 ------------------------~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                                              ..+.|.++.  |+|.+|.|++.+.++..+|+..++.
T Consensus       610 ~~~~~~~~g~~~~~~~~~~~~~~~~~f~pefl~--Rid~ii~f~~L~~~~l~~I~~~~l~  667 (758)
T PRK11034        610 RETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_pred             HHHhhcccCcccchhhHHHHHHHHHhcCHHHHc--cCCEEEEcCCCCHHHHHHHHHHHHH
Confidence                                    124577777  9999999999999999999987764

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=99.46  E-value=7.9e-13  Score=147.23  Aligned_cols=152  Identities=19%  Similarity=0.285  Sum_probs=104.0

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD  263 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~  263 (480)
                      -+|.+|++++|++.+..... .+...+..       +  ...+++||||||||||++|+++|+..+.+++.+++.. .+.
T Consensus        22 ~RP~tldd~vGQe~ii~~~~-~L~~~i~~-------~--~~~slLL~GPpGtGKTTLA~aIA~~~~~~f~~lna~~-~~i   90 (725)
T PRK13341         22 LRPRTLEEFVGQDHILGEGR-LLRRAIKA-------D--RVGSLILYGPPGVGKTTLARIIANHTRAHFSSLNAVL-AGV   90 (725)
T ss_pred             cCCCcHHHhcCcHHHhhhhH-HHHHHHhc-------C--CCceEEEECCCCCCHHHHHHHHHHHhcCcceeehhhh-hhh
Confidence            35899999999998775311 12222221       1  1237999999999999999999999999998888653 222


Q ss_pred             HHHHHHHHh-------hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEec--CCCccCcccccC
Q 011664          264 ADLKSLLLQ-------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM--NSKDHVDQALLR  334 (480)
Q Consensus       264 ~~l~~l~~~-------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT--N~~~~LD~aLlr  334 (480)
                      .+++..+..       ...+.+|||||||.+..     .....|+..++       ...+++|++|  |....+++++++
T Consensus        91 ~dir~~i~~a~~~l~~~~~~~IL~IDEIh~Ln~-----~qQdaLL~~lE-------~g~IiLI~aTTenp~~~l~~aL~S  158 (725)
T PRK13341         91 KDLRAEVDRAKERLERHGKRTILFIDEVHRFNK-----AQQDALLPWVE-------NGTITLIGATTENPYFEVNKALVS  158 (725)
T ss_pred             HHHHHHHHHHHHHhhhcCCceEEEEeChhhCCH-----HHHHHHHHHhc-------CceEEEEEecCCChHhhhhhHhhc
Confidence            233333322       23567999999998732     11244555443       1234556544  334578999998


Q ss_pred             CCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          335 PGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       335 pGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                        |+ ..+.|++++.++...+++..+.
T Consensus       159 --R~-~v~~l~pLs~edi~~IL~~~l~  182 (725)
T PRK13341        159 --RS-RLFRLKSLSDEDLHQLLKRALQ  182 (725)
T ss_pred             --cc-cceecCCCCHHHHHHHHHHHHH
Confidence              76 4799999999999999998875

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=99.46  E-value=8e-13  Score=131.08  Aligned_cols=129  Identities=20%  Similarity=0.245  Sum_probs=91.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHH---------------------------------HHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLK---------------------------------SLLL  271 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~---------------------------------~l~~  271 (480)
                      +.+||+||||||||++|+++|..+|.+++.++++.-...+++.                                 .++.
T Consensus        22 ~~vLL~G~~GtGKT~lA~~la~~lg~~~~~i~~~~~~~~~dllg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~l~~  101 (262)
T TIGR02640        22 YPVHLRGPAGTGKTTLAMHVARKRDRPVMLINGDAELTTSDLVGSYAGYTRKKVHDQFIHNVVKLEDIVRQNWVDNRLTL  101 (262)
T ss_pred             CeEEEEcCCCCCHHHHHHHHHHHhCCCEEEEeCCccCCHHHHhhhhcccchhhHHHHHHHHhhhhhcccceeecCchHHH
Confidence            4799999999999999999999999999999887543322210                                 0112


Q ss_pred             hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cc--c--------cCCceEEEEecCCC-----ccCcccccCC
Q 011664          272 QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NS--C--------CFEERVMVFTMNSK-----DHVDQALLRP  335 (480)
Q Consensus       272 ~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~--~--------~~~~~ivI~tTN~~-----~~LD~aLlrp  335 (480)
                      ....+.+|+|||||.+-     ....+.|+..|+.-. ..  .        -..+..||+|+|..     ..++++|++ 
T Consensus       102 A~~~g~~lllDEi~r~~-----~~~q~~Ll~~Le~~~~~i~~~~~~~~~i~~~~~frvIaTsN~~~~~g~~~l~~aL~~-  175 (262)
T TIGR02640       102 AVREGFTLVYDEFTRSK-----PETNNVLLSVFEEGVLELPGKRGTSRYVDVHPEFRVIFTSNPVEYAGVHETQDALLD-  175 (262)
T ss_pred             HHHcCCEEEEcchhhCC-----HHHHHHHHHHhcCCeEEccCCCCCCceEecCCCCEEEEeeCCccccceecccHHHHh-
Confidence            23456899999999763     234455666664211 00  0        01234578899965     356899999 


Q ss_pred             CceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          336 GRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       336 GRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                       || ..+.+++|+.++-.+|++.+.+
T Consensus       176 -R~-~~i~i~~P~~~~e~~Il~~~~~  199 (262)
T TIGR02640       176 -RL-ITIFMDYPDIDTETAILRAKTD  199 (262)
T ss_pred             -hc-EEEECCCCCHHHHHHHHHHhhC
Confidence             99 6899999999999999988753

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).

>PRK06620 hypothetical protein; Validated

Probab=99.45  E-value=1.8e-12  Score=124.85  Aligned_cols=159  Identities=14%  Similarity=0.188  Sum_probs=98.9

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC-CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVW-KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~-~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +..+.-+|++.+..+.-.. ....+..+..      .++..+ .+.++||||||||||+|++++++..+..+..  ....
T Consensus         8 ~~~~~~tfd~Fvvg~~N~~-a~~~~~~~~~------~~~~~~~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~--~~~~   78 (214)
T PRK06620          8 TTSSKYHPDEFIVSSSNDQ-AYNIIKNWQC------GFGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYIIK--DIFF   78 (214)
T ss_pred             CCCCCCCchhhEecccHHH-HHHHHHHHHH------ccccCCCcceEEEECCCCCCHHHHHHHHHhccCCEEcc--hhhh
Confidence            4445568999755442222 2233333322      122222 3679999999999999999999988753322  1111


Q ss_pred             CChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc--CcccccCCCce
Q 011664          261 ADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH--VDQALLRPGRI  338 (480)
Q Consensus       261 ~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~--LD~aLlrpGRf  338 (480)
                       ..    ..   .....+++|||||.+     ....+..++|.+   ..   .+..+++.++..|..  + |+|++  |+
T Consensus        79 -~~----~~---~~~~d~lliDdi~~~-----~~~~lf~l~N~~---~e---~g~~ilits~~~p~~l~l-~~L~S--Rl  136 (214)
T PRK06620         79 -NE----EI---LEKYNAFIIEDIENW-----QEPALLHIFNII---NE---KQKYLLLTSSDKSRNFTL-PDLSS--RI  136 (214)
T ss_pred             -ch----hH---HhcCCEEEEeccccc-----hHHHHHHHHHHH---Hh---cCCEEEEEcCCCccccch-HHHHH--HH
Confidence             01    11   124579999999954     112334444443   33   344566666555543  6 88998  98


Q ss_pred             e--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          339 D--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       339 d--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                      .  ..+.+..|+.+.+.+++++.+...+..+.+++
T Consensus       137 ~~gl~~~l~~pd~~~~~~~l~k~~~~~~l~l~~ev  171 (214)
T PRK06620        137 KSVLSILLNSPDDELIKILIFKHFSISSVTISRQI  171 (214)
T ss_pred             hCCceEeeCCCCHHHHHHHHHHHHHHcCCCCCHHH
Confidence            6  58999999999999999988765555666555

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=99.44  E-value=1.6e-12  Score=135.84  Aligned_cols=164  Identities=13%  Similarity=0.134  Sum_probs=111.6

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEe
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVD  256 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~  256 (480)
                      ++.+....+.+.|-++..++|...+...+..         ..+.++++|||||||||++++.+++++     +..+++++
T Consensus        22 ~l~~~~~P~~l~~Re~e~~~l~~~l~~~~~~---------~~~~~~lI~G~~GtGKT~l~~~v~~~l~~~~~~~~~v~in   92 (394)
T PRK00411         22 VLEPDYVPENLPHREEQIEELAFALRPALRG---------SRPLNVLIYGPPGTGKTTTVKKVFEELEEIAVKVVYVYIN   92 (394)
T ss_pred             hCCCCCcCCCCCCHHHHHHHHHHHHHHHhCC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEE
Confidence            3444445677889888888888777654332         123569999999999999999999876     57788898


Q ss_pred             CCCcCChH-----------------------HH-HHH---HHhhcCCcEEEEecccccccCcccccchhhhhhhcccccc
Q 011664          257 LSRVADDA-----------------------DL-KSL---LLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN  309 (480)
Q Consensus       257 ~s~~~~~~-----------------------~l-~~l---~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~  309 (480)
                      +....+..                       ++ ..+   +.....+.||+|||+|.+. .+.....+..|+..++... 
T Consensus        93 ~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~viviDE~d~l~-~~~~~~~l~~l~~~~~~~~-  170 (394)
T PRK00411         93 CQIDRTRYAIFSEIARQLFGHPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLF-EKEGNDVLYSLLRAHEEYP-  170 (394)
T ss_pred             CCcCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCHhHhh-ccCCchHHHHHHHhhhccC-
Confidence            76443211                       11 111   1122345799999999987 2333345566666554332 


Q ss_pred             cccCCceEEEEecCCC---ccCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhc
Q 011664          310 SCCFEERVMVFTMNSK---DHVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       310 ~~~~~~~ivI~tTN~~---~~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~  361 (480)
                         .....+|+++|.+   +.+++.+.+  |+. ..|+|++++.++...+++..+.
T Consensus       171 ---~~~v~vI~i~~~~~~~~~l~~~~~s--~~~~~~i~f~py~~~e~~~il~~r~~  221 (394)
T PRK00411        171 ---GARIGVIGISSDLTFLYILDPRVKS--VFRPEEIYFPPYTADEIFDILKDRVE  221 (394)
T ss_pred             ---CCeEEEEEEECCcchhhhcCHHHHh--cCCcceeecCCCCHHHHHHHHHHHHH
Confidence               2256677777755   457787776  664 6899999999999999988874

>PRK05201 hslU ATP-dependent protease ATP-binding subunit HslU; Provisional

Probab=99.44  E-value=2.5e-12  Score=133.44  Aligned_cols=215  Identities=16%  Similarity=0.262  Sum_probs=141.6

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCC-CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-----C--
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGR-VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-----D--  262 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~-~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-----~--  262 (480)
                      .|+|++++|+.+...+....++......... ..++++||+||||||||++|+++|..++.+|+.++++.+.     +  
T Consensus        16 ~IiGQe~AkkalavAl~~~~~r~~l~~~~~~e~~~~~ILliGp~G~GKT~LAr~LAk~l~~~fi~vD~t~f~e~GyvG~d   95 (443)
T PRK05201         16 YIIGQDDAKRAVAIALRNRWRRMQLPEELRDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRD   95 (443)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHhcCCcccccccCCceEEEECCCCCCHHHHHHHHHHHhCChheeecchhhccCCcccCC
Confidence            3899999999998877554333221111111 1357899999999999999999999999999999976443     2  


Q ss_pred             -hHHHHHHHHh---------------------------------------------------------------------
Q 011664          263 -DADLKSLLLQ---------------------------------------------------------------------  272 (480)
Q Consensus       263 -~~~l~~l~~~---------------------------------------------------------------------  272 (480)
                       ++.++.++..                                                                     
T Consensus        96 ~e~~ir~L~~~A~~~~~~~~~~~~~~~a~~~~e~ri~~~l~~~~~~~~~~~~~~~~~~~~r~~~~~~l~~g~ldd~~iei  175 (443)
T PRK05201         96 VESIIRDLVEIAVKMVREEKREKVREKAEEAAEERILDALLPPAKNNWGEEEEKEEISATRQKFRKKLREGELDDKEIEI  175 (443)
T ss_pred             HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhCCCccCCccccccchhhhHHHHHHHHHHHcCCcCCcEEEE
Confidence             1112222211                                                                     


Q ss_pred             -----------------------------------------------------------------------hcCCcEEEE
Q 011664          273 -----------------------------------------------------------------------TTSKSVILI  281 (480)
Q Consensus       273 -----------------------------------------------------------------------~~~~sII~I  281 (480)
                                                                                             +.+..||||
T Consensus       176 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~eA~~~l~~~e~~~lid~~~v~~~ai~~ae~~GIVfi  255 (443)
T PRK05201        176 EVAEAAPMMEIMGPPGMEEMTIQLQDMFGNLGPKKKKKRKLKVKEARKILIEEEAAKLIDMEEIKQEAIERVEQNGIVFI  255 (443)
T ss_pred             EecCCCCcccCCCCcchhHHHHHHHHHHHhhCCCCCceEEeEHHHHHHHHHHHHHHhccChHHHHHHHHHHHHcCCEEEE
Confidence                                                                                   124579999


Q ss_pred             ecccccccCccc-------ccchhhhhhhccccccc-----ccCCceEEEEe----cCCCccCcccccCCCceeEEEEcC
Q 011664          282 EDLDRFLVEKPA-------AVSLSGVLNFMDGVLNS-----CCFEERVMVFT----MNSKDHVDQALLRPGRIDVHIHFP  345 (480)
Q Consensus       282 DEiD~l~~~~~~-------~~~ls~lL~~ldg~~~~-----~~~~~~ivI~t----TN~~~~LD~aLlrpGRfd~~I~~~  345 (480)
                      ||||.++...++       ......||..++|-.-.     ...+.+++|++    ...|++|-|.|.-  ||..++.+.
T Consensus       256 DEiDKIa~~~~~~~~DvS~eGVQ~~LLki~EG~~v~~k~~~i~T~~ILFI~~GAF~~~kp~DlIPEl~G--R~Pi~v~L~  333 (443)
T PRK05201        256 DEIDKIAARGGSSGPDVSREGVQRDLLPLVEGSTVSTKYGMVKTDHILFIASGAFHVSKPSDLIPELQG--RFPIRVELD  333 (443)
T ss_pred             EcchhhcccCCCCCCCCCccchhcccccccccceeeecceeEECCceeEEecCCcCCCChhhccHHHhC--ccceEEECC
Confidence            999999864321       12345688888873211     12356677764    2467788888886  999999999


Q ss_pred             CCCHHHHHHHHHHHhccCCCCCchhHHHHHHhC---CCCCHHHHHHHHHHhh-------hcHHHHHHHHHHHHHhc
Q 011664          346 LCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNG---SSLSPAEIGELMIANR-------NSPSRALKSVITALQTD  411 (480)
Q Consensus       346 ~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~---~g~s~adI~~ll~~a~-------~~~~~al~~~i~~~~~~  411 (480)
                      .++.+++..|+..    ....+-.+...|+...   -.||...|.++...|.       .-..|.|+.+++.+-..
T Consensus       334 ~L~~~dL~~ILte----P~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtI~E~~L~d  405 (443)
T PRK05201        334 ALTEEDFVRILTE----PKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQVNEKTENIGARRLHTVMEKLLED  405 (443)
T ss_pred             CCCHHHHHHHhcC----ChhHHHHHHHHHHhhcCcEEEEcHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHHH
Confidence            9999998887631    1122333444554321   1467777777766543       44567888888877654

>TIGR00390 hslU ATP-dependent protease HslVU, ATPase subunit

Probab=99.44  E-value=3.5e-12  Score=132.33  Aligned_cols=215  Identities=16%  Similarity=0.255  Sum_probs=142.6

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-----C--
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-----D--  262 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-----~--  262 (480)
                      -|+|++++|+.+...+....++......++ ...|+++||+||||||||++|+++|..++.+|+.++.+.+.     +  
T Consensus        13 ~IiGQ~eAkk~lsvAl~n~~~r~~~~~~~~~e~~p~~ILLiGppG~GKT~lAraLA~~l~~~fi~vdat~~~e~g~vG~d   92 (441)
T TIGR00390        13 YIIGQDNAKKSVAIALRNRYRRSQLNEELKDEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRD   92 (441)
T ss_pred             hccCHHHHHHHHHHHHHhhhhhhccccccccccCCceEEEECCCCCCHHHHHHHHHHHhCCeEEEeecceeecCCcccCC
Confidence            378999999999877765433332211111 22457999999999999999999999999999999976432     2  


Q ss_pred             -hHHHHHHHH----------------------------------------------------------------------
Q 011664          263 -DADLKSLLL----------------------------------------------------------------------  271 (480)
Q Consensus       263 -~~~l~~l~~----------------------------------------------------------------------  271 (480)
                       ++.++.++.                                                                      
T Consensus        93 vE~i~r~l~e~A~~~i~~d~i~~~r~~a~~~ae~riv~~Ll~~~~~~~~~~~~~~~~~~~r~~~~~~l~~g~ldd~~iei  172 (441)
T TIGR00390        93 VESMVRDLTDAAVKLVKEEAIEKVRDRAEELAEERIVDVLLPPAKNQWGQTEQQQEPESAREAFRKKLREGELDDKEIEI  172 (441)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHhcCCccccccccccccchHHHHHHHHHHHhcCCccCcEEEE
Confidence             111222211                                                                      


Q ss_pred             -----------------------------------------------------------------------hhcCCcEEE
Q 011664          272 -----------------------------------------------------------------------QTTSKSVIL  280 (480)
Q Consensus       272 -----------------------------------------------------------------------~~~~~sII~  280 (480)
                                                                                             .+.+..|||
T Consensus       173 ~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ea~~~l~~~e~~~lid~~~v~~~a~~~~e~~GIVf  252 (441)
T TIGR00390       173 DVSAKMPSGIEIMAPPGMEEMTMQLQSLFQNLGGQKKKKRKLKIKDAKKALIAEEAAKLVDPEEIKQEAIDAVEQSGIIF  252 (441)
T ss_pred             eecCCCCCccccCCCcchhHHHhhHHHHHHhhcCCCCceEEeEHHHHHHHHHHHHHHhccChHHHHHHHHHHHHcCCEEE
Confidence                                                                                   113557999


Q ss_pred             EecccccccCcc-------cccchhhhhhhccccccc-----ccCCceEEEEec----CCCccCcccccCCCceeEEEEc
Q 011664          281 IEDLDRFLVEKP-------AAVSLSGVLNFMDGVLNS-----CCFEERVMVFTM----NSKDHVDQALLRPGRIDVHIHF  344 (480)
Q Consensus       281 IDEiD~l~~~~~-------~~~~ls~lL~~ldg~~~~-----~~~~~~ivI~tT----N~~~~LD~aLlrpGRfd~~I~~  344 (480)
                      |||||.++....       +......||..++|-.-.     ...+++++|++-    ..|++|=|.|.-  ||..++.+
T Consensus       253 iDEiDKIa~~~~~~~~DvS~eGVQ~~LLkilEGt~v~~k~~~v~T~~ILFI~~GAF~~~kp~DlIPEl~G--R~Pi~v~L  330 (441)
T TIGR00390       253 IDEIDKIAKKGESSGADVSREGVQRDLLPIVEGSTVNTKYGMVKTDHILFIAAGAFQLAKPSDLIPELQG--RFPIRVEL  330 (441)
T ss_pred             EEchhhhcccCCCCCCCCCccchhccccccccCceeeecceeEECCceeEEecCCcCCCChhhccHHHhC--ccceEEEC
Confidence            999999986431       112356688888873221     223556777642    357777788875  99999999


Q ss_pred             CCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhC---CCCCHHHHHHHHHHhh-------hcHHHHHHHHHHHHHhc
Q 011664          345 PLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNG---SSLSPAEIGELMIANR-------NSPSRALKSVITALQTD  411 (480)
Q Consensus       345 ~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~---~g~s~adI~~ll~~a~-------~~~~~al~~~i~~~~~~  411 (480)
                      ..++.+++..|+.    .....+-.+...|++..   -.||..-+.++...|.       .-..|.|+.+++.+-..
T Consensus       331 ~~L~~edL~rILt----eP~nsLikQy~~Lf~~egv~L~Ftd~Al~~IA~~A~~~N~~~~~iGAR~LrtilE~~l~d  403 (441)
T TIGR00390       331 QALTTDDFERILT----EPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAYNVNEKTENIGARRLHTVLERLLED  403 (441)
T ss_pred             CCCCHHHHHHHhc----CChhHHHHHHHHHHhhcCcEEEEeHHHHHHHHHHHHHhcccccccchhhHHHHHHHHHHH
Confidence            9999999887763    11223344555555432   1468877777766543       45567888888777554

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.

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.43  E-value=6.6e-13  Score=151.46  Aligned_cols=158  Identities=16%  Similarity=0.195  Sum_probs=111.8

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .+..++.++|.++..+.+.+.+.             ...+.+++|+||||||||++++++|..+          +.+++.
T Consensus       168 ~~~~~~~~igr~~ei~~~~~~l~-------------r~~~~n~lL~G~pGvGKT~l~~~la~~i~~~~~p~~l~~~~~~~  234 (852)
T TIGR03346       168 REGKLDPVIGRDEEIRRTIQVLS-------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIVNGDVPESLKNKRLLA  234 (852)
T ss_pred             hCCCCCcCCCcHHHHHHHHHHHh-------------cCCCCceEEEcCCCCCHHHHHHHHHHHHhccCCchhhcCCeEEE
Confidence            45678999999886666554332             1245678999999999999999999875          678898


Q ss_pred             EeCCCcCC--------hHHHHHHHHhh---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC
Q 011664          255 VDLSRVAD--------DADLKSLLLQT---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~~~---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      ++++.+..        +..++.++...   ..++|||||||+.+.+.+..... ....+.+.....   .....+|++|+
T Consensus       235 l~~~~l~a~~~~~g~~e~~l~~~l~~~~~~~~~~ILfIDEih~l~~~g~~~~~-~d~~~~Lk~~l~---~g~i~~IgaTt  310 (852)
T TIGR03346       235 LDMGALIAGAKYRGEFEERLKAVLNEVTKSEGQIILFIDELHTLVGAGKAEGA-MDAGNMLKPALA---RGELHCIGATT  310 (852)
T ss_pred             eeHHHHhhcchhhhhHHHHHHHHHHHHHhcCCCeEEEeccHHHhhcCCCCcch-hHHHHHhchhhh---cCceEEEEeCc
Confidence            88766531        23466666543   35899999999999853322211 122233333323   35577788777


Q ss_pred             CC-----ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhcc
Q 011664          324 SK-----DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       324 ~~-----~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~  362 (480)
                      ..     -.+|+|+.|  ||. .|.++.|+.+++..|++.+...
T Consensus       311 ~~e~r~~~~~d~al~r--Rf~-~i~v~~p~~~~~~~iL~~~~~~  351 (852)
T TIGR03346       311 LDEYRKYIEKDAALER--RFQ-PVFVDEPTVEDTISILRGLKER  351 (852)
T ss_pred             HHHHHHHhhcCHHHHh--cCC-EEEeCCCCHHHHHHHHHHHHHH
Confidence            55     347999999  996 5899999999999999876543

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.

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.42  E-value=7e-13  Score=150.80  Aligned_cols=151  Identities=17%  Similarity=0.217  Sum_probs=109.1

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEe
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVD  256 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~  256 (480)
                      -.++.++|.++..+.+.+.+..             ..+++++|+||||||||++|+++|..+          +..++.++
T Consensus       176 ~~~~~~igr~~ei~~~~~~L~r-------------~~~~n~lL~G~pGvGKTal~~~la~~i~~~~vp~~l~~~~i~~l~  242 (821)
T CHL00095        176 GNLDPVIGREKEIERVIQILGR-------------RTKNNPILIGEPGVGKTAIAEGLAQRIVNRDVPDILEDKLVITLD  242 (821)
T ss_pred             CCCCCCCCcHHHHHHHHHHHcc-------------cccCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEEee
Confidence            3578899999888887765432             245689999999999999999999876          47899999


Q ss_pred             CCCcC------C--hHHHHHHHHhh--cCCcEEEEecccccccCcccc--cchhhhhhhcccccccccCCceEEEEecCC
Q 011664          257 LSRVA------D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA--VSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       257 ~s~~~------~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~--~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      ++.+.      +  +..++.++...  ..++||||||||.+.+.....  ...+.+|.   ....   .+...+|++|+.
T Consensus       243 ~~~l~ag~~~~ge~e~rl~~i~~~~~~~~~~ILfiDEih~l~~~g~~~g~~~~a~lLk---p~l~---rg~l~~IgaTt~  316 (821)
T CHL00095        243 IGLLLAGTKYRGEFEERLKRIFDEIQENNNIILVIDEVHTLIGAGAAEGAIDAANILK---PALA---RGELQCIGATTL  316 (821)
T ss_pred             HHHHhccCCCccHHHHHHHHHHHHHHhcCCeEEEEecHHHHhcCCCCCCcccHHHHhH---HHHh---CCCcEEEEeCCH
Confidence            76543      2  33577777543  468899999999998654322  22233332   2222   345667777775


Q ss_pred             Cc-----cCcccccCCCceeEEEEcCCCCHHHHHHHHHHH
Q 011664          325 KD-----HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSY  359 (480)
Q Consensus       325 ~~-----~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~  359 (480)
                      .+     ..|++|.+  ||. .|.++.|+.++...|++..
T Consensus       317 ~ey~~~ie~D~aL~r--Rf~-~I~v~ep~~~e~~aILr~l  353 (821)
T CHL00095        317 DEYRKHIEKDPALER--RFQ-PVYVGEPSVEETIEILFGL  353 (821)
T ss_pred             HHHHHHHhcCHHHHh--cce-EEecCCCCHHHHHHHHHHH
Confidence            43     47999999  997 5899999999988887654

>COG2607 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=99.42  E-value=8.6e-12  Score=119.27  Aligned_cols=178  Identities=20%  Similarity=0.261  Sum_probs=139.2

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEE
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVY  253 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~  253 (480)
                      ....+|..+++.+.+|+|.+.+|+.+.+....|+++.         +-..+||||..|||||+|++|+-++.   |..++
T Consensus        47 ~L~pv~~~~~i~L~~l~Gvd~qk~~L~~NT~~F~~G~---------pANnVLLwGaRGtGKSSLVKA~~~e~~~~glrLV  117 (287)
T COG2607          47 YLEPVPDPDPIDLADLVGVDRQKEALVRNTEQFAEGL---------PANNVLLWGARGTGKSSLVKALLNEYADEGLRLV  117 (287)
T ss_pred             cccCCCCCCCcCHHHHhCchHHHHHHHHHHHHHHcCC---------cccceEEecCCCCChHHHHHHHHHHHHhcCCeEE
Confidence            4567888889999999999999999999888887652         44689999999999999999999876   56788


Q ss_pred             EEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc---
Q 011664          254 DVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ---  330 (480)
Q Consensus       254 ~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~---  330 (480)
                      .|+-.++.+-..+...+.....+-|||+||+--    ..+....-.|-..|||-.. ..+.+++|.+|+|+..-|..   
T Consensus       118 EV~k~dl~~Lp~l~~~Lr~~~~kFIlFcDDLSF----e~gd~~yK~LKs~LeG~ve-~rP~NVl~YATSNRRHLl~e~~~  192 (287)
T COG2607         118 EVDKEDLATLPDLVELLRARPEKFILFCDDLSF----EEGDDAYKALKSALEGGVE-GRPANVLFYATSNRRHLLPEDMK  192 (287)
T ss_pred             EEcHHHHhhHHHHHHHHhcCCceEEEEecCCCC----CCCchHHHHHHHHhcCCcc-cCCCeEEEEEecCCcccccHhhh
Confidence            888777777777778888888999999999752    1122334556677887665 45678888889997543321   


Q ss_pred             -----------------cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc
Q 011664          331 -----------------ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF  368 (480)
Q Consensus       331 -----------------aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~  368 (480)
                                       .+-=..||...+.|++|+.++..+|+..|.+..+....
T Consensus       193 dn~~~~~eih~~eaveEKlSlSDRFGLwL~F~~~~Q~~YL~~V~~~a~~~~l~~~  247 (287)
T COG2607         193 DNEGSTGEIHPSEAVEEKLSLSDRFGLWLSFYPCDQDEYLKIVDHYAKHFGLDIS  247 (287)
T ss_pred             hCCCcccccChhHHHHHhhchhhhcceeecccCCCHHHHHHHHHHHHHHcCCCCC
Confidence                             11112499999999999999999999999987766664

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

Probab=99.41  E-value=4.1e-12  Score=142.93  Aligned_cols=156  Identities=19%  Similarity=0.316  Sum_probs=110.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCC----CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRV----WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDAD  265 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~----~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~  265 (480)
                      ..|+|++++++.|.+.+...        +.|..    +...+||+||||||||++|+++|..++.+++.++++++.....
T Consensus       454 ~~v~GQ~~ai~~l~~~i~~~--------~~g~~~~~~p~~~~lf~Gp~GvGKT~lA~~la~~l~~~~~~~d~se~~~~~~  525 (731)
T TIGR02639       454 AKIFGQDEAIDSLVSSIKRS--------RAGLGNPNKPVGSFLFTGPTGVGKTELAKQLAEALGVHLERFDMSEYMEKHT  525 (731)
T ss_pred             cceeCcHHHHHHHHHHHHHH--------hcCCCCCCCCceeEEEECCCCccHHHHHHHHHHHhcCCeEEEeCchhhhccc
Confidence            35677777777777655432        22321    2335899999999999999999999999999999887654211


Q ss_pred             -------------------HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccc-c-----cccCCceEEEE
Q 011664          266 -------------------LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-N-----SCCFEERVMVF  320 (480)
Q Consensus       266 -------------------l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~-----~~~~~~~ivI~  320 (480)
                                         +...+ +..+.+||+|||||.+.     ....+.|++.||.-. .     .....+.+||+
T Consensus       526 ~~~lig~~~gyvg~~~~~~l~~~~-~~~p~~VvllDEieka~-----~~~~~~Ll~~ld~g~~~d~~g~~vd~~~~iii~  599 (731)
T TIGR02639       526 VSRLIGAPPGYVGFEQGGLLTEAV-RKHPHCVLLLDEIEKAH-----PDIYNILLQVMDYATLTDNNGRKADFRNVILIM  599 (731)
T ss_pred             HHHHhcCCCCCcccchhhHHHHHH-HhCCCeEEEEechhhcC-----HHHHHHHHHhhccCeeecCCCcccCCCCCEEEE
Confidence                               22212 23466999999999774     234566777776321 1     01134678999


Q ss_pred             ecCCCc-------------------------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          321 TMNSKD-------------------------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       321 tTN~~~-------------------------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      |||...                         .+.|.++.  |||.+|.|.+.+.++..+|++..+.
T Consensus       600 Tsn~g~~~~~~~~~~f~~~~~~~~~~~~~~~~f~pef~~--Rid~Vi~F~pLs~e~l~~Iv~~~L~  663 (731)
T TIGR02639       600 TSNAGASEMSKPPIGFGSENVESKSDKAIKKLFSPEFRN--RLDAIIHFNPLSEEVLEKIVQKFVD  663 (731)
T ss_pred             CCCcchhhhhhccCCcchhhhHHHHHHHHHhhcChHHHh--cCCeEEEcCCCCHHHHHHHHHHHHH
Confidence            998531                         14566766  9999999999999999999998875

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=99.40  E-value=2.2e-12  Score=137.24  Aligned_cols=188  Identities=14%  Similarity=0.230  Sum_probs=119.2

Q ss_pred             CCCccccc-cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCC
Q 011664          186 PSTFDTIS-METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSR  259 (480)
Q Consensus       186 ~~~~~~i~-g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~  259 (480)
                      +.||++.+ |..+ .. ....+..+...+      |.. ..+++||||+|||||+|++|+++++     +..++++++.+
T Consensus       111 ~~tFdnFv~g~~n-~~-A~~aa~~~a~~~------~~~-~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~  181 (450)
T PRK14087        111 ENTFENFVIGSSN-EQ-AFIAVQTVSKNP------GIS-YNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDE  181 (450)
T ss_pred             ccchhcccCCCcH-HH-HHHHHHHHHhCc------Ccc-cCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHH
Confidence            46888875 4433 22 223333332222      222 2479999999999999999999954     56788888765


Q ss_pred             cCCh---------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC-CCcc--
Q 011664          260 VADD---------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKDH--  327 (480)
Q Consensus       260 ~~~~---------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~~--  327 (480)
                      +...         ..+...........+|+|||++.+.......   .+|...++....   .+. .+|+|+| .|..  
T Consensus       182 f~~~~~~~l~~~~~~~~~~~~~~~~~dvLiIDDiq~l~~k~~~~---e~lf~l~N~~~~---~~k-~iIltsd~~P~~l~  254 (450)
T PRK14087        182 FARKAVDILQKTHKEIEQFKNEICQNDVLIIDDVQFLSYKEKTN---EIFFTIFNNFIE---NDK-QLFFSSDKSPELLN  254 (450)
T ss_pred             HHHHHHHHHHHhhhHHHHHHHHhccCCEEEEeccccccCCHHHH---HHHHHHHHHHHH---cCC-cEEEECCCCHHHHh
Confidence            4321         1222233344678899999999885433333   344444444433   233 3555655 4433  


Q ss_pred             -CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCC--CCchhH-HHHHHhCCCCCHHHHHHHHHH
Q 011664          328 -VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDH--KLFPQV-EEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       328 -LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~--~l~~~i-~~l~~~~~g~s~adI~~ll~~  392 (480)
                       +++.|++  ||.  ..+.+..|+.++|.+|+++.+...+.  .+.+++ +.|+... +-++..+..+|..
T Consensus       255 ~l~~rL~S--R~~~Gl~~~L~~pd~e~r~~iL~~~~~~~gl~~~l~~evl~~Ia~~~-~gd~R~L~gaL~~  322 (450)
T PRK14087        255 GFDNRLIT--RFNMGLSIAIQKLDNKTATAIIKKEIKNQNIKQEVTEEAINFISNYY-SDDVRKIKGSVSR  322 (450)
T ss_pred             hccHHHHH--HHhCCceeccCCcCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHcc-CCCHHHHHHHHHH
Confidence             5789999  985  88999999999999999999876543  455554 4454443 4566666665543

>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]

Probab=99.37  E-value=3.3e-12  Score=136.02  Aligned_cols=162  Identities=16%  Similarity=0.333  Sum_probs=123.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc-------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD-------------  251 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~-------------  251 (480)
                      +|.+|++++|++.+.+.|...+..            .....+|||.||-|||||++|+.+|..+++.             
T Consensus        11 RP~~F~evvGQe~v~~~L~nal~~------------~ri~hAYlfsG~RGvGKTt~Ari~AkalNC~~~~~~ePC~~C~~   78 (515)
T COG2812          11 RPKTFDDVVGQEHVVKTLSNALEN------------GRIAHAYLFSGPRGVGKTTIARILAKALNCENGPTAEPCGKCIS   78 (515)
T ss_pred             CcccHHHhcccHHHHHHHHHHHHh------------CcchhhhhhcCCCCcCchhHHHHHHHHhcCCCCCCCCcchhhhh
Confidence            478999999999999998876652            1234589999999999999999999977553             


Q ss_pred             -----------EEEEeCCCcCChHHHHHHHHhhc------CCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          252 -----------VYDVDLSRVADDADLKSLLLQTT------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       252 -----------~~~i~~s~~~~~~~l~~l~~~~~------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                 ++.+|..+-.+-.++|.+..+..      ...|.+|||++.+.     ....+.||..++.     .+.
T Consensus        79 Ck~I~~g~~~DviEiDaASn~gVddiR~i~e~v~y~P~~~ryKVyiIDEvHMLS-----~~afNALLKTLEE-----PP~  148 (515)
T COG2812          79 CKEINEGSLIDVIEIDAASNTGVDDIREIIEKVNYAPSEGRYKVYIIDEVHMLS-----KQAFNALLKTLEE-----PPS  148 (515)
T ss_pred             hHhhhcCCcccchhhhhhhccChHHHHHHHHHhccCCccccceEEEEecHHhhh-----HHHHHHHhccccc-----Ccc
Confidence                       22222222223455777765542      45799999999883     4456778877753     356


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                      .+++|++|..+..+++.+++  |+. ++.|...+.++....+...+..++...+++.
T Consensus       149 hV~FIlATTe~~Kip~TIlS--Rcq-~f~fkri~~~~I~~~L~~i~~~E~I~~e~~a  202 (515)
T COG2812         149 HVKFILATTEPQKIPNTILS--RCQ-RFDFKRLDLEEIAKHLAAILDKEGINIEEDA  202 (515)
T ss_pred             CeEEEEecCCcCcCchhhhh--ccc-cccccCCCHHHHHHHHHHHHHhcCCccCHHH
Confidence            78899999999999999999  995 8899999999988889999887777766544

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=99.37  E-value=3.2e-11  Score=124.33  Aligned_cols=181  Identities=14%  Similarity=0.160  Sum_probs=121.4

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD------------  251 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~------------  251 (480)
                      .||..+++|+|++++++.+...+..           | ..+..+||+||+|+|||++|..+|+.+.+.            
T Consensus        17 ~~P~~~~~l~Gh~~a~~~L~~a~~~-----------g-rl~ha~L~~G~~G~GKttlA~~lA~~Llc~~~~~~~~~~~~~   84 (351)
T PRK09112         17 PSPSENTRLFGHEEAEAFLAQAYRE-----------G-KLHHALLFEGPEGIGKATLAFHLANHILSHPDPAEAPETLAD   84 (351)
T ss_pred             CCCCchhhccCcHHHHHHHHHHHHc-----------C-CCCeeEeeECCCCCCHHHHHHHHHHHHcCCCccccCccccCC
Confidence            4899999999999999988865431           2 245589999999999999999999977431            


Q ss_pred             ------------------EEEEeCC---------CcCChHHHHHHH---Hhh---cCCcEEEEecccccccCcccccchh
Q 011664          252 ------------------VYDVDLS---------RVADDADLKSLL---LQT---TSKSVILIEDLDRFLVEKPAAVSLS  298 (480)
Q Consensus       252 ------------------~~~i~~s---------~~~~~~~l~~l~---~~~---~~~sII~IDEiD~l~~~~~~~~~ls  298 (480)
                                        ++.+...         ...+-.+++.+.   ...   ....|++|||+|.+-     ....+
T Consensus        85 ~~~~c~~c~~i~~~~hPdl~~l~~~~~~~~~~~~~~I~vd~iR~l~~~l~~~~~~g~~rVviIDeAd~l~-----~~aan  159 (351)
T PRK09112         85 PDPASPVWRQIAQGAHPNLLHITRPFDEKTGKFKTAITVDEIRRVGHFLSQTSGDGNWRIVIIDPADDMN-----RNAAN  159 (351)
T ss_pred             CCCCCHHHHHHHcCCCCCEEEeecccccccccccccCCHHHHHHHHHHhhhccccCCceEEEEEchhhcC-----HHHHH
Confidence                              1112110         011123344432   221   245799999999883     33456


Q ss_pred             hhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHh
Q 011664          299 GVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQN  377 (480)
Q Consensus       299 ~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~  377 (480)
                      .||..++.-     ....++|+.|+.|+.+.|.+++  |+ .++.|++|+.++...++.......+  +.++ +..++..
T Consensus       160 aLLk~LEEp-----p~~~~fiLit~~~~~llptIrS--Rc-~~i~l~pl~~~~~~~~L~~~~~~~~--~~~~~~~~i~~~  229 (351)
T PRK09112        160 AILKTLEEP-----PARALFILISHSSGRLLPTIRS--RC-QPISLKPLDDDELKKALSHLGSSQG--SDGEITEALLQR  229 (351)
T ss_pred             HHHHHHhcC-----CCCceEEEEECChhhccHHHHh--hc-cEEEecCCCHHHHHHHHHHhhcccC--CCHHHHHHHHHH
Confidence            788888642     3456677778889999999998  98 5999999999999888887432211  2233 3444444


Q ss_pred             CCCCCHHHHHHHHHH
Q 011664          378 GSSLSPAEIGELMIA  392 (480)
Q Consensus       378 ~~g~s~adI~~ll~~  392 (480)
                      . +-+|....+++..
T Consensus       230 s-~G~pr~Al~ll~~  243 (351)
T PRK09112        230 S-KGSVRKALLLLNY  243 (351)
T ss_pred             c-CCCHHHHHHHHhc
Confidence            3 5666665555543

>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=99.36  E-value=3.9e-12  Score=111.55  Aligned_cols=117  Identities=24%  Similarity=0.364  Sum_probs=81.1

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHH-----------HHHHhhcCCcEEEEecccccc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLK-----------SLLLQTTSKSVILIEDLDRFL  288 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~-----------~l~~~~~~~sII~IDEiD~l~  288 (480)
                      ..++++++||||||||++++++++.+   +.+++.++++.........           ........+.+|+|||++.+.
T Consensus        18 ~~~~v~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lilDe~~~~~   97 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLS   97 (151)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHhhcCCCCeEEEehhhhhhhhHHHHHhhhhhHhHHHHhhccCCCeEEEEeChhhhh
Confidence            34589999999999999999999998   8899999987765433221           112233578999999999772


Q ss_pred             cCcccccchhhhhhhccccccc-ccCCceEEEEecCCCc--cCcccccCCCceeEEEEcCC
Q 011664          289 VEKPAAVSLSGVLNFMDGVLNS-CCFEERVMVFTMNSKD--HVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       289 ~~~~~~~~ls~lL~~ldg~~~~-~~~~~~ivI~tTN~~~--~LD~aLlrpGRfd~~I~~~~  346 (480)
                      .     ....+++..+...... ....+..+|++||...  .+++.+..  ||+.++.+++
T Consensus        98 ~-----~~~~~~~~~i~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~~--r~~~~i~~~~  151 (151)
T cd00009          98 R-----GAQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYD--RLDIRIVIPL  151 (151)
T ss_pred             H-----HHHHHHHHHHHhcCceeccCCCeEEEEecCccccCCcChhHHh--hhccEeecCC
Confidence            1     1224444444433220 0024567788888776  77888888  9998888763

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.

>TIGR02903 spore_lon_C ATP-dependent protease, Lon family

Probab=99.36  E-value=1.5e-11  Score=135.44  Aligned_cols=166  Identities=16%  Similarity=0.231  Sum_probs=108.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|.+|++++|.+...+.+...+.             .+.+..++|+||||||||++|+++++..          +.+|+.
T Consensus       149 rp~~~~~iiGqs~~~~~l~~~ia-------------~~~~~~vlL~Gp~GtGKTTLAr~i~~~~~~~~~~~~~~~~~fv~  215 (615)
T TIGR02903       149 RPRAFSEIVGQERAIKALLAKVA-------------SPFPQHIILYGPPGVGKTTAARLALEEAKKLKHTPFAEDAPFVE  215 (615)
T ss_pred             CcCcHHhceeCcHHHHHHHHHHh-------------cCCCCeEEEECCCCCCHHHHHHHHHHhhhhccCCcccCCCCeEE
Confidence            57899999999998887654432             1234579999999999999999998755          356888


Q ss_pred             EeCCCcCCh-HHH----------------HHHHHh------------hcCCcEEEEecccccccCcccccchhhhhhhcc
Q 011664          255 VDLSRVADD-ADL----------------KSLLLQ------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD  305 (480)
Q Consensus       255 i~~s~~~~~-~~l----------------~~l~~~------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld  305 (480)
                      +++..+..+ ..+                +..+..            ..+..+|||||++.+-.     .....|+..|+
T Consensus       216 i~~~~l~~d~~~i~~~llg~~~~~~~~~a~~~l~~~gl~~~~~g~v~~asgGvL~LDEi~~Ld~-----~~Q~~Ll~~Le  290 (615)
T TIGR02903       216 VDGTTLRWDPREVTNPLLGSVHDPIYQGARRDLAETGVPEPKTGLVTDAHGGVLFIDEIGELDP-----LLQNKLLKVLE  290 (615)
T ss_pred             EechhccCCHHHHhHHhcCCccHHHHHHHHHHHHHcCCCchhcCchhhcCCCeEEEeccccCCH-----HHHHHHHHHHh
Confidence            887654211 111                011111            12457999999998732     12233444432


Q ss_pred             cc--------c---------------ccccCCceEEEE-ecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          306 GV--------L---------------NSCCFEERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       306 g~--------~---------------~~~~~~~~ivI~-tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      .-        +               ........++|+ ||+.++.++++|++  ||. .+++++++.++...|++..+.
T Consensus       291 ~~~v~~~~~~~~~~~~~~~~~ik~~~~~~~~~~~VLI~aTt~~~~~l~~aLrS--R~~-~i~~~pls~edi~~Il~~~a~  367 (615)
T TIGR02903       291 DKRVEFSSSYYDPDDPNVPKYIKKLFEEGAPADFVLIGATTRDPEEINPALRS--RCA-EVFFEPLTPEDIALIVLNAAE  367 (615)
T ss_pred             hCeEEeecceeccCCcccchhhhhhcccCccceEEEEEeccccccccCHHHHh--cee-EEEeCCCCHHHHHHHHHHHHH
Confidence            10        0               000112345555 56778899999998  997 678999999999999999876


Q ss_pred             cCCCCCchhH
Q 011664          362 LKDHKLFPQV  371 (480)
Q Consensus       362 ~~~~~l~~~i  371 (480)
                      ..+..+.+++
T Consensus       368 ~~~v~ls~ea  377 (615)
T TIGR02903       368 KINVHLAAGV  377 (615)
T ss_pred             HcCCCCCHHH
Confidence            5443344433

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.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=99.35  E-value=4.5e-11  Score=123.82  Aligned_cols=152  Identities=14%  Similarity=0.230  Sum_probs=110.9

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-------------  250 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------  250 (480)
                      .+|+++++|+|++++++.+...+..           | ..+.++||+||+|+||+++|.++|+.+-+             
T Consensus        13 ~~P~~~~~iiGq~~~~~~L~~~~~~-----------~-rl~HA~Lf~Gp~G~GK~~lA~~~A~~Llc~~~~~~~~~~~~~   80 (365)
T PRK07471         13 PHPRETTALFGHAAAEAALLDAYRS-----------G-RLHHAWLIGGPQGIGKATLAYRMARFLLATPPPGGDGAVPPP   80 (365)
T ss_pred             CCCCchhhccChHHHHHHHHHHHHc-----------C-CCCceEEEECCCCCCHHHHHHHHHHHHhCCCCCCCCcccccc
Confidence            4899999999999999998865542           2 34668999999999999999999986521             


Q ss_pred             ---------------------cEEEEeCC--C-------cCChHHHHHHHHhh------cCCcEEEEecccccccCcccc
Q 011664          251 ---------------------DVYDVDLS--R-------VADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAA  294 (480)
Q Consensus       251 ---------------------~~~~i~~s--~-------~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~  294 (480)
                                           +++.+...  +       ...-.+++.+....      ..+.|++|||+|.+     +.
T Consensus        81 ~~l~~~~~c~~c~~i~~~~HPDl~~i~~~~~~~~~~~~~~I~VdqiR~l~~~~~~~~~~~~~kVviIDead~m-----~~  155 (365)
T PRK07471         81 TSLAIDPDHPVARRIAAGAHGGLLTLERSWNEKGKRLRTVITVDEVRELISFFGLTAAEGGWRVVIVDTADEM-----NA  155 (365)
T ss_pred             ccccCCCCChHHHHHHccCCCCeEEEecccccccccccccccHHHHHHHHHHhCcCcccCCCEEEEEechHhc-----CH
Confidence                                 22333221  1       11123455544321      35789999999987     23


Q ss_pred             cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          295 VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       295 ~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                      ...+.||..++..     ....++|++|+.++.+.|.+++  |+ ..+.|++|+.++-.+++....
T Consensus       156 ~aanaLLK~LEep-----p~~~~~IL~t~~~~~llpti~S--Rc-~~i~l~~l~~~~i~~~L~~~~  213 (365)
T PRK07471        156 NAANALLKVLEEP-----PARSLFLLVSHAPARLLPTIRS--RC-RKLRLRPLAPEDVIDALAAAG  213 (365)
T ss_pred             HHHHHHHHHHhcC-----CCCeEEEEEECCchhchHHhhc--cc-eEEECCCCCHHHHHHHHHHhc
Confidence            4556788777532     3456788899999999999988  88 489999999999888887754

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=99.35  E-value=1.4e-11  Score=135.93  Aligned_cols=166  Identities=15%  Similarity=0.202  Sum_probs=110.6

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeCC
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDLS  258 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~s  258 (480)
                      .+.|.+-++..++|...+...+..        ..+...++++||||||||++++.+.+++          .+.+++|+|.
T Consensus       754 PD~LPhREeEIeeLasfL~paIkg--------sgpnnvLYIyG~PGTGKTATVK~VLrELqeeaeqk~lp~f~vVYINCm  825 (1164)
T PTZ00112        754 PKYLPCREKEIKEVHGFLESGIKQ--------SGSNQILYISGMPGTGKTATVYSVIQLLQHKTKQKLLPSFNVFEINGM  825 (1164)
T ss_pred             CCcCCChHHHHHHHHHHHHHHHhc--------CCCCceEEEECCCCCCHHHHHHHHHHHHHHHHhhccCCCceEEEEeCC
Confidence            367888888888888777665543        1123345799999999999999998765          2567899986


Q ss_pred             CcCChHH-----------------------HHHHHHhh----cCCcEEEEecccccccCcccccchhhhhhhcccccccc
Q 011664          259 RVADDAD-----------------------LKSLLLQT----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSC  311 (480)
Q Consensus       259 ~~~~~~~-----------------------l~~l~~~~----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~  311 (480)
                      .+.....                       +..+|...    ....||+|||||.+...  .+..   |++.++....  
T Consensus       826 ~Lstp~sIYqvI~qqL~g~~P~~GlsS~evLerLF~~L~k~~r~v~IIILDEID~L~kK--~QDV---LYnLFR~~~~--  898 (1164)
T PTZ00112        826 NVVHPNAAYQVLYKQLFNKKPPNALNSFKILDRLFNQNKKDNRNVSILIIDEIDYLITK--TQKV---LFTLFDWPTK--  898 (1164)
T ss_pred             ccCCHHHHHHHHHHHHcCCCCCccccHHHHHHHHHhhhhcccccceEEEeehHhhhCcc--HHHH---HHHHHHHhhc--
Confidence            5543221                       22333322    23469999999999753  2223   3444432221  


Q ss_pred             cCCceEEEEecCC---CccCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          312 CFEERVMVFTMNS---KDHVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       312 ~~~~~ivI~tTN~---~~~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                      .....+||+++|.   ++.|+|.+.+  ||. ..|.|++++.+++..|++..+......+.+++
T Consensus       899 s~SKLiLIGISNdlDLperLdPRLRS--RLg~eeIvF~PYTaEQL~dILk~RAe~A~gVLdDdA  960 (1164)
T PTZ00112        899 INSKLVLIAISNTMDLPERLIPRCRS--RLAFGRLVFSPYKGDEIEKIIKERLENCKEIIDHTA  960 (1164)
T ss_pred             cCCeEEEEEecCchhcchhhhhhhhh--ccccccccCCCCCHHHHHHHHHHHHHhCCCCCCHHH
Confidence            1345667778874   6778899988  776 35899999999999999988764333344443

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

Probab=99.34  E-value=4.2e-12  Score=127.36  Aligned_cols=148  Identities=21%  Similarity=0.339  Sum_probs=99.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc---EEEEeCCCcC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD---VYDVDLSRVA  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~~i~~s~~~  261 (480)
                      +|.+++|.+|++.+... ...+...+..       +  .-.+++||||||||||+||+.||+....+   |+.++...- 
T Consensus       133 RPktL~dyvGQ~hlv~q-~gllrs~ieq-------~--~ipSmIlWGppG~GKTtlArlia~tsk~~SyrfvelSAt~a-  201 (554)
T KOG2028|consen  133 RPKTLDDYVGQSHLVGQ-DGLLRSLIEQ-------N--RIPSMILWGPPGTGKTTLARLIASTSKKHSYRFVELSATNA-  201 (554)
T ss_pred             CcchHHHhcchhhhcCc-chHHHHHHHc-------C--CCCceEEecCCCCchHHHHHHHHhhcCCCceEEEEEecccc-
Confidence            57889999998876654 2223333222       1  12379999999999999999999877554   555554432 


Q ss_pred             ChHHHHHHHHhh-------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEe-c-CCCccCcccc
Q 011664          262 DDADLKSLLLQT-------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFT-M-NSKDHVDQAL  332 (480)
Q Consensus       262 ~~~~l~~l~~~~-------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~t-T-N~~~~LD~aL  332 (480)
                      +..+++.+|.++       ..+.|||||||+.+-  +..+   ..||-.+   .    .+.+++|++ | |..-.|..||
T Consensus       202 ~t~dvR~ife~aq~~~~l~krkTilFiDEiHRFN--ksQQ---D~fLP~V---E----~G~I~lIGATTENPSFqln~aL  269 (554)
T KOG2028|consen  202 KTNDVRDIFEQAQNEKSLTKRKTILFIDEIHRFN--KSQQ---DTFLPHV---E----NGDITLIGATTENPSFQLNAAL  269 (554)
T ss_pred             chHHHHHHHHHHHHHHhhhcceeEEEeHHhhhhh--hhhh---hccccee---c----cCceEEEecccCCCccchhHHH
Confidence            345678888554       467999999999883  2222   2233222   1    345667774 4 5557899999


Q ss_pred             cCCCceeEEEEcCCCCHHHHHHHHHH
Q 011664          333 LRPGRIDVHIHFPLCDFSSFKTLASS  358 (480)
Q Consensus       333 lrpGRfd~~I~~~~p~~~~r~~il~~  358 (480)
                      ++  |+- ++.+...+.+....|+.+
T Consensus       270 lS--RC~-VfvLekL~~n~v~~iL~r  292 (554)
T KOG2028|consen  270 LS--RCR-VFVLEKLPVNAVVTILMR  292 (554)
T ss_pred             Hh--ccc-eeEeccCCHHHHHHHHHH
Confidence            99  884 667777777777777766

>PRK09087 hypothetical protein; Validated

Probab=99.33  E-value=1.7e-11  Score=119.11  Aligned_cols=132  Identities=14%  Similarity=0.154  Sum_probs=87.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD  305 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld  305 (480)
                      .++||||+|||||||+++++...+..++.  ...+.. .    .+... ...+|+|||+|.+.   ...   .+|+..++
T Consensus        46 ~l~l~G~~GsGKThLl~~~~~~~~~~~i~--~~~~~~-~----~~~~~-~~~~l~iDDi~~~~---~~~---~~lf~l~n  111 (226)
T PRK09087         46 VVVLAGPVGSGKTHLASIWREKSDALLIH--PNEIGS-D----AANAA-AEGPVLIEDIDAGG---FDE---TGLFHLIN  111 (226)
T ss_pred             eEEEECCCCCCHHHHHHHHHHhcCCEEec--HHHcch-H----HHHhh-hcCeEEEECCCCCC---CCH---HHHHHHHH
Confidence            49999999999999999999987665433  322211 1    11111 22589999999762   122   34555554


Q ss_pred             cccccccCCceEEEEecCCCc--c-CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHH
Q 011664          306 GVLNSCCFEERVMVFTMNSKD--H-VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQ  376 (480)
Q Consensus       306 g~~~~~~~~~~ivI~tTN~~~--~-LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~  376 (480)
                      .+..   .+..+|+.++..|.  . ..++|++  |+.  ..+++..|+.+.+.+++++.+...+..+.+++ +.|+.
T Consensus       112 ~~~~---~g~~ilits~~~p~~~~~~~~dL~S--Rl~~gl~~~l~~pd~e~~~~iL~~~~~~~~~~l~~ev~~~La~  183 (226)
T PRK09087        112 SVRQ---AGTSLLMTSRLWPSSWNVKLPDLKS--RLKAATVVEIGEPDDALLSQVIFKLFADRQLYVDPHVVYYLVS  183 (226)
T ss_pred             HHHh---CCCeEEEECCCChHHhccccccHHH--HHhCCceeecCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence            4443   23344444444443  2 3688999  996  89999999999999999999877666666554 33443

>PRK13407 bchI magnesium chelatase subunit I; Provisional

Probab=99.31  E-value=3.3e-11  Score=123.16  Aligned_cols=157  Identities=16%  Similarity=0.178  Sum_probs=101.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-------CCc--EEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-------SYD--VYDV  255 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-------~~~--~~~i  255 (480)
                      .|.+|++|+|++++++.+.-.+..             +-..++||+||||||||++|+++|+.+       +.+  +..+
T Consensus         3 ~~~~f~~i~Gq~~~~~~l~~~~~~-------------~~~~~vLl~G~pG~gKT~lar~la~llP~~~~~e~~~~~~~~~   69 (334)
T PRK13407          3 KPFPFSAIVGQEEMKQAMVLTAID-------------PGIGGVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARP   69 (334)
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHhc-------------cCCCcEEEEcCCCCCHHHHHHHHHHHCCCcchhcccccccCcc
Confidence            467899999999999987643221             112479999999999999999999987       331  1111


Q ss_pred             eCC----------------------------CcCChHHHHHHHHh-----------hcCCcEEEEecccccccCcccccc
Q 011664          256 DLS----------------------------RVADDADLKSLLLQ-----------TTSKSVILIEDLDRFLVEKPAAVS  296 (480)
Q Consensus       256 ~~s----------------------------~~~~~~~l~~l~~~-----------~~~~sII~IDEiD~l~~~~~~~~~  296 (480)
                      ...                            .+.+.-.+...+..           .....+||+|||+.+.     ...
T Consensus        70 ~~~~~~~~~~~~~~~~~~~p~~~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~l~~A~~GiL~lDEInrl~-----~~~  144 (334)
T PRK13407         70 EDCPEWAHVSSTTMIERPTPVVDLPLGVTEDRVVGALDIERALTRGEKAFEPGLLARANRGYLYIDEVNLLE-----DHI  144 (334)
T ss_pred             cCCcccccccCCcccccCCccccCCCCCCcceeecchhhhhhhhcCCeeecCCceEEcCCCeEEecChHhCC-----HHH
Confidence            100                            01222222222110           1234699999999873     345


Q ss_pred             hhhhhhhccccc---c-----cccCCceEEEEecCCCc-cCcccccCCCceeEEEEcCCCCH-HHHHHHHHHHhc
Q 011664          297 LSGVLNFMDGVL---N-----SCCFEERVMVFTMNSKD-HVDQALLRPGRIDVHIHFPLCDF-SSFKTLASSYLG  361 (480)
Q Consensus       297 ls~lL~~ldg~~---~-----~~~~~~~ivI~tTN~~~-~LD~aLlrpGRfd~~I~~~~p~~-~~r~~il~~~l~  361 (480)
                      ++.|++.|+.-.   .     .......++|+|+|..+ .+.++|+.  ||...|.+++|.. +++.+++.+...
T Consensus       145 q~~Lle~mee~~v~v~r~G~~~~~p~rfiviAt~NP~e~~l~~aLld--RF~~~v~v~~~~~~~e~~~il~~~~~  217 (334)
T PRK13407        145 VDLLLDVAQSGENVVEREGLSIRHPARFVLVGSGNPEEGELRPQLLD--RFGLSVEVRSPRDVETRVEVIRRRDA  217 (334)
T ss_pred             HHHHHHHHHcCCeEEEECCeEEecCCCEEEEecCCcccCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHhhc
Confidence            566777764211   0     01123345666777544 58999999  9999999999988 889999987643

>PRK05564 DNA polymerase III subunit delta'; Validated

Probab=99.30  E-value=1.3e-10  Score=118.11  Aligned_cols=148  Identities=16%  Similarity=0.250  Sum_probs=108.2

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------cEEEEeCC-
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------DVYDVDLS-  258 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------~~~~i~~s-  258 (480)
                      +|++|+|++.+++.+...+.            ....+..|||+||+|+|||++|+++|+.+-+        +++.+... 
T Consensus         2 ~~~~i~g~~~~~~~l~~~~~------------~~~~~ha~Lf~G~~G~Gk~~la~~~a~~l~c~~~~~~h~D~~~~~~~~   69 (313)
T PRK05564          2 SFHTIIGHENIKNRIKNSII------------KNRFSHAHIIVGEDGIGKSLLAKEIALKILGKSQQREYVDIIEFKPIN   69 (313)
T ss_pred             ChhhccCcHHHHHHHHHHHH------------cCCCCceEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCeEEecccc
Confidence            69999999999998876552            1234568999999999999999999996522        44444431 


Q ss_pred             -CcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCccc
Q 011664          259 -RVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQA  331 (480)
Q Consensus       259 -~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~a  331 (480)
                       .-.+-.+++.+....      ....|++|||+|.+.     ....+.||..++.-     +++.++|++|+.++.+-|.
T Consensus        70 ~~~i~v~~ir~~~~~~~~~p~~~~~kv~iI~~ad~m~-----~~a~naLLK~LEep-----p~~t~~il~~~~~~~ll~T  139 (313)
T PRK05564         70 KKSIGVDDIRNIIEEVNKKPYEGDKKVIIIYNSEKMT-----EQAQNAFLKTIEEP-----PKGVFIILLCENLEQILDT  139 (313)
T ss_pred             CCCCCHHHHHHHHHHHhcCcccCCceEEEEechhhcC-----HHHHHHHHHHhcCC-----CCCeEEEEEeCChHhCcHH
Confidence             122334566665422      245799999999873     23456788888642     4567788888889999999


Q ss_pred             ccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          332 LLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       332 LlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                      +++  |+. .++|+.|+.++....+....
T Consensus       140 I~S--Rc~-~~~~~~~~~~~~~~~l~~~~  165 (313)
T PRK05564        140 IKS--RCQ-IYKLNRLSKEEIEKFISYKY  165 (313)
T ss_pred             HHh--hce-eeeCCCcCHHHHHHHHHHHh
Confidence            999  884 99999999998877776554

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=99.30  E-value=4.7e-11  Score=136.40  Aligned_cols=161  Identities=20%  Similarity=0.350  Sum_probs=111.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADL  266 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l  266 (480)
                      ..|+|++.+.+.+.+.+......-   .. ...+...+||+||||||||++|+++|..+   +.+++.++++.+.....+
T Consensus       565 ~~v~GQ~~av~~v~~~i~~~~~gl---~~-~~~p~~~~Lf~Gp~GvGKt~lA~~La~~l~~~~~~~i~~d~s~~~~~~~~  640 (852)
T TIGR03346       565 ERVVGQDEAVEAVSDAIRRSRAGL---SD-PNRPIGSFLFLGPTGVGKTELAKALAEFLFDDEDAMVRIDMSEYMEKHSV  640 (852)
T ss_pred             cccCCChHHHHHHHHHHHHHhccC---CC-CCCCCeEEEEEcCCCCCHHHHHHHHHHHhcCCCCcEEEEechhhcccchH
Confidence            568999999999888776542110   00 01133468999999999999999999977   468999999876543333


Q ss_pred             HHHH------------------HhhcCCcEEEEecccccccCcccccchhhhhhhcc-cccc-----cccCCceEEEEec
Q 011664          267 KSLL------------------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-GVLN-----SCCFEERVMVFTM  322 (480)
Q Consensus       267 ~~l~------------------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-g~~~-----~~~~~~~ivI~tT  322 (480)
                      ..++                  .+....+||+|||||.+-     ....+.|++.|+ |...     .....+.+||+||
T Consensus       641 ~~l~g~~~g~~g~~~~g~l~~~v~~~p~~vlllDeieka~-----~~v~~~Ll~~l~~g~l~d~~g~~vd~rn~iiI~TS  715 (852)
T TIGR03346       641 ARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAH-----PDVFNVLLQVLDDGRLTDGQGRTVDFRNTVIIMTS  715 (852)
T ss_pred             HHhcCCCCCccCcccccHHHHHHHcCCCcEEEEeccccCC-----HHHHHHHHHHHhcCceecCCCeEEecCCcEEEEeC
Confidence            2221                  122355899999999763     334566777774 2211     0123567899999


Q ss_pred             CCCcc-------------------------CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          323 NSKDH-------------------------VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       323 N~~~~-------------------------LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      |....                         +.|.|+.  |+|.++.|.+++.+....|+...+.
T Consensus       716 n~g~~~~~~~~~~~~~~~~~~~~~~~~~~~F~pel~~--Rid~IivF~PL~~e~l~~I~~l~L~  777 (852)
T TIGR03346       716 NLGSQFIQELAGGDDYEEMREAVMEVLRAHFRPEFLN--RIDEIVVFHPLGREQIARIVEIQLG  777 (852)
T ss_pred             CcchHhHhhhcccccHHHHHHHHHHHHHhhcCHHHhc--CcCeEEecCCcCHHHHHHHHHHHHH
Confidence            96211                         2356666  9999999999999999999887764

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=99.28  E-value=3.7e-11  Score=136.97  Aligned_cols=174  Identities=21%  Similarity=0.355  Sum_probs=117.7

Q ss_pred             cceeCCCCCCC-------------CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHH
Q 011664          177 RWRSVPFTHPS-------------TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAA  243 (480)
Q Consensus       177 ~w~~v~~~~~~-------------~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~a  243 (480)
                      .|..+|...-.             -.+.|+|++.+.+.|...+......-.   .. ..+...+||+||||||||++|++
T Consensus       542 ~~tgip~~~~~~~~~~~l~~l~~~l~~~viGQ~~ai~~l~~~i~~~~~gl~---~~-~~p~~~~Lf~Gp~G~GKT~lA~a  617 (857)
T PRK10865        542 RWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLS---DP-NRPIGSFLFLGPTGVGKTELCKA  617 (857)
T ss_pred             HHHCCCchhhhhhHHHHHHHHHHHhCCeEeCCHHHHHHHHHHHHHHHhccc---CC-CCCCceEEEECCCCCCHHHHHHH
Confidence            58888765321             245789999999998888765421100   00 01223689999999999999999


Q ss_pred             HHHcC---CCcEEEEeCCCcCChHHHHHHH---------------H---hhcCCcEEEEecccccccCcccccchhhhhh
Q 011664          244 MASFM---SYDVYDVDLSRVADDADLKSLL---------------L---QTTSKSVILIEDLDRFLVEKPAAVSLSGVLN  302 (480)
Q Consensus       244 iA~~l---~~~~~~i~~s~~~~~~~l~~l~---------------~---~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~  302 (480)
                      +|..+   +.+++.++++.+........++               .   +..+.+||+|||++.+-     ....+.|++
T Consensus       618 La~~l~~~~~~~i~id~se~~~~~~~~~LiG~~pgy~g~~~~g~l~~~v~~~p~~vLllDEieka~-----~~v~~~Ll~  692 (857)
T PRK10865        618 LANFMFDSDDAMVRIDMSEFMEKHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAH-----PDVFNILLQ  692 (857)
T ss_pred             HHHHhhcCCCcEEEEEhHHhhhhhhHHHHhCCCCcccccchhHHHHHHHHhCCCCeEEEeehhhCC-----HHHHHHHHH
Confidence            99977   4578999988765433333222               1   12345899999999763     234566677


Q ss_pred             hcc-cccc-----cccCCceEEEEecCCC-------------------------ccCcccccCCCceeEEEEcCCCCHHH
Q 011664          303 FMD-GVLN-----SCCFEERVMVFTMNSK-------------------------DHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       303 ~ld-g~~~-----~~~~~~~ivI~tTN~~-------------------------~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                      .++ |...     .....+.+||+|||..                         ..+.|+|+.  |+|.++.|.+++.+.
T Consensus       693 ile~g~l~d~~gr~vd~rn~iiI~TSN~g~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PELln--Rld~iivF~PL~~ed  770 (857)
T PRK10865        693 VLDDGRLTDGQGRTVDFRNTVVIMTSNLGSDLIQERFGELDYAHMKELVLGVVSHNFRPEFIN--RIDEVVVFHPLGEQH  770 (857)
T ss_pred             HHhhCceecCCceEEeecccEEEEeCCcchHHHHHhccccchHHHHHHHHHHHcccccHHHHH--hCCeeEecCCCCHHH
Confidence            664 2111     0112456789999962                         124568887  999999999999999


Q ss_pred             HHHHHHHHhc
Q 011664          352 FKTLASSYLG  361 (480)
Q Consensus       352 r~~il~~~l~  361 (480)
                      ...|++.++.
T Consensus       771 l~~Iv~~~L~  780 (857)
T PRK10865        771 IASIAQIQLQ  780 (857)
T ss_pred             HHHHHHHHHH
Confidence            9999888874

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=99.28  E-value=4e-11  Score=112.74  Aligned_cols=124  Identities=18%  Similarity=0.288  Sum_probs=89.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC------------------------cEEEEeCCC-cCChHHHHHHHHhh----
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY------------------------DVYDVDLSR-VADDADLKSLLLQT----  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~------------------------~~~~i~~s~-~~~~~~l~~l~~~~----  273 (480)
                      .+..+|||||||+|||++|+++|+.+..                        ++..++... -.+-..++.+....    
T Consensus        13 ~~~~~L~~G~~G~gkt~~a~~~~~~l~~~~~~~~~~c~~~~~c~~~~~~~~~d~~~~~~~~~~~~~~~i~~i~~~~~~~~   92 (188)
T TIGR00678        13 LAHAYLFAGPEGVGKELLALALAKALLCEQPGGGEPCGECPSCRLIEAGNHPDLHRLEPEGQSIKVDQVRELVEFLSRTP   92 (188)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCcEEEeccccCcCCHHHHHHHHHHHccCc
Confidence            4568999999999999999999998633                        234443322 12334555555332    


Q ss_pred             --cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHH
Q 011664          274 --TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       274 --~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                        ..+.||+|||+|.+..     ...+.||..|+..     ++..++|++||.+..+.+++++  |+. .+++++|+.++
T Consensus        93 ~~~~~kviiide~~~l~~-----~~~~~Ll~~le~~-----~~~~~~il~~~~~~~l~~~i~s--r~~-~~~~~~~~~~~  159 (188)
T TIGR00678        93 QESGRRVVIIEDAERMNE-----AAANALLKTLEEP-----PPNTLFILITPSPEKLLPTIRS--RCQ-VLPFPPLSEEA  159 (188)
T ss_pred             ccCCeEEEEEechhhhCH-----HHHHHHHHHhcCC-----CCCeEEEEEECChHhChHHHHh--hcE-EeeCCCCCHHH
Confidence              2457999999998842     3356688888652     3456778888888999999999  884 89999999999


Q ss_pred             HHHHHHHH
Q 011664          352 FKTLASSY  359 (480)
Q Consensus       352 r~~il~~~  359 (480)
                      ...++...
T Consensus       160 ~~~~l~~~  167 (188)
T TIGR00678       160 LLQWLIRQ  167 (188)
T ss_pred             HHHHHHHc
Confidence            88777665

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.

>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=99.28  E-value=2.2e-10  Score=123.63  Aligned_cols=179  Identities=18%  Similarity=0.212  Sum_probs=120.1

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHh---h--------------hhHHh----hhCCCCCceEEEEccCCCcHHH
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLK---A--------------KHYYH----RLGRVWKRSYLLYGPSGTGKSS  239 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~---~--------------~~~~~----~~g~~~~rgiLL~GPpGTGKT~  239 (480)
                      |..-.|..|.++.|++.+-..+...+..|=-   +              ++.+.    ..+.|.++-+||+||||-||||
T Consensus       262 Vdky~Pk~FtdLLsDe~tNR~~L~WLK~WD~~VFg~~vsrl~~s~~~~~ke~~~~~~~~s~RP~kKilLL~GppGlGKTT  341 (877)
T KOG1969|consen  262 VDKYRPKKFTDLLSDEKTNRRMLGWLKQWDPCVFGQKVSRLLASKGPTEKEVLDMELDPSKRPPKKILLLCGPPGLGKTT  341 (877)
T ss_pred             ecccChhHHHHHhcchhHHHHHHHHHHhhcHHhhcchHhhhccccccchhhhhhcccCccCCCccceEEeecCCCCChhH
Confidence            4666889999999999999999888875510   1              01111    1245667788999999999999


Q ss_pred             HHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHh----------hcCCcEEEEecccccccCcccccchhhhhhhcc----
Q 011664          240 FAAAMASFMSYDVYDVDLSRVADDADLKSLLLQ----------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD----  305 (480)
Q Consensus       240 La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~----------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld----  305 (480)
                      ||+.||+.+|+.++.|+.|+-.+...+++.+..          -.+|..|+|||||.-.     ...+..++..+.    
T Consensus       342 LAHViAkqaGYsVvEINASDeRt~~~v~~kI~~avq~~s~l~adsrP~CLViDEIDGa~-----~~~Vdvilslv~a~~k  416 (877)
T KOG1969|consen  342 LAHVIAKQAGYSVVEINASDERTAPMVKEKIENAVQNHSVLDADSRPVCLVIDEIDGAP-----RAAVDVILSLVKATNK  416 (877)
T ss_pred             HHHHHHHhcCceEEEecccccccHHHHHHHHHHHHhhccccccCCCcceEEEecccCCc-----HHHHHHHHHHHHhhcc
Confidence            999999999999999999998876666554422          1478899999999532     111122222221    


Q ss_pred             ---ccccc---------ccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCC
Q 011664          306 ---GVLNS---------CCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHK  366 (480)
Q Consensus       306 ---g~~~~---------~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~  366 (480)
                         |-...         ...=.|-||+.+|..  .-|||+----+-..|+|+.|......+-++..+..++..
T Consensus       417 ~~~Gkq~~~~~~rkkkr~~~L~RPIICICNdL--YaPaLR~Lr~~A~ii~f~~p~~s~Lv~RL~~IC~rE~mr  487 (877)
T KOG1969|consen  417 QATGKQAKKDKKRKKKRSKLLTRPIICICNDL--YAPALRPLRPFAEIIAFVPPSQSRLVERLNEICHRENMR  487 (877)
T ss_pred             hhhcCcccchhhhhhhccccccCCEEEEecCc--cchhhhhcccceEEEEecCCChhHHHHHHHHHHhhhcCC
Confidence               11110         000125688888853  357775222577899999999887666666666555443

>COG0714 MoxR-like ATPases [General function prediction only]

Probab=99.27  E-value=5.1e-11  Score=122.00  Aligned_cols=131  Identities=18%  Similarity=0.197  Sum_probs=90.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHH--HHh----------hcCC------cEEEEeccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSL--LLQ----------TTSK------SVILIEDLD  285 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l--~~~----------~~~~------sII~IDEiD  285 (480)
                      .+.+||-||||||||++|+++|..++.+++.+.|+.-...+++.-.  +..          ...|      +|+++|||+
T Consensus        43 ~~~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEIn  122 (329)
T COG0714          43 GGHVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLGTYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEIN  122 (329)
T ss_pred             CCCEEEECCCCccHHHHHHHHHHHhCCCeEEEecCCCCCHHHhcCchhHhhhhccCCeEEEecCCcccccceEEEEeccc
Confidence            4579999999999999999999999999999999866554442111  110          0111      399999999


Q ss_pred             ccccCcccccchhhhhhhcccc----ccc---ccCCceEEEEecC-----CCccCcccccCCCceeEEEEcCCC-CHHHH
Q 011664          286 RFLVEKPAAVSLSGVLNFMDGV----LNS---CCFEERVMVFTMN-----SKDHVDQALLRPGRIDVHIHFPLC-DFSSF  352 (480)
Q Consensus       286 ~l~~~~~~~~~ls~lL~~ldg~----~~~---~~~~~~ivI~tTN-----~~~~LD~aLlrpGRfd~~I~~~~p-~~~~r  352 (480)
                      ..     ...+.+.||..|+.-    ...   .-....++|+|+|     .-..|++|+++  ||-..+++++| +.++.
T Consensus       123 ra-----~p~~q~aLl~~l~e~~vtv~~~~~~~~~~~f~viaT~Np~e~~g~~~l~eA~ld--Rf~~~~~v~yp~~~~e~  195 (329)
T COG0714         123 RA-----PPEVQNALLEALEERQVTVPGLTTIRLPPPFIVIATQNPGEYEGTYPLPEALLD--RFLLRIYVDYPDSEEEE  195 (329)
T ss_pred             cC-----CHHHHHHHHHHHhCcEEEECCcCCcCCCCCCEEEEccCccccCCCcCCCHHHHh--hEEEEEecCCCCchHHH
Confidence            65     345567777777541    110   1123445666778     34568999999  99999999999 55555


Q ss_pred             HHHHHHHhc
Q 011664          353 KTLASSYLG  361 (480)
Q Consensus       353 ~~il~~~l~  361 (480)
                      ..+......
T Consensus       196 ~~i~~~~~~  204 (329)
T COG0714         196 RIILARVGG  204 (329)
T ss_pred             HHHHHhCcc
Confidence            555555443

>PF07728 AAA_5: AAA domain (dynein-related subfamily); InterPro: IPR011704 The ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.27  E-value=4.7e-12  Score=112.91  Aligned_cols=106  Identities=24%  Similarity=0.384  Sum_probs=71.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHH---------------hhcCCcEEEEecccccccC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLL---------------QTTSKSVILIEDLDRFLVE  290 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~---------------~~~~~sII~IDEiD~l~~~  290 (480)
                      ++||+||||||||++|+.+|..++.+++.+.++...+..++.....               ....++|++||||+..-  
T Consensus         1 ~vlL~G~~G~GKt~l~~~la~~~~~~~~~i~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~il~lDEin~a~--   78 (139)
T PF07728_consen    1 PVLLVGPPGTGKTTLARELAALLGRPVIRINCSSDTTEEDLIGSYDPSNGQFEFKDGPLVRAMRKGGILVLDEINRAP--   78 (139)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHTCEEEEEE-TTTSTHHHHHCEEET-TTTTCEEE-CCCTTHHEEEEEEESSCGG----
T ss_pred             CEEEECCCCCCHHHHHHHHHHHhhcceEEEEeccccccccceeeeeecccccccccccccccccceeEEEECCcccCC--
Confidence            5899999999999999999999999999999988776655422110               11257899999999652  


Q ss_pred             cccccchhhhhhhccccccc-------c-cCC------ceEEEEecCCCc----cCcccccCCCce
Q 011664          291 KPAAVSLSGVLNFMDGVLNS-------C-CFE------ERVMVFTMNSKD----HVDQALLRPGRI  338 (480)
Q Consensus       291 ~~~~~~ls~lL~~ldg~~~~-------~-~~~------~~ivI~tTN~~~----~LD~aLlrpGRf  338 (480)
                         ...+..|+..++.-.-.       . ...      +..+|+|+|..+    .+++||++  ||
T Consensus        79 ---~~v~~~L~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ii~t~N~~~~~~~~l~~al~~--Rf  139 (139)
T PF07728_consen   79 ---PEVLESLLSLLEERRIQLPEGGEEIKEPNNDLASPNFRIIATMNPRDKGRKELSPALLD--RF  139 (139)
T ss_dssp             ---HHHHHTTHHHHSSSEEEE-TSSSEEE--TT------EEEEEEESSST--TTTTCHHHHT--T-
T ss_pred             ---HHHHHHHHHHHhhCcccccCCCcEEecCcccccccceEEEEEEcCCCCCcCcCCHHHHh--hC
Confidence               23334444444321100       0 011      367889999888    89999999  87

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.

>TIGR01650 PD_CobS cobaltochelatase, CobS subunit

Probab=99.26  E-value=1e-11  Score=125.71  Aligned_cols=131  Identities=15%  Similarity=0.193  Sum_probs=90.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHH------------------HHH-HhhcCCcEEEEec
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLK------------------SLL-LQTTSKSVILIED  283 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~------------------~l~-~~~~~~sII~IDE  283 (480)
                      ..+.+||.||||||||++++++|..++.+++.++++......++.                  ..+ .....++++++||
T Consensus        63 ~~~~ilL~G~pGtGKTtla~~lA~~l~~~~~rV~~~~~l~~~DliG~~~~~l~~g~~~~~f~~GpL~~A~~~g~illlDE  142 (327)
T TIGR01650        63 YDRRVMVQGYHGTGKSTHIEQIAARLNWPCVRVNLDSHVSRIDLVGKDAIVLKDGKQITEFRDGILPWALQHNVALCFDE  142 (327)
T ss_pred             cCCcEEEEeCCCChHHHHHHHHHHHHCCCeEEEEecCCCChhhcCCCceeeccCCcceeEEecCcchhHHhCCeEEEech
Confidence            356899999999999999999999999999999876544322110                  011 1124678899999


Q ss_pred             ccccccCcccccchhhhhhhccc--------ccccc-cCCceEEEEecCCCc------------cCcccccCCCceeEEE
Q 011664          284 LDRFLVEKPAAVSLSGVLNFMDG--------VLNSC-CFEERVMVFTMNSKD------------HVDQALLRPGRIDVHI  342 (480)
Q Consensus       284 iD~l~~~~~~~~~ls~lL~~ldg--------~~~~~-~~~~~ivI~tTN~~~------------~LD~aLlrpGRfd~~I  342 (480)
                      +|..-+     .+++.|...++.        ..... ....-.+|+|+|..+            .+++|++.  ||-.++
T Consensus       143 in~a~p-----~~~~~L~~lLE~~~~l~i~~~~~~i~~hp~FrviAT~Np~g~Gd~~G~y~Gt~~l~~A~lD--RF~i~~  215 (327)
T TIGR01650       143 YDAGRP-----DVMFVIQRVLEAGGKLTLLDQNRVIRAHPAFRLFATANTIGLGDTTGLYHGTQQINQAQMD--RWSIVT  215 (327)
T ss_pred             hhccCH-----HHHHHHHHHhccCCeEEECCCceEecCCCCeEEEEeeCCCCcCCCCcceeeeecCCHHHHh--heeeEe
Confidence            997632     233443333331        10101 122445788888754            36889999  998889


Q ss_pred             EcCCCCHHHHHHHHHHHh
Q 011664          343 HFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       343 ~~~~p~~~~r~~il~~~l  360 (480)
                      .++||+.+.-.+|+....
T Consensus       216 ~~~Yp~~e~E~~Il~~~~  233 (327)
T TIGR01650       216 TLNYLEHDNEAAIVLAKA  233 (327)
T ss_pred             eCCCCCHHHHHHHHHhhc
Confidence            999999999999987664

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.

>PHA02244 ATPase-like protein

Probab=99.25  E-value=6.5e-11  Score=121.25  Aligned_cols=120  Identities=19%  Similarity=0.337  Sum_probs=78.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC----CcC----ChHHHH--HHHHhhcCCcEEEEecccccccCcccc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS----RVA----DDADLK--SLLLQTTSKSVILIEDLDRFLVEKPAA  294 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s----~~~----~~~~l~--~l~~~~~~~sII~IDEiD~l~~~~~~~  294 (480)
                      ..+||+||||||||++|+++|..++.+++.++..    .+.    ....+.  .++.......+|+|||++.+.++  ..
T Consensus       120 ~PVLL~GppGtGKTtLA~aLA~~lg~pfv~In~l~d~~~L~G~i~~~g~~~dgpLl~A~~~GgvLiLDEId~a~p~--vq  197 (383)
T PHA02244        120 IPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGLFFIDEIDASIPE--AL  197 (383)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEEEecChHHHhhcccccccccccchHHHHHhhcCCEEEEeCcCcCCHH--HH
Confidence            4699999999999999999999999999988732    011    000111  22333467899999999976421  11


Q ss_pred             cchhhhh-----hhcccccccccCCceEEEEecCCC-----------ccCcccccCCCceeEEEEcCCCCHHH
Q 011664          295 VSLSGVL-----NFMDGVLNSCCFEERVMVFTMNSK-----------DHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       295 ~~ls~lL-----~~ldg~~~~~~~~~~ivI~tTN~~-----------~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                      ..+..++     ...++...  ...+..+|+|+|.+           ..|++|++.  || .+|++++|+..+
T Consensus       198 ~~L~~lLd~r~l~l~g~~i~--~h~~FRlIATsN~~~~G~~~~y~G~k~L~~AllD--RF-v~I~~dyp~~~E  265 (383)
T PHA02244        198 IIINSAIANKFFDFADERVT--AHEDFRVISAGNTLGKGADHIYVARNKIDGATLD--RF-APIEFDYDEKIE  265 (383)
T ss_pred             HHHHHHhccCeEEecCcEEe--cCCCEEEEEeeCCCccCcccccCCCcccCHHHHh--hc-EEeeCCCCcHHH
Confidence            2222222     12222211  12456788888863           568999999  99 589999998433

>CHL00081 chlI Mg-protoporyphyrin IX chelatase

Probab=99.23  E-value=9.5e-11  Score=120.21  Aligned_cols=154  Identities=16%  Similarity=0.198  Sum_probs=100.4

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-------CcEE-----
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-------YDVY-----  253 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-------~~~~-----  253 (480)
                      .-+|++|+|++++|..|.-.+..+             ...|+||.||+|||||++|++++..+.       .+|.     
T Consensus        13 ~~pf~~ivGq~~~k~al~~~~~~p-------------~~~~vli~G~~GtGKs~~ar~~~~~l~~~~~~~~~pf~~~p~~   79 (350)
T CHL00081         13 VFPFTAIVGQEEMKLALILNVIDP-------------KIGGVMIMGDRGTGKSTTIRALVDLLPEIEVVKDDPFNSHPSD   79 (350)
T ss_pred             CCCHHHHhChHHHHHHHHHhccCC-------------CCCeEEEEcCCCCCHHHHHHHHHHHHhhcCccCCCCCCCCCCC
Confidence            347999999999999988655432             335899999999999999999987652       1111     


Q ss_pred             ----------------------------EEeCC----CcCChHHHHHHHHh-----------hcCCcEEEEecccccccC
Q 011664          254 ----------------------------DVDLS----RVADDADLKSLLLQ-----------TTSKSVILIEDLDRFLVE  290 (480)
Q Consensus       254 ----------------------------~i~~s----~~~~~~~l~~l~~~-----------~~~~sII~IDEiD~l~~~  290 (480)
                                                  .+..+    .+.+.-++.+.|..           .....+||+|||+.+.  
T Consensus        80 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~~ted~l~G~iD~~~al~~g~~~~~~GlL~~A~~GiL~lDEInrL~--  157 (350)
T CHL00081         80 PELMSDEVREAIQNGETIETEKIKIPMVDLPLGATEDRVCGTIDIEKALTEGVKAFEPGLLAKANRGILYVDEVNLLD--  157 (350)
T ss_pred             hhhhchhhhhhhcccccccceeccccceecCCCCchhhccCcccHHHHhhcCcccccCCeeeecCCCEEEecChHhCC--
Confidence                                        11110    01111122222211           1235899999999874  


Q ss_pred             cccccchhhhhhhccc---------ccccccCCceEEEEecCCCc-cCcccccCCCceeEEEEcCCCC-HHHHHHHHHHH
Q 011664          291 KPAAVSLSGVLNFMDG---------VLNSCCFEERVMVFTMNSKD-HVDQALLRPGRIDVHIHFPLCD-FSSFKTLASSY  359 (480)
Q Consensus       291 ~~~~~~ls~lL~~ldg---------~~~~~~~~~~ivI~tTN~~~-~LD~aLlrpGRfd~~I~~~~p~-~~~r~~il~~~  359 (480)
                         ....+.|++.|+.         ... ......++|+|.|..+ .+.++|+.  ||..++.+.+|+ .+.+.+|+++.
T Consensus       158 ---~~~Q~~LLeam~e~~~~ier~G~s~-~~p~rfiviaT~np~eg~l~~~Lld--Rf~l~i~l~~~~~~~~e~~il~~~  231 (350)
T CHL00081        158 ---DHLVDILLDSAASGWNTVEREGISI-RHPARFVLVGSGNPEEGELRPQLLD--RFGMHAEIRTVKDPELRVKIVEQR  231 (350)
T ss_pred             ---HHHHHHHHHHHHhCCeEEeeCCeee-ecCCCEEEEeccCcccCCCCHHHHH--HhCceeecCCCCChHHHHHHHHhh
Confidence               2344667776642         111 1122334445556444 58999999  999999999998 58999999876


Q ss_pred             h
Q 011664          360 L  360 (480)
Q Consensus       360 l  360 (480)
                      .
T Consensus       232 ~  232 (350)
T CHL00081        232 T  232 (350)
T ss_pred             h
Confidence            4

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=99.22  E-value=1.8e-10  Score=119.30  Aligned_cols=154  Identities=14%  Similarity=0.225  Sum_probs=109.3

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc-----EEEEeCCCcCChH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD-----VYDVDLSRVADDA  264 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~-----~~~i~~s~~~~~~  264 (480)
                      +.+.+-++..+.+...+..++.+.         .|.++++|||||||||..++-++.++...     +++|||-...+..
T Consensus        17 ~~l~~Re~ei~~l~~~l~~~~~~~---------~p~n~~iyG~~GTGKT~~~~~v~~~l~~~~~~~~~~yINc~~~~t~~   87 (366)
T COG1474          17 EELPHREEEINQLASFLAPALRGE---------RPSNIIIYGPTGTGKTATVKFVMEELEESSANVEVVYINCLELRTPY   87 (366)
T ss_pred             ccccccHHHHHHHHHHHHHHhcCC---------CCccEEEECCCCCCHhHHHHHHHHHHHhhhccCceEEEeeeeCCCHH
Confidence            348888888888887766655442         34469999999999999999999987443     8999987665432


Q ss_pred             HH-------------------------HHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEE
Q 011664          265 DL-------------------------KSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMV  319 (480)
Q Consensus       265 ~l-------------------------~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI  319 (480)
                      .+                         .+.+.......||++||+|.+....+  ..+-.|+...+..     ...+.+|
T Consensus        88 ~i~~~i~~~~~~~p~~g~~~~~~~~~l~~~~~~~~~~~IvvLDEid~L~~~~~--~~LY~L~r~~~~~-----~~~v~vi  160 (366)
T COG1474          88 QVLSKILNKLGKVPLTGDSSLEILKRLYDNLSKKGKTVIVILDEVDALVDKDG--EVLYSLLRAPGEN-----KVKVSII  160 (366)
T ss_pred             HHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHhcCCeEEEEEcchhhhccccc--hHHHHHHhhcccc-----ceeEEEE
Confidence            21                         11122223567999999999976544  3444444433222     2345677


Q ss_pred             EecCCC---ccCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhc
Q 011664          320 FTMNSK---DHVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       320 ~tTN~~---~~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      +.+|..   +.+||.+.+  ++. .+|.||+++.++...|+.....
T Consensus       161 ~i~n~~~~~~~ld~rv~s--~l~~~~I~F~pY~a~el~~Il~~R~~  204 (366)
T COG1474         161 AVSNDDKFLDYLDPRVKS--SLGPSEIVFPPYTAEELYDILRERVE  204 (366)
T ss_pred             EEeccHHHHHHhhhhhhh--ccCcceeeeCCCCHHHHHHHHHHHHH
Confidence            777754   578999988  775 6799999999999999988765

>CHL00095 clpC Clp protease ATP binding subunit

Probab=99.22  E-value=1.7e-10  Score=131.41  Aligned_cols=161  Identities=19%  Similarity=0.286  Sum_probs=108.8

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADL  266 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l  266 (480)
                      +.|+|++++.+.|...+.....+-   .. ...+...+||+||||||||++|+++|..+   +.+++.++++++.....+
T Consensus       509 ~~v~GQ~~ai~~l~~~i~~~~~gl---~~-~~~p~~~~lf~Gp~GvGKt~lA~~LA~~l~~~~~~~~~~d~s~~~~~~~~  584 (821)
T CHL00095        509 KRIIGQDEAVVAVSKAIRRARVGL---KN-PNRPIASFLFSGPTGVGKTELTKALASYFFGSEDAMIRLDMSEYMEKHTV  584 (821)
T ss_pred             CcCcChHHHHHHHHHHHHHHhhcc---cC-CCCCceEEEEECCCCCcHHHHHHHHHHHhcCCccceEEEEchhccccccH
Confidence            568899999998887775432110   00 01122358999999999999999999987   467899998876532222


Q ss_pred             HHH----------------H--HhhcCCcEEEEecccccccCcccccchhhhhhhccc-cccc-----ccCCceEEEEec
Q 011664          267 KSL----------------L--LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG-VLNS-----CCFEERVMVFTM  322 (480)
Q Consensus       267 ~~l----------------~--~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg-~~~~-----~~~~~~ivI~tT  322 (480)
                      ..+                .  .+..+.+||+|||+|...     ....+.|+..||. ....     ....+.+||+||
T Consensus       585 ~~l~g~~~gyvg~~~~~~l~~~~~~~p~~VvllDeieka~-----~~v~~~Llq~le~g~~~d~~g~~v~~~~~i~I~Ts  659 (821)
T CHL00095        585 SKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAH-----PDIFNLLLQILDDGRLTDSKGRTIDFKNTLIIMTS  659 (821)
T ss_pred             HHhcCCCCcccCcCccchHHHHHHhCCCeEEEECChhhCC-----HHHHHHHHHHhccCceecCCCcEEecCceEEEEeC
Confidence            211                1  122345899999999763     3345667777763 2110     113567899999


Q ss_pred             CCCcc-------------------------------------CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          323 NSKDH-------------------------------------VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       323 N~~~~-------------------------------------LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      |....                                     +.|.++.  |+|.+|.|.+.+.++..+|+...+.
T Consensus       660 n~g~~~i~~~~~~~gf~~~~~~~~~~~~~~~~~~~~~~~~~~f~pefln--Rid~ii~F~pL~~~~l~~Iv~~~l~  733 (821)
T CHL00095        660 NLGSKVIETNSGGLGFELSENQLSEKQYKRLSNLVNEELKQFFRPEFLN--RLDEIIVFRQLTKNDVWEIAEIMLK  733 (821)
T ss_pred             CcchHHHHhhccccCCcccccccccccHHHHHHHHHHHHHHhcCHHHhc--cCCeEEEeCCCCHHHHHHHHHHHHH
Confidence            84311                                     1245666  9999999999999999999888774

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=99.21  E-value=1.1e-10  Score=121.25  Aligned_cols=191  Identities=12%  Similarity=0.167  Sum_probs=119.2

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEe
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVD  256 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~  256 (480)
                      .+.+.-||++.+..+.-..... ....+-      ...|. ....++||||+|+|||+|++|++++..     ..++++.
T Consensus        79 ~l~~~ytFdnFv~g~~N~~A~a-a~~~va------~~~g~-~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~  150 (408)
T COG0593          79 GLNPKYTFDNFVVGPSNRLAYA-AAKAVA------ENPGG-AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLT  150 (408)
T ss_pred             cCCCCCchhheeeCCchHHHHH-HHHHHH------hccCC-cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEecc
Confidence            4556678999755544333222 111111      12232 344799999999999999999999762     3456665


Q ss_pred             CCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC-
Q 011664          257 LSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV-  328 (480)
Q Consensus       257 ~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L-  328 (480)
                      ...+..+       ..+.+.=... +-.+++||||+.+.+....+   .+|...+..+..   .++.|++.+...|..+ 
T Consensus       151 se~f~~~~v~a~~~~~~~~Fk~~y-~~dlllIDDiq~l~gk~~~q---eefFh~FN~l~~---~~kqIvltsdr~P~~l~  223 (408)
T COG0593         151 SEDFTNDFVKALRDNEMEKFKEKY-SLDLLLIDDIQFLAGKERTQ---EEFFHTFNALLE---NGKQIVLTSDRPPKELN  223 (408)
T ss_pred             HHHHHHHHHHHHHhhhHHHHHHhh-ccCeeeechHhHhcCChhHH---HHHHHHHHHHHh---cCCEEEEEcCCCchhhc
Confidence            4433211       1111111223 66799999999987654444   444444444443   3445555555566554 


Q ss_pred             --cccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHH-HHHhCCCCCHHHHHHHH
Q 011664          329 --DQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEE-IFQNGSSLSPAEIGELM  390 (480)
Q Consensus       329 --D~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~-l~~~~~g~s~adI~~ll  390 (480)
                        +|.|++  ||.  ..+.+.+|+.+.|.++++......+..+.+++.. ++.+. .-+..++...+
T Consensus       224 ~~~~rL~S--R~~~Gl~~~I~~Pd~e~r~aiL~kka~~~~~~i~~ev~~~la~~~-~~nvReLegaL  287 (408)
T COG0593         224 GLEDRLRS--RLEWGLVVEIEPPDDETRLAILRKKAEDRGIEIPDEVLEFLAKRL-DRNVRELEGAL  287 (408)
T ss_pred             cccHHHHH--HHhceeEEeeCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHh-hccHHHHHHHH
Confidence              689999  997  8899999999999999999888888888877643 44332 33444444433

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

Probab=99.19  E-value=6.7e-11  Score=130.68  Aligned_cols=157  Identities=22%  Similarity=0.359  Sum_probs=117.8

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCC----CCceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEeCCCcCC
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRV----WKRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVDLSRVAD  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~----~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~~s~~~~  262 (480)
                      ..|+|++++.+.+.+.+..-        +.|+.    |-.++||.||+|+|||.||+++|..+.   ..++.+|+|+++.
T Consensus       491 ~rViGQd~AV~avs~aIrra--------RaGL~dp~rPigsFlF~GPTGVGKTELAkaLA~~Lfg~e~aliR~DMSEy~E  562 (786)
T COG0542         491 KRVIGQDEAVEAVSDAIRRA--------RAGLGDPNRPIGSFLFLGPTGVGKTELAKALAEALFGDEQALIRIDMSEYME  562 (786)
T ss_pred             cceeChHHHHHHHHHHHHHH--------hcCCCCCCCCceEEEeeCCCcccHHHHHHHHHHHhcCCCccceeechHHHHH
Confidence            56899999999888877654        22322    334688899999999999999999986   7899999999987


Q ss_pred             hHHHHHHHHh------------------hcCCcEEEEecccccccCcccccchhhhhhhcc-ccccc-----ccCCceEE
Q 011664          263 DADLKSLLLQ------------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-GVLNS-----CCFEERVM  318 (480)
Q Consensus       263 ~~~l~~l~~~------------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-g~~~~-----~~~~~~iv  318 (480)
                      ...+.+++..                  ..+.|||++|||+.-     ....++-||+.|| |...+     ....+.||
T Consensus       563 kHsVSrLIGaPPGYVGyeeGG~LTEaVRr~PySViLlDEIEKA-----HpdV~nilLQVlDdGrLTD~~Gr~VdFrNtiI  637 (786)
T COG0542         563 KHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSVILLDEIEKA-----HPDVFNLLLQVLDDGRLTDGQGRTVDFRNTII  637 (786)
T ss_pred             HHHHHHHhCCCCCCceeccccchhHhhhcCCCeEEEechhhhc-----CHHHHHHHHHHhcCCeeecCCCCEEecceeEE
Confidence            7777776522                  234699999999964     4456677888886 22221     22345689


Q ss_pred             EEecCCCc----------------------------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          319 VFTMNSKD----------------------------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       319 I~tTN~~~----------------------------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      |||||--.                            ...|+++.  |+|.+|.|.+.+.+...+|+...+.
T Consensus       638 ImTSN~Gs~~i~~~~~~~~~~~~~~~~~~v~~~l~~~F~PEFLN--Rid~II~F~~L~~~~l~~Iv~~~L~  706 (786)
T COG0542         638 IMTSNAGSEEILRDADGDDFADKEALKEAVMEELKKHFRPEFLN--RIDEIIPFNPLSKEVLERIVDLQLN  706 (786)
T ss_pred             EEecccchHHHHhhccccccchhhhHHHHHHHHHHhhCCHHHHh--hcccEEeccCCCHHHHHHHHHHHHH
Confidence            99998320                            02355666  9999999999999999999988775

>PRK07952 DNA replication protein DnaC; Validated

Probab=99.19  E-value=8.8e-11  Score=115.15  Aligned_cols=130  Identities=17%  Similarity=0.288  Sum_probs=81.6

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      +..+..+|++.....+-.+.+...+..+...   +..    ...+++|+||||||||+|+.|||+++   +..++.+++.
T Consensus        64 ~~~~~~tFdnf~~~~~~q~~al~~a~~~~~~---~~~----~~~~~~l~G~~GtGKThLa~aia~~l~~~g~~v~~it~~  136 (244)
T PRK07952         64 PLHQNCSFENYRVECEGQMNALSKARQYVEE---FDG----NIASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVA  136 (244)
T ss_pred             ccccCCccccccCCCchHHHHHHHHHHHHHh---hcc----CCceEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEHH
Confidence            3445678999865544444445455555432   111    13489999999999999999999987   7788888876


Q ss_pred             CcCC---------hHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          259 RVAD---------DADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       259 ~~~~---------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ++..         +.....++......++|+|||+++..........   +...++.-.    ....-+|+|||..
T Consensus       137 ~l~~~l~~~~~~~~~~~~~~l~~l~~~dlLvIDDig~~~~s~~~~~~---l~~Ii~~Ry----~~~~~tiitSNl~  205 (244)
T PRK07952        137 DIMSAMKDTFSNSETSEEQLLNDLSNVDLLVIDEIGVQTESRYEKVI---INQIVDRRS----SSKRPTGMLTNSN  205 (244)
T ss_pred             HHHHHHHHHHhhccccHHHHHHHhccCCEEEEeCCCCCCCCHHHHHH---HHHHHHHHH----hCCCCEEEeCCCC
Confidence            6542         1122345555667899999999986422212222   333444322    2345678889843

>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I

Probab=99.19  E-value=1.6e-10  Score=118.39  Aligned_cols=153  Identities=18%  Similarity=0.226  Sum_probs=100.1

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-------CCcEE-------
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-------SYDVY-------  253 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-------~~~~~-------  253 (480)
                      .|..|+|++++|..+.-.+..+             ...+++|.||||||||++++++++.+       +.++-       
T Consensus         2 pf~~ivgq~~~~~al~~~~~~~-------------~~g~vli~G~~G~gKttl~r~~~~~~~~~~~~~~~~~~~~~~~~~   68 (337)
T TIGR02030         2 PFTAIVGQDEMKLALLLNVIDP-------------KIGGVMVMGDRGTGKSTAVRALAALLPEIKAVAGCPFNSSPSDPE   68 (337)
T ss_pred             CccccccHHHHHHHHHHHhcCC-------------CCCeEEEEcCCCCCHHHHHHHHHHhhcccccccCCCCCCCCCCcc
Confidence            4889999999999886544332             23579999999999999999999766       22111       


Q ss_pred             ------E------------------EeCC------CcCChHHHHHHHH-----------hhcCCcEEEEecccccccCcc
Q 011664          254 ------D------------------VDLS------RVADDADLKSLLL-----------QTTSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       254 ------~------------------i~~s------~~~~~~~l~~l~~-----------~~~~~sII~IDEiD~l~~~~~  292 (480)
                            .                  +++.      .+.+.-++...+.           ....+.+||||||+.+.    
T Consensus        69 ~~~~~~r~~~~~~~~~~~~~~~~~~~~lP~~~t~d~l~G~~d~~~~l~~g~~~~~~GlL~~A~~GvL~lDEi~~L~----  144 (337)
T TIGR02030        69 MMCEEVRIRVDSQEPLSIIKKPVPVVDLPLGATEDRVCGTLDIERALTEGVKAFEPGLLARANRGILYIDEVNLLE----  144 (337)
T ss_pred             ccChHHhhhhhcccccccccCCCCcCCCCCCCcccceecchhHhhHhhcCCEEeecCcceeccCCEEEecChHhCC----
Confidence                  0                  1111      1222223333221           12345899999999873    


Q ss_pred             cccchhhhhhhccc---------ccccccCCceEEEEecCCCc-cCcccccCCCceeEEEEcCCCCH-HHHHHHHHHHhc
Q 011664          293 AAVSLSGVLNFMDG---------VLNSCCFEERVMVFTMNSKD-HVDQALLRPGRIDVHIHFPLCDF-SSFKTLASSYLG  361 (480)
Q Consensus       293 ~~~~ls~lL~~ldg---------~~~~~~~~~~ivI~tTN~~~-~LD~aLlrpGRfd~~I~~~~p~~-~~r~~il~~~l~  361 (480)
                       ....+.|++.|+.         ... ......++|+|+|..+ .+.++|+.  ||..++.+++|+. +++.+|+++...
T Consensus       145 -~~~Q~~Ll~~l~~g~~~v~r~G~~~-~~~~r~iviat~np~eg~l~~~Lld--Rf~l~i~l~~p~~~eer~eIL~~~~~  220 (337)
T TIGR02030       145 -DHLVDVLLDVAASGWNVVEREGISI-RHPARFVLVGSGNPEEGELRPQLLD--RFGLHAEIRTVRDVELRVEIVERRTE  220 (337)
T ss_pred             -HHHHHHHHHHHHhCCeEEEECCEEE-EcCCCEEEEeccccccCCCCHHHHh--hcceEEECCCCCCHHHHHHHHHhhhh
Confidence             3345666776642         211 1122345555666444 68999999  9999999999986 888999987543

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.

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=99.19  E-value=8.2e-11  Score=133.90  Aligned_cols=157  Identities=18%  Similarity=0.289  Sum_probs=108.2

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCC-CCCc-eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGR-VWKR-SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA  264 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~-~~~r-giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~  264 (480)
                      ..|+|++++.+.+.+.+.....+      +.. ..|. .+||+||||||||.+|+++|..+   +..++.++++.+....
T Consensus       566 ~~v~GQ~~Av~~v~~~i~~~~~g------l~~~~~p~~~~lf~Gp~GvGKT~lA~~La~~l~~~~~~~~~~dmse~~~~~  639 (852)
T TIGR03345       566 ERVIGQDHALEAIAERIRTARAG------LEDPRKPLGVFLLVGPSGVGKTETALALAELLYGGEQNLITINMSEFQEAH  639 (852)
T ss_pred             CeEcChHHHHHHHHHHHHHHhcC------CCCCCCCceEEEEECCCCCCHHHHHHHHHHHHhCCCcceEEEeHHHhhhhh
Confidence            47899999999998888654211      111 1233 47999999999999999999988   4578899987664322


Q ss_pred             H-------------------HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccc-c-----cccCCceEEE
Q 011664          265 D-------------------LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-N-----SCCFEERVMV  319 (480)
Q Consensus       265 ~-------------------l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~-----~~~~~~~ivI  319 (480)
                      .                   +...+ +..+.+||+|||||...     ....+-|++.+|.-. .     .....+.+||
T Consensus       640 ~~~~l~g~~~gyvg~~~~g~L~~~v-~~~p~svvllDEieka~-----~~v~~~Llq~ld~g~l~d~~Gr~vd~~n~iiI  713 (852)
T TIGR03345       640 TVSRLKGSPPGYVGYGEGGVLTEAV-RRKPYSVVLLDEVEKAH-----PDVLELFYQVFDKGVMEDGEGREIDFKNTVIL  713 (852)
T ss_pred             hhccccCCCCCcccccccchHHHHH-HhCCCcEEEEechhhcC-----HHHHHHHHHHhhcceeecCCCcEEeccccEEE
Confidence            2                   22222 23577999999999653     234455666665221 1     0112467899


Q ss_pred             EecCCCc-----------------------------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          320 FTMNSKD-----------------------------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       320 ~tTN~~~-----------------------------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      +|||...                             .+.|+++.  |++ .|.|.+.+.++..+|+...+.
T Consensus       714 ~TSNlg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEfln--Ri~-iI~F~pLs~e~l~~Iv~~~L~  781 (852)
T TIGR03345       714 LTSNAGSDLIMALCADPETAPDPEALLEALRPELLKVFKPAFLG--RMT-VIPYLPLDDDVLAAIVRLKLD  781 (852)
T ss_pred             EeCCCchHHHHHhccCcccCcchHHHHHHHHHHHHHhccHHHhc--cee-EEEeCCCCHHHHHHHHHHHHH
Confidence            9998421                             14467777  998 899999999999999988764

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.

>PRK08116 hypothetical protein; Validated

Probab=99.16  E-value=1.2e-10  Score=115.97  Aligned_cols=117  Identities=19%  Similarity=0.281  Sum_probs=78.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh----------HHHHHHHHhhcCCcEEEEecccccccC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD----------ADLKSLLLQTTSKSVILIEDLDRFLVE  290 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~----------~~l~~l~~~~~~~sII~IDEiD~l~~~  290 (480)
                      ..|++||||||||||+||.|||+++   +.+++.++.+++...          .....++.......+|+|||+....  
T Consensus       114 ~~gl~l~G~~GtGKThLa~aia~~l~~~~~~v~~~~~~~ll~~i~~~~~~~~~~~~~~~~~~l~~~dlLviDDlg~e~--  191 (268)
T PRK08116        114 NVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFVNFPQLLNRIKSTYKSSGKEDENEIIRSLVNADLLILDDLGAER--  191 (268)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhccccccHHHHHHHhcCCCEEEEecccCCC--
Confidence            4589999999999999999999976   778888886654321          1122344445567899999997532  


Q ss_pred             cccccchhhhhhhcccccccccCCceEEEEecCCC-cc----CcccccCCCce---eEEEEcCCCCH
Q 011664          291 KPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK-DH----VDQALLRPGRI---DVHIHFPLCDF  349 (480)
Q Consensus       291 ~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~-~~----LD~aLlrpGRf---d~~I~~~~p~~  349 (480)
                       .+......|.+.++....    .+..+|+|||.+ +.    +++++.+  |+   ...|.++-++.
T Consensus       192 -~t~~~~~~l~~iin~r~~----~~~~~IiTsN~~~~eL~~~~~~ri~s--Rl~e~~~~v~~~g~d~  251 (268)
T PRK08116        192 -DTEWAREKVYNIIDSRYR----KGLPTIVTTNLSLEELKNQYGKRIYD--RILEMCTPVENEGKSY  251 (268)
T ss_pred             -CCHHHHHHHHHHHHHHHH----CCCCEEEECCCCHHHHHHHHhHHHHH--HHHHcCEEEEeeCcCh
Confidence             223344566777765443    345578888854 34    4677777  75   35577777765

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=99.14  E-value=1.8e-09  Score=110.56  Aligned_cols=198  Identities=14%  Similarity=0.125  Sum_probs=130.3

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA  264 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~  264 (480)
                      .+++++|....-+.+.+.+......           ...|||+|++||||+++|++|....   +.+|+.++|..+.. .
T Consensus         4 ~~~~liG~S~~~~~~~~~i~~~a~~-----------~~pVlI~GE~GtGK~~lA~~iH~~s~r~~~pfv~v~c~~~~~-~   71 (326)
T PRK11608          4 YKDNLLGEANSFLEVLEQVSRLAPL-----------DKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNE-N   71 (326)
T ss_pred             ccCccEECCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHHhCCccCCCeEEEeCCCCCH-H
Confidence            4678999998888888887766432           3469999999999999999998765   46899999998753 3


Q ss_pred             HHH-HHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cc-----ccCCceEEEE
Q 011664          265 DLK-SLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NS-----CCFEERVMVF  320 (480)
Q Consensus       265 ~l~-~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~-----~~~~~~ivI~  320 (480)
                      .+. .+|.                 .......|||||||.+..     .....|++.++.-. ..     .......||+
T Consensus        72 ~~~~~lfg~~~~~~~g~~~~~~g~l~~a~gGtL~l~~i~~L~~-----~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~  146 (326)
T PRK11608         72 LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPM-----LVQEKLLRVIEYGELERVGGSQPLQVNVRLVC  146 (326)
T ss_pred             HHHHHHccccccccCCcccccCCchhccCCCeEEeCChhhCCH-----HHHHHHHHHHhcCcEEeCCCCceeeccEEEEE
Confidence            332 2221                 123467899999998842     23345555554211 10     0011345677


Q ss_pred             ecCCC-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHh-CCCCCHHHHHHH
Q 011664          321 TMNSK-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQN-GSSLSPAEIGEL  389 (480)
Q Consensus       321 tTN~~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~-~~g~s~adI~~l  389 (480)
                      ||+..       ..+.+.|..  ||. ..|.+|+...  ++...|+..|+....       ..+... ..+++++-+..+
T Consensus       147 ~s~~~l~~l~~~g~f~~dL~~--~l~~~~i~lPpLReR~eDI~~L~~~fl~~~~-------~~~~~~~~~~~s~~al~~L  217 (326)
T PRK11608        147 ATNADLPAMVAEGKFRADLLD--RLAFDVVQLPPLRERQSDIMLMAEHFAIQMC-------RELGLPLFPGFTERARETL  217 (326)
T ss_pred             eCchhHHHHHHcCCchHHHHH--hcCCCEEECCChhhhhhhHHHHHHHHHHHHH-------HHhCCCCCCCCCHHHHHHH
Confidence            66642       345567776  774 5667766543  344556666653211       111111 148999999999


Q ss_pred             HHHhhhcHHHHHHHHHHHHHhc
Q 011664          390 MIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~~  411 (480)
                      ....+...++.|+.+++.+-..
T Consensus       218 ~~y~WPGNvrEL~~vl~~a~~~  239 (326)
T PRK11608        218 LNYRWPGNIRELKNVVERSVYR  239 (326)
T ss_pred             HhCCCCcHHHHHHHHHHHHHHh
Confidence            9999999999999999876553

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=99.12  E-value=1e-09  Score=112.49  Aligned_cols=194  Identities=15%  Similarity=0.157  Sum_probs=121.5

Q ss_pred             ccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHHHH
Q 011664          193 SMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLKSL  269 (480)
Q Consensus       193 ~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~~l  269 (480)
                      +|....-+.+.+.+.....           ....|||+|++||||+++|++|....   +.+|+.++|..+..+.--..+
T Consensus         2 iG~S~~m~~~~~~~~~~a~-----------~~~pVLI~GE~GtGK~~lAr~iH~~s~r~~~pfv~vnc~~~~~~~l~~~l   70 (329)
T TIGR02974         2 IGESNAFLEVLEQVSRLAP-----------LDRPVLIIGERGTGKELIAARLHYLSKRWQGPLVKLNCAALSENLLDSEL   70 (329)
T ss_pred             CcCCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCChHHHHHHHHHHhcCccCCCeEEEeCCCCChHHHHHHH
Confidence            4555556666666655422           23479999999999999999998755   468999999876542211233


Q ss_pred             HH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cc-----ccCCceEEEEecCCC-
Q 011664          270 LL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NS-----CCFEERVMVFTMNSK-  325 (480)
Q Consensus       270 ~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~-----~~~~~~ivI~tTN~~-  325 (480)
                      |.                 ......+|||||||.+..     .....|+..++.-. ..     ....+.-+|+|||.. 
T Consensus        71 fG~~~g~~~ga~~~~~G~~~~a~gGtL~Ldei~~L~~-----~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~at~~~l  145 (329)
T TIGR02974        71 FGHEAGAFTGAQKRHQGRFERADGGTLFLDELATASL-----LVQEKLLRVIEYGEFERVGGSQTLQVDVRLVCATNADL  145 (329)
T ss_pred             hccccccccCcccccCCchhhCCCCEEEeCChHhCCH-----HHHHHHHHHHHcCcEEecCCCceeccceEEEEechhhH
Confidence            31                 123568999999998842     23345555553211 00     001234567777632 


Q ss_pred             ------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhC-CCCCHHHHHHHHHHhhh
Q 011664          326 ------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNG-SSLSPAEIGELMIANRN  395 (480)
Q Consensus       326 ------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~-~g~s~adI~~ll~~a~~  395 (480)
                            ..+.+.|..  |+. ..|++|+...  ++...|+..|+....       ....... .++++.-+..++...+.
T Consensus       146 ~~~~~~g~fr~dL~~--rl~~~~i~lPpLReR~eDI~~L~~~fl~~~~-------~~~~~~~~~~ls~~a~~~L~~y~WP  216 (329)
T TIGR02974       146 PALAAEGRFRADLLD--RLAFDVITLPPLRERQEDIMLLAEHFAIRMA-------RELGLPLFPGFTPQAREQLLEYHWP  216 (329)
T ss_pred             HHHhhcCchHHHHHH--HhcchhcCCCchhhhhhhHHHHHHHHHHHHH-------HHhCCCCCCCcCHHHHHHHHhCCCC
Confidence                  234566666  774 4556665542  345556666653210       1111122 48999999999999999


Q ss_pred             cHHHHHHHHHHHHHhc
Q 011664          396 SPSRALKSVITALQTD  411 (480)
Q Consensus       396 ~~~~al~~~i~~~~~~  411 (480)
                      ..++.|+++++.+-..
T Consensus       217 GNvrEL~n~i~~~~~~  232 (329)
T TIGR02974       217 GNVRELKNVVERSVYR  232 (329)
T ss_pred             chHHHHHHHHHHHHHh
Confidence            9999999999876654

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

>PRK08058 DNA polymerase III subunit delta'; Validated

Probab=99.12  E-value=1.3e-09  Score=111.79  Aligned_cols=146  Identities=18%  Similarity=0.258  Sum_probs=103.8

Q ss_pred             Ccccccc-ChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC----------------
Q 011664          188 TFDTISM-ETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY----------------  250 (480)
Q Consensus       188 ~~~~i~g-~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~----------------  250 (480)
                      .|++|.| ++.+++.+...+.            ....+..+|||||+|+||+++|+++|+.+-+                
T Consensus         3 ~~~~i~~~q~~~~~~L~~~~~------------~~~l~ha~Lf~G~~G~gk~~~a~~la~~l~c~~~~~~~~cg~C~~c~   70 (329)
T PRK08058          3 TWEQLTALQPVVVKMLQNSIA------------KNRLSHAYLFEGAKGTGKKATALWLAKSLFCLERNGVEPCGTCTNCK   70 (329)
T ss_pred             cHHHHHhhHHHHHHHHHHHHH------------cCCCCceEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCcCHHHH
Confidence            4788888 8878887775543            1224668999999999999999999987522                


Q ss_pred             --------cEEEEeCCC-cCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCc
Q 011664          251 --------DVYDVDLSR-VADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEE  315 (480)
Q Consensus       251 --------~~~~i~~s~-~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~  315 (480)
                              ++..+.... -.+-.+++.+....      ....|++|||+|.+.     ....+.||..|+.-     ++.
T Consensus        71 ~~~~~~hpD~~~i~~~~~~i~id~ir~l~~~~~~~~~~~~~kvviI~~a~~~~-----~~a~NaLLK~LEEP-----p~~  140 (329)
T PRK08058         71 RIDSGNHPDVHLVAPDGQSIKKDQIRYLKEEFSKSGVESNKKVYIIEHADKMT-----ASAANSLLKFLEEP-----SGG  140 (329)
T ss_pred             HHhcCCCCCEEEeccccccCCHHHHHHHHHHHhhCCcccCceEEEeehHhhhC-----HHHHHHHHHHhcCC-----CCC
Confidence                    244443321 12234555554322      245799999999873     23457788888642     456


Q ss_pred             eEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHH
Q 011664          316 RVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASS  358 (480)
Q Consensus       316 ~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~  358 (480)
                      .++|++|+.+..|-|++++  |+ .+++|++|+.++....+..
T Consensus       141 ~~~Il~t~~~~~ll~TIrS--Rc-~~i~~~~~~~~~~~~~L~~  180 (329)
T PRK08058        141 TTAILLTENKHQILPTILS--RC-QVVEFRPLPPESLIQRLQE  180 (329)
T ss_pred             ceEEEEeCChHhCcHHHHh--hc-eeeeCCCCCHHHHHHHHHH
Confidence            7788889899999999999  88 4899999999887666653

>TIGR01817 nifA Nif-specific regulatory protein

Probab=99.12  E-value=1.5e-09  Score=118.26  Aligned_cols=200  Identities=18%  Similarity=0.190  Sum_probs=130.8

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD  262 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~  262 (480)
                      ..+|+.++|.....+.+.+.+.....           ....+||+|++||||+++|++|....   +.+|+.++|..+..
T Consensus       192 ~~~~~~liG~s~~~~~~~~~~~~~a~-----------~~~pvli~Ge~GtGK~~lA~~ih~~s~r~~~pfv~i~c~~~~~  260 (534)
T TIGR01817       192 SGKEDGIIGKSPAMRQVVDQARVVAR-----------SNSTVLLRGESGTGKELIAKAIHYLSPRAKRPFVKVNCAALSE  260 (534)
T ss_pred             cCccCceEECCHHHHHHHHHHHHHhC-----------cCCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeecCCCCH
Confidence            35789999999999998888776542           23469999999999999999999875   56899999998754


Q ss_pred             hHHHHHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cccc-----CCceEEE
Q 011664          263 DADLKSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NSCC-----FEERVMV  319 (480)
Q Consensus       263 ~~~l~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~~~-----~~~~ivI  319 (480)
                      +.--..+|.                 ......+|||||||.+..     .....|+..++.-. ....     ....-+|
T Consensus       261 ~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~GtL~ldei~~L~~-----~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI  335 (534)
T TIGR01817       261 TLLESELFGHEKGAFTGAIAQRKGRFELADGGTLFLDEIGEISP-----AFQAKLLRVLQEGEFERVGGNRTLKVDVRLV  335 (534)
T ss_pred             HHHHHHHcCCCCCccCCCCcCCCCcccccCCCeEEEechhhCCH-----HHHHHHHHHHhcCcEEECCCCceEeecEEEE
Confidence            221222332                 123467999999998842     23355666664211 1000     0124466


Q ss_pred             EecCCC-c------cCcccccCCCcee-EEEEcCCCC--HHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHH
Q 011664          320 FTMNSK-D------HVDQALLRPGRID-VHIHFPLCD--FSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGEL  389 (480)
Q Consensus       320 ~tTN~~-~------~LD~aLlrpGRfd-~~I~~~~p~--~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~l  389 (480)
                      +||+.. +      .+.+.|..  |+. ..|.+|+..  .++...|+..++....       ...... .++|++-+..+
T Consensus       336 ~~s~~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLreR~eDi~~L~~~~l~~~~-------~~~~~~-~~~s~~a~~~L  405 (534)
T TIGR01817       336 AATNRDLEEAVAKGEFRADLYY--RINVVPIFLPPLRERREDIPLLAEAFLEKFN-------RENGRP-LTITPSAIRVL  405 (534)
T ss_pred             EeCCCCHHHHHHcCCCCHHHHH--HhcCCeeeCCCcccccccHHHHHHHHHHHHH-------HHcCCC-CCCCHHHHHHH
Confidence            666532 1      23344444  554 466777665  3455667777764211       011112 48999999999


Q ss_pred             HHHhhhcHHHHHHHHHHHHHhc
Q 011664          390 MIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~~  411 (480)
                      ....+...++.|+.+++.+-..
T Consensus       406 ~~~~WPGNvrEL~~v~~~a~~~  427 (534)
T TIGR01817       406 MSCKWPGNVRELENCLERTATL  427 (534)
T ss_pred             HhCCCCChHHHHHHHHHHHHHh
Confidence            9989999999999999876543

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.

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=99.12  E-value=2.5e-10  Score=98.84  Aligned_cols=119  Identities=24%  Similarity=0.308  Sum_probs=73.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc---EEEEeCCCcCC--------------------hHHHHHHHHhh--cCCcE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD---VYDVDLSRVAD--------------------DADLKSLLLQT--TSKSV  278 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~~i~~s~~~~--------------------~~~l~~l~~~~--~~~sI  278 (480)
                      +..++|+||||||||++++++|..+...   ++.++++....                    .......+..+  ..+.+
T Consensus         2 ~~~~~l~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v   81 (148)
T smart00382        2 GEVILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLRLALALARKLKPDV   81 (148)
T ss_pred             CCEEEEECCCCCcHHHHHHHHHhccCCCCCCEEEECCEEccccCHHHHHhhhhhccCCCCCHHHHHHHHHHHHHhcCCCE
Confidence            3579999999999999999999999775   88888765321                    22233333332  34699


Q ss_pred             EEEecccccccCcccccchhhh-hhhcccccccccCCceEEEEecCC-CccCcccccCCCceeEEEEcCCC
Q 011664          279 ILIEDLDRFLVEKPAAVSLSGV-LNFMDGVLNSCCFEERVMVFTMNS-KDHVDQALLRPGRIDVHIHFPLC  347 (480)
Q Consensus       279 I~IDEiD~l~~~~~~~~~ls~l-L~~ldg~~~~~~~~~~ivI~tTN~-~~~LD~aLlrpGRfd~~I~~~~p  347 (480)
                      |+|||++.+............. .......   .......+|+++|. ....+..+.+  |++.++.++.+
T Consensus        82 iiiDei~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~i~~~~~~~~~~~~~~~~--~~~~~~~~~~~  147 (148)
T smart00382       82 LILDEITSLLDAEQEALLLLLEELRLLLLL---KSEKNLTVILTTNDEKDLGPALLRR--RFDRRIVLLLI  147 (148)
T ss_pred             EEEECCcccCCHHHHHHHHhhhhhHHHHHH---HhcCCCEEEEEeCCCccCchhhhhh--ccceEEEecCC
Confidence            9999999886433211110000 0000111   11345677888886 3344555555  88888887655

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.

>PRK07399 DNA polymerase III subunit delta'; Validated

Probab=99.11  E-value=2.6e-09  Score=108.71  Aligned_cols=175  Identities=13%  Similarity=0.140  Sum_probs=117.3

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-----------------
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-----------------  250 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-----------------  250 (480)
                      .|++|+|++++++.+...+..           | ..+..+||+||+|+||+++|.++|+.+-+                 
T Consensus         2 ~f~~iiGq~~~~~~L~~~i~~-----------~-rl~ha~Lf~G~~G~Gk~~~A~~~a~~llc~~~c~~c~~~~~~~~~h   69 (314)
T PRK07399          2 LFANLIGQPLAIELLTAAIKQ-----------N-RIAPAYLFAGPEGVGRKLAALCFIEGLLSQGSPSKNIRRRLEEGNH   69 (314)
T ss_pred             cHHHhCCHHHHHHHHHHHHHh-----------C-CCCceEEEECCCCCCHHHHHHHHHHHHcCCCCCCCcHhcccccCCC
Confidence            489999999999988876542           2 23558999999999999999999987521                 


Q ss_pred             -cEEEEeCCC-----c------------------CChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhh
Q 011664          251 -DVYDVDLSR-----V------------------ADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGV  300 (480)
Q Consensus       251 -~~~~i~~s~-----~------------------~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~l  300 (480)
                       +++.+....     .                  ..-..++.+....      ....|++||++|.+.     ....+.|
T Consensus        70 PDl~~i~p~~~~~g~~~~~~~~~~~~~~~~~~~~I~id~ir~i~~~l~~~p~~~~~kVvII~~ae~m~-----~~aaNaL  144 (314)
T PRK07399         70 PDLLWVEPTYQHQGKLITASEAEEAGLKRKAPPQIRLEQIREIKRFLSRPPLEAPRKVVVIEDAETMN-----EAAANAL  144 (314)
T ss_pred             CCEEEEeccccccccccchhhhhhccccccccccCcHHHHHHHHHHHccCcccCCceEEEEEchhhcC-----HHHHHHH
Confidence             223332210     0                  0112345543222      246899999999883     2344678


Q ss_pred             hhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCC
Q 011664          301 LNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSS  380 (480)
Q Consensus       301 L~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g  380 (480)
                      |..|+.-     + ..++|++|+.++.|-|.+++  |+ ..++|+.++.++..+++........  ...+...++.. .+
T Consensus       145 LK~LEEP-----p-~~~fILi~~~~~~Ll~TI~S--Rc-q~i~f~~l~~~~~~~~L~~~~~~~~--~~~~~~~l~~~-a~  212 (314)
T PRK07399        145 LKTLEEP-----G-NGTLILIAPSPESLLPTIVS--RC-QIIPFYRLSDEQLEQVLKRLGDEEI--LNINFPELLAL-AQ  212 (314)
T ss_pred             HHHHhCC-----C-CCeEEEEECChHhCcHHHHh--hc-eEEecCCCCHHHHHHHHHHhhcccc--chhHHHHHHHH-cC
Confidence            8887542     3 45788888899999999999  98 5899999999998888887643221  11123445443 35


Q ss_pred             CCHHHHHHHHH
Q 011664          381 LSPAEIGELMI  391 (480)
Q Consensus       381 ~s~adI~~ll~  391 (480)
                      -+|....+++.
T Consensus       213 Gs~~~al~~l~  223 (314)
T PRK07399        213 GSPGAAIANIE  223 (314)
T ss_pred             CCHHHHHHHHH
Confidence            56665555553

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=99.10  E-value=8.3e-10  Score=115.94  Aligned_cols=113  Identities=27%  Similarity=0.376  Sum_probs=69.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc-----EEEEeCC------CcC-C-----------hHHHHHHHHhh----cCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD-----VYDVDLS------RVA-D-----------DADLKSLLLQT----TSK  276 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~-----~~~i~~s------~~~-~-----------~~~l~~l~~~~----~~~  276 (480)
                      +++++|+||||||||++|+++|..++..     +..+..+      ++. +           ...+.++..++    ..|
T Consensus       194 ~~~iil~GppGtGKT~lA~~la~~l~~~~~~~~v~~VtFHpsySYeDFI~G~rP~~vgy~~~~G~f~~~~~~A~~~p~~~  273 (459)
T PRK11331        194 KKNIILQGPPGVGKTFVARRLAYLLTGEKAPQRVNMVQFHQSYSYEDFIQGYRPNGVGFRRKDGIFYNFCQQAKEQPEKK  273 (459)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHhcCCcccceeeEEeecccccHHHHhcccCCCCCCeEecCchHHHHHHHHHhcccCC
Confidence            4689999999999999999999987431     1122221      111 0           11122222222    357


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcc--------------------cccccccCCceEEEEecCCCc----cCcccc
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMD--------------------GVLNSCCFEERVMVFTMNSKD----HVDQAL  332 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ld--------------------g~~~~~~~~~~ivI~tTN~~~----~LD~aL  332 (480)
                      ++||||||+..-..    ....+++..|+                    .+.   -+.+..||+|+|..+    .+|.||
T Consensus       274 ~vliIDEINRani~----kiFGel~~lLE~~~rg~~~~v~l~y~e~d~e~f~---iP~Nl~IIgTMNt~Drs~~~lD~Al  346 (459)
T PRK11331        274 YVFIIDEINRANLS----KVFGEVMMLMEHDKRGENWSVPLTYSENDEERFY---VPENVYIIGLMNTADRSLAVVDYAL  346 (459)
T ss_pred             cEEEEehhhccCHH----Hhhhhhhhhccccccccccceeeecccccccccc---CCCCeEEEEecCccccchhhccHHH
Confidence            99999999964221    11223333332                    111   246778899999887    689999


Q ss_pred             cCCCceeEEEEcCC
Q 011664          333 LRPGRIDVHIHFPL  346 (480)
Q Consensus       333 lrpGRfd~~I~~~~  346 (480)
                      +|  ||. .|++.+
T Consensus       347 rR--RF~-fi~i~p  357 (459)
T PRK11331        347 RR--RFS-FIDIEP  357 (459)
T ss_pred             Hh--hhh-eEEecC
Confidence            99  995 566654

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=99.07  E-value=3.5e-09  Score=108.39  Aligned_cols=124  Identities=17%  Similarity=0.266  Sum_probs=93.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC------------------------cEEEEeCC---CcCChHHHHHHHHhh--
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY------------------------DVYDVDLS---RVADDADLKSLLLQT--  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~------------------------~~~~i~~s---~~~~~~~l~~l~~~~--  273 (480)
                      .+.++||+||+|+|||++|.++|+.+.+                        +++.+...   ...+-.+++.+....  
T Consensus        21 ~~ha~Lf~G~~G~GK~~~A~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~~~~~~~~i~id~iR~l~~~~~~  100 (328)
T PRK05707         21 HPHAYLLHGPAGIGKRALAERLAAALLCEAPQGGGACGSCKGCQLLRAGSHPDNFVLEPEEADKTIKVDQVRELVSFVVQ  100 (328)
T ss_pred             cceeeeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccCCCCCCCHHHHHHHHHHHhh
Confidence            4568999999999999999999987633                        45555432   223445666665332  


Q ss_pred             ----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          274 ----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       274 ----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                          ....|++||++|.+-     ....+.||..|+.-     +++.++|++|+.++.|.|.+++  |+. .+.|++|+.
T Consensus       101 ~~~~~~~kv~iI~~a~~m~-----~~aaNaLLK~LEEP-----p~~~~fiL~t~~~~~ll~TI~S--Rc~-~~~~~~~~~  167 (328)
T PRK05707        101 TAQLGGRKVVLIEPAEAMN-----RNAANALLKSLEEP-----SGDTVLLLISHQPSRLLPTIKS--RCQ-QQACPLPSN  167 (328)
T ss_pred             ccccCCCeEEEECChhhCC-----HHHHHHHHHHHhCC-----CCCeEEEEEECChhhCcHHHHh--hce-eeeCCCcCH
Confidence                245799999999883     34457788888642     4567888999999999999999  996 699999999


Q ss_pred             HHHHHHHHHH
Q 011664          350 SSFKTLASSY  359 (480)
Q Consensus       350 ~~r~~il~~~  359 (480)
                      ++-.+.+...
T Consensus       168 ~~~~~~L~~~  177 (328)
T PRK05707        168 EESLQWLQQA  177 (328)
T ss_pred             HHHHHHHHHh
Confidence            8877776654

>PRK13531 regulatory ATPase RavA; Provisional

Probab=99.07  E-value=8e-10  Score=116.94  Aligned_cols=130  Identities=15%  Similarity=0.213  Sum_probs=83.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCC-----CcCChHHHHHH-----HHhh-----cCCcEEEEeccc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLS-----RVADDADLKSL-----LLQT-----TSKSVILIEDLD  285 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s-----~~~~~~~l~~l-----~~~~-----~~~sII~IDEiD  285 (480)
                      ....+||+||||||||++|+++|..++.  +|..+.+.     ++.+...+...     |.+.     ....++|+|||.
T Consensus        38 ag~hVLL~GpPGTGKT~LAraLa~~~~~~~~F~~~~~~fttp~DLfG~l~i~~~~~~g~f~r~~~G~L~~A~lLfLDEI~  117 (498)
T PRK13531         38 SGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRFSTPEEVFGPLSIQALKDEGRYQRLTSGYLPEAEIVFLDEIW  117 (498)
T ss_pred             cCCCEEEECCCChhHHHHHHHHHHHhcccCcceeeeeeecCcHHhcCcHHHhhhhhcCchhhhcCCccccccEEeecccc
Confidence            3457999999999999999999997643  33333221     22222111111     1111     123599999998


Q ss_pred             ccccCcccccchhhhhhhcc-ccccc----ccCCceEEEEecCCCc---cCcccccCCCceeEEEEcCCCC-HHHHHHHH
Q 011664          286 RFLVEKPAAVSLSGVLNFMD-GVLNS----CCFEERVMVFTMNSKD---HVDQALLRPGRIDVHIHFPLCD-FSSFKTLA  356 (480)
Q Consensus       286 ~l~~~~~~~~~ls~lL~~ld-g~~~~----~~~~~~ivI~tTN~~~---~LD~aLlrpGRfd~~I~~~~p~-~~~r~~il  356 (480)
                      .+     +..+.+.||..|. +....    ...+.+++++|||...   ...+|+..  ||-.++.+|+|+ .++..+|+
T Consensus       118 ra-----sp~~QsaLLeam~Er~~t~g~~~~~lp~rfiv~ATN~LPE~g~~leAL~D--RFliri~vp~l~~~~~e~~lL  190 (498)
T PRK13531        118 KA-----GPAILNTLLTAINERRFRNGAHEEKIPMRLLVTASNELPEADSSLEALYD--RMLIRLWLDKVQDKANFRSML  190 (498)
T ss_pred             cC-----CHHHHHHHHHHHHhCeEecCCeEEeCCCcEEEEECCCCcccCCchHHhHh--hEEEEEECCCCCchHHHHHHH
Confidence            54     4566788888883 22110    1123467788888332   23359999  999999999997 56778888


Q ss_pred             HHH
Q 011664          357 SSY  359 (480)
Q Consensus       357 ~~~  359 (480)
                      ...
T Consensus       191 ~~~  193 (498)
T PRK13531        191 TSQ  193 (498)
T ss_pred             Hcc
Confidence            764

>smart00763 AAA_PrkA PrkA AAA domain

Probab=99.07  E-value=3.7e-09  Score=108.34  Aligned_cols=64  Identities=23%  Similarity=0.279  Sum_probs=51.1

Q ss_pred             CCcc-ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-------cEEEEeC
Q 011664          187 STFD-TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-------DVYDVDL  257 (480)
Q Consensus       187 ~~~~-~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------~~~~i~~  257 (480)
                      .-|+ ++.|+++.++++.+.+.....+      . ...++.++|+||||||||+||+++|+.++.       ++|.+..
T Consensus        47 ~~F~~~~~G~~~~i~~lv~~l~~~a~g------~-~~~r~il~L~GPPGsGKStla~~La~~l~~ys~t~eG~~Y~~~~  118 (361)
T smart00763       47 RFFDHDFFGMEEAIERFVNYFKSAAQG------L-EERKQILYLLGPVGGGKSSLVECLKRGLEEYSKTPEGRRYTFKW  118 (361)
T ss_pred             cccchhccCcHHHHHHHHHHHHHHHhc------C-CCCCcEEEEECCCCCCHHHHHHHHHHHHhhhcccccCceEEEEe
Confidence            4577 9999999999988776655421      1 224567899999999999999999999976       8888876

This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=99.07  E-value=3.1e-09  Score=118.20  Aligned_cols=199  Identities=16%  Similarity=0.178  Sum_probs=125.6

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD  263 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~  263 (480)
                      .+|++++|.....+.+.+.+....+.           ...+||+|++||||+++|++|.+..   +.+|+.+||..+..+
T Consensus       322 ~~~~~l~g~s~~~~~~~~~~~~~a~~-----------~~pvli~Ge~GtGK~~~A~~ih~~s~r~~~pfv~vnc~~~~~~  390 (638)
T PRK11388        322 HTFDHMPQDSPQMRRLIHFGRQAAKS-----------SFPVLLCGEEGVGKALLAQAIHNESERAAGPYIAVNCQLYPDE  390 (638)
T ss_pred             ccccceEECCHHHHHHHHHHHHHhCc-----------CCCEEEECCCCcCHHHHHHHHHHhCCccCCCeEEEECCCCChH
Confidence            46888999888888777776655332           3469999999999999999999875   468999999988653


Q ss_pred             HHHHHHHHh--------------hcCCcEEEEecccccccCcccccchhhhhhhccccc-ccccC-----CceEEEEecC
Q 011664          264 ADLKSLLLQ--------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NSCCF-----EERVMVFTMN  323 (480)
Q Consensus       264 ~~l~~l~~~--------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~~~~-----~~~ivI~tTN  323 (480)
                      .-...+|..              ......||||||+.+..     .....|+..++.-. ....+     -..-||+|||
T Consensus       391 ~~~~elfg~~~~~~~~~~~g~~~~a~~GtL~ldei~~l~~-----~~Q~~Ll~~l~~~~~~~~~~~~~~~~~~riI~~t~  465 (638)
T PRK11388        391 ALAEEFLGSDRTDSENGRLSKFELAHGGTLFLEKVEYLSP-----ELQSALLQVLKTGVITRLDSRRLIPVDVRVIATTT  465 (638)
T ss_pred             HHHHHhcCCCCcCccCCCCCceeECCCCEEEEcChhhCCH-----HHHHHHHHHHhcCcEEeCCCCceEEeeEEEEEecc
Confidence            323344431              13467999999998842     22345565554211 10001     1234777777


Q ss_pred             CC-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SK-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      ..       ..+.+.|.-  |+. ..|.+|+...  ++...|+..++....       ... ....++|+.-+..|....
T Consensus       466 ~~l~~~~~~~~f~~dL~~--~l~~~~i~lPpLreR~~Di~~L~~~~l~~~~-------~~~-~~~~~~s~~a~~~L~~y~  535 (638)
T PRK11388        466 ADLAMLVEQNRFSRQLYY--ALHAFEITIPPLRMRREDIPALVNNKLRSLE-------KRF-STRLKIDDDALARLVSYR  535 (638)
T ss_pred             CCHHHHHhcCCChHHHhh--hhceeEEeCCChhhhhhHHHHHHHHHHHHHH-------HHh-CCCCCcCHHHHHHHHcCC
Confidence            43       122233333  442 4455555443  234456666653211       011 112378999999999989


Q ss_pred             hhcHHHHHHHHHHHHHhc
Q 011664          394 RNSPSRALKSVITALQTD  411 (480)
Q Consensus       394 ~~~~~~al~~~i~~~~~~  411 (480)
                      +...++.|+.+++.+-..
T Consensus       536 WPGNvreL~~~l~~~~~~  553 (638)
T PRK11388        536 WPGNDFELRSVIENLALS  553 (638)
T ss_pred             CCChHHHHHHHHHHHHHh
Confidence            999999999999876544

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=99.06  E-value=1.1e-09  Score=110.74  Aligned_cols=141  Identities=16%  Similarity=0.218  Sum_probs=98.0

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------------------
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------------------  249 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------------------  249 (480)
                      ++++.+.+...+.......          | ..+..+||+||||||||++|.++|+++.                     
T Consensus         2 ~~~~~~~~~~~l~~~~~~~----------~-~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~   70 (325)
T COG0470           2 ELVPWQEAVKRLLVQALES----------G-RLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPA   70 (325)
T ss_pred             CcccchhHHHHHHHHHHhc----------C-CCCceeeeeCCCCCCHHHHHHHHHHHHhCCCcccCCcccchhhhhHHhh
Confidence            4555666555555443322          1 1233799999999999999999999886                     


Q ss_pred             ---CcEEEEeCCCcCC----hHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCce
Q 011664          250 ---YDVYDVDLSRVAD----DADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEER  316 (480)
Q Consensus       250 ---~~~~~i~~s~~~~----~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~  316 (480)
                         .+++.++.++...    ...++.+....      ....|++|||+|.+..     ...+.++..+.-     .....
T Consensus        71 ~~~~d~lel~~s~~~~~~i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~-----~A~nallk~lEe-----p~~~~  140 (325)
T COG0470          71 GNHPDFLELNPSDLRKIDIIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTE-----DAANALLKTLEE-----PPKNT  140 (325)
T ss_pred             cCCCceEEecccccCCCcchHHHHHHHHHHhccCCCCCCceEEEeCcHHHHhH-----HHHHHHHHHhcc-----CCCCe
Confidence               5788888887655    33354443322      2458999999998843     334566666642     24567


Q ss_pred             EEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHH
Q 011664          317 VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTL  355 (480)
Q Consensus       317 ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~i  355 (480)
                      .+|++||.++.+-+.+++  |+. .+.|++|+...+...
T Consensus       141 ~~il~~n~~~~il~tI~S--Rc~-~i~f~~~~~~~~i~~  176 (325)
T COG0470         141 RFILITNDPSKILPTIRS--RCQ-RIRFKPPSRLEAIAW  176 (325)
T ss_pred             EEEEEcCChhhccchhhh--cce-eeecCCchHHHHHHH
Confidence            889999999999999999  884 888888665554433

>PF07724 AAA_2: AAA domain (Cdc48 subfamily); InterPro: IPR013093 ATPases Associated to a variety of cellular Activities (AAA) are a family distinguished by a highly conserved module of 230 amino acids []

Probab=99.06  E-value=2.8e-10  Score=105.91  Aligned_cols=104  Identities=22%  Similarity=0.390  Sum_probs=72.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC----cEEEEeCCCcCC----hHHHHHHHHhh------cCCcEEEEecccccc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY----DVYDVDLSRVAD----DADLKSLLLQT------TSKSVILIEDLDRFL  288 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~----~~~~i~~s~~~~----~~~l~~l~~~~------~~~sII~IDEiD~l~  288 (480)
                      +...+||.||+|||||.+|+++|..+..    +++.+|++.+..    +..+..++...      ....||||||||...
T Consensus         2 p~~~~ll~GpsGvGKT~la~~la~~l~~~~~~~~~~~d~s~~~~~~~~~~~~~~l~~~~~~~v~~~~~gVVllDEidKa~   81 (171)
T PF07724_consen    2 PKSNFLLAGPSGVGKTELAKALAELLFVGSERPLIRIDMSEYSEGDDVESSVSKLLGSPPGYVGAEEGGVVLLDEIDKAH   81 (171)
T ss_dssp             -SEEEEEESSTTSSHHHHHHHHHHHHT-SSCCEEEEEEGGGHCSHHHCSCHCHHHHHHTTCHHHHHHHTEEEEETGGGCS
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHhccCCccchHHHhhhcccccchHHhhhhhhhhcccceeeccchhhhhhHHHhhcc
Confidence            3457899999999999999999999996    999999999887    44455554332      234699999999987


Q ss_pred             cCcccc------cchhhhhhhcccccc------cccCCceEEEEecCCCc
Q 011664          289 VEKPAA------VSLSGVLNFMDGVLN------SCCFEERVMVFTMNSKD  326 (480)
Q Consensus       289 ~~~~~~------~~ls~lL~~ldg~~~------~~~~~~~ivI~tTN~~~  326 (480)
                      +..+..      .....||..||+-.-      ...-.+.++|+|+|.-.
T Consensus        82 ~~~~~~~~v~~~~V~~~LL~~le~g~~~d~~g~~vd~~n~ifI~Tsn~~~  131 (171)
T PF07724_consen   82 PSNSGGADVSGEGVQNSLLQLLEGGTLTDSYGRTVDTSNIIFIMTSNFGA  131 (171)
T ss_dssp             HTTTTCSHHHHHHHHHHHHHHHHHSEEEETTCCEEEGTTEEEEEEESSST
T ss_pred             ccccccchhhHHHHHHHHHHHhcccceecccceEEEeCCceEEEeccccc
Confidence            632211      235567777753211      12235678999999543

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 ....

>TIGR00602 rad24 checkpoint protein rad24

Probab=99.06  E-value=1.8e-09  Score=118.51  Aligned_cols=169  Identities=20%  Similarity=0.279  Sum_probs=102.5

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEE-E
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYD-V  255 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~-i  255 (480)
                      .|.  ..-.|.++++++|+++..+.+...+....        .+....+.++|+||||||||++++++|++++..+.. .
T Consensus        73 pW~--eKyrP~~ldel~~~~~ki~~l~~~l~~~~--------~~~~~~~illL~GP~GsGKTTl~~~la~~l~~~~~Ew~  142 (637)
T TIGR00602        73 PWV--EKYKPETQHELAVHKKKIEEVETWLKAQV--------LENAPKRILLITGPSGCGKSTTIKILSKELGIQVQEWS  142 (637)
T ss_pred             chH--HHhCCCCHHHhcCcHHHHHHHHHHHHhcc--------cccCCCcEEEEECCCCCCHHHHHHHHHHHhhhHHHHHh
Confidence            463  45578999999999998888776554321        122334569999999999999999999999875432 1


Q ss_pred             e---CC-----------------Cc-CChHHHHHHHHhh------------cCCcEEEEecccccccCcccccchhhhhh
Q 011664          256 D---LS-----------------RV-ADDADLKSLLLQT------------TSKSVILIEDLDRFLVEKPAAVSLSGVLN  302 (480)
Q Consensus       256 ~---~s-----------------~~-~~~~~l~~l~~~~------------~~~sII~IDEiD~l~~~~~~~~~ls~lL~  302 (480)
                      +   +.                 .+ .....+..++..+            ..+.||+|||++.+...  ....+..+|.
T Consensus       143 npv~~~~~~~~~~~~~s~~~~~~~~~s~~~~F~~fl~~a~~~~~~~g~~~~~~~~IILIDEiPn~~~r--~~~~lq~lLr  220 (637)
T TIGR00602       143 NPTLPDFQKNDHKVTLSLESCFSNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDLPNQFYR--DTRALHEILR  220 (637)
T ss_pred             hhhhhcccccccccchhhhhccccccchHHHHHHHHHHHHhhhcccccccCCceeEEEeecchhhchh--hHHHHHHHHH
Confidence            1   00                 00 1112233333322            24579999999987642  2223444444


Q ss_pred             -hcccccccccCCceEEEEecCCCc----------c----CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccC
Q 011664          303 -FMDGVLNSCCFEERVMVFTMNSKD----------H----VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK  363 (480)
Q Consensus       303 -~ldg~~~~~~~~~~ivI~tTN~~~----------~----LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~  363 (480)
                       ...  ..   +.-.+|+++|..+.          .    |.++++..-|+ .+|.|++.+....++.+...+..+
T Consensus       221 ~~~~--e~---~~~pLI~I~TE~~~~~~~~~~~~f~~~~lL~~eLls~~rv-~~I~FnPia~t~l~K~L~rIl~~E  290 (637)
T TIGR00602       221 WKYV--SI---GRCPLVFIITESLEGDNNQRRLLFPAETIMNKEILEEPRV-SNISFNPIAPTIMKKFLNRIVTIE  290 (637)
T ss_pred             HHhh--cC---CCceEEEEecCCccccccccccccchhcccCHhHhcccce-eEEEeCCCCHHHHHHHHHHHHHhh
Confidence             211  11   11223333442221          1    33677743355 489999999999888888887543

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

>PRK08181 transposase; Validated

Probab=99.05  E-value=5.5e-10  Score=111.09  Aligned_cols=94  Identities=20%  Similarity=0.396  Sum_probs=63.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC-------hHHHHHHHHhhcCCcEEEEecccccccCccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD-------DADLKSLLLQTTSKSVILIEDLDRFLVEKPA  293 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~-------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~  293 (480)
                      ..+++|+||||||||+|+.|+|+++   |..+++++..++..       +..+.+.+.....+.+|+|||++........
T Consensus       106 ~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~~~~~~~~l~~l~~~dLLIIDDlg~~~~~~~~  185 (269)
T PRK08181        106 GANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARRELQLESAIAKLDKFDLLILDDLAYVTKDQAE  185 (269)
T ss_pred             CceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHhCCcHHHHHHHHhcCCEEEEeccccccCCHHH
Confidence            4589999999999999999999754   77788887655443       1223445566678899999999987544333


Q ss_pred             ccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          294 AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ...   |++.++....     ..-+|+|||.+
T Consensus       186 ~~~---Lf~lin~R~~-----~~s~IiTSN~~  209 (269)
T PRK08181        186 TSV---LFELISARYE-----RRSILITANQP  209 (269)
T ss_pred             HHH---HHHHHHHHHh-----CCCEEEEcCCC
Confidence            333   4444443222     13477888865

>PRK12377 putative replication protein; Provisional

Probab=99.03  E-value=7.8e-10  Score=108.72  Aligned_cols=95  Identities=17%  Similarity=0.218  Sum_probs=64.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh--------HHHHHHHHhhcCCcEEEEecccccccCcc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD--------ADLKSLLLQTTSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~--------~~l~~l~~~~~~~sII~IDEiD~l~~~~~  292 (480)
                      ..+++|+||||||||+||.|||+++   |..+..++..++...        .....++.......+|+|||++.......
T Consensus       101 ~~~l~l~G~~GtGKThLa~AIa~~l~~~g~~v~~i~~~~l~~~l~~~~~~~~~~~~~l~~l~~~dLLiIDDlg~~~~s~~  180 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLAAAIGNRLLAKGRSVIVVTVPDVMSRLHESYDNGQSGEKFLQELCKVDLLVLDEIGIQRETKN  180 (248)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEHHHHHHHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCCCCHH
Confidence            3589999999999999999999987   667777776654321        11234556667889999999986543332


Q ss_pred             cccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          293 AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       293 ~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                         ....|.+.++.-..    ...-+|+|||..
T Consensus       181 ---~~~~l~~ii~~R~~----~~~ptiitSNl~  206 (248)
T PRK12377        181 ---EQVVLNQIIDRRTA----SMRSVGMLTNLN  206 (248)
T ss_pred             ---HHHHHHHHHHHHHh----cCCCEEEEcCCC
Confidence               23344555544322    345578899954

>PF07726 AAA_3: ATPase family associated with various cellular activities (AAA); InterPro: IPR011703 This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model

Probab=99.02  E-value=1.7e-10  Score=101.32  Aligned_cols=106  Identities=20%  Similarity=0.264  Sum_probs=60.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHH--HHh-------hcC---CcEEEEecccccccCccc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSL--LLQ-------TTS---KSVILIEDLDRFLVEKPA  293 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l--~~~-------~~~---~sII~IDEiD~l~~~~~~  293 (480)
                      .+||.|+||+|||++|+++|..++..|..|.++.-...+++.-.  +..       ...   ..|+++|||...     .
T Consensus         1 HvLleg~PG~GKT~la~~lA~~~~~~f~RIq~tpdllPsDi~G~~v~~~~~~~f~~~~GPif~~ill~DEiNra-----p   75 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALARSLGLSFKRIQFTPDLLPSDILGFPVYDQETGEFEFRPGPIFTNILLADEINRA-----P   75 (131)
T ss_dssp             -EEEES---HHHHHHHHHHHHHTT--EEEEE--TT--HHHHHEEEEEETTTTEEEEEE-TT-SSEEEEETGGGS------
T ss_pred             CEeeECCCccHHHHHHHHHHHHcCCceeEEEecCCCCcccceeeeeeccCCCeeEeecChhhhceeeecccccC-----C
Confidence            38999999999999999999999999999988643333333211  000       012   269999999965     4


Q ss_pred             ccchhhhhhhcccccc------cccCCceEEEEecCCCc-----cCcccccCCCce
Q 011664          294 AVSLSGVLNFMDGVLN------SCCFEERVMVFTMNSKD-----HVDQALLRPGRI  338 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~------~~~~~~~ivI~tTN~~~-----~LD~aLlrpGRf  338 (480)
                      ..+.+.||+.|..-.-      ....+..+||+|-|..+     .|++|++.  ||
T Consensus        76 pktQsAlLeam~Er~Vt~~g~~~~lp~pf~ViATqNp~e~~Gty~Lpea~~D--RF  129 (131)
T PF07726_consen   76 PKTQSALLEAMEERQVTIDGQTYPLPDPFFVIATQNPVEQEGTYPLPEAQLD--RF  129 (131)
T ss_dssp             HHHHHHHHHHHHHSEEEETTEEEE--SS-EEEEEE-TT--S------HHHHT--TS
T ss_pred             HHHHHHHHHHHHcCeEEeCCEEEECCCcEEEEEecCccccCceecCCHHHhc--cc
Confidence            4667888888852111      02234456777778665     57888887  77

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.

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=99.01  E-value=4.9e-09  Score=113.79  Aligned_cols=202  Identities=15%  Similarity=0.173  Sum_probs=125.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~  261 (480)
                      ...+|++++|....-+.+.+.+......           ...+||+|++||||+++|+++....   +.+|+.++|+.+.
T Consensus       199 ~~~~f~~~ig~s~~~~~~~~~~~~~A~~-----------~~pvlI~GE~GtGK~~lA~aiH~~s~r~~~pfv~inca~~~  267 (520)
T PRK10820        199 DDSAFSQIVAVSPKMRQVVEQARKLAML-----------DAPLLITGDTGTGKDLLAYACHLRSPRGKKPFLALNCASIP  267 (520)
T ss_pred             ccccccceeECCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCccHHHHHHHHHHhCCCCCCCeEEeccccCC
Confidence            3457999999998877777766554222           3359999999999999999997654   4689999998876


Q ss_pred             ChHHHHHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccc-cccccc-----CCceEE
Q 011664          262 DDADLKSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG-VLNSCC-----FEERVM  318 (480)
Q Consensus       262 ~~~~l~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg-~~~~~~-----~~~~iv  318 (480)
                      .+.--..+|.                 +......|||||||.+..     .....|++.++. ......     ...+-|
T Consensus       268 ~~~~e~elFG~~~~~~~~~~~~~~g~~e~a~~GtL~LdeI~~L~~-----~~Q~~Ll~~l~~~~~~~~g~~~~~~~~vRi  342 (520)
T PRK10820        268 DDVVESELFGHAPGAYPNALEGKKGFFEQANGGSVLLDEIGEMSP-----RMQAKLLRFLNDGTFRRVGEDHEVHVDVRV  342 (520)
T ss_pred             HHHHHHHhcCCCCCCcCCcccCCCChhhhcCCCEEEEeChhhCCH-----HHHHHHHHHHhcCCcccCCCCcceeeeeEE
Confidence            4222223332                 123457899999998843     223455555532 111000     112346


Q ss_pred             EEecCCC-c------cCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHH
Q 011664          319 VFTMNSK-D------HVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       319 I~tTN~~-~------~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~  388 (480)
                      |+||+.+ .      .+.+.|..  |+. ..|.+|+...  ++...++..++....       .+......+++++-+..
T Consensus       343 I~st~~~l~~l~~~g~f~~dL~~--rL~~~~i~lPpLreR~~Di~~L~~~fl~~~~-------~~~g~~~~~ls~~a~~~  413 (520)
T PRK10820        343 ICATQKNLVELVQKGEFREDLYY--RLNVLTLNLPPLRDRPQDIMPLTELFVARFA-------DEQGVPRPKLAADLNTV  413 (520)
T ss_pred             EEecCCCHHHHHHcCCccHHHHh--hcCeeEEeCCCcccChhHHHHHHHHHHHHHH-------HHcCCCCCCcCHHHHHH
Confidence            6666543 2      23455665  764 4555555543  234445555543210       01111124789998888


Q ss_pred             HHHHhhhcHHHHHHHHHHHHHhc
Q 011664          389 LMIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       389 ll~~a~~~~~~al~~~i~~~~~~  411 (480)
                      |....+...++.|++++..+-..
T Consensus       414 L~~y~WPGNvreL~nvl~~a~~~  436 (520)
T PRK10820        414 LTRYGWPGNVRQLKNAIYRALTQ  436 (520)
T ss_pred             HhcCCCCCHHHHHHHHHHHHHHh
Confidence            88888999999999998876654

>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional

Probab=99.00  E-value=3.6e-09  Score=118.57  Aligned_cols=199  Identities=15%  Similarity=0.165  Sum_probs=125.6

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD  263 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~  263 (480)
                      .+|++++|.....+.+.+.+......           ...+||+|++|||||++|++|....   +.+++.++|..+..+
T Consensus       373 ~~~~~liG~S~~~~~~~~~~~~~a~~-----------~~pVLI~GE~GTGK~~lA~~ih~~s~r~~~~~v~i~c~~~~~~  441 (686)
T PRK15429        373 SEFGEIIGRSEAMYSVLKQVEMVAQS-----------DSTVLILGETGTGKELIARAIHNLSGRNNRRMVKMNCAAMPAG  441 (686)
T ss_pred             ccccceeecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCcCHHHHHHHHHHhcCCCCCCeEEEecccCChh
Confidence            57899999999999998888765332           3479999999999999999998854   578999999876432


Q ss_pred             HHHHHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-----cc-ccCCceEEEE
Q 011664          264 ADLKSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----NS-CCFEERVMVF  320 (480)
Q Consensus       264 ~~l~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----~~-~~~~~~ivI~  320 (480)
                      .--..+|.                 .....++||||||+.+..     .....|+..++.-.     +. .-..+.-+|+
T Consensus       442 ~~~~~lfg~~~~~~~g~~~~~~g~le~a~~GtL~Ldei~~L~~-----~~Q~~L~~~l~~~~~~~~g~~~~~~~~~RiI~  516 (686)
T PRK15429        442 LLESDLFGHERGAFTGASAQRIGRFELADKSSLFLDEVGDMPL-----ELQPKLLRVLQEQEFERLGSNKIIQTDVRLIA  516 (686)
T ss_pred             HhhhhhcCcccccccccccchhhHHHhcCCCeEEEechhhCCH-----HHHHHHHHHHHhCCEEeCCCCCcccceEEEEE
Confidence            11111111                 223568999999998732     23355666554211     00 0012344677


Q ss_pred             ecCCC-c------cCcccccCCCceeEEEEcCCCCHHHH----HHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHH
Q 011664          321 TMNSK-D------HVDQALLRPGRIDVHIHFPLCDFSSF----KTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGEL  389 (480)
Q Consensus       321 tTN~~-~------~LD~aLlrpGRfd~~I~~~~p~~~~r----~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~l  389 (480)
                      ||+.. .      .+.+.|..  |+. .+.+..|...+|    ..|++.|+....       ........++|+.-+..+
T Consensus       517 ~t~~~l~~~~~~~~f~~~L~~--~l~-~~~i~lPpLreR~~Di~~L~~~~l~~~~-------~~~~~~~~~~s~~al~~L  586 (686)
T PRK15429        517 ATNRDLKKMVADREFRSDLYY--RLN-VFPIHLPPLRERPEDIPLLVKAFTFKIA-------RRMGRNIDSIPAETLRTL  586 (686)
T ss_pred             eCCCCHHHHHHcCcccHHHHh--ccC-eeEEeCCChhhhHhHHHHHHHHHHHHHH-------HHcCCCCCCcCHHHHHHH
Confidence            77643 2      12233333  443 334444444444    345555543211       011112247999999999


Q ss_pred             HHHhhhcHHHHHHHHHHHHHhc
Q 011664          390 MIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~~  411 (480)
                      ....+...++.|+++++.+-..
T Consensus       587 ~~y~WPGNvrEL~~~i~~a~~~  608 (686)
T PRK15429        587 SNMEWPGNVRELENVIERAVLL  608 (686)
T ss_pred             HhCCCCCcHHHHHHHHHHHHHh
Confidence            9999999999999999877654

>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR

Probab=99.00  E-value=3.8e-09  Score=114.34  Aligned_cols=199  Identities=15%  Similarity=0.198  Sum_probs=126.8

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~  261 (480)
                      ..-+|++++|.....+.+.+.+..+...           ...+||+|++||||+++|++|.+..   +.+|+.+||..+.
T Consensus       207 ~~~~f~~iiG~S~~m~~~~~~i~~~A~~-----------~~pVLI~GE~GTGKe~lA~~IH~~S~r~~~pfv~inC~~l~  275 (526)
T TIGR02329       207 TRYRLDDLLGASAPMEQVRALVRLYARS-----------DATVLILGESGTGKELVAQAIHQLSGRRDFPFVAINCGAIA  275 (526)
T ss_pred             cccchhheeeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCcCHHHHHHHHHHhcCcCCCCEEEeccccCC
Confidence            3467999999999888888877765332           3479999999999999999999764   5689999998875


Q ss_pred             ChHHHHHHHH------------------hhcCCcEEEEecccccccCcccccchhhhhhhcccc-----ccc-ccCCceE
Q 011664          262 DDADLKSLLL------------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV-----LNS-CCFEERV  317 (480)
Q Consensus       262 ~~~~l~~l~~------------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~-----~~~-~~~~~~i  317 (480)
                      ...--..+|.                  +......||||||+.+..     .....|+..++.-     .+. ...-++-
T Consensus       276 e~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~-----~~Q~~Ll~~L~~~~~~r~g~~~~~~~dvR  350 (526)
T TIGR02329       276 ESLLEAELFGYEEGAFTGARRGGRTGLIEAAHRGTLFLDEIGEMPL-----PLQTRLLRVLEEREVVRVGGTEPVPVDVR  350 (526)
T ss_pred             hhHHHHHhcCCcccccccccccccccchhhcCCceEEecChHhCCH-----HHHHHHHHHHhcCcEEecCCCceeeecce
Confidence            4221122332                  113457899999998842     2335566555321     110 0001224


Q ss_pred             EEEecCCC-cc------CcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHH
Q 011664          318 MVFTMNSK-DH------VDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIG  387 (480)
Q Consensus       318 vI~tTN~~-~~------LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~  387 (480)
                      +|+|||.. ..      +.+.|..  |+. ..|++|+...  ++...|+..|+.....          ....+++++.+.
T Consensus       351 iIaat~~~l~~~v~~g~fr~dL~~--rL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~----------~~~~~~~~~a~~  418 (526)
T TIGR02329       351 VVAATHCALTTAVQQGRFRRDLFY--RLSILRIALPPLRERPGDILPLAAEYLVQAAA----------ALRLPDSEAAAQ  418 (526)
T ss_pred             EEeccCCCHHHHhhhcchhHHHHH--hcCCcEEeCCCchhchhHHHHHHHHHHHHHHH----------HcCCCCCHHHHH
Confidence            66666643 21      2233443  553 5666666544  3455666676643211          112257777776


Q ss_pred             H-------HHHHhhhcHHHHHHHHHHHHHhc
Q 011664          388 E-------LMIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       388 ~-------ll~~a~~~~~~al~~~i~~~~~~  411 (480)
                      .       +....+...++.|+++++.+...
T Consensus       419 ~~~~~~~~L~~y~WPGNvrEL~nvier~~i~  449 (526)
T TIGR02329       419 VLAGVADPLQRYPWPGNVRELRNLVERLALE  449 (526)
T ss_pred             HhHHHHHHHHhCCCCchHHHHHHHHHHHHHh
Confidence            6       77888999999999999887653

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.

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

Probab=99.00  E-value=3e-09  Score=112.44  Aligned_cols=202  Identities=18%  Similarity=0.205  Sum_probs=133.4

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      +....+|++|+|....-..+++.+..+-           +..-.||+.|.+||||..+|++|.+..   +-+|+.+||..
T Consensus       238 ~~a~y~f~~Iig~S~~m~~~~~~akr~A-----------~tdstVLi~GESGTGKElfA~~IH~~S~R~~~PFIaiNCaA  306 (560)
T COG3829         238 LKAKYTFDDIIGESPAMLRVLELAKRIA-----------KTDSTVLILGESGTGKELFARAIHNLSPRANGPFIAINCAA  306 (560)
T ss_pred             cccccchhhhccCCHHHHHHHHHHHhhc-----------CCCCcEEEecCCCccHHHHHHHHHhcCcccCCCeEEEeccc
Confidence            3456789999999988888877665442           234579999999999999999999876   56899999988


Q ss_pred             cCChHHHHHHHHh------------------hcCCcEEEEecccccccCcccccchhhhhhhcc-----ccccc-ccCCc
Q 011664          260 VADDADLKSLLLQ------------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-----GVLNS-CCFEE  315 (480)
Q Consensus       260 ~~~~~~l~~l~~~------------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-----g~~~~-~~~~~  315 (480)
                      +-..--=..+|..                  .....-||+|||..+.     ....+.||..+.     .+.+. .-.-.
T Consensus       307 iPe~LlESELFGye~GAFTGA~~~GK~GlfE~A~gGTLFLDEIgemp-----l~LQaKLLRVLQEkei~rvG~t~~~~vD  381 (560)
T COG3829         307 IPETLLESELFGYEKGAFTGASKGGKPGLFELANGGTLFLDEIGEMP-----LPLQAKLLRVLQEKEIERVGGTKPIPVD  381 (560)
T ss_pred             CCHHHHHHHHhCcCCccccccccCCCCcceeeccCCeEEehhhccCC-----HHHHHHHHHHHhhceEEecCCCCceeeE
Confidence            7542111233311                  1234789999999773     233466776664     12211 01123


Q ss_pred             eEEEEecCCC-c------cCcccccCCCceeEEEEcCCCCHHHHH----HHHHHHhccCCCCCchhHHHHHHhCCCCCHH
Q 011664          316 RVMVFTMNSK-D------HVDQALLRPGRIDVHIHFPLCDFSSFK----TLASSYLGLKDHKLFPQVEEIFQNGSSLSPA  384 (480)
Q Consensus       316 ~ivI~tTN~~-~------~LD~aLlrpGRfd~~I~~~~p~~~~r~----~il~~~l~~~~~~l~~~i~~l~~~~~g~s~a  384 (480)
                      +-||+|||.. .      .+-..|.-  |+. ++.+..|...+|.    .+...++......+.       ....|++|.
T Consensus       382 VRIIAATN~nL~~~i~~G~FReDLYY--RLN-V~~i~iPPLReR~eDI~~L~~~Fl~k~s~~~~-------~~v~~ls~~  451 (560)
T COG3829         382 VRIIAATNRNLEKMIAEGTFREDLYY--RLN-VIPITIPPLRERKEDIPLLAEYFLDKFSRRYG-------RNVKGLSPD  451 (560)
T ss_pred             EEEEeccCcCHHHHHhcCcchhhhee--eec-eeeecCCCcccCcchHHHHHHHHHHHHHHHcC-------CCcccCCHH
Confidence            5589999953 2      22233333  553 5566666655543    344444432222221       234689999


Q ss_pred             HHHHHHHHhhhcHHHHHHHHHHHHHh
Q 011664          385 EIGELMIANRNSPSRALKSVITALQT  410 (480)
Q Consensus       385 dI~~ll~~a~~~~~~al~~~i~~~~~  410 (480)
                      .+..++..+|...+|.|+++++.+-.
T Consensus       452 a~~~L~~y~WPGNVRELeNviER~v~  477 (560)
T COG3829         452 ALALLLRYDWPGNVRELENVIERAVN  477 (560)
T ss_pred             HHHHHHhCCCCchHHHHHHHHHHHHh
Confidence            99999999999999999999998875

>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional

Probab=98.99  E-value=5.1e-09  Score=113.44  Aligned_cols=199  Identities=14%  Similarity=0.165  Sum_probs=127.1

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA  264 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~  264 (480)
                      ++.+++|.....+.+.+.+.....           ....|||+|++||||+++|++|....   +.+|+.++|..+..+.
T Consensus       185 ~~~~iig~s~~~~~~~~~i~~~a~-----------~~~pVlI~Ge~GtGK~~~A~~ih~~s~r~~~p~v~v~c~~~~~~~  253 (509)
T PRK05022        185 KEGEMIGQSPAMQQLKKEIEVVAA-----------SDLNVLILGETGVGKELVARAIHAASPRADKPLVYLNCAALPESL  253 (509)
T ss_pred             cCCceeecCHHHHHHHHHHHHHhC-----------CCCcEEEECCCCccHHHHHHHHHHhCCcCCCCeEEEEcccCChHH
Confidence            578899999999988888776532           24479999999999999999999875   5689999999875421


Q ss_pred             HHHHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-----cc-ccCCceEEEEe
Q 011664          265 DLKSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----NS-CCFEERVMVFT  321 (480)
Q Consensus       265 ~l~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----~~-~~~~~~ivI~t  321 (480)
                      --..+|.                 .......|||||||.+..     .....|+..++.-.     +. ....+.-||+|
T Consensus       254 ~e~~lfG~~~g~~~ga~~~~~g~~~~a~gGtL~ldeI~~L~~-----~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~  328 (509)
T PRK05022        254 AESELFGHVKGAFTGAISNRSGKFELADGGTLFLDEIGELPL-----ALQAKLLRVLQYGEIQRVGSDRSLRVDVRVIAA  328 (509)
T ss_pred             HHHHhcCccccccCCCcccCCcchhhcCCCEEEecChhhCCH-----HHHHHHHHHHhcCCEeeCCCCcceecceEEEEe
Confidence            1122332                 123457899999998842     23345565553211     10 00113346776


Q ss_pred             cCCC-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          322 MNSK-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       322 TN~~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      ||..       ..+.+.|..  |+. ..|++|+...  ++...|++.++....       ..+.....++++.-+..|..
T Consensus       329 t~~~l~~~~~~~~f~~dL~~--rl~~~~i~lPpLreR~eDI~~L~~~fl~~~~-------~~~~~~~~~~s~~a~~~L~~  399 (509)
T PRK05022        329 TNRDLREEVRAGRFRADLYH--RLSVFPLSVPPLRERGDDVLLLAGYFLEQNR-------ARLGLRSLRLSPAAQAALLA  399 (509)
T ss_pred             cCCCHHHHHHcCCccHHHHh--cccccEeeCCCchhchhhHHHHHHHHHHHHH-------HHcCCCCCCCCHHHHHHHHh
Confidence            6643       224444544  554 3455554433  233345555543211       11111235899999999999


Q ss_pred             HhhhcHHHHHHHHHHHHHhc
Q 011664          392 ANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       392 ~a~~~~~~al~~~i~~~~~~  411 (480)
                      ..+...++.|+++++.+...
T Consensus       400 y~WPGNvrEL~~~i~ra~~~  419 (509)
T PRK05022        400 YDWPGNVRELEHVISRAALL  419 (509)
T ss_pred             CCCCCcHHHHHHHHHHHHHh
Confidence            99999999999999887654

>TIGR02442 Cob-chelat-sub cobaltochelatase subunit

Probab=98.99  E-value=2.1e-09  Score=119.16  Aligned_cols=153  Identities=19%  Similarity=0.231  Sum_probs=100.5

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-------------------
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-------------------  248 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-------------------  248 (480)
                      .|.+|+|++.+|..+.-....+             ...||||+||||||||++|+++++.+                   
T Consensus         2 pf~~ivGq~~~~~al~~~av~~-------------~~g~vli~G~~GtgKs~lar~l~~~lp~~~~~~~~~~~c~p~~~~   68 (633)
T TIGR02442         2 PFTAIVGQEDLKLALLLNAVDP-------------RIGGVLIRGEKGTAKSTAARGLAALLPPIDVVAGCPFSCDPDDPE   68 (633)
T ss_pred             CcchhcChHHHHHHHHHHhhCC-------------CCCeEEEEcCCCCcHHHHHHHHHHhCCCceeccCCcCCCCCCCcc
Confidence            4889999999887765333211             12479999999999999999999887                   


Q ss_pred             ----------------CCcEEEEeCCC----cCChHHHHHHHHh-----------hcCCcEEEEecccccccCcccccch
Q 011664          249 ----------------SYDVYDVDLSR----VADDADLKSLLLQ-----------TTSKSVILIEDLDRFLVEKPAAVSL  297 (480)
Q Consensus       249 ----------------~~~~~~i~~s~----~~~~~~l~~l~~~-----------~~~~sII~IDEiD~l~~~~~~~~~l  297 (480)
                                      ..+|+.+.++.    +.+..++...+..           .....|||||||+.+.     ...+
T Consensus        69 ~~~~~~~~~~~~~~~~~~pfv~~p~~~t~~~l~G~~d~~~~l~~g~~~~~~G~L~~A~~GiL~lDEi~~l~-----~~~q  143 (633)
T TIGR02442        69 EWCEECRRKYRPSEQRPVPFVNLPLGATEDRVVGSLDIERALREGEKAFQPGLLAEAHRGILYIDEVNLLD-----DHLV  143 (633)
T ss_pred             ccChhhhhcccccccCCCCeeeCCCCCcHHHcCCcccHHHHhhcCCeeecCcceeecCCCeEEeChhhhCC-----HHHH
Confidence                            24566655442    2232233332211           1244799999999883     3445


Q ss_pred             hhhhhhcc-ccc---c----cccCCceEEEEecCCC-ccCcccccCCCceeEEEEcCCCC-HHHHHHHHHHHh
Q 011664          298 SGVLNFMD-GVL---N----SCCFEERVMVFTMNSK-DHVDQALLRPGRIDVHIHFPLCD-FSSFKTLASSYL  360 (480)
Q Consensus       298 s~lL~~ld-g~~---~----~~~~~~~ivI~tTN~~-~~LD~aLlrpGRfd~~I~~~~p~-~~~r~~il~~~l  360 (480)
                      +.|++.|+ |..   .    .......++|+|+|.. ..+.++|+.  ||+.+|.++++. .+++.+++...+
T Consensus       144 ~~Ll~~le~g~~~v~r~g~~~~~~~~~~lIat~np~eg~l~~~L~d--R~~l~i~v~~~~~~~~~~~il~~~~  214 (633)
T TIGR02442       144 DVLLDAAAMGVNRVEREGLSVSHPARFVLIGTMNPEEGDLRPQLLD--RFGLCVDVAAPRDPEERVEIIRRRL  214 (633)
T ss_pred             HHHHHHHhcCCEEEEECCceeeecCCeEEEEecCCCCCCCCHHHHh--hcceEEEccCCCchHHHHHHHHHHH
Confidence            66777774 210   0    0111235677788843 368899999  999999999886 466777776543

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.

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

Probab=98.99  E-value=4.3e-09  Score=104.52  Aligned_cols=119  Identities=18%  Similarity=0.291  Sum_probs=79.4

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhh-hCC-CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHR-LGR-VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------  262 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~-~g~-~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------  262 (480)
                      -++|++..|+.+.=++....++-..... -.. -.+.++||.||.|||||.||+.+|..++.+|-.-|++.+..      
T Consensus        62 YVIGQe~AKKvLsVAVYNHYKRl~~~~~~~dvEL~KSNILLiGPTGsGKTlLAqTLAk~LnVPFaiADATtLTEAGYVGE  141 (408)
T COG1219          62 YVIGQEQAKKVLSVAVYNHYKRLNNKEDNDDVELSKSNILLIGPTGSGKTLLAQTLAKILNVPFAIADATTLTEAGYVGE  141 (408)
T ss_pred             heecchhhhceeeeeehhHHHHHhccCCCCceeeeeccEEEECCCCCcHHHHHHHHHHHhCCCeeeccccchhhccccch
Confidence            3688888888776554433222111100 001 12457999999999999999999999999999999887653      


Q ss_pred             --hHHHHHHHHhh------cCCcEEEEecccccccCccc---------ccchhhhhhhcccccc
Q 011664          263 --DADLKSLLLQT------TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLN  309 (480)
Q Consensus       263 --~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~  309 (480)
                        +.-+.+++..+      ..+.||+|||||.+.....+         ......||..++|-..
T Consensus       142 DVENillkLlqaadydV~rAerGIIyIDEIDKIarkSeN~SITRDVSGEGVQQALLKiiEGTva  205 (408)
T COG1219         142 DVENILLKLLQAADYDVERAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKIIEGTVA  205 (408)
T ss_pred             hHHHHHHHHHHHcccCHHHHhCCeEEEechhhhhccCCCCCcccccCchHHHHHHHHHHcCcee
Confidence              22355666443      47899999999999753321         1223457887776543

>PRK08939 primosomal protein DnaI; Reviewed

Probab=98.98  E-value=1.2e-09  Score=110.72  Aligned_cols=128  Identities=21%  Similarity=0.265  Sum_probs=81.0

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD  262 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~  262 (480)
                      ..+|+++...+.-+..+.+....|+..   |.. + +..+|++|+||||||||+|+.|+|+++   |..+..+.++.+..
T Consensus       123 ~atf~~~~~~~~~~~~~~~~~~~fi~~---~~~-~-~~~~gl~L~G~~G~GKThLa~Aia~~l~~~g~~v~~~~~~~l~~  197 (306)
T PRK08939        123 QASLADIDLDDRDRLDALMAALDFLEA---YPP-G-EKVKGLYLYGDFGVGKSYLLAAIANELAKKGVSSTLLHFPEFIR  197 (306)
T ss_pred             cCcHHHhcCCChHHHHHHHHHHHHHHH---hhc-c-CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEEHHHHHH
Confidence            367888776654455555555555543   221 1 245799999999999999999999987   77777777655432


Q ss_pred             -------hHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhc-ccccccccCCceEEEEecCCC
Q 011664          263 -------DADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFM-DGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       263 -------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~l-dg~~~~~~~~~~ivI~tTN~~  325 (480)
                             +..+...+.......+|+|||+.......   -...+++..+ +.-.    .++.-+|+|||.+
T Consensus       198 ~lk~~~~~~~~~~~l~~l~~~dlLiIDDiG~e~~s~---~~~~~ll~~Il~~R~----~~~~~ti~TSNl~  261 (306)
T PRK08939        198 ELKNSISDGSVKEKIDAVKEAPVLMLDDIGAEQMSS---WVRDEVLGVILQYRM----QEELPTFFTSNFD  261 (306)
T ss_pred             HHHHHHhcCcHHHHHHHhcCCCEEEEecCCCccccH---HHHHHHHHHHHHHHH----HCCCeEEEECCCC
Confidence                   12244556666788999999998653211   1112344332 2211    2456689999954

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=98.96  E-value=6.3e-09  Score=112.69  Aligned_cols=199  Identities=13%  Similarity=0.170  Sum_probs=119.4

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHc-----------CCCcEEEE
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF-----------MSYDVYDV  255 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~-----------l~~~~~~i  255 (480)
                      .+|++++|.....+.+++.+..+...           ...+||+|++||||+++|++|.+.           .+.+|+.+
T Consensus       216 ~~f~~iiG~S~~m~~~~~~i~~~A~s-----------~~pVLI~GE~GTGKe~~A~~IH~~~~~~~~~~S~r~~~pfv~i  284 (538)
T PRK15424        216 YVLGDLLGQSPQMEQVRQTILLYARS-----------SAAVLIQGETGTGKELAAQAIHREYFARHDARQGKKSHPFVAV  284 (538)
T ss_pred             cchhheeeCCHHHHHHHHHHHHHhCC-----------CCcEEEECCCCCCHHHHHHHHHHhhcccccccCccCCCCeEEe
Confidence            46999999999888888877665332           347999999999999999999887           35689999


Q ss_pred             eCCCcCChHHHHHHHH------------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cccc----
Q 011664          256 DLSRVADDADLKSLLL------------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NSCC----  312 (480)
Q Consensus       256 ~~s~~~~~~~l~~l~~------------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~~~----  312 (480)
                      ||+.+..+.--..+|.                  +......||||||+.+..     .....|+..++.-. ....    
T Consensus       285 nCaal~e~lleseLFG~~~gaftga~~~~~~Gl~e~A~gGTLfLdeI~~Lp~-----~~Q~kLl~~L~e~~~~r~G~~~~  359 (538)
T PRK15424        285 NCGAIAESLLEAELFGYEEGAFTGSRRGGRAGLFEIAHGGTLFLDEIGEMPL-----PLQTRLLRVLEEKEVTRVGGHQP  359 (538)
T ss_pred             ecccCChhhHHHHhcCCccccccCccccccCCchhccCCCEEEEcChHhCCH-----HHHHHHHhhhhcCeEEecCCCce
Confidence            9998764221222332                  123457899999998842     23355666664211 0000    


Q ss_pred             -CCceEEEEecCCC-cc------CcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccC----CCCCchhHHHHHHh
Q 011664          313 -FEERVMVFTMNSK-DH------VDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLK----DHKLFPQVEEIFQN  377 (480)
Q Consensus       313 -~~~~ivI~tTN~~-~~------LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~----~~~l~~~i~~l~~~  377 (480)
                       .-++-+|+|||.. +.      +.+.|.-  |+. ..|++|+...  ++...|+..|+...    +..+..+.      
T Consensus       360 ~~~dvRiIaat~~~L~~~v~~g~Fr~dL~y--rL~~~~I~lPPLReR~eDI~~L~~~fl~~~~~~~~~~~~~~a------  431 (538)
T PRK15424        360 VPVDVRVISATHCDLEEDVRQGRFRRDLFY--RLSILRLQLPPLRERVADILPLAESFLKQSLAALSAPFSAAL------  431 (538)
T ss_pred             eccceEEEEecCCCHHHHHhcccchHHHHH--HhcCCeecCCChhhchhHHHHHHHHHHHHHHHHcCCCCCHHH------
Confidence             1123467776643 21      2223333  443 3444554432  23445666665431    11111111      


Q ss_pred             CCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHHh
Q 011664          378 GSSLSPAEIGELMIANRNSPSRALKSVITALQT  410 (480)
Q Consensus       378 ~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~~  410 (480)
                       .++.++-+..++...+...++.|+++++.+..
T Consensus       432 -~~~~~~a~~~L~~y~WPGNvREL~nvier~~i  463 (538)
T PRK15424        432 -RQGLQQCETLLLHYDWPGNVRELRNLMERLAL  463 (538)
T ss_pred             -HHhhHHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence             12222333566677889999999999987665

>PRK04132 replication factor C small subunit; Provisional

Probab=98.95  E-value=8.3e-09  Score=116.22  Aligned_cols=128  Identities=11%  Similarity=0.105  Sum_probs=99.9

Q ss_pred             EEEEc--cCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcCChHHHHHHHHhh---c-----CCcEEEEecccccccCc
Q 011664          227 YLLYG--PSGTGKSSFAAAMASFM-----SYDVYDVDLSRVADDADLKSLLLQT---T-----SKSVILIEDLDRFLVEK  291 (480)
Q Consensus       227 iLL~G--PpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~~~~~l~~l~~~~---~-----~~sII~IDEiD~l~~~~  291 (480)
                      .+..|  |++.||||+|+|+|+++     +.+++.+|+++..+-..++..+...   .     +..|++|||+|.+.   
T Consensus       567 ~~~~G~lPh~lGKTT~A~ala~~l~g~~~~~~~lElNASd~rgid~IR~iIk~~a~~~~~~~~~~KVvIIDEaD~Lt---  643 (846)
T PRK04132        567 NFIGGNLPTVLHNTTAALALARELFGENWRHNFLELNASDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALT---  643 (846)
T ss_pred             hhhcCCCCCcccHHHHHHHHHHhhhcccccCeEEEEeCCCcccHHHHHHHHHHHHhcCCcCCCCCEEEEEECcccCC---
Confidence            35568  99999999999999998     5689999999877777777765332   1     23699999999983   


Q ss_pred             ccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCC
Q 011664          292 PAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL  367 (480)
Q Consensus       292 ~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l  367 (480)
                        ....+.|+..|+..     .....+|++||.+..+.+++++  |+ ..+.|++|+.++....+...+...+..+
T Consensus       644 --~~AQnALLk~lEep-----~~~~~FILi~N~~~kIi~tIrS--RC-~~i~F~~ls~~~i~~~L~~I~~~Egi~i  709 (846)
T PRK04132        644 --QDAQQALRRTMEMF-----SSNVRFILSCNYSSKIIEPIQS--RC-AIFRFRPLRDEDIAKRLRYIAENEGLEL  709 (846)
T ss_pred             --HHHHHHHHHHhhCC-----CCCeEEEEEeCChhhCchHHhh--hc-eEEeCCCCCHHHHHHHHHHHHHhcCCCC
Confidence              23456788877643     3457789999999999999999  98 5899999999888887777765544443

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=98.94  E-value=2.7e-09  Score=101.88  Aligned_cols=185  Identities=14%  Similarity=0.207  Sum_probs=113.0

Q ss_pred             eCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-C----CcEEE
Q 011664          180 SVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-S----YDVYD  254 (480)
Q Consensus       180 ~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~----~~~~~  254 (480)
                      +|..-+|+.+.||+|.++..+.+.-.           .+-|--|  .+++.||||||||+-+.++|+++ |    .-+..
T Consensus        17 wVeKYrP~~l~dIVGNe~tv~rl~vi-----------a~~gnmP--~liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLE   83 (333)
T KOG0991|consen   17 WVEKYRPSVLQDIVGNEDTVERLSVI-----------AKEGNMP--NLIISGPPGTGKTTSILCLARELLGDSYKEAVLE   83 (333)
T ss_pred             HHHhhCchHHHHhhCCHHHHHHHHHH-----------HHcCCCC--ceEeeCCCCCchhhHHHHHHHHHhChhhhhHhhh
Confidence            35667889999999999988776531           2223222  69999999999999999999986 4    24677


Q ss_pred             EeCCCcCChHHHH---HHHHhhc------CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          255 VDLSRVADDADLK---SLLLQTT------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       255 i~~s~~~~~~~l~---~l~~~~~------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ++.|+-.+-.-++   +.|++..      ...||++||.|++...  .+   ..|-..|+-. +    +..-+.+++|..
T Consensus        84 LNASdeRGIDvVRn~IK~FAQ~kv~lp~grhKIiILDEADSMT~g--AQ---QAlRRtMEiy-S----~ttRFalaCN~s  153 (333)
T KOG0991|consen   84 LNASDERGIDVVRNKIKMFAQKKVTLPPGRHKIIILDEADSMTAG--AQ---QALRRTMEIY-S----NTTRFALACNQS  153 (333)
T ss_pred             ccCccccccHHHHHHHHHHHHhhccCCCCceeEEEeeccchhhhH--HH---HHHHHHHHHH-c----ccchhhhhhcch
Confidence            8888766654444   4565542      2379999999988421  12   2233333322 2    234477788988


Q ss_pred             ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHH
Q 011664          326 DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSV  404 (480)
Q Consensus       326 ~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~  404 (480)
                      +.+-+.+-+  |+- .+.+.-.+.++...-+....+              .+...|++.-++.++..+..+...++..+
T Consensus       154 ~KIiEPIQS--RCA-iLRysklsd~qiL~Rl~~v~k--------------~Ekv~yt~dgLeaiifta~GDMRQalNnL  215 (333)
T KOG0991|consen  154 EKIIEPIQS--RCA-ILRYSKLSDQQILKRLLEVAK--------------AEKVNYTDDGLEAIIFTAQGDMRQALNNL  215 (333)
T ss_pred             hhhhhhHHh--hhH-hhhhcccCHHHHHHHHHHHHH--------------HhCCCCCcchHHHhhhhccchHHHHHHHH
Confidence            887666666  553 333333343332221211111              12346777777777666655555555444

>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=98.93  E-value=1.4e-08  Score=93.70  Aligned_cols=112  Identities=19%  Similarity=0.292  Sum_probs=79.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC-----------------------CCcEEEEeCCCc---CChHHHHHHHHhh---
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM-----------------------SYDVYDVDLSRV---ADDADLKSLLLQT---  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l-----------------------~~~~~~i~~s~~---~~~~~l~~l~~~~---  273 (480)
                      .+..+||+||+|+||+++|.++|+.+                       ..+++.++...-   .+-.+++.+....   
T Consensus        18 l~ha~L~~G~~g~gk~~~a~~~a~~ll~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~i~i~~ir~i~~~~~~~   97 (162)
T PF13177_consen   18 LPHALLFHGPSGSGKKTLALAFARALLCSNPNEDPCGECRSCRRIEEGNHPDFIIIKPDKKKKSIKIDQIREIIEFLSLS   97 (162)
T ss_dssp             --SEEEEECSTTSSHHHHHHHHHHHHC-TT-CTT--SSSHHHHHHHTT-CTTEEEEETTTSSSSBSHHHHHHHHHHCTSS
T ss_pred             cceeEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHhccCcceEEEecccccchhhHHHHHHHHHHHHHH
Confidence            45689999999999999999999854                       235667765543   3456677665433   


Q ss_pred             ---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCC
Q 011664          274 ---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLC  347 (480)
Q Consensus       274 ---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p  347 (480)
                         ....|++|||+|.+.     ....+.||..|+.-     +...++|++|+.++.|-|.+++  |+ ..+.|+..
T Consensus        98 ~~~~~~KviiI~~ad~l~-----~~a~NaLLK~LEep-----p~~~~fiL~t~~~~~il~TI~S--Rc-~~i~~~~l  161 (162)
T PF13177_consen   98 PSEGKYKVIIIDEADKLT-----EEAQNALLKTLEEP-----PENTYFILITNNPSKILPTIRS--RC-QVIRFRPL  161 (162)
T ss_dssp             -TTSSSEEEEEETGGGS------HHHHHHHHHHHHST-----TTTEEEEEEES-GGGS-HHHHT--TS-EEEEE---
T ss_pred             HhcCCceEEEeehHhhhh-----HHHHHHHHHHhcCC-----CCCEEEEEEECChHHChHHHHh--hc-eEEecCCC
Confidence               245799999999883     34568888888643     4578899999999999999999  98 47777654

...

>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=98.93  E-value=1.2e-08  Score=104.01  Aligned_cols=66  Identities=23%  Similarity=0.368  Sum_probs=46.5

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC--CcEEEEeCCCcC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS--YDVYDVDLSRVA  261 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~--~~~~~i~~s~~~  261 (480)
                      ..+.++|+.++++..--.+. .++.       |+--.+++||.||||||||.||-+||++||  .||..++.|++.
T Consensus        22 ~~~GlVGQ~~AReAagiiv~-mIk~-------~K~aGr~iLiaGppGtGKTAlA~~ia~eLG~~~PF~~isgSEiy   89 (398)
T PF06068_consen   22 IADGLVGQEKAREAAGIIVD-MIKE-------GKIAGRAILIAGPPGTGKTALAMAIAKELGEDVPFVSISGSEIY   89 (398)
T ss_dssp             EETTEES-HHHHHHHHHHHH-HHHT-------T--TT-EEEEEE-TTSSHHHHHHHHHHHCTTTS-EEEEEGGGG-
T ss_pred             ccccccChHHHHHHHHHHHH-HHhc-------ccccCcEEEEeCCCCCCchHHHHHHHHHhCCCCCeeEcccceee
Confidence            35789999999998764333 3333       223467999999999999999999999997  678888777654

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.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=98.92  E-value=6.5e-10  Score=104.10  Aligned_cols=94  Identities=24%  Similarity=0.406  Sum_probs=59.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC-------hHHHHHHHHhhcCCcEEEEecccccccCccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD-------DADLKSLLLQTTSKSVILIEDLDRFLVEKPA  293 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~-------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~  293 (480)
                      ..|++|+||||||||+||.|+|+++   |..+..++.+++..       +....+.+.+.....+|+|||+.....+.  
T Consensus        47 ~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~~~~~~~~~~~~l~~~dlLilDDlG~~~~~~--  124 (178)
T PF01695_consen   47 GENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSRSDGSYEELLKRLKRVDLLILDDLGYEPLSE--  124 (178)
T ss_dssp             --EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCHCCTTHCHHHHHHHTSSCEEEETCTSS---H--
T ss_pred             CeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccccccchhhhcCccccccEecccccceeeecc--
Confidence            4689999999999999999999865   78888888765432       22244556666788999999997543222  


Q ss_pred             ccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          294 AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                       .....|.+.++.-..     ..-+|+|||..
T Consensus       125 -~~~~~l~~ii~~R~~-----~~~tIiTSN~~  150 (178)
T PF01695_consen  125 -WEAELLFEIIDERYE-----RKPTIITSNLS  150 (178)
T ss_dssp             -HHHHCTHHHHHHHHH-----T-EEEEEESS-
T ss_pred             -cccccchhhhhHhhc-----ccCeEeeCCCc
Confidence             223445555554332     23467799954

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.

>PRK06835 DNA replication protein DnaC; Validated

Probab=98.92  E-value=3.2e-09  Score=108.50  Aligned_cols=115  Identities=19%  Similarity=0.291  Sum_probs=74.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh---------HHHHHHHHhhcCCcEEEEecccccccCcc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD---------ADLKSLLLQTTSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~---------~~l~~l~~~~~~~sII~IDEiD~l~~~~~  292 (480)
                      .+++||||||||||+|+.|||+++   |..+++++..++...         ......+.......+|+|||+......  
T Consensus       184 ~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~~~l~~~DLLIIDDlG~e~~t--  261 (329)
T PRK06835        184 ENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVYDLLINCDLLIIDDLGTEKIT--  261 (329)
T ss_pred             CcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHHHHhccCCEEEEeccCCCCCC--
Confidence            689999999999999999999986   778888887654321         111222444557789999999876432  


Q ss_pred             cccchhhhhhhcccccccccCCceEEEEecCC-Ccc----CcccccCCCcee---EEEEcCCCC
Q 011664          293 AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS-KDH----VDQALLRPGRID---VHIHFPLCD  348 (480)
Q Consensus       293 ~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~-~~~----LD~aLlrpGRfd---~~I~~~~p~  348 (480)
                       ....+.|++.++....    .+.-+|+|||. |+.    +++++.+  |+-   ..|.|.-.|
T Consensus       262 -~~~~~~Lf~iin~R~~----~~k~tIiTSNl~~~el~~~~~eri~S--RL~~~~~~i~~~G~d  318 (329)
T PRK06835        262 -EFSKSELFNLINKRLL----RQKKMIISTNLSLEELLKTYSERISS--RLLGNFTLLKFYGED  318 (329)
T ss_pred             -HHHHHHHHHHHHHHHH----CCCCEEEECCCCHHHHHHHHhHHHHH--HHHcCCEEEEecCcC
Confidence             2334556666654433    23457788884 333    3566666  653   345554444

>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=98.91  E-value=3.8e-09  Score=105.41  Aligned_cols=135  Identities=27%  Similarity=0.373  Sum_probs=84.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc---EEEEeCCCcCChHHHHHHHHhh-------------cCCcEEEEeccccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD---VYDVDLSRVADDADLKSLLLQT-------------TSKSVILIEDLDRF  287 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~~i~~s~~~~~~~l~~l~~~~-------------~~~sII~IDEiD~l  287 (480)
                      .+.+||+||+|||||++++..-..+.-.   ...++++.......++..+...             ..+.|+||||+..-
T Consensus        33 ~~pvLl~G~~GtGKT~li~~~l~~l~~~~~~~~~~~~s~~Tts~~~q~~ie~~l~k~~~~~~gP~~~k~lv~fiDDlN~p  112 (272)
T PF12775_consen   33 GRPVLLVGPSGTGKTSLIQNFLSSLDSDKYLVITINFSAQTTSNQLQKIIESKLEKRRGRVYGPPGGKKLVLFIDDLNMP  112 (272)
T ss_dssp             TEEEEEESSTTSSHHHHHHHHHHCSTTCCEEEEEEES-TTHHHHHHHHCCCTTECECTTEEEEEESSSEEEEEEETTT-S
T ss_pred             CCcEEEECCCCCchhHHHHhhhccCCccccceeEeeccCCCCHHHHHHHHhhcEEcCCCCCCCCCCCcEEEEEecccCCC
Confidence            4689999999999999999877766432   3456676655555555544221             13479999999987


Q ss_pred             ccCcccccchhhhhhhc---ccccccc-----cCCceEEEEecCCC---ccCcccccCCCceeEEEEcCCCCHHHHHHHH
Q 011664          288 LVEKPAAVSLSGVLNFM---DGVLNSC-----CFEERVMVFTMNSK---DHVDQALLRPGRIDVHIHFPLCDFSSFKTLA  356 (480)
Q Consensus       288 ~~~~~~~~~ls~lL~~l---dg~~~~~-----~~~~~ivI~tTN~~---~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il  356 (480)
                      ..+..+.....+||.++   .|..+..     .-.+..+|+|+|.+   ..+++.++|  .| ..+.++.|+.+....|+
T Consensus       113 ~~d~ygtq~~iElLRQ~i~~~g~yd~~~~~~~~i~~i~~vaa~~p~~Gr~~is~R~~r--~f-~i~~~~~p~~~sl~~If  189 (272)
T PF12775_consen  113 QPDKYGTQPPIELLRQLIDYGGFYDRKKLEWKSIEDIQFVAAMNPTGGRNPISPRFLR--HF-NILNIPYPSDESLNTIF  189 (272)
T ss_dssp             ---TTS--HHHHHHHHHHHCSEEECTTTTEEEEECSEEEEEEESSTTT--SHHHHHHT--TE-EEEE----TCCHHHHHH
T ss_pred             CCCCCCCcCHHHHHHHHHHhcCcccCCCcEEEEEeeeEEEEecCCCCCCCCCChHHhh--he-EEEEecCCChHHHHHHH
Confidence            77666666566777665   2433310     11345577777743   248889998  77 58999999999888887


Q ss_pred             HHHhc
Q 011664          357 SSYLG  361 (480)
Q Consensus       357 ~~~l~  361 (480)
                      ..++.
T Consensus       190 ~~il~  194 (272)
T PF12775_consen  190 SSILQ  194 (272)
T ss_dssp             HHHHH
T ss_pred             HHHHh
Confidence            77664

>smart00350 MCM minichromosome maintenance proteins

Probab=98.91  E-value=6.6e-09  Score=112.50  Aligned_cols=160  Identities=18%  Similarity=0.169  Sum_probs=95.0

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCC--CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEE----eCCCcCC--
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRV--WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV----DLSRVAD--  262 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~--~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i----~~s~~~~--  262 (480)
                      .|.|++.+|..+.-.+.   .+......-|..  -.-.+||+|+||||||++|+++++......+..    ++..+..  
T Consensus       204 ~i~G~~~~k~~l~l~l~---gg~~~~~~~~~~~r~~~~vLL~G~pGtGKs~lar~l~~~~~r~~~~~~~~~~~~~l~~~~  280 (509)
T smart00350      204 SIYGHEDIKKAILLLLF---GGVHKNLPDGMKIRGDINILLLGDPGTAKSQLLKYVEKTAPRAVYTTGKGSSAVGLTAAV  280 (509)
T ss_pred             cccCcHHHHHHHHHHHh---CCCccccCCCccccccceEEEeCCCChhHHHHHHHHHHHcCcceEcCCCCCCcCCccccc
Confidence            47888888877653331   111000000111  122699999999999999999999775443332    1111211  


Q ss_pred             -------hHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccc---------ccccccCCceEEEEecCCCc
Q 011664          263 -------DADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG---------VLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 -------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg---------~~~~~~~~~~ivI~tTN~~~  326 (480)
                             +..++.-........+++|||+|.+-     ....+.|+..|+.         ... .-.....||+|+|..+
T Consensus       281 ~~~~~~g~~~~~~G~l~~A~~Gil~iDEi~~l~-----~~~q~~L~e~me~~~i~i~k~G~~~-~l~~~~~viAa~NP~~  354 (509)
T smart00350      281 TRDPETREFTLEGGALVLADNGVCCIDEFDKMD-----DSDRTAIHEAMEQQTISIAKAGITT-TLNARCSVLAAANPIG  354 (509)
T ss_pred             eEccCcceEEecCccEEecCCCEEEEechhhCC-----HHHHHHHHHHHhcCEEEEEeCCEEE-EecCCcEEEEEeCCCC
Confidence                   00000000112356899999999873     2334556666632         111 1123345778888542


Q ss_pred             -------------cCcccccCCCceeEE-EEcCCCCHHHHHHHHHHHhc
Q 011664          327 -------------HVDQALLRPGRIDVH-IHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       327 -------------~LD~aLlrpGRfd~~-I~~~~p~~~~r~~il~~~l~  361 (480)
                                   .|++++++  |||.. +-..+|+.+...+|++..+.
T Consensus       355 g~y~~~~~~~~n~~l~~~lLs--RFdLi~~~~d~~~~~~d~~i~~~i~~  401 (509)
T smart00350      355 GRYDPKLTPEENIDLPAPILS--RFDLLFVVLDEVDEERDRELAKHVVD  401 (509)
T ss_pred             cccCCCcChhhccCCChHHhC--ceeeEEEecCCCChHHHHHHHHHHHH
Confidence                         58999999  99965 55578999999999988764

>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=98.90  E-value=4.9e-09  Score=99.63  Aligned_cols=46  Identities=30%  Similarity=0.528  Sum_probs=36.0

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .|++|.|++.+|..+.-...            |   ..++|++||||||||++|++++.-+
T Consensus         1 Df~dI~GQe~aKrAL~iAAa------------G---~h~lLl~GppGtGKTmlA~~l~~lL   46 (206)
T PF01078_consen    1 DFSDIVGQEEAKRALEIAAA------------G---GHHLLLIGPPGTGKTMLARRLPSLL   46 (206)
T ss_dssp             -TCCSSSTHHHHHHHHHHHH------------C---C--EEEES-CCCTHHHHHHHHHHCS
T ss_pred             ChhhhcCcHHHHHHHHHHHc------------C---CCCeEEECCCCCCHHHHHHHHHHhC
Confidence            48999999999998874332            3   3589999999999999999999865

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.

>PRK06526 transposase; Provisional

Probab=98.88  E-value=1.1e-09  Score=108.05  Aligned_cols=94  Identities=17%  Similarity=0.267  Sum_probs=60.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh-------HHHHHHHHhhcCCcEEEEecccccccCccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPA  293 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~  293 (480)
                      +.+++|+||||||||+|+.+++.++   |..++.++++++...       ..+...+.+...+.+|+|||++.+..+...
T Consensus        98 ~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~~~~~~~~~l~~l~~~dlLIIDD~g~~~~~~~~  177 (254)
T PRK06526         98 KENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAHHAGRLQAELVKLGRYPLLIVDEVGYIPFEPEA  177 (254)
T ss_pred             CceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHHhcCcHHHHHHHhccCCEEEEcccccCCCCHHH
Confidence            4589999999999999999999865   666666655443321       122334445567899999999977543333


Q ss_pred             ccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          294 AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ...+.++++   ....    . .-+|+|||.+
T Consensus       178 ~~~L~~li~---~r~~----~-~s~IitSn~~  201 (254)
T PRK06526        178 ANLFFQLVS---SRYE----R-ASLIVTSNKP  201 (254)
T ss_pred             HHHHHHHHH---HHHh----c-CCEEEEcCCC
Confidence            333334443   3222    1 2377888865

>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=98.87  E-value=6.7e-08  Score=97.46  Aligned_cols=66  Identities=21%  Similarity=0.354  Sum_probs=49.2

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC--CcEEEEeCCCcCC
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS--YDVYDVDLSRVAD  262 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~--~~~~~i~~s~~~~  262 (480)
                      =+-++|+.++++..-- +...++.       |.-..+|+|+.||||||||.||-+||++||  .||..++.|++.+
T Consensus        38 ~dG~VGQ~~AReAaGv-Iv~mik~-------gk~aGrgiLi~GppgTGKTAlA~gIa~eLG~dvPF~~isgsEiYS  105 (450)
T COG1224          38 GDGLVGQEEAREAAGV-IVKMIKQ-------GKMAGRGILIVGPPGTGKTALAMGIARELGEDVPFVAISGSEIYS  105 (450)
T ss_pred             CCcccchHHHHHhhhH-HHHHHHh-------CcccccEEEEECCCCCcHHHHHHHHHHHhCCCCCceeeccceeee
Confidence            4678999998887432 2222222       444578999999999999999999999997  5777777776543

>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=98.87  E-value=1.6e-08  Score=93.89  Aligned_cols=98  Identities=13%  Similarity=0.210  Sum_probs=66.3

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHHH
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLKS  268 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~~  268 (480)
                      |+|....-+++.+.+.....           .+..|||+|++||||+.+|++|.+..   +.+|+.++|+.+..+.--..
T Consensus         1 liG~s~~m~~~~~~~~~~a~-----------~~~pVlI~GE~GtGK~~lA~~IH~~s~r~~~pfi~vnc~~~~~~~~e~~   69 (168)
T PF00158_consen    1 LIGESPAMKRLREQAKRAAS-----------SDLPVLITGETGTGKELLARAIHNNSPRKNGPFISVNCAALPEELLESE   69 (168)
T ss_dssp             SS--SHHHHHHHHHHHHHTT-----------STS-EEEECSTTSSHHHHHHHHHHCSTTTTS-EEEEETTTS-HHHHHHH
T ss_pred             CEeCCHHHHHHHHHHHHHhC-----------CCCCEEEEcCCCCcHHHHHHHHHHhhhcccCCeEEEehhhhhcchhhhh
Confidence            45666666666666655433           34579999999999999999999976   46899999998865443445


Q ss_pred             HHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhcc
Q 011664          269 LLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD  305 (480)
Q Consensus       269 l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld  305 (480)
                      +|..                 .....+||||||+.+..     .....|++.|+
T Consensus        70 LFG~~~~~~~~~~~~~~G~l~~A~~GtL~Ld~I~~L~~-----~~Q~~Ll~~l~  118 (168)
T PF00158_consen   70 LFGHEKGAFTGARSDKKGLLEQANGGTLFLDEIEDLPP-----ELQAKLLRVLE  118 (168)
T ss_dssp             HHEBCSSSSTTTSSEBEHHHHHTTTSEEEEETGGGS-H-----HHHHHHHHHHH
T ss_pred             hhccccccccccccccCCceeeccceEEeecchhhhHH-----HHHHHHHHHHh
Confidence            5532                 13568999999999842     33456666665

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 ....

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

Probab=98.86  E-value=3.4e-08  Score=103.67  Aligned_cols=129  Identities=20%  Similarity=0.365  Sum_probs=89.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe-CCCcCC--h----HHHHHHHHhh--cCCcEEEEeccccccc-----
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD-LSRVAD--D----ADLKSLLLQT--TSKSVILIEDLDRFLV-----  289 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~-~s~~~~--~----~~l~~l~~~~--~~~sII~IDEiD~l~~-----  289 (480)
                      -.++||+||||+|||.||..+|...+++|+.+= ..++.+  +    ..+.+.|..+  ..-+||++|||+.+..     
T Consensus       538 lvSvLl~Gp~~sGKTaLAA~iA~~S~FPFvKiiSpe~miG~sEsaKc~~i~k~F~DAYkS~lsiivvDdiErLiD~vpIG  617 (744)
T KOG0741|consen  538 LVSVLLEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIGLSESAKCAHIKKIFEDAYKSPLSIIVVDDIERLLDYVPIG  617 (744)
T ss_pred             ceEEEEecCCCCChHHHHHHHHhhcCCCeEEEeChHHccCccHHHHHHHHHHHHHHhhcCcceEEEEcchhhhhcccccC
Confidence            357999999999999999999999999999763 333433  2    2366777544  3459999999998864     


Q ss_pred             CcccccchhhhhhhcccccccccCCceEEEE-ecCCCccCc-ccccCCCceeEEEEcCCCCH-HHHHHHHH
Q 011664          290 EKPAAVSLSGVLNFMDGVLNSCCFEERVMVF-TMNSKDHVD-QALLRPGRIDVHIHFPLCDF-SSFKTLAS  357 (480)
Q Consensus       290 ~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~-tTN~~~~LD-~aLlrpGRfd~~I~~~~p~~-~~r~~il~  357 (480)
                      .|-++..+..|+..+.....   .+.+++|+ ||...+-|. -.++.  .|+..|++|..+. ++...++.
T Consensus       618 PRfSN~vlQaL~VllK~~pp---kg~kLli~~TTS~~~vL~~m~i~~--~F~~~i~Vpnl~~~~~~~~vl~  683 (744)
T KOG0741|consen  618 PRFSNLVLQALLVLLKKQPP---KGRKLLIFGTTSRREVLQEMGILD--CFSSTIHVPNLTTGEQLLEVLE  683 (744)
T ss_pred             chhhHHHHHHHHHHhccCCC---CCceEEEEecccHHHHHHHcCHHH--hhhheeecCccCchHHHHHHHH
Confidence            34455556666666655443   34456555 555555442 35566  8899999998776 45555544

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=98.85  E-value=2.5e-08  Score=102.33  Aligned_cols=125  Identities=15%  Similarity=0.160  Sum_probs=92.3

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCC-------------------------cEEEEeCC------------------
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSY-------------------------DVYDVDLS------------------  258 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------------------~~~~i~~s------------------  258 (480)
                      ..+.++||+||+|+||+++|.++|+.+.+                         +++.+...                  
T Consensus        19 rl~ha~Lf~Gp~G~GK~~lA~~~A~~LlC~~~~~~~~~Cg~C~~C~~~~~~~HPD~~~i~p~~~~~~~~~~~~~~~~~~~   98 (342)
T PRK06964         19 RLPHALLLHGQAGIGKLDFAQHLAQGLLCETPQPDGEPCGTCAACNWFAQGNHPDYRIVRPEALAAEAPGAADEAKEADA   98 (342)
T ss_pred             CcceEEEEECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccccccccccccchh
Confidence            45679999999999999999999986633                         13333211                  


Q ss_pred             -----------CcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEe
Q 011664          259 -----------RVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFT  321 (480)
Q Consensus       259 -----------~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~t  321 (480)
                                 ...+-.+++.+....      ....|++||++|.+.     ....+.||..++.-     +++.++|++
T Consensus        99 ~~~~~k~~~~~~~I~idqiR~l~~~~~~~~~~~~~kV~iI~~ae~m~-----~~AaNaLLKtLEEP-----p~~t~fiL~  168 (342)
T PRK06964         99 DEGGKKTKAPSKEIKIEQVRALLDFCGVGTHRGGARVVVLYPAEALN-----VAAANALLKTLEEP-----PPGTVFLLV  168 (342)
T ss_pred             hcccccccccccccCHHHHHHHHHHhccCCccCCceEEEEechhhcC-----HHHHHHHHHHhcCC-----CcCcEEEEE
Confidence                       112234566655432      234699999999883     34457888888742     567889999


Q ss_pred             cCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHH
Q 011664          322 MNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSY  359 (480)
Q Consensus       322 TN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~  359 (480)
                      |++++.|.|.+++  |+ ..+.|++|+.++..+.+...
T Consensus       169 t~~~~~LLpTI~S--Rc-q~i~~~~~~~~~~~~~L~~~  203 (342)
T PRK06964        169 SARIDRLLPTILS--RC-RQFPMTVPAPEAAAAWLAAQ  203 (342)
T ss_pred             ECChhhCcHHHHh--cC-EEEEecCCCHHHHHHHHHHc
Confidence            9999999999999  99 59999999999888777653

>COG1221 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=98.84  E-value=1.5e-08  Score=105.24  Aligned_cols=204  Identities=16%  Similarity=0.201  Sum_probs=130.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHc----CCCcEEEEeCCCc
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF----MSYDVYDVDLSRV  260 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~----l~~~~~~i~~s~~  260 (480)
                      ....+++++|....-+++++.+..+       ..    ....+|++|++||||+.+|++|...    .+.+|+.+||..+
T Consensus        73 ~~~~~~~LIG~~~~~~~~~eqik~~-------ap----~~~~vLi~GetGtGKel~A~~iH~~s~r~~~~PFI~~NCa~~  141 (403)
T COG1221          73 KSEALDDLIGESPSLQELREQIKAY-------AP----SGLPVLIIGETGTGKELFARLIHALSARRAEAPFIAFNCAAY  141 (403)
T ss_pred             cchhhhhhhccCHHHHHHHHHHHhh-------CC----CCCcEEEecCCCccHHHHHHHHHHhhhcccCCCEEEEEHHHh
Confidence            3456899999999988888888762       22    2346999999999999999999853    3668999999998


Q ss_pred             CChHHHHHHHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhccc-----cccc-ccCCceE
Q 011664          261 ADDADLKSLLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG-----VLNS-CCFEERV  317 (480)
Q Consensus       261 ~~~~~l~~l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg-----~~~~-~~~~~~i  317 (480)
                      ..+-...++|.-                 .....+||+|||..+-+.     ....|+..||.     +.+. .-...+-
T Consensus       142 ~en~~~~eLFG~~kGaftGa~~~k~Glfe~A~GGtLfLDEI~~LP~~-----~Q~kLl~~le~g~~~rvG~~~~~~~dVR  216 (403)
T COG1221         142 SENLQEAELFGHEKGAFTGAQGGKAGLFEQANGGTLFLDEIHRLPPE-----GQEKLLRVLEEGEYRRVGGSQPRPVDVR  216 (403)
T ss_pred             CcCHHHHHHhccccceeecccCCcCchheecCCCEEehhhhhhCCHh-----HHHHHHHHHHcCceEecCCCCCcCCCce
Confidence            877666566631                 124589999999988432     22446666653     1110 1123456


Q ss_pred             EEEecC-CC-ccCcc--cccCCCceeEEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          318 MVFTMN-SK-DHVDQ--ALLRPGRIDVHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       318 vI~tTN-~~-~~LD~--aLlrpGRfd~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      +|+||| .+ +.+-.  .|.+ -|....|.+|+...  +++..++..++......+.       ......+|.-+..++.
T Consensus       217 li~AT~~~l~~~~~~g~dl~~-rl~~~~I~LPpLrER~~Di~~L~e~Fl~~~~~~l~-------~~~~~~~~~a~~~L~~  288 (403)
T COG1221         217 LICATTEDLEEAVLAGADLTR-RLNILTITLPPLRERKEDILLLAEHFLKSEARRLG-------LPLSVDSPEALRALLA  288 (403)
T ss_pred             eeeccccCHHHHHHhhcchhh-hhcCceecCCChhhchhhHHHHHHHHHHHHHHHcC-------CCCCCCCHHHHHHHHh
Confidence            777776 22 22322  3433 15556667666544  3344556665543211111       1112344566777777


Q ss_pred             HhhhcHHHHHHHHHHHHHhcC
Q 011664          392 ANRNSPSRALKSVITALQTDG  412 (480)
Q Consensus       392 ~a~~~~~~al~~~i~~~~~~~  412 (480)
                      ..+.+.++.|+++++.+....
T Consensus       289 y~~pGNirELkN~Ve~~~~~~  309 (403)
T COG1221         289 YDWPGNIRELKNLVERAVAQA  309 (403)
T ss_pred             CCCCCcHHHHHHHHHHHHHHh
Confidence            788889999999998887664

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=98.84  E-value=2e-08  Score=99.20  Aligned_cols=124  Identities=16%  Similarity=0.308  Sum_probs=77.2

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD  262 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~  262 (480)
                      ...+.++-+.+...+.....+..+..   +|.     -..+++||||||||||+||.|||+++   |..++.+...++..
T Consensus        75 ~~~~~d~~~~~~~~~~~l~~~~~~~~---~~~-----~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~  146 (254)
T COG1484          75 TFEEFDFEFQPGIDKKALEDLASLVE---FFE-----RGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLS  146 (254)
T ss_pred             CcccccccCCcchhHHHHHHHHHHHH---Hhc-----cCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHH
Confidence            34455666666555555544444432   222     35689999999999999999999987   67888888776653


Q ss_pred             h-------HHHH-HHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          263 D-------ADLK-SLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       263 ~-------~~l~-~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      +       .... ++........+|+|||+...-......   +.+++.++....    .... ++|||.+
T Consensus       147 ~Lk~~~~~~~~~~~l~~~l~~~dlLIiDDlG~~~~~~~~~---~~~~q~I~~r~~----~~~~-~~tsN~~  209 (254)
T COG1484         147 KLKAAFDEGRLEEKLLRELKKVDLLIIDDIGYEPFSQEEA---DLLFQLISRRYE----SRSL-IITSNLS  209 (254)
T ss_pred             HHHHHHhcCchHHHHHHHhhcCCEEEEecccCccCCHHHH---HHHHHHHHHHHh----hccc-eeecCCC
Confidence            1       1122 222336678999999999763322222   334444443332    2233 8899965

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=98.83  E-value=1e-07  Score=97.09  Aligned_cols=123  Identities=15%  Similarity=0.199  Sum_probs=88.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC---------------------cEEEEe--CCC-------cCChHHHHHHHHh
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY---------------------DVYDVD--LSR-------VADDADLKSLLLQ  272 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~---------------------~~~~i~--~s~-------~~~~~~l~~l~~~  272 (480)
                      .+.++||+||+|+||+++|.++|+.+-+                     +++.+.  .++       -..-..++.+...
T Consensus        25 l~HA~Lf~Gp~G~GK~~lA~~lA~~LlC~~~~~~~~c~~c~~~~~g~HPD~~~i~~~p~~~~~k~~~~I~idqIR~l~~~  104 (319)
T PRK08769         25 LGHGLLICGPEGLGKRAVALALAEHVLASGPDPAAAQRTRQLIAAGTHPDLQLVSFIPNRTGDKLRTEIVIEQVREISQK  104 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHHhCCCCCCCCcchHHHHHhcCCCCCEEEEecCCCcccccccccccHHHHHHHHHH
Confidence            4568999999999999999999975521                     344442  111       1123345555432


Q ss_pred             h------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCC
Q 011664          273 T------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       273 ~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~  346 (480)
                      .      ....|++||++|.+.     ....+.||..|+.-     +.+.+||++|+.++.|-|.+++  |+. .+.|+.
T Consensus       105 ~~~~p~~g~~kV~iI~~ae~m~-----~~AaNaLLKtLEEP-----p~~~~fiL~~~~~~~lLpTIrS--RCq-~i~~~~  171 (319)
T PRK08769        105 LALTPQYGIAQVVIVDPADAIN-----RAACNALLKTLEEP-----SPGRYLWLISAQPARLPATIRS--RCQ-RLEFKL  171 (319)
T ss_pred             HhhCcccCCcEEEEeccHhhhC-----HHHHHHHHHHhhCC-----CCCCeEEEEECChhhCchHHHh--hhe-EeeCCC
Confidence            2      134799999999883     34457788887542     4567888899999999999999  995 889999


Q ss_pred             CCHHHHHHHHHH
Q 011664          347 CDFSSFKTLASS  358 (480)
Q Consensus       347 p~~~~r~~il~~  358 (480)
                      |+.++-.+.+..
T Consensus       172 ~~~~~~~~~L~~  183 (319)
T PRK08769        172 PPAHEALAWLLA  183 (319)
T ss_pred             cCHHHHHHHHHH
Confidence            999877666653

>PRK06921 hypothetical protein; Provisional

Probab=98.83  E-value=9e-09  Score=102.42  Aligned_cols=107  Identities=20%  Similarity=0.241  Sum_probs=64.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCCcCCh-----HHHHHHHHhhcCCcEEEEecccc-cccC-cc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSRVADD-----ADLKSLLLQTTSKSVILIEDLDR-FLVE-KP  292 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~~~~~-----~~l~~l~~~~~~~sII~IDEiD~-l~~~-~~  292 (480)
                      ..+++|+||||||||+|+.|||+++    |..+++++..++...     ......+.......+|+|||++. +.+. ..
T Consensus       117 ~~~l~l~G~~G~GKThLa~aia~~l~~~~g~~v~y~~~~~l~~~l~~~~~~~~~~~~~~~~~dlLiIDDl~~~~~g~e~~  196 (266)
T PRK06921        117 KNSIALLGQPGSGKTHLLTAAANELMRKKGVPVLYFPFVEGFGDLKDDFDLLEAKLNRMKKVEVLFIDDLFKPVNGKPRA  196 (266)
T ss_pred             CCeEEEECCCCCcHHHHHHHHHHHHhhhcCceEEEEEHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEeccccccCCCccC
Confidence            4689999999999999999999976    567778776543221     11222334456789999999954 1111 11


Q ss_pred             cccchhhhhhhcccccccccCCceEEEEecCC-CccC---cccccC
Q 011664          293 AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS-KDHV---DQALLR  334 (480)
Q Consensus       293 ~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~-~~~L---D~aLlr  334 (480)
                      +.-....|...++....    .+.-+|+|||. |+.+   ++++.+
T Consensus       197 t~~~~~~lf~iin~R~~----~~k~tIitsn~~~~el~~~~~~l~s  238 (266)
T PRK06921        197 TEWQIEQMYSVLNYRYL----NHKPILISSELTIDELLDIDEALGS  238 (266)
T ss_pred             CHHHHHHHHHHHHHHHH----CCCCEEEECCCCHHHHhhhhhHHHH
Confidence            12223445555554332    22346778884 4443   345544

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=98.82  E-value=4.6e-08  Score=104.72  Aligned_cols=199  Identities=15%  Similarity=0.174  Sum_probs=125.5

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA  264 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~  264 (480)
                      .+.+++|.....+.+.+.+....           .....+|+.|++|||||++|+++....   +.+|+.++|+.+..+.
T Consensus       136 ~~~~lig~s~~~~~l~~~~~~~~-----------~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~i~i~c~~~~~~~  204 (469)
T PRK10923        136 PTTDIIGEAPAMQDVFRIIGRLS-----------RSSISVLINGESGTGKELVAHALHRHSPRAKAPFIALNMAAIPKDL  204 (469)
T ss_pred             ccccceecCHHHHHHHHHHHHHh-----------ccCCeEEEEeCCCCcHHHHHHHHHhcCCCCCCCeEeeeCCCCCHHH
Confidence            35678887776666665554321           124469999999999999999999876   4689999998874432


Q ss_pred             HHHHHHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhccccc-cccc-----CCceEEEEe
Q 011664          265 DLKSLLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NSCC-----FEERVMVFT  321 (480)
Q Consensus       265 ~l~~l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~~~-----~~~~ivI~t  321 (480)
                      --..+|..                 ...+..|||||||.+..     .....|+..++.-. ....     ..+.-+|+|
T Consensus       205 ~~~~lfg~~~g~~~~~~~~~~g~~~~a~~Gtl~l~~i~~l~~-----~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~  279 (469)
T PRK10923        205 IESELFGHEKGAFTGANTIRQGRFEQADGGTLFLDEIGDMPL-----DVQTRLLRVLADGQFYRVGGYAPVKVDVRIIAA  279 (469)
T ss_pred             HHHHhcCCCCCCCCCCCcCCCCCeeECCCCEEEEeccccCCH-----HHHHHHHHHHhcCcEEeCCCCCeEEeeEEEEEe
Confidence            22233321                 22457899999998843     22345565554211 0000     112346666


Q ss_pred             cCCC-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          322 MNSK-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       322 TN~~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      |+..       ..+.+.|..  |+. ..|.+|+...  ++...|+..|+....       ........++|+.-+..++.
T Consensus       280 ~~~~l~~~~~~~~~~~~L~~--~l~~~~i~~PpLreR~~Di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L~~  350 (469)
T PRK10923        280 THQNLEQRVQEGKFREDLFH--RLNVIRVHLPPLRERREDIPRLARHFLQVAA-------RELGVEAKLLHPETEAALTR  350 (469)
T ss_pred             CCCCHHHHHHcCCchHHHHH--HhcceeecCCCcccchhhHHHHHHHHHHHHH-------HHcCCCCCCcCHHHHHHHHh
Confidence            6532       235566666  773 5666665543  345556666653211       11111234799999999999


Q ss_pred             HhhhcHHHHHHHHHHHHHhc
Q 011664          392 ANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       392 ~a~~~~~~al~~~i~~~~~~  411 (480)
                      ..+...++.|+++++.+-..
T Consensus       351 ~~wpgNv~eL~~~i~~~~~~  370 (469)
T PRK10923        351 LAWPGNVRQLENTCRWLTVM  370 (469)
T ss_pred             CCCCChHHHHHHHHHHHHHh
Confidence            99999999999999887654

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

Probab=98.80  E-value=3.1e-08  Score=109.87  Aligned_cols=152  Identities=18%  Similarity=0.242  Sum_probs=105.6

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEe
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVD  256 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~  256 (480)
                      -.+|.++|-++-.+.+.+.+.+.             .+.+-+|.|+||+|||.++..+|...          +..++.+|
T Consensus       167 gklDPvIGRd~EI~r~iqIL~RR-------------~KNNPvLiGEpGVGKTAIvEGLA~rIv~g~VP~~L~~~~i~sLD  233 (786)
T COG0542         167 GKLDPVIGRDEEIRRTIQILSRR-------------TKNNPVLVGEPGVGKTAIVEGLAQRIVNGDVPESLKDKRIYSLD  233 (786)
T ss_pred             CCCCCCcChHHHHHHHHHHHhcc-------------CCCCCeEecCCCCCHHHHHHHHHHHHhcCCCCHHHcCCEEEEec
Confidence            35888999998888887766532             45578899999999999999999754          56789999


Q ss_pred             CCCcCC--------hHHHHHHHHhh--cCCcEEEEecccccccCcccc---cchhhhhhhcccccccccCCceEEEEecC
Q 011664          257 LSRVAD--------DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA---VSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       257 ~s~~~~--------~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~---~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      ++.+..        +..++.++...  ..+.|||||||+.+.+.....   ...+.+|.-+   ..  .++-++|-+||-
T Consensus       234 ~g~LvAGakyRGeFEeRlk~vl~ev~~~~~vILFIDEiHtiVGAG~~~G~a~DAaNiLKPa---LA--RGeL~~IGATT~  308 (786)
T COG0542         234 LGSLVAGAKYRGEFEERLKAVLKEVEKSKNVILFIDEIHTIVGAGATEGGAMDAANLLKPA---LA--RGELRCIGATTL  308 (786)
T ss_pred             HHHHhccccccCcHHHHHHHHHHHHhcCCCeEEEEechhhhcCCCcccccccchhhhhHHH---Hh--cCCeEEEEeccH
Confidence            876543        44566666433  348999999999998754431   2233344332   22  133344444542


Q ss_pred             CC----ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHH
Q 011664          324 SK----DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSY  359 (480)
Q Consensus       324 ~~----~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~  359 (480)
                      .-    =.=|+||-|  ||. .|.+..|+.++-..|++-.
T Consensus       309 ~EYRk~iEKD~AL~R--RFQ-~V~V~EPs~e~ti~ILrGl  345 (786)
T COG0542         309 DEYRKYIEKDAALER--RFQ-KVLVDEPSVEDTIAILRGL  345 (786)
T ss_pred             HHHHHHhhhchHHHh--cCc-eeeCCCCCHHHHHHHHHHH
Confidence            11    123999999  996 8999999999888777654

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=98.79  E-value=7.5e-08  Score=98.82  Aligned_cols=123  Identities=11%  Similarity=0.103  Sum_probs=91.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC------------------------cEEEEeCC---CcCChHHHHHHHHhh--
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY------------------------DVYDVDLS---RVADDADLKSLLLQT--  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~------------------------~~~~i~~s---~~~~~~~l~~l~~~~--  273 (480)
                      .+.++||+||+|+||+++|.++|..+-+                        +++.+...   ...+-.+++.+....  
T Consensus        23 l~HA~Lf~G~~G~Gk~~lA~~~A~~LlC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~  102 (334)
T PRK07993         23 GHHALLIQALPGMGDDALIYALSRWLMCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLTPEKGKSSLGVDAVREVTEKLYE  102 (334)
T ss_pred             cceEEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecccccccCCHHHHHHHHHHHhh
Confidence            4568999999999999999999986521                        34455332   123445566655432  


Q ss_pred             ----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          274 ----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       274 ----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                          ....|++||++|.+-     ....+.||..|+.     .+++.++|++|+.++.|-|.+++  |+. .+.|+.|+.
T Consensus       103 ~~~~g~~kV~iI~~ae~m~-----~~AaNaLLKtLEE-----Pp~~t~fiL~t~~~~~lLpTIrS--RCq-~~~~~~~~~  169 (334)
T PRK07993        103 HARLGGAKVVWLPDAALLT-----DAAANALLKTLEE-----PPENTWFFLACREPARLLATLRS--RCR-LHYLAPPPE  169 (334)
T ss_pred             ccccCCceEEEEcchHhhC-----HHHHHHHHHHhcC-----CCCCeEEEEEECChhhChHHHHh--ccc-cccCCCCCH
Confidence                245799999999883     3445788888864     25678899999999999999999  996 789999998


Q ss_pred             HHHHHHHHH
Q 011664          350 SSFKTLASS  358 (480)
Q Consensus       350 ~~r~~il~~  358 (480)
                      ++-...+..
T Consensus       170 ~~~~~~L~~  178 (334)
T PRK07993        170 QYALTWLSR  178 (334)
T ss_pred             HHHHHHHHH
Confidence            887766643

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=98.75  E-value=2.2e-07  Score=94.89  Aligned_cols=124  Identities=10%  Similarity=0.130  Sum_probs=92.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC------------------------cEEEEeC--CCcCChHHHHHHHHhh---
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY------------------------DVYDVDL--SRVADDADLKSLLLQT---  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~------------------------~~~~i~~--s~~~~~~~l~~l~~~~---  273 (480)
                      .+.++||+||+|+||+++|.++|+.+-+                        +++.+..  +.-.+-.++|.+....   
T Consensus        23 l~HA~Lf~G~~G~GK~~lA~~~A~~llC~~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~I~id~iR~l~~~~~~~  102 (325)
T PRK06871         23 GHHALLFKADSGLGTEQLIRALAQWLMCQTPQGDQPCGQCHSCHLFQAGNHPDFHILEPIDNKDIGVDQVREINEKVSQH  102 (325)
T ss_pred             cceeEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEccccCCCCCHHHHHHHHHHHhhc
Confidence            4568999999999999999999986522                        3444533  1223455666654332   


Q ss_pred             ---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHH
Q 011664          274 ---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFS  350 (480)
Q Consensus       274 ---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~  350 (480)
                         ....|++||++|.+.     ....+.||..++.-     +...++|++|+.++.|-|.+++  |+. .+.|++|+.+
T Consensus       103 ~~~g~~KV~iI~~a~~m~-----~~AaNaLLKtLEEP-----p~~~~fiL~t~~~~~llpTI~S--RC~-~~~~~~~~~~  169 (325)
T PRK06871        103 AQQGGNKVVYIQGAERLT-----EAAANALLKTLEEP-----RPNTYFLLQADLSAALLPTIYS--RCQ-TWLIHPPEEQ  169 (325)
T ss_pred             cccCCceEEEEechhhhC-----HHHHHHHHHHhcCC-----CCCeEEEEEECChHhCchHHHh--hce-EEeCCCCCHH
Confidence               244799999999883     34557888888642     5677888999999999999999  984 8899999998


Q ss_pred             HHHHHHHHH
Q 011664          351 SFKTLASSY  359 (480)
Q Consensus       351 ~r~~il~~~  359 (480)
                      +..+.+...
T Consensus       170 ~~~~~L~~~  178 (325)
T PRK06871        170 QALDWLQAQ  178 (325)
T ss_pred             HHHHHHHHH
Confidence            877766654

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

Probab=98.74  E-value=1.2e-07  Score=94.99  Aligned_cols=70  Identities=21%  Similarity=0.319  Sum_probs=54.1

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      -|+|++++|+.+.-++..-.++.+.-..+. --.|+++|..||.|+|||.+|+-+|...+.||+.+..+.+
T Consensus        16 yIIGQ~~AKkaVAIALRNR~RR~qL~~~lr~EV~PKNILMIGpTGVGKTEIARRLAkl~~aPFiKVEATKf   86 (444)
T COG1220          16 YIIGQDEAKKAVAIALRNRWRRMQLEEELRDEVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKF   86 (444)
T ss_pred             HhcCcHHHHHHHHHHHHHHHHHHhcCHHHhhccCccceEEECCCCCcHHHHHHHHHHHhCCCeEEEEeeee
Confidence            378999999998877765544443333332 2357899999999999999999999999999999865443

>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D

Probab=98.73  E-value=3.9e-08  Score=108.10  Aligned_cols=128  Identities=16%  Similarity=0.216  Sum_probs=87.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCCC----cCChHHHHHHHH-----------hhcCCcEEEEeccccc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLSR----VADDADLKSLLL-----------QTTSKSVILIEDLDRF  287 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s~----~~~~~~l~~l~~-----------~~~~~sII~IDEiD~l  287 (480)
                      .++||.|+||||||++|++++..+..  +|..++++.    +.+.-.+...+.           ......+||||||+.+
T Consensus        17 g~vLl~G~~GtgKs~lar~l~~~~~~~~pfv~i~~~~t~d~L~G~idl~~~~~~g~~~~~~G~L~~A~~GvL~lDEi~rl   96 (589)
T TIGR02031        17 GGVAIRARAGTGKTALARALAEILPPIMPFVELPLGVTEDRLIGGIDVEESLAGGQRVTQPGLLDEAPRGVLYVDMANLL   96 (589)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhCCcCCCeEecCcccchhhcccchhhhhhhhcCcccCCCCCeeeCCCCcEeccchhhC
Confidence            48999999999999999999998754  577777521    222222222111           1124479999999987


Q ss_pred             ccCcccccchhhhhhhcc-cc--------cccccCCceEEEEecCCCc---cCcccccCCCceeEEEEcCCC-CHHHHHH
Q 011664          288 LVEKPAAVSLSGVLNFMD-GV--------LNSCCFEERVMVFTMNSKD---HVDQALLRPGRIDVHIHFPLC-DFSSFKT  354 (480)
Q Consensus       288 ~~~~~~~~~ls~lL~~ld-g~--------~~~~~~~~~ivI~tTN~~~---~LD~aLlrpGRfd~~I~~~~p-~~~~r~~  354 (480)
                      .     ....+.|++.|+ |.        .. .......+|+|+|..+   .|.++|+.  ||+.+|.+.++ +.++|.+
T Consensus        97 ~-----~~~q~~Ll~al~~g~v~i~r~G~~~-~~p~~f~lIAt~np~e~~g~L~~~Lld--Rf~l~v~~~~~~~~~er~e  168 (589)
T TIGR02031        97 D-----DGLSNRLLQALDEGVVIVEREGISV-VHPAKFALIATYDPAEGGGGLPDHLLD--RLALHVSLEDVASQDLRVE  168 (589)
T ss_pred             C-----HHHHHHHHHHHHcCCeEEEECCCce-eecCceEEEEecCCccccCCCCHHHHH--hccCeeecCCCCCHHHHHH
Confidence            3     345577777775 21        11 1123456777888665   68999999  99998888754 5667889


Q ss_pred             HHHHHh
Q 011664          355 LASSYL  360 (480)
Q Consensus       355 il~~~l  360 (480)
                      |++..+
T Consensus       169 il~~~~  174 (589)
T TIGR02031       169 IVRRER  174 (589)
T ss_pred             HHHHHH
Confidence            888876

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=98.73  E-value=9.1e-08  Score=101.66  Aligned_cols=197  Identities=15%  Similarity=0.201  Sum_probs=118.6

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA  264 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~  264 (480)
                      .+..++|.....+.+.+.+....           .....++++|++||||+++|+++....   +.+|+.++|..+.. .
T Consensus       137 ~~~~lig~s~~~~~l~~~i~~~a-----------~~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~v~v~c~~~~~-~  204 (445)
T TIGR02915       137 ALRGLITSSPGMQKICRTIEKIA-----------PSDITVLLLGESGTGKEVLARALHQLSDRKDKRFVAINCAAIPE-N  204 (445)
T ss_pred             cccceeecCHHHHHHHHHHHHHh-----------CCCCCEEEECCCCcCHHHHHHHHHHhCCcCCCCeEEEECCCCCh-H
Confidence            34567777666666665443321           123469999999999999999998765   46899999998754 2


Q ss_pred             HHHH-HHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhccccc-cccc-----CCceEEEE
Q 011664          265 DLKS-LLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NSCC-----FEERVMVF  320 (480)
Q Consensus       265 ~l~~-l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~~~-----~~~~ivI~  320 (480)
                      .+.. +|..                 ...+.+|||||||.+..     .....|+..++.-. ....     ..+.-+|+
T Consensus       205 ~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~i~~l~~-----~~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~  279 (445)
T TIGR02915       205 LLESELFGYEKGAFTGAVKQTLGKIEYAHGGTLFLDEIGDLPL-----NLQAKLLRFLQERVIERLGGREEIPVDVRIVC  279 (445)
T ss_pred             HHHHHhcCCCCCCcCCCccCCCCceeECCCCEEEEechhhCCH-----HHHHHHHHHHhhCeEEeCCCCceeeeceEEEE
Confidence            3322 2321                 13467999999998842     22345555553211 0000     11334666


Q ss_pred             ecCCC-------ccCcccccCCCceeEEEEcCCCCHHHHH----HHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHH
Q 011664          321 TMNSK-------DHVDQALLRPGRIDVHIHFPLCDFSSFK----TLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGEL  389 (480)
Q Consensus       321 tTN~~-------~~LD~aLlrpGRfd~~I~~~~p~~~~r~----~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~l  389 (480)
                      ||+..       ..+.+.|..  |+. .+.+..|...+|.    .++..++....       ........++|+.-+..+
T Consensus       280 ~~~~~l~~~~~~~~~~~~L~~--~l~-~~~i~lPpLr~R~~Di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L  349 (445)
T TIGR02915       280 ATNQDLKRMIAEGTFREDLFY--RIA-EISITIPPLRSRDGDAVLLANAFLERFA-------RELKRKTKGFTDDALRAL  349 (445)
T ss_pred             ecCCCHHHHHHcCCccHHHHH--Hhc-cceecCCCchhchhhHHHHHHHHHHHHH-------HHhCCCCCCCCHHHHHHH
Confidence            66543       233444544  553 3444444444443    35555543210       011112357999999999


Q ss_pred             HHHhhhcHHHHHHHHHHHHHhc
Q 011664          390 MIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~~  411 (480)
                      ....+...++.|+.+++.+-..
T Consensus       350 ~~~~wpgNvreL~~~i~~a~~~  371 (445)
T TIGR02915       350 EAHAWPGNVRELENKVKRAVIM  371 (445)
T ss_pred             HhCCCCChHHHHHHHHHHHHHh
Confidence            9999999999999999877654

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).

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

Probab=98.72  E-value=8.9e-08  Score=101.16  Aligned_cols=201  Identities=16%  Similarity=0.177  Sum_probs=133.4

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD  263 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~  263 (480)
                      ..+..++|....-+++.+.+......           .-.||++|++||||-.+|++|....   +.+|+.+||..+..+
T Consensus       138 ~~~~~liG~S~am~~l~~~i~kvA~s-----------~a~VLI~GESGtGKElvAr~IH~~S~R~~~PFVavNcaAip~~  206 (464)
T COG2204         138 SLGGELVGESPAMQQLRRLIAKVAPS-----------DASVLITGESGTGKELVARAIHQASPRAKGPFIAVNCAAIPEN  206 (464)
T ss_pred             cccCCceecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCCcHHHHHHHHHhhCcccCCCceeeecccCCHH
Confidence            35678899999888888777655322           3469999999999999999999876   459999999988654


Q ss_pred             HHHHHHHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhcc-----ccccc-ccCCceEEEE
Q 011664          264 ADLKSLLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-----GVLNS-CCFEERVMVF  320 (480)
Q Consensus       264 ~~l~~l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-----g~~~~-~~~~~~ivI~  320 (480)
                      --=..+|..                 ......||+|||..+..     .....||..+.     .+.+. .-.-.+-||+
T Consensus       207 l~ESELFGhekGAFTGA~~~r~G~fE~A~GGTLfLDEI~~mpl-----~~Q~kLLRvLqe~~~~rvG~~~~i~vdvRiIa  281 (464)
T COG2204         207 LLESELFGHEKGAFTGAITRRIGRFEQANGGTLFLDEIGEMPL-----ELQVKLLRVLQEREFERVGGNKPIKVDVRIIA  281 (464)
T ss_pred             HHHHHhhcccccCcCCcccccCcceeEcCCceEEeeccccCCH-----HHHHHHHHHHHcCeeEecCCCcccceeeEEEe
Confidence            333345531                 13468999999998732     23355665553     22110 0011344788


Q ss_pred             ecCCC-------ccCcccccCCCceeEEEEcCCCCHHHHHH----HHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHH
Q 011664          321 TMNSK-------DHVDQALLRPGRIDVHIHFPLCDFSSFKT----LASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGEL  389 (480)
Q Consensus       321 tTN~~-------~~LD~aLlrpGRfd~~I~~~~p~~~~r~~----il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~l  389 (480)
                      |||..       ..+-+.|.-  |+ .++.+..|...+|.+    |+..++....       .+.-....++|+..++.+
T Consensus       282 aT~~dL~~~v~~G~FReDLyy--RL-nV~~i~iPpLRER~EDIp~L~~hfl~~~~-------~~~~~~~~~~s~~a~~~L  351 (464)
T COG2204         282 ATNRDLEEEVAAGRFREDLYY--RL-NVVPLRLPPLRERKEDIPLLAEHFLKRFA-------AELGRPPKGFSPEALAAL  351 (464)
T ss_pred             ecCcCHHHHHHcCCcHHHHHh--hh-ccceecCCcccccchhHHHHHHHHHHHHH-------HHcCCCCCCCCHHHHHHH
Confidence            88843       122334444  55 366666666655543    5555543211       111123468999999999


Q ss_pred             HHHhhhcHHHHHHHHHHHHHhcCC
Q 011664          390 MIANRNSPSRALKSVITALQTDGE  413 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~~~~  413 (480)
                      +...|...+|.|+++++....-.+
T Consensus       352 ~~y~WPGNVREL~N~ver~~il~~  375 (464)
T COG2204         352 LAYDWPGNVRELENVVERAVILSE  375 (464)
T ss_pred             HhCCCChHHHHHHHHHHHHHhcCC
Confidence            999999999999999998876644

>KOG0745 consensus Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones]

Probab=98.71  E-value=2.5e-08  Score=102.57  Aligned_cols=123  Identities=20%  Similarity=0.354  Sum_probs=85.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--------hHHHHHHHHhh------cCCcEEEEeccccccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--------DADLKSLLLQT------TSKSVILIEDLDRFLV  289 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--------~~~l~~l~~~~------~~~sII~IDEiD~l~~  289 (480)
                      +.++||.||+|+|||.||+.+|..++.+|.-.||+.+..        ++-+.+++..+      .+..|+||||+|.+..
T Consensus       226 KSNvLllGPtGsGKTllaqTLAr~ldVPfaIcDcTtLTQAGYVGeDVEsvi~KLl~~A~~nVekAQqGIVflDEvDKi~~  305 (564)
T KOG0745|consen  226 KSNVLLLGPTGSGKTLLAQTLARVLDVPFAICDCTTLTQAGYVGEDVESVIQKLLQEAEYNVEKAQQGIVFLDEVDKITK  305 (564)
T ss_pred             cccEEEECCCCCchhHHHHHHHHHhCCCeEEecccchhhcccccccHHHHHHHHHHHccCCHHHHhcCeEEEehhhhhcc
Confidence            457999999999999999999999999999999987753        34467777543      4779999999999874


Q ss_pred             Ccc---------cccchhhhhhhccccccc--------ccCCceEEEEecCC-------CccCcccccCCCcee-EEEEc
Q 011664          290 EKP---------AAVSLSGVLNFMDGVLNS--------CCFEERVMVFTMNS-------KDHVDQALLRPGRID-VHIHF  344 (480)
Q Consensus       290 ~~~---------~~~~ls~lL~~ldg~~~~--------~~~~~~ivI~tTN~-------~~~LD~aLlrpGRfd-~~I~~  344 (480)
                      ...         +......||..++|-.-.        ...+..|.|=|||-       -..||.-+-|  |++ ..+-|
T Consensus       306 ~~~~i~~~RDVsGEGVQQaLLKllEGtvVnVpeK~~~~~~rgd~vqiDTtnILFiasGAF~~Ldk~I~r--R~~d~slGF  383 (564)
T KOG0745|consen  306 KAESIHTSRDVSGEGVQQALLKLLEGTVVNVPEKGSRRKPRGDTVQIDTTNILFIASGAFVGLDKIISR--RLDDKSLGF  383 (564)
T ss_pred             cCccccccccccchhHHHHHHHHhcccEEcccCCCCCCCCCCCeEEEeccceEEEecccccchHHHHHH--hhcchhccc
Confidence            221         122345578777753211        11223444445542       3457777777  775 67778


Q ss_pred             CCCC
Q 011664          345 PLCD  348 (480)
Q Consensus       345 ~~p~  348 (480)
                      ..|+
T Consensus       384 g~~s  387 (564)
T KOG0745|consen  384 GAPS  387 (564)
T ss_pred             CCCC
Confidence            8773

>PF14532 Sigma54_activ_2: Sigma-54 interaction domain; PDB: 3CO5_B 3N70_H

Probab=98.71  E-value=1.8e-08  Score=90.16  Aligned_cols=126  Identities=21%  Similarity=0.333  Sum_probs=75.2

Q ss_pred             cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC---cEEEEeCCCcCChHHHHHHH
Q 011664          194 METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY---DVYDVDLSRVADDADLKSLL  270 (480)
Q Consensus       194 g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~---~~~~i~~s~~~~~~~l~~l~  270 (480)
                      |....-+++++.+.....           ....+||+|+|||||+++|+++....+.   +++.+++....     .+++
T Consensus         2 G~S~~~~~l~~~l~~~a~-----------~~~pvli~GE~GtGK~~~A~~lh~~~~~~~~~~~~~~~~~~~-----~~~l   65 (138)
T PF14532_consen    2 GKSPAMRRLRRQLERLAK-----------SSSPVLITGEPGTGKSLLARALHRYSGRANGPFIVIDCASLP-----AELL   65 (138)
T ss_dssp             -SCHHHHHHHHHHHHHHC-----------SSS-EEEECCTTSSHHHHHHCCHHTTTTCCS-CCCCCHHCTC-----HHHH
T ss_pred             CCCHHHHHHHHHHHHHhC-----------CCCcEEEEcCCCCCHHHHHHHHHhhcCccCCCeEEechhhCc-----HHHH
Confidence            445556666666665532           2456999999999999999999987754   45555655433     3344


Q ss_pred             HhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc------CcccccCCCcee-EEEE
Q 011664          271 LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH------VDQALLRPGRID-VHIH  343 (480)
Q Consensus       271 ~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~------LD~aLlrpGRfd-~~I~  343 (480)
                      .++ .+..|+|+|||.+..     .....|++.++....   .+-++|..++..++.      +++.|..  |+. ..|.
T Consensus        66 ~~a-~~gtL~l~~i~~L~~-----~~Q~~L~~~l~~~~~---~~~RlI~ss~~~l~~l~~~~~~~~~L~~--~l~~~~i~  134 (138)
T PF14532_consen   66 EQA-KGGTLYLKNIDRLSP-----EAQRRLLDLLKRQER---SNVRLIASSSQDLEELVEEGRFSPDLYY--RLSQLEIH  134 (138)
T ss_dssp             HHC-TTSEEEEECGCCS-H-----HHHHHHHHHHHHCTT---TTSEEEEEECC-CCCHHHHSTHHHHHHH--HCSTCEEE
T ss_pred             HHc-CCCEEEECChHHCCH-----HHHHHHHHHHHhcCC---CCeEEEEEeCCCHHHHhhccchhHHHHH--HhCCCEEe
Confidence            443 788999999999842     233445555543222   234544444444433      5666666  665 5666


Q ss_pred             cCC
Q 011664          344 FPL  346 (480)
Q Consensus       344 ~~~  346 (480)
                      +|+
T Consensus       135 lPp  137 (138)
T PF14532_consen  135 LPP  137 (138)
T ss_dssp             E--
T ss_pred             CCC
Confidence            664

>TIGR00368 Mg chelatase-related protein

Probab=98.71  E-value=7.4e-08  Score=103.68  Aligned_cols=144  Identities=18%  Similarity=0.292  Sum_probs=85.4

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc--EEEEeCCCcCC-
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD--VYDVDLSRVAD-  262 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~--~~~i~~s~~~~-  262 (480)
                      +..|+++.|++.+++.+.-.+               .....++|.||||||||+++++++..+-..  -..++.+.+.+ 
T Consensus       188 ~~d~~dv~Gq~~~~~al~~aa---------------~~g~~vlliG~pGsGKTtlar~l~~llp~~~~~~~le~~~i~s~  252 (499)
T TIGR00368       188 DLDLKDIKGQQHAKRALEIAA---------------AGGHNLLLFGPPGSGKTMLASRLQGILPPLTNEEAIETARIWSL  252 (499)
T ss_pred             CCCHHHhcCcHHHHhhhhhhc---------------cCCCEEEEEecCCCCHHHHHHHHhcccCCCCCcEEEeccccccc
Confidence            348999999988877655322               123479999999999999999999754110  00111111000 


Q ss_pred             --------------------hHHHHHHH----------HhhcCCcEEEEecccccccCcccccchhhhhhhccccc---c
Q 011664          263 --------------------DADLKSLL----------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL---N  309 (480)
Q Consensus       263 --------------------~~~l~~l~----------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~---~  309 (480)
                                          ......++          .......+|||||++.+.     ...+..|++.|+.-.   .
T Consensus       253 ~g~~~~~~~~~~~Pf~~p~~s~s~~~~~ggg~~~~pG~i~lA~~GvLfLDEi~e~~-----~~~~~~L~~~LE~~~v~i~  327 (499)
T TIGR00368       253 VGKLIDRKQIKQRPFRSPHHSASKPALVGGGPIPLPGEISLAHNGVLFLDELPEFK-----RSVLDALREPIEDGSISIS  327 (499)
T ss_pred             hhhhccccccccCCccccccccchhhhhCCccccchhhhhccCCCeEecCChhhCC-----HHHHHHHHHHHHcCcEEEE
Confidence                                00000111          122345899999999773     233444555553211   0


Q ss_pred             c-----ccCCceEEEEecCCC-----c------------------cCcccccCCCceeEEEEcCCCCHHH
Q 011664          310 S-----CCFEERVMVFTMNSK-----D------------------HVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       310 ~-----~~~~~~ivI~tTN~~-----~------------------~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                      .     .......+|+|+|.-     .                  .+..+|+.  |||.++.++.++.++
T Consensus       328 r~g~~~~~pa~frlIaa~Npcpcg~~~~~~~~c~c~~~~~~~y~~~is~pllD--R~dl~~~~~~~~~~~  395 (499)
T TIGR00368       328 RASAKIFYPARFQLVAAMNPCPCGHYGGKNTHCRCSPQQISRYWNKLSGPFLD--RIDLSVEVPLLPPEK  395 (499)
T ss_pred             ecCcceeccCCeEEEEecCCcccCcCCCCcccccCCHHHHHHHhhhccHhHHh--hCCEEEEEcCCCHHH
Confidence            0     012345677788742     1                  47888999  999999999987663

The N-terminal end matches very strongly a pfam Mg_chelatase domain.

>PRK09183 transposase/IS protein; Provisional

Probab=98.70  E-value=1.7e-08  Score=100.05  Aligned_cols=94  Identities=18%  Similarity=0.276  Sum_probs=60.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh-------HHHHHHHHh-hcCCcEEEEecccccccCcc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD-------ADLKSLLLQ-TTSKSVILIEDLDRFLVEKP  292 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~-------~~l~~l~~~-~~~~sII~IDEiD~l~~~~~  292 (480)
                      ..+++|+||||||||+|+.+++..+   |..+..++..++...       ..+...+.+ ...+.+++|||++....+..
T Consensus       102 ~~~v~l~Gp~GtGKThLa~al~~~a~~~G~~v~~~~~~~l~~~l~~a~~~~~~~~~~~~~~~~~dlLiiDdlg~~~~~~~  181 (259)
T PRK09183        102 NENIVLLGPSGVGKTHLAIALGYEAVRAGIKVRFTTAADLLLQLSTAQRQGRYKTTLQRGVMAPRLLIIDEIGYLPFSQE  181 (259)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeHHHHHHHHHHHHHCCcHHHHHHHHhcCCCEEEEcccccCCCChH
Confidence            4579999999999999999998653   777877776554311       123334433 45778999999987643333


Q ss_pred             cccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          293 AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       293 ~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ..   ..|++.++....    .+ -+|+|||.+
T Consensus       182 ~~---~~lf~li~~r~~----~~-s~iiTsn~~  206 (259)
T PRK09183        182 EA---NLFFQVIAKRYE----KG-SMILTSNLP  206 (259)
T ss_pred             HH---HHHHHHHHHHHh----cC-cEEEecCCC
Confidence            22   234444443322    12 367788854

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=7.4e-08  Score=98.51  Aligned_cols=124  Identities=16%  Similarity=0.226  Sum_probs=88.7

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCC-------------------------CcEEEEeCCC----------cCChHHH
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMS-------------------------YDVYDVDLSR----------VADDADL  266 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~-------------------------~~~~~i~~s~----------~~~~~~l  266 (480)
                      ..+.++||+||+|+|||++|+++|+.+.                         .+++.++...          ..+-..+
T Consensus        19 r~~hA~Lf~G~~G~GK~~la~~~a~~llC~~~~~~~~~Cg~C~~C~~~~~~~HpD~~~~~p~~~~~~~g~~~~~I~id~i   98 (325)
T PRK08699         19 RRPNAWLFAGKKGIGKTAFARFAAQALLCETPAPGHKPCGECMSCHLFGQGSHPDFYEITPLSDEPENGRKLLQIKIDAV   98 (325)
T ss_pred             CcceEEEeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCcCHHHHHHhcCCCCCEEEEecccccccccccCCCcCHHHH
Confidence            3566899999999999999999998652                         2466665421          1234456


Q ss_pred             HHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeE
Q 011664          267 KSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDV  340 (480)
Q Consensus       267 ~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~  340 (480)
                      |.+....      ....|++||+++.+-     ....+.++..++...     .+..+|++|+.++.+.+.+.+  |+ .
T Consensus        99 R~l~~~~~~~p~~~~~kV~iiEp~~~Ld-----~~a~naLLk~LEep~-----~~~~~Ilvth~~~~ll~ti~S--Rc-~  165 (325)
T PRK08699         99 REIIDNVYLTSVRGGLRVILIHPAESMN-----LQAANSLLKVLEEPP-----PQVVFLLVSHAADKVLPTIKS--RC-R  165 (325)
T ss_pred             HHHHHHHhhCcccCCceEEEEechhhCC-----HHHHHHHHHHHHhCc-----CCCEEEEEeCChHhChHHHHH--Hh-h
Confidence            6655332      245799999999883     234466777665432     346678889999999999998  88 5


Q ss_pred             EEEcCCCCHHHHHHHHHH
Q 011664          341 HIHFPLCDFSSFKTLASS  358 (480)
Q Consensus       341 ~I~~~~p~~~~r~~il~~  358 (480)
                      .+.|++|+.++..+.+..
T Consensus       166 ~~~~~~~~~~~~~~~L~~  183 (325)
T PRK08699        166 KMVLPAPSHEEALAYLRE  183 (325)
T ss_pred             hhcCCCCCHHHHHHHHHh
Confidence            899999999887666543

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=98.69  E-value=1.2e-06  Score=86.39  Aligned_cols=156  Identities=17%  Similarity=0.223  Sum_probs=84.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC-cEEEEe--CCCcC-----------------Ch--H----HHHHHHH---hhcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY-DVYDVD--LSRVA-----------------DD--A----DLKSLLL---QTTSK  276 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~-~~~~i~--~s~~~-----------------~~--~----~l~~l~~---~~~~~  276 (480)
                      -++|+||+|+|||++++.+++.+.. .+....  .+...                 +.  .    .+...+.   ....+
T Consensus        45 ~~~l~G~~G~GKTtl~~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~i~~~lG~~~~~~~~~~~~~~l~~~l~~~~~~~~~  124 (269)
T TIGR03015        45 FILITGEVGAGKTTLIRNLLKRLDQERVVAAKLVNTRVDAEDLLRMVAADFGLETEGRDKAALLRELEDFLIEQFAAGKR  124 (269)
T ss_pred             EEEEEcCCCCCHHHHHHHHHHhcCCCCeEEeeeeCCCCCHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHhCCCC
Confidence            5889999999999999999998763 222111  11110                 00  0    1111111   12457


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc---cCc----ccccCCCceeEEEEcCCCCH
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD---HVD----QALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~---~LD----~aLlrpGRfd~~I~~~~p~~  349 (480)
                      .+|+|||++.+...  ....+..+.+..   ..  ......||++ ..++   .+.    ..+.+  |+...+++++.+.
T Consensus       125 ~vliiDe~~~l~~~--~~~~l~~l~~~~---~~--~~~~~~vvl~-g~~~~~~~l~~~~~~~l~~--r~~~~~~l~~l~~  194 (269)
T TIGR03015       125 ALLVVDEAQNLTPE--LLEELRMLSNFQ---TD--NAKLLQIFLV-GQPEFRETLQSPQLQQLRQ--RIIASCHLGPLDR  194 (269)
T ss_pred             eEEEEECcccCCHH--HHHHHHHHhCcc---cC--CCCeEEEEEc-CCHHHHHHHcCchhHHHHh--heeeeeeCCCCCH
Confidence            89999999987321  111122222221   11  0112223333 2222   221    23555  8888999999999


Q ss_pred             HHHHHHHHHHhccCC----CCCch-hHHHHHHhCCCCCHHHHHHHHHH
Q 011664          350 SSFKTLASSYLGLKD----HKLFP-QVEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       350 ~~r~~il~~~l~~~~----~~l~~-~i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      ++...++...+...+    ..+.+ .++.|...+.|. |..|..+|..
T Consensus       195 ~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~-p~~i~~l~~~  241 (269)
T TIGR03015       195 EETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGI-PRLINILCDR  241 (269)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCc-ccHHHHHHHH
Confidence            999998887775322    22332 345566666554 4446665543

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.

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=98.69  E-value=2.7e-07  Score=93.98  Aligned_cols=123  Identities=9%  Similarity=0.095  Sum_probs=91.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC-----------------------CcEEEEeCC---CcCChHHHHHHHHhh---
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS-----------------------YDVYDVDLS---RVADDADLKSLLLQT---  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~-----------------------~~~~~i~~s---~~~~~~~l~~l~~~~---  273 (480)
                      .+.++||+||.|+||+++|.++|..+-                       -+++.+...   ...+-.+++.+....   
T Consensus        24 l~hA~L~~G~~G~Gk~~lA~~~a~~llC~~~~~~~Cg~C~sC~~~~~g~HPD~~~i~p~~~~~~I~vdqiR~l~~~~~~~  103 (319)
T PRK06090         24 IPGALLLQSDEGLGVESLVELFSRALLCQNYQSEACGFCHSCELMQSGNHPDLHVIKPEKEGKSITVEQIRQCNRLAQES  103 (319)
T ss_pred             cceeEeeECCCCCCHHHHHHHHHHHHcCCCCCCCCCCCCHHHHHHHcCCCCCEEEEecCcCCCcCCHHHHHHHHHHHhhC
Confidence            456899999999999999999998552                       246666543   223445566654322   


Q ss_pred             ---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHH
Q 011664          274 ---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFS  350 (480)
Q Consensus       274 ---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~  350 (480)
                         ....|++||++|.+.     ....+.||..++.-     +.+.++|++|+.++.|-|.+++  |+. .+.|+.|+.+
T Consensus       104 ~~~~~~kV~iI~~ae~m~-----~~AaNaLLKtLEEP-----p~~t~fiL~t~~~~~lLpTI~S--RCq-~~~~~~~~~~  170 (319)
T PRK06090        104 SQLNGYRLFVIEPADAMN-----ESASNALLKTLEEP-----APNCLFLLVTHNQKRLLPTIVS--RCQ-QWVVTPPSTA  170 (319)
T ss_pred             cccCCceEEEecchhhhC-----HHHHHHHHHHhcCC-----CCCeEEEEEECChhhChHHHHh--cce-eEeCCCCCHH
Confidence               235799999999883     34457788888642     4568889999999999999999  995 8999999998


Q ss_pred             HHHHHHHH
Q 011664          351 SFKTLASS  358 (480)
Q Consensus       351 ~r~~il~~  358 (480)
                      +..+.+..
T Consensus       171 ~~~~~L~~  178 (319)
T PRK06090        171 QAMQWLKG  178 (319)
T ss_pred             HHHHHHHH
Confidence            87776654

>PF13173 AAA_14: AAA domain

Probab=98.67  E-value=9.8e-08  Score=84.23  Aligned_cols=114  Identities=18%  Similarity=0.316  Sum_probs=72.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC--CcEEEEeCCCcCChHH----HHHHHHhh--cCCcEEEEecccccccCcccccc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS--YDVYDVDLSRVADDAD----LKSLLLQT--TSKSVILIEDLDRFLVEKPAAVS  296 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~--~~~~~i~~s~~~~~~~----l~~l~~~~--~~~sII~IDEiD~l~~~~~~~~~  296 (480)
                      +.++|+||.|||||++++.++..+.  .+++++++.+......    +.+.+.+.  ..+.+|||||++.+         
T Consensus         3 ~~~~l~G~R~vGKTtll~~~~~~~~~~~~~~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~iDEiq~~---------   73 (128)
T PF13173_consen    3 KIIILTGPRGVGKTTLLKQLAKDLLPPENILYINFDDPRDRRLADPDLLEYFLELIKPGKKYIFIDEIQYL---------   73 (128)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhcccccceeeccCCHHHHHHhhhhhHHHHHHhhccCCcEEEEehhhhh---------
Confidence            4689999999999999999998876  8899999876543211    23334333  36799999999977         


Q ss_pred             hhhhhhhcccccccccCCceEEEEecCCCc---cCcccccCCCceeEEEEcCCCCHHHH
Q 011664          297 LSGVLNFMDGVLNSCCFEERVMVFTMNSKD---HVDQALLRPGRIDVHIHFPLCDFSSF  352 (480)
Q Consensus       297 ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~---~LD~aLlrpGRfd~~I~~~~p~~~~r  352 (480)
                       ..+...+..+... ..+..+++.+++...   .....|  +||.. .+++.+.+..++
T Consensus        74 -~~~~~~lk~l~d~-~~~~~ii~tgS~~~~l~~~~~~~l--~gr~~-~~~l~Plsf~E~  127 (128)
T PF13173_consen   74 -PDWEDALKFLVDN-GPNIKIILTGSSSSLLSKDIAESL--AGRVI-EIELYPLSFREF  127 (128)
T ss_pred             -ccHHHHHHHHHHh-ccCceEEEEccchHHHhhcccccC--CCeEE-EEEECCCCHHHh
Confidence             2222233333221 112344454444322   223334  35885 889999888764

>PF03215 Rad17: Rad17 cell cycle checkpoint protein

Probab=98.66  E-value=1.3e-07  Score=102.22  Aligned_cols=168  Identities=24%  Similarity=0.333  Sum_probs=100.0

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEE-
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV-  255 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i-  255 (480)
                      .|.  ..-.|.+.++|+.+....++++..+...+.        +....+-+||+||||||||++++++|+++|..+..- 
T Consensus         8 ~W~--~ky~P~~~~eLavhkkKv~eV~~wl~~~~~--------~~~~~~iLlLtGP~G~GKtttv~~La~elg~~v~Ew~   77 (519)
T PF03215_consen    8 PWV--EKYAPKTLDELAVHKKKVEEVRSWLEEMFS--------GSSPKRILLLTGPSGCGKTTTVKVLAKELGFEVQEWI   77 (519)
T ss_pred             ccc--hhcCCCCHHHhhccHHHHHHHHHHHHHHhc--------cCCCcceEEEECCCCCCHHHHHHHHHHHhCCeeEEec
Confidence            463  456789999999998888888777765332        233455678999999999999999999999877653 


Q ss_pred             eCCCc----------CC-----h---HH---HHHH-HHh-------------hcCCcEEEEecccccccCcccccchhhh
Q 011664          256 DLSRV----------AD-----D---AD---LKSL-LLQ-------------TTSKSVILIEDLDRFLVEKPAAVSLSGV  300 (480)
Q Consensus       256 ~~s~~----------~~-----~---~~---l~~l-~~~-------------~~~~sII~IDEiD~l~~~~~~~~~ls~l  300 (480)
                      +...+          .+     +   +.   ...+ +..             ...+.||+|||+-.++....     ..|
T Consensus        78 np~~~~~~~~~~~d~~s~~~~~~~f~sq~~~F~~f~l~~s~y~~l~~~g~~~~~~~kvILVEDlPN~~~~~~-----~~f  152 (519)
T PF03215_consen   78 NPVSFRESDNQEDDFESDFNKFDEFLSQSDKFSEFLLRASKYSSLSMSGSNSSSNKKVILVEDLPNVFHRDT-----SRF  152 (519)
T ss_pred             CCCCccccccccccccccccccccccchhhhhccccccccccccccccCCCcCCCceEEEeeccccccchhH-----HHH
Confidence            21111          00     0   01   1111 100             12468999999987654332     222


Q ss_pred             hhhcccccccccCC-ceEEEEe-c------CCCc--------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          301 LNFMDGVLNSCCFE-ERVMVFT-M------NSKD--------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       301 L~~ldg~~~~~~~~-~~ivI~t-T------N~~~--------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      -+.|..... .... ..|||+| +      |...        -+++.++.-.++ .+|.|.+-.....++.+++.+.
T Consensus       153 ~~~L~~~l~-~~~~~PlV~iiSe~~~~~~~~~~~~~~~t~~~L~~~~il~~~~i-~~I~FNpIa~T~mkKaL~rI~~  227 (519)
T PF03215_consen  153 REALRQYLR-SSRCLPLVFIISETESLSGDNSYRSNSFTAERLFPKEILNHPGI-TRIKFNPIAPTFMKKALKRILK  227 (519)
T ss_pred             HHHHHHHHH-cCCCCCEEEEEecccccCCCCcccccchhhhhccCHHHHhCCCc-eEEEecCCCHHHHHHHHHHHHH
Confidence            222222211 1112 4555665 1      1111        245555543344 5899998888777777776654

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=98.66  E-value=2.4e-07  Score=98.88  Aligned_cols=198  Identities=16%  Similarity=0.204  Sum_probs=124.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADL  266 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l  266 (480)
                      ..++|....-.++.+.+....           .....+++.|.+||||+++|+++....   +.+|+.++|..+..+.--
T Consensus       134 ~~lig~s~~~~~v~~~i~~~a-----------~~~~~vli~Ge~GtGK~~~A~~ih~~~~~~~~~~~~~~c~~~~~~~~~  202 (463)
T TIGR01818       134 AELIGEAPAMQEVFRAIGRLS-----------RSDITVLINGESGTGKELVARALHRHSPRANGPFIALNMAAIPKDLIE  202 (463)
T ss_pred             cceeecCHHHHHHHHHHHHHh-----------CcCCeEEEECCCCCCHHHHHHHHHHhCCCCCCCeEEEeCCCCCHHHHH
Confidence            457777776666665554321           123469999999999999999998865   568999999887432222


Q ss_pred             HHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cc-----ccCCceEEEEecC
Q 011664          267 KSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NS-----CCFEERVMVFTMN  323 (480)
Q Consensus       267 ~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~-----~~~~~~ivI~tTN  323 (480)
                      ..+|.                 ....++.|||||||.+..     .....|+..++.-. ..     ....+.-+|+||+
T Consensus       203 ~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~ei~~l~~-----~~q~~ll~~l~~~~~~~~~~~~~~~~~~rii~~~~  277 (463)
T TIGR01818       203 SELFGHEKGAFTGANTRRQGRFEQADGGTLFLDEIGDMPL-----DAQTRLLRVLADGEFYRVGGRTPIKVDVRIVAATH  277 (463)
T ss_pred             HHhcCCCCCCCCCcccCCCCcEEECCCCeEEEEchhhCCH-----HHHHHHHHHHhcCcEEECCCCceeeeeeEEEEeCC
Confidence            22322                 112468899999998843     22355665554211 00     0011234666665


Q ss_pred             CC-c------cCcccccCCCcee-EEEEcCCCC--HHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SK-D------HVDQALLRPGRID-VHIHFPLCD--FSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~-~------~LD~aLlrpGRfd-~~I~~~~p~--~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .. +      .+.+.|..  |+. .+|++|+..  .++...++..++....       ........++|+..+..++...
T Consensus       278 ~~l~~~~~~~~f~~~L~~--rl~~~~i~lPpLr~R~~Di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L~~~~  348 (463)
T TIGR01818       278 QNLEALVRQGKFREDLFH--RLNVIRIHLPPLRERREDIPRLARHFLALAA-------RELDVEPKLLDPEALERLKQLR  348 (463)
T ss_pred             CCHHHHHHcCCcHHHHHH--HhCcceecCCCcccchhhHHHHHHHHHHHHH-------HHhCCCCCCcCHHHHHHHHhCC
Confidence            32 2      33445555  554 477777766  4566667777663211       0111122589999999999999


Q ss_pred             hhcHHHHHHHHHHHHHhcC
Q 011664          394 RNSPSRALKSVITALQTDG  412 (480)
Q Consensus       394 ~~~~~~al~~~i~~~~~~~  412 (480)
                      +...++.|+.+++.+-...
T Consensus       349 wpgNvreL~~~~~~~~~~~  367 (463)
T TIGR01818       349 WPGNVRQLENLCRWLTVMA  367 (463)
T ss_pred             CCChHHHHHHHHHHHHHhC
Confidence            9999999999998876543

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.

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=98.65  E-value=2.2e-07  Score=88.64  Aligned_cols=156  Identities=19%  Similarity=0.292  Sum_probs=81.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc---EEEEeCCCcCC--------------------------------------
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD---VYDVDLSRVAD--------------------------------------  262 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~~i~~s~~~~--------------------------------------  262 (480)
                      ...++|+||.|+|||+|++.+.+.+...   .++++......                                      
T Consensus        20 ~~~~~l~G~rg~GKTsLl~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   99 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSLLKEFINELKEKGYKVVYIDFLEESNESSLRSFIEETSLADELSEALGISIPSITLEKISKDLS   99 (234)
T ss_dssp             SSEEEEEESTTSSHHHHHHHHHHHCT--EECCCHHCCTTBSHHHHHHHHHHHHHHHCHCHHHHHHHCCTSTTEEEECTS-
T ss_pred             CcEEEEEcCCcCCHHHHHHHHHHHhhhcCCcEEEEecccchhhhHHHHHHHHHHHHHHHHHHHhhhcccccchhhhhcch
Confidence            4579999999999999999999988321   11221111110                                      


Q ss_pred             ---hHHHHHHH---HhhcCCcEEEEecccccc-cCcccccchhhhhhhcccccccccCCceEEEE-ecCCC---c--cCc
Q 011664          263 ---DADLKSLL---LQTTSKSVILIEDLDRFL-VEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF-TMNSK---D--HVD  329 (480)
Q Consensus       263 ---~~~l~~l~---~~~~~~sII~IDEiD~l~-~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~-tTN~~---~--~LD  329 (480)
                         ...+..++   .+...+.||+|||++.+. ........+..|.+.++....   ..+..+|+ ++...   +  .-.
T Consensus       100 ~~~~~~l~~~~~~l~~~~~~~iiviDe~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~~~~v~~~S~~~~~~~~~~~~  176 (234)
T PF01637_consen  100 EDSFSALERLLEKLKKKGKKVIIVIDEFQYLAIASEEDKDFLKSLRSLLDSLLS---QQNVSIVITGSSDSLMEEFLDDK  176 (234)
T ss_dssp             GG-G--HHHHHHHHHHCHCCEEEEEETGGGGGBCTTTTHHHHHHHHHHHHH-------TTEEEEEEESSHHHHHHTT-TT
T ss_pred             hhHHHHHHHHHHHHHhcCCcEEEEEecHHHHhhcccchHHHHHHHHHHHhhccc---cCCceEEEECCchHHHHHhhccc
Confidence               01122222   222345899999999997 333334445666666665433   33444444 44311   1  122


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCC---chhHHHHHHhCCCCCHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL---FPQVEEIFQNGSSLSPAEIG  387 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l---~~~i~~l~~~~~g~s~adI~  387 (480)
                      ..+..  |+.. +.+++.+.++..+++...+... ..+   ..+++++...+ |-.|.-|.
T Consensus       177 ~~~~~--~~~~-~~l~~l~~~e~~~~~~~~~~~~-~~~~~~~~~~~~i~~~~-gG~P~~l~  232 (234)
T PF01637_consen  177 SPLFG--RFSH-IELKPLSKEEAREFLKELFKEL-IKLPFSDEDIEEIYSLT-GGNPRYLQ  232 (234)
T ss_dssp             STTTT-----E-EEE----HHHHHHHHHHHHHCC-------HHHHHHHHHHH-TT-HHHHH
T ss_pred             Ccccc--ccce-EEEeeCCHHHHHHHHHHHHHHh-hcccCCHHHHHHHHHHh-CCCHHHHh
Confidence            34444  8876 9999999999999998876544 322   23455665555 44454443

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=98.63  E-value=3.2e-07  Score=97.76  Aligned_cols=197  Identities=17%  Similarity=0.180  Sum_probs=117.1

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHH
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDAD  265 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~  265 (480)
                      +..++|....-..+.+.+.....           ....+|++|++||||+++|+++....   +.+|+.++|..+..+.-
T Consensus       142 ~~~ii~~S~~~~~~~~~~~~~a~-----------~~~~vli~Ge~GtGK~~lA~~ih~~s~~~~~~~~~i~c~~~~~~~~  210 (457)
T PRK11361        142 WGHILTNSPAMMDICKDTAKIAL-----------SQASVLISGESGTGKELIARAIHYNSRRAKGPFIKVNCAALPESLL  210 (457)
T ss_pred             ccceecccHHHhHHHHHHHHHcC-----------CCcEEEEEcCCCccHHHHHHHHHHhCCCCCCCeEEEECCCCCHHHH
Confidence            34566665555555544443321           23479999999999999999998764   57899999998754322


Q ss_pred             HHHHHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhccccc-----cc-ccCCceEEEEec
Q 011664          266 LKSLLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----NS-CCFEERVMVFTM  322 (480)
Q Consensus       266 l~~l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----~~-~~~~~~ivI~tT  322 (480)
                      -..+|..                 .....+|||||||.+..     .....|+..++.-.     .. ....+..||+||
T Consensus       211 ~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ld~i~~l~~-----~~q~~L~~~l~~~~~~~~~~~~~~~~~~rii~~t  285 (457)
T PRK11361        211 ESELFGHEKGAFTGAQTLRQGLFERANEGTLLLDEIGEMPL-----VLQAKLLRILQEREFERIGGHQTIKVDIRIIAAT  285 (457)
T ss_pred             HHHhcCCCCCCCCCCCCCCCCceEECCCCEEEEechhhCCH-----HHHHHHHHHHhcCcEEeCCCCceeeeceEEEEeC
Confidence            2233321                 12457999999999843     22355565554211     00 001124577777


Q ss_pred             CCC-c------cCcccccCCCceeEEEEcCCCCHHHHH----HHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          323 NSK-D------HVDQALLRPGRIDVHIHFPLCDFSSFK----TLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       323 N~~-~------~LD~aLlrpGRfd~~I~~~~p~~~~r~----~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      |.. .      .+.+.|..  |+. .+.+..|...+|.    .++..++....       ........++++..+..+..
T Consensus       286 ~~~l~~~~~~g~~~~~l~~--~l~-~~~i~~ppLreR~~di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L~~  355 (457)
T PRK11361        286 NRDLQAMVKEGTFREDLFY--RLN-VIHLILPPLRDRREDISLLANHFLQKFS-------SENQRDIIDIDPMAMSLLTA  355 (457)
T ss_pred             CCCHHHHHHcCCchHHHHH--Hhc-cceecCCChhhchhhHHHHHHHHHHHHH-------HHcCCCCCCcCHHHHHHHHc
Confidence            643 1      23333443  442 3455555555543    34444442110       01111235899999999998


Q ss_pred             HhhhcHHHHHHHHHHHHHhc
Q 011664          392 ANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       392 ~a~~~~~~al~~~i~~~~~~  411 (480)
                      ..+...++.|+.+++.+-..
T Consensus       356 ~~wpgNv~eL~~~~~~~~~~  375 (457)
T PRK11361        356 WSWPGNIRELSNVIERAVVM  375 (457)
T ss_pred             CCCCCcHHHHHHHHHHHHHh
Confidence            88999999999999876554

>PF00910 RNA_helicase: RNA helicase; InterPro: IPR000605 Helicases have been classified in 5 superfamilies (SF1-SF5)

Probab=98.61  E-value=3.3e-08  Score=84.71  Aligned_cols=97  Identities=18%  Similarity=0.239  Sum_probs=54.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG  306 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg  306 (480)
                      |.||||||+|||++|+.+|..+...+-......+.....-.+.+.......++++||+....... .....+++++.++.
T Consensus         1 I~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~vy~~~~~~~~w~gY~~q~vvi~DD~~~~~~~~-~~~~~~~l~~l~s~   79 (107)
T PF00910_consen    1 IWIYGPPGIGKSTLAKELAKDLLKHIGEPTKDSVYTRNPGDKFWDGYQGQPVVIIDDFGQDNDGY-NYSDESELIRLISS   79 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHhccCCCCcEEeCCCccchhhccCCCcEEEEeecCcccccc-chHHHHHHHHHHhc
Confidence            57999999999999999998664322111111110001111334445567899999999775332 22245556665542


Q ss_pred             c---------ccc-ccCCceEEEEecCC
Q 011664          307 V---------LNS-CCFEERVMVFTMNS  324 (480)
Q Consensus       307 ~---------~~~-~~~~~~ivI~tTN~  324 (480)
                      .         ... ..-...+||+|||.
T Consensus        80 ~~~~~~~a~~~~K~~~~~s~~vi~tsN~  107 (107)
T PF00910_consen   80 NPFQPNMADLEDKGTPFNSKLVIITSNF  107 (107)
T ss_pred             CCcccccccHhhCCCccCCCEEEEcCCC
Confidence            2         110 11233688889984

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

>PRK15115 response regulator GlrR; Provisional

Probab=98.58  E-value=4.4e-07  Score=96.41  Aligned_cols=173  Identities=16%  Similarity=0.154  Sum_probs=104.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHHHHHHh-----------------hcCCcEEEEec
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLKSLLLQ-----------------TTSKSVILIED  283 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~~l~~~-----------------~~~~sII~IDE  283 (480)
                      ...++++|++|||||++|+++....   +.+|+.++|..+..+.--..+|..                 ......|||||
T Consensus       157 ~~~vli~Ge~GtGk~~lA~~ih~~s~r~~~~f~~i~c~~~~~~~~~~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~l~~  236 (444)
T PRK15115        157 DVSVLINGQSGTGKEILAQAIHNASPRASKPFIAINCGALPEQLLESELFGHARGAFTGAVSNREGLFQAAEGGTLFLDE  236 (444)
T ss_pred             CCeEEEEcCCcchHHHHHHHHHHhcCCCCCCeEEEeCCCCCHHHHHHHhcCCCcCCCCCCccCCCCcEEECCCCEEEEEc
Confidence            3469999999999999999998865   478999999887433222233321                 22457999999


Q ss_pred             ccccccCcccccchhhhhhhccccc-cccc-----CCceEEEEecCCCccCcccccCCCcee-------EEEEcCCCCHH
Q 011664          284 LDRFLVEKPAAVSLSGVLNFMDGVL-NSCC-----FEERVMVFTMNSKDHVDQALLRPGRID-------VHIHFPLCDFS  350 (480)
Q Consensus       284 iD~l~~~~~~~~~ls~lL~~ldg~~-~~~~-----~~~~ivI~tTN~~~~LD~aLlrpGRfd-------~~I~~~~p~~~  350 (480)
                      ||.+..     .....|+..++.-. ....     .....+|+||+..  ++..+. .|+|.       ..+.+..|...
T Consensus       237 i~~l~~-----~~q~~L~~~l~~~~~~~~g~~~~~~~~~rii~~~~~~--l~~~~~-~~~f~~~l~~~l~~~~i~lPpLr  308 (444)
T PRK15115        237 IGDMPA-----PLQVKLLRVLQERKVRPLGSNRDIDIDVRIISATHRD--LPKAMA-RGEFREDLYYRLNVVSLKIPALA  308 (444)
T ss_pred             cccCCH-----HHHHHHHHHHhhCCEEeCCCCceeeeeEEEEEeCCCC--HHHHHH-cCCccHHHHHhhceeeecCCChH
Confidence            998843     22344555553211 0000     1134567777642  332222 23441       23455555555


Q ss_pred             HHH----HHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHHhc
Q 011664          351 SFK----TLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       351 ~r~----~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~~~  411 (480)
                      +|.    .|++.++....       ........++|+.-+..+....+...++.|+.+++.+-..
T Consensus       309 ~R~eDi~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L~~~~WpgNvreL~~~i~~~~~~  366 (444)
T PRK15115        309 ERTEDIPLLANHLLRQAA-------ERHKPFVRAFSTDAMKRLMTASWPGNVRQLVNVIEQCVAL  366 (444)
T ss_pred             hccccHHHHHHHHHHHHH-------HHhCCCCCCcCHHHHHHHHhCCCCChHHHHHHHHHHHHHh
Confidence            553    34444442110       0011122479999999999999999999999999876543

>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]

Probab=98.54  E-value=1.6e-06  Score=85.51  Aligned_cols=64  Identities=23%  Similarity=0.281  Sum_probs=45.2

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCCCc
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLSRV  260 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s~~  260 (480)
                      -..++|++++++..- .+...++.+..       ..|++||.||||||||.||-+|++++|.  +|+....|++
T Consensus        37 ~~g~vGQ~~AReAag-iivdlik~Kkm-------aGravLlaGppgtGKTAlAlaisqELG~kvPFcpmvgSEv  102 (456)
T KOG1942|consen   37 AAGFVGQENAREAAG-IIVDLIKSKKM-------AGRAVLLAGPPGTGKTALALAISQELGPKVPFCPMVGSEV  102 (456)
T ss_pred             ccccccchhhhhhhh-HHHHHHHhhhc-------cCcEEEEecCCCCchhHHHHHHHHHhCCCCCcccccchhh
Confidence            356789988887643 33344444332       4578999999999999999999999975  4554444443

>KOG0990 consensus Replication factor C, subunit RFC5 [Replication, recombination and repair]

Probab=98.53  E-value=2.4e-07  Score=92.42  Aligned_cols=159  Identities=14%  Similarity=0.152  Sum_probs=103.2

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc------EEE
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD------VYD  254 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~------~~~  254 (480)
                      ++..+|..++++++++++...+.+.           ...+.  -...|+|||||||||+.+.|.|+.+-.+      +..
T Consensus        32 vekyrP~~l~dv~~~~ei~st~~~~-----------~~~~~--lPh~L~YgPPGtGktsti~a~a~~ly~~~~~~~m~le   98 (360)
T KOG0990|consen   32 VEKYRPPFLGIVIKQEPIWSTENRY-----------SGMPG--LPHLLFYGPPGTGKTSTILANARDFYSPHPTTSMLLE   98 (360)
T ss_pred             ccCCCCchhhhHhcCCchhhHHHHh-----------ccCCC--CCcccccCCCCCCCCCchhhhhhhhcCCCCchhHHHH
Confidence            4677889999999998877766542           22221  1279999999999999999999977442      223


Q ss_pred             EeCCCcCCh---HHHHHHHHhhc---------CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEec
Q 011664          255 VDLSRVADD---ADLKSLLLQTT---------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM  322 (480)
Q Consensus       255 i~~s~~~~~---~~l~~l~~~~~---------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT  322 (480)
                      +++|+-.+-   ..-...|+.+.         ....+++||.|++..  .   ..++|-..+...     ..+.-|+.-+
T Consensus        99 lnaSd~rgid~vr~qi~~fast~~~~~fst~~~fKlvILDEADaMT~--~---AQnALRRviek~-----t~n~rF~ii~  168 (360)
T KOG0990|consen   99 LNASDDRGIDPVRQQIHLFASTQQPTTYSTHAAFKLVILDEADAMTR--D---AQNALRRVIEKY-----TANTRFATIS  168 (360)
T ss_pred             hhccCccCCcchHHHHHHHHhhccceeccccCceeEEEecchhHhhH--H---HHHHHHHHHHHh-----ccceEEEEec
Confidence            344443331   11223344333         568999999998742  2   223333333322     2334455678


Q ss_pred             CCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCC
Q 011664          323 NSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDH  365 (480)
Q Consensus       323 N~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~  365 (480)
                      |++..+.|++.+  ||. ...|.+.+.+.-....+.++.....
T Consensus       169 n~~~ki~pa~qs--Rct-rfrf~pl~~~~~~~r~shi~e~e~~  208 (360)
T KOG0990|consen  169 NPPQKIHPAQQS--RCT-RFRFAPLTMAQQTERQSHIRESEQK  208 (360)
T ss_pred             cChhhcCchhhc--ccc-cCCCCCCChhhhhhHHHHHHhcchh
Confidence            999999999999  885 6677777766666666666654443

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=98.52  E-value=5.9e-07  Score=89.92  Aligned_cols=191  Identities=19%  Similarity=0.215  Sum_probs=108.3

Q ss_pred             cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCCcCChH
Q 011664          194 METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSRVADDA  264 (480)
Q Consensus       194 g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~~~~~~  264 (480)
                      |.+.+++ +.+.+...+..|..      ....++||+|++|.|||++++..+...         ..+++.+.+..-.++.
T Consensus        38 gY~~A~~-~L~~L~~Ll~~P~~------~Rmp~lLivG~snnGKT~Ii~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~  110 (302)
T PF05621_consen   38 GYPRAKE-ALDRLEELLEYPKR------HRMPNLLIVGDSNNGKTMIIERFRRLHPPQSDEDAERIPVVYVQMPPEPDER  110 (302)
T ss_pred             cCHHHHH-HHHHHHHHHhCCcc------cCCCceEEecCCCCcHHHHHHHHHHHCCCCCCCCCccccEEEEecCCCCChH
Confidence            3344443 34455555555432      223489999999999999999998643         2467777765444333


Q ss_pred             HHHHH------------------------HHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEE
Q 011664          265 DLKSL------------------------LLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF  320 (480)
Q Consensus       265 ~l~~l------------------------~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~  320 (480)
                      .+...                        +.+..+..+|+|||++.++....  ....+++|.+..+.+. ..=..|.++
T Consensus       111 ~~Y~~IL~~lgaP~~~~~~~~~~~~~~~~llr~~~vrmLIIDE~H~lLaGs~--~~qr~~Ln~LK~L~Ne-L~ipiV~vG  187 (302)
T PF05621_consen  111 RFYSAILEALGAPYRPRDRVAKLEQQVLRLLRRLGVRMLIIDEFHNLLAGSY--RKQREFLNALKFLGNE-LQIPIVGVG  187 (302)
T ss_pred             HHHHHHHHHhCcccCCCCCHHHHHHHHHHHHHHcCCcEEEeechHHHhcccH--HHHHHHHHHHHHHhhc-cCCCeEEec
Confidence            22111                        12234668999999999764332  2345667777666441 111223333


Q ss_pred             ecCC--CccCcccccCCCceeEEEEcCCCCH-HHHHHHHHHHhccCCC----CCc-hhH-HHHHHhCCCCCHHHHHHHHH
Q 011664          321 TMNS--KDHVDQALLRPGRIDVHIHFPLCDF-SSFKTLASSYLGLKDH----KLF-PQV-EEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       321 tTN~--~~~LD~aLlrpGRfd~~I~~~~p~~-~~r~~il~~~l~~~~~----~l~-~~i-~~l~~~~~g~s~adI~~ll~  391 (480)
                      |..-  .=.-|+.|-+  ||+ .+.+|.... +++..++..+-...+.    .+. .++ ..|...+.|.+| ++..++.
T Consensus       188 t~~A~~al~~D~QLa~--RF~-~~~Lp~W~~d~ef~~LL~s~e~~LPLr~~S~l~~~~la~~i~~~s~G~iG-~l~~ll~  263 (302)
T PF05621_consen  188 TREAYRALRTDPQLAS--RFE-PFELPRWELDEEFRRLLASFERALPLRKPSNLASPELARRIHERSEGLIG-ELSRLLN  263 (302)
T ss_pred             cHHHHHHhccCHHHHh--ccC-CccCCCCCCCcHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHcCCchH-HHHHHHH
Confidence            3221  1223788888  997 566665443 4566676665432221    122 233 567777767666 6777776


Q ss_pred             HhhhcHH
Q 011664          392 ANRNSPS  398 (480)
Q Consensus       392 ~a~~~~~  398 (480)
                      .+...+.
T Consensus       264 ~aA~~AI  270 (302)
T PF05621_consen  264 AAAIAAI  270 (302)
T ss_pred             HHHHHHH
Confidence            5544333

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]

Probab=98.50  E-value=6e-07  Score=92.86  Aligned_cols=155  Identities=16%  Similarity=0.223  Sum_probs=100.7

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-------Cc--------
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-------YD--------  251 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-------~~--------  251 (480)
                      -.|.-++|++..|..|.-....             +.-.|+|+-|+.|||||++++|+|..|.       ++        
T Consensus        14 ~pf~aivGqd~lk~aL~l~av~-------------P~iggvLI~G~kGtaKSt~~Rala~LLp~~~~V~gc~f~cdP~~P   80 (423)
T COG1239          14 LPFTAIVGQDPLKLALGLNAVD-------------PQIGGALIAGEKGTAKSTLARALADLLPEIEVVIGCPFNCDPDDP   80 (423)
T ss_pred             cchhhhcCchHHHHHHhhhhcc-------------cccceeEEecCCCccHHHHHHHHHHhCCccceecCCCCCCCCCCh
Confidence            4588899999999887633221             2335899999999999999999998772       21        


Q ss_pred             -------------------------EEEEeCCC----cCChHHHHHHHH-----------hhcCCcEEEEecccccccCc
Q 011664          252 -------------------------VYDVDLSR----VADDADLKSLLL-----------QTTSKSVILIEDLDRFLVEK  291 (480)
Q Consensus       252 -------------------------~~~i~~s~----~~~~~~l~~l~~-----------~~~~~sII~IDEiD~l~~~~  291 (480)
                                               |..+.++.    +.+.-++.+.+.           ...+..|++|||+..+-   
T Consensus        81 ~~~c~~c~~k~~e~~~~~~~~r~v~~v~lPl~ateDrvvGslDi~ka~~~g~~af~PGlLa~AnRGIlYvDEvnlL~---  157 (423)
T COG1239          81 EEMCDECRAKGDELEWLPREKRKVPFVALPLGATEDRLVGSLDIEKALEEGPKAFQPGLLARANRGILYVDEVNLLD---  157 (423)
T ss_pred             hhhhHHHHhhccccccccccceecceecCCCccchhhhccccCHHHHHhcCccccCCcchhhccCCEEEEecccccc---
Confidence                                     11111110    112222333321           12356899999999773   


Q ss_pred             ccccchhhhhhhcc---------cccccccCCceEEEEecCCC-ccCcccccCCCceeEEEEcCCCC-HHHHHHHHHHHh
Q 011664          292 PAAVSLSGVLNFMD---------GVLNSCCFEERVMVFTMNSK-DHVDQALLRPGRIDVHIHFPLCD-FSSFKTLASSYL  360 (480)
Q Consensus       292 ~~~~~ls~lL~~ld---------g~~~~~~~~~~ivI~tTN~~-~~LD~aLlrpGRfd~~I~~~~p~-~~~r~~il~~~l  360 (480)
                        ......||+.+.         |+.- ...-..++|+|+|.- ..|-|.|+.  ||...|.+.+|. .+.|.+|..+-+
T Consensus       158 --d~lvd~LLd~aaeG~n~vereGisi-~hpa~fvligTmNPEeGeLrpqLlD--Rfg~~v~~~~~~~~~~rv~Ii~r~~  232 (423)
T COG1239         158 --DHLVDALLDVAAEGVNDVEREGISI-RHPARFLLIGTMNPEEGELRPQLLD--RFGLEVDTHYPLDLEERVEIIRRRL  232 (423)
T ss_pred             --HHHHHHHHHHHHhCCceeeeCceee-ccCccEEEEeecCccccccchhhHh--hhcceeeccCCCCHHHHHHHHHHHH
Confidence              334456666553         3322 223345778888844 578899999  999999998875 467888887766


Q ss_pred             cc
Q 011664          361 GL  362 (480)
Q Consensus       361 ~~  362 (480)
                      ..
T Consensus       233 ~f  234 (423)
T COG1239         233 AF  234 (423)
T ss_pred             Hh
Confidence            53

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=98.47  E-value=1.3e-06  Score=92.45  Aligned_cols=194  Identities=13%  Similarity=0.127  Sum_probs=112.0

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLK  267 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~  267 (480)
                      .+.|.......+.+.+....           .....++++|.+||||+++++++....   +.+|+.++|+.+.. ..+.
T Consensus       140 ~lig~s~~~~~~~~~i~~~~-----------~~~~~vli~ge~g~gk~~~a~~ih~~s~~~~~~~i~~~c~~~~~-~~~~  207 (441)
T PRK10365        140 GMVGKSPAMQHLLSEIALVA-----------PSEATVLIHGDSGTGKELVARAIHASSARSEKPLVTLNCAALNE-SLLE  207 (441)
T ss_pred             ceEecCHHHHHHHHHHhhcc-----------CCCCeEEEEecCCCCHHHHHHHHHHcCCCCCCCeeeeeCCCCCH-HHHH
Confidence            35555555555554443221           124579999999999999999998765   46899999997653 3333


Q ss_pred             H-HHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhcccccccc------cCCceEEEEecC
Q 011664          268 S-LLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSC------CFEERVMVFTMN  323 (480)
Q Consensus       268 ~-l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~------~~~~~ivI~tTN  323 (480)
                      . +|.                 ....+++|||||||.+...     ....|+..++.-.-..      -.-+..+|+||+
T Consensus       208 ~~lfg~~~~~~~~~~~~~~g~~~~a~~gtl~ldei~~l~~~-----~q~~l~~~l~~~~~~~~~~~~~~~~~~rii~~t~  282 (441)
T PRK10365        208 SELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISPM-----MQVRLLRAIQEREVQRVGSNQTISVDVRLIAATH  282 (441)
T ss_pred             HHhcCCCCCCcCCCCcCCCCceeECCCCEEEEeccccCCHH-----HHHHHHHHHccCcEEeCCCCceeeeceEEEEeCC
Confidence            3 332                 1124678999999998532     2244555543211000      001233565554


Q ss_pred             CCccCcccccCCCcee-------EEEEcCCCCHHH----HHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHH
Q 011664          324 SKDHVDQALLRPGRID-------VHIHFPLCDFSS----FKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd-------~~I~~~~p~~~~----r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      .+-   ..+..+|+|.       ..+.+..|...+    ...+++.++....       ........++|+..+..++..
T Consensus       283 ~~~---~~~~~~~~~~~~l~~~l~~~~i~~ppLreR~~Di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L~~~  352 (441)
T PRK10365        283 RDL---AAEVNAGRFRQDLYYRLNVVAIEVPSLRQRREDIPLLAGHFLQRFA-------ERNRKAVKGFTPQAMDLLIHY  352 (441)
T ss_pred             CCH---HHHHHcCCchHHHHHHhccceecCCChhhcchhHHHHHHHHHHHHH-------HHhCCCCCCcCHHHHHHHHhC
Confidence            321   1222334442       134444444443    3445555543210       111112247999999999998


Q ss_pred             hhhcHHHHHHHHHHHHHhc
Q 011664          393 NRNSPSRALKSVITALQTD  411 (480)
Q Consensus       393 a~~~~~~al~~~i~~~~~~  411 (480)
                      .+...++.|+.+++.+-..
T Consensus       353 ~wpgN~reL~~~~~~~~~~  371 (441)
T PRK10365        353 DWPGNIRELENAVERAVVL  371 (441)
T ss_pred             CCCCHHHHHHHHHHHHHHh
Confidence            9999999999999876543

>PRK09862 putative ATP-dependent protease; Provisional

Probab=98.47  E-value=3.8e-07  Score=98.06  Aligned_cols=142  Identities=18%  Similarity=0.315  Sum_probs=86.5

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC----------cEEEEe
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY----------DVYDVD  256 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~----------~~~~i~  256 (480)
                      ..|.++.|...+++.+.-               -......++|+||||||||++++.+++.+..          .++.+.
T Consensus       188 ~d~~~v~Gq~~~~~al~l---------------aa~~G~~llliG~~GsGKTtLak~L~gllpp~~g~e~le~~~i~s~~  252 (506)
T PRK09862        188 HDLSDVIGQEQGKRGLEI---------------TAAGGHNLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLV  252 (506)
T ss_pred             cCeEEEECcHHHHhhhhe---------------eccCCcEEEEECCCCCcHHHHHHHHhccCCCCCCcEEEecchhhhhh
Confidence            478888888776665431               1123357999999999999999999986531          112111


Q ss_pred             CC-----Cc-----CC---hHHHHHHH----------HhhcCCcEEEEecccccccCcccccchhhhhhhcc-ccc--cc
Q 011664          257 LS-----RV-----AD---DADLKSLL----------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-GVL--NS  310 (480)
Q Consensus       257 ~s-----~~-----~~---~~~l~~l~----------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-g~~--~~  310 (480)
                      ..     .+     ..   ......++          .......+||+||++.+-     ...+..|++.|+ +..  ..
T Consensus       253 g~~~~~~~~~~rPfr~ph~~~s~~~l~GGg~~~~pG~l~~A~gGvLfLDEi~e~~-----~~~~~~L~~~LE~g~v~I~r  327 (506)
T PRK09862        253 NAESVQKQWRQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFE-----RRTLDALREPIESGQIHLSR  327 (506)
T ss_pred             ccccccCCcCCCCccCCCccchHHHHhCCCceehhhHhhhccCCEEecCCchhCC-----HHHHHHHHHHHHcCcEEEec
Confidence            00     00     00   00111122          122345899999998762     244566666663 221  00


Q ss_pred             -----ccCCceEEEEecCCCc---------------------cCcccccCCCceeEEEEcCCCCHH
Q 011664          311 -----CCFEERVMVFTMNSKD---------------------HVDQALLRPGRIDVHIHFPLCDFS  350 (480)
Q Consensus       311 -----~~~~~~ivI~tTN~~~---------------------~LD~aLlrpGRfd~~I~~~~p~~~  350 (480)
                           .......+|+|+|...                     .|..+++.  |||.++.+++|+.+
T Consensus       328 ~g~~~~~pa~f~lIAa~NP~pcG~~~~~~c~c~~~~~~~Y~~~ls~plLD--RfdL~v~v~~~~~~  391 (506)
T PRK09862        328 TRAKITYPARFQLVAAMNPSPTGHYQGNHNRCTPEQTLRYLNRLSGPFLD--RFDLSLEIPLPPPG  391 (506)
T ss_pred             CCcceeccCCEEEEEeecCccceecCCCCCCcCHHHHHHHHhhCCHhHHh--hccEEEEeCCCCHH
Confidence                 1123456788888542                     47779999  99999999999876

>KOG1514 consensus Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair]

Probab=98.44  E-value=1.8e-06  Score=93.75  Aligned_cols=129  Identities=19%  Similarity=0.259  Sum_probs=85.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeCCCcCChHH----------------------HHHHHH--
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDLSRVADDAD----------------------LKSLLL--  271 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~s~~~~~~~----------------------l~~l~~--  271 (480)
                      .+++.|-||||||.+++.+-.+|          .+.++.||.-.+.+..+                      +...|.  
T Consensus       424 ~mYIsGvPGtGKT~tV~~Vm~~Lq~~s~~~e~p~f~yveINgm~l~~~~~~Y~~I~~~lsg~~~~~~~al~~L~~~f~~~  503 (767)
T KOG1514|consen  424 CMYISGVPGTGKTATVLEVMKELQTSSAQKELPKFDYVEINGLRLASPREIYEKIWEALSGERVTWDAALEALNFRFTVP  503 (767)
T ss_pred             eEEEecCCCCCceehHHHHHHHHHHHHhhcCCCCccEEEEcceeecCHHHHHHHHHHhcccCcccHHHHHHHHHHhhccC
Confidence            57889999999999999998755          34566777655554222                      122222  


Q ss_pred             -hhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCC---CccC-cccccCCCcee-EEEEcC
Q 011664          272 -QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS---KDHV-DQALLRPGRID-VHIHFP  345 (480)
Q Consensus       272 -~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~---~~~L-D~aLlrpGRfd-~~I~~~  345 (480)
                       ....++||+|||+|.++..+     ..-|.|++|....  .+...+||+..|.   |+.+ ....-+  |++ .+|.|.
T Consensus       504 k~~~~~~VvLiDElD~Lvtr~-----QdVlYn~fdWpt~--~~sKLvvi~IaNTmdlPEr~l~nrvsS--Rlg~tRi~F~  574 (767)
T KOG1514|consen  504 KPKRSTTVVLIDELDILVTRS-----QDVLYNIFDWPTL--KNSKLVVIAIANTMDLPERLLMNRVSS--RLGLTRICFQ  574 (767)
T ss_pred             CCCCCCEEEEeccHHHHhccc-----HHHHHHHhcCCcC--CCCceEEEEecccccCHHHHhccchhh--hccceeeecC
Confidence             12357999999999997533     2446677765543  2334444544443   3332 233334  776 789999


Q ss_pred             CCCHHHHHHHHHHHhccC
Q 011664          346 LCDFSSFKTLASSYLGLK  363 (480)
Q Consensus       346 ~p~~~~r~~il~~~l~~~  363 (480)
                      +++.++..+|+...|...
T Consensus       575 pYth~qLq~Ii~~RL~~~  592 (767)
T KOG1514|consen  575 PYTHEQLQEIISARLKGL  592 (767)
T ss_pred             CCCHHHHHHHHHHhhcch
Confidence            999999999999888654

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

Probab=98.43  E-value=9.1e-07  Score=99.61  Aligned_cols=124  Identities=19%  Similarity=0.311  Sum_probs=83.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCC-CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC---
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRV-WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD---  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~-~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~---  262 (480)
                      +.|+|++++...|.+.+...-.+      ++.+ +.-.+||.||.|+|||-||+|+|..+   .-.++.+|++++..   
T Consensus       562 ~~V~gQ~eAv~aIa~AI~~sr~g------l~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evsk  635 (898)
T KOG1051|consen  562 ERVIGQDEAVAAIAAAIRRSRAG------LKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSK  635 (898)
T ss_pred             hhccchHHHHHHHHHHHHhhhcc------cCCCCCCeEEEEECCCchhHHHHHHHHHHHHcCCccceEEechhhhhhhhh
Confidence            46889999999888888765332      2222 44568999999999999999999987   34699999986332   


Q ss_pred             ----------hHHHHHHHH--hhcCCcEEEEecccccccCcccccchhhhhhhcccccc------cccCCceEEEEecCC
Q 011664          263 ----------DADLKSLLL--QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN------SCCFEERVMVFTMNS  324 (480)
Q Consensus       263 ----------~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~------~~~~~~~ivI~tTN~  324 (480)
                                ....-.+..  +..+.+||+|||||.-     +...++.|+..+|.-.-      ...-.+.|||+|+|.
T Consensus       636 ligsp~gyvG~e~gg~LteavrrrP~sVVLfdeIEkA-----h~~v~n~llq~lD~GrltDs~Gr~Vd~kN~I~IMTsn~  710 (898)
T KOG1051|consen  636 LIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKA-----HPDVLNILLQLLDRGRLTDSHGREVDFKNAIFIMTSNV  710 (898)
T ss_pred             ccCCCcccccchhHHHHHHHHhcCCceEEEEechhhc-----CHHHHHHHHHHHhcCccccCCCcEeeccceEEEEeccc
Confidence                      222223332  2245699999999964     33445666666652211      122346789999874

>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.43  E-value=1.5e-06  Score=85.25  Aligned_cols=168  Identities=21%  Similarity=0.306  Sum_probs=112.2

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-CCcEE---------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-SYDVY---------  253 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~~~~~---------  253 (480)
                      -.|.+++.+.+.++....++....    .       + ..| .+|+|||+|+||-|.+.++-+++ |..+.         
T Consensus         7 yrpksl~~l~~~~e~~~~Lksl~~----~-------~-d~P-Hll~yGPSGaGKKTrimclL~elYG~gveklki~~~t~   73 (351)
T KOG2035|consen    7 YRPKSLDELIYHEELANLLKSLSS----T-------G-DFP-HLLVYGPSGAGKKTRIMCLLRELYGVGVEKLKIETRTF   73 (351)
T ss_pred             cCcchhhhcccHHHHHHHHHHhcc----c-------C-CCC-eEEEECCCCCCchhhHHHHHHHHhCCCchheeeeeEEE
Confidence            357788899999888887774322    0       1 112 69999999999999999998876 32111         


Q ss_pred             -------------------EEeCCCcCC-h-HHHHHHHH---hhc--------CCcEEEEecccccccCcccccchhhhh
Q 011664          254 -------------------DVDLSRVAD-D-ADLKSLLL---QTT--------SKSVILIEDLDRFLVEKPAAVSLSGVL  301 (480)
Q Consensus       254 -------------------~i~~s~~~~-~-~~l~~l~~---~~~--------~~sII~IDEiD~l~~~~~~~~~ls~lL  301 (480)
                                         .++.|+... + --+++++.   +..        .-.+++|-|+|.+..     .....|-
T Consensus        74 ~tpS~kklEistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~-----dAQ~aLR  148 (351)
T KOG2035|consen   74 TTPSKKKLEISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTR-----DAQHALR  148 (351)
T ss_pred             ecCCCceEEEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhH-----HHHHHHH
Confidence                               111121111 1 11344442   221        236999999998842     2234455


Q ss_pred             hhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHh
Q 011664          302 NFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQN  377 (480)
Q Consensus       302 ~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~  377 (480)
                      ..|+...+     ..-+|+.+|....+-+++++  |+ ..|.+|.|+.++-..+++..+..++..+..++ ..+++.
T Consensus       149 RTMEkYs~-----~~RlIl~cns~SriIepIrS--RC-l~iRvpaps~eeI~~vl~~v~~kE~l~lp~~~l~rIa~k  217 (351)
T KOG2035|consen  149 RTMEKYSS-----NCRLILVCNSTSRIIEPIRS--RC-LFIRVPAPSDEEITSVLSKVLKKEGLQLPKELLKRIAEK  217 (351)
T ss_pred             HHHHHHhc-----CceEEEEecCcccchhHHhh--he-eEEeCCCCCHHHHHHHHHHHHHHhcccCcHHHHHHHHHH
Confidence            56655443     34577788999999999999  88 58999999999999999999988887776554 344443

>PTZ00111 DNA replication licensing factor MCM4; Provisional

Probab=98.41  E-value=7.8e-07  Score=100.32  Aligned_cols=160  Identities=18%  Similarity=0.183  Sum_probs=91.2

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhh--H--------HhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-------CcEE
Q 011664          191 TISMETDLKNRVKSDLESFLKAKH--Y--------YHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-------YDVY  253 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~--~--------~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-------~~~~  253 (480)
                      .|.|++++|+.|.-.+  |-..+.  .        |........-.+||.|+||||||.+|+++++...       .++.
T Consensus       451 ~I~G~e~vK~ailL~L--~gG~~k~~~~~~~~dg~~~~~~iRgdihVLLvGDPGTGKSqLAr~Ih~lspR~~ytsG~~~s  528 (915)
T PTZ00111        451 SIKARNNVKIGLLCQL--FSGNKNSSDFNKSPDACYKVDNFRGIINVLLCGDPGTAKSQLLHYTHLLSPRSIYTSGKSSS  528 (915)
T ss_pred             eEECCHHHHHHHHHHH--hcCCccccccccccccccccccccCCceEEEeCCCCccHHHHHHHHHHhCCccccCCCCCCc
Confidence            5788888888775332  211110  0        0001122233799999999999999999998543       3344


Q ss_pred             EEeCCCcCC--h---HH--HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccc---------ccccccCCceE
Q 011664          254 DVDLSRVAD--D---AD--LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG---------VLNSCCFEERV  317 (480)
Q Consensus       254 ~i~~s~~~~--~---~~--l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg---------~~~~~~~~~~i  317 (480)
                      .++++....  +   ..  +..-........+++|||+|.+.     ....+.|++.|+.         +.. .-....-
T Consensus       529 ~vgLTa~~~~~d~~tG~~~le~GaLvlAdgGtL~IDEidkms-----~~~Q~aLlEaMEqqtIsI~KaGi~~-tL~ar~r  602 (915)
T PTZ00111        529 SVGLTASIKFNESDNGRAMIQPGAVVLANGGVCCIDELDKCH-----NESRLSLYEVMEQQTVTIAKAGIVA-TLKAETA  602 (915)
T ss_pred             cccccchhhhcccccCcccccCCcEEEcCCCeEEecchhhCC-----HHHHHHHHHHHhCCEEEEecCCcce-ecCCCeE
Confidence            444433211  0   00  00000112345799999999873     2233556666632         111 1123445


Q ss_pred             EEEecCCC-------------ccCcccccCCCceeEE-EEcCCCCHHHHHHHHHHHh
Q 011664          318 MVFTMNSK-------------DHVDQALLRPGRIDVH-IHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       318 vI~tTN~~-------------~~LD~aLlrpGRfd~~-I~~~~p~~~~r~~il~~~l  360 (480)
                      ||+|+|..             -.|+++|++  |||.. +-++.|+.+.=+.|+.+.+
T Consensus       603 VIAAaNP~~gryd~~~s~~eni~Lp~~LLS--RFDLIf~l~D~~d~~~D~~lA~hI~  657 (915)
T PTZ00111        603 ILASCNPINSRYNKNKAVIENINISPSLFT--RFDLIYLVLDHIDQDTDQLISLSIA  657 (915)
T ss_pred             EEEEcCCcccccCcccCcccccCCChHHhh--hhcEEEEecCCCChHHHHHHHHHHH
Confidence            77888864             136799999  99954 5677888776566655544

>TIGR00764 lon_rel lon-related putative ATP-dependent protease

Probab=98.40  E-value=9.4e-06  Score=89.73  Aligned_cols=51  Identities=29%  Similarity=0.406  Sum_probs=42.0

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ..-|++++|++++++.+...+.               .+++++|+||||||||++++++|+.++.+
T Consensus        14 ~~~~~~viG~~~a~~~l~~a~~---------------~~~~~ll~G~pG~GKT~la~~la~~l~~~   64 (608)
T TIGR00764        14 ERLIDQVIGQEEAVEIIKKAAK---------------QKRNVLLIGEPGVGKSMLAKAMAELLPDE   64 (608)
T ss_pred             hhhHhhccCHHHHHHHHHHHHH---------------cCCCEEEECCCCCCHHHHHHHHHHHcCch
Confidence            3578999999999887775553               12479999999999999999999998654

Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.

>PF05729 NACHT: NACHT domain

Probab=98.39  E-value=1.9e-06  Score=77.94  Aligned_cols=130  Identities=15%  Similarity=0.263  Sum_probs=72.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC---------cEEEEeCCCcCChH---HHHHH------------------HHhhc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY---------DVYDVDLSRVADDA---DLKSL------------------LLQTT  274 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~---------~~~~i~~s~~~~~~---~l~~l------------------~~~~~  274 (480)
                      |-++++|+||+|||++++.++..+..         -++.+.+.......   .+...                  +....
T Consensus         1 r~l~I~G~~G~GKStll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    1 RVLWISGEPGSGKSTLLRKLAQQLAEEEPPPSKFPYPFFFSLRDISDSNNSRSLADLLFDQLPESIAPIEELLQELLEKN   80 (166)
T ss_pred             CEEEEECCCCCChHHHHHHHHHHHHhcCcccccceEEEEEeehhhhhccccchHHHHHHHhhccchhhhHHHHHHHHHcC
Confidence            35789999999999999999975511         13344443332211   12111                  12234


Q ss_pred             CCcEEEEecccccccCccc--ccchhhhh-hhcccccccccCCceEEEEecCCCc-cCcccccCCCceeEEEEcCCCCHH
Q 011664          275 SKSVILIEDLDRFLVEKPA--AVSLSGVL-NFMDGVLNSCCFEERVMVFTMNSKD-HVDQALLRPGRIDVHIHFPLCDFS  350 (480)
Q Consensus       275 ~~sII~IDEiD~l~~~~~~--~~~ls~lL-~~ldg~~~~~~~~~~ivI~tTN~~~-~LD~aLlrpGRfd~~I~~~~p~~~  350 (480)
                      .+.+|+||.+|.+......  ......++ +.+..-   ...+-+++|.+..... .+...+-.   . ..++++..+.+
T Consensus        81 ~~~llilDglDE~~~~~~~~~~~~~~~~l~~l~~~~---~~~~~~liit~r~~~~~~~~~~~~~---~-~~~~l~~~~~~  153 (166)
T PF05729_consen   81 KRVLLILDGLDELEEQDQSQERQRLLDLLSQLLPQA---LPPGVKLIITSRPRAFPDLRRRLKQ---A-QILELEPFSEE  153 (166)
T ss_pred             CceEEEEechHhcccchhhhHHHHHHHHHHHHhhhc---cCCCCeEEEEEcCChHHHHHHhcCC---C-cEEEECCCCHH
Confidence            6789999999998753322  11222222 223221   1123344444332221 22222222   1 57899999999


Q ss_pred             HHHHHHHHHhc
Q 011664          351 SFKTLASSYLG  361 (480)
Q Consensus       351 ~r~~il~~~l~  361 (480)
                      +..++++.|+.
T Consensus       154 ~~~~~~~~~f~  164 (166)
T PF05729_consen  154 DIKQYLRKYFS  164 (166)
T ss_pred             HHHHHHHHHhh
Confidence            99999999875

>PRK07132 DNA polymerase III subunit delta'; Validated

Probab=98.38  E-value=2.3e-05  Score=79.29  Aligned_cols=123  Identities=11%  Similarity=0.156  Sum_probs=88.1

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC-------------cEEEEeC-CCcCChHHHHHHHHhh-------cCCcEEEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY-------------DVYDVDL-SRVADDADLKSLLLQT-------TSKSVILI  281 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------~~~~i~~-s~~~~~~~l~~l~~~~-------~~~sII~I  281 (480)
                      .+..|||+|+.|+||+.++.++|+.+-+             ++..++. ..-.+-.+++.+....       ....|++|
T Consensus        17 l~haYLf~G~eg~gk~~~a~~~a~~l~c~~~~~~~~~~~p~n~~~~d~~g~~i~vd~Ir~l~~~~~~~~~~~~~~KvvII   96 (299)
T PRK07132         17 ISHSFLLKSNYNEDIDEKILYFLNKFNNLQITNLNEQELPANIILFDIFDKDLSKSEFLSAINKLYFSSFVQSQKKILII   96 (299)
T ss_pred             CCeEEEEeCCCCCCHHHHHHHHHHHHcCcCCCCCCCCCCCcceEEeccCCCcCCHHHHHHHHHHhccCCcccCCceEEEE
Confidence            4568999999999999999999987611             3344441 1122334566554332       26689999


Q ss_pred             ecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHH
Q 011664          282 EDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASS  358 (480)
Q Consensus       282 DEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~  358 (480)
                      |++|.+.     ....+.||..++.-     ++..++|++|+.++.|-|.+++  |+. .++|++++.++....+..
T Consensus        97 ~~~e~m~-----~~a~NaLLK~LEEP-----p~~t~~il~~~~~~kll~TI~S--Rc~-~~~f~~l~~~~l~~~l~~  160 (299)
T PRK07132         97 KNIEKTS-----NSLLNALLKTIEEP-----PKDTYFLLTTKNINKVLPTIVS--RCQ-VFNVKEPDQQKILAKLLS  160 (299)
T ss_pred             ecccccC-----HHHHHHHHHHhhCC-----CCCeEEEEEeCChHhChHHHHh--CeE-EEECCCCCHHHHHHHHHH
Confidence            9998773     33456788888653     4567888888888999999998  884 899999998887665543

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=98.38  E-value=9.2e-07  Score=77.35  Aligned_cols=65  Identities=25%  Similarity=0.470  Sum_probs=43.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC--------CCcEEEEeCCCcCChHHHH---------------------HHHHh--
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM--------SYDVYDVDLSRVADDADLK---------------------SLLLQ--  272 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l--------~~~~~~i~~s~~~~~~~l~---------------------~l~~~--  272 (480)
                      .+.++++||||+|||++++.++..+        +.+++.+++....+...+.                     ..+.+  
T Consensus         4 ~~~~~i~G~~G~GKT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~l~~~~~~~l   83 (131)
T PF13401_consen    4 QRILVISGPPGSGKTTLIKRLARQLNAEAEIKNHPDVIYVNCPSSRTPRDFAQEILEALGLPLKSRQTSDELRSLLIDAL   83 (131)
T ss_dssp             ---EEEEE-TTSSHHHHHHHHHHHHHHHHHHCCCEEEEEEEHHHHSSHHHHHHHHHHHHT-SSSSTS-HHHHHHHHHHHH
T ss_pred             CcccEEEcCCCCCHHHHHHHHHHHhHHhhhccCCCcEEEEEeCCCCCHHHHHHHHHHHhCccccccCCHHHHHHHHHHHH
Confidence            3568999999999999999999987        7788888765544322221                     11111  


Q ss_pred             -hcCCcEEEEecccccc
Q 011664          273 -TTSKSVILIEDLDRFL  288 (480)
Q Consensus       273 -~~~~sII~IDEiD~l~  288 (480)
                       .....+|+|||+|.+.
T Consensus        84 ~~~~~~~lviDe~~~l~  100 (131)
T PF13401_consen   84 DRRRVVLLVIDEADHLF  100 (131)
T ss_dssp             HHCTEEEEEEETTHHHH
T ss_pred             HhcCCeEEEEeChHhcC
Confidence             1122599999999974

>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=98.35  E-value=3.1e-06  Score=82.54  Aligned_cols=129  Identities=19%  Similarity=0.197  Sum_probs=75.5

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHh-hcCCcEEEEecccccccCcccccchhhhh
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQ-TTSKSVILIEDLDRFLVEKPAAVSLSGVL  301 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~-~~~~sII~IDEiD~l~~~~~~~~~ls~lL  301 (480)
                      ...|-.++||+|||||..++++|..+|..++..+|++-.+...+.++|.. +...+-+++||++.+-.+-  -..+++.+
T Consensus        31 ~~~~~~~~GpagtGKtetik~La~~lG~~~~vfnc~~~~~~~~l~ril~G~~~~GaW~cfdefnrl~~~v--LS~i~~~i  108 (231)
T PF12774_consen   31 LNLGGALSGPAGTGKTETIKDLARALGRFVVVFNCSEQMDYQSLSRILKGLAQSGAWLCFDEFNRLSEEV--LSVISQQI  108 (231)
T ss_dssp             TTTEEEEESSTTSSHHHHHHHHHHCTT--EEEEETTSSS-HHHHHHHHHHHHHHT-EEEEETCCCSSHHH--HHHHHHHH
T ss_pred             cCCCCCCcCCCCCCchhHHHHHHHHhCCeEEEecccccccHHHHHHHHHHHhhcCchhhhhhhhhhhHHH--HHHHHHHH
Confidence            34577899999999999999999999999999999999988888888854 4578999999999873211  11112212


Q ss_pred             hhc-cccccc-----------ccCCceEEEEecC----CCccCcccccCCCceeEEEEcCCCCHHHHHHHH
Q 011664          302 NFM-DGVLNS-----------CCFEERVMVFTMN----SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLA  356 (480)
Q Consensus       302 ~~l-dg~~~~-----------~~~~~~ivI~tTN----~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il  356 (480)
                      ..+ +.+...           .-..+.-+++|.|    ....|++.|+.  -| +-|.+..||.+...++.
T Consensus       109 ~~i~~al~~~~~~~~~~g~~i~l~~~~~iFiT~np~y~gr~~LP~nLk~--lF-Rpvam~~PD~~~I~ei~  176 (231)
T PF12774_consen  109 QSIQDALRAKQKSFTLEGQEIKLNPNCGIFITMNPGYAGRSELPENLKA--LF-RPVAMMVPDLSLIAEIL  176 (231)
T ss_dssp             HHHHHHHHCTSSEEEETTCEEE--TT-EEEEEE-B-CCCC--S-HHHCT--TE-EEEE--S--HHHHHHHH
T ss_pred             HHHHHhhcccccccccCCCEEEEccceeEEEeeccccCCcccCCHhHHH--Hh-heeEEeCCCHHHHHHHH
Confidence            111 111110           0011122344555    23567877764  34 78999999987655443

>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]

Probab=98.34  E-value=5.7e-07  Score=94.29  Aligned_cols=48  Identities=23%  Similarity=0.431  Sum_probs=39.7

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..+|.||.|++..|+.+.....               -..++|++||||||||++|+-+..-+
T Consensus       175 ~~D~~DV~GQ~~AKrAleiAAA---------------GgHnLl~~GpPGtGKTmla~Rl~~lL  222 (490)
T COG0606         175 APDFKDVKGQEQAKRALEIAAA---------------GGHNLLLVGPPGTGKTMLASRLPGLL  222 (490)
T ss_pred             CcchhhhcCcHHHHHHHHHHHh---------------cCCcEEEecCCCCchHHhhhhhcccC
Confidence            4589999999999998874332               24589999999999999999987644

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

Probab=98.33  E-value=2.4e-06  Score=89.88  Aligned_cols=201  Identities=13%  Similarity=0.141  Sum_probs=128.6

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD  262 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~  262 (480)
                      ...+..|+|....-..+.+.+......           .-.|||.|.+||||-.+|++|....   ..+|+.+||..+..
T Consensus       219 ~~~~~~iIG~S~am~~ll~~i~~VA~S-----------d~tVLi~GETGtGKElvAraIH~~S~R~~kPfV~~NCAAlPe  287 (550)
T COG3604         219 VLEVGGIIGRSPAMRQLLKEIEVVAKS-----------DSTVLIRGETGTGKELVARAIHQLSPRRDKPFVKLNCAALPE  287 (550)
T ss_pred             hcccccceecCHHHHHHHHHHHHHhcC-----------CCeEEEecCCCccHHHHHHHHHhhCcccCCCceeeeccccch
Confidence            457889999999999988887755332           3479999999999999999999876   56899999988764


Q ss_pred             hHHHHHHHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhcc-----ccccc-ccCCceEEE
Q 011664          263 DADLKSLLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-----GVLNS-CCFEERVMV  319 (480)
Q Consensus       263 ~~~l~~l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-----g~~~~-~~~~~~ivI  319 (480)
                      .--=.++|..                 .....-||+|||..+..     .....||..+.     .+.++ .-.-.+-||
T Consensus       288 sLlESELFGHeKGAFTGA~~~r~GrFElAdGGTLFLDEIGelPL-----~lQaKLLRvLQegEieRvG~~r~ikVDVRiI  362 (550)
T COG3604         288 SLLESELFGHEKGAFTGAINTRRGRFELADGGTLFLDEIGELPL-----ALQAKLLRVLQEGEIERVGGDRTIKVDVRVI  362 (550)
T ss_pred             HHHHHHHhcccccccccchhccCcceeecCCCeEechhhccCCH-----HHHHHHHHHHhhcceeecCCCceeEEEEEEE
Confidence            2111233411                 13568999999987632     12244555443     22221 001134589


Q ss_pred             EecCCCccCcccccCCCcee-------EEEEcCCCCHHHHH----HHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHH
Q 011664          320 FTMNSKDHVDQALLRPGRID-------VHIHFPLCDFSSFK----TLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       320 ~tTN~~~~LD~aLlrpGRfd-------~~I~~~~p~~~~r~----~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~  388 (480)
                      +|||+  +|-.+.. .|+|-       .++.+..|...+|.    -++..|+....       .++......+|+..+..
T Consensus       363 AATNR--DL~~~V~-~G~FRaDLYyRLsV~Pl~lPPLRER~~DIplLA~~Fle~~~-------~~~gr~~l~ls~~Al~~  432 (550)
T COG3604         363 AATNR--DLEEMVR-DGEFRADLYYRLSVFPLELPPLRERPEDIPLLAGYFLEKFR-------RRLGRAILSLSAEALEL  432 (550)
T ss_pred             eccch--hHHHHHH-cCcchhhhhhcccccccCCCCcccCCccHHHHHHHHHHHHH-------HhcCCcccccCHHHHHH
Confidence            99995  3333332 24442       24445555554442    23333432211       11222245789999999


Q ss_pred             HHHHhhhcHHHHHHHHHHHHHhcC
Q 011664          389 LMIANRNSPSRALKSVITALQTDG  412 (480)
Q Consensus       389 ll~~a~~~~~~al~~~i~~~~~~~  412 (480)
                      ++...+...+|.|+++++.....+
T Consensus       433 L~~y~wPGNVRELen~veRavlla  456 (550)
T COG3604         433 LSSYEWPGNVRELENVVERAVLLA  456 (550)
T ss_pred             HHcCCCCCcHHHHHHHHHHHHHHh
Confidence            998889999999999998877754

>PHA00729 NTP-binding motif containing protein

Probab=98.32  E-value=7e-07  Score=86.31  Aligned_cols=104  Identities=15%  Similarity=0.256  Sum_probs=56.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC----------cCChHHHHHH----HHhhcCCcEEEEecccccccCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR----------VADDADLKSL----LLQTTSKSVILIEDLDRFLVEK  291 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~----------~~~~~~l~~l----~~~~~~~sII~IDEiD~l~~~~  291 (480)
                      .++++||||||||+||.++|..++..+..+....          +.+...+...    +.......+|+|||+..-....
T Consensus        19 nIlItG~pGvGKT~LA~aLa~~l~~~l~~l~~~~~~~d~~~~~~fid~~~Ll~~L~~a~~~~~~~dlLIIDd~G~~~~~~   98 (226)
T PHA00729         19 SAVIFGKQGSGKTTYALKVARDVFWKLNNLSTKDDAWQYVQNSYFFELPDALEKIQDAIDNDYRIPLIIFDDAGIWLSKY   98 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhcccccchhhHHhcCCcEEEEEHHHHHHHHHHHHhcCCCCCEEEEeCCchhhccc
Confidence            7999999999999999999998764333321110          1112222222    2222234689999976544321


Q ss_pred             ccc----cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCC
Q 011664          292 PAA----VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPG  336 (480)
Q Consensus       292 ~~~----~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpG  336 (480)
                      .-.    .....+.+.+.   +    .-.++++++..++.|-..|+..|
T Consensus        99 ~wh~~~~~~yf~L~~aLr---S----R~~l~il~~ls~edL~~~Lr~Rg  140 (226)
T PHA00729         99 VWYEDYMKTFYKIYALIR---T----RVSAVIFTTPSPEDLAFYLREKG  140 (226)
T ss_pred             chhhhccchHHHHHHHHH---h----hCcEEEEecCCHHHHHHHHHhCC
Confidence            000    11112222221   1    23456777777777776666533

>PHA02624 large T antigen; Provisional

Probab=98.32  E-value=2.3e-06  Score=92.60  Aligned_cols=119  Identities=20%  Similarity=0.286  Sum_probs=79.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccC------ccc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVE------KPA  293 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~------~~~  293 (480)
                      |.|.++.++||||||||||++++++++.++-..+.++.+.-    .+...+.-.....+.+|||+-.-+-.      ...
T Consensus       427 giPKk~~il~~GPpnTGKTtf~~sLl~~L~G~vlsVNsPt~----ks~FwL~pl~D~~~~l~dD~t~~~~~~~~Lp~G~~  502 (647)
T PHA02624        427 NVPKRRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPPD----KLNFELGCAIDQFMVVFEDVKGQPADNKDLPSGQG  502 (647)
T ss_pred             cCCCCeEEEEECCCCCCHHHHHHHHHHHcCCeEEEeeCCcc----hhHHHhhhhhhceEEEeeeccccccccccCCcccc
Confidence            56778899999999999999999999999766777764432    23333444456679999999643321      112


Q ss_pred             ccchhhhhhhcccccccccCC-----c-----eEEEEecCCCccCcccccCCCceeEEEEcCC
Q 011664          294 AVSLSGVLNFMDGVLNSCCFE-----E-----RVMVFTMNSKDHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~~~~~~-----~-----~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~  346 (480)
                      -..+.-|-+.+||-.. .+-+     .     --.|+|||. ..|+..+.-  ||-+++.|..
T Consensus       503 ~dNl~~lRn~LDG~V~-v~ld~KH~n~~q~~~PPlliT~Ne-y~iP~T~~~--Rf~~~~~F~~  561 (647)
T PHA02624        503 MNNLDNLRDYLDGSVP-VNLEKKHLNKRSQIFPPGIVTMNE-YLIPQTVKA--RFAKVLDFKP  561 (647)
T ss_pred             cchhhHHHhhcCCCCc-cccchhccCchhccCCCeEEeecC-cccchhHHH--HHHHhccccc
Confidence            2234567788888621 0000     1     125778884 356777777  9988888865

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=98.32  E-value=5.1e-07  Score=93.54  Aligned_cols=99  Identities=15%  Similarity=0.226  Sum_probs=61.7

Q ss_pred             CCCCceEEEEccCCCcHHHHHHHHHHcCCC-cEEEEeCCCcCC------------hHHHHHHHHhhcC-CcEEEEecccc
Q 011664          221 RVWKRSYLLYGPSGTGKSSFAAAMASFMSY-DVYDVDLSRVAD------------DADLKSLLLQTTS-KSVILIEDLDR  286 (480)
Q Consensus       221 ~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-~~~~i~~s~~~~------------~~~l~~l~~~~~~-~sII~IDEiD~  286 (480)
                      .+.++|++||||+|+|||+|+-...+.+.. .--.+-...++.            ...+..+..+..+ -.||+|||+..
T Consensus        59 ~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh~Fm~~vh~~l~~~~~~~~~l~~va~~l~~~~~lLcfDEF~V  138 (362)
T PF03969_consen   59 PPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFHEFMLDVHSRLHQLRGQDDPLPQVADELAKESRLLCFDEFQV  138 (362)
T ss_pred             CCCCceEEEECCCCCchhHHHHHHHHhCCccccccccccHHHHHHHHHHHHHhCCCccHHHHHHHHHhcCCEEEEeeeec
Confidence            457899999999999999999999887743 111111111111            1112222222233 34999999985


Q ss_pred             cccCcccccchhhhhhhcccccccccCCceEEEEecC-CCccC
Q 011664          287 FLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKDHV  328 (480)
Q Consensus       287 l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~~L  328 (480)
                      -  +..+...+..|++.+   .    ..++++|+|+| .|++|
T Consensus       139 ~--DiaDAmil~rLf~~l---~----~~gvvlVaTSN~~P~~L  172 (362)
T PF03969_consen  139 T--DIADAMILKRLFEAL---F----KRGVVLVATSNRPPEDL  172 (362)
T ss_pred             c--chhHHHHHHHHHHHH---H----HCCCEEEecCCCChHHH
Confidence            3  344555667777655   2    36788999999 45555

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

>PLN03210 Resistant to P

Probab=98.27  E-value=2.2e-05  Score=93.16  Aligned_cols=156  Identities=22%  Similarity=0.187  Sum_probs=91.2

Q ss_pred             eCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcE---EEEe
Q 011664          180 SVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDV---YDVD  256 (480)
Q Consensus       180 ~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~---~~i~  256 (480)
                      .+...++..+++++|.++..+++.+.+.           .+....+-+-++||+|+||||||+++++.+...|   +.++
T Consensus       174 ~l~~~~~~~~~~~vG~~~~l~~l~~lL~-----------l~~~~~~vvgI~G~gGiGKTTLA~~l~~~l~~~F~g~vfv~  242 (1153)
T PLN03210        174 KLNLTPSNDFEDFVGIEDHIAKMSSLLH-----------LESEEVRMVGIWGSSGIGKTTIARALFSRLSRQFQSSVFID  242 (1153)
T ss_pred             hhccccCcccccccchHHHHHHHHHHHc-----------cccCceEEEEEEcCCCCchHHHHHHHHHHHhhcCCeEEEee
Confidence            3445566788999999988888776543           1222345688999999999999999988764332   1121


Q ss_pred             C---CC---cCC---------hHH-----HHHHHH--------------h-hcCCcEEEEecccccccCcccccchhhhh
Q 011664          257 L---SR---VAD---------DAD-----LKSLLL--------------Q-TTSKSVILIEDLDRFLVEKPAAVSLSGVL  301 (480)
Q Consensus       257 ~---s~---~~~---------~~~-----l~~l~~--------------~-~~~~sII~IDEiD~l~~~~~~~~~ls~lL  301 (480)
                      .   +.   ...         ...     +..++.              . ...+.+|++||+|..       ..+..+.
T Consensus       243 ~~~v~~~~~~~~~~~~~~~~~~~~l~~~~l~~il~~~~~~~~~~~~~~~~L~~krvLLVLDdv~~~-------~~l~~L~  315 (1153)
T PLN03210        243 RAFISKSMEIYSSANPDDYNMKLHLQRAFLSEILDKKDIKIYHLGAMEERLKHRKVLIFIDDLDDQ-------DVLDALA  315 (1153)
T ss_pred             ccccccchhhcccccccccchhHHHHHHHHHHHhCCCCcccCCHHHHHHHHhCCeEEEEEeCCCCH-------HHHHHHH
Confidence            1   00   000         000     111110              0 135679999999742       1122222


Q ss_pred             hhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccC
Q 011664          302 NFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK  363 (480)
Q Consensus       302 ~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~  363 (480)
                      ...+..     +.+.-||+||....     +++....+..++++.|+.++-.+++..+....
T Consensus       316 ~~~~~~-----~~GsrIIiTTrd~~-----vl~~~~~~~~~~v~~l~~~ea~~LF~~~Af~~  367 (1153)
T PLN03210        316 GQTQWF-----GSGSRIIVITKDKH-----FLRAHGIDHIYEVCLPSNELALEMFCRSAFKK  367 (1153)
T ss_pred             hhCccC-----CCCcEEEEEeCcHH-----HHHhcCCCeEEEecCCCHHHHHHHHHHHhcCC
Confidence            222211     22334566666433     33323467789999999999899998886543

syringae 6; Provisional

>KOG2227 consensus Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]

Probab=98.26  E-value=2.5e-05  Score=81.65  Aligned_cols=185  Identities=13%  Similarity=0.129  Sum_probs=115.3

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcCCh
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSRVADD  263 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~~~  263 (480)
                      -.++.|-++....+.+.+...+..         .-.+++.+.|-||||||.+..-+-..+     +...++++|.++...
T Consensus       149 p~~l~gRe~e~~~v~~F~~~hle~---------~t~gSlYVsG~PGtgkt~~l~rvl~~~~~~~~~~~~v~inc~sl~~~  219 (529)
T KOG2227|consen  149 PGTLKGRELEMDIVREFFSLHLEL---------NTSGSLYVSGQPGTGKTALLSRVLDSLSKSSKSPVTVYINCTSLTEA  219 (529)
T ss_pred             CCCccchHHHHHHHHHHHHhhhhc---------ccCcceEeeCCCCcchHHHHHHHHHhhhhhcccceeEEEeeccccch
Confidence            456777777777666554444332         245689999999999999888665544     235688888875532


Q ss_pred             HH---------------------HHHHHHh----hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEE
Q 011664          264 AD---------------------LKSLLLQ----TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVM  318 (480)
Q Consensus       264 ~~---------------------l~~l~~~----~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~iv  318 (480)
                      ..                     ....|.+    ...+-|+++||+|.++...  +..+-.+. +++.+    .....++
T Consensus       220 ~aiF~kI~~~~~q~~~s~~~~~~~~~~~~~h~~q~k~~~llVlDEmD~L~tr~--~~vLy~lF-ewp~l----p~sr~iL  292 (529)
T KOG2227|consen  220 SAIFKKIFSSLLQDLVSPGTGMQHLEKFEKHTKQSKFMLLLVLDEMDHLITRS--QTVLYTLF-EWPKL----PNSRIIL  292 (529)
T ss_pred             HHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHhcccceEEEEechhhHHhhcc--cceeeeeh-hcccC----Ccceeee
Confidence            21                     1122221    2246799999999997322  22222222 22222    2355677


Q ss_pred             EEecCCCccCcccccC----CCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc--hhHHHHHHhCCCCCHHHHHHHH
Q 011664          319 VFTMNSKDHVDQALLR----PGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF--PQVEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       319 I~tTN~~~~LD~aLlr----pGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~--~~i~~l~~~~~g~s~adI~~ll  390 (480)
                      |+..|..+.=|..|-|    -+--...+.|++++.++..+|++..+.......+  ..++-.|....+.|| |+..++
T Consensus       293 iGiANslDlTdR~LprL~~~~~~~P~~l~F~PYTk~qI~~Il~~rl~~~~t~~~~~~Aie~~ArKvaa~SG-DlRkaL  369 (529)
T KOG2227|consen  293 IGIANSLDLTDRFLPRLNLDLTIKPKLLVFPPYTKDQIVEILQQRLSEESTSIFLNAAIELCARKVAAPSG-DLRKAL  369 (529)
T ss_pred             eeehhhhhHHHHHhhhhhhccCCCCceeeecCCCHHHHHHHHHHHHhcccccccchHHHHHHHHHhccCch-hHHHHH
Confidence            7788876654443321    1233478999999999999999999876544332  245566667777776 666554

>KOG1968 consensus Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair]

Probab=98.24  E-value=3.5e-06  Score=95.49  Aligned_cols=194  Identities=20%  Similarity=0.246  Sum_probs=122.2

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHh-hhhHHhhhCCCC-Cc-eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLK-AKHYYHRLGRVW-KR-SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~-~~~~~~~~g~~~-~r-giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      ..|....++.|....-..+.+.+..+-+ .+..|...+... .. ..|++||||.|||+.++++|.++|+.++..|.+..
T Consensus       314 ~~p~~~k~~~~~~~~~~~~~~~l~~~k~~~~~sy~~~~~~ss~~~~~l~~G~pGigKT~~~h~~~k~~g~~v~E~Nas~~  393 (871)
T KOG1968|consen  314 YQPTSSKALEGNASSSKKASKWLAKSKDKEKSSYKENEPDSSKKKALLLSGPPGIGKTTAAHKAAKELGFKVVEKNASDV  393 (871)
T ss_pred             cccccHHhhhcccchhhhhhhHHHhhhccccccccccCcchhhHHHHHhcCCCCCCchhhHhhhhhhcccceeecCcccc
Confidence            3555667787777777777766665521 111232222111 11 36999999999999999999999999999999988


Q ss_pred             CChHHHHHHHHhh-------------------cC-CcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEE
Q 011664          261 ADDADLKSLLLQT-------------------TS-KSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF  320 (480)
Q Consensus       261 ~~~~~l~~l~~~~-------------------~~-~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~  320 (480)
                      .+...+...+...                   .. ..||++||+|.+..  .+...++++-..+.       ...+-+|+
T Consensus       394 RSk~~l~~~~~~~~~s~si~~~~~~~~~~~~~~~~~~vil~devD~~~~--~dRg~v~~l~~l~~-------ks~~Piv~  464 (871)
T KOG1968|consen  394 RSKKELLNKLGNATSSHSIKGSKKKKGNRQSLNSDHFLILMDEVDGMFG--EDRGGVSKLSSLCK-------KSSRPLVC  464 (871)
T ss_pred             ccccHHHhhhhccccccchhhhhcccccccccccceeEEEEeccccccc--hhhhhHHHHHHHHH-------hccCCeEE
Confidence            7665544433211                   11 24999999998875  22222222222221       23455788


Q ss_pred             ecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch-hHHHHHHhCCCCCHHHHHHHHHH
Q 011664          321 TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP-QVEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       321 tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~-~i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      ++|..+......+.  |-..-++|+.|+.+....-+..++......+.. .++++.+    .+++||.+.+..
T Consensus       465 ~cndr~~p~sr~~~--~~~~~l~f~kP~~~~i~~ri~si~~se~~ki~~~~l~~~s~----~~~~DiR~~i~~  531 (871)
T KOG1968|consen  465 TCNDRNLPKSRALS--RACSDLRFSKPSSELIRSRIMSICKSEGIKISDDVLEEISK----LSGGDIRQIIMQ  531 (871)
T ss_pred             EecCCCCccccchh--hhcceeeecCCcHHHHHhhhhhhhcccceecCcHHHHHHHH----hcccCHHHHHHH
Confidence            88866655543333  544689999999999888888887666555544 3455543    336677665543

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=98.22  E-value=1.3e-05  Score=80.35  Aligned_cols=112  Identities=17%  Similarity=0.233  Sum_probs=80.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC----------------CcEEEEeCCC---cCChHHHHHHHHhh------cCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS----------------YDVYDVDLSR---VADDADLKSLLLQT------TSKS  277 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~----------------~~~~~i~~s~---~~~~~~l~~l~~~~------~~~s  277 (480)
                      .+..|||+||+|+||+.+|.++|..+-                -+++.+....   ..+-..++.+....      ....
T Consensus        18 l~HAyLf~G~~G~Gk~~lA~~~A~~llC~~~~~~c~~~~~~~HPD~~~i~p~~~~~~I~idqiR~l~~~~~~~p~e~~~k   97 (290)
T PRK05917         18 VPSAIILHGQDLSNLSARAYELASLILKETSPEAAYKISQKIHPDIHEFSPQGKGRLHSIETPRAIKKQIWIHPYESPYK   97 (290)
T ss_pred             cCeeEeeECCCCCcHHHHHHHHHHHHhCCCCccHHHHHhcCCCCCEEEEecCCCCCcCcHHHHHHHHHHHhhCccCCCce
Confidence            456899999999999999999998652                2354453221   22344555554332      2347


Q ss_pred             EEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCC
Q 011664          278 VILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLC  347 (480)
Q Consensus       278 II~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p  347 (480)
                      |++||++|.+.     ....+.||..++.-     +++.++|+.|+.++.|-|.+++  |+. .+.|+++
T Consensus        98 v~ii~~ad~mt-----~~AaNaLLK~LEEP-----p~~~~fiL~~~~~~~ll~TI~S--Rcq-~~~~~~~  154 (290)
T PRK05917         98 IYIIHEADRMT-----LDAISAFLKVLEDP-----PQHGVIILTSAKPQRLPPTIRS--RSL-SIHIPME  154 (290)
T ss_pred             EEEEechhhcC-----HHHHHHHHHHhhcC-----CCCeEEEEEeCChhhCcHHHHh--cce-EEEccch
Confidence            99999999883     34457788888642     5678888899999999999999  985 6777754

>KOG1970 consensus Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]

Probab=98.22  E-value=2.7e-05  Score=82.77  Aligned_cols=175  Identities=22%  Similarity=0.315  Sum_probs=99.9

Q ss_pred             CcceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          176 GRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       176 ~~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-|-  ..-.|.+.++|+-+..-..++++.+..+....      .....+-+||+||+|||||+.++.+|.++|+.+..-
T Consensus        70 elW~--eKy~P~t~eeLAVHkkKI~eVk~WL~~~~~~~------~~l~~~iLLltGPsGcGKSTtvkvLskelg~~~~Ew  141 (634)
T KOG1970|consen   70 ELWV--EKYKPRTLEELAVHKKKISEVKQWLKQVAEFT------PKLGSRILLLTGPSGCGKSTTVKVLSKELGYQLIEW  141 (634)
T ss_pred             chhH--HhcCcccHHHHhhhHHhHHHHHHHHHHHHHhc------cCCCceEEEEeCCCCCCchhHHHHHHHhhCceeeee
Confidence            3463  34468899999999888887777666221111      111245688999999999999999999999987654


Q ss_pred             e-------CCCcCC---------hHHHHH---HHHh--------------hcCCcEEEEecccccccCcccccchhhhhh
Q 011664          256 D-------LSRVAD---------DADLKS---LLLQ--------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLN  302 (480)
Q Consensus       256 ~-------~s~~~~---------~~~l~~---l~~~--------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~  302 (480)
                      .       .+.+..         .+.+..   .+..              ...+.+|+|||+-..+... ....+.+.|.
T Consensus       142 ~Npi~~~~~~~~h~~t~~~~~~~~s~L~~fesFler~~kyg~l~~~g~~~~~~~~liLveDLPn~~~~d-~~~~f~evL~  220 (634)
T KOG1970|consen  142 SNPINLKEPENLHNETSFLMFPYQSQLAVFESFLLRATKYGSLQMSGDDLRTDKKLILVEDLPNQFYRD-DSETFREVLR  220 (634)
T ss_pred             cCCccccccccccccchhcccchhhHHHHHHHHHHHHHhhchhhhcccccccCceEEEeeccchhhhhh-hHHHHHHHHH
Confidence            3       111111         111111   1111              1246799999997765432 3334444444


Q ss_pred             hcccccccccCCceEEEEe-cCCCccCcccccCC------CceeEEEEcCCCCHHHHHHHHHHHhccCC
Q 011664          303 FMDGVLNSCCFEERVMVFT-MNSKDHVDQALLRP------GRIDVHIHFPLCDFSSFKTLASSYLGLKD  364 (480)
Q Consensus       303 ~ldg~~~~~~~~~~ivI~t-TN~~~~LD~aLlrp------GRfd~~I~~~~p~~~~r~~il~~~l~~~~  364 (480)
                      ..-...    .-..|||.| ++.++..++..+.|      .|+ .+|.|.+-...-.++.++.++....
T Consensus       221 ~y~s~g----~~PlIf~iTd~~~~g~nnq~rlf~~d~q~~~ri-~~IsFNPIa~T~MKK~L~ric~~e~  284 (634)
T KOG1970|consen  221 LYVSIG----RCPLIFIITDSLSNGNNNQDRLFPKDIQEEPRI-SNISFNPIAPTIMKKFLKRICRIEA  284 (634)
T ss_pred             HHHhcC----CCcEEEEEeccccCCCcchhhhchhhhhhccCc-ceEeecCCcHHHHHHHHHHHHHHhc
Confidence            332111    112344443 22334444433322      255 3788887777777777777765443

>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=98.22  E-value=3.7e-05  Score=76.50  Aligned_cols=150  Identities=19%  Similarity=0.175  Sum_probs=80.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHc--CCC--c-EEEEeCCCcCCh------------------------HHHHHHHHh-
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASF--MSY--D-VYDVDLSRVADD------------------------ADLKSLLLQ-  272 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~--l~~--~-~~~i~~s~~~~~------------------------~~l~~l~~~-  272 (480)
                      ..+-+.|+|++|+|||+||..+++.  ...  + ++.++++.....                        ..+...+.+ 
T Consensus        18 ~~~~v~I~G~~G~GKT~LA~~~~~~~~~~~~f~~v~wv~~~~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~~~l~~~   97 (287)
T PF00931_consen   18 EVRVVAIVGMGGIGKTTLARQVARDLRIKNRFDGVIWVSLSKNPSLEQLLEQILRQLGEPDSSISDPKDIEELQDQLREL   97 (287)
T ss_dssp             SSEEEEEEESTTSSHHHHHHHHHCHHHHCCCCTEEEEEEEES-SCCHHHHHHHHHHHTCC-STSSCCSSHHHHHHHHHHH
T ss_pred             CeEEEEEEcCCcCCcceeeeecccccccccccccccccccccccccccccccccccccccccccccccccccccccchhh
Confidence            4567889999999999999999976  322  2 344444332211                        111122221 


Q ss_pred             -hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHH
Q 011664          273 -TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       273 -~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                       ...+++|+|||++...       .+..+...+.   . . ..+.-||+||.... +-...-   .-...++++..+.++
T Consensus        98 L~~~~~LlVlDdv~~~~-------~~~~l~~~~~---~-~-~~~~kilvTTR~~~-v~~~~~---~~~~~~~l~~L~~~e  161 (287)
T PF00931_consen   98 LKDKRCLLVLDDVWDEE-------DLEELREPLP---S-F-SSGSKILVTTRDRS-VAGSLG---GTDKVIELEPLSEEE  161 (287)
T ss_dssp             HCCTSEEEEEEEE-SHH-------HH-------H---C-H-HSS-EEEEEESCGG-GGTTHH---SCEEEEECSS--HHH
T ss_pred             hccccceeeeeeecccc-------cccccccccc---c-c-cccccccccccccc-cccccc---ccccccccccccccc
Confidence             1348999999998542       2222222221   1 1 22334566776432 211111   115789999999999


Q ss_pred             HHHHHHHHhccCC----CCCchhHHHHHHhCCCCCHHHHHHH
Q 011664          352 FKTLASSYLGLKD----HKLFPQVEEIFQNGSSLSPAEIGEL  389 (480)
Q Consensus       352 r~~il~~~l~~~~----~~l~~~i~~l~~~~~g~s~adI~~l  389 (480)
                      -.+++..+.....    ........++++.. |..|--|.-+
T Consensus       162 a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~c-~glPLal~~~  202 (287)
T PF00931_consen  162 ALELFKKRAGRKESESPEDLEDLAKEIVEKC-GGLPLALKLI  202 (287)
T ss_dssp             HHHHHHHHHTSHS----TTSCTHHHHHHHHT-TT-HHHHHHH
T ss_pred             ccccccccccccccccccccccccccccccc-cccccccccc
Confidence            9999999876544    22334456777776 5556555443

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.

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=98.21  E-value=5.2e-06  Score=74.43  Aligned_cols=63  Identities=27%  Similarity=0.492  Sum_probs=42.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC-----------------------------hHHHH---HHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD-----------------------------DADLK---SLLL  271 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~-----------------------------~~~l~---~l~~  271 (480)
                      ++++||||+|||+++.+++..+   +.+++.++......                             .....   ..+.
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~~~~~~~v~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNIATKGGKVVYVDIEEEIEELTERLIGESLKGALDNLIIVFATADDPAAARLLSKAERLR   81 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHHHhcCCEEEEEECCcchHHHHHHHhhhhhccccccEEEEEcCCCCCcHHHHHHHHHHHH
Confidence            6899999999999999998876   45666665432210                             01111   1223


Q ss_pred             hhcCCcEEEEeccccccc
Q 011664          272 QTTSKSVILIEDLDRFLV  289 (480)
Q Consensus       272 ~~~~~sII~IDEiD~l~~  289 (480)
                      ....+.+|+|||+..+..
T Consensus        82 ~~~~~~~lviDe~~~~~~   99 (165)
T cd01120          82 ERGGDDLIILDELTRLVR   99 (165)
T ss_pred             hCCCCEEEEEEcHHHHHH
Confidence            445788999999998764

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.

>PRK07276 DNA polymerase III subunit delta'; Validated

Probab=98.16  E-value=6.4e-05  Score=75.63  Aligned_cols=145  Identities=19%  Similarity=0.278  Sum_probs=93.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC------------------------CcEEEEeCC-CcCChHHHHHHHHhh----
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS------------------------YDVYDVDLS-RVADDADLKSLLLQT----  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~------------------------~~~~~i~~s-~~~~~~~l~~l~~~~----  273 (480)
                      .+.+|||+||  +||+++|.++|..+-                        .+++.+... ...+-.+++.+....    
T Consensus        23 l~hAyLf~G~--~G~~~~A~~~A~~llC~~~~~~~~Cg~C~~C~~i~~~~HPD~~~i~p~~~~I~idqIR~l~~~~~~~p  100 (290)
T PRK07276         23 LNHAYLFSGD--FASFEMALFLAQSLFCEQKEGVLPCGHCRSCRLIEQGEFSDVTVIEPQGQVIKTDTIRELVKNFSQSG  100 (290)
T ss_pred             cceeeeeeCC--ccHHHHHHHHHHHHcCCCCCCCCCCCCCHHHHHHhcCCCCCeeeecCCCCcCCHHHHHHHHHHHhhCc
Confidence            4568999996  689999999997542                        134444332 122345566654332    


Q ss_pred             --cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHH
Q 011664          274 --TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       274 --~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                        ....|++||++|.+.     ....+.||..++.-     +.+.++|++|+.++.|-|.+++  |+ .+|.|+. +.+.
T Consensus       101 ~~~~~kV~II~~ad~m~-----~~AaNaLLKtLEEP-----p~~t~~iL~t~~~~~lLpTI~S--Rc-q~i~f~~-~~~~  166 (290)
T PRK07276        101 YEGKQQVFIIKDADKMH-----VNAANSLLKVIEEP-----QSEIYIFLLTNDENKVLPTIKS--RT-QIFHFPK-NEAY  166 (290)
T ss_pred             ccCCcEEEEeehhhhcC-----HHHHHHHHHHhcCC-----CCCeEEEEEECChhhCchHHHH--cc-eeeeCCC-cHHH
Confidence              234799999999883     34457788888642     4567889999999999999999  99 4888876 5555


Q ss_pred             HHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHH
Q 011664          352 FKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       352 r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll  390 (480)
                      ..+++..    .+  +..+..+++....| ++....++.
T Consensus       167 ~~~~L~~----~g--~~~~~a~~la~~~~-s~~~A~~l~  198 (290)
T PRK07276        167 LIQLLEQ----KG--LLKTQAELLAKLAQ-STSEAEKLA  198 (290)
T ss_pred             HHHHHHH----cC--CChHHHHHHHHHCC-CHHHHHHHh
Confidence            4444432    22  22333344444445 676666665

>PF05707 Zot: Zonular occludens toxin (Zot); InterPro: IPR008900 This entry consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot)

Probab=98.14  E-value=5.1e-06  Score=78.67  Aligned_cols=113  Identities=18%  Similarity=0.287  Sum_probs=60.2

Q ss_pred             EEEEccCCCcHHHHHHHH-HHc---CCCcEEEEeCCCcC-----C---------------------hHHHHHHHHhhcCC
Q 011664          227 YLLYGPSGTGKSSFAAAM-ASF---MSYDVYDVDLSRVA-----D---------------------DADLKSLLLQTTSK  276 (480)
Q Consensus       227 iLL~GPpGTGKT~La~ai-A~~---l~~~~~~i~~s~~~-----~---------------------~~~l~~l~~~~~~~  276 (480)
                      ++++|.||+|||..|-.. ...   -|.+++. ++..+.     .                     ...+ .........
T Consensus         3 ~~~~G~pGsGKS~~av~~~i~~~l~~gr~V~t-ni~gL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (193)
T PF05707_consen    3 YLITGKPGSGKSYYAVSYVIIPALKKGRPVYT-NIPGLNIEKIQPVLGYDIPTRLIDLSDPDFEEDWDDP-DDWRKLPKG   80 (193)
T ss_dssp             EEEE--TTSSHHHHHHHHHHH-GGGS---EEE---TTB-S--EEEE--TTT-S-----S--SSSEEGGGH-HHHTTSGTT
T ss_pred             EEEEcCCCCcHhHHHHHHHHHHHHhCCCEEEE-ccCCcchhhhhhhccccccccccccccccchhhhhhh-hhhcccCCC
Confidence            688999999999887655 332   2666554 443221     1                     0011 111222368


Q ss_pred             cEEEEecccccccCcccc-cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCC
Q 011664          277 SVILIEDLDRFLVEKPAA-VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLC  347 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~-~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p  347 (480)
                      ++|+|||+...++.+... ....+.++.+.-..    ..+.-||++|.++..||+.+++  ..+.++++.-+
T Consensus        81 ~liviDEa~~~~~~r~~~~~~~~~~~~~l~~hR----h~g~diiliTQ~~~~id~~ir~--lve~~~~~~k~  146 (193)
T PF05707_consen   81 SLIVIDEAQNFFPSRSWKGKKVPEIIEFLAQHR----HYGWDIILITQSPSQIDKFIRD--LVEYHYHCRKL  146 (193)
T ss_dssp             -EEEETTGGGTSB---T-T----HHHHGGGGCC----CTT-EEEEEES-GGGB-HHHHC--CEEEEEEEEE-
T ss_pred             cEEEEECChhhcCCCccccccchHHHHHHHHhC----cCCcEEEEEeCCHHHHhHHHHH--HHheEEEEEee
Confidence            999999999999877663 22333444442221    3466788999999999999987  88888877654

Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2R2A_B.

>KOG0478 consensus DNA replication licensing factor, MCM4 component [Replication, recombination and repair]

Probab=98.07  E-value=6e-06  Score=89.35  Aligned_cols=158  Identities=22%  Similarity=0.288  Sum_probs=89.9

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe-------CCCc-C
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD-------LSRV-A  261 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~-------~s~~-~  261 (480)
                      .|.|++++|+.+.  +..|--..+.+...| ..-.-+|||+|-||||||.+.+.+++-+-...|.-.       ++.. .
T Consensus       430 sIye~edvKkglL--LqLfGGt~k~~~~~~~~R~~INILL~GDPGtsKSqlLqyv~~l~pRg~yTSGkGsSavGLTayVt  507 (804)
T KOG0478|consen  430 SIYELEDVKKGLL--LQLFGGTRKEDEKSGRFRGDINILLVGDPGTSKSQLLQYCHRLLPRGVYTSGKGSSAVGLTAYVT  507 (804)
T ss_pred             hhhcccchhhhHH--HHHhcCCcccccccccccccceEEEecCCCcCHHHHHHHHHHhCCcceeecCCccchhcceeeEE
Confidence            5788889888876  333433333333333 111236999999999999999999997755444321       1100 0


Q ss_pred             ChHHHHHHHHhh-----cCCcEEEEecccccccCcccccchhhhhhhcc---------cccccccCCceEEEEecCCC--
Q 011664          262 DDADLKSLLLQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD---------GVLNSCCFEERVMVFTMNSK--  325 (480)
Q Consensus       262 ~~~~l~~l~~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld---------g~~~~~~~~~~ivI~tTN~~--  325 (480)
                      .+.+-+++..+.     ....|.+|||+|.+..     .+.+-|++.|+         |+.. .-+...-|+++.|..  
T Consensus       508 rd~dtkqlVLesGALVLSD~GiCCIDEFDKM~d-----StrSvLhEvMEQQTvSIAKAGII~-sLNAR~SVLAaANP~~s  581 (804)
T KOG0478|consen  508 KDPDTRQLVLESGALVLSDNGICCIDEFDKMSD-----STRSVLHEVMEQQTLSIAKAGIIA-SLNARCSVLAAANPIRS  581 (804)
T ss_pred             ecCccceeeeecCcEEEcCCceEEchhhhhhhH-----HHHHHHHHHHHHhhhhHhhcceee-eccccceeeeeeccccc
Confidence            111222222221     3678999999999842     22244444443         3332 111222366677732  


Q ss_pred             ---------c--cCcccccCCCceeEE-EEcCCCCHHHHHHHHHH
Q 011664          326 ---------D--HVDQALLRPGRIDVH-IHFPLCDFSSFKTLASS  358 (480)
Q Consensus       326 ---------~--~LD~aLlrpGRfd~~-I~~~~p~~~~r~~il~~  358 (480)
                               +  .|+|.|++  |||.+ +-+..||+..=+.|..+
T Consensus       582 kynp~k~i~eNI~LpptLLS--RFDLIylllD~~DE~~Dr~La~H  624 (804)
T KOG0478|consen  582 KYNPNKSIIENINLPPTLLS--RFDLIFLLLDKPDERSDRRLADH  624 (804)
T ss_pred             cCCCCCchhhccCCChhhhh--hhcEEEEEecCcchhHHHHHHHH
Confidence                     1  26899999  99944 45667777643444443

>PHA02774 E1; Provisional

Probab=98.04  E-value=2.8e-05  Score=84.03  Aligned_cols=58  Identities=28%  Similarity=0.458  Sum_probs=42.3

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEE-EeCCCcCChHHHHHHHHhhcCCcEEEEecc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYD-VDLSRVADDADLKSLLLQTTSKSVILIEDL  284 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~-i~~s~~~~~~~l~~l~~~~~~~sII~IDEi  284 (480)
                      |.|.+++++||||||||||+++.+|++.++..++. ++..+   .    ..+.......|++|||+
T Consensus       430 ~~PKknciv~~GPP~TGKS~fa~sL~~~L~G~vi~fvN~~s---~----FwLqpl~d~ki~vlDD~  488 (613)
T PHA02774        430 GIPKKNCLVIYGPPDTGKSMFCMSLIKFLKGKVISFVNSKS---H----FWLQPLADAKIALLDDA  488 (613)
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCEEEEEECcc---c----cccchhccCCEEEEecC
Confidence            45556789999999999999999999998655543 65421   1    11333445679999999

>PRK05818 DNA polymerase III subunit delta'; Validated

Probab=98.03  E-value=4.4e-05  Score=75.34  Aligned_cols=112  Identities=14%  Similarity=0.166  Sum_probs=79.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC----------------------cEEEEeCC-CcCChHHHHHHHHh---h---
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY----------------------DVYDVDLS-RVADDADLKSLLLQ---T---  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~----------------------~~~~i~~s-~~~~~~~l~~l~~~---~---  273 (480)
                      .+.++||+||+|+||..+|.++|..+-+                      +++.+... .-.+-.+++.+...   .   
T Consensus         6 ~~HA~Lf~G~~G~G~~~lA~~~A~~llC~~~~~~Cg~C~sC~~i~~~~HPDl~~i~p~~~~I~id~ir~l~~~l~~~s~e   85 (261)
T PRK05818          6 KTHPLLLIERKGSFLKPFLYEYLTSIVCTKANGFCKTCESCLKILNGKYNDFYLIFDQKNPIKKEDALSIINKLNRPSVE   85 (261)
T ss_pred             CCcceeeeCCCCCcHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHhcCCCCCEEEecCCcccCCHHHHHHHHHHHccCchh
Confidence            5678999999999999999999975521                      23333211 12233445554432   1   


Q ss_pred             -cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCC
Q 011664          274 -TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLC  347 (480)
Q Consensus       274 -~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p  347 (480)
                       ....|++|+++|.+.     ....+.||..++.     .+.+.++|++|+.++.+-|.+++  |+. .+.++.+
T Consensus        86 ~~~~KV~II~~ae~m~-----~~AaNaLLK~LEE-----Pp~~t~fiLit~~~~~lLpTI~S--RCq-~~~~~~~  147 (261)
T PRK05818         86 SNGKKIYIIYGIEKLN-----KQSANSLLKLIEE-----PPKNTYGIFTTRNENNILNTILS--RCV-QYVVLSK  147 (261)
T ss_pred             cCCCEEEEeccHhhhC-----HHHHHHHHHhhcC-----CCCCeEEEEEECChHhCchHhhh--hee-eeecCCh
Confidence             235799999999883     3445778888864     25678899999999999999999  985 5667766

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=98.01  E-value=2.1e-05  Score=74.95  Aligned_cols=40  Identities=25%  Similarity=0.369  Sum_probs=33.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~  259 (480)
                      |++...-++++||||||||+++..+|..   .+...++++...
T Consensus         8 Gi~~g~i~~i~G~~GsGKT~l~~~~~~~~~~~g~~v~yi~~e~   50 (209)
T TIGR02237         8 GVERGTITQIYGPPGSGKTNICMILAVNAARQGKKVVYIDTEG   50 (209)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCC
Confidence            6677777899999999999999988854   367788888865

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

>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=97.90  E-value=8.8e-06  Score=70.33  Aligned_cols=31  Identities=32%  Similarity=0.629  Sum_probs=27.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      |++.|||||||||+|+.+|..+|+.++.++-
T Consensus         2 I~I~G~~gsGKST~a~~La~~~~~~~i~~d~   32 (121)
T PF13207_consen    2 IIISGPPGSGKSTLAKELAERLGFPVISMDD   32 (121)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHTCEEEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEEecc
Confidence            7899999999999999999999988776653

...

>PRK13406 bchD magnesium chelatase subunit D; Provisional

Probab=97.90  E-value=3.8e-05  Score=84.37  Aligned_cols=119  Identities=13%  Similarity=0.167  Sum_probs=82.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCC----CcCChHHHHHHHHh-----------hcCCcEEEEeccccc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLS----RVADDADLKSLLLQ-----------TTSKSVILIEDLDRF  287 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s----~~~~~~~l~~l~~~-----------~~~~sII~IDEiD~l  287 (480)
                      .|+||-|++|||||+++++++..+..  +|..+..+    .+.+.-++...+..           .....|||+||+..+
T Consensus        26 gGv~i~g~~G~~ks~~~r~l~~llp~~~p~r~~p~~~t~~~L~Gg~Dl~~~l~~g~~~~~pGlla~Ah~GvL~lDe~n~~  105 (584)
T PRK13406         26 GGVVLRARAGPVRDRWLAALRALLPAGTPLRRLPPGIADDRLLGGLDLAATLRAGRPVAQRGLLAEADGGVLVLAMAERL  105 (584)
T ss_pred             ceEEEEcCCCcHHHHHHHHHHHhcCCCCCcccCCCCCcHHHccCCchHHhHhhcCCcCCCCCceeeccCCEEEecCcccC
Confidence            58999999999999999999998754  77666543    24454445444422           123579999999976


Q ss_pred             ccCcccccchhhhhhhccc---------ccccccCCceEEEEecCCC---ccCcccccCCCceeEEEEcCCCCHHH
Q 011664          288 LVEKPAAVSLSGVLNFMDG---------VLNSCCFEERVMVFTMNSK---DHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       288 ~~~~~~~~~ls~lL~~ldg---------~~~~~~~~~~ivI~tTN~~---~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                           ...+++.|++.|+.         ... ......++|+|-|..   ..|.++++.  ||+.+|.+++|+..+
T Consensus       106 -----~~~~~~aLleame~G~vtIeR~G~s~-~~Pa~F~LIat~~~~~~~~~L~~~lLD--Rf~l~v~v~~~~~~~  173 (584)
T PRK13406        106 -----EPGTAARLAAALDTGEVRLERDGLAL-RLPARFGLVALDEGAEEDERAPAALAD--RLAFHLDLDGLALRD  173 (584)
T ss_pred             -----CHHHHHHHHHHHhCCcEEEEECCcEE-ecCCCcEEEecCCChhcccCCCHHhHh--heEEEEEcCCCChHH
Confidence                 34567888888752         111 112233455553322   458899999  999999999988654

>PRK15455 PrkA family serine protein kinase; Provisional

Probab=97.89  E-value=1.8e-05  Score=85.61  Aligned_cols=66  Identities=24%  Similarity=0.326  Sum_probs=50.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-CCcEEEEeC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-SYDVYDVDL  257 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i~~  257 (480)
                      .-.-|+++.|++++++.|.+.+......      ++ ..++-++|.||||+|||+||+++|+.+ .+++|.+..
T Consensus        71 ry~fF~d~yGlee~ieriv~~l~~Aa~g------l~-~~~~IL~LvGPpG~GKSsLa~~la~~le~~~~Y~~kg  137 (644)
T PRK15455         71 RYPAFEEFYGMEEAIEQIVSYFRHAAQG------LE-EKKQILYLLGPVGGGKSSLAERLKSLMERVPIYVLKA  137 (644)
T ss_pred             cccchhcccCcHHHHHHHHHHHHHHHHh------cC-CCCceEEEecCCCCCchHHHHHHHHHHHhCcceeecC
Confidence            3446999999999999999877554333      12 234578899999999999999999977 357777644

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.88  E-value=3.7e-05  Score=79.92  Aligned_cols=103  Identities=19%  Similarity=0.324  Sum_probs=64.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC----C-CcEEEEeCCCcC----------------------ChHHHHHHHHhhcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM----S-YDVYDVDLSRVA----------------------DDADLKSLLLQTTSK  276 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l----~-~~~~~i~~s~~~----------------------~~~~l~~l~~~~~~~  276 (480)
                      ...++|.||+|+|||+++..+|..+    | ..+..+....+.                      ...++...+.+....
T Consensus       137 g~ii~lvGptGvGKTTtiakLA~~~~~~~G~~~V~lit~D~~R~ga~EqL~~~a~~~gv~~~~~~~~~~l~~~l~~l~~~  216 (374)
T PRK14722        137 GGVFALMGPTGVGKTTTTAKLAARCVMRFGASKVALLTTDSYRIGGHEQLRIFGKILGVPVHAVKDGGDLQLALAELRNK  216 (374)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEecccccccHHHHHHHHHHHcCCceEecCCcccHHHHHHHhcCC
Confidence            4568899999999999999999753    3 345455443321                      123344555666778


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEE-ecCCCccCccccc
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF-TMNSKDHVDQALL  333 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~-tTN~~~~LD~aLl  333 (480)
                      .+|+||......    ....+.+.+..+.+...   ...+++|+ +|+..+.++..+.
T Consensus       217 DlVLIDTaG~~~----~d~~l~e~La~L~~~~~---~~~~lLVLsAts~~~~l~evi~  267 (374)
T PRK14722        217 HMVLIDTIGMSQ----RDRTVSDQIAMLHGADT---PVQRLLLLNATSHGDTLNEVVQ  267 (374)
T ss_pred             CEEEEcCCCCCc----ccHHHHHHHHHHhccCC---CCeEEEEecCccChHHHHHHHH
Confidence            999999997432    22335556666654433   23445554 7777777765543

>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]

Probab=97.85  E-value=0.00017  Score=71.79  Aligned_cols=56  Identities=14%  Similarity=0.207  Sum_probs=40.1

Q ss_pred             eEEEEecCC------------CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHH
Q 011664          316 RVMVFTMNS------------KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEI  374 (480)
Q Consensus       316 ~ivI~tTN~------------~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l  374 (480)
                      .++|++||+            |.-++-.|+.  |+ ..|...+++.++.++|++..+..++..+.++.-.+
T Consensus       318 PiiimaTNrgit~iRGTn~~SphGiP~D~lD--R~-lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~  385 (454)
T KOG2680|consen  318 PIIIMATNRGITRIRGTNYRSPHGIPIDLLD--RM-LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDL  385 (454)
T ss_pred             cEEEEEcCCceEEeecCCCCCCCCCcHHHhh--hh-heeecccCcHHHHHHHHHhhhhhhccccCHHHHHH
Confidence            466777764            4556667777  77 57788888888899999988877776666655333

>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=97.84  E-value=6.9e-05  Score=69.62  Aligned_cols=31  Identities=35%  Similarity=0.329  Sum_probs=24.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      +|++||||||||+++..++.+.   |.++.++++
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~g~~v~~~s~   35 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLARGEPGLYVTL   35 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHCCCcEEEEEC
Confidence            7899999999999999886643   566666654

A related protein is found in archaea.

>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite

Probab=97.84  E-value=1e-05  Score=83.17  Aligned_cols=164  Identities=19%  Similarity=0.165  Sum_probs=80.5

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC----Cc------
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS----RV------  260 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s----~~------  260 (480)
                      +|.|.+.+|..|.=.+..-...... ........-.+||.|.||||||.|.+.+++..-..++...-+    .+      
T Consensus        25 ~i~g~~~iK~aill~L~~~~~~~~~-~~~~~r~~ihiLlvGdpg~gKS~ll~~~~~~~pr~v~~~g~~~s~~gLta~~~~  103 (331)
T PF00493_consen   25 SIYGHEDIKKAILLQLFGGVEKNDP-DGTRIRGNIHILLVGDPGTGKSQLLKYVAKLAPRSVYTSGKGSSAAGLTASVSR  103 (331)
T ss_dssp             TTTT-HHHHHHHCCCCTT--SCCCC-T-TEE--S--EEEECSCHHCHHHHHHCCCCT-SSEEEEECCGSTCCCCCEEECC
T ss_pred             cCcCcHHHHHHHHHHHHhccccccc-cccccccccceeeccchhhhHHHHHHHHHhhCCceEEECCCCcccCCccceecc
Confidence            4678888877765222111100000 000011223699999999999999998876654444332110    01      


Q ss_pred             ---CChHHHHH-HHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccccc--------CCceEEEEecCCCc--
Q 011664          261 ---ADDADLKS-LLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC--------FEERVMVFTMNSKD--  326 (480)
Q Consensus       261 ---~~~~~l~~-l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~--------~~~~ivI~tTN~~~--  326 (480)
                         .++..+.. .+. .....|++|||+|.+-.     .....|+..|+.-.-...        +-..-|++|+|...  
T Consensus       104 d~~~~~~~leaGalv-lad~GiccIDe~dk~~~-----~~~~~l~eaMEqq~isi~kagi~~~l~ar~svlaa~NP~~g~  177 (331)
T PF00493_consen  104 DPVTGEWVLEAGALV-LADGGICCIDEFDKMKE-----DDRDALHEAMEQQTISIAKAGIVTTLNARCSVLAAANPKFGR  177 (331)
T ss_dssp             CGGTSSECEEE-HHH-HCTTSEEEECTTTT--C-----HHHHHHHHHHHCSCEEECTSSSEEEEE---EEEEEE--TT--
T ss_pred             ccccceeEEeCCchh-cccCceeeecccccccc-----hHHHHHHHHHHcCeeccchhhhcccccchhhhHHHHhhhhhh
Confidence               01111110 111 23678999999998732     224555666642110011        11234677877554  


Q ss_pred             -----------cCcccccCCCceeEEEEc-CCCCHHHHHHHHHHHhccC
Q 011664          327 -----------HVDQALLRPGRIDVHIHF-PLCDFSSFKTLASSYLGLK  363 (480)
Q Consensus       327 -----------~LD~aLlrpGRfd~~I~~-~~p~~~~r~~il~~~l~~~  363 (480)
                                 .++++|++  |||..+.+ ..|+.+.=..+.+..+...
T Consensus       178 ~~~~~~~~~ni~l~~~LLS--RFDLif~l~D~~d~~~D~~la~~il~~~  224 (331)
T PF00493_consen  178 YDPNKSLSENINLPPPLLS--RFDLIFLLRDKPDEEEDERLAEHILDSH  224 (331)
T ss_dssp             S-TTS-CGCCT-S-CCCHC--C-SEEECC--TTT-HHHHHHHHHHHTTT
T ss_pred             cchhhhhHHhcccchhhHh--hcCEEEEeccccccccccccceEEEecc
Confidence                       47889999  99977665 5677666666777666543

; 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.

>KOG0480 consensus DNA replication licensing factor, MCM6 component [Replication, recombination and repair]

Probab=97.83  E-value=2.9e-05  Score=83.67  Aligned_cols=190  Identities=18%  Similarity=0.279  Sum_probs=111.7

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC--CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe-CCCcC----
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVW--KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD-LSRVA----  261 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~--~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~-~s~~~----  261 (480)
                      |..|.|++.+|.-|.=  ..| -+-..+..-|.+.  --++++.|-||||||-+.+++++.+-..+|... .+.-.    
T Consensus       344 ~PsIyGhe~VK~GilL--~Lf-GGv~K~a~eg~~lRGDinv~iVGDPgt~KSQfLk~v~~fsPR~vYtsGkaSSaAGLTa  420 (764)
T KOG0480|consen  344 FPSIYGHELVKAGILL--SLF-GGVHKSAGEGTSLRGDINVCIVGDPGTGKSQFLKAVCAFSPRSVYTSGKASSAAGLTA  420 (764)
T ss_pred             CccccchHHHHhhHHH--HHh-CCccccCCCCccccCCceEEEeCCCCccHHHHHHHHhccCCcceEecCcccccccceE
Confidence            6678999999988762  222 1212222222222  226999999999999999999998876666542 11111    


Q ss_pred             ---ChHHHHHHHHhh-----cCCcEEEEecccccccCcccccchhhhhhhcc---------cccccccCCceEEEEecCC
Q 011664          262 ---DDADLKSLLLQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD---------GVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ---~~~~l~~l~~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld---------g~~~~~~~~~~ivI~tTN~  324 (480)
                         .+++--....++     ....|.+|||+|.+-.     ...-.++..|+         |+... -+...-|++|+|.
T Consensus       421 aVvkD~esgdf~iEAGALmLADnGICCIDEFDKMd~-----~dqvAihEAMEQQtISIaKAGv~aT-LnARtSIlAAANP  494 (764)
T KOG0480|consen  421 AVVKDEESGDFTIEAGALMLADNGICCIDEFDKMDV-----KDQVAIHEAMEQQTISIAKAGVVAT-LNARTSILAAANP  494 (764)
T ss_pred             EEEecCCCCceeeecCcEEEccCceEEechhcccCh-----HhHHHHHHHHHhheehheecceEEe-ecchhhhhhhcCC
Confidence               111100111111     3578999999998832     12234455553         22210 0111235667774


Q ss_pred             C-----------c--cCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHH
Q 011664          325 K-----------D--HVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       325 ~-----------~--~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll  390 (480)
                      .           +  .+++++++  ||| ..|-+..|++..=..|.++.+..+..     +++-......|+-.++...+
T Consensus       495 v~GhYdR~ktl~eNi~msApimS--RFDL~FiLlD~~nE~~D~~ia~hIld~h~~-----i~~~~~~~~~~~~e~vrkYi  567 (764)
T KOG0480|consen  495 VGGHYDRKKTLRENINMSAPIMS--RFDLFFILLDDCNEVVDYAIARHILDLHRG-----IDDATERVCVYTLEQVRKYI  567 (764)
T ss_pred             cCCccccccchhhhcCCCchhhh--hhcEEEEEecCCchHHHHHHHHHHHHHhcc-----ccccccccccccHHHHHHHH
Confidence            3           1  25889999  999 66788999998888888887754211     11111222477888888777


Q ss_pred             HHhh
Q 011664          391 IANR  394 (480)
Q Consensus       391 ~~a~  394 (480)
                      .-+|
T Consensus       568 ~yAR  571 (764)
T KOG0480|consen  568 RYAR  571 (764)
T ss_pred             HHHH
Confidence            7665

>PRK00131 aroK shikimate kinase; Reviewed

Probab=97.80  E-value=2e-05  Score=72.13  Aligned_cols=34  Identities=32%  Similarity=0.474  Sum_probs=30.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .+..++|+||||||||++++++|..++.++++.+
T Consensus         3 ~~~~i~l~G~~GsGKstla~~La~~l~~~~~d~d   36 (175)
T PRK00131          3 KGPNIVLIGFMGAGKSTIGRLLAKRLGYDFIDTD   36 (175)
T ss_pred             CCCeEEEEcCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            4568999999999999999999999999888764

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.78  E-value=0.00013  Score=76.49  Aligned_cols=129  Identities=16%  Similarity=0.284  Sum_probs=72.1

Q ss_pred             hHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-------CCcEEEEeCCCcC-------
Q 011664          196 TDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-------SYDVYDVDLSRVA-------  261 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-------~~~~~~i~~s~~~-------  261 (480)
                      +.+++.+.+.+...+.....+  .....++.++|+||+|+||||.+..+|..+       +..+..+++....       
T Consensus       148 ~~v~~~l~~~l~~~i~~~~~~--~~~~~~~vi~lvGptGvGKTTT~aKLA~~~~~~~~~~g~~V~lit~Dt~R~aa~eQL  225 (388)
T PRK12723        148 DKVRDSVIIYIAKTIKCSGSI--IDNLKKRVFILVGPTGVGKTTTIAKLAAIYGINSDDKSLNIKIITIDNYRIGAKKQI  225 (388)
T ss_pred             HHHHHHHHHHHHHHhhccCcc--ccCCCCeEEEEECCCCCCHHHHHHHHHHHHHhhhccCCCeEEEEeccCccHHHHHHH
Confidence            445555555554444322111  112345678999999999999999999754       3444444433321       


Q ss_pred             ---------------ChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEE-ecCCC
Q 011664          262 ---------------DDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF-TMNSK  325 (480)
Q Consensus       262 ---------------~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~-tTN~~  325 (480)
                                     ....+...+.+.....+|+||.+.....   ....+.++...++....   ..++++|+ +|...
T Consensus       226 ~~~a~~lgvpv~~~~~~~~l~~~L~~~~~~DlVLIDTaGr~~~---~~~~l~el~~~l~~~~~---~~e~~LVlsat~~~  299 (388)
T PRK12723        226 QTYGDIMGIPVKAIESFKDLKEEITQSKDFDLVLVDTIGKSPK---DFMKLAEMKELLNACGR---DAEFHLAVSSTTKT  299 (388)
T ss_pred             HHHhhcCCcceEeeCcHHHHHHHHHHhCCCCEEEEcCCCCCcc---CHHHHHHHHHHHHhcCC---CCeEEEEEcCCCCH
Confidence                           1233444455556778999999987632   12224455555543322   22455554 66666


Q ss_pred             ccCcccc
Q 011664          326 DHVDQAL  332 (480)
Q Consensus       326 ~~LD~aL  332 (480)
                      ..+...+
T Consensus       300 ~~~~~~~  306 (388)
T PRK12723        300 SDVKEIF  306 (388)
T ss_pred             HHHHHHH
Confidence            6665443

>COG5245 DYN1 Dynein, heavy chain [Cytoskeleton]

Probab=97.77  E-value=0.0001  Score=85.45  Aligned_cols=138  Identities=16%  Similarity=0.183  Sum_probs=89.6

Q ss_pred             CCCCceEEEEccCCCcHHHH-HHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhh-------------cC----CcEEEEe
Q 011664          221 RVWKRSYLLYGPSGTGKSSF-AAAMASFMSYDVYDVDLSRVADDADLKSLLLQT-------------TS----KSVILIE  282 (480)
Q Consensus       221 ~~~~rgiLL~GPpGTGKT~L-a~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~-------------~~----~sII~ID  282 (480)
                      +...|+|+++||||+|||+| .-++-+++-..++.++.+.-.....+-..+.+.             +.    .-|+|.|
T Consensus      1491 lnt~R~~i~cGppGSgK~mlM~~sLrs~~~~ev~~~Nfs~~t~T~s~ls~Ler~t~yy~~tg~~~l~PK~~vK~lVLFcD 1570 (3164)
T COG5245        1491 LNTLRSYIYCGPPGSGKEMLMCPSLRSELITEVKYFNFSTCTMTPSKLSVLERETEYYPNTGVVRLYPKPVVKDLVLFCD 1570 (3164)
T ss_pred             HhccceEEEECCCCCccchhcchhhhhhhheeeeEEeeccccCCHHHHHHHHhhceeeccCCeEEEccCcchhheEEEee
Confidence            44678999999999999985 458888999999999988655444333344332             11    2589999


Q ss_pred             cccccccCcccccchhhhhh---hcccccccc-----cCCceEEEEecCCCccCc-----ccccCCCceeEEEEcCCCCH
Q 011664          283 DLDRFLVEKPAAVSLSGVLN---FMDGVLNSC-----CFEERVMVFTMNSKDHVD-----QALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       283 EiD~l~~~~~~~~~ls~lL~---~ldg~~~~~-----~~~~~ivI~tTN~~~~LD-----~aLlrpGRfd~~I~~~~p~~  349 (480)
                      ||..--.......+.--+|.   .-+|+|+..     .-.+.++++++|.+.+..     ..++|  | ...+++.+|..
T Consensus      1571 eInLp~~~~y~~~~vI~FlR~l~e~QGfw~s~~~~wvTI~~i~l~Gacnp~td~gRv~~~eRf~r--~-~v~vf~~ype~ 1647 (3164)
T COG5245        1571 EINLPYGFEYYPPTVIVFLRPLVERQGFWSSIAVSWVTICGIILYGACNPGTDEGRVKYYERFIR--K-PVFVFCCYPEL 1647 (3164)
T ss_pred             ccCCccccccCCCceEEeeHHHHHhcccccchhhhHhhhcceEEEccCCCCCCcccCccHHHHhc--C-ceEEEecCcch
Confidence            99932222222223222332   235677631     123567778999876542     44554  3 26788999999


Q ss_pred             HHHHHHHHHHhc
Q 011664          350 SSFKTLASSYLG  361 (480)
Q Consensus       350 ~~r~~il~~~l~  361 (480)
                      .....|...++.
T Consensus      1648 ~SL~~Iyea~l~ 1659 (3164)
T COG5245        1648 ASLRNIYEAVLM 1659 (3164)
T ss_pred             hhHHHHHHHHHH
Confidence            999888887764

>cd01394 radB RadB

Probab=97.73  E-value=0.00014  Score=69.67  Aligned_cols=39  Identities=31%  Similarity=0.401  Sum_probs=31.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      |++...-++++||||||||+++..+|.+.   +.++++++..
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~g~~v~yi~~e   56 (218)
T cd01394          15 GVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTE   56 (218)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEECC
Confidence            56666678999999999999999998654   5677777654

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

>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=97.73  E-value=0.00038  Score=73.38  Aligned_cols=130  Identities=15%  Similarity=0.173  Sum_probs=79.3

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc-CChHHHH---HHHHhhc--CCcEEEEecccccccCccc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV-ADDADLK---SLLLQTT--SKSVILIEDLDRFLVEKPA  293 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~-~~~~~l~---~l~~~~~--~~sII~IDEiD~l~~~~~~  293 (480)
                      ...++ -++++||-+||||++++.+...+...+++++..+. .....+.   ..+....  ....||+|||+++      
T Consensus        34 ~~~~~-i~~i~GpR~~GKTtll~~l~~~~~~~~iy~~~~d~~~~~~~l~d~~~~~~~~~~~~~~yifLDEIq~v------  106 (398)
T COG1373          34 DLRPF-IILILGPRQVGKTTLLKLLIKGLLEEIIYINFDDLRLDRIELLDLLRAYIELKEREKSYIFLDEIQNV------  106 (398)
T ss_pred             ccCCc-EEEEECCccccHHHHHHHHHhhCCcceEEEEecchhcchhhHHHHHHHHHHhhccCCceEEEecccCc------
Confidence            33343 78999999999999999888877655555554443 3333332   2222222  4589999999987      


Q ss_pred             ccchhhhhhhcccccccccCCceEEEEecCCCccC-cccccCCCceeEEEEcCCCCHHHHHH-------------HHHHH
Q 011664          294 AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV-DQALLRPGRIDVHIHFPLCDFSSFKT-------------LASSY  359 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L-D~aLlrpGRfd~~I~~~~p~~~~r~~-------------il~~~  359 (480)
                          .++...++.+...  +...++|.++|..-.+ ..+-.=|||. ..+++.+.++.++..             .+..|
T Consensus       107 ----~~W~~~lk~l~d~--~~~~v~itgsss~ll~~~~~~~L~GR~-~~~~l~PlSF~Efl~~~~~~~~~~~~~~~f~~Y  179 (398)
T COG1373         107 ----PDWERALKYLYDR--GNLDVLITGSSSSLLSKEISESLAGRG-KDLELYPLSFREFLKLKGEEIEPSKLELLFEKY  179 (398)
T ss_pred             ----hhHHHHHHHHHcc--ccceEEEECCchhhhccchhhhcCCCc-eeEEECCCCHHHHHhhcccccchhHHHHHHHHH
Confidence                2233344443331  1114666666644322 2222335795 688999999999864             57777


Q ss_pred             hccC
Q 011664          360 LGLK  363 (480)
Q Consensus       360 l~~~  363 (480)
                      +..-
T Consensus       180 l~~G  183 (398)
T COG1373         180 LETG  183 (398)
T ss_pred             HHhC
Confidence            7543

>PRK07261 topology modulation protein; Provisional

Probab=97.72  E-value=5.8e-05  Score=70.12  Aligned_cols=100  Identities=16%  Similarity=0.183  Sum_probs=61.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG  306 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg  306 (480)
                      +++.|+||+||||||+.++..++.+.+.+|.-.+...                            .......+++..+..
T Consensus         3 i~i~G~~GsGKSTla~~l~~~~~~~~i~~D~~~~~~~----------------------------~~~~~~~~~~~~~~~   54 (171)
T PRK07261          3 IAIIGYSGSGKSTLARKLSQHYNCPVLHLDTLHFQPN----------------------------WQERDDDDMIADISN   54 (171)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHhCCCeEecCCEEeccc----------------------------cccCCHHHHHHHHHH
Confidence            7899999999999999999999888776653221100                            000011223333332


Q ss_pred             ccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          307 VLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       307 ~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      +..   . +. .|+-.|....+-+..+.  +.|.+|.+..|.......++++.+.
T Consensus        55 ~~~---~-~~-wIidg~~~~~~~~~~l~--~ad~vI~Ld~p~~~~~~R~lkR~~~  102 (171)
T PRK07261         55 FLL---K-HD-WIIDGNYSWCLYEERMQ--EADQIIFLNFSRFNCLYRAFKRYLK  102 (171)
T ss_pred             HHh---C-CC-EEEcCcchhhhHHHHHH--HCCEEEEEcCCHHHHHHHHHHHHHH
Confidence            222   2 23 34433433333234444  7899999999988888888888764

>PRK08118 topology modulation protein; Reviewed

Probab=97.68  E-value=8.6e-05  Score=68.74  Aligned_cols=100  Identities=17%  Similarity=0.154  Sum_probs=62.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD  305 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld  305 (480)
                      .|++.||||+||||+|+.+++.++.+++.+|.--+.              |.-      .    .. .......++..+ 
T Consensus         3 rI~I~G~~GsGKSTlak~L~~~l~~~~~~lD~l~~~--------------~~w------~----~~-~~~~~~~~~~~~-   56 (167)
T PRK08118          3 KIILIGSGGSGKSTLARQLGEKLNIPVHHLDALFWK--------------PNW------E----GV-PKEEQITVQNEL-   56 (167)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCceecchhhcc--------------cCC------c----CC-CHHHHHHHHHHH-
Confidence            489999999999999999999999998888732110              000      0    00 000111122211 


Q ss_pred             cccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          306 GVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       306 g~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                        ..   .++  .|+-.|.+..++..+ .  +.|..|.+..|...-...++++.+.
T Consensus        57 --~~---~~~--wVidG~~~~~~~~~l-~--~~d~vi~Ld~p~~~~~~R~~~R~~~  102 (167)
T PRK08118         57 --VK---EDE--WIIDGNYGGTMDIRL-N--AADTIIFLDIPRTICLYRAFKRRVQ  102 (167)
T ss_pred             --hc---CCC--EEEeCCcchHHHHHH-H--hCCEEEEEeCCHHHHHHHHHHHHHH
Confidence              11   122  344555555565443 2  7899999999988887888888764

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=97.67  E-value=0.00016  Score=70.46  Aligned_cols=102  Identities=25%  Similarity=0.354  Sum_probs=57.3

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC---------------------------------Ch
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA---------------------------------DD  263 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~---------------------------------~~  263 (480)
                      |.+...-+++.||||||||+++..++..+   |....+++...-.                                 +.
T Consensus        20 gi~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~g~~~~yi~~e~~~~~~~~~~~~~g~~~~~~~~~~~l~~~~~~~~~~~~   99 (230)
T PRK08533         20 GIPAGSLILIEGDESTGKSILSQRLAYGFLQNGYSVSYVSTQLTTTEFIKQMMSLGYDINKKLISGKLLYIPVYPLLSGN   99 (230)
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEeCCCCHHHHHHHHHHhCCchHHHhhcCcEEEEEecccccCh
Confidence            46666779999999999999975554422   5566666532110                                 00


Q ss_pred             ----HHHHHHHHh--hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          264 ----ADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       264 ----~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                          ..+..++..  ...|.+++||++-.......+......+++.+..+..    .+..+++|++..
T Consensus       100 ~~~~~~l~~il~~~~~~~~~~lVIDe~t~~l~~~~d~~~~~~l~~~l~~l~~----~g~tvi~t~~~~  163 (230)
T PRK08533        100 SEKRKFLKKLMNTRRFYEKDVIIIDSLSSLISNDASEVAVNDLMAFFKRISS----LNKVIILTANPK  163 (230)
T ss_pred             HHHHHHHHHHHHHHHhcCCCEEEEECccHHhcCCcchHHHHHHHHHHHHHHh----CCCEEEEEeccc
Confidence                111122222  1368999999998865322222233445555544433    234666666633

>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]

Probab=97.66  E-value=0.0027  Score=64.82  Aligned_cols=207  Identities=16%  Similarity=0.213  Sum_probs=124.1

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEE
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVY  253 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~  253 (480)
                      ....++..+...|+.+++....-+.+.+....+       .-    ..-.+|+.|..||||-.+|+|.....   ..+|+
T Consensus       191 ~~~~~~~~~~~~F~~~v~~S~~mk~~v~qA~k~-------Am----lDAPLLI~GeTGTGKdLlAkaCH~~S~R~~~pFl  259 (511)
T COG3283         191 QLQNVAAQDVSGFEQIVAVSPKMKHVVEQAQKL-------AM----LDAPLLITGETGTGKDLLAKACHLASPRHSKPFL  259 (511)
T ss_pred             HHhhcccccccchHHHhhccHHHHHHHHHHHHh-------hc----cCCCeEEecCCCchHHHHHHHHhhcCcccCCCee
Confidence            345566777788999999887777666544433       11    12359999999999999999987654   67899


Q ss_pred             EEeCCCcCChHHHHHHHHhh------------cCCcEEEEecccccccCcccccchhhhhhhc-ccccccccCC-----c
Q 011664          254 DVDLSRVADDADLKSLLLQT------------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFM-DGVLNSCCFE-----E  315 (480)
Q Consensus       254 ~i~~s~~~~~~~l~~l~~~~------------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~l-dg~~~~~~~~-----~  315 (480)
                      .++|..+-.+..-.++|..+            ....-+|+|||..+.+     .....||.++ ||-..+...+     +
T Consensus       260 alNCA~lPe~~aEsElFG~apg~~gk~GffE~AngGTVlLDeIgEmSp-----~lQaKLLRFL~DGtFRRVGee~Ev~vd  334 (511)
T COG3283         260 ALNCASLPEDAAESELFGHAPGDEGKKGFFEQANGGTVLLDEIGEMSP-----RLQAKLLRFLNDGTFRRVGEDHEVHVD  334 (511)
T ss_pred             EeecCCCchhHhHHHHhcCCCCCCCccchhhhccCCeEEeehhhhcCH-----HHHHHHHHHhcCCceeecCCcceEEEE
Confidence            99999887654445555433            3457889999987743     3345566666 3433211111     2


Q ss_pred             eEEEEecCCC--c-----cCcccccCCCceeEEEEcCCCCHHHH----HHHHHHHhccCCCCCchhHHHHHHhCCCCCHH
Q 011664          316 RVMVFTMNSK--D-----HVDQALLRPGRIDVHIHFPLCDFSSF----KTLASSYLGLKDHKLFPQVEEIFQNGSSLSPA  384 (480)
Q Consensus       316 ~ivI~tTN~~--~-----~LD~aLlrpGRfd~~I~~~~p~~~~r----~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~a  384 (480)
                      +-||+||..+  +     ..-+.|.-  |+. +..+..|...+|    .-+.+.++...       -+++......+++.
T Consensus       335 VRVIcatq~nL~~lv~~g~fReDLfy--RLN-VLtl~~PpLRer~~di~pL~e~Fv~q~-------s~elg~p~pkl~~~  404 (511)
T COG3283         335 VRVICATQVNLVELVQKGKFREDLFY--RLN-VLTLNLPPLRERPQDIMPLAELFVQQF-------SDELGVPRPKLAAD  404 (511)
T ss_pred             EEEEecccccHHHHHhcCchHHHHHH--Hhh-eeeecCCccccCcccchHHHHHHHHHH-------HHHhCCCCCccCHH
Confidence            4578888654  1     12233333  553 444444443333    22333332110       12222223456666


Q ss_pred             HHHHHHHHhhhcHHHHHHHHHHHHH
Q 011664          385 EIGELMIANRNSPSRALKSVITALQ  409 (480)
Q Consensus       385 dI~~ll~~a~~~~~~al~~~i~~~~  409 (480)
                      -+..+....|...++.+++++-...
T Consensus       405 ~~~~L~~y~WpGNVRqL~N~iyRA~  429 (511)
T COG3283         405 LLTVLTRYAWPGNVRQLKNAIYRAL  429 (511)
T ss_pred             HHHHHHHcCCCccHHHHHHHHHHHH
Confidence            6666666678888888888764443

>COG1485 Predicted ATPase [General function prediction only]

Probab=97.65  E-value=5e-05  Score=77.23  Aligned_cols=98  Identities=17%  Similarity=0.231  Sum_probs=59.9

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCCcE-EEEeCCCc-----------CChHHHHHHHH-h-hcCCcEEEEeccccc
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSYDV-YDVDLSRV-----------ADDADLKSLLL-Q-TTSKSVILIEDLDRF  287 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~-~~i~~s~~-----------~~~~~l~~l~~-~-~~~~sII~IDEiD~l  287 (480)
                      .+++|+.||||-|+|||+|+-..-..+-.+- ..+-...+           .+.++.....+ + ..+-.||+|||+.--
T Consensus        63 ~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh~FM~~vH~~l~~l~g~~dpl~~iA~~~~~~~~vLCfDEF~Vt  142 (367)
T COG1485          63 GPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFHRFMARVHQRLHTLQGQTDPLPPIADELAAETRVLCFDEFEVT  142 (367)
T ss_pred             CCCceEEEECCCCccHHHHHHHHHhhCCccccccccHHHHHHHHHHHHHHHcCCCCccHHHHHHHHhcCCEEEeeeeeec
Confidence            4678999999999999999999887663321 11111111           11111000111 1 124479999999732


Q ss_pred             ccCcccccchhhhhhhcccccccccCCceEEEEecC-CCccC
Q 011664          288 LVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKDHV  328 (480)
Q Consensus       288 ~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~~L  328 (480)
                        +-.+...++.|++.|=       .+++++|+|+| .|+.|
T Consensus       143 --DI~DAMiL~rL~~~Lf-------~~GV~lvaTSN~~P~~L  175 (367)
T COG1485         143 --DIADAMILGRLLEALF-------ARGVVLVATSNTAPDNL  175 (367)
T ss_pred             --ChHHHHHHHHHHHHHH-------HCCcEEEEeCCCChHHh
Confidence              3445566777777662       35788999999 55655

>TIGR02012 tigrfam_recA protein RecA

Probab=97.64  E-value=0.00011  Score=75.03  Aligned_cols=101  Identities=19%  Similarity=0.305  Sum_probs=59.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC----------------------hHHHH--HHHHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD----------------------DADLK--SLLLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~----------------------~~~l~--~l~~~  272 (480)
                      |++..+.++++||||||||+|+..++.+.   |..+.+++...-.+                      +..+.  ..+.+
T Consensus        51 Glp~G~iteI~G~~GsGKTtLaL~~~~~~~~~g~~v~yId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~~~~~li~  130 (321)
T TIGR02012        51 GLPRGRIIEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYARKLGVDIDNLLVSQPDTGEQALEIAETLVR  130 (321)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEcccchhHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            56666678999999999999988765433   56677776533111                      11111  11223


Q ss_pred             hcCCcEEEEecccccccCcc------c------ccchhhhhhhcccccccccCCceEEEEecC
Q 011664          273 TTSKSVILIEDLDRFLVEKP------A------AVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~~~~------~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      ...+.+|+||-+.++.+..+      +      .+.+++++..|.+...   ..+..+|+|..
T Consensus       131 ~~~~~lIVIDSv~al~~~~E~e~~~g~~~~~~~aR~m~~~lr~L~~~l~---~~~~tvi~tNQ  190 (321)
T TIGR02012       131 SGAVDIIVVDSVAALVPKAEIEGEMGDSHVGLQARLMSQALRKLTGALS---KSNTTAIFINQ  190 (321)
T ss_pred             ccCCcEEEEcchhhhccchhhcccccccchhHHHHHHHHHHHHHHHHHH---hCCCEEEEEec
Confidence            35789999999998875311      0      1223445555555443   45566666543

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=97.63  E-value=0.00017  Score=70.13  Aligned_cols=38  Identities=26%  Similarity=0.330  Sum_probs=30.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~  257 (480)
                      |++....++++||||||||+++.+++.+   .|.+++++++
T Consensus        21 G~~~g~~~~i~G~~GsGKt~l~~~~~~~~~~~g~~~~y~~~   61 (234)
T PRK06067         21 GIPFPSLILIEGDHGTGKSVLSQQFVYGALKQGKKVYVITT   61 (234)
T ss_pred             CCcCCcEEEEECCCCCChHHHHHHHHHHHHhCCCEEEEEEc
Confidence            6777788999999999999999999754   3667776664

>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=97.62  E-value=0.00024  Score=69.34  Aligned_cols=23  Identities=35%  Similarity=0.551  Sum_probs=20.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      =+-+.||+|||||||.+.||+..
T Consensus        31 fvsilGpSGcGKSTLLriiAGL~   53 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAGLE   53 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            37789999999999999999855

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=97.61  E-value=9.5e-05  Score=65.04  Aligned_cols=53  Identities=15%  Similarity=0.085  Sum_probs=42.0

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..|.|++-+++.|...+..++..+.-      ..|--+-|+||||||||.+++.||+.+
T Consensus        25 ~~l~GQhla~~~v~~ai~~~l~~~~p------~KpLVlSfHG~tGtGKn~v~~liA~~l   77 (127)
T PF06309_consen   25 RNLFGQHLAVEVVVNAIKGHLANPNP------RKPLVLSFHGWTGTGKNFVSRLIAEHL   77 (127)
T ss_pred             HHccCcHHHHHHHHHHHHHHHcCCCC------CCCEEEEeecCCCCcHHHHHHHHHHHH
Confidence            35889999999999999999866421      122344599999999999999999874

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

>TIGR01618 phage_P_loop phage nucleotide-binding protein

Probab=97.60  E-value=6.1e-05  Score=72.83  Aligned_cols=23  Identities=39%  Similarity=0.690  Sum_probs=20.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      +.-+|+||+||+|||++|+.++.
T Consensus        12 ~~~~liyG~~G~GKtt~a~~~~~   34 (220)
T TIGR01618        12 PNMYLIYGKPGTGKTSTIKYLPG   34 (220)
T ss_pred             CcEEEEECCCCCCHHHHHHhcCC
Confidence            34599999999999999999974

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.

>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]

Probab=97.59  E-value=5.1e-05  Score=83.91  Aligned_cols=161  Identities=20%  Similarity=0.174  Sum_probs=85.8

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe-CCCcCC-----
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD-LSRVAD-----  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~-~s~~~~-----  262 (480)
                      -.|.|++++|+.|.=  ..|--.++.....+ +.---++||.|-||||||.|.+.+++.+-..+|.-- .++-.+     
T Consensus       286 PsIyG~e~VKkAilL--qLfgGv~k~~~~g~~iRGDInILLvGDPgtaKSqlLk~v~~~aPr~vytsgkgss~~GLTAav  363 (682)
T COG1241         286 PSIYGHEDVKKAILL--QLFGGVKKNLPDGTRIRGDIHILLVGDPGTAKSQLLKYVAKLAPRGVYTSGKGSSAAGLTAAV  363 (682)
T ss_pred             ccccCcHHHHHHHHH--HhcCCCcccCCCCcccccceeEEEcCCCchhHHHHHHHHHhhCCceEEEccccccccCceeEE
Confidence            467888888888752  22211111111100 001125899999999999999999987765555321 111111     


Q ss_pred             --hHHHHHHHHh-----hcCCcEEEEecccccccCcccccchhhhhhhcc---------cccccccCCceEEEEecCCCc
Q 011664          263 --DADLKSLLLQ-----TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD---------GVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 --~~~l~~l~~~-----~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld---------g~~~~~~~~~~ivI~tTN~~~  326 (480)
                        +...-+...+     ...++|.+|||+|.+-.     ...+.+...|+         |+.. .-+...-|++|+|.+.
T Consensus       364 ~rd~~tge~~LeaGALVlAD~Gv~cIDEfdKm~~-----~dr~aihEaMEQQtIsIaKAGI~a-tLnARcsvLAAaNP~~  437 (682)
T COG1241         364 VRDKVTGEWVLEAGALVLADGGVCCIDEFDKMNE-----EDRVAIHEAMEQQTISIAKAGITA-TLNARCSVLAAANPKF  437 (682)
T ss_pred             EEccCCCeEEEeCCEEEEecCCEEEEEeccCCCh-----HHHHHHHHHHHhcEeeecccceee-ecchhhhhhhhhCCCC
Confidence              1100011111     14689999999998732     22234444443         1111 0011123566777553


Q ss_pred             -------------cCcccccCCCceeEEEEc-CCCCHHHHHHHHHHHh
Q 011664          327 -------------HVDQALLRPGRIDVHIHF-PLCDFSSFKTLASSYL  360 (480)
Q Consensus       327 -------------~LD~aLlrpGRfd~~I~~-~~p~~~~r~~il~~~l  360 (480)
                                   +|+++|++  |||..+-+ ..|+.+.=..++...+
T Consensus       438 Gryd~~~~~~enI~l~~~lLS--RFDLifvl~D~~d~~~D~~ia~hil  483 (682)
T COG1241         438 GRYDPKKTVAENINLPAPLLS--RFDLIFVLKDDPDEEKDEEIAEHIL  483 (682)
T ss_pred             CcCCCCCCHHHhcCCChhHHh--hCCeeEEecCCCCccchHHHHHHHH
Confidence                         36789999  99965544 4566654344444433

>COG3267 ExeA Type II secretory pathway, component ExeA (predicted ATPase) [Intracellular trafficking and secretion]

Probab=97.58  E-value=0.0012  Score=64.72  Aligned_cols=157  Identities=18%  Similarity=0.235  Sum_probs=88.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCc-E--EEEeCCCcCC--------------------------hHHHHHHHHhhcCCc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYD-V--YDVDLSRVAD--------------------------DADLKSLLLQTTSKS  277 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~-~--~~i~~s~~~~--------------------------~~~l~~l~~~~~~~s  277 (480)
                      +.++|+-|||||.+.+|+...+.-+ +  +.++-..+..                          +..+..++.+-..|-
T Consensus        54 ~~vtGevGsGKTv~~Ral~~s~~~d~~~~v~i~~~~~s~~~~~~ai~~~l~~~p~~~~~~~~e~~~~~L~al~~~g~r~v  133 (269)
T COG3267          54 LAVTGEVGSGKTVLRRALLASLNEDQVAVVVIDKPTLSDATLLEAIVADLESQPKVNVNAVLEQIDRELAALVKKGKRPV  133 (269)
T ss_pred             EEEEecCCCchhHHHHHHHHhcCCCceEEEEecCcchhHHHHHHHHHHHhccCccchhHHHHHHHHHHHHHHHHhCCCCe
Confidence            5689999999999999887766432 2  2333222211                          111222333445678


Q ss_pred             EEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc--------cccCCCceeEEEEcCCCCH
Q 011664          278 VILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ--------ALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       278 II~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~--------aLlrpGRfd~~I~~~~p~~  349 (480)
                      ++++||.+.+..     ..+..+.-++.........-.++.|+   .| .|.+        .+..  |++..|++++.+.
T Consensus       134 ~l~vdEah~L~~-----~~le~Lrll~nl~~~~~~~l~ivL~G---qp-~L~~~lr~~~l~e~~~--R~~ir~~l~P~~~  202 (269)
T COG3267         134 VLMVDEAHDLND-----SALEALRLLTNLEEDSSKLLSIVLIG---QP-KLRPRLRLPVLRELEQ--RIDIRIELPPLTE  202 (269)
T ss_pred             EEeehhHhhhCh-----hHHHHHHHHHhhcccccCceeeeecC---Cc-ccchhhchHHHHhhhh--eEEEEEecCCcCh
Confidence            999999998742     22233222222222201112233333   11 2333        2334  8988899999999


Q ss_pred             HHHHHHHHHHhccC--CCCCch--hHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          350 SSFKTLASSYLGLK--DHKLFP--QVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       350 ~~r~~il~~~l~~~--~~~l~~--~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      ++-...++..++..  +.+++.  -+..+.....| .|..|.++|..|..
T Consensus       203 ~~t~~yl~~~Le~a~~~~~l~~~~a~~~i~~~sqg-~P~lin~~~~~Al~  251 (269)
T COG3267         203 AETGLYLRHRLEGAGLPEPLFSDDALLLIHEASQG-IPRLINNLATLALD  251 (269)
T ss_pred             HHHHHHHHHHHhccCCCcccCChhHHHHHHHHhcc-chHHHHHHHHHHHH
Confidence            97777777777643  223332  33455556656 68888888766544

>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=97.57  E-value=4.2e-05  Score=67.88  Aligned_cols=28  Identities=36%  Similarity=0.579  Sum_probs=24.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ++++||||||||++|+.++..++..++.
T Consensus         2 ii~~G~pgsGKSt~a~~l~~~~~~~~i~   29 (143)
T PF13671_consen    2 IILCGPPGSGKSTLAKRLAKRLGAVVIS   29 (143)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHSTEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCEEEe
Confidence            6899999999999999999999944433

...

>PRK13947 shikimate kinase; Provisional

Probab=97.55  E-value=6.9e-05  Score=68.92  Aligned_cols=31  Identities=32%  Similarity=0.544  Sum_probs=29.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .|+|.|+||||||++++.+|+.+|.++++.+
T Consensus         3 ~I~l~G~~GsGKst~a~~La~~lg~~~id~d   33 (171)
T PRK13947          3 NIVLIGFMGTGKTTVGKRVATTLSFGFIDTD   33 (171)
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            5899999999999999999999999998876

>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants

Probab=97.55  E-value=6.6e-05  Score=67.50  Aligned_cols=31  Identities=26%  Similarity=0.459  Sum_probs=28.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .|+|+||||+|||++++.+|..++.+++..+
T Consensus         1 ~i~l~G~~GsGKstla~~la~~l~~~~~~~d   31 (154)
T cd00464           1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD   31 (154)
T ss_pred             CEEEEcCCCCCHHHHHHHHHHHhCCCEEEch
Confidence            3799999999999999999999999988765

Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.

>PRK09361 radB DNA repair and recombination protein RadB; Provisional

Probab=97.55  E-value=0.00017  Score=69.66  Aligned_cols=39  Identities=26%  Similarity=0.377  Sum_probs=32.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      |++...-++++||||||||+++..+|.+.   +.+++++++.
T Consensus        19 Gi~~g~i~~i~G~~GsGKT~l~~~la~~~~~~~~~v~yi~~e   60 (225)
T PRK09361         19 GFERGTITQIYGPPGSGKTNICLQLAVEAAKNGKKVIYIDTE   60 (225)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            56666678999999999999999998643   7788888876

>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]

Probab=97.54  E-value=0.00031  Score=82.29  Aligned_cols=127  Identities=17%  Similarity=0.294  Sum_probs=83.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-----------h--HH--H--HHHHHhhcCCcEEEEecccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-----------D--AD--L--KSLLLQTTSKSVILIEDLDR  286 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-----------~--~~--l--~~l~~~~~~~sII~IDEiD~  286 (480)
                      .+++||-|.||.|||+|+.|+|+..|-..+.|++|+-.+           +  .+  +  ..++.......-+++||+..
T Consensus      1543 ~kpilLEGsPGVGKTSlItaLAr~tG~kliRINLSeQTdL~DLfGsd~Pve~~Gef~w~dapfL~amr~G~WVlLDEiNL 1622 (4600)
T COG5271        1543 GKPILLEGSPGVGKTSLITALARKTGKKLIRINLSEQTDLCDLFGSDLPVEEGGEFRWMDAPFLHAMRDGGWVLLDEINL 1622 (4600)
T ss_pred             CCceeecCCCCccHHHHHHHHHHHhcCceEEeeccccchHHHHhCCCCCcccCceeEecccHHHHHhhcCCEEEeehhhh
Confidence            467999999999999999999999999999999876432           1  01  0  12234456678899999984


Q ss_pred             cccCcccccchhhhhhhcc-----------cccccccCCceEEEEecCCC------ccCcccccCCCceeEEEEcCCCCH
Q 011664          287 FLVEKPAAVSLSGVLNFMD-----------GVLNSCCFEERVMVFTMNSK------DHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       287 l~~~~~~~~~ls~lL~~ld-----------g~~~~~~~~~~ivI~tTN~~------~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                      .     ++..+.+|-..+|           ...+  |..+-.|++|-|..      ..|+..++.  ||. +|.+...+.
T Consensus      1623 a-----SQSVlEGLNacLDhR~eayIPEld~~f~--~HpnfrVFAaqNPq~qggGRKgLPkSF~n--RFs-vV~~d~lt~ 1692 (4600)
T COG5271        1623 A-----SQSVLEGLNACLDHRREAYIPELDKTFD--VHPNFRVFAAQNPQDQGGGRKGLPKSFLN--RFS-VVKMDGLTT 1692 (4600)
T ss_pred             h-----HHHHHHHHHHHHhhccccccccccceee--ccCCeeeeeecCchhcCCCcccCCHHHhh--hhh-eEEeccccc
Confidence            3     2233344444443           2222  12233344444432      347888888  995 788888877


Q ss_pred             HHHHHHHHHHh
Q 011664          350 SSFKTLASSYL  360 (480)
Q Consensus       350 ~~r~~il~~~l  360 (480)
                      +....|+....
T Consensus      1693 dDi~~Ia~~~y 1703 (4600)
T COG5271        1693 DDITHIANKMY 1703 (4600)
T ss_pred             chHHHHHHhhC
Confidence            77666665544

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

Probab=97.53  E-value=0.00026  Score=68.07  Aligned_cols=40  Identities=23%  Similarity=0.248  Sum_probs=31.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---C------CcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---S------YDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~------~~~~~i~~s~  259 (480)
                      |++...-+.++||||+|||+++..+|...   +      ..+++++...
T Consensus        15 G~~~g~v~~I~G~~GsGKT~l~~~ia~~~~~~~~~~g~~~~v~yi~~e~   63 (226)
T cd01393          15 GIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYIDTEG   63 (226)
T ss_pred             CCcCCcEEEEeCCCCCChhHHHHHHHHHhhcccccCCCcceEEEEecCC
Confidence            56666778999999999999999998643   3      5667777644

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK03839 putative kinase; Provisional

Probab=97.52  E-value=6.9e-05  Score=69.74  Aligned_cols=30  Identities=23%  Similarity=0.503  Sum_probs=27.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      |+|.|+||+||||+++.+|+.+++++++++
T Consensus         3 I~l~G~pGsGKsT~~~~La~~~~~~~id~d   32 (180)
T PRK03839          3 IAITGTPGVGKTTVSKLLAEKLGYEYVDLT   32 (180)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEehh
Confidence            889999999999999999999999887754

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=97.50  E-value=0.00028  Score=70.36  Aligned_cols=121  Identities=19%  Similarity=0.272  Sum_probs=72.6

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CC--cEE--EEeCCCcCCh
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SY--DVY--DVDLSRVADD  263 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~--~~~--~i~~s~~~~~  263 (480)
                      .|.|+.-+++.|...+..++.++.-      ..|-.+=|+|+|||||+..++.||+.+   |.  +++  .+.-..+-.+
T Consensus        83 ~lfGQHla~~~Vv~alk~~~~n~~p------~KPLvLSfHG~tGTGKN~Va~iiA~n~~~~Gl~S~~V~~fvat~hFP~~  156 (344)
T KOG2170|consen   83 ALFGQHLAKQLVVNALKSHWANPNP------RKPLVLSFHGWTGTGKNYVAEIIAENLYRGGLRSPFVHHFVATLHFPHA  156 (344)
T ss_pred             HhhchHHHHHHHHHHHHHHhcCCCC------CCCeEEEecCCCCCchhHHHHHHHHHHHhccccchhHHHhhhhccCCCh
Confidence            4789999999999999988776531      112234488999999999999999865   22  111  1111111112


Q ss_pred             H-------HHHHHH---HhhcCCcEEEEecccccccCcccccchhhhhhhcccccc------cccCCceEEEEecCCCc
Q 011664          264 A-------DLKSLL---LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN------SCCFEERVMVFTMNSKD  326 (480)
Q Consensus       264 ~-------~l~~l~---~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~------~~~~~~~ivI~tTN~~~  326 (480)
                      +       +++..+   .+..+.+|.++||+|.+-         ++|+..+.++..      .....+-|+|+-+|.-.
T Consensus       157 ~~ie~Yk~eL~~~v~~~v~~C~rslFIFDE~DKmp---------~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg  226 (344)
T KOG2170|consen  157 SKIEDYKEELKNRVRGTVQACQRSLFIFDEVDKLP---------PGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGG  226 (344)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCceEEechhhhcC---------HhHHHHHhhhhccccccccccccceEEEEEcCCcc
Confidence            1       122222   223578999999999884         333333322211      01235668888887543

>PRK05973 replicative DNA helicase; Provisional

Probab=97.49  E-value=0.00057  Score=66.88  Aligned_cols=38  Identities=18%  Similarity=-0.000  Sum_probs=28.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      |.++..-+++.|+||+|||+++-.+|.+.   |.+++++++
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~Ge~vlyfSl  100 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKSGRTGVFFTL  100 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEEE
Confidence            55566678999999999999998876543   666655553

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

Probab=97.48  E-value=0.00024  Score=72.53  Aligned_cols=70  Identities=19%  Similarity=0.323  Sum_probs=46.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCCcCC---------------------hHHHHHH---HHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSRVAD---------------------DADLKSL---LLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~~~~---------------------~~~l~~l---~~~  272 (480)
                      |++..+-+.+|||||||||+|+-.++.+   .|....+++...-.+                     ..+....   +.+
T Consensus        51 Glp~G~iteI~Gp~GsGKTtLal~~~~~~~~~g~~~vyId~E~~~~~~~a~~lGvd~~~l~v~~p~~~eq~l~i~~~li~  130 (325)
T cd00983          51 GYPKGRIIEIYGPESSGKTTLALHAIAEAQKLGGTVAFIDAEHALDPVYAKKLGVDLDNLLISQPDTGEQALEIADSLVR  130 (325)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCCEEEECccccHHHHHHHHcCCCHHHheecCCCCHHHHHHHHHHHHh
Confidence            5666667889999999999999987643   366777776533111                     1111111   223


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|+||-+-++.+
T Consensus       131 s~~~~lIVIDSvaal~~  147 (325)
T cd00983         131 SGAVDLIVVDSVAALVP  147 (325)
T ss_pred             ccCCCEEEEcchHhhcc
Confidence            35789999999998875

RecA couples ATP hydrolysis to DNA strand exchange.

>PF10443 RNA12: RNA12 protein; InterPro: IPR018850 Mitochondrial escape protein 2 (also known as RNA12) plays a role in maintaining the mitochondrial genome and in controlling mtDNA escape [, ]

Probab=97.47  E-value=0.0033  Score=65.96  Aligned_cols=126  Identities=17%  Similarity=0.171  Sum_probs=73.7

Q ss_pred             CcEEEEecccccccCcccccchhhhhhhcc-cccccccCCceEEEEecC--CCccCcccccCCCceeEEEEcCCCCHHHH
Q 011664          276 KSVILIEDLDRFLVEKPAAVSLSGVLNFMD-GVLNSCCFEERVMVFTMN--SKDHVDQALLRPGRIDVHIHFPLCDFSSF  352 (480)
Q Consensus       276 ~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-g~~~~~~~~~~ivI~tTN--~~~~LD~aLlrpGRfd~~I~~~~p~~~~r  352 (480)
                      ..||+||.+..-...   +..+-..|..+- .+..  .+-..||+.|++  ....|..||  |.|.-+.|.++.++.+.-
T Consensus       149 ~PVVVIdnF~~k~~~---~~~iy~~laeWAa~Lv~--~nIAHVIFlT~dv~~~k~LskaL--Pn~vf~tI~L~Das~~~A  221 (431)
T PF10443_consen  149 RPVVVIDNFLHKAEE---NDFIYDKLAEWAASLVQ--NNIAHVIFLTDDVSYSKPLSKAL--PNRVFKTISLSDASPESA  221 (431)
T ss_pred             CCEEEEcchhccCcc---cchHHHHHHHHHHHHHh--cCccEEEEECCCCchhhhHHHhC--CCCceeEEeecCCCHHHH
Confidence            369999998753211   222222222111 1111  122345555544  234567777  448778999999999998


Q ss_pred             HHHHHHHhccCCC---------------------CCchhHHHHHHhCCCCCHHHHHHHHHH--hhhcHHHHHHHHHHHHH
Q 011664          353 KTLASSYLGLKDH---------------------KLFPQVEEIFQNGSSLSPAEIGELMIA--NRNSPSRALKSVITALQ  409 (480)
Q Consensus       353 ~~il~~~l~~~~~---------------------~l~~~i~~l~~~~~g~s~adI~~ll~~--a~~~~~~al~~~i~~~~  409 (480)
                      +..+...|.....                     ....+++...... |---.||+.++++  ....|..|++++++.-.
T Consensus       222 k~yV~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~eld~~i~~L-GGRltDLe~lvrRiksGe~p~~Av~~iI~qsa  300 (431)
T PF10443_consen  222 KQYVLSQLDEDTEDSSDSKESNEQNKNDKSAENEKDLAELDECIEPL-GGRLTDLEFLVRRIKSGESPEEAVEEIISQSA  300 (431)
T ss_pred             HHHHHHHhcccccccccccccccccccccccccccchHHHHHHHHHc-CCcHHHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence            8888888865311                     1223444444433 6666788888876  34678888888886543

It is also involved in the regulation of mtDNA nucleotide structure and number []. Additionally, this protein have a dispensable role in the early maturation of pre-rRNA [].

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=97.47  E-value=0.00042  Score=66.02  Aligned_cols=98  Identities=16%  Similarity=0.290  Sum_probs=55.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH-----cCCCcEE-------------EEeCCC-cC--------ChHHHHHHHHhhc--
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVY-------------DVDLSR-VA--------DDADLKSLLLQTT--  274 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~-----~l~~~~~-------------~i~~s~-~~--------~~~~l~~l~~~~~--  274 (480)
                      .+-++|.||+|+|||+++++++.     ..|.++.             .+...+ +.        .-..+..++....  
T Consensus        25 g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~l~~~~s~~~~e~~~~~~iL~~~~~~  104 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELPPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKG  104 (199)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcccceEEEeccchhccccccChHHHHHHHHHHHHHhccCC
Confidence            35789999999999999999985     3344321             111100 00        0123556666666  


Q ss_pred             CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          275 SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       275 ~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      .|.++++||.-.-............+++.+   ..    .+..+|++|..++.+
T Consensus       105 ~p~llllDEp~~glD~~~~~~l~~~ll~~l---~~----~~~tiiivTH~~~~~  151 (199)
T cd03283         105 EPVLFLLDEIFKGTNSRERQAASAAVLKFL---KN----KNTIGIISTHDLELA  151 (199)
T ss_pred             CCeEEEEecccCCCCHHHHHHHHHHHHHHH---HH----CCCEEEEEcCcHHHH
Confidence            899999999754322111111123344443   11    245677777766544

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid

>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]

Probab=97.46  E-value=0.00047  Score=63.05  Aligned_cols=24  Identities=21%  Similarity=0.434  Sum_probs=21.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      --+.+.||||+|||+++.-+|..+
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L   29 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKL   29 (179)
T ss_pred             eEEEEeCCCCccHHHHHHHHHHHH
Confidence            358999999999999999999766

>PRK00625 shikimate kinase; Provisional

Probab=97.46  E-value=0.0001  Score=68.77  Aligned_cols=31  Identities=39%  Similarity=0.675  Sum_probs=29.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .|+|.|+||+|||++++.+|+.++++++++|
T Consensus         2 ~I~LiG~pGsGKTT~~k~La~~l~~~~id~D   32 (173)
T PRK00625          2 QIFLCGLPTVGKTSFGKALAKFLSLPFFDTD   32 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCEEEhh
Confidence            4899999999999999999999999998886

>PRK13949 shikimate kinase; Provisional

Probab=97.46  E-value=0.0001  Score=68.41  Aligned_cols=31  Identities=29%  Similarity=0.495  Sum_probs=29.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .|+|.||||+|||++++.+|+.+++++++.|
T Consensus         3 ~I~liG~~GsGKstl~~~La~~l~~~~id~D   33 (169)
T PRK13949          3 RIFLVGYMGAGKTTLGKALARELGLSFIDLD   33 (169)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCCeeccc
Confidence            5999999999999999999999999988876

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=97.45  E-value=0.00027  Score=68.12  Aligned_cols=104  Identities=20%  Similarity=0.275  Sum_probs=55.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH-----cCCCcEE-------EEe--CCCcCC-----------hHH---HHHHHHhhcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS-----FMSYDVY-------DVD--LSRVAD-----------DAD---LKSLLLQTTSK  276 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~-----~l~~~~~-------~i~--~s~~~~-----------~~~---l~~l~~~~~~~  276 (480)
                      +.++|.||.|+|||++.+.++.     ..|..+.       ..+  .+.+..           ..+   +..++..+..+
T Consensus        30 ~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~~~~si~~~~S~f~~el~~l~~~l~~~~~~  109 (213)
T cd03281          30 SIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRR  109 (213)
T ss_pred             eEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeCCccChhhccchHHHHHHHHHHHHHhCCCC
Confidence            6799999999999999999983     2343221       110  111111           112   22333455789


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccc
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQAL  332 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aL  332 (480)
                      ++++|||+..-............++..+   .. .......+|++|...+.+....
T Consensus       110 slvllDE~~~gtd~~~~~~~~~ail~~l---~~-~~~~~~~vli~TH~~~l~~~~~  161 (213)
T cd03281         110 SLVLIDEFGKGTDTEDGAGLLIATIEHL---LK-RGPECPRVIVSTHFHELFNRSL  161 (213)
T ss_pred             cEEEeccccCCCCHHHHHHHHHHHHHHH---Hh-cCCCCcEEEEEcChHHHHHhhh
Confidence            9999999975432111112223344433   11 0012346777887666554443

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=97.45  E-value=0.00063  Score=68.35  Aligned_cols=37  Identities=24%  Similarity=0.302  Sum_probs=29.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC----C-CcEEEEeCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM----S-YDVYDVDLSRV  260 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l----~-~~~~~i~~s~~  260 (480)
                      ++.++|.||+|+|||+++..+|..+    | ..+..+++...
T Consensus       194 ~~vi~~vGptGvGKTTt~~kLa~~~~~~~g~~~V~li~~D~~  235 (282)
T TIGR03499       194 GGVIALVGPTGVGKTTTLAKLAARFVLEHGNKKVALITTDTY  235 (282)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHHcCCCeEEEEECCcc
Confidence            4468899999999999999999765    3 67777776654

>PRK05800 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated

Probab=97.44  E-value=0.00031  Score=65.28  Aligned_cols=63  Identities=27%  Similarity=0.399  Sum_probs=45.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH-----------------------HHHHHHHh-hcCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA-----------------------DLKSLLLQ-TTSKSVILI  281 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~-----------------------~l~~l~~~-~~~~sII~I  281 (480)
                      -+|+.||||||||++|..++..++.+++++......+++                       ++..++.. ..++.+++|
T Consensus         3 ~ili~G~~~sGKS~~a~~l~~~~~~~~~~iat~~~~~~e~~~ri~~h~~~R~~~w~t~E~~~~l~~~i~~~~~~~~~VlI   82 (170)
T PRK05800          3 LILVTGGARSGKSRFAERLAAQSGLQVLYIATAQPFDDEMAARIAHHRQRRPAHWQTVEEPLDLAELLRADAAPGRCVLV   82 (170)
T ss_pred             EEEEECCCCccHHHHHHHHHHHcCCCcEeCcCCCCChHHHHHHHHHHHhcCCCCCeEecccccHHHHHHhhcCCCCEEEe
Confidence            379999999999999999999988888888765544332                       12233333 344678999


Q ss_pred             ecccccc
Q 011664          282 EDLDRFL  288 (480)
Q Consensus       282 DEiD~l~  288 (480)
                      |-+..+.
T Consensus        83 D~Lt~~~   89 (170)
T PRK05800         83 DCLTTWV   89 (170)
T ss_pred             hhHHHHH
Confidence            9887764

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=97.43  E-value=0.00081  Score=68.09  Aligned_cols=154  Identities=16%  Similarity=0.212  Sum_probs=95.2

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHH-H--HcCCCcEEEEeCCCcCCh----
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAM-A--SFMSYDVYDVDLSRVADD----  263 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~ai-A--~~l~~~~~~i~~s~~~~~----  263 (480)
                      .+.|..+..+.+.+.+..-+-.       |  -..++++.||.|+|||.++... +  .+.|.+++.+.+......    
T Consensus        25 ~l~g~~~~~~~l~~~lkqt~~~-------g--EsnsviiigprgsgkT~li~~~Ls~~q~~~E~~l~v~Lng~~~~dk~a   95 (408)
T KOG2228|consen   25 NLFGVQDEQKHLSELLKQTILH-------G--ESNSVIIIGPRGSGKTILIDTRLSDIQENGENFLLVRLNGELQTDKIA   95 (408)
T ss_pred             ceeehHHHHHHHHHHHHHHHHh-------c--CCCceEEEccCCCCceEeeHHHHhhHHhcCCeEEEEEECccchhhHHH
Confidence            4567777777777666544332       2  2357999999999999877643 3  377889988877643211    


Q ss_pred             -----------------------HHHHHHHHh------hc-CCcEEEEecccccccCcccccchhhhhhhcccccccccC
Q 011664          264 -----------------------ADLKSLLLQ------TT-SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCF  313 (480)
Q Consensus       264 -----------------------~~l~~l~~~------~~-~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~  313 (480)
                                             ..+.+++..      .+ .+-|.++||+|.+++..    ...-+.|.+|-..+.  .
T Consensus        96 l~~I~rql~~e~~~~~k~~gsfte~l~~lL~~L~~~~~~t~~~ViFIldEfDlf~~h~----rQtllYnlfDisqs~--r  169 (408)
T KOG2228|consen   96 LKGITRQLALELNRIVKSFGSFTENLSKLLEALKKGDETTSGKVIFILDEFDLFAPHS----RQTLLYNLFDISQSA--R  169 (408)
T ss_pred             HHHHHHHHHHHHhhhheeecccchhHHHHHHHHhcCCCCCCceEEEEeehhhccccch----hhHHHHHHHHHHhhc--C
Confidence                                   111122211      11 23455567999886532    123466777766542  3


Q ss_pred             CceEEEEecCCC---ccCcccccCCCcee-EEEEcCCC-CHHHHHHHHHHHhc
Q 011664          314 EERVMVFTMNSK---DHVDQALLRPGRID-VHIHFPLC-DFSSFKTLASSYLG  361 (480)
Q Consensus       314 ~~~ivI~tTN~~---~~LD~aLlrpGRfd-~~I~~~~p-~~~~r~~il~~~l~  361 (480)
                      ..+.||+.|.+-   +.|.....+  ||. ++|+++++ ...+...+++..+.
T Consensus       170 ~Piciig~Ttrld~lE~LEKRVKS--RFshr~I~m~~~~~l~~yv~l~r~ll~  220 (408)
T KOG2228|consen  170 APICIIGVTTRLDILELLEKRVKS--RFSHRVIFMLPSLPLGDYVDLYRKLLS  220 (408)
T ss_pred             CCeEEEEeeccccHHHHHHHHHHh--hcccceeeccCCCChHHHHHHHHHHhc
Confidence            456677755443   556778888  998 44776654 56888888888874

>PRK13765 ATP-dependent protease Lon; Provisional

Probab=97.42  E-value=0.00029  Score=78.08  Aligned_cols=51  Identities=25%  Similarity=0.388  Sum_probs=42.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      +|..|++++|++++++.+...+..               ++.++|+||||||||++++++|..+..
T Consensus        26 ~~~~~~~vigq~~a~~~L~~~~~~---------------~~~~l~~G~~G~GKttla~~l~~~l~~   76 (637)
T PRK13765         26 PERLIDQVIGQEHAVEVIKKAAKQ---------------RRHVMMIGSPGTGKSMLAKAMAELLPK   76 (637)
T ss_pred             CcccHHHcCChHHHHHHHHHHHHh---------------CCeEEEECCCCCcHHHHHHHHHHHcCh
Confidence            578999999999998877754431               237999999999999999999998753

>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=97.41  E-value=0.0004  Score=68.93  Aligned_cols=91  Identities=18%  Similarity=0.379  Sum_probs=57.0

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEeCC-Cc
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVDLS-RV  260 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~~s-~~  260 (480)
                      .+.++++++-.+...+.+.+.+...++           ..+.+++.||+|||||++++++..++.   ..++.+.-. ++
T Consensus        99 ~~~sle~l~~~~~~~~~~~~~l~~~v~-----------~~~~ili~G~tGSGKTT~l~all~~i~~~~~~iv~iEd~~E~  167 (270)
T PF00437_consen   99 KPFSLEDLGESGSIPEEIAEFLRSAVR-----------GRGNILISGPTGSGKTTLLNALLEEIPPEDERIVTIEDPPEL  167 (270)
T ss_dssp             S--CHCCCCHTHHCHHHHHHHHHHCHH-----------TTEEEEEEESTTSSHHHHHHHHHHHCHTTTSEEEEEESSS-S
T ss_pred             ccccHhhccCchhhHHHHHHHHhhccc-----------cceEEEEECCCccccchHHHHHhhhccccccceEEeccccce
Confidence            455888988877766666655543322           256899999999999999999998773   445554311 11


Q ss_pred             -------------CChHHHHHHHHhh--cCCcEEEEecccc
Q 011664          261 -------------ADDADLKSLLLQT--TSKSVILIEDLDR  286 (480)
Q Consensus       261 -------------~~~~~l~~l~~~~--~~~sII~IDEiD~  286 (480)
                                   .+...+.+++..+  ..|++|+|.||-.
T Consensus       168 ~l~~~~~~~~~~~~~~~~~~~~l~~~LR~~pD~iiigEiR~  208 (270)
T PF00437_consen  168 RLPGPNQIQIQTRRDEISYEDLLKSALRQDPDVIIIGEIRD  208 (270)
T ss_dssp             --SCSSEEEEEEETTTBSHHHHHHHHTTS--SEEEESCE-S
T ss_pred             eecccceEEEEeecCcccHHHHHHHHhcCCCCcccccccCC
Confidence                         0122345555433  5799999999973

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 ....

>PF14516 AAA_35: AAA-like domain

Probab=97.41  E-value=0.0045  Score=63.61  Aligned_cols=161  Identities=16%  Similarity=0.185  Sum_probs=90.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC-----hHH------------------------------
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD-----DAD------------------------------  265 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~-----~~~------------------------------  265 (480)
                      ..-+.++||..+|||++...+.+.+   |+..+.+|+..+..     ...                              
T Consensus        31 G~~~~I~apRq~GKTSll~~l~~~l~~~~~~~v~id~~~~~~~~~~~~~~f~~~~~~~i~~~L~l~~~l~~~w~~~~~~~  110 (331)
T PF14516_consen   31 GSYIRIKAPRQMGKTSLLLRLLERLQQQGYRCVYIDLQQLGSAIFSDLEQFLRWFCEEISRQLKLDEKLDEYWDEEIGSK  110 (331)
T ss_pred             CCEEEEECcccCCHHHHHHHHHHHHHHCCCEEEEEEeecCCCcccCCHHHHHHHHHHHHHHHcCCChhHHHHHHHhcCCh
Confidence            3457899999999999999887654   78888888765432     000                              


Q ss_pred             --HHH-----HHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccccc----CCc-eEEEEecCCCccCccccc
Q 011664          266 --LKS-----LLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC----FEE-RVMVFTMNSKDHVDQALL  333 (480)
Q Consensus       266 --l~~-----l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~----~~~-~ivI~tTN~~~~LD~aLl  333 (480)
                        ...     ++.+...|-||+|||||.++....   ...+|+..+......+.    ... +++++.+..+......-.
T Consensus       111 ~~~~~~~~~~ll~~~~~~lVL~iDEiD~l~~~~~---~~~dF~~~LR~~~~~~~~~~~~~~L~li~~~~t~~~~~~~~~~  187 (331)
T PF14516_consen  111 ISCTEYFEEYLLKQIDKPLVLFIDEIDRLFEYPQ---IADDFFGLLRSWYEQRKNNPIWQKLRLILAGSTEDYIILDINQ  187 (331)
T ss_pred             hhHHHHHHHHHHhcCCCCEEEEEechhhhccCcc---hHHHHHHHHHHHHHhcccCcccceEEEEEecCcccccccCCCC
Confidence              000     112234678999999999975332   22344544433322110    011 233332222222211223


Q ss_pred             CCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          334 RPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       334 rpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      +|=-+...|.++.-+.++-..+++.|-....   ...++.+...+.| -|-=+..+|.
T Consensus       188 SPFNIg~~i~L~~Ft~~ev~~L~~~~~~~~~---~~~~~~l~~~tgG-hP~Lv~~~~~  241 (331)
T PF14516_consen  188 SPFNIGQPIELPDFTPEEVQELAQRYGLEFS---QEQLEQLMDWTGG-HPYLVQKACY  241 (331)
T ss_pred             CCcccccceeCCCCCHHHHHHHHHhhhccCC---HHHHHHHHHHHCC-CHHHHHHHHH
Confidence            4444556788888899998888887732211   1235666666644 4544444443

>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B

Probab=97.40  E-value=0.00042  Score=67.03  Aligned_cols=40  Identities=18%  Similarity=0.214  Sum_probs=30.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~  259 (480)
                      |++...-+.|+||||||||+++..+|...         +..+++++...
T Consensus        15 Gi~~g~i~~i~G~~GsGKT~l~~~l~~~~~~~~~~~g~~~~viyi~~e~   63 (235)
T cd01123          15 GIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYIDTEG   63 (235)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHeeCccccCCCCccEEEEeCCC
Confidence            56666678999999999999999997432         25677777654

This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=97.40  E-value=0.00042  Score=69.19  Aligned_cols=26  Identities=23%  Similarity=0.406  Sum_probs=23.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .++++.||||+|||++.+++++.+..
T Consensus       112 ~~~~i~g~~g~GKttl~~~l~~~~~~  137 (270)
T TIGR02858       112 LNTLIISPPQCGKTTLLRDLARILST  137 (270)
T ss_pred             eEEEEEcCCCCCHHHHHHHHhCccCC
Confidence            48999999999999999999998743

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.

>PRK11823 DNA repair protein RadA; Provisional

Probab=97.40  E-value=0.00033  Score=74.84  Aligned_cols=70  Identities=21%  Similarity=0.328  Sum_probs=48.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC--------------------hHHHHHHHH--hhc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD--------------------DADLKSLLL--QTT  274 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~--------------------~~~l~~l~~--~~~  274 (480)
                      |++...-+||+||||+|||+|+..+|...   +.++++++..+-..                    +..+..++.  +..
T Consensus        76 Gi~~Gs~~lI~G~pG~GKTtL~lq~a~~~a~~g~~vlYvs~Ees~~qi~~ra~rlg~~~~~l~~~~e~~l~~i~~~i~~~  155 (446)
T PRK11823         76 GLVPGSVVLIGGDPGIGKSTLLLQVAARLAAAGGKVLYVSGEESASQIKLRAERLGLPSDNLYLLAETNLEAILATIEEE  155 (446)
T ss_pred             CccCCEEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccccHHHHHHHHHHcCCChhcEEEeCCCCHHHHHHHHHhh
Confidence            56666678999999999999999998754   67788887543211                    111222222  224


Q ss_pred             CCcEEEEeccccccc
Q 011664          275 SKSVILIEDLDRFLV  289 (480)
Q Consensus       275 ~~sII~IDEiD~l~~  289 (480)
                      .|.+|+||.|..+..
T Consensus       156 ~~~lVVIDSIq~l~~  170 (446)
T PRK11823        156 KPDLVVIDSIQTMYS  170 (446)
T ss_pred             CCCEEEEechhhhcc
Confidence            789999999998764

>COG0703 AroK Shikimate kinase [Amino acid transport and metabolism]

Probab=97.39  E-value=0.00012  Score=67.89  Aligned_cols=32  Identities=31%  Similarity=0.457  Sum_probs=30.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.+.|.|++|+||||+.+++|+.++.+|++.|
T Consensus         3 ~~IvLiG~mGaGKSTIGr~LAk~L~~~F~D~D   34 (172)
T COG0703           3 MNIVLIGFMGAGKSTIGRALAKALNLPFIDTD   34 (172)
T ss_pred             ccEEEEcCCCCCHhHHHHHHHHHcCCCcccch
Confidence            46999999999999999999999999999987

>PF05272 VirE: Virulence-associated protein E; InterPro: IPR007936 This family contains several bacterial virulence-associated protein E like proteins

Probab=97.39  E-value=0.00031  Score=67.00  Aligned_cols=114  Identities=25%  Similarity=0.257  Sum_probs=65.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSG  299 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~  299 (480)
                      |......++|.|+.|+|||++++.|+.+     +..+......+.+.   .......-|+.+||++.+.  +.....+-.
T Consensus        48 g~k~d~~lvl~G~QG~GKStf~~~L~~~-----~~~d~~~~~~~kd~---~~~l~~~~iveldEl~~~~--k~~~~~lK~  117 (198)
T PF05272_consen   48 GCKNDTVLVLVGKQGIGKSTFFRKLGPE-----YFSDSINDFDDKDF---LEQLQGKWIVELDELDGLS--KKDVEALKS  117 (198)
T ss_pred             CCcCceeeeEecCCcccHHHHHHHHhHH-----hccCccccCCCcHH---HHHHHHhHheeHHHHhhcc--hhhHHHHHH
Confidence            5555667889999999999999999765     22221111122222   2233455799999999875  222223333


Q ss_pred             hhhhc-ccccc------cccCCceEEEEecCCCccC-cccccCCCceeEEEEcCC
Q 011664          300 VLNFM-DGVLN------SCCFEERVMVFTMNSKDHV-DQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       300 lL~~l-dg~~~------~~~~~~~ivI~tTN~~~~L-D~aLlrpGRfd~~I~~~~  346 (480)
                      ++..- +.+..      .......++|+|||..+-| |+.=-|  || ..|+++.
T Consensus       118 ~iT~~~~~~R~pY~~~~~~~~R~~~figTtN~~~~L~D~TGnR--Rf-~~v~v~~  169 (198)
T PF05272_consen  118 FITRRTDTYRPPYGRDPEEFPRRAVFIGTTNDDDFLKDPTGNR--RF-WPVEVSK  169 (198)
T ss_pred             HhcccceeeecCCcCcceeeceeEEEEeccCCcceeeCCCCCe--EE-EEEEEcC
Confidence            33221 11111      0112344678899987755 666667  88 4566554

>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules

Probab=97.38  E-value=0.00043  Score=62.91  Aligned_cols=98  Identities=16%  Similarity=0.260  Sum_probs=55.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc--EEEEeCCCc-----------------CChHHHHHH-HH--hhcCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD--VYDVDLSRV-----------------ADDADLKSL-LL--QTTSKSVILI  281 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~--~~~i~~s~~-----------------~~~~~l~~l-~~--~~~~~sII~I  281 (480)
                      ..-+.|.||+|+|||+|++++++.+...  -+.++...+                 .+..+.+++ ++  -..+|.++++
T Consensus        25 g~~~~i~G~nGsGKStll~~l~g~~~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS~G~~~r~~l~~~l~~~~~i~il  104 (157)
T cd00267          25 GEIVALVGPNGSGKSTLLRAIAGLLKPTSGEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALLLNPDLLLL  104 (157)
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCCCCccEEEECCEEcccCCHHHHHhceEEEeeCCHHHHHHHHHHHHHhcCCCEEEE
Confidence            3468899999999999999999876432  122221110                 111222222 22  2357999999


Q ss_pred             ecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          282 EDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       282 DEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                      ||...-+..    .+...+.+.+.....   . +..+|++|+.++.+.
T Consensus       105 DEp~~~lD~----~~~~~l~~~l~~~~~---~-~~tii~~sh~~~~~~  144 (157)
T cd00267         105 DEPTSGLDP----ASRERLLELLRELAE---E-GRTVIIVTHDPELAE  144 (157)
T ss_pred             eCCCcCCCH----HHHHHHHHHHHHHHH---C-CCEEEEEeCCHHHHH
Confidence            998864422    222333343333222   2 356677777665443

The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate

Probab=97.37  E-value=0.00016  Score=65.04  Aligned_cols=28  Identities=32%  Similarity=0.483  Sum_probs=24.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ++|+||||+|||++++.++..++..+++
T Consensus         2 i~l~G~~GsGKST~a~~l~~~~~~~~i~   29 (150)
T cd02021           2 IVVMGVSGSGKSTVGKALAERLGAPFID   29 (150)
T ss_pred             EEEEcCCCCCHHHHHHHHHhhcCCEEEe
Confidence            6899999999999999999998776554

The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.

>cd00544 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU)

Probab=97.36  E-value=0.00059  Score=63.43  Aligned_cols=62  Identities=31%  Similarity=0.382  Sum_probs=44.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh-----------------------HHHHHHHHhhcCCcEEEEec
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD-----------------------ADLKSLLLQTTSKSVILIED  283 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~-----------------------~~l~~l~~~~~~~sII~IDE  283 (480)
                      +|+.||||+|||++|..++...+.+.+++....-.+.                       .++.+.+.+...+.+|+||-
T Consensus         2 ~li~G~~~sGKS~~a~~~~~~~~~~~~y~at~~~~d~em~~rI~~H~~~R~~~w~t~E~~~~l~~~l~~~~~~~~VLIDc   81 (169)
T cd00544           2 ILVTGGARSGKSRFAERLAAELGGPVTYIATAEAFDDEMAERIARHRKRRPAHWRTIETPRDLVSALKELDPGDVVLIDC   81 (169)
T ss_pred             EEEECCCCCCHHHHHHHHHHhcCCCeEEEEccCcCCHHHHHHHHHHHHhCCCCceEeecHHHHHHHHHhcCCCCEEEEEc
Confidence            6899999999999999999888888888876543321                       12333333323567899998


Q ss_pred             ccccc
Q 011664          284 LDRFL  288 (480)
Q Consensus       284 iD~l~  288 (480)
                      +..+.
T Consensus        82 lt~~~   86 (169)
T cd00544          82 LTLWV   86 (169)
T ss_pred             HhHHH
Confidence            87654

CobU is bifunctional cobalbumin biosynthesis enzymes which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity. This enzyme is a homotrimer with a propeller-like shape.

>PRK14532 adenylate kinase; Provisional

Probab=97.36  E-value=0.00017  Score=67.58  Aligned_cols=30  Identities=20%  Similarity=0.366  Sum_probs=26.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .+++.||||||||++++.+|..+|+..++.
T Consensus         2 ~i~~~G~pGsGKsT~a~~la~~~g~~~is~   31 (188)
T PRK14532          2 NLILFGPPAAGKGTQAKRLVEERGMVQLST   31 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCeEEeC
Confidence            489999999999999999999998766554

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=97.35  E-value=0.0025  Score=66.97  Aligned_cols=76  Identities=16%  Similarity=0.287  Sum_probs=45.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc----CCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhh
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF----MSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSG  299 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~----l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~  299 (480)
                      ..++++.||||||||+++.+++.+    .|   ..+....+..+-. ...+.......+|+|||+..+.-.+. ...++.
T Consensus       209 ~~Nli~lGp~GTGKThla~~l~~~~a~~sG---~f~T~a~Lf~~L~-~~~lg~v~~~DlLI~DEvgylp~~~~-~~~v~i  283 (449)
T TIGR02688       209 NYNLIELGPKGTGKSYIYNNLSPYVILISG---GTITVAKLFYNIS-TRQIGLVGRWDVVAFDEVATLKFAKP-KELIGI  283 (449)
T ss_pred             CCcEEEECCCCCCHHHHHHHHhHHHHHHcC---CcCcHHHHHHHHH-HHHHhhhccCCEEEEEcCCCCcCCch-HHHHHH
Confidence            347999999999999999998876    23   1111212111111 13334456789999999998543222 222344


Q ss_pred             hhhhc
Q 011664          300 VLNFM  304 (480)
Q Consensus       300 lL~~l  304 (480)
                      |-+.|
T Consensus       284 mK~yM  288 (449)
T TIGR02688       284 LKNYM  288 (449)
T ss_pred             HHHHH
Confidence            44545

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.

>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family

Probab=97.35  E-value=0.00016  Score=67.19  Aligned_cols=28  Identities=18%  Similarity=0.395  Sum_probs=24.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      +++.||||||||++++.+|..+|...+.
T Consensus         2 i~i~G~pGsGKst~a~~la~~~~~~~is   29 (183)
T TIGR01359         2 VFVLGGPGSGKGTQCAKIVENFGFTHLS   29 (183)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEE
Confidence            6899999999999999999999864444

This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.

>PRK13948 shikimate kinase; Provisional

Probab=97.34  E-value=0.00022  Score=67.08  Aligned_cols=34  Identities=26%  Similarity=0.213  Sum_probs=31.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +++.++|.|++|||||++++.+|..++.+|++.|
T Consensus         9 ~~~~I~LiG~~GsGKSTvg~~La~~lg~~~iD~D   42 (182)
T PRK13948          9 PVTWVALAGFMGTGKSRIGWELSRALMLHFIDTD   42 (182)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCCEEECC
Confidence            5678999999999999999999999999999876

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=97.33  E-value=0.00074  Score=70.41  Aligned_cols=94  Identities=13%  Similarity=0.162  Sum_probs=53.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCC-Cc----------------CCh-HHHHHHHHh--hcCCcEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLS-RV----------------ADD-ADLKSLLLQ--TTSKSVI  279 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s-~~----------------~~~-~~l~~l~~~--~~~~sII  279 (480)
                      ..+|++||+|+||||+++++.+++     +..++.+.-. ++                ..+ ..+...+..  ...|.+|
T Consensus       150 GlilI~G~TGSGKTT~l~al~~~i~~~~~~~~IvtiEdp~E~~~~~~~~~~~~~q~evg~~~~~~~~~l~~aLR~~PD~I  229 (372)
T TIGR02525       150 GLGLICGETGSGKSTLAASIYQHCGETYPDRKIVTYEDPIEYILGSPDDLLPPAQSQIGRDVDSFANGIRLALRRAPKII  229 (372)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEecCchhccCCCceeecccccccCCCccCHHHHHHHhhccCCCEE
Confidence            358999999999999999998876     2345555311 10                000 012222221  2489999


Q ss_pred             EEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccC
Q 011664          280 LIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLR  334 (480)
Q Consensus       280 ~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlr  334 (480)
                      ++.|+-.-       .+...+++..        ..+.. ++||=|..+...++-|
T Consensus       230 ~vGEiRd~-------et~~~al~aa--------~TGH~-v~tTlHa~s~~~ai~R  268 (372)
T TIGR02525       230 GVGEIRDL-------ETFQAAVLAG--------QSGHF-CLGTLHVKSPGEAISR  268 (372)
T ss_pred             eeCCCCCH-------HHHHHHHHHH--------hcCCc-EEEeeCCCCHHHHHHH
Confidence            99999732       2233334332        22344 5566566555556554

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK14531 adenylate kinase; Provisional

Probab=97.32  E-value=0.0002  Score=67.00  Aligned_cols=31  Identities=26%  Similarity=0.450  Sum_probs=27.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +-++++||||+|||++++.+|..+|...++.
T Consensus         3 ~~i~i~G~pGsGKsT~~~~la~~~g~~~is~   33 (183)
T PRK14531          3 QRLLFLGPPGAGKGTQAARLCAAHGLRHLST   33 (183)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCCeEec
Confidence            4599999999999999999999998776554

>PRK06217 hypothetical protein; Validated

Probab=97.32  E-value=0.00019  Score=67.11  Aligned_cols=31  Identities=29%  Similarity=0.472  Sum_probs=28.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -|+|.|+||+||||+++++|..++.++++.|
T Consensus         3 ~I~i~G~~GsGKSTla~~L~~~l~~~~~~~D   33 (183)
T PRK06217          3 RIHITGASGSGTTTLGAALAERLDIPHLDTD   33 (183)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEEEcC
Confidence            4899999999999999999999998877665

>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family

Probab=97.31  E-value=0.00018  Score=65.80  Aligned_cols=33  Identities=27%  Similarity=0.479  Sum_probs=26.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ++|.||||||||++++.+++.++..++  +...+.
T Consensus         1 i~l~G~~GsGKSTla~~l~~~l~~~~v--~~D~~~   33 (163)
T TIGR01313         1 FVLMGVAGSGKSTIASALAHRLGAKFI--EGDDLH   33 (163)
T ss_pred             CEEECCCCCCHHHHHHHHHHhcCCeEE--eCcccc
Confidence            578999999999999999999986554  444443

This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases.

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=97.30  E-value=0.0014  Score=69.74  Aligned_cols=62  Identities=23%  Similarity=0.254  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      .+.+.+.+.+...+.......... ..|..++++||||+|||+++..+|..+   |..+..+++..
T Consensus        69 ~~~~~v~~~L~~~l~~~~~~~~~~-~~p~vI~lvG~~GsGKTTtaakLA~~L~~~g~kV~lV~~D~  133 (437)
T PRK00771         69 HVIKIVYEELVKLLGEETEPLVLP-LKPQTIMLVGLQGSGKTTTAAKLARYFKKKGLKVGLVAADT  133 (437)
T ss_pred             HHHHHHHHHHHHHhCCCccccccC-CCCeEEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEecCCC
Confidence            345556656655544322111111 246689999999999999999999866   55666665543

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=97.30  E-value=0.00058  Score=71.28  Aligned_cols=70  Identities=20%  Similarity=0.305  Sum_probs=47.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC--------------------ChHHHHHHHH--hhc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA--------------------DDADLKSLLL--QTT  274 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~--------------------~~~~l~~l~~--~~~  274 (480)
                      |+.+..-++++||||+|||+|+..+|..+   +.++++++..+-.                    .+..+..++.  ...
T Consensus        78 Gi~~GslvLI~G~pG~GKStLllq~a~~~a~~g~~VlYvs~EEs~~qi~~Ra~rlg~~~~~l~l~~e~~le~I~~~i~~~  157 (372)
T cd01121          78 GLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGGKVLYVSGEESPEQIKLRADRLGISTENLYLLAETNLEDILASIEEL  157 (372)
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEEECCcCHHHHHHHHHHcCCCcccEEEEccCcHHHHHHHHHhc
Confidence            56666678999999999999999998754   3567777654211                    0111222222  234


Q ss_pred             CCcEEEEeccccccc
Q 011664          275 SKSVILIEDLDRFLV  289 (480)
Q Consensus       275 ~~sII~IDEiD~l~~  289 (480)
                      .|.+|+||+|..+..
T Consensus       158 ~~~lVVIDSIq~l~~  172 (372)
T cd01121         158 KPDLVIIDSIQTVYS  172 (372)
T ss_pred             CCcEEEEcchHHhhc
Confidence            789999999988753

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.

>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor

Probab=97.30  E-value=0.00019  Score=63.74  Aligned_cols=30  Identities=30%  Similarity=0.491  Sum_probs=28.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      |.+.|+||||||++|+.+|..++.+++..+
T Consensus         2 I~i~G~~GsGKst~a~~la~~~~~~~~~~~   31 (147)
T cd02020           2 IAIDGPAGSGKSTVAKLLAKKLGLPYLDTG   31 (147)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceeccc
Confidence            679999999999999999999999988876

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=97.30  E-value=0.00096  Score=66.43  Aligned_cols=86  Identities=14%  Similarity=0.273  Sum_probs=53.9

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEe------
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVD------  256 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~------  256 (480)
                      +.++++++..++..+.+.+.+..              ....+++.||+|+|||++++++..++.   ..++.+.      
T Consensus        56 ~~~l~~lg~~~~~~~~l~~~~~~--------------~~GlilisG~tGSGKTT~l~all~~i~~~~~~iitiEdp~E~~  121 (264)
T cd01129          56 ILDLEKLGLKPENLEIFRKLLEK--------------PHGIILVTGPTGSGKTTTLYSALSELNTPEKNIITVEDPVEYQ  121 (264)
T ss_pred             CCCHHHcCCCHHHHHHHHHHHhc--------------CCCEEEEECCCCCcHHHHHHHHHhhhCCCCCeEEEECCCceec
Confidence            35788888888777766543321              233588999999999999999987663   3455542      


Q ss_pred             CCCcC-----Ch--HHHHHHHHh--hcCCcEEEEeccc
Q 011664          257 LSRVA-----DD--ADLKSLLLQ--TTSKSVILIEDLD  285 (480)
Q Consensus       257 ~s~~~-----~~--~~l~~l~~~--~~~~sII~IDEiD  285 (480)
                      +..+.     .+  ......+..  ...|.+|+++|+.
T Consensus       122 ~~~~~q~~v~~~~~~~~~~~l~~~lR~~PD~i~vgEiR  159 (264)
T cd01129         122 IPGINQVQVNEKAGLTFARGLRAILRQDPDIIMVGEIR  159 (264)
T ss_pred             CCCceEEEeCCcCCcCHHHHHHHHhccCCCEEEeccCC
Confidence            11110     01  112233322  2589999999996

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.

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

Probab=97.30  E-value=0.00079  Score=64.96  Aligned_cols=38  Identities=26%  Similarity=0.313  Sum_probs=28.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~  257 (480)
                      |++....+|+.||||||||+++..++.+.    |.++++++.
T Consensus        15 Gip~gs~~li~G~~GsGKT~l~~q~l~~~~~~~ge~vlyvs~   56 (226)
T PF06745_consen   15 GIPKGSVVLISGPPGSGKTTLALQFLYNGLKNFGEKVLYVSF   56 (226)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHT--EEEEES
T ss_pred             CCCCCcEEEEEeCCCCCcHHHHHHHHHHhhhhcCCcEEEEEe
Confidence            67777889999999999999998776432    677777764

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=97.28  E-value=0.0013  Score=62.57  Aligned_cols=63  Identities=25%  Similarity=0.452  Sum_probs=39.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh----------HHHHHHHHh-----------hcCCcEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD----------ADLKSLLLQ-----------TTSKSVIL  280 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~----------~~l~~l~~~-----------~~~~sII~  280 (480)
                      +-.++.||||||||+++++++..+   +..++.+..+.-...          ..+..++..           .....+|+
T Consensus        19 ~~~~l~G~aGtGKT~~l~~~~~~~~~~g~~v~~~apT~~Aa~~L~~~~~~~a~Ti~~~l~~~~~~~~~~~~~~~~~~vli   98 (196)
T PF13604_consen   19 RVSVLQGPAGTGKTTLLKALAEALEAAGKRVIGLAPTNKAAKELREKTGIEAQTIHSFLYRIPNGDDEGRPELPKKDVLI   98 (196)
T ss_dssp             SEEEEEESTTSTHHHHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHHTS-EEEHHHHTTEECCEECCSSCC-TSTSEEE
T ss_pred             eEEEEEECCCCCHHHHHHHHHHHHHhCCCeEEEECCcHHHHHHHHHhhCcchhhHHHHHhcCCcccccccccCCcccEEE
Confidence            467889999999999999987644   667777766532111          112222211           12348999


Q ss_pred             Eeccccc
Q 011664          281 IEDLDRF  287 (480)
Q Consensus       281 IDEiD~l  287 (480)
                      |||+-.+
T Consensus        99 VDEasmv  105 (196)
T PF13604_consen   99 VDEASMV  105 (196)
T ss_dssp             ESSGGG-
T ss_pred             Eeccccc
Confidence            9999876

>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=97.28  E-value=0.0039  Score=63.19  Aligned_cols=77  Identities=22%  Similarity=0.379  Sum_probs=47.5

Q ss_pred             CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCccc----------------ccCCCce
Q 011664          275 SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQA----------------LLRPGRI  338 (480)
Q Consensus       275 ~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~a----------------LlrpGRf  338 (480)
                      .+-||+|||+|++.+     ...-++|+.+.-+.+   ..+.++|++.+.. .|..+                .+. =-+
T Consensus       172 ~~iViiIDdLDR~~~-----~~i~~~l~~ik~~~~---~~~i~~Il~~D~~-~l~~ai~~~~~~~~~~~~~~~yLe-Kii  241 (325)
T PF07693_consen  172 KRIVIIIDDLDRCSP-----EEIVELLEAIKLLLD---FPNIIFILAFDPE-ILEKAIEKNYGEGFDEIDGREYLE-KII  241 (325)
T ss_pred             ceEEEEEcchhcCCc-----HHHHHHHHHHHHhcC---CCCeEEEEEecHH-HHHHHHHhhcCcccccccHHHHHH-hhc
Confidence            457999999998843     223455555544444   3567777776521 22111                122 045


Q ss_pred             eEEEEcCCCCHHHHHHHHHHHhc
Q 011664          339 DVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       339 d~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      +..+.+|.|+..+...++...+.
T Consensus       242 q~~~~lP~~~~~~~~~~~~~~~~  264 (325)
T PF07693_consen  242 QVPFSLPPPSPSDLERYLNELLE  264 (325)
T ss_pred             CeEEEeCCCCHHHHHHHHHHHHH
Confidence            68899999999888777776643

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 [].

>PRK04841 transcriptional regulator MalT; Provisional

Probab=97.27  E-value=0.0063  Score=70.31  Aligned_cols=33  Identities=24%  Similarity=0.274  Sum_probs=26.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      .+-++++||+|.|||+++...+...+ ++.-+++
T Consensus        32 ~~~~~v~apaG~GKTtl~~~~~~~~~-~~~w~~l   64 (903)
T PRK04841         32 YRLVLVTSPAGYGKTTLISQWAAGKN-NLGWYSL   64 (903)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhCC-CeEEEec
Confidence            34689999999999999999987776 6655554

>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP)

Probab=97.26  E-value=0.00023  Score=66.59  Aligned_cols=29  Identities=31%  Similarity=0.463  Sum_probs=25.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |++.||||+|||++++.+|..+|...+.+
T Consensus         2 I~i~G~pGsGKst~a~~La~~~~~~~i~~   30 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGLPHIST   30 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCeEEEC
Confidence            79999999999999999999988766554

This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.

>KOG3347 consensus Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]

Probab=97.24  E-value=0.00022  Score=64.26  Aligned_cols=42  Identities=26%  Similarity=0.448  Sum_probs=33.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKS  268 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~  268 (480)
                      ..||+.|-||||||+++..+|...+...+.+  +++..+.++..
T Consensus         8 PNILvtGTPG~GKstl~~~lae~~~~~~i~i--sd~vkEn~l~~   49 (176)
T KOG3347|consen    8 PNILVTGTPGTGKSTLAERLAEKTGLEYIEI--SDLVKENNLYE   49 (176)
T ss_pred             CCEEEeCCCCCCchhHHHHHHHHhCCceEeh--hhHHhhhcchh
Confidence            3699999999999999999999888776554  56655555433

>PRK05057 aroK shikimate kinase I; Reviewed

Probab=97.23  E-value=0.0003  Score=65.37  Aligned_cols=34  Identities=38%  Similarity=0.695  Sum_probs=30.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      ++.++|.||+|+|||++++.+|+.++.+++..|.
T Consensus         4 ~~~I~liG~~GaGKStl~~~La~~l~~~~vd~D~   37 (172)
T PRK05057          4 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQ   37 (172)
T ss_pred             CCEEEEECCCCcCHHHHHHHHHHHcCCcEEECCc
Confidence            3469999999999999999999999999888764

>PRK13946 shikimate kinase; Provisional

Probab=97.23  E-value=0.00026  Score=66.44  Aligned_cols=34  Identities=32%  Similarity=0.541  Sum_probs=31.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      ++.|+|.|+||||||++++.+|..+|+++++.|.
T Consensus        10 ~~~I~l~G~~GsGKsti~~~LA~~Lg~~~id~D~   43 (184)
T PRK13946         10 KRTVVLVGLMGAGKSTVGRRLATMLGLPFLDADT   43 (184)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHcCCCeECcCH
Confidence            4579999999999999999999999999998773

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=97.22  E-value=0.0033  Score=66.79  Aligned_cols=63  Identities=30%  Similarity=0.354  Sum_probs=42.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcC----------------------ChHHHHHHHHhhcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSRVA----------------------DDADLKSLLLQTTSK  276 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~----------------------~~~~l~~l~~~~~~~  276 (480)
                      .+.++|.||+|+||||++..+|..+     +..+..+++....                      ...++...+.+....
T Consensus       221 ~~~i~~vGptGvGKTTt~~kLA~~~~~~~~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~~~~~  300 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLAKLAARYALLYGKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQLRDC  300 (424)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcCCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHHhCCC
Confidence            4568899999999999999888643     4567777665432                      122333344444567


Q ss_pred             cEEEEecccc
Q 011664          277 SVILIEDLDR  286 (480)
Q Consensus       277 sII~IDEiD~  286 (480)
                      .+|+||....
T Consensus       301 DlVlIDt~G~  310 (424)
T PRK05703        301 DVILIDTAGR  310 (424)
T ss_pred             CEEEEeCCCC
Confidence            8899998764

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=97.22  E-value=0.00065  Score=69.18  Aligned_cols=57  Identities=23%  Similarity=0.351  Sum_probs=40.2

Q ss_pred             ChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          195 ETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       195 ~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .++.++.+.+.+...+....     ...+...|.|.|+||||||++++.+|..+|+++++++
T Consensus       109 ~~~~~~~~~~~l~~~~~~~~-----~~~~~~~I~l~G~~GsGKStvg~~La~~Lg~~~id~D  165 (309)
T PRK08154        109 SPAQLARVRDALSGMLGAGR-----RAARRRRIALIGLRGAGKSTLGRMLAARLGVPFVELN  165 (309)
T ss_pred             CHHHHHHHHHHHHHHHhhhh-----hccCCCEEEEECCCCCCHHHHHHHHHHHcCCCEEeHH
Confidence            33444445544444333221     2345668999999999999999999999999999655

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=97.19  E-value=0.0015  Score=66.31  Aligned_cols=25  Identities=28%  Similarity=0.607  Sum_probs=23.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ++++++.||+|+|||++++++++++
T Consensus       132 ~~~ilI~G~tGSGKTTll~al~~~i  156 (299)
T TIGR02782       132 RKNILVVGGTGSGKTTLANALLAEI  156 (299)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHh
Confidence            4689999999999999999999876

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK03731 aroL shikimate kinase II; Reviewed

Probab=97.19  E-value=0.00034  Score=64.37  Aligned_cols=31  Identities=32%  Similarity=0.596  Sum_probs=28.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .++|.|+||||||++++.+|..+|.++++.|
T Consensus         4 ~i~~~G~~GsGKst~~~~la~~lg~~~~d~D   34 (171)
T PRK03731          4 PLFLVGARGCGKTTVGMALAQALGYRFVDTD   34 (171)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEEcc
Confidence            5899999999999999999999999998775

>PRK06762 hypothetical protein; Provisional

Probab=97.19  E-value=0.00041  Score=63.54  Aligned_cols=33  Identities=21%  Similarity=0.340  Sum_probs=27.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.-++++|+||||||++|+.++..++..++.++
T Consensus         2 ~~li~i~G~~GsGKST~A~~L~~~l~~~~~~i~   34 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERLGRGTLLVS   34 (166)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeEEec
Confidence            346889999999999999999999866666664

>PRK08233 hypothetical protein; Provisional

Probab=97.18  E-value=0.0011  Score=61.24  Aligned_cols=32  Identities=16%  Similarity=0.203  Sum_probs=25.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC-CcEEEEeC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS-YDVYDVDL  257 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~-~~~~~i~~  257 (480)
                      -+.+.|+||+||||+|+.+|..++ ..++..+.
T Consensus         5 iI~I~G~~GsGKtTla~~L~~~l~~~~~~~~d~   37 (182)
T PRK08233          5 IITIAAVSGGGKTTLTERLTHKLKNSKALYFDR   37 (182)
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCCCCceEEECC
Confidence            467889999999999999999885 45555543

>COG4650 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription / Signal transduction mechanisms]

Probab=97.17  E-value=0.00085  Score=66.72  Aligned_cols=67  Identities=19%  Similarity=0.367  Sum_probs=55.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH------cCCCcEEEEeCCCcCChHHHHHHHHhh-----------------cCCcEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS------FMSYDVYDVDLSRVADDADLKSLLLQT-----------------TSKSVI  279 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~------~l~~~~~~i~~s~~~~~~~l~~l~~~~-----------------~~~sII  279 (480)
                      ....+||.||.|.|||.||+-|-.      .+.-.|+.++|..+.++..+..+|...                 .....+
T Consensus       207 sr~p~ll~gptgagksflarriyelk~arhq~sg~fvevncatlrgd~amsalfghvkgaftga~~~r~gllrsadggml  286 (531)
T COG4650         207 SRAPILLNGPTGAGKSFLARRIYELKQARHQFSGAFVEVNCATLRGDTAMSALFGHVKGAFTGARESREGLLRSADGGML  286 (531)
T ss_pred             ccCCeEeecCCCcchhHHHHHHHHHHHHHHhcCCceEEEeeeeecCchHHHHHHhhhccccccchhhhhhhhccCCCceE
Confidence            344699999999999999998863      567789999999999998888887431                 345899


Q ss_pred             EEeccccccc
Q 011664          280 LIEDLDRFLV  289 (480)
Q Consensus       280 ~IDEiD~l~~  289 (480)
                      |+|||..+..
T Consensus       287 fldeigelga  296 (531)
T COG4650         287 FLDEIGELGA  296 (531)
T ss_pred             ehHhhhhcCc
Confidence            9999988754

>PRK13764 ATPase; Provisional

Probab=97.17  E-value=0.0012  Score=72.62  Aligned_cols=26  Identities=42%  Similarity=0.733  Sum_probs=23.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .+++|++|||||||||+++|++.++.
T Consensus       257 ~~~ILIsG~TGSGKTTll~AL~~~i~  282 (602)
T PRK13764        257 AEGILIAGAPGAGKSTFAQALAEFYA  282 (602)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHh
Confidence            56899999999999999999998774

>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=97.17  E-value=0.001  Score=61.07  Aligned_cols=98  Identities=16%  Similarity=0.241  Sum_probs=53.5

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCc--EEEEe---CCCc---------------CChHHHHHH-HHh--hcCCcEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYD--VYDVD---LSRV---------------ADDADLKSL-LLQ--TTSKSVI  279 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~--~~~i~---~s~~---------------~~~~~l~~l-~~~--~~~~sII  279 (480)
                      +..-+.|.||+|+|||+|.+.+++.....  -+.++   ....               .+..+.+++ +++  ..+|.++
T Consensus        25 ~Ge~~~l~G~nGsGKSTLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~~qrl~laral~~~p~il  104 (163)
T cd03216          25 RGEVHALLGENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSVGERQMVEIARALARNARLL  104 (163)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCCCCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCHHHHHHHHHHHHHhcCCCEE
Confidence            34468899999999999999999875321  11221   1111               111112222 222  3589999


Q ss_pred             EEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          280 LIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       280 ~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      ++||-..-+. ......+.+++..+   ..    .+..+|++|.+++.+
T Consensus       105 llDEP~~~LD-~~~~~~l~~~l~~~---~~----~~~tiii~sh~~~~~  145 (163)
T cd03216         105 ILDEPTAALT-PAEVERLFKVIRRL---RA----QGVAVIFISHRLDEV  145 (163)
T ss_pred             EEECCCcCCC-HHHHHHHHHHHHHH---HH----CCCEEEEEeCCHHHH
Confidence            9999875432 22222333344333   21    245667777665543

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

>PF13191 AAA_16: AAA ATPase domain; PDB: 2V1U_A

Probab=97.16  E-value=0.00019  Score=66.25  Aligned_cols=59  Identities=22%  Similarity=0.263  Sum_probs=33.8

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc---EEEEeCCCc
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD---VYDVDLSRV  260 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~~i~~s~~  260 (480)
                      ++|-++..+++...+. .         .....++.++++||||+|||++++++...+..+   ++.+++...
T Consensus         2 fvgR~~e~~~l~~~l~-~---------~~~~~~~~~ll~G~~G~GKT~ll~~~~~~~~~~~~~~~~~~~~~~   63 (185)
T PF13191_consen    2 FVGREEEIERLRDLLD-A---------AQSGSPRNLLLTGESGSGKTSLLRALLDRLAERGGYVISINCDDS   63 (185)
T ss_dssp             -TT-HHHHHHHHHTTG-G---------TSS-----EEE-B-TTSSHHHHHHHHHHHHHHHT--EEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHH-H---------HHcCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCEEEEEEEecc
Confidence            3555666666654442 1         111234689999999999999999988766433   777776554

>PRK14530 adenylate kinase; Provisional

Probab=97.16  E-value=0.00038  Score=66.83  Aligned_cols=30  Identities=23%  Similarity=0.386  Sum_probs=27.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .++|.||||+||||+++.+|..++.+++..
T Consensus         5 ~I~i~G~pGsGKsT~~~~La~~~~~~~i~~   34 (215)
T PRK14530          5 RILLLGAPGAGKGTQSSNLAEEFGVEHVTT   34 (215)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEec
Confidence            589999999999999999999999876654

>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT)

Probab=97.15  E-value=0.00031  Score=65.21  Aligned_cols=33  Identities=33%  Similarity=0.409  Sum_probs=28.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      +-++|.||||+|||+++++++..++..++.++.
T Consensus         3 ~~i~l~G~~gsGKst~a~~l~~~~~~~~~~~~~   35 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWLHFGV   35 (175)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhhCCCccccCc
Confidence            468999999999999999999998877665543

Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=97.14  E-value=0.0012  Score=61.71  Aligned_cols=65  Identities=15%  Similarity=0.227  Sum_probs=39.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc--EEEEe-------CCC--cCChHHHHHHHHh--hcCCcEEEEecccccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD--VYDVD-------LSR--VADDADLKSLLLQ--TTSKSVILIEDLDRFL  288 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~--~~~i~-------~s~--~~~~~~l~~l~~~--~~~~sII~IDEiD~l~  288 (480)
                      ..-+.|.||.|+|||||++.+++.+..+  -+.++       ...  +.+...-+-.+++  ...|.++++||--.-+
T Consensus        25 Ge~~~l~G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~~q~~~LSgGq~qrv~laral~~~p~lllLDEPts~L  102 (177)
T cd03222          25 GEVIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAALLRNATFYLFDEPSAYL  102 (177)
T ss_pred             CCEEEEECCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEEcccCCCCHHHHHHHHHHHHHhcCCCEEEEECCcccC
Confidence            3457899999999999999999865321  11111       111  2222222222232  3589999999987544

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain

Probab=97.13  E-value=0.0018  Score=65.68  Aligned_cols=137  Identities=15%  Similarity=0.240  Sum_probs=76.0

Q ss_pred             ccccc-ChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe----CCCcCChH
Q 011664          190 DTISM-ETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD----LSRVADDA  264 (480)
Q Consensus       190 ~~i~g-~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~----~s~~~~~~  264 (480)
                      +++.+ ++++++.+.+.+-..+...       .+...-++|+|+.|+|||+++..+...+|-....+.    +.++.+. 
T Consensus        48 ~~~~~~d~~~~~~l~~~lg~~L~~~-------~~~~~~~~l~G~g~nGKStl~~~l~~l~G~~~~~~~~~~~~~~~~~~-  119 (304)
T TIGR01613        48 LETFGGDNELIEYLQRVIGYSLTGN-------YTEQKLFFLYGNGGNGKSTFQNLLSNLLGDYATTAVASLKMNEFQEH-  119 (304)
T ss_pred             HHHhCCCHHHHHHHHHHHhHHhcCC-------CCceEEEEEECCCCCcHHHHHHHHHHHhChhhccCCcchhhhhccCC-
Confidence            44443 4456666666555444331       235667899999999999999999998876542222    2222110 


Q ss_pred             HHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccc---cccc-c------cCCceEEEEecCCCccC---ccc
Q 011664          265 DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG---VLNS-C------CFEERVMVFTMNSKDHV---DQA  331 (480)
Q Consensus       265 ~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg---~~~~-~------~~~~~ivI~tTN~~~~L---D~a  331 (480)
                        +..++.....-+++.||++.-.  ...    .+.+..|-|   +... .      -.....+|++||++-.+   |.+
T Consensus       120 --~f~~a~l~gk~l~~~~E~~~~~--~~~----~~~lK~lt~gd~i~~~~k~k~~~~~~~~~~~i~~tN~~P~~~~~~~a  191 (304)
T TIGR01613       120 --RFGLARLEGKRAVIGDEVQKGY--RDD----ESTFKSLTGGDTITARFKNKDPFEFTPKFTLVQSTNHLPRIRGFDGG  191 (304)
T ss_pred             --CchhhhhcCCEEEEecCCCCCc--ccc----HHhhhhhhcCCeEEeecccCCcEEEEEeeEEEEEcCCCCccCCCChh
Confidence              1123344567899999987421  111    122222211   1100 0      01123467788865333   678


Q ss_pred             ccCCCceeEEEEcC
Q 011664          332 LLRPGRIDVHIHFP  345 (480)
Q Consensus       332 LlrpGRfd~~I~~~  345 (480)
                      +.|  |+ ..|.|+
T Consensus       192 ~~R--R~-~vi~f~  202 (304)
T TIGR01613       192 IKR--RL-RIIPFT  202 (304)
T ss_pred             hee--eE-EEEecc
Confidence            999  88 577765

This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.

>PRK09354 recA recombinase A; Provisional

Probab=97.13  E-value=0.001  Score=68.65  Aligned_cols=70  Identities=17%  Similarity=0.286  Sum_probs=46.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCCcCC---------------------hHHH---HHHHHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSRVAD---------------------DADL---KSLLLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~~~~---------------------~~~l---~~l~~~  272 (480)
                      |++..+-+++|||||||||+|+-.++.+   .|...++++...-.+                     ..+.   ...+.+
T Consensus        56 Gip~G~IteI~G~~GsGKTtLal~~~~~~~~~G~~~~yId~E~s~~~~~a~~lGvdld~lli~qp~~~Eq~l~i~~~li~  135 (349)
T PRK09354         56 GLPRGRIVEIYGPESSGKTTLALHAIAEAQKAGGTAAFIDAEHALDPVYAKKLGVDIDNLLVSQPDTGEQALEIADTLVR  135 (349)
T ss_pred             CCcCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchHHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHhh
Confidence            5666667889999999999999876643   366677776543111                     0111   111223


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|+||-+-++.+
T Consensus       136 s~~~~lIVIDSvaaL~~  152 (349)
T PRK09354        136 SGAVDLIVVDSVAALVP  152 (349)
T ss_pred             cCCCCEEEEeChhhhcc
Confidence            35789999999998875

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=97.11  E-value=0.0015  Score=60.39  Aligned_cols=24  Identities=38%  Similarity=0.596  Sum_probs=21.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..+++.||+|||||+|.+++|+..
T Consensus        30 e~iaitGPSG~GKStllk~va~Li   53 (223)
T COG4619          30 EFIAITGPSGCGKSTLLKIVASLI   53 (223)
T ss_pred             ceEEEeCCCCccHHHHHHHHHhcc
Confidence            358999999999999999999855

>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]

Probab=97.10  E-value=0.00039  Score=63.55  Aligned_cols=29  Identities=21%  Similarity=0.423  Sum_probs=26.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +-+.|||||||||+++-+|..+|+++++-
T Consensus         3 ItIsG~pGsG~TTva~~lAe~~gl~~vsa   31 (179)
T COG1102           3 ITISGLPGSGKTTVARELAEHLGLKLVSA   31 (179)
T ss_pred             EEeccCCCCChhHHHHHHHHHhCCceeec
Confidence            56889999999999999999999998873

>PRK06547 hypothetical protein; Provisional

Probab=97.09  E-value=0.00055  Score=63.75  Aligned_cols=34  Identities=29%  Similarity=0.483  Sum_probs=29.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .+.-|++.||+|||||++++.+|..++..++..+
T Consensus        14 ~~~~i~i~G~~GsGKTt~a~~l~~~~~~~~~~~d   47 (172)
T PRK06547         14 GMITVLIDGRSGSGKTTLAGALAARTGFQLVHLD   47 (172)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhCCCeeccc
Confidence            4557889999999999999999999988777654

>PRK04296 thymidine kinase; Provisional

Probab=97.09  E-value=0.0019  Score=61.02  Aligned_cols=30  Identities=23%  Similarity=0.213  Sum_probs=23.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i  255 (480)
                      -.+++||||+|||+++..++..+   +..++.+
T Consensus         4 i~litG~~GsGKTT~~l~~~~~~~~~g~~v~i~   36 (190)
T PRK04296          4 LEFIYGAMNSGKSTELLQRAYNYEERGMKVLVF   36 (190)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHcCCeEEEE
Confidence            46899999999999998887654   5555555

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=97.09  E-value=0.0019  Score=60.03  Aligned_cols=26  Identities=27%  Similarity=0.383  Sum_probs=22.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...-+.|.||+|+|||+|++++++..
T Consensus        27 ~Ge~~~i~G~nGsGKStLl~~l~G~~   52 (178)
T cd03247          27 QGEKIALLGRSGSGKSTLLQLLTGDL   52 (178)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccC
Confidence            34568899999999999999999865

The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=97.08  E-value=0.0016  Score=61.21  Aligned_cols=62  Identities=21%  Similarity=0.301  Sum_probs=38.5

Q ss_pred             EEEEccCCCcHHHHHHHHHH-----cCCCcE--------------EEEeCCCcCC---------hHHHHHHHHhhcCCcE
Q 011664          227 YLLYGPSGTGKSSFAAAMAS-----FMSYDV--------------YDVDLSRVAD---------DADLKSLLLQTTSKSV  278 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~-----~l~~~~--------------~~i~~s~~~~---------~~~l~~l~~~~~~~sI  278 (480)
                      ++|.||.|+|||++.++++-     ..|..+              ..+...+...         -..+..++.....|++
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~l   81 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSL   81 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeE
Confidence            68999999999999999982     233321              1111211111         1123344455568999


Q ss_pred             EEEecccccc
Q 011664          279 ILIEDLDRFL  288 (480)
Q Consensus       279 I~IDEiD~l~  288 (480)
                      +++||...-.
T Consensus        82 lllDEp~~g~   91 (185)
T smart00534       82 VLLDELGRGT   91 (185)
T ss_pred             EEEecCCCCC
Confidence            9999997543

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=97.08  E-value=0.0034  Score=65.63  Aligned_cols=59  Identities=20%  Similarity=0.289  Sum_probs=39.1

Q ss_pred             hHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          196 TDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .++++.+.+.+...+..+..+    ...++-++|.||+|+||||++..+|..+   |..+..+++.
T Consensus       217 ~~~~~~l~~~l~~~l~~~~~~----~~~~~vI~LVGptGvGKTTTiaKLA~~L~~~GkkVglI~aD  278 (436)
T PRK11889        217 EEVIEYILEDMRSHFNTENVF----EKEVQTIALIGPTGVGKTTTLAKMAWQFHGKKKTVGFITTD  278 (436)
T ss_pred             HHHHHHHHHHHHHHhcccccc----ccCCcEEEEECCCCCcHHHHHHHHHHHHHHcCCcEEEEecC
Confidence            456666666666555443221    1124678999999999999999999866   4455555543

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=97.07  E-value=0.0012  Score=56.52  Aligned_cols=23  Identities=30%  Similarity=0.340  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +++++||+|+|||.++.+.+..+
T Consensus         2 ~~~i~~~~G~GKT~~~~~~~~~~   24 (144)
T cd00046           2 DVLLAAPTGSGKTLAALLPILEL   24 (144)
T ss_pred             CEEEECCCCCchhHHHHHHHHHH
Confidence            68999999999998888777654

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

>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily

Probab=97.07  E-value=0.00049  Score=63.94  Aligned_cols=30  Identities=13%  Similarity=0.304  Sum_probs=25.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -+++.||||+||||+++.+|..+|...+..
T Consensus         5 ii~i~G~~GsGKsTl~~~l~~~~g~~~~~~   34 (188)
T TIGR01360         5 IIFIVGGPGSGKGTQCEKIVEKYGFTHLST   34 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            578999999999999999999988665543

Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=97.07  E-value=0.0017  Score=59.93  Aligned_cols=26  Identities=27%  Similarity=0.439  Sum_probs=22.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...-+.|.||+|+|||+|++++++.+
T Consensus        27 ~G~~~~l~G~nGsGKstLl~~i~G~~   52 (171)
T cd03228          27 PGEKVAIVGPSGSGKSTLLKLLLRLY   52 (171)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHcCC
Confidence            44468899999999999999999875

They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK02496 adk adenylate kinase; Provisional

Probab=97.05  E-value=0.00046  Score=64.45  Aligned_cols=29  Identities=24%  Similarity=0.490  Sum_probs=26.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +++.||||+|||++++.+|..++...+..
T Consensus         4 i~i~G~pGsGKst~a~~la~~~~~~~i~~   32 (184)
T PRK02496          4 LIFLGPPGAGKGTQAVVLAEHLHIPHIST   32 (184)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEh
Confidence            88999999999999999999998776654

>PF13245 AAA_19: Part of AAA domain

Probab=97.05  E-value=0.00081  Score=54.04  Aligned_cols=33  Identities=30%  Similarity=0.573  Sum_probs=22.3

Q ss_pred             eEEEEccCCCcHH-HHHHHHHHcC------CCcEEEEeCC
Q 011664          226 SYLLYGPSGTGKS-SFAAAMASFM------SYDVYDVDLS  258 (480)
Q Consensus       226 giLL~GPpGTGKT-~La~aiA~~l------~~~~~~i~~s  258 (480)
                      -+++.|||||||| ++++.++...      +..+..+..+
T Consensus        12 ~~vv~g~pGtGKT~~~~~~i~~l~~~~~~~~~~vlv~a~t   51 (76)
T PF13245_consen   12 LFVVQGPPGTGKTTTLAARIAELLAARADPGKRVLVLAPT   51 (76)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHHHhcCCCCeEEEECCC
Confidence            3556999999999 5556666554      4456666544

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

Probab=97.04  E-value=0.0044  Score=70.55  Aligned_cols=126  Identities=17%  Similarity=0.243  Sum_probs=81.1

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeCCCcCC--------hHHHHHHHHh---hcCCcEEEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDLSRVAD--------DADLKSLLLQ---TTSKSVILI  281 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~s~~~~--------~~~l~~l~~~---~~~~sII~I  281 (480)
                      -+++-+|.|.||+|||.++.-+|+..          +..++.+++..+..        +..+..+...   ....-||||
T Consensus       207 tk~NPvLVG~~gvgktaiv~gla~ri~~G~vp~~l~~~~l~~l~~g~l~aGa~~rge~E~rlk~l~k~v~~~~~gvILfi  286 (898)
T KOG1051|consen  207 TKNNPVLVGEPGVGKTAIVEGLAQRIATGDVPETLKDKKLIALDFGSLVAGAKRRGEFEERLKELLKEVESGGGGVILFL  286 (898)
T ss_pred             CCCCceEEecCCCCchhHHHHHHHHhhcCCCCccccccceEEEEhhhcccCcccchHHHHHHHHHHHHHhcCCCcEEEEe
Confidence            34678999999999999999999754          34677888765442        3335555543   346789999


Q ss_pred             ecccccccCcccc--cchhhhhhhcccccccccCCceEEEEe-cCCC----ccCcccccCCCceeEEEEcCCCCHHHHHH
Q 011664          282 EDLDRFLVEKPAA--VSLSGVLNFMDGVLNSCCFEERVMVFT-MNSK----DHVDQALLRPGRIDVHIHFPLCDFSSFKT  354 (480)
Q Consensus       282 DEiD~l~~~~~~~--~~ls~lL~~ldg~~~~~~~~~~ivI~t-TN~~----~~LD~aLlrpGRfd~~I~~~~p~~~~r~~  354 (480)
                      ||++.+.+.....  .....+|..+   ..   .++.-+|+| |+.-    -.=||+|-|  ||+ .+.++.|+.+.-..
T Consensus       287 gelh~lvg~g~~~~~~d~~nlLkp~---L~---rg~l~~IGatT~e~Y~k~iekdPalEr--rw~-l~~v~~pS~~~~~~  357 (898)
T KOG1051|consen  287 GELHWLVGSGSNYGAIDAANLLKPL---LA---RGGLWCIGATTLETYRKCIEKDPALER--RWQ-LVLVPIPSVENLSL  357 (898)
T ss_pred             cceeeeecCCCcchHHHHHHhhHHH---Hh---cCCeEEEecccHHHHHHHHhhCcchhh--Ccc-eeEeccCcccchhh
Confidence            9999998765441  1222233332   22   233556664 4421    123999999  998 67788888665444


Q ss_pred             HHH
Q 011664          355 LAS  357 (480)
Q Consensus       355 il~  357 (480)
                      ++.
T Consensus       358 iL~  360 (898)
T KOG1051|consen  358 ILP  360 (898)
T ss_pred             hhh
Confidence            443

>KOG2383 consensus Predicted ATPase [General function prediction only]

Probab=97.03  E-value=0.00064  Score=70.15  Aligned_cols=26  Identities=23%  Similarity=0.405  Sum_probs=22.5

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +|+|++|||.-|||||+|.-..-..+
T Consensus       113 ~PkGlYlYG~VGcGKTmLMDlFy~~~  138 (467)
T KOG2383|consen  113 PPKGLYLYGSVGCGKTMLMDLFYDAL  138 (467)
T ss_pred             CCceEEEecccCcchhHHHHHHhhcC
Confidence            58899999999999999998776443

>COG3854 SpoIIIAA ncharacterized protein conserved in bacteria [Function unknown]

Probab=97.02  E-value=0.0017  Score=62.73  Aligned_cols=62  Identities=23%  Similarity=0.387  Sum_probs=40.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC--------CcEEEEeCCC-cCC---------------------hHHHHHHHHhhcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS--------YDVYDVDLSR-VAD---------------------DADLKSLLLQTTS  275 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~--------~~~~~i~~s~-~~~---------------------~~~l~~l~~~~~~  275 (480)
                      +.|+.||||||||++.+-+|+.+.        ..+.-+|-++ +.+                     ..+......+...
T Consensus       139 ntLiigpP~~GKTTlLRdiaR~~s~g~~~~l~kkv~IiDersEIag~~~gvpq~~~g~R~dVld~cpk~~gmmmaIrsm~  218 (308)
T COG3854         139 NTLIIGPPQVGKTTLLRDIARLLSDGINQFLPKKVGIIDERSEIAGCLNGVPQHGRGRRMDVLDPCPKAEGMMMAIRSMS  218 (308)
T ss_pred             eeEEecCCCCChHHHHHHHHHHhhccccccCCceEEEEeccchhhccccCCchhhhhhhhhhcccchHHHHHHHHHHhcC
Confidence            689999999999999999998653        3455555322 211                     0111112234568


Q ss_pred             CcEEEEeccccc
Q 011664          276 KSVILIEDLDRF  287 (480)
Q Consensus       276 ~sII~IDEiD~l  287 (480)
                      |.||++|||...
T Consensus       219 PEViIvDEIGt~  230 (308)
T COG3854         219 PEVIIVDEIGTE  230 (308)
T ss_pred             CcEEEEeccccH
Confidence            999999999753

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=97.02  E-value=0.0023  Score=60.78  Aligned_cols=64  Identities=25%  Similarity=0.353  Sum_probs=39.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH-----cCCCc--------------EEEEeCCCcC----C-----hHHHHHHHHhhcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS-----FMSYD--------------VYDVDLSRVA----D-----DADLKSLLLQTTSK  276 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~-----~l~~~--------------~~~i~~s~~~----~-----~~~l~~l~~~~~~~  276 (480)
                      .-++|.||.|+|||++.++++.     ..|..              +..++..+-.    +     ...+..++.....|
T Consensus        30 ~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~~~~~~~~~i~~~dqi~~~~~~~d~i~~~~s~~~~e~~~l~~i~~~~~~~  109 (202)
T cd03243          30 RLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPR  109 (202)
T ss_pred             eEEEEECCCCCccHHHHHHHHHHHHHHHcCCCccccccccCCcCEEEEEecCcccccCCceeHHHHHHHHHHHHHhccCC
Confidence            4689999999999999999993     22321              1111111110    0     12233444556789


Q ss_pred             cEEEEecccccc
Q 011664          277 SVILIEDLDRFL  288 (480)
Q Consensus       277 sII~IDEiD~l~  288 (480)
                      .++++||.-.-.
T Consensus       110 ~llllDEp~~gl  121 (202)
T cd03243         110 SLVLIDELGRGT  121 (202)
T ss_pred             eEEEEecCCCCC
Confidence            999999997543

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>PRK14528 adenylate kinase; Provisional

Probab=97.01  E-value=0.00059  Score=64.21  Aligned_cols=30  Identities=23%  Similarity=0.435  Sum_probs=26.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .+++.||||+|||++++.+|..+|++.+..
T Consensus         3 ~i~i~G~pGsGKtt~a~~la~~~~~~~is~   32 (186)
T PRK14528          3 NIIFMGPPGAGKGTQAKILCERLSIPQIST   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCCeeeC
Confidence            489999999999999999999998776554

>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain

Probab=97.01  E-value=0.002  Score=59.67  Aligned_cols=25  Identities=36%  Similarity=0.660  Sum_probs=21.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||+|+|||+|++++++..
T Consensus        28 Ge~~~i~G~nGsGKStLl~~l~G~~   52 (173)
T cd03246          28 GESLAIIGPSGSGKSTLARLILGLL   52 (173)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcc
Confidence            3458899999999999999999865

They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substra

>PLN02200 adenylate kinase family protein

Probab=97.00  E-value=0.00072  Score=66.12  Aligned_cols=36  Identities=11%  Similarity=0.253  Sum_probs=28.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      .+.-+++.||||||||++++.+|..+|..  .++.+++
T Consensus        42 ~~~ii~I~G~PGSGKsT~a~~La~~~g~~--his~gdl   77 (234)
T PLN02200         42 TPFITFVLGGPGSGKGTQCEKIVETFGFK--HLSAGDL   77 (234)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhCCe--EEEccHH
Confidence            34568899999999999999999999865  4555443

>KOG0477 consensus DNA replication licensing factor, MCM2 component [Replication, recombination and repair]

Probab=97.00  E-value=0.0015  Score=70.52  Aligned_cols=95  Identities=25%  Similarity=0.294  Sum_probs=53.1

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC---CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC--CcC----
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVW---KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS--RVA----  261 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~---~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s--~~~----  261 (480)
                      +|.|+.++|..+.-.+  |---++  ..-|...   --++||+|-||||||-+.+.++.-....++.-..+  .+.    
T Consensus       450 sIyGh~~VK~AvAlaL--fGGv~k--n~~~khkvRGDinvLL~GDPGTaKSQFLKY~eK~s~RAV~tTGqGASavGLTa~  525 (854)
T KOG0477|consen  450 SIYGHEDVKRAVALAL--FGGVPK--NPGGKHKVRGDINVLLLGDPGTAKSQFLKYAEKTSPRAVFTTGQGASAVGLTAY  525 (854)
T ss_pred             hhhchHHHHHHHHHHH--hcCCcc--CCCCCceeccceeEEEecCCCccHHHHHHHHHhcCcceeEeccCCccccceeEE
Confidence            4678888877765322  111110  0001111   12599999999999999999998776655543211  110    


Q ss_pred             --ChHHHHHHHHh-----hcCCcEEEEeccccccc
Q 011664          262 --DDADLKSLLLQ-----TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       262 --~~~~l~~l~~~-----~~~~sII~IDEiD~l~~  289 (480)
                        .+.-.++...+     ...+.|.+|||+|.+-.
T Consensus       526 v~KdPvtrEWTLEaGALVLADkGvClIDEFDKMnd  560 (854)
T KOG0477|consen  526 VRKDPVTREWTLEAGALVLADKGVCLIDEFDKMND  560 (854)
T ss_pred             EeeCCccceeeeccCeEEEccCceEEeehhhhhcc
Confidence              00001111111     13678999999999854

>PTZ00088 adenylate kinase 1; Provisional

Probab=97.00  E-value=0.00057  Score=66.65  Aligned_cols=31  Identities=23%  Similarity=0.493  Sum_probs=27.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -++|.||||+||||+++.+|..+|+..++++
T Consensus         8 rIvl~G~PGsGK~T~a~~La~~~g~~~is~g   38 (229)
T PTZ00088          8 KIVLFGAPGVGKGTFAEILSKKENLKHINMG   38 (229)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEECC
Confidence            4999999999999999999999987666553

>PF06431 Polyoma_lg_T_C: Polyomavirus large T antigen C-terminus; InterPro: IPR010932 The group of polyomaviruses is formed by the homonymous murine virus (Py) as well as other representative members such as the simian virus 40 (SV40) and the human BK and JC viruses []

Probab=96.98  E-value=0.0019  Score=66.17  Aligned_cols=120  Identities=20%  Similarity=0.277  Sum_probs=66.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccC------ccc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVE------KPA  293 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~------~~~  293 (480)
                      +.|.+|.+|+-||-.||||++|+|+-+.+|-....|++..    ..+..-+.-+-..-.++++|+---...      ..+
T Consensus       151 N~PKkRy~lFkGPvNsGKTTlAAAlLdL~gG~~LNvN~p~----dkl~FELG~AiDQfmVvFEDVKGq~~~~~~Lp~G~G  226 (417)
T PF06431_consen  151 NIPKKRYWLFKGPVNSGKTTLAAALLDLCGGKSLNVNCPP----DKLNFELGCAIDQFMVVFEDVKGQPSDNKDLPPGQG  226 (417)
T ss_dssp             TBTTB-EEEEE-STTSSHHHHHHHHHHHH-EEEE-TSS-T----TTHHHHHCCCTT-SEEEEEEE--SSTTTTT----SH
T ss_pred             CCCcceeEEEecCcCCchHHHHHHHHHhcCCceeecCCCh----hhcchhhheeeceEEEEEEecCCCcCCCCCCCCCCC
Confidence            3566788999999999999999999999998888888753    234444444556678888887532111      111


Q ss_pred             ccchhhhhhhccccccc----ccC--CceE---EEEecCCCccCcccccCCCceeEEEEcCC
Q 011664          294 AVSLSGVLNFMDGVLNS----CCF--EERV---MVFTMNSKDHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       294 ~~~ls~lL~~ldg~~~~----~~~--~~~i---vI~tTN~~~~LD~aLlrpGRfd~~I~~~~  346 (480)
                      -..+..|-..+||...-    ...  ...|   -|+|+|. ..|+..+.-  ||...+.|..
T Consensus       227 ~~NLDNLRD~LDG~V~VNLErKH~NK~sQiFPPgIvTmNe-Y~iP~Tv~v--Rf~~~~~F~~  285 (417)
T PF06431_consen  227 MNNLDNLRDYLDGAVKVNLERKHQNKRSQIFPPGIVTMNE-YKIPQTVKV--RFCKVLDFRP  285 (417)
T ss_dssp             HHHHHTTHHHHH-SS-EEEECSSSEEEEE----EEEEESS--B--HHHHT--TEEEEEE---
T ss_pred             cccchhhhhhccCceeechhhhhcccccccCCCceEeecc-ccCCcceee--eeEeeEeccc
Confidence            12344455566664321    001  1123   3677774 357778887  9998888865

Their large T antigen (T-ag) protein binds to and activates DNA replication from the origin of DNA replication (ori). Insofar as is known, the T-ag binds to the origin first as a monomer to its pentanucleotide recognition element. The monomers are then thought to assemble into hexamers and double hexamers, which constitute the form that is active in initiation of DNA replication. When bound to the ori, T-ag double hexamers encircle DNA []. T-ag is a multidomain protein that contains an N-terminal J domain, which mediates protein interactions (see PDOC00553 from PROSITEDOC, IPR001623 from INTERPRO), a central origin-binding domain (OBD), and a C-terminal superfamily 3 helicase domain (see PDOC51206 from PROSITEDOC, IPR010932 from INTERPRO) []. This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA []. ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA []. These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 2H1L_H 1SVO_A 1SVM_E 1SVL_B 1N25_A 4E2I_K.

>TIGR01351 adk adenylate kinases

Probab=96.98  E-value=0.00062  Score=65.14  Aligned_cols=29  Identities=28%  Similarity=0.439  Sum_probs=25.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +++.||||+|||++++.+|..+|+..+..
T Consensus         2 I~i~G~pGsGKsT~a~~La~~~g~~~is~   30 (210)
T TIGR01351         2 LVLLGPPGSGKGTQAKRIAEKYGLPHIST   30 (210)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeeeh
Confidence            78999999999999999999998766654

Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=96.97  E-value=0.0017  Score=67.19  Aligned_cols=24  Identities=33%  Similarity=0.519  Sum_probs=21.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+++.|.||||||.||-.+|..+
T Consensus         2 ~v~~I~G~aGTGKTvla~~l~~~l   25 (352)
T PF09848_consen    2 QVILITGGAGTGKTVLALNLAKEL   25 (352)
T ss_pred             eEEEEEecCCcCHHHHHHHHHHHh
Confidence            357899999999999999999987

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>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=96.96  E-value=0.0011  Score=52.09  Aligned_cols=22  Identities=36%  Similarity=0.533  Sum_probs=20.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +.+.|+||+|||+++++++..+
T Consensus         2 i~i~G~~gsGKst~~~~l~~~l   23 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHh
Confidence            5789999999999999999986

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=96.95  E-value=0.002  Score=66.06  Aligned_cols=66  Identities=26%  Similarity=0.341  Sum_probs=48.7

Q ss_pred             Ccc-ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-CCcEEEEeCCCc
Q 011664          188 TFD-TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-SYDVYDVDLSRV  260 (480)
Q Consensus       188 ~~~-~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i~~s~~  260 (480)
                      .|+ ++.|.++..+++.+.+...-++       +-.-++-++|.||+|+|||++++.+-+.+ .+++|.+..+.+
T Consensus        58 ~f~~~~~G~~~~i~~lV~~fk~AA~g-------~~~~krIl~L~GPvg~GKSsl~~~Lk~~le~y~~Y~l~~~Pm  125 (358)
T PF08298_consen   58 FFEDEFYGMEETIERLVNYFKSAAQG-------LEERKRILLLLGPVGGGKSSLAELLKRGLEEYPIYTLKGCPM  125 (358)
T ss_pred             CccccccCcHHHHHHHHHHHHHHHhc-------cCccceEEEEECCCCCCHHHHHHHHHHHhheEEEEEecCCcc
Confidence            355 8999999999888766544332       12345678899999999999999999877 347777754433

PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.

>PRK06696 uridine kinase; Validated

Probab=96.95  E-value=0.0026  Score=61.52  Aligned_cols=41  Identities=17%  Similarity=0.263  Sum_probs=33.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA  264 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~  264 (480)
                      +.-|.+.|+||+||||+|+.|+..+   |.+++.+.+.++....
T Consensus        22 ~~iI~I~G~sgsGKSTlA~~L~~~l~~~g~~v~~~~~Ddf~~~~   65 (223)
T PRK06696         22 PLRVAIDGITASGKTTFADELAEEIKKRGRPVIRASIDDFHNPR   65 (223)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeccccccCCH
Confidence            4468899999999999999999988   6778887777765433

>PRK13695 putative NTPase; Provisional

Probab=96.94  E-value=0.0037  Score=57.86  Aligned_cols=22  Identities=27%  Similarity=0.610  Sum_probs=19.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ++|.|+||+|||++++.+++.+
T Consensus         3 i~ltG~~G~GKTTll~~i~~~l   24 (174)
T PRK13695          3 IGITGPPGVGKTTLVLKIAELL   24 (174)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            7899999999999999988764

>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]

Probab=96.94  E-value=0.0031  Score=68.65  Aligned_cols=170  Identities=18%  Similarity=0.186  Sum_probs=106.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC--CCcEEEEeCCCcCChHHHHHHHHh------------------hcCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM--SYDVYDVDLSRVADDADLKSLLLQ------------------TTSKSVILIE  282 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l--~~~~~~i~~s~~~~~~~l~~l~~~------------------~~~~sII~ID  282 (480)
                      +.-.+|+.|.|||||-.+++++....  .-+|+.++|..+...-.=.++|..                  ......+|+|
T Consensus       335 ~~~pvll~GEtGtGKe~laraiH~~s~~~gpfvAvNCaAip~~liesELFGy~~GafTga~~kG~~g~~~~A~gGtlFld  414 (606)
T COG3284         335 TDLPVLLQGETGTGKEVLARAIHQNSEAAGPFVAVNCAAIPEALIESELFGYVAGAFTGARRKGYKGKLEQADGGTLFLD  414 (606)
T ss_pred             cCCCeEecCCcchhHHHHHHHHHhcccccCCeEEEEeccchHHhhhHHHhccCccccccchhccccccceecCCCccHHH
Confidence            34469999999999999999998765  457999999876542222233311                  1234789999


Q ss_pred             cccccccCcccccchhhhhhhcc-ccccccc----CCceEEEEecCCCccCcccccCCCcee---------EEEEcCCCC
Q 011664          283 DLDRFLVEKPAAVSLSGVLNFMD-GVLNSCC----FEERVMVFTMNSKDHVDQALLRPGRID---------VHIHFPLCD  348 (480)
Q Consensus       283 EiD~l~~~~~~~~~ls~lL~~ld-g~~~~~~----~~~~ivI~tTN~~~~LD~aLlrpGRfd---------~~I~~~~p~  348 (480)
                      ||..+.     -...+.||..+. |......    .-.+-||.||+++=   ..|.+-|||-         ..|.+|+..
T Consensus       415 eIgd~p-----~~~Qs~LLrVl~e~~v~p~g~~~~~vdirvi~ath~dl---~~lv~~g~fredLyyrL~~~~i~lP~lr  486 (606)
T COG3284         415 EIGDMP-----LALQSRLLRVLQEGVVTPLGGTRIKVDIRVIAATHRDL---AQLVEQGRFREDLYYRLNAFVITLPPLR  486 (606)
T ss_pred             Hhhhch-----HHHHHHHHHHHhhCceeccCCcceeEEEEEEeccCcCH---HHHHHcCCchHHHHHHhcCeeeccCchh
Confidence            998763     123466776653 2111111    11234677776531   2455666664         344444332


Q ss_pred             H-HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHHhc
Q 011664          349 F-SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       349 ~-~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~~~  411 (480)
                      . .++..++.+++..++.           ....++++-+..++...+...++.+..+++.+...
T Consensus       487 ~R~d~~~~l~~~~~~~~~-----------~~~~l~~~~~~~l~~~~WPGNirel~~v~~~~~~l  539 (606)
T COG3284         487 ERSDRIPLLDRILKREND-----------WRLQLDDDALARLLAYRWPGNIRELDNVIERLAAL  539 (606)
T ss_pred             cccccHHHHHHHHHHccC-----------CCccCCHHHHHHHHhCCCCCcHHHHHHHHHHHHHc
Confidence            2 3355566666654432           12357777788888889999999999999988765

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=96.94  E-value=0.0054  Score=62.74  Aligned_cols=61  Identities=20%  Similarity=0.212  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHHHHhhh-hHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          197 DLKNRVKSDLESFLKAK-HYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~-~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .+++.+.+.+...+... ..+. .....+.-++|.||+|+||||++..+|..+   +..+.-+++.
T Consensus        87 ~~~~~l~~~l~~~l~~~~~~~~-~~~~~~~vi~lvGpnGsGKTTt~~kLA~~l~~~g~~V~Li~~D  151 (318)
T PRK10416         87 ELKELLKEELAEILEPVEKPLN-IEEKKPFVILVVGVNGVGKTTTIGKLAHKYKAQGKKVLLAAGD  151 (318)
T ss_pred             HHHHHHHHHHHHHhCcCCcccc-ccCCCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCeEEEEecC
Confidence            45666666666665421 1111 122234568899999999999999999866   4455555543

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=96.94  E-value=0.0019  Score=61.31  Aligned_cols=21  Identities=24%  Similarity=0.498  Sum_probs=19.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA  245 (480)
                      +.++|.||.|+|||++.+.++
T Consensus        29 ~~~~ltG~Ng~GKStll~~i~   49 (200)
T cd03280          29 RVLVITGPNAGGKTVTLKTLG   49 (200)
T ss_pred             eEEEEECCCCCChHHHHHHHH
Confidence            469999999999999999998

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=96.93  E-value=0.0032  Score=61.13  Aligned_cols=98  Identities=18%  Similarity=0.259  Sum_probs=54.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH-c----CCCcE--------------EEEeCCC-cC-------C-hHHHHHHHHhhcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS-F----MSYDV--------------YDVDLSR-VA-------D-DADLKSLLLQTTS  275 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~-~----l~~~~--------------~~i~~s~-~~-------~-~~~l~~l~~~~~~  275 (480)
                      .+-++|.||.|+|||++.+.++. .    .|..+              ..+...+ +.       . -.++..++..+..
T Consensus        31 g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  110 (222)
T cd03287          31 GYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTS  110 (222)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCccccccccchHHHHHHHHHHHHHhCCC
Confidence            34689999999999999999987 2    23211              1111111 11       1 1235556677788


Q ss_pred             CcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          276 KSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       276 ~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      +++++|||+..=............+++.+   ..   ..+..+|++|...+-
T Consensus       111 ~sLvllDE~~~gT~~~d~~~i~~~il~~l---~~---~~~~~~i~~TH~~~l  156 (222)
T cd03287         111 RSLVILDELGRGTSTHDGIAIAYATLHYL---LE---EKKCLVLFVTHYPSL  156 (222)
T ss_pred             CeEEEEccCCCCCChhhHHHHHHHHHHHH---Hh---ccCCeEEEEcccHHH
Confidence            99999999864221111111122344443   22   124567777776654

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PRK00279 adk adenylate kinase; Reviewed

Probab=96.93  E-value=0.00073  Score=64.90  Aligned_cols=29  Identities=28%  Similarity=0.413  Sum_probs=25.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+++||||+|||++++.+|..+++..+.+
T Consensus         3 I~v~G~pGsGKsT~a~~la~~~~~~~is~   31 (215)
T PRK00279          3 LILLGPPGAGKGTQAKFIAEKYGIPHIST   31 (215)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEEC
Confidence            89999999999999999999998766554

>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=96.92  E-value=0.00057  Score=58.99  Aligned_cols=22  Identities=27%  Similarity=0.442  Sum_probs=20.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l  248 (480)
                      |+|.|+|||||||+|+.++..+
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            6899999999999999999987

...

>PRK04040 adenylate kinase; Provisional

Probab=96.91  E-value=0.00091  Score=63.18  Aligned_cols=29  Identities=17%  Similarity=0.389  Sum_probs=25.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC--CCcEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM--SYDVY  253 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l--~~~~~  253 (480)
                      .-++++|+||||||++++.++..+  +..++
T Consensus         3 ~~i~v~G~pG~GKtt~~~~l~~~l~~~~~~~   33 (188)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKIV   33 (188)
T ss_pred             eEEEEEeCCCCCHHHHHHHHHHHhccCCeEE
Confidence            468999999999999999999999  55553

>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]

Probab=96.90  E-value=0.00059  Score=63.07  Aligned_cols=29  Identities=21%  Similarity=0.503  Sum_probs=26.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +++.|.|||||||+++.++ ++|++.+.++
T Consensus         3 I~ITGTPGvGKTT~~~~L~-~lg~~~i~l~   31 (180)
T COG1936           3 IAITGTPGVGKTTVCKLLR-ELGYKVIELN   31 (180)
T ss_pred             EEEeCCCCCchHHHHHHHH-HhCCceeeHH
Confidence            7899999999999999999 9998887764

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=96.90  E-value=0.0022  Score=61.90  Aligned_cols=22  Identities=32%  Similarity=0.536  Sum_probs=19.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      +-++|.||+|+|||++.+.++.
T Consensus        31 ~~~~l~Gpn~sGKstllr~i~~   52 (216)
T cd03284          31 QILLITGPNMAGKSTYLRQVAL   52 (216)
T ss_pred             eEEEEECCCCCChHHHHHHHHH
Confidence            4588999999999999999974

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>PRK14974 cell division protein FtsY; Provisional

Probab=96.90  E-value=0.0051  Score=63.32  Aligned_cols=61  Identities=21%  Similarity=0.328  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHhhhhHHh---hh-CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          198 LKNRVKSDLESFLKAKHYYH---RL-GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       198 ~k~~l~e~l~~~l~~~~~~~---~~-g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      +++.+.+.+...+.....+.   .. ....+.-++|.||||+||||+++.+|..+   |..+..+++.
T Consensus       110 ~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~vi~~~G~~GvGKTTtiakLA~~l~~~g~~V~li~~D  177 (336)
T PRK14974        110 VKNALKEALLEVLSVGDLFDLIEEIKSKGKPVVIVFVGVNGTGKTTTIAKLAYYLKKNGFSVVIAAGD  177 (336)
T ss_pred             HHHHHHHHHHHHhCCCcchhhhhhhhccCCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            45556666665554322111   11 11234578999999999999999998765   4555555544

>PRK06581 DNA polymerase III subunit delta'; Validated

Probab=96.89  E-value=0.016  Score=56.79  Aligned_cols=125  Identities=9%  Similarity=0.088  Sum_probs=91.1

Q ss_pred             CceEEEEccCC-CcHHHHHHHHHHcC---------CCcEEEEeCC-------CcCChHHHHHHHHhh------cCCcEEE
Q 011664          224 KRSYLLYGPSG-TGKSSFAAAMASFM---------SYDVYDVDLS-------RVADDADLKSLLLQT------TSKSVIL  280 (480)
Q Consensus       224 ~rgiLL~GPpG-TGKT~La~aiA~~l---------~~~~~~i~~s-------~~~~~~~l~~l~~~~------~~~sII~  280 (480)
                      ...||+.|..+ +||.-++.-++..+         +-+++.+...       ...+-.++|++....      ...-|++
T Consensus        15 shAYLfeG~n~~~~~~~~~~f~~~~l~~~~i~~~~HPD~~~I~pe~~~~~~~~~I~IdqIReL~~~l~~~p~~g~~KViI   94 (263)
T PRK06581         15 YNSWLIEAENIEQALKDLEKFIYIKLFKNSIPLENNPDYHFIARETSATSNAKNISIEQIRKLQDFLSKTSAISGYKVAI   94 (263)
T ss_pred             hheeeEeCCChhhHHHHHHHHHHHHHhccCcccCCCCCEEEEeccccccccCCcccHHHHHHHHHHHhhCcccCCcEEEE
Confidence            45799999998 99999988877644         2356666533       233455566654332      2457999


Q ss_pred             EecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          281 IEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       281 IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                      |+++|.+.     ....+.||..++.     .+.+.++|+.|..++.|-|.+++  |+ ..+.++.|+...-.++...++
T Consensus        95 I~~ae~mt-----~~AANALLKtLEE-----PP~~t~fILit~~~~~LLpTIrS--RC-q~i~~~~p~~~~~~e~~~~~~  161 (263)
T PRK06581         95 IYSAELMN-----LNAANSCLKILED-----APKNSYIFLITSRAASIISTIRS--RC-FKINVRSSILHAYNELYSQFI  161 (263)
T ss_pred             EechHHhC-----HHHHHHHHHhhcC-----CCCCeEEEEEeCChhhCchhHhh--ce-EEEeCCCCCHHHHHHHHHHhc
Confidence            99999883     3445778888764     24567888888899999999999  99 489999999877777766665


Q ss_pred             c
Q 011664          361 G  361 (480)
Q Consensus       361 ~  361 (480)
                      .
T Consensus       162 ~  162 (263)
T PRK06581        162 Q  162 (263)
T ss_pred             c
Confidence            4

>PRK04182 cytidylate kinase; Provisional

Probab=96.87  E-value=0.00093  Score=61.53  Aligned_cols=30  Identities=23%  Similarity=0.408  Sum_probs=27.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -|.|.|+||||||++++++|..+|++++..
T Consensus         2 ~I~i~G~~GsGKstia~~la~~lg~~~id~   31 (180)
T PRK04182          2 IITISGPPGSGKTTVARLLAEKLGLKHVSA   31 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCCcEecH
Confidence            378999999999999999999999988763

>COG1855 ATPase (PilT family) [General function prediction only]

Probab=96.86  E-value=0.00091  Score=69.94  Aligned_cols=45  Identities=31%  Similarity=0.585  Sum_probs=39.1

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .++++-...+.+++.|.+                  ..+|+|+.||||.|||++|+|+|..+.
T Consensus       244 ~~ledY~L~dkl~eRL~e------------------raeGILIAG~PGaGKsTFaqAlAefy~  288 (604)
T COG1855         244 LSLEDYGLSDKLKERLEE------------------RAEGILIAGAPGAGKSTFAQALAEFYA  288 (604)
T ss_pred             echhhcCCCHHHHHHHHh------------------hhcceEEecCCCCChhHHHHHHHHHHH
Confidence            478999999999988875                  246999999999999999999998763

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=96.86  E-value=0.00064  Score=64.65  Aligned_cols=22  Identities=36%  Similarity=0.649  Sum_probs=17.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .++.||||||||+++.+++..+
T Consensus        20 ~~i~GpPGTGKT~~l~~~i~~~   41 (236)
T PF13086_consen   20 TLIQGPPGTGKTTTLASIIAQL   41 (236)
T ss_dssp             EEEE-STTSSHHHHHHHHHHHH
T ss_pred             EEEECCCCCChHHHHHHHHHHh
Confidence            8899999999998777766654

>PHA00350 putative assembly protein

Probab=96.85  E-value=0.0022  Score=67.16  Aligned_cols=107  Identities=10%  Similarity=0.104  Sum_probs=60.5

Q ss_pred             EEEEccCCCcHHHHHHH--HH--HcCCCcEEEEeCCCcCCh--------------------------HHHHHHHHhhcCC
Q 011664          227 YLLYGPSGTGKSSFAAA--MA--SFMSYDVYDVDLSRVADD--------------------------ADLKSLLLQTTSK  276 (480)
Q Consensus       227 iLL~GPpGTGKT~La~a--iA--~~l~~~~~~i~~s~~~~~--------------------------~~l~~l~~~~~~~  276 (480)
                      ++++|+||+|||.-|-.  +-  -..|..++. ++..+.-+                          ..+...+.-....
T Consensus         4 ~l~tG~pGSGKT~~aV~~~i~palk~GR~V~T-NI~Gl~le~i~~~~~~~p~~~~li~i~~~~~~~~~~~~~~~~w~p~g   82 (399)
T PHA00350          4 YAIVGRPGSYKSYEAVVYHIIPALKDGRKVIT-NIPGLNLDVFEKVFGEFPSTARLIRIVDRNLEGFESMNRPFSWRPRG   82 (399)
T ss_pred             EEEecCCCCchhHHHHHHHHHHHHHCCCEEEE-CCCCCCHHHHHhhcccCcccceeEEeccccccchhhhccccccCCCC
Confidence            68899999999987765  32  233655543 43322111                          0011111113466


Q ss_pred             cEEEEecccccccCcccc------------------cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCce
Q 011664          277 SVILIEDLDRFLVEKPAA------------------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRI  338 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~------------------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRf  338 (480)
                      ++|+|||+..+.+.+...                  .....+++.+.--    ...+.=||++|.++..||..++.  +.
T Consensus        83 aLIViDEaq~~~p~r~~~~~~~~~~~p~~~~~~~~~~~p~~~i~~l~~H----RH~G~DIiliTQ~~~~Id~~iR~--lv  156 (399)
T PHA00350         83 ALYVIDEAQMIFPKRLGFKMANIFKRPFTDFEPHLPEGPENFLEAFMRH----RHYNWDIILLTPNIRKIHSDIRA--MI  156 (399)
T ss_pred             CEEEEECchhhcCCCccccccccccccccccccccccCCHHHHHHHHHh----cccCceEEEEeCCHHHhhHHHHH--hh
Confidence            899999999998765431                  0012233333211    12344478888889899988775  65


Q ss_pred             eE
Q 011664          339 DV  340 (480)
Q Consensus       339 d~  340 (480)
                      +.
T Consensus       157 E~  158 (399)
T PHA00350        157 EM  158 (399)
T ss_pred             hh
Confidence            54

>PRK14527 adenylate kinase; Provisional

Probab=96.84  E-value=0.00085  Score=63.15  Aligned_cols=32  Identities=22%  Similarity=0.448  Sum_probs=26.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +.-++++||||+|||++++.+|..++...+..
T Consensus         6 ~~~i~i~G~pGsGKsT~a~~La~~~~~~~is~   37 (191)
T PRK14527          6 NKVVIFLGPPGAGKGTQAERLAQELGLKKLST   37 (191)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCCCCCc
Confidence            34689999999999999999999988655443

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=96.83  E-value=0.0047  Score=63.85  Aligned_cols=62  Identities=23%  Similarity=0.404  Sum_probs=39.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC----CcEEEEeCC-Cc---------C----C--hHHHHHHHHh--hcCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS----YDVYDVDLS-RV---------A----D--DADLKSLLLQ--TTSKSVILI  281 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~----~~~~~i~~s-~~---------~----~--~~~l~~l~~~--~~~~sII~I  281 (480)
                      ...+++.||+|+||||+++++.+++.    ..++.+.-. ++         .    +  ...+...+..  ...|.+|++
T Consensus       122 ~g~ili~G~tGSGKTT~l~al~~~i~~~~~~~i~tiEdp~E~~~~~~~~~i~q~evg~~~~~~~~~l~~~lr~~pd~i~v  201 (343)
T TIGR01420       122 RGLILVTGPTGSGKSTTLASMIDYINKNAAGHIITIEDPIEYVHRNKRSLINQREVGLDTLSFANALRAALREDPDVILI  201 (343)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCcCCCCEEEEEcCChhhhccCccceEEccccCCCCcCHHHHHHHhhccCCCEEEE
Confidence            34688999999999999999998664    234433200 00         0    0  1123333332  258999999


Q ss_pred             eccc
Q 011664          282 EDLD  285 (480)
Q Consensus       282 DEiD  285 (480)
                      ||+-
T Consensus       202 gEir  205 (343)
T TIGR01420       202 GEMR  205 (343)
T ss_pred             eCCC
Confidence            9995

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK01184 hypothetical protein; Provisional

Probab=96.82  E-value=0.001  Score=62.06  Aligned_cols=29  Identities=28%  Similarity=0.343  Sum_probs=24.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -++|.||||+||||+++ ++.++|++++..
T Consensus         3 ~i~l~G~~GsGKsT~a~-~~~~~g~~~i~~   31 (184)
T PRK01184          3 IIGVVGMPGSGKGEFSK-IAREMGIPVVVM   31 (184)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHcCCcEEEh
Confidence            47899999999999987 788888877664

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

Probab=96.80  E-value=0.0034  Score=60.03  Aligned_cols=115  Identities=30%  Similarity=0.376  Sum_probs=66.8

Q ss_pred             hHHhhhC--CCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEE----------------------------------E
Q 011664          214 HYYHRLG--RVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVY----------------------------------D  254 (480)
Q Consensus       214 ~~~~~~g--~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~----------------------------------~  254 (480)
                      +.-+++|  +|.+.=+++.|+.|||||-|.+.++.-+   |..+.                                  .
T Consensus        16 elDkrLGGGiP~GsL~lIEGd~~tGKSvLsqr~~YG~L~~g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~   95 (235)
T COG2874          16 ELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNGYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFP   95 (235)
T ss_pred             HHHhhccCCCccCeEEEEECCCCccHHHHHHHHHHHHHhCCceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEE
Confidence            3444554  5666567889999999999999998421   23332                                  3


Q ss_pred             EeCCCcCChHH-----HHHHH--HhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          255 VDLSRVADDAD-----LKSLL--LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       255 i~~s~~~~~~~-----l~~l~--~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      +++..+..+..     +..++  .+.....||+||-+..+.... +.   .+.+++|..+.. .|..+++||+|. ||..
T Consensus        96 ~~~~~~~~~~~~~~~~L~~l~~~~k~~~~dViIIDSls~~~~~~-~~---~~vl~fm~~~r~-l~d~gKvIilTv-hp~~  169 (235)
T COG2874          96 VNLEPVNWGRRSARKLLDLLLEFIKRWEKDVIIIDSLSAFATYD-SE---DAVLNFMTFLRK-LSDLGKVIILTV-HPSA  169 (235)
T ss_pred             ecccccccChHHHHHHHHHHHhhHHhhcCCEEEEecccHHhhcc-cH---HHHHHHHHHHHH-HHhCCCEEEEEe-Chhh
Confidence            33222222111     22222  233467899999999876432 22   334444443333 334677777665 5778


Q ss_pred             CcccccC
Q 011664          328 VDQALLR  334 (480)
Q Consensus       328 LD~aLlr  334 (480)
                      ++++++-
T Consensus       170 l~e~~~~  176 (235)
T COG2874         170 LDEDVLT  176 (235)
T ss_pred             cCHHHHH
Confidence            8887765

>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells

Probab=96.79  E-value=0.0008  Score=60.77  Aligned_cols=26  Identities=27%  Similarity=0.427  Sum_probs=22.3

Q ss_pred             EEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          229 LYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       229 L~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      |.||||+|||++++.||...|...+.
T Consensus         1 i~G~PgsGK~t~~~~la~~~~~~~is   26 (151)
T PF00406_consen    1 ILGPPGSGKGTQAKRLAKRYGLVHIS   26 (151)
T ss_dssp             EEESTTSSHHHHHHHHHHHHTSEEEE
T ss_pred             CcCCCCCChHHHHHHHHHhcCcceec
Confidence            57999999999999999998765444

Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....

>TIGR02173 cyt_kin_arch cytidylate kinase, putative

Probab=96.78  E-value=0.0012  Score=60.32  Aligned_cols=29  Identities=28%  Similarity=0.518  Sum_probs=26.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +.++|+||+|||++++.+|+.+|++++..
T Consensus         3 I~i~G~~GSGKstia~~la~~lg~~~~~~   31 (171)
T TIGR02173         3 ITISGPPGSGKTTVAKILAEKLSLKLISA   31 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCceecH
Confidence            78999999999999999999999887664

Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=96.78  E-value=0.0024  Score=61.19  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=19.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      +-++|.||.|+|||++.+.++.
T Consensus        30 ~~~~l~G~n~~GKstll~~i~~   51 (204)
T cd03282          30 RFHIITGPNMSGKSTYLKQIAL   51 (204)
T ss_pred             cEEEEECCCCCCHHHHHHHHHH
Confidence            5689999999999999999973

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

>PF10236 DAP3: Mitochondrial ribosomal death-associated protein 3; InterPro: IPR019368 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=96.78  E-value=0.031  Score=56.98  Aligned_cols=86  Identities=12%  Similarity=0.169  Sum_probs=48.0

Q ss_pred             CCcEEEEecccccccCccc-----c------cc-hhhhhhhcccccccccCCceEE--EEecC---CCc--cCcccccCC
Q 011664          275 SKSVILIEDLDRFLVEKPA-----A------VS-LSGVLNFMDGVLNSCCFEERVM--VFTMN---SKD--HVDQALLRP  335 (480)
Q Consensus       275 ~~sII~IDEiD~l~~~~~~-----~------~~-ls~lL~~ldg~~~~~~~~~~iv--I~tTN---~~~--~LD~aLlrp  335 (480)
                      -|.++.||++.+++....-     .      -+ ...|+..+.|-.+ - .++.++  +.+|.   .+.  .++.+|...
T Consensus       156 ~PVL~avD~~n~l~~~S~Y~~~~~~~I~~~~L~l~~~f~~~~s~~~~-~-~nG~~v~~l~~t~~~~~~~~~~l~~~L~~~  233 (309)
T PF10236_consen  156 PPVLVAVDGFNALFGPSAYRDPDFKPIHPHDLTLVRLFLDLLSGKRD-F-KNGAVVTALAATSVSNAPKSPTLPVALGGK  233 (309)
T ss_pred             CceEEEehhhHHhhCCccccCCCCccccHHHhhHHHHHHHHhcCccc-c-CCCeEEEEEeccccccccCCccchhhhccc
Confidence            4778899999998864210     0      11 2334555443332 1 234443  44432   333  456666531


Q ss_pred             Cce---e----------------EEEEcCCCCHHHHHHHHHHHhcc
Q 011664          336 GRI---D----------------VHIHFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       336 GRf---d----------------~~I~~~~p~~~~r~~il~~~l~~  362 (480)
                      .-+   |                ..|+++..+.++.+.+++.|...
T Consensus       234 ~~~~~~dPy~~~d~~~~~~l~~~~~i~v~~~s~~E~~~ll~yy~~~  279 (309)
T PF10236_consen  234 EGFPHLDPYVKRDPRVAESLKGVKPIEVPRLSKEEARSLLEYYADS  279 (309)
T ss_pred             cCCCCCCCcccccHHHHHHhcCCceEEeCCCCHHHHHHHHHHHHHC
Confidence            111   1                16788899999998888888653

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).

>PLN03187 meiotic recombination protein DMC1 homolog; Provisional

Probab=96.78  E-value=0.004  Score=64.28  Aligned_cols=40  Identities=18%  Similarity=0.121  Sum_probs=29.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---------CCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---------MSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---------l~~~~~~i~~s~  259 (480)
                      |++...-+.++||||||||.|+..+|-.         .+..+++++...
T Consensus       122 Gi~~G~ItEI~G~~GsGKTql~lqlav~~qlp~~~gg~~~~vvyIdTE~  170 (344)
T PLN03187        122 GIETRCITEAFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEG  170 (344)
T ss_pred             CCCCCeEEEEecCCCCChhHHHHHHHHHHhcchhhCCCCceEEEEEcCC
Confidence            5666666789999999999999988631         134677777643

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=96.78  E-value=0.0038  Score=56.20  Aligned_cols=65  Identities=20%  Similarity=0.319  Sum_probs=40.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCc---EE-----EEe-CCCcCChHHHHHH-HHh--hcCCcEEEEecccccc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYD---VY-----DVD-LSRVADDADLKSL-LLQ--TTSKSVILIEDLDRFL  288 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~-----~i~-~s~~~~~~~l~~l-~~~--~~~~sII~IDEiD~l~  288 (480)
                      ....+.+.||+|+|||+|++++++.....   ++     .+. +.++. ..+.+++ +++  ..+|.++++||-..-+
T Consensus        25 ~Ge~~~i~G~nGsGKStLl~~l~G~~~~~~G~i~~~~~~~i~~~~~lS-~G~~~rv~laral~~~p~illlDEP~~~L  101 (144)
T cd03221          25 PGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLS-GGEKMRLALAKLLLENPNLLLLDEPTNHL  101 (144)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHcCCCCCCceEEEECCeEEEEEEccCC-HHHHHHHHHHHHHhcCCCEEEEeCCccCC
Confidence            34468899999999999999999976321   10     111 11122 2232222 232  3689999999987544

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PHA02530 pseT polynucleotide kinase; Provisional

Probab=96.78  E-value=0.0013  Score=66.21  Aligned_cols=31  Identities=26%  Similarity=0.276  Sum_probs=25.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-CCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-SYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i  255 (480)
                      .-+++.|||||||||+|+.++..+ +..+++.
T Consensus         3 ~liil~G~pGSGKSTla~~L~~~~~~~~~l~~   34 (300)
T PHA02530          3 KIILTVGVPGSGKSTWAREFAAKNPKAVNVNR   34 (300)
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHCCCCEEEec
Confidence            458899999999999999999998 5544443

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=96.77  E-value=0.0021  Score=58.92  Aligned_cols=96  Identities=17%  Similarity=0.266  Sum_probs=52.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc---------------CCCcEEEEe----C--CCcCC-hHH---HHHHHHhhc--CCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF---------------MSYDVYDVD----L--SRVAD-DAD---LKSLLLQTT--SKS  277 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~---------------l~~~~~~i~----~--s~~~~-~~~---l~~l~~~~~--~~s  277 (480)
                      +-.++.||.|+|||++.++++-.               .+......+    .  ..+.+ ..+   +...+....  .|+
T Consensus        22 ~~~~i~G~NgsGKS~~l~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~i~~~~~lS~G~~~~~~la~~L~~~~~~~~~  101 (162)
T cd03227          22 SLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAELIFTRLQLSGGEKELSALALILALASLKPRP  101 (162)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHhcchhhhccCcccCCCcceeeEEEEehheeeccccHHHHHHHHHHHHhcCCCCCC
Confidence            47889999999999999998632               233222222    1  11221 222   333344333  789


Q ss_pred             EEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          278 VILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       278 II~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      ++++||...-...... ..+...+..   ...   . +..+|++|..++..
T Consensus       102 llllDEp~~gld~~~~-~~l~~~l~~---~~~---~-~~~vii~TH~~~~~  144 (162)
T cd03227         102 LYILDEIDRGLDPRDG-QALAEAILE---HLV---K-GAQVIVITHLPELA  144 (162)
T ss_pred             EEEEeCCCCCCCHHHH-HHHHHHHHH---HHh---c-CCEEEEEcCCHHHH
Confidence            9999999865432221 122222222   111   1 34677778766543

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.77  E-value=0.004  Score=66.40  Aligned_cols=83  Identities=19%  Similarity=0.339  Sum_probs=55.6

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCce-EEEEccCCCcHHHHHHHHHHcCCCc---EEEEe-----
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRS-YLLYGPSGTGKSSFAAAMASFMSYD---VYDVD-----  256 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rg-iLL~GPpGTGKT~La~aiA~~l~~~---~~~i~-----  256 (480)
                      ..+|+++++.+...+.+.+.+.               .|.| +|+.||.|+|||+..-++-++++.+   ++.+.     
T Consensus       234 ~l~l~~Lg~~~~~~~~~~~~~~---------------~p~GliLvTGPTGSGKTTTLY~~L~~ln~~~~nI~TiEDPVE~  298 (500)
T COG2804         234 ILDLEKLGMSPFQLARLLRLLN---------------RPQGLILVTGPTGSGKTTTLYAALSELNTPERNIITIEDPVEY  298 (500)
T ss_pred             cCCHHHhCCCHHHHHHHHHHHh---------------CCCeEEEEeCCCCCCHHHHHHHHHHHhcCCCceEEEeeCCeee
Confidence            4578999999988888776554               2345 5677999999999999999888543   44332     


Q ss_pred             -CCCcC--------C---hHHHHHHHHhhcCCcEEEEeccc
Q 011664          257 -LSRVA--------D---DADLKSLLLQTTSKSVILIEDLD  285 (480)
Q Consensus       257 -~s~~~--------~---~~~l~~l~~~~~~~sII~IDEiD  285 (480)
                       .+.+.        +   ...++.++  .+.|.||++.||-
T Consensus       299 ~~~gI~Q~qVN~k~gltfa~~LRa~L--RqDPDvImVGEIR  337 (500)
T COG2804         299 QLPGINQVQVNPKIGLTFARALRAIL--RQDPDVIMVGEIR  337 (500)
T ss_pred             ecCCcceeecccccCCCHHHHHHHHh--ccCCCeEEEeccC
Confidence             11111        0   12233333  2589999999996

>PTZ00035 Rad51 protein; Provisional

Probab=96.76  E-value=0.0046  Score=63.78  Aligned_cols=40  Identities=20%  Similarity=0.176  Sum_probs=29.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~  259 (480)
                      |++...-+.++||||||||+++..+|...         +..+++++...
T Consensus       114 Gi~~G~iteI~G~~GsGKT~l~~~l~~~~qlp~~~gg~~g~vvyIdtE~  162 (337)
T PTZ00035        114 GIETGSITELFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEG  162 (337)
T ss_pred             CCCCCeEEEEECCCCCchhHHHHHHHHHhccccccCCCCceEEEEEccC
Confidence            56666667899999999999999887422         34566776543

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=96.76  E-value=0.0049  Score=63.11  Aligned_cols=25  Identities=24%  Similarity=0.505  Sum_probs=22.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +.++|+.||+|+|||++++|++.++
T Consensus       144 ~~nilI~G~tGSGKTTll~aL~~~i  168 (323)
T PRK13833        144 RLNIVISGGTGSGKTTLANAVIAEI  168 (323)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHH
Confidence            4589999999999999999999875

>PF13521 AAA_28: AAA domain; PDB: 1LW7_A

Probab=96.75  E-value=0.0011  Score=60.48  Aligned_cols=26  Identities=31%  Similarity=0.508  Sum_probs=20.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      |.|.|+||||||||+++++.. |.+++
T Consensus         2 I~i~G~~stGKTTL~~~L~~~-g~~~v   27 (163)
T PF13521_consen    2 IVITGGPSTGKTTLIEALAAR-GYPVV   27 (163)
T ss_dssp             EEEE--TTSHHHHHHHHHHHH-T-EEE
T ss_pred             EEEECCCCCCHHHHHHHHHHc-CCeEE
Confidence            789999999999999999998 76655

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.74  E-value=0.0077  Score=63.57  Aligned_cols=63  Identities=19%  Similarity=0.319  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHHHHHhhh-hHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCC
Q 011664          197 DLKNRVKSDLESFLKAK-HYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSR  259 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~-~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~  259 (480)
                      ++.+.+.+.+...+.-. ..+...|...+.-+++.||+|+||||++..+|...    |..+..+++..
T Consensus       195 ~~~~~l~~~L~~~l~~~~~~~~~~g~~~~~vi~lvGptGvGKTTtaaKLA~~~~~~~G~~V~Lit~Dt  262 (432)
T PRK12724        195 NVTERAVTYLEERVSVDSDLFSGTGKNQRKVVFFVGPTGSGKTTSIAKLAAKYFLHMGKSVSLYTTDN  262 (432)
T ss_pred             HHHHHHHHHHHHhcccchhhhhhcccCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEecccc
Confidence            45555555555544321 11222222234458899999999999999999643    44555555443

>TIGR00416 sms DNA repair protein RadA

Probab=96.74  E-value=0.0038  Score=66.89  Aligned_cols=70  Identities=17%  Similarity=0.247  Sum_probs=47.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC--------------------hHHHHHHHH--hhc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD--------------------DADLKSLLL--QTT  274 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~--------------------~~~l~~l~~--~~~  274 (480)
                      |++...-+|++|+||+|||+|+..+|..+   +.++++++..+-..                    +..+..+..  ...
T Consensus        90 Gi~~GsvilI~G~pGsGKTTL~lq~a~~~a~~g~kvlYvs~EEs~~qi~~ra~rlg~~~~~l~~~~e~~~~~I~~~i~~~  169 (454)
T TIGR00416        90 GIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMKVLYVSGEESLQQIKMRAIRLGLPEPNLYVLSETNWEQICANIEEE  169 (454)
T ss_pred             CccCCeEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEECcCCHHHHHHHHHHcCCChHHeEEcCCCCHHHHHHHHHhc
Confidence            56666678999999999999999987754   45677776532210                    111222221  234


Q ss_pred             CCcEEEEeccccccc
Q 011664          275 SKSVILIEDLDRFLV  289 (480)
Q Consensus       275 ~~sII~IDEiD~l~~  289 (480)
                      .|.+|+||.|..+..
T Consensus       170 ~~~~vVIDSIq~l~~  184 (454)
T TIGR00416       170 NPQACVIDSIQTLYS  184 (454)
T ss_pred             CCcEEEEecchhhcc
Confidence            789999999988754

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=96.72  E-value=0.0078  Score=65.08  Aligned_cols=86  Identities=17%  Similarity=0.342  Sum_probs=54.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCce-EEEEccCCCcHHHHHHHHHHcCC---CcEEEEe----
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRS-YLLYGPSGTGKSSFAAAMASFMS---YDVYDVD----  256 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rg-iLL~GPpGTGKT~La~aiA~~l~---~~~~~i~----  256 (480)
                      .+.++++++..++..+.+...+.               .+.| ++++||+|+|||++..++.+++.   .+++.+.    
T Consensus       217 ~~~~l~~Lg~~~~~~~~l~~~~~---------------~~~GlilitGptGSGKTTtL~a~L~~l~~~~~~iiTiEDpvE  281 (486)
T TIGR02533       217 VRLDLETLGMSPELLSRFERLIR---------------RPHGIILVTGPTGSGKTTTLYAALSRLNTPERNILTVEDPVE  281 (486)
T ss_pred             CCCCHHHcCCCHHHHHHHHHHHh---------------cCCCEEEEEcCCCCCHHHHHHHHHhccCCCCCcEEEEcCCee
Confidence            34588999888887777665332               2334 68999999999999998887764   3455542    


Q ss_pred             --CCCcC-----Ch--HHHHHHHHh--hcCCcEEEEeccc
Q 011664          257 --LSRVA-----DD--ADLKSLLLQ--TTSKSVILIEDLD  285 (480)
Q Consensus       257 --~s~~~-----~~--~~l~~l~~~--~~~~sII~IDEiD  285 (480)
                        +..+.     ..  ......+..  ...|.||++.||-
T Consensus       282 ~~~~~~~q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEiR  321 (486)
T TIGR02533       282 YQIEGIGQIQVNPKIGLTFAAGLRAILRQDPDIIMVGEIR  321 (486)
T ss_pred             eecCCCceEEEccccCccHHHHHHHHHhcCCCEEEEeCCC
Confidence              11110     00  111122211  2589999999996

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]

Probab=96.72  E-value=0.0014  Score=61.52  Aligned_cols=31  Identities=32%  Similarity=0.555  Sum_probs=25.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS  258 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s  258 (480)
                      .+++.||||+||||+|+.+|+.  +++..++..
T Consensus         2 riiilG~pGaGK~T~A~~La~~--~~i~hlstg   32 (178)
T COG0563           2 RILILGPPGAGKSTLAKKLAKK--LGLPHLDTG   32 (178)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH--hCCcEEcHh
Confidence            4899999999999999999999  445555543

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=96.72  E-value=0.0068  Score=62.01  Aligned_cols=25  Identities=32%  Similarity=0.603  Sum_probs=22.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ++++++.||+|+|||+++++++.+.
T Consensus       148 ~~~ilI~G~tGSGKTTll~aL~~~~  172 (319)
T PRK13894        148 HRNILVIGGTGSGKTTLVNAIINEM  172 (319)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHhh
Confidence            4689999999999999999999863

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=96.71  E-value=0.0035  Score=62.78  Aligned_cols=59  Identities=24%  Similarity=0.465  Sum_probs=43.0

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCce-EEEEccCCCcHHHHHHHHHHcCCC----c
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRS-YLLYGPSGTGKSSFAAAMASFMSY----D  251 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rg-iLL~GPpGTGKT~La~aiA~~l~~----~  251 (480)
                      ..+.+|. ...+|+.++..+-+.+ +.+                  .++| ||..||.|||||+..+||-++++.    +
T Consensus        97 vlR~Ip~-~i~~~e~LglP~i~~~-~~~------------------~~~GLILVTGpTGSGKSTTlAamId~iN~~~~~H  156 (353)
T COG2805          97 VLRLIPS-KIPTLEELGLPPIVRE-LAE------------------SPRGLILVTGPTGSGKSTTLAAMIDYINKHKAKH  156 (353)
T ss_pred             EEeccCc-cCCCHHHcCCCHHHHH-HHh------------------CCCceEEEeCCCCCcHHHHHHHHHHHHhccCCcc
Confidence            5677784 4558999988876665 321                  3445 567799999999999999988754    4


Q ss_pred             EEEE
Q 011664          252 VYDV  255 (480)
Q Consensus       252 ~~~i  255 (480)
                      ++.+
T Consensus       157 IlTI  160 (353)
T COG2805         157 ILTI  160 (353)
T ss_pred             eEEe
Confidence            5555

>PRK14526 adenylate kinase; Provisional

Probab=96.70  E-value=0.0014  Score=63.10  Aligned_cols=28  Identities=25%  Similarity=0.570  Sum_probs=24.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ++|.||||||||++++.+|..++...+.
T Consensus         3 i~l~G~pGsGKsT~a~~La~~~~~~~is   30 (211)
T PRK14526          3 LVFLGPPGSGKGTIAKILSNELNYYHIS   30 (211)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceee
Confidence            7899999999999999999998866544

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=96.70  E-value=0.0041  Score=58.15  Aligned_cols=24  Identities=25%  Similarity=0.285  Sum_probs=20.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ...-+.|.||+|+|||||.+++..
T Consensus        20 ~G~~~~l~G~nG~GKSTLl~~il~   43 (176)
T cd03238          20 LNVLVVVTGVSGSGKSTLVNEGLY   43 (176)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhh
Confidence            344578999999999999999974

Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.

>TIGR00235 udk uridine kinase

Probab=96.70  E-value=0.011  Score=56.44  Aligned_cols=25  Identities=24%  Similarity=0.275  Sum_probs=21.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -+.+.||+|+|||||++++++.++.
T Consensus         8 vi~I~G~sGsGKSTl~~~l~~~l~~   32 (207)
T TIGR00235         8 IIGIGGGSGSGKTTVARKIYEQLGK   32 (207)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcc
Confidence            3568999999999999999998753

Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.70  E-value=0.0051  Score=58.53  Aligned_cols=34  Identities=26%  Similarity=0.398  Sum_probs=24.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      |+-++|.||+|+||||.+.-+|..+   +..+.-+.+
T Consensus         1 p~vi~lvGptGvGKTTt~aKLAa~~~~~~~~v~lis~   37 (196)
T PF00448_consen    1 PKVIALVGPTGVGKTTTIAKLAARLKLKGKKVALISA   37 (196)
T ss_dssp             SEEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEE
T ss_pred             CEEEEEECCCCCchHhHHHHHHHHHhhccccceeecC
Confidence            4568999999999999999998755   444444443

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK10078 ribose 1,5-bisphosphokinase; Provisional

Probab=96.69  E-value=0.0015  Score=61.26  Aligned_cols=29  Identities=34%  Similarity=0.440  Sum_probs=25.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      -+.|.||+|+||||+++.++..++.+++.
T Consensus         4 ~i~l~G~sGsGKsTl~~~l~~~~~~~~~~   32 (186)
T PRK10078          4 LIWLMGPSGSGKDSLLAALRQREQTQLLV   32 (186)
T ss_pred             EEEEECCCCCCHHHHHHHHhccCCCeEEE
Confidence            58899999999999999999988776544

>TIGR00150 HI0065_YjeE ATPase, YjeE family

Probab=96.68  E-value=0.0019  Score=57.61  Aligned_cols=29  Identities=21%  Similarity=0.373  Sum_probs=25.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ...-++|.|+.|+|||++++++++.++..
T Consensus        21 ~~~~i~l~G~lGaGKTtl~~~l~~~lg~~   49 (133)
T TIGR00150        21 FGTVVLLKGDLGAGKTTLVQGLLQGLGIQ   49 (133)
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcCCC
Confidence            34468899999999999999999999854

Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have ATPase activity.

>KOG0482 consensus DNA replication licensing factor, MCM7 component [Replication, recombination and repair]

Probab=96.67  E-value=0.0048  Score=65.47  Aligned_cols=166  Identities=18%  Similarity=0.124  Sum_probs=90.1

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC--CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe-CCCcCC--hHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVW--KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD-LSRVAD--DAD  265 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~--~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~-~s~~~~--~~~  265 (480)
                      .|.|++++|+.+.-.+.-   .+..-..-|.+.  .-+|+|.|-||..||-|.+.|.+-.-...|.-. .|+-.+  .+-
T Consensus       343 EIyGheDVKKaLLLlLVG---gvd~~~~dGMKIRGdINicLmGDPGVAKSQLLkyi~rlapRgvYTTGrGSSGVGLTAAV  419 (721)
T KOG0482|consen  343 EIYGHEDVKKALLLLLVG---GVDKSPGDGMKIRGDINICLMGDPGVAKSQLLKYISRLAPRGVYTTGRGSSGVGLTAAV  419 (721)
T ss_pred             hhccchHHHHHHHHHhhC---CCCCCCCCCceeecceeEEecCCCchhHHHHHHHHHhcCcccceecCCCCCccccchhh
Confidence            688999999988744431   211111112222  225899999999999999999987766665542 111111  000


Q ss_pred             HHHH------HH-h---hcCCcEEEEecccccccCcccccchhhhhhhc------ccccccccCCceEEEEecCCC----
Q 011664          266 LKSL------LL-Q---TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFM------DGVLNSCCFEERVMVFTMNSK----  325 (480)
Q Consensus       266 l~~l------~~-~---~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~l------dg~~~~~~~~~~ivI~tTN~~----  325 (480)
                      ++.-      +. .   .....|.+|||+|.+.......  .-+...+-      .|+.. .-+...-|++|.|..    
T Consensus       420 mkDpvTgEM~LEGGALVLAD~GICCIDEfDKM~e~DRtA--IHEVMEQQTISIaKAGI~T-tLNAR~sILaAANPayGRY  496 (721)
T KOG0482|consen  420 MKDPVTGEMVLEGGALVLADGGICCIDEFDKMDESDRTA--IHEVMEQQTISIAKAGINT-TLNARTSILAAANPAYGRY  496 (721)
T ss_pred             hcCCCCCeeEeccceEEEccCceEeehhhhhhhhhhhHH--HHHHHHhhhhhhhhhcccc-chhhhHHhhhhcCcccccc
Confidence            1100      00 0   1356799999999986432111  11111100      12211 001112355565532    


Q ss_pred             ---------ccCcccccCCCceeEEE-EcCCCCHHHHHHHHHHHhccCC
Q 011664          326 ---------DHVDQALLRPGRIDVHI-HFPLCDFSSFKTLASSYLGLKD  364 (480)
Q Consensus       326 ---------~~LD~aLlrpGRfd~~I-~~~~p~~~~r~~il~~~l~~~~  364 (480)
                               =.|++||++  |||... -...|+.+.=..++++..-.+.
T Consensus       497 nprrs~e~NI~LPaALLS--RFDll~Li~D~pdrd~D~~LA~HiTyVH~  543 (721)
T KOG0482|consen  497 NPRRSPEQNINLPAALLS--RFDLLWLIQDRPDRDNDLRLAQHITYVHQ  543 (721)
T ss_pred             CcccChhHhcCCcHHHHH--hhhhhhhhccCCcccchHHHHHHhHhhhc
Confidence                     137899999  999544 4457888777777777654443

>cd02027 APSK Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS)

Probab=96.67  E-value=0.0017  Score=58.77  Aligned_cols=30  Identities=40%  Similarity=0.547  Sum_probs=25.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      ++++|+||+|||++++.++..+   +.+.+.++
T Consensus         2 i~i~G~~GsGKSTla~~L~~~l~~~g~~~~~i~   34 (149)
T cd02027           2 IWLTGLSGSGKSTIARALEEKLFQRGRPVYVLD   34 (149)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEEc
Confidence            6899999999999999999987   66666654

The end-product PAPS is a biologically "activated" sulfate form important for the assimilation of inorganic sulfate.

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=96.65  E-value=0.0057  Score=60.40  Aligned_cols=27  Identities=19%  Similarity=0.369  Sum_probs=23.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      ..-+++.||+|||||+|++.+++.+..
T Consensus        16 Gqr~~I~G~~G~GKTTLlr~I~n~l~~   42 (249)
T cd01128          16 GQRGLIVAPPKAGKTTLLQSIANAITK   42 (249)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcccc
Confidence            346899999999999999999998754

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.

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=96.64  E-value=0.016  Score=56.75  Aligned_cols=123  Identities=18%  Similarity=0.325  Sum_probs=71.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc---EEEEeCC---------------CcCChHHHH-----------HHHHhh-
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD---VYDVDLS---------------RVADDADLK-----------SLLLQT-  273 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~---~~~i~~s---------------~~~~~~~l~-----------~l~~~~-  273 (480)
                      +-.+.+.||+|||||+++..+-..+...   ++.+...               .+....++.           +...+. 
T Consensus        13 ~fr~viIG~sGSGKT~li~~lL~~~~~~f~~I~l~t~~~n~~~~~~i~p~~i~~~~~~e~le~~l~~~k~~I~k~~~k~~   92 (241)
T PF04665_consen   13 PFRMVIIGKSGSGKTTLIKSLLYYLRHKFDHIFLITPEYNNEYYKYIWPDHIFKVFDKEELEYILIRQKEKIEKYIKKSP   92 (241)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHhhcccCCEEEEEecCCchhhhhhcchhhccccccHHHHHHHHHHHHHHHHHHhhhhc
Confidence            4468999999999999999988766432   2222110               000111111           111101 


Q ss_pred             ----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          274 ----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       274 ----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                          ..+.+|++||+..   ....+..+.++++.  |-     --+.-+|+.+...-.|++.++.  =++..+-++ -+.
T Consensus        93 ~~k~~~~~LiIlDD~~~---~~~k~~~l~~~~~~--gR-----H~~is~i~l~Q~~~~lp~~iR~--n~~y~i~~~-~s~  159 (241)
T PF04665_consen   93 QKKNNPRFLIILDDLGD---KKLKSKILRQFFNN--GR-----HYNISIIFLSQSYFHLPPNIRS--NIDYFIIFN-NSK  159 (241)
T ss_pred             ccCCCCCeEEEEeCCCC---chhhhHHHHHHHhc--cc-----ccceEEEEEeeecccCCHHHhh--cceEEEEec-CcH
Confidence                2368999999753   11112234444431  11     2345677788888899999877  777777675 466


Q ss_pred             HHHHHHHHHH
Q 011664          350 SSFKTLASSY  359 (480)
Q Consensus       350 ~~r~~il~~~  359 (480)
                      .....|++.+
T Consensus       160 ~dl~~i~~~~  169 (241)
T PF04665_consen  160 RDLENIYRNM  169 (241)
T ss_pred             HHHHHHHHhc
Confidence            6666666655

This is thought to be an ATPase involved in viral DNA packaging [].

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=96.63  E-value=0.0042  Score=56.68  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=18.7

Q ss_pred             ceEEEEccCCCcHHH-HHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSS-FAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~-La~aiA~~l  248 (480)
                      +.+++.||+|||||. ++..+...+
T Consensus        25 ~~~~i~~~~GsGKT~~~~~~~~~~~   49 (201)
T smart00487       25 RDVILAAPTGSGKTLAALLPALEAL   49 (201)
T ss_pred             CcEEEECCCCCchhHHHHHHHHHHh
Confidence            579999999999999 555555544

>PF02367 UPF0079: Uncharacterised P-loop hydrolase UPF0079; InterPro: IPR003442 This group consists of bacterial proteins, which contain a P-loop

Probab=96.63  E-value=0.0047  Score=54.33  Aligned_cols=29  Identities=31%  Similarity=0.446  Sum_probs=23.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ...-++|+|+=|+|||+++++++..+|..
T Consensus        14 ~g~vi~L~GdLGaGKTtf~r~l~~~lg~~   42 (123)
T PF02367_consen   14 PGDVILLSGDLGAGKTTFVRGLARALGID   42 (123)
T ss_dssp             S-EEEEEEESTTSSHHHHHHHHHHHTT--
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHcCCC
Confidence            34568999999999999999999998764

They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements [].; PDB: 1HTW_A 1FL9_A.

>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea

Probab=96.62  E-value=0.0035  Score=58.42  Aligned_cols=26  Identities=27%  Similarity=0.493  Sum_probs=22.5

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...-+.|.||+|+|||+|++.+++..
T Consensus        24 ~G~~~~l~G~nGsGKStLl~~i~G~~   49 (180)
T cd03214          24 AGEIVGILGPNGAGKSTLLKTLAGLL   49 (180)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCCC
Confidence            33468899999999999999999876

Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.

>PLN02199 shikimate kinase

Probab=96.62  E-value=0.0034  Score=63.21  Aligned_cols=33  Identities=33%  Similarity=0.631  Sum_probs=30.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .+.|+|.|++|||||++++.+|+.+|++|++.|
T Consensus       102 ~~~I~LIG~~GSGKSTVgr~LA~~Lg~~fIDtD  134 (303)
T PLN02199        102 GRSMYLVGMMGSGKTTVGKLMSKVLGYTFFDCD  134 (303)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEehH
Confidence            458999999999999999999999999999887

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=96.60  E-value=0.0074  Score=55.82  Aligned_cols=25  Identities=28%  Similarity=0.620  Sum_probs=21.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||+|+|||+|++.+|+..
T Consensus        26 Ge~~~i~G~nGsGKStLl~~l~G~~   50 (173)
T cd03230          26 GEIYGLLGPNGAGKTTLIKIILGLL   50 (173)
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3458899999999999999999865

In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=96.60  E-value=0.0032  Score=65.77  Aligned_cols=24  Identities=21%  Similarity=0.378  Sum_probs=21.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -.+++||||+|||+|++.|++...
T Consensus       171 R~lIvgppGvGKTTLaK~Ian~I~  194 (416)
T PRK09376        171 RGLIVAPPKAGKTVLLQNIANSIT  194 (416)
T ss_pred             eEEEeCCCCCChhHHHHHHHHHHH
Confidence            378899999999999999998664

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

Probab=96.59  E-value=0.0027  Score=62.82  Aligned_cols=40  Identities=30%  Similarity=0.298  Sum_probs=33.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      |.+..+.+|++|+||||||+++..++...   |.++++++..+
T Consensus        19 G~p~g~~~lI~G~pGsGKT~f~~qfl~~~~~~ge~vlyvs~~e   61 (260)
T COG0467          19 GLPRGSVVLITGPPGTGKTIFALQFLYEGAREGEPVLYVSTEE   61 (260)
T ss_pred             CCcCCcEEEEEcCCCCcHHHHHHHHHHHHHhcCCcEEEEEecC
Confidence            57777889999999999999999887643   77888887754

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=96.58  E-value=0.0023  Score=63.42  Aligned_cols=39  Identities=26%  Similarity=0.134  Sum_probs=31.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s  258 (480)
                      |++....++++||||||||+++..+|..   .|.++.++++.
T Consensus        32 Gip~gs~~lI~G~pGtGKT~l~~qf~~~~a~~Ge~vlyis~E   73 (259)
T TIGR03878        32 GIPAYSVINITGVSDTGKSLMVEQFAVTQASRGNPVLFVTVE   73 (259)
T ss_pred             CeECCcEEEEEcCCCCCHHHHHHHHHHHHHhCCCcEEEEEec
Confidence            6667778999999999999999987653   36788888875

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

>PF01745 IPT: Isopentenyl transferase; InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid []

Probab=96.58  E-value=0.0019  Score=61.77  Aligned_cols=32  Identities=41%  Similarity=0.648  Sum_probs=26.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      -++++||+|||||.++-++|+..|.+++..|-
T Consensus         3 v~~i~GpT~tGKt~~ai~lA~~~g~pvI~~Dr   34 (233)
T PF01745_consen    3 VYLIVGPTGTGKTALAIALAQKTGAPVISLDR   34 (233)
T ss_dssp             EEEEE-STTSSHHHHHHHHHHHH--EEEEE-S
T ss_pred             EEEEECCCCCChhHHHHHHHHHhCCCEEEecc
Confidence            47899999999999999999999999999984

; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ZE8_C 2ZE5_A 2ZE7_A 2ZE6_A.

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.57  E-value=0.0069  Score=65.55  Aligned_cols=65  Identities=25%  Similarity=0.258  Sum_probs=43.1

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcC----------------------ChHHHHHHHHhhcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSRVA----------------------DDADLKSLLLQTTS  275 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~----------------------~~~~l~~l~~~~~~  275 (480)
                      +.+.+.|.||+|+|||+++..+|..+     +..+..++.....                      ....+...+.+...
T Consensus       349 ~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyRigA~EQLk~ya~iLgv~v~~a~d~~~L~~aL~~l~~  428 (559)
T PRK12727        349 RGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQRVGGREQLHSYGRQLGIAVHEADSAESLLDLLERLRD  428 (559)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEecccccccHHHHHHHhhcccCceeEecCcHHHHHHHHHHhcc
Confidence            34578899999999999999998743     2344444432211                      12345555555667


Q ss_pred             CcEEEEeccccc
Q 011664          276 KSVILIEDLDRF  287 (480)
Q Consensus       276 ~sII~IDEiD~l  287 (480)
                      ..+|+||.....
T Consensus       429 ~DLVLIDTaG~s  440 (559)
T PRK12727        429 YKLVLIDTAGMG  440 (559)
T ss_pred             CCEEEecCCCcc
Confidence            789999988754

>COG4178 ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]

Probab=96.56  E-value=0.0032  Score=68.94  Aligned_cols=24  Identities=38%  Similarity=0.504  Sum_probs=21.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      +...+|+.||+|||||+|.||||+
T Consensus       418 ~G~~llI~G~SG~GKTsLlRaiaG  441 (604)
T COG4178         418 PGERLLITGESGAGKTSLLRALAG  441 (604)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhc
Confidence            444699999999999999999997

>PF13479 AAA_24: AAA domain

Probab=96.55  E-value=0.0045  Score=59.51  Aligned_cols=57  Identities=25%  Similarity=0.475  Sum_probs=35.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC--C-------------CcCChHHHHHHHHh----hcCCcEEEEecccc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL--S-------------RVADDADLKSLLLQ----TTSKSVILIEDLDR  286 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~--s-------------~~~~~~~l~~l~~~----~~~~sII~IDEiD~  286 (480)
                      .++||||||+|||+++..+-     +.+.+++  +             .+.+-.++...+..    ...-..|+||-++.
T Consensus         5 ~~lIyG~~G~GKTt~a~~~~-----k~l~id~E~g~~~~~~~~~~~~i~i~s~~~~~~~~~~l~~~~~~y~tiVIDsis~   79 (213)
T PF13479_consen    5 KILIYGPPGSGKTTLAASLP-----KPLFIDTENGSDSLKFLDDGDVIPITSWEDFLEALDELEEDEADYDTIVIDSISW   79 (213)
T ss_pred             EEEEECCCCCCHHHHHHhCC-----CeEEEEeCCCccchhhhcCCCeeCcCCHHHHHHHHHHHHhccCCCCEEEEECHHH
Confidence            58999999999999999882     2222222  1             01123344444422    24568999998876


Q ss_pred             c
Q 011664          287 F  287 (480)
Q Consensus       287 l  287 (480)
                      +
T Consensus        80 ~   80 (213)
T PF13479_consen   80 L   80 (213)
T ss_pred             H
Confidence            5

>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]

Probab=96.54  E-value=0.0076  Score=58.47  Aligned_cols=23  Identities=30%  Similarity=0.531  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+-+.||+|||||||...++.-.
T Consensus        33 ~vaI~GpSGSGKSTLLniig~ld   55 (226)
T COG1136          33 FVAIVGPSGSGKSTLLNLLGGLD   55 (226)
T ss_pred             EEEEECCCCCCHHHHHHHHhccc
Confidence            47799999999999999998644

>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]

Probab=96.54  E-value=0.0085  Score=57.54  Aligned_cols=22  Identities=32%  Similarity=0.664  Sum_probs=19.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      .-+.+.||+|||||||.+++..
T Consensus        29 evv~iiGpSGSGKSTlLRclN~   50 (240)
T COG1126          29 EVVVIIGPSGSGKSTLLRCLNG   50 (240)
T ss_pred             CEEEEECCCCCCHHHHHHHHHC
Confidence            3588999999999999999986

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=96.53  E-value=0.0031  Score=61.61  Aligned_cols=40  Identities=33%  Similarity=0.282  Sum_probs=32.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~  259 (480)
                      |.+....+|++||||||||+++..++.+   -|.+.+++++.+
T Consensus        17 G~~~gs~~lI~G~pGsGKT~la~~~l~~~~~~ge~~lyvs~ee   59 (237)
T TIGR03877        17 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGIYVALEE   59 (237)
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHHHHcCCcEEEEEeeC
Confidence            6777788999999999999999876643   367788887643

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>TIGR03574 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal

Probab=96.53  E-value=0.0022  Score=63.04  Aligned_cols=31  Identities=32%  Similarity=0.494  Sum_probs=25.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      |+|+|+||+|||++|+++|..+   +.+++.++.
T Consensus         2 Ivl~G~pGSGKST~a~~La~~l~~~~~~v~~i~~   35 (249)
T TIGR03574         2 IILTGLPGVGKSTFSKELAKKLSEKNIDVIILGT   35 (249)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHcCCceEEEcc
Confidence            6899999999999999999877   456666653

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity.

>PLN02674 adenylate kinase

Probab=96.53  E-value=0.0024  Score=62.83  Aligned_cols=31  Identities=19%  Similarity=0.373  Sum_probs=26.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ...++|.||||+||||+++.+|..++...+.
T Consensus        31 ~~~i~l~G~PGsGKgT~a~~La~~~~~~his   61 (244)
T PLN02674         31 DKRLILIGPPGSGKGTQSPIIKDEYCLCHLA   61 (244)
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHcCCcEEc
Confidence            3469999999999999999999998854443

>PRK10436 hypothetical protein; Provisional

Probab=96.51  E-value=0.013  Score=62.91  Aligned_cols=94  Identities=16%  Similarity=0.311  Sum_probs=57.6

Q ss_pred             ceeCCCCC-CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEE
Q 011664          178 WRSVPFTH-PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVY  253 (480)
Q Consensus       178 w~~v~~~~-~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~  253 (480)
                      ++-++... +.++++++..+...+.+.+.+..              +..-+|+.||+|+||||+..++-+++.   .+++
T Consensus       185 lRll~~~~~~~~L~~LG~~~~~~~~l~~~~~~--------------~~GliLvtGpTGSGKTTtL~a~l~~~~~~~~~i~  250 (462)
T PRK10436        185 LRLLQQVQQALDLETLGMTPAQLAQFRQALQQ--------------PQGLILVTGPTGSGKTVTLYSALQTLNTAQINIC  250 (462)
T ss_pred             EEEeccccCCCCHHHcCcCHHHHHHHHHHHHh--------------cCCeEEEECCCCCChHHHHHHHHHhhCCCCCEEE
Confidence            44444332 35889999888877776654321              233578999999999999988776663   3455


Q ss_pred             EEe------CCCcC-----C--hHHHHHHHHh--hcCCcEEEEeccc
Q 011664          254 DVD------LSRVA-----D--DADLKSLLLQ--TTSKSVILIEDLD  285 (480)
Q Consensus       254 ~i~------~s~~~-----~--~~~l~~l~~~--~~~~sII~IDEiD  285 (480)
                      .+.      +..+.     .  .......+..  ...|.||+|.||-
T Consensus       251 TiEDPvE~~l~gi~Q~~v~~~~g~~f~~~lr~~LR~dPDvI~vGEIR  297 (462)
T PRK10436        251 SVEDPVEIPLAGINQTQIHPKAGLTFQRVLRALLRQDPDVIMVGEIR  297 (462)
T ss_pred             EecCCccccCCCcceEeeCCccCcCHHHHHHHHhcCCCCEEEECCCC
Confidence            543      11110     0  1112223322  2589999999986

>PRK12339 2-phosphoglycerate kinase; Provisional

Probab=96.51  E-value=0.0028  Score=60.35  Aligned_cols=29  Identities=24%  Similarity=0.377  Sum_probs=25.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      +.-+++.|+||+|||++++.+|..++..+
T Consensus         3 ~~~i~i~G~~G~GKst~a~~l~~~~~~~~   31 (197)
T PRK12339          3 STIHFIGGIPGVGKTSISGYIARHRAIDI   31 (197)
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            34689999999999999999999988654

>PF08433 KTI12: Chromatin associated protein KTI12 ; InterPro: IPR013641 This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II []

Probab=96.49  E-value=0.0058  Score=61.07  Aligned_cols=62  Identities=15%  Similarity=0.325  Sum_probs=34.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC-------cC---ChHHHHHHH----Hhh-cCCcEEEEecccccc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR-------VA---DDADLKSLL----LQT-TSKSVILIEDLDRFL  288 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~-------~~---~~~~l~~l~----~~~-~~~sII~IDEiD~l~  288 (480)
                      ++|+|.||+|||++|+.|+..+   +..+..++-..       +.   .+...+..+    .+. ....||++|+...+-
T Consensus         4 iil~G~P~SGKTt~a~~L~~~~~~~~~~v~~i~~~~~~~~~~~y~~~~~Ek~~R~~l~s~v~r~ls~~~iVI~Dd~nYiK   83 (270)
T PF08433_consen    4 IILCGLPCSGKTTRAKELKKYLEEKGKEVVIISDDSLGIDRNDYADSKKEKEARGSLKSAVERALSKDTIVILDDNNYIK   83 (270)
T ss_dssp             EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH-TTSSS--GGGHHHHHHHHHHHHHHHHTT-SEEEE-S---SH
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHHhcCCEEEEEcccccccchhhhhchhhhHHHHHHHHHHHHHhhccCeEEEEeCCchHH
Confidence            7899999999999999999864   56666665221       11   133344333    222 456899999988763

The Elongator complex has histone acetyltransferase activity. ; PDB: 3ADB_B 3ADC_B 3A4M_B 3A4N_B 3AM1_A 3A4L_B 3ADD_A.

>KOG3354 consensus Gluconate kinase [Carbohydrate transport and metabolism]

Probab=96.49  E-value=0.0022  Score=58.31  Aligned_cols=46  Identities=24%  Similarity=0.408  Sum_probs=35.6

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHH
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSL  269 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l  269 (480)
                      +.+-.+++-|++|||||+++++++.+++.+|++-|  ++...+++.++
T Consensus        10 ~~k~~i~vmGvsGsGKSTigk~L~~~l~~~F~dgD--d~Hp~~NveKM   55 (191)
T KOG3354|consen   10 PFKYVIVVMGVSGSGKSTIGKALSEELGLKFIDGD--DLHPPANVEKM   55 (191)
T ss_pred             CCceeEEEEecCCCChhhHHHHHHHHhCCcccccc--cCCCHHHHHHH
Confidence            34557889999999999999999999998887653  55555555443

>PRK05541 adenylylsulfate kinase; Provisional

Probab=96.47  E-value=0.0032  Score=58.29  Aligned_cols=26  Identities=23%  Similarity=0.358  Sum_probs=23.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +.-++|.|+||+|||++++++++.+.
T Consensus         7 ~~~I~i~G~~GsGKst~a~~l~~~l~   32 (176)
T PRK05541          7 GYVIWITGLAGSGKTTIAKALYERLK   32 (176)
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHH
Confidence            44688999999999999999999875

>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting

Probab=96.45  E-value=0.00054  Score=52.89  Aligned_cols=48  Identities=21%  Similarity=0.190  Sum_probs=32.8

Q ss_pred             ccCCCCCCCC-----CCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC-cccccccc
Q 011664          425 DKSGSKKSTD-----ADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS-FDLAAAEN  478 (480)
Q Consensus       425 ~~~~~~~~~~-----~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~-~~~~~~~~  478 (480)
                      .+|.++++++     .++ +.+.+..++|+++||++|     |+++||||| .|+..||+
T Consensus         3 ~PCs~~dp~a~~m~~~di-~~~~l~~p~it~~DF~~A-----l~~~kpSVs~~dl~~ye~   56 (62)
T PF09336_consen    3 TPCSPSDPGAVEMSLMDI-PAEKLKEPPITMEDFEEA-----LKKVKPSVSQEDLKKYEE   56 (62)
T ss_dssp             EEESSSSTTEEEEEGTGS--GGGB-HHHBCHHHHHHH-----HHTCGGSS-HHHHHHHHH
T ss_pred             cCCCCCCccchhccHhhc-CcccccCCCCCHHHHHHH-----HHHcCCCCCHHHHHHHHH
Confidence            3455555543     233 344566678999999999     999999999 67777664

It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....

>PF02456 Adeno_IVa2: Adenovirus IVa2 protein; InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging []

Probab=96.44  E-value=0.042  Score=55.34  Aligned_cols=20  Identities=35%  Similarity=0.725  Sum_probs=17.5

Q ss_pred             eEEEEccCCCcHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA  245 (480)
                      -.++|||.|||||.|.+.+-
T Consensus        89 I~~VYGPTG~GKSqLlRNLi  108 (369)
T PF02456_consen   89 IGVVYGPTGSGKSQLLRNLI  108 (369)
T ss_pred             EEEEECCCCCCHHHHHHHhh
Confidence            45789999999999999874

During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter [].; GO: 0019083 viral transcription

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=96.44  E-value=0.0065  Score=58.19  Aligned_cols=23  Identities=39%  Similarity=0.537  Sum_probs=18.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+.+.||.|||||+||-+.|-++
T Consensus        21 ~v~~~G~AGTGKT~LA~a~Al~~   43 (205)
T PF02562_consen   21 LVIVNGPAGTGKTFLALAAALEL   43 (205)
T ss_dssp             EEEEE--TTSSTTHHHHHHHHHH
T ss_pred             eEEEECCCCCcHHHHHHHHHHHH
Confidence            58899999999999999998644

; GO: 0005524 ATP binding; PDB: 3B85_A.

>TIGR02236 recomb_radA DNA repair and recombination protein RadA

Probab=96.43  E-value=0.0077  Score=61.14  Aligned_cols=51  Identities=14%  Similarity=0.171  Sum_probs=36.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCCcCChHHHHHHH
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSRVADDADLKSLL  270 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~~~~~~~l~~l~  270 (480)
                      |++...-++++||||||||+++..+|...         +-..++++...-.....+.+..
T Consensus        91 Gi~~g~i~ei~G~~g~GKT~l~~~~~~~~~~~~~~g~~~~~~~yi~te~~f~~~rl~~~~  150 (310)
T TIGR02236        91 GIETQAITEVFGEFGSGKTQICHQLAVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMA  150 (310)
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhcCCcccCCCcceEEEEECCCCCCHHHHHHHH
Confidence            56666678899999999999999888652         2367888876533344444443

This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=96.42  E-value=0.014  Score=64.35  Aligned_cols=94  Identities=15%  Similarity=0.279  Sum_probs=57.6

Q ss_pred             ceeCCCCC-CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEE
Q 011664          178 WRSVPFTH-PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVY  253 (480)
Q Consensus       178 w~~v~~~~-~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~  253 (480)
                      ++-++... ..++++++..++..+.+.+.+..              ....+|++||+|+||||+..++.++++   .+++
T Consensus       283 lRll~~~~~~~~l~~lg~~~~~~~~l~~~~~~--------------~~Glilv~G~tGSGKTTtl~a~l~~~~~~~~~i~  348 (564)
T TIGR02538       283 LRILDSSAAQLDIDKLGFEPDQKALFLEAIHK--------------PQGMVLVTGPTGSGKTVSLYTALNILNTEEVNIS  348 (564)
T ss_pred             EEeecCccccCCHHHcCCCHHHHHHHHHHHHh--------------cCCeEEEECCCCCCHHHHHHHHHHhhCCCCceEE
Confidence            44444332 35789999988877777654432              233578999999999999988887764   3454


Q ss_pred             EEe------CCCcC-----Ch--HHHHHHHHh--hcCCcEEEEeccc
Q 011664          254 DVD------LSRVA-----DD--ADLKSLLLQ--TTSKSVILIEDLD  285 (480)
Q Consensus       254 ~i~------~s~~~-----~~--~~l~~l~~~--~~~~sII~IDEiD  285 (480)
                      .+.      +..+.     ..  ......+..  ...|.||++.||-
T Consensus       349 tiEdpvE~~~~~~~q~~v~~~~g~~~~~~l~~~LR~dPDvI~vGEiR  395 (564)
T TIGR02538       349 TAEDPVEINLPGINQVNVNPKIGLTFAAALRSFLRQDPDIIMVGEIR  395 (564)
T ss_pred             EecCCceecCCCceEEEeccccCCCHHHHHHHHhccCCCEEEeCCCC
Confidence            432      11110     00  112223322  2589999999997

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.42  E-value=0.02  Score=60.70  Aligned_cols=24  Identities=38%  Similarity=0.631  Sum_probs=21.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..-+.|.||+|+||||+++.+|..
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~  214 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAAR  214 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHH
Confidence            345889999999999999999875

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=96.42  E-value=0.017  Score=61.23  Aligned_cols=63  Identities=13%  Similarity=0.204  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHhhhh-HHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc
Q 011664          197 DLKNRVKSDLESFLKAKH-YYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV  260 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~-~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~  260 (480)
                      .+++.+.+.+...+.... .+. .....+.-++|.||+|+||||++..+|..+   |..+.-+++...
T Consensus        73 ~v~~~v~~~L~~~l~~~~~~~~-~~~~~~~vi~lvG~~GvGKTTtaaKLA~~l~~~G~kV~lV~~D~~  139 (429)
T TIGR01425        73 MIQHAVFKELCNLVDPGVEAFT-PKKGKQNVIMFVGLQGSGKTTTCTKLAYYYQRKGFKPCLVCADTF  139 (429)
T ss_pred             HHHHHHHHHHHHHhCCCCcccc-ccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEcCccc
Confidence            345555665655553211 111 111235678999999999999999999766   666766666443

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.

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

Probab=96.41  E-value=0.004  Score=58.16  Aligned_cols=23  Identities=35%  Similarity=0.665  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -.+++||||+|||+++..+|..+
T Consensus        34 l~~i~g~~g~GKT~~~~~l~~~~   56 (193)
T PF13481_consen   34 LTLIAGPPGSGKTTLALQLAAAL   56 (193)
T ss_dssp             EEEEEECSTSSHHHHHHHHHHHH
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHH
Confidence            47899999999999999888643

>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2

Probab=96.39  E-value=0.0034  Score=58.59  Aligned_cols=29  Identities=34%  Similarity=0.453  Sum_probs=25.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      |.|+|+||+|||++++.+++ +|+++++.|
T Consensus         2 i~itG~~gsGKst~~~~l~~-~g~~~i~~D   30 (179)
T cd02022           2 IGLTGGIGSGKSTVAKLLKE-LGIPVIDAD   30 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHH-CCCCEEecC
Confidence            67999999999999999999 787776655

7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.

>PRK00889 adenylylsulfate kinase; Provisional

Probab=96.38  E-value=0.0041  Score=57.54  Aligned_cols=34  Identities=32%  Similarity=0.400  Sum_probs=26.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      ..-+.|.|+||+|||++++++|..+   +.++..++.
T Consensus         4 g~~i~~~G~~GsGKST~a~~la~~l~~~g~~v~~id~   40 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTIARALAEKLREAGYPVEVLDG   40 (175)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEcC
Confidence            3468899999999999999999877   444555654

>PRK09519 recA DNA recombination protein RecA; Reviewed

Probab=96.37  E-value=0.0091  Score=67.53  Aligned_cols=70  Identities=16%  Similarity=0.275  Sum_probs=45.4

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHH---cCCCcEEEEeCCCcCC---------------------hHHHHHHH---Hh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMAS---FMSYDVYDVDLSRVAD---------------------DADLKSLL---LQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~---~l~~~~~~i~~s~~~~---------------------~~~l~~l~---~~  272 (480)
                      |++..+.++++||||||||+|+..++.   ..|..+.+++...-..                     .+......   .+
T Consensus        56 Gip~GsiteI~G~~GsGKTtLal~~~~~a~~~G~~v~yId~E~t~~~~~A~~lGvDl~~llv~~~~~~E~~l~~i~~lv~  135 (790)
T PRK09519         56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (790)
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEECCccchhHHHHHHcCCChhHeEEecCCCHHHHHHHHHHHhh
Confidence            566667789999999999999965443   3356666766443111                     11111111   22


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|+||-|..+.+
T Consensus       136 ~~~~~LVVIDSI~aL~~  152 (790)
T PRK09519        136 SGALDIVVIDSVAALVP  152 (790)
T ss_pred             cCCCeEEEEcchhhhcc
Confidence            34689999999998875

>PF00488 MutS_V: MutS domain V C-terminus

Probab=96.37  E-value=0.014  Score=57.11  Aligned_cols=97  Identities=20%  Similarity=0.273  Sum_probs=52.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH-----cCCCcE--------------EEEeCC-CcC-C-------hHHHHHHHHhhcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS-----FMSYDV--------------YDVDLS-RVA-D-------DADLKSLLLQTTSK  276 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~-----~l~~~~--------------~~i~~s-~~~-~-------~~~l~~l~~~~~~~  276 (480)
                      +.++|.||..+|||++.+++|-     .+|..+              ..+... ++. +       -..+..++......
T Consensus        44 ~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~  123 (235)
T PF00488_consen   44 RIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNATEK  123 (235)
T ss_dssp             SEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--TT
T ss_pred             eEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeecccccccccccccHHHhHHHHHhhhhhcccc
Confidence            5789999999999999999985     334311              111111 111 1       12355667777889


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      ++|+|||+-.=....++......+++.+..      ..+..+++||+..+-
T Consensus       124 sLvliDE~g~gT~~~eg~ai~~aile~l~~------~~~~~~i~~TH~~~l  168 (235)
T PF00488_consen  124 SLVLIDELGRGTNPEEGIAIAIAILEYLLE------KSGCFVIIATHFHEL  168 (235)
T ss_dssp             EEEEEESTTTTSSHHHHHHHHHHHHHHHHH------TTT-EEEEEES-GGG
T ss_pred             eeeecccccCCCChhHHHHHHHHHHHHHHH------hccccEEEEeccchh
Confidence            999999998432211111222334444421      123456778876543

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []

Probab=96.35  E-value=0.0028  Score=60.12  Aligned_cols=40  Identities=18%  Similarity=0.239  Sum_probs=30.5

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcC-CCcEEEEeCCCcC
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFM-SYDVYDVDLSRVA  261 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i~~s~~~  261 (480)
                      ..|.-+++.|+||+|||+++..+...+ +.+++.++...+.
T Consensus        13 ~~P~~~i~aG~~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r   53 (199)
T PF06414_consen   13 EKPTLIIIAGQPGSGKSTLARQLLEEFGGGGIVVIDADEFR   53 (199)
T ss_dssp             SS-EEEEEES-TTSTTHHHHHHHHHHT-TT-SEEE-GGGGG
T ss_pred             cCCEEEEEeCCCCCCHHHHHHHhhhhccCCCeEEEehHHHH
Confidence            356789999999999999999999988 7788888876654

It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.

>PRK05480 uridine/cytidine kinase; Provisional

Probab=96.35  E-value=0.0045  Score=58.98  Aligned_cols=37  Identities=16%  Similarity=0.170  Sum_probs=28.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC-CcEEEEeCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS-YDVYDVDLSRV  260 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~-~~~~~i~~s~~  260 (480)
                      +.-+.+.||+|||||||+++|+..++ ..+..++...+
T Consensus         6 ~~iI~I~G~sGsGKTTl~~~l~~~l~~~~~~~i~~D~~   43 (209)
T PRK05480          6 PIIIGIAGGSGSGKTTVASTIYEELGDESIAVIPQDSY   43 (209)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHhCCCceEEEeCCcc
Confidence            34578999999999999999999883 34555555443

>TIGR02322 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN

Probab=96.34  E-value=0.0028  Score=58.70  Aligned_cols=25  Identities=24%  Similarity=0.376  Sum_probs=22.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -+++.||||+|||+++++++..++.
T Consensus         3 ~~~i~G~sGsGKttl~~~l~~~~~~   27 (179)
T TIGR02322         3 LIYVVGPSGAGKDTLLDYARARLAG   27 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHcCc
Confidence            4789999999999999999998754

Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see PubMed:15231805), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP.

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=96.34  E-value=0.0097  Score=59.54  Aligned_cols=63  Identities=22%  Similarity=0.158  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHHHhhh-hHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc
Q 011664          197 DLKNRVKSDLESFLKAK-HYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV  260 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~-~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~  260 (480)
                      .+.+.+.+.+...+... ..+.. ....++-++|.||||+|||+++..+|..+   |..+.-+++..+
T Consensus        45 ~~~~~~~e~l~~~~~~~~~~~~~-~~~~~~vi~l~G~~G~GKTTt~akLA~~l~~~g~~V~li~~D~~  111 (272)
T TIGR00064        45 LLKEILKEYLKEILKETDLELIV-EENKPNVILFVGVNGVGKTTTIAKLANKLKKQGKSVLLAAGDTF  111 (272)
T ss_pred             HHHHHHHHHHHHHHcccchhhcc-cCCCCeEEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEeCCCC
Confidence            34555556665554332 11211 12235678899999999999999998765   556666665543

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.

>PRK14529 adenylate kinase; Provisional

Probab=96.33  E-value=0.0026  Score=61.79  Aligned_cols=28  Identities=25%  Similarity=0.515  Sum_probs=25.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ++|.||||+|||++++.+|..++...++
T Consensus         3 I~l~G~PGsGK~T~a~~La~~~~~~~is   30 (223)
T PRK14529          3 ILIFGPNGSGKGTQGALVKKKYDLAHIE   30 (223)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCcc
Confidence            8899999999999999999999876653

>PRK09825 idnK D-gluconate kinase; Provisional

Probab=96.33  E-value=0.0062  Score=56.87  Aligned_cols=36  Identities=33%  Similarity=0.492  Sum_probs=28.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD  263 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~  263 (480)
                      -+.+.||+|+|||++++++++.++..  .++...+...
T Consensus         5 ~i~l~G~sGsGKSTl~~~la~~l~~~--~i~gd~~~~~   40 (176)
T PRK09825          5 SYILMGVSGSGKSLIGSKIAALFSAK--FIDGDDLHPA   40 (176)
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCE--EECCcccCCH
Confidence            47899999999999999999998874  3444444333

>PRK12338 hypothetical protein; Provisional

Probab=96.32  E-value=0.0036  Score=63.77  Aligned_cols=30  Identities=27%  Similarity=0.334  Sum_probs=26.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      |.-+++.|+||||||++|+++|..+|...+
T Consensus         4 p~ii~i~G~sGsGKST~a~~la~~l~~~~~   33 (319)
T PRK12338          4 PYVILIGSASGIGKSTIASELARTLNIKHL   33 (319)
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHCCCeEE
Confidence            457899999999999999999999987643

>PF12780 AAA_8: P-loop containing dynein motor region D4; InterPro: IPR024317 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases

Probab=96.30  E-value=0.013  Score=58.41  Aligned_cols=63  Identities=27%  Similarity=0.434  Sum_probs=47.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh----HHHHHHHHhh---cCCcEEEEeccc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD----ADLKSLLLQT---TSKSVILIEDLD  285 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~----~~l~~l~~~~---~~~sII~IDEiD  285 (480)
                      +....||.|.+||||+++++..|.-.++.++.+..+.-.+-    .+++.++.++   ..|.+++|+|-+
T Consensus        30 ~~Gh~LLvG~~GsGr~sl~rLaa~i~~~~~~~i~~~~~y~~~~f~~dLk~~~~~ag~~~~~~vfll~d~q   99 (268)
T PF12780_consen   30 PRGHALLVGVGGSGRQSLARLAAFICGYEVFQIEITKGYSIKDFKEDLKKALQKAGIKGKPTVFLLTDSQ   99 (268)
T ss_dssp             TTEEEEEECTTTSCHHHHHHHHHHHTTEEEE-TTTSTTTHHHHHHHHHHHHHHHHHCS-S-EEEEEECCC
T ss_pred             CCCCeEEecCCCccHHHHHHHHHHHhccceEEEEeeCCcCHHHHHHHHHHHHHHHhccCCCeEEEecCcc
Confidence            34579999999999999999999999999999988764443    3466666444   367888888854

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.

>TIGR00767 rho transcription termination factor Rho

Probab=96.28  E-value=0.0085  Score=62.81  Aligned_cols=25  Identities=20%  Similarity=0.379  Sum_probs=22.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+++.||||||||+|++.+++.+.
T Consensus       169 q~~~IvG~~g~GKTtL~~~i~~~I~  193 (415)
T TIGR00767       169 QRGLIVAPPKAGKTVLLQKIAQAIT  193 (415)
T ss_pred             CEEEEECCCCCChhHHHHHHHHhhc
Confidence            3589999999999999999999764

Members of this family differ in the specificity of RNA binding.

>PRK09302 circadian clock protein KaiC; Reviewed

Probab=96.27  E-value=0.011  Score=64.25  Aligned_cols=38  Identities=29%  Similarity=0.279  Sum_probs=28.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc-C---CCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF-M---SYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~-l---~~~~~~i~~  257 (480)
                      |.+...-+|++|+||||||+|+..++.+ +   |.+++++++
T Consensus        27 G~p~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~   68 (509)
T PRK09302         27 GLPKGRPTLVSGTAGTGKTLFALQFLVNGIKRFDEPGVFVTF   68 (509)
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCEEEEEc
Confidence            5667778999999999999999977642 2   555655543

>PLN02459 probable adenylate kinase

Probab=96.26  E-value=0.0044  Score=61.45  Aligned_cols=30  Identities=17%  Similarity=0.483  Sum_probs=25.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .++|.||||+|||++++.+|..+++..+..
T Consensus        31 ~ii~~G~PGsGK~T~a~~la~~~~~~~is~   60 (261)
T PLN02459         31 NWVFLGCPGVGKGTYASRLSKLLGVPHIAT   60 (261)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEeC
Confidence            488899999999999999999988655443

>PRK04301 radA DNA repair and recombination protein RadA; Validated

Probab=96.26  E-value=0.01  Score=60.57  Aligned_cols=50  Identities=16%  Similarity=0.212  Sum_probs=35.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCCcCChHHHHHH
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSRVADDADLKSL  269 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~~~~~~~l~~l  269 (480)
                      |++...-++++||||||||.++..+|...         +..+++++...-.....+.+.
T Consensus        98 Gi~~g~vtei~G~~GsGKT~l~~~~~~~~~~~~~~gg~~~~~~yi~te~~f~~~rl~~~  156 (317)
T PRK04301         98 GIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYIDTEGTFRPERIEQM  156 (317)
T ss_pred             CccCCcEEEEECCCCCCHhHHHHHHHHHhccccccCCCCceEEEEeCCCCcCHHHHHHH
Confidence            56666778899999999999999988642         346788887653333444433

>PTZ00202 tuzin; Provisional

Probab=96.24  E-value=0.018  Score=61.05  Aligned_cols=64  Identities=20%  Similarity=0.222  Sum_probs=49.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS  258 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s  258 (480)
                      -|....+..|-+.....+...+..          .....++-+.|.||+|||||++++.++..++...+.+|+.
T Consensus       257 lPa~~~~FVGReaEla~Lr~VL~~----------~d~~~privvLtG~~G~GKTTLlR~~~~~l~~~qL~vNpr  320 (550)
T PTZ00202        257 APAVIRQFVSREAEESWVRQVLRR----------LDTAHPRIVVFTGFRGCGKSSLCRSAVRKEGMPAVFVDVR  320 (550)
T ss_pred             CCCCccCCCCcHHHHHHHHHHHhc----------cCCCCceEEEEECCCCCCHHHHHHHHHhcCCceEEEECCC
Confidence            455677888988888888765542          2223345678999999999999999999999888888876

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=96.24  E-value=0.013  Score=61.16  Aligned_cols=40  Identities=18%  Similarity=0.171  Sum_probs=30.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD  262 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~  262 (480)
                      .++-++|.||+|+|||+++..+|..+   +..+..+++.....
T Consensus       205 ~~~ii~lvGptGvGKTTt~akLA~~l~~~g~~V~lItaDtyR~  247 (407)
T PRK12726        205 NHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITTDTFRS  247 (407)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeCCccCc
Confidence            35568899999999999999999755   55666676655543

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=96.23  E-value=0.0092  Score=60.72  Aligned_cols=27  Identities=19%  Similarity=0.523  Sum_probs=24.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ....+++.||+|+|||++++++++.+.
T Consensus       143 ~~~~ili~G~tGsGKTTll~al~~~~~  169 (308)
T TIGR02788       143 SRKNIIISGGTGSGKTTFLKSLVDEIP  169 (308)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHccCC
Confidence            456899999999999999999998763

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>PRK04220 2-phosphoglycerate kinase; Provisional

Probab=96.23  E-value=0.01  Score=59.98  Aligned_cols=29  Identities=31%  Similarity=0.307  Sum_probs=26.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .|--+++.||+|||||++|..+|..++.+
T Consensus        91 ~p~iIlI~G~sgsGKStlA~~La~~l~~~  119 (301)
T PRK04220         91 EPIIILIGGASGVGTSTIAFELASRLGIR  119 (301)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            45579999999999999999999999877

>PLN02165 adenylate isopentenyltransferase

Probab=96.23  E-value=0.0042  Score=63.59  Aligned_cols=34  Identities=21%  Similarity=0.465  Sum_probs=29.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS  258 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s  258 (480)
                      .-+.|.||+|+|||+|+.++|..++..++..|--
T Consensus        44 ~iivIiGPTGSGKStLA~~LA~~l~~eIIsaDs~   77 (334)
T PLN02165         44 KVVVIMGATGSGKSRLSVDLATRFPSEIINSDKM   77 (334)
T ss_pred             CEEEEECCCCCcHHHHHHHHHHHcCCceecCChh
Confidence            3588999999999999999999999877776543

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=96.22  E-value=0.033  Score=57.59  Aligned_cols=128  Identities=21%  Similarity=0.332  Sum_probs=74.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC----------------------h------HHHHHHHHhh-
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD----------------------D------ADLKSLLLQT-  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~----------------------~------~~l~~l~~~~-  273 (480)
                      .|..+.|||-.|||||.+++++-+.++.+...+++-+...                      +      .+...+|.+. 
T Consensus        29 ~PS~~~iyG~sgTGKT~~~r~~l~~~n~~~vw~n~~ecft~~~lle~IL~~~~~~d~dg~~~~~~~en~~d~i~~l~q~~  108 (438)
T KOG2543|consen   29 IPSIVHIYGHSGTGKTYLVRQLLRKLNLENVWLNCVECFTYAILLEKILNKSQLADKDGDKVEGDAENFSDFIYLLVQWP  108 (438)
T ss_pred             cceeEEEeccCCCchhHHHHHHHhhcCCcceeeehHHhccHHHHHHHHHHHhccCCCchhhhhhHHHHHHHHHHHHHhhH
Confidence            4556799999999999999999999988877776432211                      0      1112223331 


Q ss_pred             --c---CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEe-cCCCccCcccccCCCcee-EEEEcCC
Q 011664          274 --T---SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFT-MNSKDHVDQALLRPGRID-VHIHFPL  346 (480)
Q Consensus       274 --~---~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~t-TN~~~~LD~aLlrpGRfd-~~I~~~~  346 (480)
                        .   ..-.|++|.+|.+..  -+...+..|+..- .+..   .....||+. +-.+.   .-+.+-|-++ ..++||.
T Consensus       109 ~~t~~d~~~~liLDnad~lrD--~~a~ll~~l~~L~-el~~---~~~i~iils~~~~e~---~y~~n~g~~~i~~l~fP~  179 (438)
T KOG2543|consen  109 AATNRDQKVFLILDNADALRD--MDAILLQCLFRLY-ELLN---EPTIVIILSAPSCEK---QYLINTGTLEIVVLHFPQ  179 (438)
T ss_pred             HhhccCceEEEEEcCHHhhhc--cchHHHHHHHHHH-HHhC---CCceEEEEeccccHH---HhhcccCCCCceEEecCC
Confidence              1   246889999998842  2222233333221 1111   223333332 22221   1222334554 6889999


Q ss_pred             CCHHHHHHHHHHH
Q 011664          347 CDFSSFKTLASSY  359 (480)
Q Consensus       347 p~~~~r~~il~~~  359 (480)
                      |+.++-++|+.+-
T Consensus       180 Ys~~e~~~Il~~~  192 (438)
T KOG2543|consen  180 YSVEETQVILSRD  192 (438)
T ss_pred             CCHHHHHHHHhcC
Confidence            9999988887653

>PRK04328 hypothetical protein; Provisional

Probab=96.22  E-value=0.0059  Score=60.18  Aligned_cols=40  Identities=33%  Similarity=0.279  Sum_probs=31.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~  259 (480)
                      |.+....+|++||||||||+|+..++.+   -|.+.++++..+
T Consensus        19 Gip~gs~ili~G~pGsGKT~l~~~fl~~~~~~ge~~lyis~ee   61 (249)
T PRK04328         19 GIPERNVVLLSGGPGTGKSIFSQQFLWNGLQMGEPGVYVALEE   61 (249)
T ss_pred             CCcCCcEEEEEcCCCCCHHHHHHHHHHHHHhcCCcEEEEEeeC
Confidence            5777778999999999999999876643   367788887654

>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2

Probab=96.21  E-value=0.0045  Score=57.94  Aligned_cols=35  Identities=26%  Similarity=0.425  Sum_probs=27.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA  261 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~  261 (480)
                      +.+.|+||||||++++.++..+   +.++..+++.++.
T Consensus         2 i~i~G~sgsGKttla~~l~~~l~~~~~~~~~i~~Ddf~   39 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNGIGPVVISLDDYY   39 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHcCCCEEEEehhhcc
Confidence            6789999999999999999987   4556666655443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=96.21  E-value=0.0048  Score=57.89  Aligned_cols=26  Identities=27%  Similarity=0.685  Sum_probs=23.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...+++.||+|+|||++++++++.+.
T Consensus        25 g~~i~I~G~tGSGKTTll~aL~~~i~   50 (186)
T cd01130          25 RKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhcC
Confidence            45799999999999999999998763

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.20  E-value=0.025  Score=63.88  Aligned_cols=64  Identities=25%  Similarity=0.322  Sum_probs=41.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC----C-CcEEEEeCCCcC----------------------ChHHHHHHHHhhcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM----S-YDVYDVDLSRVA----------------------DDADLKSLLLQTTSK  276 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l----~-~~~~~i~~s~~~----------------------~~~~l~~l~~~~~~~  276 (480)
                      ++-++|.||.|+||||++..+|..+    | ..+..++.....                      +..++...+.+....
T Consensus       185 g~Vi~lVGpnGvGKTTTiaKLA~~~~~~~G~kkV~lit~Dt~RigA~eQL~~~a~~~gvpv~~~~~~~~l~~al~~~~~~  264 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAKLAARCVAREGADQLALLTTDSFRIGALEQLRIYGRILGVPVHAVKDAADLRFALAALGDK  264 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHHHHhhHHHHcCCCeEEEecCcccchHHHHHHHHHHHhCCCCccccCCHHHHHHHHHHhcCC
Confidence            3468899999999999999999755    2 244444332221                      233345555555666


Q ss_pred             cEEEEeccccc
Q 011664          277 SVILIEDLDRF  287 (480)
Q Consensus       277 sII~IDEiD~l  287 (480)
                      .+|+||=....
T Consensus       265 D~VLIDTAGRs  275 (767)
T PRK14723        265 HLVLIDTVGMS  275 (767)
T ss_pred             CEEEEeCCCCC
Confidence            88888876644

>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+)

Probab=96.19  E-value=0.0044  Score=58.56  Aligned_cols=30  Identities=20%  Similarity=0.322  Sum_probs=24.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC-CCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM-SYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l-~~~~~~i~  256 (480)
                      |.+.|+||||||++|+.++..+ +..++.+|
T Consensus         2 i~i~G~sgsGKTtla~~l~~~~~~~~~i~~D   32 (187)
T cd02024           2 VGISGVTNSGKTTLAKLLQRILPNCCVIHQD   32 (187)
T ss_pred             EEEECCCCCCHHHHHHHHHHHcCCCeEEccc
Confidence            5688999999999999999998 45444443

This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=96.19  E-value=0.016  Score=63.98  Aligned_cols=28  Identities=32%  Similarity=0.445  Sum_probs=23.9

Q ss_pred             CCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          221 RVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       221 ~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +++..-+.+.||+|+|||||++.+++..
T Consensus       366 i~~G~~~aIvG~sGsGKSTLl~ll~gl~  393 (582)
T PRK11176        366 IPAGKTVALVGRSGSGKSTIANLLTRFY  393 (582)
T ss_pred             eCCCCEEEEECCCCCCHHHHHHHHHhcc
Confidence            3445569999999999999999999866

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=96.19  E-value=0.0067  Score=58.54  Aligned_cols=39  Identities=26%  Similarity=0.146  Sum_probs=30.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s  258 (480)
                      |.+....++++||||||||+++..++.+   -+...++++..
T Consensus        16 Gi~~G~~~~i~G~~G~GKT~l~~~~~~~~~~~g~~~~~is~e   57 (229)
T TIGR03881        16 GIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDPVIYVTTE   57 (229)
T ss_pred             CCcCCeEEEEECCCCCChHHHHHHHHHHHHhcCCeEEEEEcc
Confidence            5666778999999999999999987643   25566677653

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>TIGR03263 guanyl_kin guanylate kinase

Probab=96.18  E-value=0.0037  Score=57.86  Aligned_cols=25  Identities=32%  Similarity=0.460  Sum_probs=22.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -++|.||+|+|||++++.+++....
T Consensus         3 ii~l~G~~GsGKsTl~~~L~~~~~~   27 (180)
T TIGR03263         3 LIVISGPSGVGKSTLVKALLEEDPN   27 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHccCcc
Confidence            4789999999999999999997654

Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.

>PRK10646 ADP-binding protein; Provisional

Probab=96.18  E-value=0.021  Score=52.14  Aligned_cols=26  Identities=27%  Similarity=0.526  Sum_probs=23.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-++|.|+=|+|||++++++++.+|.
T Consensus        29 ~vi~L~GdLGaGKTtf~rgl~~~Lg~   54 (153)
T PRK10646         29 TVIYLYGDLGAGKTTFSRGFLQALGH   54 (153)
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCC
Confidence            35899999999999999999999875

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=96.17  E-value=0.0069  Score=58.82  Aligned_cols=40  Identities=20%  Similarity=0.179  Sum_probs=32.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~  259 (480)
                      |+++..-++|.||||+|||+++..+|...    +.+++++++..
T Consensus         9 Gl~~G~l~lI~G~~G~GKT~~~~~~~~~~~~~~g~~vly~s~E~   52 (242)
T cd00984           9 GLQPGDLIIIAARPSMGKTAFALNIAENIAKKQGKPVLFFSLEM   52 (242)
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhCCCceEEEeCCC
Confidence            66666778999999999999998887643    78888888754

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>PRK12337 2-phosphoglycerate kinase; Provisional

Probab=96.17  E-value=0.012  Score=62.72  Aligned_cols=34  Identities=32%  Similarity=0.387  Sum_probs=28.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCc-EEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYD-VYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~-~~~i~  256 (480)
                      .|.-++++|+||||||+++..+|..++.. ++..|
T Consensus       254 ~p~vil~~G~~G~GKSt~a~~LA~~lg~~~ii~tD  288 (475)
T PRK12337        254 RPLHVLIGGVSGVGKSVLASALAYRLGITRIVSTD  288 (475)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHcCCcEEeehh
Confidence            46788999999999999999999999985 44444

>PRK12608 transcription termination factor Rho; Provisional

Probab=96.16  E-value=0.0097  Score=61.86  Aligned_cols=24  Identities=21%  Similarity=0.372  Sum_probs=21.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -.++.||||||||+|++.+|+.+.
T Consensus       135 R~LIvG~pGtGKTTLl~~la~~i~  158 (380)
T PRK12608        135 RGLIVAPPRAGKTVLLQQIAAAVA  158 (380)
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHH
Confidence            369999999999999999998763

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=96.15  E-value=0.021  Score=53.71  Aligned_cols=24  Identities=25%  Similarity=0.635  Sum_probs=21.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.+.||.|+|||+|.+.+|.-+
T Consensus        29 e~~~i~G~NG~GKTtLLRilaGLl   52 (209)
T COG4133          29 EALQITGPNGAGKTTLLRILAGLL   52 (209)
T ss_pred             CEEEEECCCCCcHHHHHHHHHccc
Confidence            357789999999999999999866

>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2

Probab=96.15  E-value=0.0062  Score=57.45  Aligned_cols=33  Identities=21%  Similarity=0.272  Sum_probs=25.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCC-CcEEEEeCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMS-YDVYDVDLSR  259 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~-~~~~~i~~s~  259 (480)
                      +.|.||+|||||++++++++.++ ..+..++...
T Consensus         2 igi~G~~GsGKSTl~~~l~~~l~~~~~~v~~~D~   35 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQDS   35 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCCeEEEEecc
Confidence            56899999999999999999873 3444554443

7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=96.14  E-value=0.0085  Score=62.30  Aligned_cols=25  Identities=28%  Similarity=0.484  Sum_probs=22.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...++++||+|+||||+++++++++
T Consensus       134 ~glilI~GpTGSGKTTtL~aLl~~i  158 (358)
T TIGR02524       134 EGIVFITGATGSGKSTLLAAIIREL  158 (358)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
Confidence            3468999999999999999999876

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>TIGR01069 mutS2 MutS2 family protein

Probab=96.14  E-value=0.044  Score=62.55  Aligned_cols=23  Identities=22%  Similarity=0.387  Sum_probs=20.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      +.++|.||.|+|||++.+.++..
T Consensus       323 ~~liItGpNg~GKSTlLK~i~~~  345 (771)
T TIGR01069       323 RVLAITGPNTGGKTVTLKTLGLL  345 (771)
T ss_pred             eEEEEECCCCCCchHHHHHHHHH
Confidence            57899999999999999999865

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>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=96.14  E-value=0.0059  Score=55.96  Aligned_cols=33  Identities=33%  Similarity=0.461  Sum_probs=27.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .|.|.|.||+|||++|+++...|   |.+++.++..
T Consensus         4 vIwltGlsGsGKtTlA~~L~~~L~~~g~~~~~LDgD   39 (156)
T PF01583_consen    4 VIWLTGLSGSGKTTLARALERRLFARGIKVYLLDGD   39 (156)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHHHHHTTS-EEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEecCc
Confidence            57899999999999999999865   6778877754

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 ....

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=96.13  E-value=0.012  Score=57.00  Aligned_cols=63  Identities=22%  Similarity=0.403  Sum_probs=40.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc-----CCCc--------------EEEEeCCC-cCC--------hHHHHHHHHhhcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF-----MSYD--------------VYDVDLSR-VAD--------DADLKSLLLQTTS  275 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~-----l~~~--------------~~~i~~s~-~~~--------~~~l~~l~~~~~~  275 (480)
                      .+.++|.||.|.|||++.+.++..     .|..              +..+...+ +..        -.++..++..+..
T Consensus        30 ~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~  109 (218)
T cd03286          30 PRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATP  109 (218)
T ss_pred             CcEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCcccccccCcchHHHHHHHHHHHHHhCCC
Confidence            456899999999999999988752     2321              11111111 111        1234556777789


Q ss_pred             CcEEEEecccc
Q 011664          276 KSVILIEDLDR  286 (480)
Q Consensus       276 ~sII~IDEiD~  286 (480)
                      |++++|||+..
T Consensus       110 ~sLvLlDE~~~  120 (218)
T cd03286         110 DSLVILDELGR  120 (218)
T ss_pred             CeEEEEecccC
Confidence            99999999864

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c

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

Probab=96.13  E-value=0.015  Score=57.62  Aligned_cols=23  Identities=30%  Similarity=0.619  Sum_probs=20.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+-|.||.|||||||.+++++.+
T Consensus        30 i~~iiGpNG~GKSTLLk~l~g~l   52 (258)
T COG1120          30 ITGILGPNGSGKSTLLKCLAGLL   52 (258)
T ss_pred             EEEEECCCCCCHHHHHHHHhccC
Confidence            46688999999999999999866

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=96.13  E-value=0.0067  Score=65.64  Aligned_cols=39  Identities=31%  Similarity=0.290  Sum_probs=31.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc----CCCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF----MSYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~----l~~~~~~i~~s  258 (480)
                      |++..+.+|+.||||||||+++..++.+    .|.+.+++++.
T Consensus        17 Glp~g~~~Li~G~pGsGKT~la~qfl~~g~~~~ge~~lyvs~e   59 (484)
T TIGR02655        17 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIHFDEPGVFVTFE   59 (484)
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHHHHHHHHhCCCCEEEEEEe
Confidence            6778889999999999999999988532    36677777653

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PLN03186 DNA repair protein RAD51 homolog; Provisional

Probab=96.13  E-value=0.014  Score=60.35  Aligned_cols=40  Identities=18%  Similarity=0.160  Sum_probs=29.4

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~  259 (480)
                      |++...-+.++|+||+|||.++..+|-..         +..+++++...
T Consensus       119 G~~~g~i~~i~G~~g~GKT~l~~~l~~~~~~~~~~gg~~g~vlyIdtE~  167 (342)
T PLN03186        119 GIETGSITEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEG  167 (342)
T ss_pred             CCcCceEEEEECCCCCCccHHHHHHHHHhhcchhhCCCCceEEEEECCC
Confidence            55566667899999999999999777321         23677777654

>PRK00300 gmk guanylate kinase; Provisional

Probab=96.13  E-value=0.0059  Score=57.78  Aligned_cols=27  Identities=33%  Similarity=0.413  Sum_probs=23.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+.|.||+|||||+|++.+++.+.
T Consensus         4 ~g~~i~i~G~sGsGKstl~~~l~~~~~   30 (205)
T PRK00300          4 RGLLIVLSGPSGAGKSTLVKALLERDP   30 (205)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhhCc
Confidence            345689999999999999999999875

>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=96.12  E-value=0.0042  Score=57.66  Aligned_cols=22  Identities=23%  Similarity=0.548  Sum_probs=19.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ++|.|+||+||||+++.+...+
T Consensus         2 i~iTG~pG~GKTTll~k~i~~l   23 (168)
T PF03266_consen    2 IFITGPPGVGKTTLLKKVIEEL   23 (168)
T ss_dssp             EEEES-TTSSHHHHHHHHHHHH
T ss_pred             EEEECcCCCCHHHHHHHHHHHh
Confidence            7999999999999999999877

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.

>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2

Probab=96.12  E-value=0.0054  Score=54.81  Aligned_cols=25  Identities=32%  Similarity=0.515  Sum_probs=22.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      +.|.||+|+|||++++.++..+...
T Consensus         2 i~i~GpsGsGKstl~~~L~~~~~~~   26 (137)
T cd00071           2 IVLSGPSGVGKSTLLKRLLEEFDPN   26 (137)
T ss_pred             EEEECCCCCCHHHHHHHHHhcCCcc
Confidence            6789999999999999999987544

7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	480
4b4t_L	437	Near-Atomic Resolution Structural Model Of The Yeas		2e-05
4b4t_K	428	Near-Atomic Resolution Structural Model Of The Yeas		2e-04
1lv7_A	257	Crystal Structure Of The Aaa Domain Of Ftsh Length		6e-04

>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 437

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 70/178 (39%), Gaps = 20/178 (11%)
Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKXXXXXXXXXX 247
           TFD I   T+    ++  +E  LK    + R+G    +  LLYGP GTGK          
Sbjct: 179 TFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAAT 238
Query: 248 XXYD--------VYDVDLSRVADDADXXXXXXXXXXXXVILIEDLD----RFLVEKPAA- 294
              +        + D  +   A                +I ++++D    R   E  +A 
Sbjct: 239 IGANFIFSPASGIVDKYIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSAD 298
Query: 295 ----VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCD 348
                +L  +L  MDG  N     +  ++   N  D +D ALLRPGR+D  +  PL +
Sbjct: 299 REIQRTLMELLTQMDGFDN---LGQTKIIMATNRPDTLDPALLRPGRLDRKVEIPLPN 353

>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 428

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 63/167 (37%), Gaps = 26/167 (15%)
Query: 199 KNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKXXXXXXXXXXXXYDVYDVDLS 258
           K  ++  +E  L     Y ++G    R  LLYGP GTGK                 V+ S
Sbjct: 181 KQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGS 240
Query: 259 -----------RVADDADXXXXXXXXXXXXVILIEDLDRFLVEKPAAVS---------LS 298
                      R+  D              +I I+++D    ++  A +         L 
Sbjct: 241 EFVHKYLGEGPRMVRDV---FRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILI 297
Query: 299 GVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFP 345
            +L  MDG   S   +   ++   N  D +D ALLRPGR+D  I FP
Sbjct: 298 ELLTQMDGFDQSTNVK---VIMATNRADTLDPALLRPGRLDRKIEFP 341

>pdb|1LV7|A Chain A, Crystal Structure Of The Aaa Domain Of Ftsh Length = 257

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 72/183 (39%), Gaps = 29/183 (15%)
Query: 187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKXXXXXXXXX 246
           +TF  ++   + K  V ++L  +L+    + +LG    +  L+ GP GTGK         
Sbjct: 9   TTFADVAGCDEAKEEV-AELVEYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAG 67
Query: 247 XXXYDVY------------DVDLSRVADDADXXXXXXXXXXXXVILIEDLDRFLVEKPAA 294
                 +             V  SRV D               +I I+++D    ++ A 
Sbjct: 68  EAKVPFFTISGSDFVEMFVGVGASRVRD----MFEQAKKAAPCIIFIDEIDAVGRQRGAG 123
Query: 295 V---------SLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFP 345
           +         +L+ +L  MDG   +   E  +++   N  D +D ALLRPGR D  +   
Sbjct: 124 LGGGHDEREQTLNQMLVEMDGFEGN---EGIIVIAATNRPDVLDPALLRPGRFDRQVVVG 180
Query: 346 LCD 348
           L D
Sbjct: 181 LPD 183

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	480
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	9e-20
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	4e-15
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-09
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	2e-09
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	7e-09
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	5e-08
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	2e-07
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	3e-07
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	3e-07
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	4e-07
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	5e-07
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	2e-06
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	4e-06
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	5e-06
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	5e-06
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	2e-05
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	5e-05
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	6e-05
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	7e-05
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	2e-04
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	3e-04
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	3e-04
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	3e-04
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	6e-04

>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 = 91.8 bits (227), Expect = 9e-20
 Identities = 59/384 (15%), Positives = 120/384 (31%), Gaps = 92/384 (23%)

Query: 89  KSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATARTLVLKLRKADRRRILRPYLQHIHA 148
           +  DI+       + +D F+       +  D   +   +L   + D   + +  +     
Sbjct: 17  QYKDIL------SVFEDAFV-DNFDCKDVQDMPKS---ILSKEEIDHIIMSKDAVSGTLR 66

Query: 149 VSDELEQKKKRDLRLFVN--LRNDRDGCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDL 206
           +   L  K++  ++ FV   LR +        ++     PS    + +E   ++R+ +D 
Sbjct: 67  LFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQ-RQPSMMTRMYIEQ--RDRLYNDN 123

Query: 207 ESFLKAKHYYHRLGRVWK-RSYL----------LYGPSGTGKSSFAAAMAS------FMS 249
           + F  AK+   RL    K R  L          + G  G+GK+  A  +         M 
Sbjct: 124 QVF--AKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMD 181

Query: 250 YDVYDVDLSRVADDAD----LKSLLLQTTSKSVIL----------IED----LDRFLVEK 291
           + ++ ++L            L+ LL Q                  I      L R L  K
Sbjct: 182 FKIFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSK 241

Query: 292 PAAVSL--------SGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIH 343
           P    L        +   N  +    SC    ++++ T   +  V   L       + + 
Sbjct: 242 PYENCLLVLLNVQNAKAWNAFNL---SC----KILLTTRFKQ--VTDFLSAATTTHISLD 292

Query: 344 FPLCDFSSFKTLA--SSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSR-- 399
                 +  +  +    YL  +   L  +V       +    + I E +   R+  +   
Sbjct: 293 HHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTT----NPRRLSIIAESI---RDGLATWD 345

Query: 400 ------------ALKSVITALQTD 411
                        ++S +  L+  
Sbjct: 346 NWKHVNCDKLTTIIESSLNVLEPA 369

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 47.2 bits (111), Expect = 1e-05
 Identities = 68/527 (12%), Positives = 139/527 (26%), Gaps = 164/527 (31%)

Query: 37  FIED--CLHVHQF----FKVPEF----NEGMQENQLYRKVYAYLNSLTSIEDSDFTNLFT 86
           F+++  C  V           E           +   R  +  L+    +        F 
Sbjct: 29  FVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQK-----FV 83

Query: 87  GKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDDSATART--------------------- 125
            +        L  N      FL +P+    +  S   R                      
Sbjct: 84  EE-------VLRINY----KFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVS 132

Query: 126 ---LVLKLRKADRRRILRP--YLQHIH-------------AVSDELEQKKKRDLRLF-VN 166
                LKLR+A     LRP   +  I                    + + K D ++F +N
Sbjct: 133 RLQPYLKLRQALLE--LRPAKNVL-IDGVLGSGKTWVALDVCLSY-KVQCKMDFKIFWLN 188

Query: 167 LRNDRD---------GCCGRWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYH 217
           L+N                +      +       I +     + ++++L   LK+K Y  
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRI---HSIQAELRRLLKSKPY-- 243

Query: 218 RLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTT-SK 276
                 +   L+                     +V +   ++  +  +L   +L TT  K
Sbjct: 244 ------ENCLLVLL-------------------NVQN---AKAWNAFNLSCKILLTTRFK 275

Query: 277 SVILIEDLDR----FLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ-- 330
            V             L      ++   V + +   L+    +    V T N +  +    
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPR-RLSIIA 334

Query: 331 ALLR--PGRIDVHIHFPLCDFSSF-KTLASSYLGLK--DHK-------LFP-------QV 371
             +R      D   ++   +       + SS   L+  +++       +FP        +
Sbjct: 335 ESIRDGLATWD---NWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTIL 391

Query: 372 EEIF-QNGSSLSPAEIGELMI----ANRNSPSRA--LKSVITALQTDGEGRGAANAGRRL 424
             +   +        +   +       +        + S+   L+   E   A +    +
Sbjct: 392 LSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHR-SIV 450

Query: 425 DKSGSKKSTDADS--------------GEHGGVFSRENTVKEFRKLY 457
           D     K+ D+D               G H         +  FR ++
Sbjct: 451 DHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVF 497

>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 = 45.6 bits (107), Expect = 3e-05
 Identities = 48/307 (15%), Positives = 90/307 (29%), Gaps = 73/307 (23%)

Query: 6   IVLLVIGCLLF-----MIRVLLFKTGLIFVAKKWWRFIEDCLHVHQFFKVPEFNEGMQEN 60
           ++L  + C        ++     +  +I         I D L     +K       +  +
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSII------AESIRDGLATWDNWKH------VNCD 353

Query: 61  QLYRKVYAYLNSLTSIEDSD-FTNLFTGKKSNDIVLGLDPNQLIQDNFLGAPLSWANQDD 119
           +L   + + LN L   E    F  L     S  I     P  L+        L W +   
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHI-----PTILLS-------LIWFD-VI 400

Query: 120 SATARTLVLKLRK---ADRRRILRPYLQHIHAVSDELEQKKKRDLRL---FVNLRNDRDG 173
            +    +V KL K    +++   +     I ++  EL+ K + +  L    V+  N    
Sbjct: 401 KSDVMVVVNKLHKYSLVEKQP--KESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKT 458

Query: 174 CCGRWRSVPFT----------HPSTFDTISM--ETDLKNRVKSDLESFLKAKHYYHRLGR 221
                   P+           H      I       L   V  D   FL+ K        
Sbjct: 459 FDSDDLIPPYLDQYFYSHIGHH---LKNIEHPERMTLFRMVFLDF-RFLEQK-------- 506

Query: 222 VWKRSYLLY-GPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLL--LQTTSKSV 278
                 + +   +     S    +     Y  Y  D +    +  + ++L  L    +++
Sbjct: 507 ------IRHDSTAWNASGSILNTLQQLKFYKPYICD-NDPKYERLVNAILDFLPKIEENL 559

Query: 279 ILIEDLD 285
           I  +  D
Sbjct: 560 ICSKYTD 566

>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 = 43.7 bits (102), Expect = 1e-04
 Identities = 74/487 (15%), Positives = 148/487 (30%), Gaps = 124/487 (25%)

Query: 33  KWWRFIEDC----LHVHQFFKV----------PEFNEGMQENQLYRKVYAYLNSLTSIED 78
           K W  ++ C    +     FK+          PE    M +  L  ++     S +    
Sbjct: 163 KTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK-LLYQIDPNWTSRSDHSS 221

Query: 79  SDFTNLFTGKKSNDIVLGLDPNQ---LIQDNFLGAPLSWANQDDSA---TARTLVLKLRK 132
           +    + + +     +L   P +   L+  N          +  +A   + + L+    K
Sbjct: 222 NIKLRIHSIQAELRRLLKSKPYENCLLVLLNV------QNAKAWNAFNLSCKILLTTRFK 275

Query: 133 ADRRRILRPYLQHIHAV--SDELEQKKKRDL-RLFVNLRND---RDGCCGRWRSVPFT-- 184
                +      HI     S  L   + + L   +++ R     R+         P    
Sbjct: 276 QVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTN----PRRLS 331

Query: 185 --------HPSTFDTISMETDLKNRVKSDLESFLKA------KHYYHRLGRVWKRSYLLY 230
                     +T+D    +    +++ + +ES L        +  + RL  V+  S  + 
Sbjct: 332 IIAESIRDGLATWDNW--KHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS-VFPPSAHI- 387

Query: 231 GPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVE 290
            P+          ++      +   D+  V +     SL+ +   +S I I  +   L  
Sbjct: 388 -PTIL--------LSLIWFDVIKS-DVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKV 437

Query: 291 KPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRID----VHI--HF 344
           K             +  L+      R +V   N     D   L P  +D     HI  H 
Sbjct: 438 KLEN----------EYALH------RSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHL 481

Query: 345 PLCD----FSSFKTLASSYLGLK--DHKLFPQVEEIFQNGSSLSPAEIGEL------MIA 392
              +     + F+ +   +L  +  + K+  + +    N S      + +L      +  
Sbjct: 482 KNIEHPERMTLFRMV---FLDFRFLEQKI--RHDSTAWNASGSILNTLQQLKFYKPYICD 536

Query: 393 NRNSPSRALKSVITALQTDGEGRGAANAGRRLDKSGSKKSTD----ADSGEHGGVFSREN 448
           N     R + +++  L               L  S   K TD    A   E   +F  E 
Sbjct: 537 NDPKYERLVNAILDFLP---------KIEENLICS---KYTDLLRIALMAEDEAIF--EE 582

Query: 449 TVKEFRK 455
             K+ ++
Sbjct: 583 AHKQVQR 589

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score = 58.7 bits (142), Expect = 2e-09
 Identities = 42/176 (23%), Positives = 78/176 (44%), Gaps = 19/176 (10%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
            +D I        ++K  +E  L+    +  +G    R  LLYGP GTGK+  A A+A+ 
Sbjct: 202 GYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 261

Query: 248 MSYDVYDVD----LSRVADDAD--LKSL--LLQTTSKSVILIEDLDRFLVEKPAAVS--- 296
                + ++    +S++A +++  L+      +  + ++I I++LD    ++        
Sbjct: 262 TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE 321

Query: 297 ---LSGVLNFMDGVLNSCCFEERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCD 348
              +S +L  MDG+         V+V    N  + +D AL R GR D  +   + D
Sbjct: 322 RRIVSQLLTLMDGLKQ----RAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPD 373

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus} Length = 301

 Score = 56.1 bits (136), Expect = 7e-09
 Identities = 52/271 (19%), Positives = 101/271 (37%), Gaps = 63/271 (23%)

Query: 197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMS-- 249
           D+K  ++  ++  ++    + + G    +  L YGP G GK+  A A+A+     F+S  
Sbjct: 22  DVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIK 81

Query: 250 ----YDVYDV--------DLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSL 297
                 ++          ++   A  A          +  V+  ++LD     +   +  
Sbjct: 82  GPELLTMW-FGESEANVREIFDKARQA----------APCVLFFDELDSIAKARGGNIGD 130

Query: 298 SG---------VLNFMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDVHIHFP 345
            G         +L  MDG+        +  VF +   N  D +D A+LRPGR+D  I+ P
Sbjct: 131 GGGAADRVINQILTEMDGM------STKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIP 184

Query: 346 LCDFSS----FKTLASSYLGLKDHKLFPQV--EEIFQNGSSLSPAEIGELMIANRNSPSR 399
           L D  S     K        L+   +   V  E + +  +  S A++ E+    + +   
Sbjct: 185 LPDEKSRVAILKAN------LRKSPVAKDVDLEFLAKMTNGFSGADLTEIC---QRACKL 235

Query: 400 ALKSVITALQTDGEGRGAANAGRRLDKSGSK 430
           A++  I +       R    +   +++    
Sbjct: 236 AIRESIESEIRRERERQTNPSAMEVEEDDPV 266

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii} Length = 285

 Score = 53.0 bits (128), Expect = 5e-08
 Identities = 43/162 (26%), Positives = 68/162 (41%), Gaps = 32/162 (19%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMS------YDVYDVDLS 258
           LK    + ++G    +  LLYGP GTGK+  A A+A+     F+          +  + +
Sbjct: 37  LKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELVKKFIGEGA 96

Query: 259 RVADDADLKSLLLQTTSKSVILIEDLD-----RFLVEKPAAV----SLSGVLNFMDGVLN 309
            +  D      L +  + S+I I+++D     R             +L  +L  MDG   
Sbjct: 97  SLVKDI---FKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDG--- 150

Query: 310 SCCFEER---VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCD 348
              F+ R    ++   N  D +D A+LRPGR D  I  P  D
Sbjct: 151 ---FDARGDVKIIGATNRPDILDPAILRPGRFDRIIEVPAPD 189

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A* Length = 272

 Score = 51.3 bits (123), Expect = 2e-07
 Identities = 34/167 (20%), Positives = 58/167 (34%), Gaps = 34/167 (20%)

Query: 200 NRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA-------------S 246
            RV  D E  ++      R       S LL GP  +GK++ AA +A              
Sbjct: 43  TRVLDDGELLVQQTKNSDRTPL---VSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPD 99

Query: 247 FMS--YDVYDVD-LSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAA--VS---LS 298
            M    +      + ++ DDA    L       S ++++D++R L   P     S   L 
Sbjct: 100 KMIGFSETAKCQAMKKIFDDAYKSQL-------SCVVVDDIERLLDYVPIGPRFSNLVLQ 152

Query: 299 GVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFP 345
            +L  +           ++++    S+  V Q +         IH P
Sbjct: 153 ALLVLLKKAPPQ---GRKLLIIGTTSRKDVLQEMEMLNAFSTTIHVP 196

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20 Length = 257

 Score = 50.8 bits (122), Expect = 3e-07
 Identities = 50/188 (26%), Positives = 80/188 (42%), Gaps = 41/188 (21%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS- 246
           TF  ++   + K  V   +E +L+    + +LG    +  L+ GP GTGK+  A A+A  
Sbjct: 10  TFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68

Query: 247 ----FMSYDVYD-------VDLSRVADDADLKSLLLQTTSKS---VILIEDLDRFLVEKP 292
               F +    D       V  SRV D       + +   K+   +I I+++D    ++ 
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRD-------MFEQAKKAAPCIIFIDEIDAVGRQRG 121

Query: 293 AAV---------SLSGVLNFMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDV 340
           A +         +L+ +L  MDG      FE    +  +   N  D +D ALLRPGR D 
Sbjct: 122 AGLGGGHDEREQTLNQMLVEMDG------FEGNEGIIVIAATNRPDVLDPALLRPGRFDR 175

Query: 341 HIHFPLCD 348
            +   L D
Sbjct: 176 QVVVGLPD 183

>1ixz_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 2.20A {Thermus thermophilus} SCOP: c.37.1.20 PDB: 1iy0_A* 1iy1_A* Length = 254

 Score = 50.8 bits (122), Expect = 3e-07
 Identities = 52/188 (27%), Positives = 81/188 (43%), Gaps = 41/188 (21%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS- 246
           TF  ++   + K  +K  +E FLK    +H +G    +  LL GP G GK+  A A+A  
Sbjct: 14  TFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 72

Query: 247 ----FMSYDVYD-------VDLSRVADDADLKSLLLQTTSKS---VILIEDLDRFLVEKP 292
               F++    D       V  +RV D       L +T  +    ++ I+++D    ++ 
Sbjct: 73  ARVPFITASGSDFVEMFVGVGAARVRD-------LFETAKRHAPCIVFIDEIDAVGRKRG 125

Query: 293 AAV---------SLSGVLNFMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDV 340
           + V         +L+ +L  MDG      FE+   +  M   N  D +D ALLRPGR D 
Sbjct: 126 SGVGGGNDEREQTLNQLLVEMDG------FEKDTAIVVMAATNRPDILDPALLRPGRFDR 179

Query: 341 HIHFPLCD 348
            I     D
Sbjct: 180 QIAIDAPD 187

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20 Length = 278

 Score = 50.4 bits (121), Expect = 4e-07
 Identities = 52/188 (27%), Positives = 81/188 (43%), Gaps = 41/188 (21%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS- 246
           TF  ++   + K  +K  +E FLK    +H +G    +  LL GP G GK+  A A+A  
Sbjct: 38  TFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 96

Query: 247 ----FMSYDVYD-------VDLSRVADDADLKSLLLQTTSKS---VILIEDLDRFLVEKP 292
               F++    D       V  +RV D       L +T  +    ++ I+++D    ++ 
Sbjct: 97  ARVPFITASGSDFVEMFVGVGAARVRD-------LFETAKRHAPCIVFIDEIDAVGRKRG 149

Query: 293 AAV---------SLSGVLNFMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDV 340
           + V         +L+ +L  MDG      FE+   +  M   N  D +D ALLRPGR D 
Sbjct: 150 SGVGGGNDEREQTLNQLLVEMDG------FEKDTAIVVMAATNRPDILDPALLRPGRFDR 203

Query: 341 HIHFPLCD 348
            I     D
Sbjct: 204 QIAIDAPD 211

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens} Length = 262

 Score = 49.9 bits (120), Expect = 5e-07
 Identities = 42/171 (24%), Positives = 69/171 (40%), Gaps = 45/171 (26%)

Query: 208 SFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYD-------V 255
            +LK+   + +LG    +  LL GP G GK+  A A+A+     F++    +       +
Sbjct: 23  DYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVIGGL 82

Query: 256 DLSRVADDADLKSLLLQTTSK---SVILIEDLDRFLVEKPAAVSLSGV--------LN-- 302
             +RV         L +        ++ I+++D   V K  + ++SG         LN  
Sbjct: 83  GAARVRS-------LFKEARARAPCIVYIDEIDA--VGKKRSTTMSGFSNTEEEQTLNQL 133

Query: 303 --FMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDVHIHFPLCD 348
              MDG            V  +   N  D +D AL+RPGR+D H+   L  
Sbjct: 134 LVEMDG------MGTTDHVIVLASTNRADILDGALMRPGRLDRHVFIDLPT 178

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A Length = 293

 Score = 48.7 bits (116), Expect = 2e-06
 Identities = 27/174 (15%), Positives = 51/174 (29%), Gaps = 46/174 (26%)

Query: 212 AKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV---------------- 255
            K++             ++G  G GKS     +   M  +   +                
Sbjct: 24  TKNFLKLPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKL 83

Query: 256 --DLSRVADDADLKSLLLQTTSKSVILIEDLD----RFLVEKPAAVS-------LSGVLN 302
                R A +      +++  +   + I DLD    R        V+       L  + +
Sbjct: 84  IRQRYREAAE------IIRKGNMCCLFINDLDAGAGRMGGTTQYTVNNQMVNATLMNIAD 137

Query: 303 F-----MDGVLNSCCFEERVMVF---TMNSKDHVDQALLRPGRIDVHIHFPLCD 348
                 + G+ N    +E   V    T N    +   L+R GR++     P  +
Sbjct: 138 NPTNVQLPGMYNK---QENARVPIIVTGNDFSTLYAPLIRDGRMEKFYWAPTRE 188

>2r62_A Cell division protease FTSH homolog; ATPase domain, ATP-binding, cell CELL division, hydrolase, membrane, metal-binding; 3.30A {Helicobacter pylori} PDB: 2r65_A* Length = 268

 Score = 47.3 bits (113), Expect = 4e-06
 Identities = 47/171 (27%), Positives = 66/171 (38%), Gaps = 44/171 (25%)

Query: 209 FLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYD-------VD 256
           FLK    Y  LG    +  LL GP GTGK+  A A+A      F S            + 
Sbjct: 29  FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEMFVGLG 88

Query: 257 LSRVADDADLKSLLLQTTSKS--VILIEDLDRFLVEKPAAVSLSG-----------VLNF 303
            SRV D      L      ++  +I I+++D  + +  AA  +             +L  
Sbjct: 89  ASRVRD------LFETAKKQAPSIIFIDEIDA-IGKSRAAGGVVSGNDEREQTLNQLLAE 141

Query: 304 MDGVLNSCCFEER-----VMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF 349
           MDG      F        V+  T N  + +D AL+RPGR D  +     DF
Sbjct: 142 MDG------FGSENAPVIVLAAT-NRPEILDPALMRPGRFDRQVLVDKPDF 185

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens} Length = 389

 Score = 47.5 bits (113), Expect = 5e-06
 Identities = 39/174 (22%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYDVDLSR-VADD 263
                 +  L    +   LL+GP G GK+  A A+A+     F +     +  S+ V + 
Sbjct: 135 SLRPELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASL-TSKYVGEG 192

Query: 264 ADLKSLLLQTTSK---SVILIEDLDRFLVEKPAAVSLSG------VLNFMDGVLNSCCFE 314
             L   L     +   S+I I+ +D  L E+      +        L   DGV ++   +
Sbjct: 193 EKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAG--D 250

Query: 315 ERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL 367
           +RV+V    N    +D+A+LR  R    ++  L +  +   L  + L  +   L
Sbjct: 251 DRVLVMGATNRPQELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPL 302

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens} Length = 357

 Score = 47.5 bits (113), Expect = 5e-06
 Identities = 40/174 (22%), Positives = 70/174 (40%), Gaps = 22/174 (12%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYDVDLSR-VADD 263
           +     +  L    K   LL+GP GTGK+     +AS     F S     +  S+ V + 
Sbjct: 104 MLRPDIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSL-TSKWVGEG 161

Query: 264 ADLKSLLLQTTSK---SVILIEDLDRFLVEKPAAVSLSG------VLNFMDGVLNSCCFE 314
             +   L         +VI I+++D  L ++      S        L  +DG   S   E
Sbjct: 162 EKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATTSS--E 219

Query: 315 ERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL 367
           +R++V    N    +D+A  R  R+   ++ PL + S+ K +  + +  +   L
Sbjct: 220 DRILVVGATNRPQEIDEAARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCL 271

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens} Length = 274

 Score = 45.6 bits (109), Expect = 2e-05
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 9/54 (16%)

Query: 301 LNFMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDVHIHFPLCDFSS 351
           L  MDG+      E R  VF M   N  D +D A+LRPGR+D  +   L   + 
Sbjct: 135 LTEMDGL------EARQQVFIMAATNRPDIIDPAILRPGRLDKTLFVGLPPPAD 182

>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 Length = 377

 Score = 44.6 bits (105), Expect = 5e-05
 Identities = 20/94 (21%), Positives = 36/94 (38%), Gaps = 10/94 (10%)

Query: 224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIED 283
           KR +L  GP  +GK++ AAA+            L+       L   L     + +++ ED
Sbjct: 169 KRYWLFKGPIDSGKTTLAAALLELCGGKA----LNVNLPLDRLNFELGVAIDQFLVVFED 224

Query: 284 LDRFLVEKPAAVS------LSGVLNFMDGVLNSC 311
           +     E     S      L  + +++DG +   
Sbjct: 225 VKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVN 258

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster} Length = 297

 Score = 43.8 bits (104), Expect = 6e-05
 Identities = 40/181 (22%), Positives = 71/181 (39%), Gaps = 23/181 (12%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYDVDLSR-VADD 263
                 +  L    K   LL+GP G GK+  A A+A+     F++     +  S+ V D 
Sbjct: 41  SVRPELFTGLRAPAK-GLLLFGPPGNGKTLLARAVATECSATFLNISAASL-TSKYVGDG 98

Query: 264 ADLKSLLLQTTSK---SVILIEDLDRFLVEKPAAVSLSG------VLNFMDGVLNSCCFE 314
             L   L         S+I I+++D  L E+ ++   +        L   DG+  +    
Sbjct: 99  EKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPD-G 157

Query: 315 ERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEE 373
           +R++V    N    +D+A LR  R    ++  L D  + + L +    L+        E 
Sbjct: 158 DRIVVLAATNRPQELDEAALR--RFTKRVYVSLPDEQTRELLLNRL--LQKQGSPLDTEA 213

Query: 374 I 374
           +
Sbjct: 214 L 214

>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 = 44.1 bits (104), Expect = 7e-05
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 4/71 (5%)

Query: 186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRL----GRVWKRSYLLYGPSGTGKSSFA 241
           P+    +        ++K+ L ++  +K    +     G    R+ +LYGP G GK++ A
Sbjct: 35  PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA 94

Query: 242 AAMASFMSYDV 252
             +A  + YD+
Sbjct: 95  HLVAQELGYDI 105

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens} Length = 322

 Score = 42.4 bits (100), Expect = 2e-04
 Identities = 42/174 (24%), Positives = 70/174 (40%), Gaps = 22/174 (12%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS------FMSYDVYDVDLSRVADD 263
           +K  H +      W+   LL+GP GTGKS  A A+A+      F S    D+    + + 
Sbjct: 32  IKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGES 90

Query: 264 ADLKSLLLQTTSK---SVILIEDLDRFLVEKPAAVSLSG------VLNFMDGVLNSCCFE 314
             L   L Q   +   S+I I+++D     +    S +        L  M GV       
Sbjct: 91  EKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVD---N 147

Query: 315 ERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL 367
           + ++V    N    +D A+ R  R +  I+ PL +  +   +   +LG   + L
Sbjct: 148 DGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSL 199

>2zan_A Vacuolar protein sorting-associating protein 4B; SKD1, VPS4B, AAA ATPase, ATP-binding, coiled coil, membrane, nucleotide-binding, phosphorylation; HET: ATP; 3.00A {Mus musculus} PDB: 2zam_A* 2zao_A* 2jqh_A 2jqk_A 1wr0_A 2jq9_A 2k3w_A 1yxr_A Length = 444

 Score = 42.2 bits (99), Expect = 3e-04
 Identities = 42/174 (24%), Positives = 69/174 (39%), Gaps = 22/174 (12%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS------FMSYDVYDVDLSRVADD 263
           +K  H +      W+   LL+GP GTGKS  A A+A+      F S    D+    + + 
Sbjct: 154 IKFPHLFTGKRTPWR-GILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVSKWLGES 212

Query: 264 ADLKSLLLQ---TTSKSVILIEDLDRFLVEKPAAVSLSG------VLNFMDGVLNSCCFE 314
             L   L Q       S+I I+++D     +    S +        L  M GV       
Sbjct: 213 EKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVD---N 269

Query: 315 ERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL 367
           + ++V    N    +D A+ R  R +  I+ PL +  +   +   +LG   + L
Sbjct: 270 DGILVLGATNIPWVLDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSL 321

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus} Length = 499

 Score = 42.2 bits (100), Expect = 3e-04
 Identities = 47/180 (26%), Positives = 66/180 (36%), Gaps = 66/180 (36%)

Query: 209 FLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYD-------VD 256
           FLK    +H +G    +  LL GP G GK+  A A+A      F++    D       V 
Sbjct: 49  FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMFVGVG 108

Query: 257 LSRVADDADLKSLLLQTTSKS---VILIEDLD----------------------RFLVEK 291
            +RV D       L +T  +    ++ I+++D                      + LVE 
Sbjct: 109 AARVRD-------LFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVE- 160

Query: 292 PAAVSLSGVLNFMDGVLNSCCFEERVMVFTM---NSKDHVDQALLRPGRIDVHIHFPLCD 348
                       MDG      FE+   +  M   N  D +D ALLRPGR D  I     D
Sbjct: 161 ------------MDG------FEKDTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPD 202

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A* Length = 355

 Score = 41.7 bits (98), Expect = 3e-04
 Identities = 45/195 (23%), Positives = 80/195 (41%), Gaps = 21/195 (10%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
            ++ ++     K  +K  +   +K  H +    +      LLYGP GTGKS  A A+A+ 
Sbjct: 49  KWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATE 107

Query: 248 MSYDVYDVDLSRVA------DDADLKSL--LLQTTSKSVILIEDLDRFLVEKPAAVSLSG 299
            +   + V  S +        +  +K L  + +    S+I I+ +D     +    S + 
Sbjct: 108 ANSTFFSVSSSDLVSKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEAS 167

Query: 300 ------VLNFMDGVLNSCCFEERVMVFT-MNSKDHVDQALLRPGRIDVHIHFPLCDFSSF 352
                 +L  M+GV N     + V+V    N    +D A+ R  R +  I+ PL D ++ 
Sbjct: 168 RRIKTELLVQMNGVGND---SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAAR 222

Query: 353 KTLASSYLGLKDHKL 367
            T+    +G     L
Sbjct: 223 TTMFEINVGDTPSVL 237

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C Length = 322

 Score = 40.8 bits (96), Expect = 6e-04
 Identities = 45/187 (24%), Positives = 71/187 (37%), Gaps = 49/187 (26%)

Query: 210 LKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS-----FMSYDVYDVDLSR-VADD 263
           +K  H +    +      LLYGP GTGKS  A A+A+     F S    D+ +S+ + + 
Sbjct: 38  VKFPHLFKGNRKPTS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDL-VSKWMGES 95

Query: 264 ADLKSLLLQTTSK---SVILIEDLD-------------------RFLVEKPAAVSLSGVL 301
             L   L     +   S+I I+ +D                     LV+           
Sbjct: 96  EKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQ----------- 144

Query: 302 NFMDGVLNSCCFEERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYL 360
             M+GV N     + V+V    N    +D A+ R  R +  I+ PL D ++  T+    +
Sbjct: 145 --MNGVGND---SQGVLVLGATNIPWQLDSAIRR--RFERRIYIPLPDLAARTTMFEINV 197

Query: 361 GLKDHKL 367
           G     L
Sbjct: 198 GDTPCVL 204

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	480
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	100.0
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	100.0
4b4t_I	437	26S protease regulatory subunit 4 homolog; hydrola	100.0
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	100.0
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	100.0
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	100.0
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	100.0
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	100.0
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	100.0
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	100.0
2zan_A	444	Vacuolar protein sorting-associating protein 4B; S	100.0
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	100.0
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	99.98
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	99.97
2ce7_A	476	Cell division protein FTSH; metalloprotease; HET:	99.97
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.97
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	99.97
3b9p_A	297	CG5977-PA, isoform A; AAA ATPase, ATP-binding, nuc	99.97
3d8b_A	357	Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, s	99.97
2dhr_A	499	FTSH; AAA+ protein, hexameric Zn metalloprotease,	99.96
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	99.96
2r62_A	268	Cell division protease FTSH homolog; ATPase domain	99.96
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.96
1ixz_A	254	ATP-dependent metalloprotease FTSH; AAA domain fol	99.96
1iy2_A	278	ATP-dependent metalloprotease FTSH; AAA domain fol	99.95
3t15_A	293	Ribulose bisphosphate carboxylase/oxygenase activ	99.93
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.93
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	99.87
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	99.84
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	99.83
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	99.81
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	99.79
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	99.79
2chg_A	226	Replication factor C small subunit; DNA-binding pr	99.77
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	99.76
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	99.75
3uk6_A	368	RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding	99.75
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	99.75
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	99.73
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	99.73
3pvs_A	447	Replication-associated recombination protein A; ma	99.72
1sxj_A	516	Activator 1 95 kDa subunit; clamp loader, processi	99.7
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	99.7
2chq_A	319	Replication factor C small subunit; DNA-binding pr	99.69
4fcw_A	311	Chaperone protein CLPB; AAA domain; HET: ADP; 2.35	99.69
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	99.68
1um8_A	376	ATP-dependent CLP protease ATP-binding subunit CL;	99.67
3bos_A	242	Putative DNA replication factor; P-loop containing	99.66
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	99.66
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	99.66
2r44_A	331	Uncharacterized protein; putative ATPase, structur	99.65
1in4_A	334	RUVB, holliday junction DNA helicase RUVB; AAA+-cl	99.65
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	99.65
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	99.65
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	99.64
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	99.64
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	99.64
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	99.61
3pxg_A	468	Negative regulator of genetic competence CLPC/MEC;	99.6
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	99.6
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.59
1r6b_X	758	CLPA protein; AAA+, N-terminal domain, CLPS, cryst	99.58
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	99.58
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.58
1g8p_A	350	Magnesium-chelatase 38 kDa subunit; parallel beta	99.57
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	99.57
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	99.56
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	99.56
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.55
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	99.54
3pxi_A	758	Negative regulator of genetic competence CLPC/MEC;	99.54
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	99.49
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	99.48
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	99.46
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	99.46
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	99.46
3co5_A	143	Putative two-component system transcriptional RES	99.41
3f9v_A	595	Minichromosome maintenance protein MCM; replicativ	99.36
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	99.33
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	99.31
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	99.28
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	99.26
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	99.16
1svm_A	377	Large T antigen; AAA+ fold, viral protein; HET: AT	99.11
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	99.1
3k1j_A	604	LON protease, ATP-dependent protease LON; ATP-bind	99.07
2qgz_A	308	Helicase loader, putative primosome component; str	99.01
2fna_A	357	Conserved hypothetical protein; structural genomic	98.97
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	98.96
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	98.92
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	98.92
2r2a_A	199	Uncharacterized protein; zonular occludens toxin,	98.92
1tue_A	212	Replication protein E1; helicase, replication, E1E	98.91
2vhj_A	331	Ntpase P4, P4; non- hydrolysable ATP analogue, hyd	98.88
2qen_A	350	Walker-type ATPase; unknown function; HET: ADP; 2.	98.83
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.8
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	98.67
4akg_A	2695	Glutathione S-transferase class-MU 26 kDa isozyme	98.64
3aji_B	83	S6C, proteasome (prosome, macropain) 26S subunit,	98.61
2krk_A	86	26S protease regulatory subunit 8; structural geno	98.56
3kw6_A	78	26S protease regulatory subunit 8; structural geno	98.5
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	98.38
3f8t_A	506	Predicted ATPase involved in replication control,	98.36
3vlf_B	88	26S protease regulatory subunit 7 homolog; heat re	98.33
3vkg_A	3245	Dynein heavy chain, cytoplasmic; AAA+ protein, mol	98.25
1jr3_D	343	DNA polymerase III, delta subunit; processivity, p	98.21
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	98.04
1z6t_A	591	APAF-1, apoptotic protease activating factor 1; ca	98.03
2cvh_A	220	DNA repair and recombination protein RADB; filamen	97.87
3sfz_A	1249	APAF-1, apoptotic peptidase activating factor 1; a	97.83
2dzn_B	82	26S protease regulatory subunit 6B homolog; ankyri	97.8
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	97.74
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	97.74
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	97.74
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	97.69
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	97.67
2z43_A	324	DNA repair and recombination protein RADA; archaea	97.67
1xp8_A	366	RECA protein, recombinase A; recombination, radior	97.66
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	97.65
1u94_A	356	RECA protein, recombinase A; homologous recombinat	97.65
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	97.63
1qhx_A	178	CPT, protein (chloramphenicol phosphotransferase);	97.61
3trf_A	185	Shikimate kinase, SK; amino acid biosynthesis, tra	97.6
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	97.58
3vaa_A	199	Shikimate kinase, SK; structural genomics, center	97.52
1pzn_A	349	RAD51, DNA repair and recombination protein RAD51,	97.52
2rhm_A	193	Putative kinase; P-loop containing nucleoside trip	97.51
2a5y_B	549	CED-4; apoptosis; HET: ATP; 2.60A {Caenorhabditis	97.5
3kb2_A	173	SPBC2 prophage-derived uncharacterized protein YOR	97.43
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	97.42
1via_A	175	Shikimate kinase; structural genomics, transferase	97.38
3iij_A	180	Coilin-interacting nuclear ATPase protein; alpha a	97.37
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	97.36
1gvn_B	287	Zeta; postsegregational killing system, plasmid; 1	97.36
1y63_A	184	LMAJ004144AAA protein; structural genomics, protei	97.34
2iyv_A	184	Shikimate kinase, SK; transferase, aromatic amino	97.34
2r8r_A	228	Sensor protein; KDPD, PFAM02702, MCSG, structural	97.34
1kag_A	173	SKI, shikimate kinase I; transferase, structural g	97.34
1zuh_A	168	Shikimate kinase; alpha-beta protein, transferase;	97.31
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	97.28
3lw7_A	179	Adenylate kinase related protein (ADKA-like); AMP,	97.27
2ze6_A	253	Isopentenyl transferase; crown GALL tumor, cytokin	97.27
3io5_A	333	Recombination and repair protein; storage dimer, i	97.27
1zp6_A	191	Hypothetical protein ATU3015; alpha-beta protein.,	97.24
1e6c_A	173	Shikimate kinase; phosphoryl transfer, ADP, shikim	97.24
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	97.22
2cdn_A	201	Adenylate kinase; phosphoryl transfer, associative	97.22
1tev_A	196	UMP-CMP kinase; ploop, NMP binding region, LID reg	97.21
1qf9_A	194	UMP/CMP kinase, protein (uridylmonophosphate/cytid	97.21
1ly1_A	181	Polynucleotide kinase; PNK, phosphatase, transfera	97.19
2p5t_B	253	PEZT; postsegregational killing system, phosphoryl	97.19
2c95_A	196	Adenylate kinase 1; transferase, AP4A, nucleotide	97.19
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	97.18
1zd8_A	227	GTP:AMP phosphotransferase mitochondrial; ATP:AMP	97.16
3jvv_A	356	Twitching mobility protein; hexameric P-loop ATPas	97.15
3t61_A	202	Gluconokinase; PSI-biology, structural genomics, p	97.15
3cm0_A	186	Adenylate kinase; ATP-binding, cytoplasm, nucleoti	97.14
2bwj_A	199	Adenylate kinase 5; phosphoryl transfer reaction,	97.14
1g41_A	444	Heat shock protein HSLU; AAA-ATPase, CLPY, ATP-dep	97.14
3dl0_A	216	Adenylate kinase; phosphotransferase, zinc coordin	97.14
3be4_A	217	Adenylate kinase; malaria, cryptosporidium parvum	97.13
2pt5_A	168	Shikimate kinase, SK; aromatic amino acid biosynth	97.13
1kht_A	192	Adenylate kinase; phosphotransferase, signaling pr	97.11
1aky_A	220	Adenylate kinase; ATP:AMP phosphotransferase, myok	97.1
3fb4_A	216	Adenylate kinase; psychrophIle, phosphotransferase	97.07
1ukz_A	203	Uridylate kinase; transferase; HET: ADP AMP; 1.90A	97.06
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	97.06
2vli_A	183	Antibiotic resistance protein; transferase, tunica	97.05
1knq_A	175	Gluconate kinase; ALFA/beta structure, transferase	97.04
2c9o_A	456	RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-	97.02
1zak_A	222	Adenylate kinase; ATP:AMP-phosphotransferase, tran	97.0
1ak2_A	233	Adenylate kinase isoenzyme-2; nucleoside monophosp	96.99
3crm_A	323	TRNA delta(2)-isopentenylpyrophosphate transferase	96.97
4eun_A	200	Thermoresistant glucokinase; putative sugar kinase	96.97
2pez_A	179	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	96.96
2pbr_A	195	DTMP kinase, thymidylate kinase; transferase, nucl	96.94
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	96.93
2px0_A	296	Flagellar biosynthesis protein FLHF; SRP GTPase, f	96.93
1e4v_A	214	Adenylate kinase; transferase(phosphotransferase);	96.92
3umf_A	217	Adenylate kinase; rossmann fold, transferase; 2.05	96.91
3tlx_A	243	Adenylate kinase 2; structural genomics, structura	96.91
2if2_A	204	Dephospho-COA kinase; alpha-beta protein, structur	96.89
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	96.88
2bbw_A	246	Adenylate kinase 4, AK4; nucleotide kinase, nucleo	96.84
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	96.82
2r6a_A	454	DNAB helicase, replicative helicase; replication,	96.81
2v54_A	204	DTMP kinase, thymidylate kinase; nucleotide biosyn	96.81
2jaq_A	205	Deoxyguanosine kinase; transferase, deoxyribonucle	96.8
1cke_A	227	CK, MSSA, protein (cytidine monophosphate kinase);	96.79
3sr0_A	206	Adenylate kinase; phosphoryl transfer analogue, AL	96.79
2xb4_A	223	Adenylate kinase; ATP-binding, nucleotide-binding,	96.77
1nks_A	194	Adenylate kinase; thermophilic, transferase; HET:	96.76
1jjv_A	206	Dephospho-COA kinase; P-loop nucleotide-binding fo	96.76
2z0h_A	197	DTMP kinase, thymidylate kinase; ATP-binding, nucl	96.74
3uie_A	200	Adenylyl-sulfate kinase 1, chloroplastic; rossmann	96.74
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	96.74
3a4m_A	260	L-seryl-tRNA(SEC) kinase; P-loop motif, walker A m	96.7
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	96.66
1uf9_A	203	TT1252 protein; P-loop, nucleotide binding domain,	96.65
3ake_A	208	Cytidylate kinase; CMP kinase, CMP complex, open c	96.64
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	96.63
1vma_A	306	Cell division protein FTSY; TM0570, structural gen	96.63
3nwj_A	250	ATSK2; P loop, shikimate, nucleoside monophosphate	96.62
2plr_A	213	DTMP kinase, probable thymidylate kinase; TMP-bind	96.62
4a74_A	231	DNA repair and recombination protein RADA; hydrola	96.61
3r20_A	233	Cytidylate kinase; structural genomics, seattle st	96.6
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	96.59
2grj_A	192	Dephospho-COA kinase; TM1387, EC 2.7.1.24, dephosp	96.58
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.53
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	96.52
2iut_A	574	DNA translocase FTSK; nucleotide-binding, chromoso	96.51
2wwf_A	212	Thymidilate kinase, putative; transferase, malaria	96.51
2ga8_A	359	Hypothetical 39.9 kDa protein; YFR007W, YFH7, unkn	96.5
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	96.5
3a8t_A	339	Adenylate isopentenyltransferase; rossmann fold pr	96.48
2pt7_A	330	CAG-ALFA; ATPase, protein-protein complex, type IV	96.43
2h92_A	219	Cytidylate kinase; rossmann fold, transferase; HET	96.43
1vht_A	218	Dephospho-COA kinase; structural genomics, transfe	96.43
2qt1_A	207	Nicotinamide riboside kinase 1; non-protein kinase	96.42
2ius_A	512	DNA translocase FTSK; nucleotide-binding, chromoso	96.41
4e22_A	252	Cytidylate kinase; P-loop, CMP/ATP binding, transf	96.39
2bdt_A	189	BH3686; alpha-beta protein, structural genomics, P	96.39
2qor_A	204	Guanylate kinase; phosphotransferase, purine metab	96.39
1nn5_A	215	Similar to deoxythymidylate kinase (thymidylate K;	96.38
1ltq_A	301	Polynucleotide kinase; phosphatase, alpha/beta, P-	96.37
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	96.37
3foz_A	316	TRNA delta(2)-isopentenylpyrophosphate transferas;	96.35
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	96.34
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	96.32
2j41_A	207	Guanylate kinase; GMP, GMK, transferase, ATP-bindi	96.29
1q3t_A	236	Cytidylate kinase; nucleotide monophosphate kinase	96.28
1uj2_A	252	Uridine-cytidine kinase 2; alpha/beta mononucleoti	96.26
2yvu_A	186	Probable adenylyl-sulfate kinase; transferase, str	96.24
1rz3_A	201	Hypothetical protein rbstp0775; MCSG, structural g	96.16
2qmh_A	205	HPR kinase/phosphorylase; V267F mutation, ATP-bind	96.16
3zvl_A	416	Bifunctional polynucleotide phosphatase/kinase; hy	96.15
3d3q_A	340	TRNA delta(2)-isopentenylpyrophosphate transferase	96.15
3tau_A	208	Guanylate kinase, GMP kinase; structural genomics,	96.14
2f6r_A	281	COA synthase, bifunctional coenzyme A synthase; 18	96.1
3exa_A	322	TRNA delta(2)-isopentenylpyrophosphate transferase	96.04
1m7g_A	211	Adenylylsulfate kinase; APS kinase, transferase, s	96.04
2v3c_C	432	SRP54, signal recognition 54 kDa protein; nucleoti	96.02
3c8u_A	208	Fructokinase; YP_612366.1, putative fructose trans	96.02
1ex7_A	186	Guanylate kinase; substrate-induced FIT, domain mo	96.0
3tr0_A	205	Guanylate kinase, GMP kinase; purines, pyrimidines	95.98
3fdi_A	201	Uncharacterized protein; cytidylate kinase like pr	95.98
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	95.93
3b9q_A	302	Chloroplast SRP receptor homolog, alpha subunit CP	95.92
3a00_A	186	Guanylate kinase, GMP kinase; domain movement, dim	95.9
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	95.88
1c9k_A	180	COBU, adenosylcobinamide kinase; alpha/beta struct	95.82
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	95.81
3asz_A	211	Uridine kinase; cytidine phosphorylation, transfer	95.73
2og2_A	359	Putative signal recognition particle receptor; nuc	95.67
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	95.67
1htw_A	158	HI0065; nucleotide-binding fold, structural genomi	95.65
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	95.64
3eph_A	409	TRNA isopentenyltransferase; transferase, alternat	95.62
1gtv_A	214	TMK, thymidylate kinase; transferase, transferase	95.61
2yhs_A	503	FTSY, cell division protein FTSY; cell cycle, prot	95.58
2ce2_X	166	GTPase HRAS; signaling protein, guanine nucleotide	95.54
2j37_W	504	Signal recognition particle 54 kDa protein (SRP54)	95.54
1odf_A	290	YGR205W, hypothetical 33.3 kDa protein in ADE3-Ser	95.54
1z6g_A	218	Guanylate kinase; structural genomics, SGC, struct	95.51
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	95.51
1znw_A	207	Guanylate kinase, GMP kinase; ATP:GMP-phosphotrans	95.5
3ney_A	197	55 kDa erythrocyte membrane protein; structural ge	95.5
3b6e_A	216	Interferon-induced helicase C domain-containing P;	95.49
1zu4_A	320	FTSY; GTPase, signal recognition particle, SRP, re	95.49
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	95.48
2v9p_A	305	Replication protein E1; AAA+ molecular motor, DNA	95.43
1x6v_B	630	Bifunctional 3'-phosphoadenosine 5'- phosphosulfat	95.36
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	95.29
3gmt_A	230	Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucle	95.28
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	95.27
2eyu_A	261	Twitching motility protein PILT; pilus retraction	95.26
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	95.25
1j8m_F	297	SRP54, signal recognition 54 kDa protein; signalin	95.24
1s96_A	219	Guanylate kinase, GMP kinase; E.coli, dimer, SAD,	95.24
3tqf_A	181	HPR(Ser) kinase; transferase, hydrolase; 2.80A {Co	95.22
1kao_A	167	RAP2A; GTP-binding protein, small G protein, GDP,	95.2
3hdt_A	223	Putative kinase; structura genomics, PSI-2, protei	95.19
1nrj_B	218	SR-beta, signal recognition particle receptor beta	95.16
3e70_C	328	DPA, signal recognition particle receptor; FTSY, S	95.12
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	95.11
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	95.11
4eaq_A	229	DTMP kinase, thymidylate kinase; structural genomi	95.08
2jeo_A	245	Uridine-cytidine kinase 1; UCK, transferase, ATP-b	95.06
2ewv_A	372	Twitching motility protein PILT; pilus retraction	95.05
2p5s_A	199	RAS and EF-hand domain containing; G-protein, RAB,	94.99
2i3b_A	189	HCR-ntpase, human cancer-related ntpase; AAA, ross	94.96
1p9r_A	418	General secretion pathway protein E; bacterial typ	94.9
1r8s_A	164	ADP-ribosylation factor 1; protein transport/excha	94.83
3lnc_A	231	Guanylate kinase, GMP kinase; ALS collaborative cr	94.8
1u8z_A	168	RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNH	94.8
2ged_A	193	SR-beta, signal recognition particle receptor beta	94.79
1np6_A	174	Molybdopterin-guanine dinucleotide biosynthesis pr	94.73
2erx_A	172	GTP-binding protein DI-RAS2; GTP hydrolysis, trans	94.72
3kta_A	182	Chromosome segregation protein SMC; structural mai	94.71
1a7j_A	290	Phosphoribulokinase; transferase, calvin cycle; 2.	94.7
3tkl_A	196	RAS-related protein RAB-1A; vesicle trafficking, p	94.68
2fg5_A	192	RAB-22B, RAS-related protein RAB-31; G-protein, GT	94.68
1c1y_A	167	RAS-related protein RAP-1A; GTP-binding proteins,	94.68
1x3s_A	195	RAS-related protein RAB-18; GTPase, GNP, structura	94.62
4a82_A	578	Cystic fibrosis transmembrane conductance regulat;	94.62
3tqc_A	321	Pantothenate kinase; biosynthesis of cofactors, pr	94.55
2axn_A	520	6-phosphofructo-2-kinase/fructose-2,6- biphosphata	94.53
2a9k_A	187	RAS-related protein RAL-A; bacterial ADP-ribosyltr	94.48
2xxa_A	433	Signal recognition particle protein; protein trans	94.44
1p5z_B	263	DCK, deoxycytidine kinase; nucleoside kinase, P-lo	94.44
3t1o_A	198	Gliding protein MGLA; G domain containing protein,	94.39
2ocp_A	241	DGK, deoxyguanosine kinase; protein-nucleotide com	94.36
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	94.35
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	94.34
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	94.34
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.34
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	94.32
1sq5_A	308	Pantothenate kinase; P-loop, transferase; HET: PAU	94.31
1m8p_A	573	Sulfate adenylyltransferase; rossmann fold, phosph	94.3
3aez_A	312	Pantothenate kinase; transferase, homodimer, COA b	94.28
1rj9_A	304	FTSY, signal recognition protein; SRP-GTPase domai	94.28
1fzq_A	181	ADP-ribosylation factor-like protein 3; protein-GD	94.23
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	94.21
1xjc_A	169	MOBB protein homolog; structural genomics, midwest	94.2
2bov_A	206	RAla, RAS-related protein RAL-A; C3BOT, exoenzyme,	94.2
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	94.18
4i1u_A	210	Dephospho-COA kinase; structural genomics, niaid,	94.16
1oix_A	191	RAS-related protein RAB-11A; small G protein, intr	94.12
2f9l_A	199	RAB11B, member RAS oncogene family; RAB11B GTPase,	94.11
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	94.11
2f7s_A	217	C25KG, RAS-related protein RAB-27B; G-protein, str	94.11
1q57_A	503	DNA primase/helicase; dntpase, DNA replication, tr	94.03
1lw7_A	365	Transcriptional regulator NADR; NMN, NMN adenylyl	94.03
3bgw_A	444	DNAB-like replicative helicase; ATPase, replicatio	93.99
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	93.99
1sgw_A	214	Putative ABC transporter; structural genomics, P p	93.96
2dyk_A	161	GTP-binding protein; GTPase, ribosome-binding prot	93.96
1g6h_A	257	High-affinity branched-chain amino acid transport	93.94
2ffh_A	425	Protein (FFH); SRP54, signal recognition particle,	93.93
1b0u_A	262	Histidine permease; ABC transporter, transport pro	93.93
2gf0_A	199	GTP-binding protein DI-RAS1; GDP/GTP binding, GTP	93.93
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	93.9
3sop_A	270	Neuronal-specific septin-3; hydrolase; HET: GDP; 2	93.9
2pze_A	229	Cystic fibrosis transmembrane conductance regulat;	93.85
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	93.85
1z2a_A	168	RAS-related protein RAB-23; RAB GTPase, vesicular	93.84
1bif_A	469	6-phosphofructo-2-kinase/ fructose-2,6-bisphospha;	93.82
1ji0_A	240	ABC transporter; ATP binding protein, structural g	93.78
2ghi_A	260	Transport protein; multidrug resistance protein, M	93.77
2d2e_A	250	SUFC protein; ABC-ATPase, SUF protein, 310-helix,	93.76
2h57_A	190	ADP-ribosylation factor-like protein 6; GTP, GTPas	93.76
2ff7_A	247	Alpha-hemolysin translocation ATP-binding protein	93.76
2qi9_C	249	Vitamin B12 import ATP-binding protein BTUD; inner	93.75
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	93.75
2fh5_B	214	SR-beta, signal recognition particle receptor beta	93.74
2olj_A	263	Amino acid ABC transporter; ABC domain, ATPase, hy	93.73
4edh_A	213	DTMP kinase, thymidylate kinase; structural genomi	93.72
2ixe_A	271	Antigen peptide transporter 1; ABC ATPase, hydrola	93.72
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	93.62
1ek0_A	170	Protein (GTP-binding protein YPT51); vesicular tra	93.61
2zu0_C	267	Probable ATP-dependent transporter SUFC; iron-sulf	93.6
2wji_A	165	Ferrous iron transport protein B homolog; membrane	93.6
2ihy_A	279	ABC transporter, ATP-binding protein; ATPase, ABC	93.58
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	93.57
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	93.52
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	93.5
2nq2_C	253	Hypothetical ABC transporter ATP-binding protein H	93.48
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	93.48
1g16_A	170	RAS-related protein SEC4; G protein RAB, signaling	93.48
1z0j_A	170	RAB-22, RAS-related protein RAB-22A; RAB GTPase, R	93.48
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	93.48
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	93.48
3v9p_A	227	DTMP kinase, thymidylate kinase; ssgcid, STRU geno	93.47
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	93.44
1wms_A	177	RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, p	93.43
2nzj_A	175	GTP-binding protein REM 1; GDP/GTP binding, GTP hy	93.42
2zej_A	184	Dardarin, leucine-rich repeat kinase 2; parkinson'	93.41
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	93.41
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	93.37
2www_A	349	Methylmalonic aciduria type A protein, mitochondri	93.37
1z08_A	170	RAS-related protein RAB-21; RAB GTPase, vesicular	93.36
3tmk_A	216	Thymidylate kinase; phosphotransferase; HET: T5A;	93.35
1ky3_A	182	GTP-binding protein YPT7P; vesicular traffic, GTP	93.32
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	93.32
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	93.28
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	93.27
1r2q_A	170	RAS-related protein RAB-5A; GTPase, GNP, atomic re	93.27
1g8f_A	511	Sulfate adenylyltransferase; alpha-beta protein, b	93.25
2f1r_A	171	Molybdopterin-guanine dinucleotide biosynthesis pr	93.21
2wjg_A	188	FEOB, ferrous iron transport protein B homolog; me	93.19
3d31_A	348	Sulfate/molybdate ABC transporter, ATP-binding pro	93.17
3cr8_A	552	Sulfate adenylyltranferase, adenylylsulfate kinase	93.17
2obl_A	347	ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O	93.15
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	93.14
2hxs_A	178	RAB-26, RAS-related protein RAB-28; GTPase, signal	93.1
2y8e_A	179	RAB-protein 6, GH09086P, RAB6; hydrolase, nucleoti	93.1
3bc1_A	195	RAS-related protein RAB-27A; RAB27, GTPase, RAB, s	93.1
1f2t_A	149	RAD50 ABC-ATPase; DNA double-strand break repair,	93.07
3q85_A	169	GTP-binding protein REM 2; G-domain, CAV2 beta, si	93.05
3p32_A	355	Probable GTPase RV1496/MT1543; structural genomics	93.02
3q72_A	166	GTP-binding protein RAD; G-domain, CAV2 beta, sign	93.0
1upt_A	171	ARL1, ADP-ribosylation factor-like protein 1; hydr	92.91
2atv_A	196	RERG, RAS-like estrogen-regulated growth inhibitor	92.88
3gd7_A	390	Fusion complex of cystic fibrosis transmembrane co	92.88
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	92.88
4dsu_A	189	GTPase KRAS, isoform 2B; small G-protein, signalin	92.88
1z0f_A	179	RAB14, member RAS oncogene family; RAB GTPase, ves	92.88
3clv_A	208	RAB5 protein, putative; malaria, GTPase, structura	92.87
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	92.87
1svi_A	195	GTP-binding protein YSXC; ENGB, GTPase, GDP, hydro	92.85
2fn4_A	181	P23, RAS-related protein R-RAS; GDP/GTP binding, G	92.84
1tf7_A	525	KAIC; homohexamer, hexamer, circadian clock protei	92.84
2gj8_A	172	MNME, tRNA modification GTPase TRME; G-domain dime	92.83
2lkc_A	178	Translation initiation factor IF-2; NMR {Geobacill	92.83
3lv8_A	236	DTMP kinase, thymidylate kinase; structural genomi	92.83
1tq4_A	413	IIGP1, interferon-inducible GTPase; interferon gam	92.83
2bbs_A	290	Cystic fibrosis transmembrane conductance regulato	92.82
1moz_A	183	ARL1, ADP-ribosylation factor-like protein 1; GTP-	92.81
1oxx_K	353	GLCV, glucose, ABC transporter, ATP binding protei	92.8
1m7b_A	184	RND3/RHOE small GTP-binding protein; small GTPase,	92.8
2bme_A	186	RAB4A, RAS-related protein RAB4A; GTP-binding prot	92.8
2oil_A	193	CATX-8, RAS-related protein RAB-25; G-protein, GDP	92.77
2efe_B	181	Small GTP-binding protein-like; GEF, GTPase, VPS9,	92.75
2dpy_A	438	FLII, flagellum-specific ATP synthase; beta barrel	92.72
3con_A	190	GTPase NRAS; structural genomics consortium, SGC,	92.69
2cxx_A	190	Probable GTP-binding protein ENGB; structural geno	92.61
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	92.57
3b1v_A	272	Ferrous iron uptake transporter protein B; G prote	92.56
3tw8_B	181	RAS-related protein RAB-35; longin domain, RAB GTP	92.56
1yrb_A	262	ATP(GTP)binding protein; GTPase, P-loop, rossman f	92.48
2npi_A	460	Protein CLP1; CLP1-PCF11 complex, ATP binding, ter	92.43
2g6b_A	180	RAS-related protein RAB-26; G-protein, GTP analogu	92.43
1mh1_A	186	RAC1; GTP-binding, GTPase, small G-protein, RHO fa	92.42
2gf9_A	189	RAS-related protein RAB-3D; G-protein, structural	92.41
3kkq_A	183	RAS-related protein M-RAS; GTP-binding, GTPase, si	92.41
1m2o_B	190	GTP-binding protein SAR1, GTP binding protein; zin	92.35
1ko7_A	314	HPR kinase/phosphatase; protein kinase, phosphotra	92.32
1pui_A	210	ENGB, probable GTP-binding protein ENGB; structura	92.31
4tmk_A	213	Protein (thymidylate kinase); ATP:DTMP phosphotran	92.31
3k53_A	271	Ferrous iron transport protein B; GTPase fold, hel	92.27
3pqc_A	195	Probable GTP-binding protein ENGB; rossmann fold,	92.26
2wsm_A	221	Hydrogenase expression/formation protein (HYPB); m	92.26
2qm8_A	337	GTPase/ATPase; G protein, G3E, metallochaperone, c	92.24
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	92.24
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	92.24
2b6h_A	192	ADP-ribosylation factor 5; membrane trafficking, G	92.24
3bwd_D	182	RAC-like GTP-binding protein ARAC6; G domain, cyto	92.19
3ld9_A	223	DTMP kinase, thymidylate kinase; ssgcid, NIH, niai	92.16
3dz8_A	191	RAS-related protein RAB-3B; GDP, GTPase, structura	92.14
3c5c_A	187	RAS-like protein 12; GDP, GTPase, structural genom	92.06
1knx_A	312	Probable HPR(Ser) kinase/phosphatase; HPR kinase,	92.05
1vg8_A	207	RAS-related protein RAB-7; GTP-binding protein, pr	92.05
3t5g_A	181	GTP-binding protein RHEB; immunoglobulin-like beta	92.04
1z06_A	189	RAS-related protein RAB-33B; RAB GTPase, RAB33B GT	92.02
1zd9_A	188	ADP-ribosylation factor-like 10B; transport protei	92.01
1zbd_A	203	Rabphilin-3A; G protein, effector, RABCDR, synapti	91.98
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	91.97
2bcg_Y	206	Protein YP2, GTP-binding protein YPT1; RABGTPase,	91.97
3ihw_A	184	Centg3; RAS, centaurin, GTPase, structural genomic	91.96
2vp4_A	230	Deoxynucleoside kinase; ATP-binding, DNA synthesis	91.95
2iwr_A	178	Centaurin gamma 1; ANK repeat, zinc-finger, GTP-bi	91.94
2a5j_A	191	RAS-related protein RAB-2B; GTPase, signal transdu	91.93
3reg_A	194	RHO-like small GTPase; cytoskeleton, nucleotide-bi	91.88
2rcn_A	358	Probable GTPase ENGC; YJEQ, circularly permuted, G	91.83
3cph_A	213	RAS-related protein SEC4; RAB GTPase, prenylation,	91.82
3oes_A	201	GTPase rhebl1; small GTPase, structural genomics,	91.8
1u0l_A	301	Probable GTPase ENGC; permutation, OB-fold, zinc-f	91.78
2gks_A	546	Bifunctional SAT/APS kinase; transferase, sulfuryl	91.72
1ksh_A	186	ARF-like protein 2; small GTPase, small GTP-bindin	91.69
1gwn_A	205	RHO-related GTP-binding protein RHOE; GTPase, inac	91.63
3lxx_A	239	GTPase IMAP family member 4; structural genomics c	91.58
2qag_B	427	Septin-6, protein NEDD5; cell cycle, cell division	91.58
4f4c_A	1321	Multidrug resistance protein PGP-1; ABC transporte	91.54
1zj6_A	187	ADP-ribosylation factor-like protein 5; ARL, GTP-b	91.53
2hf9_A	226	Probable hydrogenase nickel incorporation protein	91.42
2h17_A	181	ADP-ribosylation factor-like protein 5A; GDP, GTPa	91.4
2ew1_A	201	RAS-related protein RAB-30; G-protein, GTP analogu	91.38
2fu5_C	183	RAS-related protein RAB-8A; MSS4:RAB8 protein comp	91.35
1f6b_A	198	SAR1; gtpases, N-terminal helix, Mg-containing com	91.3
2yv5_A	302	YJEQ protein; hydrolase, GTPase, permutation, stru	91.25
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	91.24
2atx_A	194	Small GTP binding protein TC10; GTPase, P-loop, al	91.19
2qtf_A	364	Protein HFLX, GTP-binding protein; beta-alpha-barr	91.18
3qks_A	203	DNA double-strand break repair RAD50 ATPase; RECA-	91.16
3t34_A	360	Dynamin-related protein 1A, linker, dynamin-relat	91.13
2o52_A	200	RAS-related protein RAB-4B; G-protein, GDP, struct	91.11
2fv8_A	207	H6, RHO-related GTP-binding protein RHOB; GDP/GTP	91.07
2q3h_A	201	RAS homolog gene family, member U; GTPase, structu	90.96
4hlc_A	205	DTMP kinase, thymidylate kinase; TMK, MRSA, pipiri	90.93
2gco_A	201	H9, RHO-related GTP-binding protein RHOC; GTPase,s	90.85
3ice_A	422	Transcription termination factor RHO; transcriptio	90.84
2cjw_A	192	GTP-binding protein GEM; nucleotide-binding, small	90.82
2hup_A	201	RAS-related protein RAB-43; G-protein, GDP, struct	90.76
1qhl_A	227	Protein (cell division protein MUKB); SMC, chromos	90.68
2j0v_A	212	RAC-like GTP-binding protein ARAC7; nucleotide-bin	90.67
2p67_A	341	LAO/AO transport system kinase; ARGK, structural G	90.61
2il1_A	192	RAB12; G-protein, GDP, GTPase, predicted, structur	90.61
1dek_A	241	Deoxynucleoside monophosphate kinase; transferase,	90.59

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.3e-46  Score=388.98  Aligned_cols=211  Identities=22%  Similarity=0.303  Sum_probs=189.4

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...|.++|+||+|++++|++|++.+..|+++|+.|.++|.++|+|+|||||||||||++|+|+|++++.+|+.++++++.
T Consensus       140 ~~~p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi~~prGvLL~GPPGTGKTllAkAiA~e~~~~f~~v~~s~l~  219 (405)
T 4b4t_J          140 EKVPDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGIAQPKGVILYGPPGTGKTLLARAVAHHTDCKFIRVSGAELV  219 (405)
T ss_dssp             ECSCSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCCEEEESCSSSSHHHHHHHHHHHHTCEEEEEEGGGGS
T ss_pred             cCCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCceEEeCCCCCCHHHHHHHHHHhhCCCceEEEhHHhh
Confidence            34467999999999999999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             ----C--hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 ----D--DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ----~--~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                          +  +..++.+|..  ..+||||||||||++++.+..         ..++++||++|||+.+   ..+++||+|||+
T Consensus       220 sk~vGese~~vr~lF~~Ar~~aP~IIFiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~---~~~V~vIaATNr  296 (405)
T 4b4t_J          220 QKYIGEGSRMVRELFVMAREHAPSIIFMDEIDSIGSTRVEGSGGGDSEVQRTMLELLNQLDGFET---SKNIKIIMATNR  296 (405)
T ss_dssp             CSSTTHHHHHHHHHHHHHHHTCSEEEEEESSSCCTTSCSCSSSGGGGHHHHHHHHHHHHHHTTTC---CCCEEEEEEESC
T ss_pred             ccccchHHHHHHHHHHHHHHhCCceEeeecchhhccCCCCCCCCCcHHHHHHHHHHHHhhhccCC---CCCeEEEeccCC
Confidence                3  4558888854  468999999999999876532         2357899999999987   578899999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |+.|||||+||||||++|+||+|+.++|.+|++.++...+..-..+++.||..+.|||||||.++|..|..
T Consensus       297 pd~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~l~~dvdl~~lA~~t~G~SGADi~~l~~eA~~  367 (405)
T 4b4t_J          297 LDILDPALLRPGRIDRKIEFPPPSVAARAEILRIHSRKMNLTRGINLRKVAEKMNGCSGADVKGVCTEAGM  367 (405)
T ss_dssp             SSSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSBCCSSCCHHHHHHHCCSCCHHHHHHHHHHHHH
T ss_pred             hhhCCHhHcCCCcCceEEEcCCcCHHHHHHHHHHHhcCCCCCccCCHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999987766555678999999999999999999987644

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=3.3e-46  Score=390.65  Aligned_cols=211  Identities=18%  Similarity=0.250  Sum_probs=188.8

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...++++|+||+|++++|++|.+.+..|+++|+.|.+.|.++|+|||||||||||||++|+|+|++++.+|+.++++++.
T Consensus       173 ~~~p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~~~prGvLLyGPPGTGKTllAkAiA~e~~~~f~~v~~s~l~  252 (434)
T 4b4t_M          173 DEKPTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGIRAPKGALMYGPPGTGKTLLARACAAQTNATFLKLAAPQLV  252 (434)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGGC
T ss_pred             CCCCCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeeEEECcCCCCHHHHHHHHHHHhCCCEEEEehhhhh
Confidence            44678999999999999999999999999999999999999999999999999999999999999999999999988765


Q ss_pred             C------hHHHHHHHH--hhcCCcEEEEecccccccCcccc---------cchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 D------DADLKSLLL--QTTSKSVILIEDLDRFLVEKPAA---------VSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ~------~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~~~---------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      +      +..++.+|.  +..+||||||||+|++++.+...         .++++||+.|||+.+   .++++||+|||+
T Consensus       253 ~~~vGese~~ir~lF~~A~~~aP~IifiDEiDal~~~R~~~~~~~~~~~~~~~~~lL~~ldg~~~---~~~ViVIaaTNr  329 (434)
T 4b4t_M          253 QMYIGEGAKLVRDAFALAKEKAPTIIFIDELDAIGTKRFDSEKSGDREVQRTMLELLNQLDGFSS---DDRVKVLAATNR  329 (434)
T ss_dssp             SSCSSHHHHHHHHHHHHHHHHCSEEEEEECTHHHHCCCSSGGGGTTHHHHHHHHHHHHHHTTSCS---SCSSEEEEECSS
T ss_pred             hcccchHHHHHHHHHHHHHhcCCeEEeecchhhhhhccCCCCCCCchHHHHHHHHHHHHhhccCC---CCCEEEEEeCCC
Confidence            3      345788885  45689999999999998766322         347889999999987   578899999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |+.|||||+||||||++|+||+|+.++|.+||+.++......-..+++.||..+.|||||||.++|..|..
T Consensus       330 p~~LD~AllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~sGADi~~l~~eA~~  400 (434)
T 4b4t_M          330 VDVLDPALLRSGRLDRKIEFPLPSEDSRAQILQIHSRKMTTDDDINWQELARSTDEFNGAQLKAVTVEAGM  400 (434)
T ss_dssp             CCCCCTTTCSTTSEEEEEECCCCCHHHHHHHHHHHHHHSCBCSCCCHHHHHHHCSSCCHHHHHHHHHHHHH
T ss_pred             chhcCHhHhcCCceeEEEEeCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999987665555578999999999999999999987644

>4b4t_I 26S protease regulatory subunit 4 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.5e-46  Score=388.05  Aligned_cols=211  Identities=21%  Similarity=0.280  Sum_probs=188.9

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...+.++|+||+|++++|++|++.+..|+++|++|...|.+|++|||||||||||||++|+|+|++++.+|+.++++++.
T Consensus       174 ~~~p~v~~~DIgGld~~k~~L~e~v~~Pl~~pe~f~~~Gi~~prGvLLyGPPGTGKTlLAkAiA~e~~~~fi~v~~s~l~  253 (437)
T 4b4t_I          174 DKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPKGVILYGAPGTGKTLLAKAVANQTSATFLRIVGSELI  253 (437)
T ss_dssp             ESSCCCCGGGTCSCHHHHHHHHHHHHHHHHCCHHHHHHTCCCCSEEEEESSTTTTHHHHHHHHHHHHTCEEEEEESGGGC
T ss_pred             ccCCCCcceecCcHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCCCceECCCCchHHHHHHHHHHHhCCCEEEEEHHHhh
Confidence            34577899999999999999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             ----C--hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 ----D--DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ----~--~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                          +  +..++.+|..  ..+||||||||||+++..+..         ..++++||++|||+.+   .++++||+|||+
T Consensus       254 sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~LL~~lDg~~~---~~~ViVIaATNr  330 (437)
T 4b4t_I          254 QKYLGDGPRLCRQIFKVAGENAPSIVFIDEIDAIGTKRYDSNSGGEREIQRTMLELLNQLDGFDD---RGDVKVIMATNK  330 (437)
T ss_dssp             CSSSSHHHHHHHHHHHHHHHTCSEEEEEEEESSSSCCCSCSSCSSCCHHHHHHHHHHHHHHHCCC---SSSEEEEEEESC
T ss_pred             hccCchHHHHHHHHHHHHHhcCCcEEEEehhhhhcccCCCCCCCccHHHHHHHHHHHHHhhCcCC---CCCEEEEEeCCC
Confidence                3  3457888854  468999999999999986632         2457899999999877   678999999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |+.|||||+||||||++|+|++|+.++|.+|++.|+...+..-..+++.||..+.|||||||.++|..|..
T Consensus       331 pd~LDpALlRpGRfD~~I~v~lPd~~~R~~Il~~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~eA~~  401 (437)
T 4b4t_I          331 IETLDPALIRPGRIDRKILFENPDLSTKKKILGIHTSKMNLSEDVNLETLVTTKDDLSGADIQAMCTEAGL  401 (437)
T ss_dssp             STTCCTTSSCTTTEEEEECCCCCCHHHHHHHHHHHHTTSCBCSCCCHHHHHHHCCSCCHHHHHHHHHHHHH
T ss_pred             hhhcCHHHhcCCceeEEEEcCCcCHHHHHHHHHHHhcCCCCCCcCCHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999987665555678999999999999999999987644

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=2.5e-45  Score=384.30  Aligned_cols=209  Identities=23%  Similarity=0.303  Sum_probs=187.7

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      .+.++|+||+|++++|++|.+.+..|+++|+.|.++|.++++|+|||||||||||++|+|+|++++.+|+.++++++.+ 
T Consensus       175 ~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~~~prGvLL~GPPGtGKTllAkAiA~e~~~~~~~v~~s~l~sk  254 (437)
T 4b4t_L          175 QGEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPKGVLLYGPPGTGKTLLAKAVAATIGANFIFSPASGIVDK  254 (437)
T ss_dssp             SCSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTSSHHHHHHHHHHHHTCEEEEEEGGGTCCS
T ss_pred             CCCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehhhhccc
Confidence            4678999999999999999999999999999999999999999999999999999999999999999999999887653 


Q ss_pred             -----hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          263 -----DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 -----~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                           +..++.+|..  ..+||||||||||++++.+..         ..++++||++|||+.+   .++++||+|||+|+
T Consensus       255 ~~Gese~~ir~~F~~A~~~~P~IifiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~---~~~vivI~ATNrp~  331 (437)
T 4b4t_L          255 YIGESARIIREMFAYAKEHEPCIIFMDEVDAIGGRRFSEGTSADREIQRTLMELLTQMDGFDN---LGQTKIIMATNRPD  331 (437)
T ss_dssp             SSSHHHHHHHHHHHHHHHSCSEEEEEECCCSSSCCCSSSCCSSTTHHHHHHHHHHHHHHSSSC---TTSSEEEEEESSTT
T ss_pred             cchHHHHHHHHHHHHHHhcCCceeeeecccccccccccCCCCcchHHHHHHHHHHHHhhcccC---CCCeEEEEecCCch
Confidence                 3447788854  468999999999999876532         2357889999999987   57899999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      .|||||+||||||++|+||+|+.++|.+||+.|+......-..+++.++..|.|||||||.++|..|..
T Consensus       332 ~LDpAllRpGRfD~~I~i~lPd~~~R~~Il~~~~~~~~~~~d~dl~~lA~~t~G~sGADi~~l~~eA~~  400 (437)
T 4b4t_L          332 TLDPALLRPGRLDRKVEIPLPNEAGRLEIFKIHTAKVKKTGEFDFEAAVKMSDGFNGADIRNCATEAGF  400 (437)
T ss_dssp             SSCTTTTSTTSEEEEECCCCCCHHHHHHHHHHHHHTSCBCSCCCHHHHHHTCCSCCHHHHHHHHHHHHH
T ss_pred             hhCHHHhCCCccceeeecCCcCHHHHHHHHHHHhcCCCCCcccCHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999987666555678999999999999999999986643

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.7e-44  Score=377.44  Aligned_cols=211  Identities=24%  Similarity=0.318  Sum_probs=188.3

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...+.++|+||+|++++|+.|.+.+..|+++|++|..+|.+|++|+|||||||||||++|+|+|++++.+|+.++++++.
T Consensus       164 ~~~p~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g~~~prGiLL~GPPGtGKT~lakAiA~~~~~~~~~v~~~~l~  243 (428)
T 4b4t_K          164 NEKPDVTYADVGGLDMQKQEIREAVELPLVQADLYEQIGIDPPRGVLLYGPPGTGKTMLVKAVANSTKAAFIRVNGSEFV  243 (428)
T ss_dssp             ESSCSCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCCEEEEESCTTTTHHHHHHHHHHHHTCEEEEEEGGGTC
T ss_pred             CCCCCCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCeEEEecchhh
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999988764


Q ss_pred             C------hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 D------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      +      +..++.+|..  ..+||||||||+|+++..+..         .+++++||++|||+.+   ..+++||+|||+
T Consensus       244 ~~~~Ge~e~~ir~lF~~A~~~aP~IifiDEiD~i~~~R~~~~~~~~~~~~r~l~~lL~~ldg~~~---~~~v~vI~aTN~  320 (428)
T 4b4t_K          244 HKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGSDREVQRILIELLTQMDGFDQ---STNVKVIMATNR  320 (428)
T ss_dssp             CSSCSHHHHHHHHHHHHHHHTCSEEEEEECTHHHHCSCSSSCSCCCCHHHHHHHHHHHHHHHSCS---SCSEEEEEEESC
T ss_pred             ccccchhHHHHHHHHHHHHHcCCCeeechhhhhhhccccCCCCCCChHHHHHHHHHHHHhhCCCC---CCCEEEEEecCC
Confidence            3      3458888854  468999999999999876522         2458999999999987   577999999999


Q ss_pred             CccCcccccCCCceeEEEEcC-CCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFP-LCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~-~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |+.|||||+||||||++|+|| +|+.++|..|++.++...+.....+++.|+..|.|||||||.++|+.|..
T Consensus       321 ~~~LD~AllRpGRfd~~I~~p~lPd~~~R~~Il~~~~~~~~l~~~~dl~~lA~~t~G~sgadi~~l~~eA~~  392 (428)
T 4b4t_K          321 ADTLDPALLRPGRLDRKIEFPSLRDRRERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGL  392 (428)
T ss_dssp             SSSCCHHHHSSSSEEEEEECCSSCCHHHHHHHHHHHHHSSCBCTTCCHHHHHHHTTTCCHHHHHHHHHHHHH
T ss_pred             hhhcChhhhcCCcceEEEEcCCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            999999999999999999997 89999999999999987665555678999999999999999999986643

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.9e-44  Score=377.19  Aligned_cols=211  Identities=21%  Similarity=0.230  Sum_probs=189.0

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...|.++|+||+|++++|++|++.+..|+.+|+.|.++|+++++|+|||||||||||++|+|+|++++.+|+.++++++.
T Consensus       201 ~e~P~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~Gi~pprGILLyGPPGTGKTlLAkAiA~e~~~~fi~vs~s~L~  280 (467)
T 4b4t_H          201 EEKPDVTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPKGILLYGPPGTGKTLCARAVANRTDATFIRVIGSELV  280 (467)
T ss_dssp             ESSCSCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCSEEEECSCTTSSHHHHHHHHHHHHTCEEEEEEGGGGC
T ss_pred             cCCCCCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCCCCCCCceEeeCCCCCcHHHHHHHHHhccCCCeEEEEhHHhh
Confidence            34577999999999999999999999999999999999999999999999999999999999999999999999987765


Q ss_pred             C------hHHHHHHHHh--hcCCcEEEEecccccccCcccc---------cchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 D------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA---------VSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~---------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      +      +..++.+|..  ..+||||||||+|+++..+...         .+++++|++|||...   .++++||+|||+
T Consensus       281 sk~vGesek~ir~lF~~Ar~~aP~IIfiDEiDai~~~R~~~~~~~~~~~~~~l~~lL~~lDg~~~---~~~ViVIaATNr  357 (467)
T 4b4t_H          281 QKYVGEGARMVRELFEMARTKKACIIFFDEIDAVGGARFDDGAGGDNEVQRTMLELITQLDGFDP---RGNIKVMFATNR  357 (467)
T ss_dssp             CCSSSHHHHHHHHHHHHHHHTCSEEEEEECCTTTSBCCSSSSCGGGGHHHHHHHHHHHHHHSSCC---TTTEEEEEECSC
T ss_pred             cccCCHHHHHHHHHHHHHHhcCCceEeecccccccccccCcCCCccHHHHHHHHHHHHHhhccCC---CCcEEEEeCCCC
Confidence            3      3458888854  4689999999999999765322         357889999999876   678899999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |+.|||||+||||||++|+|++|+.++|.+||+.++.........+++.|+..+.|||||||.++|..|..
T Consensus       358 pd~LDpALlRpGRFD~~I~i~lPd~~~R~~Ilk~~l~~~~l~~dvdl~~LA~~T~GfSGADI~~l~~eAa~  428 (467)
T 4b4t_H          358 PNTLDPALLRPGRIDRKVEFSLPDLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGM  428 (467)
T ss_dssp             TTSBCHHHHSTTTCCEEECCCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHHCCSCCHHHHHHHHHHHHH
T ss_pred             cccCChhhhccccccEEEEeCCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999987766655678999999999999999999987644

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=3.4e-43  Score=391.44  Aligned_cols=271  Identities=20%  Similarity=0.258  Sum_probs=176.4

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc-
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV-  260 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~-  260 (480)
                      ...+.++|++|+|++++|+.|.+.+..++++++.|.+.|..+++|+|||||||||||++|+|+|++++.+|+.++.+++ 
T Consensus       469 ~~~p~v~w~diggl~~~k~~l~e~v~~p~~~p~~f~~~g~~~~~gvLl~GPPGtGKT~lAkaiA~e~~~~f~~v~~~~l~  548 (806)
T 3cf2_A          469 VEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELL  548 (806)
T ss_dssp             CBCCCCCSTTCCSCHHHHHHHTTTTTTTTTCSGGGSSSCCCCCSCCEEESSTTSSHHHHHHHHHHTTTCEEEECCHHHHH
T ss_pred             ccCCCCCHHHhCCHHHHHHHHHHHHHhhhhCHHHHHhcCCCCCceEEEecCCCCCchHHHHHHHHHhCCceEEeccchhh
Confidence            3456789999999999999999999999999999999999999999999999999999999999999999999986554 


Q ss_pred             ---CC--hHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          261 ---AD--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       261 ---~~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                         .+  +..++.+|..+  .+||||||||||++++.|+.         .+.+++||++|||+.+   ..+++||+|||+
T Consensus       549 s~~vGese~~vr~lF~~Ar~~~P~IifiDEiDsl~~~R~~~~~~~~~~~~rv~~~lL~~mdg~~~---~~~V~vi~aTN~  625 (806)
T 3cf2_A          549 TMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST---KKNVFIIGATNR  625 (806)
T ss_dssp             TTTCSSCHHHHHHHHHHHHTTCSEEEECSCGGGCC--------------CHHHHHHHHHHHSSCS---SSSEEEECC-CC
T ss_pred             ccccchHHHHHHHHHHHHHHcCCceeechhhhHHhhccCCCCCCCchHHHHHHHHHHHHHhCCCC---CCCEEEEEeCCC
Confidence               33  56699999655  58999999999999976532         2458999999999987   567888899999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHH
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSV  404 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~  404 (480)
                      |+.||||++||||||++|+||+|+.++|.+|++.++...+.....+++.|++.++|||||||.++|+.|..   .++++.
T Consensus       626 p~~lD~AllRpgRfd~~i~v~lPd~~~R~~il~~~l~~~~~~~~~dl~~la~~t~g~SGadi~~l~~~A~~---~a~r~~  702 (806)
T 3cf2_A          626 PDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACK---LAIRES  702 (806)
T ss_dssp             SSSSCHHHHSTTTSCCEEEC-----CHHHHTTTTTSSCC--CCC----------------CHHHHHHHHHH---HHHHHH
T ss_pred             chhCCHhHcCCCcceEEEEECCcCHHHHHHHHHHHhcCCCCCCCCCHHHHHHhCCCCCHHHHHHHHHHHHH---HHHHHH
Confidence            99999999999999999999999999999999999987666555678899999999999999999987644   445555


Q ss_pred             HHHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcC-cccccccc
Q 011664          405 ITALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQS-FDLAAAEN  478 (480)
Q Consensus       405 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~-~~~~~~~~  478 (480)
                      ++..........       .   .+   ...+  .......++|+++||++|     +++++|||| .++..||+
T Consensus       703 ~~~~~~~~~~~~-------~---~~---~~~~--~~~~~~~~~i~~~df~~a-----l~~~~pSvs~~~l~~y~~  757 (806)
T 3cf2_A          703 IESEIRRERERQ-------T---NP---SAME--VEEDDPVPEIRRDHFEEA-----MRFARRSVSDNDIRKYEM  757 (806)
T ss_dssp             HC--------------------------------------CCC----CCTTT-----C---------------CC
T ss_pred             HHhhhhhhhhhc-------c---Cc---cccc--cccccccCccCHHHHHHH-----HHhCCCCCCHHHHHHHHH
Confidence            433222111000       0   00   0000  011112377999999999     999999999 45566664

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=100.00  E-value=5.5e-39  Score=357.65  Aligned_cols=208  Identities=20%  Similarity=0.266  Sum_probs=186.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      +.++|+||+|.+++|++|++.+..++++|+.|..+|..+|+|+|||||||||||+||+++|++++.+++.++++++.   
T Consensus       199 ~~v~~~dIgGl~~~~~~l~e~v~~pl~~p~~f~~~g~~~p~GILL~GPPGTGKT~LAraiA~elg~~~~~v~~~~l~sk~  278 (806)
T 3cf2_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (806)
T ss_dssp             SSCCGGGCCSCCTTHHHHHHHHHHHHHCCGGGTSCCCCCCCEEEEECCTTSCHHHHHHHHHTTTTCEEEEEEHHHHHSSC
T ss_pred             CCCChhhhcCHHHHHHHHHHHHHHHccCHHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCeEEEEEhHHhhccc
Confidence            45899999999999999999999999999999999999999999999999999999999999999999999976543   


Q ss_pred             -C--hHHHHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          262 -D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       262 -~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                       +  +..++.+|..+  .+||||||||||.+++.++..      ..+++|+..|||+.+   ..+++||+|||+|+.||+
T Consensus       279 ~gese~~lr~lF~~A~~~~PsIIfIDEiDal~~~r~~~~~~~~~riv~~LL~~mdg~~~---~~~V~VIaaTN~~d~LD~  355 (806)
T 3cf2_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQ---RAHVIVMAATNRPNSIDP  355 (806)
T ss_dssp             TTHHHHHHHHHHHHHTTSCSEEEEEESGGGTCCTTTTCCCTTHHHHHHHHHTHHHHCCG---GGCEEEEEECSSTTTSCT
T ss_pred             chHHHHHHHHHHHHHHHcCCeEEEEehhcccccccCCCCChHHHHHHHHHHHHHhcccc---cCCEEEEEecCChhhcCH
Confidence             3  34588888655  589999999999999865432      457899999999977   467889999999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      ||+||||||++|+++.|+.++|.+|++.++.........++..++..|.||+++||..+|..+..
T Consensus       356 ALrR~GRFd~~I~i~~Pd~~~R~~IL~~~l~~~~~~~dvdl~~lA~~T~GfsgaDL~~Lv~eA~~  420 (806)
T 3cf2_A          356 ALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL  420 (806)
T ss_dssp             TTTSTTSSCEEEECCCCCHHHHHHHHHHTCSSSEECTTCCHHHHHHHCCSCCHHHHHHHHHHHHH
T ss_pred             HHhCCcccceEEecCCCCHHHHHHHHHHHhcCCCCCcccCHHHHHHhcCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999987666666688999999999999999999987644

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=100.00  E-value=1.6e-36  Score=307.29  Aligned_cols=280  Identities=20%  Similarity=0.236  Sum_probs=211.3

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-CCcEEEEeCCCcCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-SYDVYDVDLSRVAD  262 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i~~s~~~~  262 (480)
                      .++++|++|+|++++|+.|.+.+..+++.++.|.. +..+++|+|||||||||||++|+++|+++ +.+++.++++++.+
T Consensus         6 ~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~~i~~~~l~~   84 (322)
T 1xwi_A            6 RPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLVS   84 (322)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCGGGSCT-TCCCCSEEEEESSSSSCHHHHHHHHHHHTTSCEEEEEECCSSCC
T ss_pred             CCCCCHHHhcCHHHHHHHHHHHHHHHHhCHHHHhC-CCCCCceEEEECCCCccHHHHHHHHHHHcCCCcEEEEEhHHHHh
Confidence            35789999999999999999999999999999875 35567899999999999999999999999 89999999887643


Q ss_pred             ------hHHHHHHHHh--hcCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          263 ------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       263 ------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                            +..++.+|..  ..+|+||||||||.+++.+...      ..+++|+..||++...  ..+++||+|||+|+.+
T Consensus        85 ~~~g~~~~~~~~lf~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~ld~~~~~--~~~v~vI~atn~~~~l  162 (322)
T 1xwi_A           85 KWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVD--NDGILVLGATNIPWVL  162 (322)
T ss_dssp             SSCCSCHHHHHHHHHHHHHTSSEEEEEETTTGGGCCSSSCCTTHHHHHHHHHHHHHHCSSSC--CTTEEEEEEESCTTTS
T ss_pred             hhhhHHHHHHHHHHHHHHhcCCcEEEeecHHHhccccccccchHHHHHHHHHHHHHhccccc--CCCEEEEEecCCcccC
Confidence                  4457777754  3579999999999998765432      3467899999998642  4678889999999999


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc-hhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHH
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF-PQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITA  407 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~-~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~  407 (480)
                      |++++|  ||+..+++++|+.++|.+|++.++...+..+. .+++.|+..+.|||++||..+|..+...+.+   +....
T Consensus       163 d~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~A~~~a~r---~~~~~  237 (322)
T 1xwi_A          163 DSAIRR--RFEKRIYIPLPEPHARAAMFKLHLGTTQNSLTEADFRELGRKTDGYSGADISIIVRDALMQPVR---KVQSA  237 (322)
T ss_dssp             CHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTCCBCCCHHHHHHHHHTCTTCCHHHHHHHHHHHHTHHHH---HHHHC
T ss_pred             CHHHHh--hcCeEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH---HHHhh
Confidence            999999  99999999999999999999999987665543 4678999999999999999999887665543   33221


Q ss_pred             HHh---cCCCC-c-ccccccccccCCCCCCCCC-----CCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc-ccccc
Q 011664          408 LQT---DGEGR-G-AANAGRRLDKSGSKKSTDA-----DSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF-DLAAA  476 (480)
Q Consensus       408 ~~~---~~~~~-~-~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~-~~~~~  476 (480)
                      ...   .+... . .......+..|...+.+..     +. +.+.+..++|+++||++|     ++.++||+|. |+..|
T Consensus       238 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~v~~~df~~a-----l~~~~ps~~~~~~~~~  311 (322)
T 1xwi_A          238 THFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEMTWMDV-PGDKLLEPVVSMSDMLRS-----LSNTKPTVNEHDLLKL  311 (322)
T ss_dssp             SEEEEEEEECSSCTTSEEEEEEEECCSSSTTEEECCGGGS-CGGGBCCCCBCHHHHHHH-----HHTCCCSCCHHHHHHH
T ss_pred             hhhhhhccccccccccccccccccccccccchhhcccccc-ccccccCCCcCHHHHHHH-----HHhCCCCCCHHHHHHH
Confidence            000   00000 0 0001112233333322211     11 122344578999999999     9999999995 44555


Q ss_pred             c
Q 011664          477 E  477 (480)
Q Consensus       477 ~  477 (480)
                      +
T Consensus       312 ~  312 (322)
T 1xwi_A          312 K  312 (322)
T ss_dssp             H
T ss_pred             H
Confidence            4

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=100.00  E-value=1.1e-35  Score=294.57  Aligned_cols=248  Identities=19%  Similarity=0.270  Sum_probs=189.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--  262 (480)
                      +.++|++|+|.+++|+.|.+.+..++.+++.|+.++...++|++|+||||||||+|++++|++++.+++.++..++.+  
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLakala~~~~~~~i~i~g~~l~~~~   84 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAILAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLAKAVANESGLNFISVKGPELLNMY   84 (274)
T ss_dssp             -------CCHHHHHHHHHHHHHTHHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEEETTTTCSST
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHHHHHHHHcCCCEEEEEcHHHHhhh
Confidence            568999999999999999999999999999999999999999999999999999999999999999999999877643  


Q ss_pred             ----hHHHHHHHHhh--cCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          263 ----DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       263 ----~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                          ...+..+|...  ..|+++|+||+|.++..+..      ...+++++..|+|...   ....+++++||+|+.||+
T Consensus        85 ~~~~~~~i~~vf~~a~~~~p~i~~~Deid~~~~~r~~~~~~~~~~~~~~~l~~Lsgg~~---~~~~i~ia~tn~p~~LD~  161 (274)
T 2x8a_A           85 VGESERAVRQVFQRAKNSAPCVIFFDEVDALCPRRSDRETGASVRVVNQLLTEMDGLEA---RQQVFIMAATNRPDIIDP  161 (274)
T ss_dssp             THHHHHHHHHHHHHHHHTCSEEEEEETCTTTCC---------CTTHHHHHHHHHHTCCS---TTCEEEEEEESCGGGSCH
T ss_pred             hhHHHHHHHHHHHHHHhcCCCeEeeehhhhhhcccCCCcchHHHHHHHHHHHhhhcccc---cCCEEEEeecCChhhCCH
Confidence                23466777653  57999999999998754321      2346788999998866   466788889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCC---CCCchhHHHHHHhC--CCCCHHHHHHHHHHhhhcHHHHHHHHH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKD---HKLFPQVEEIFQNG--SSLSPAEIGELMIANRNSPSRALKSVI  405 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~---~~l~~~i~~l~~~~--~g~s~adI~~ll~~a~~~~~~al~~~i  405 (480)
                      |++||||||++|++++|+.++|.+|++.++....   .....+++.++..+  +|||||||..+|+.+..   .++++.+
T Consensus       162 al~r~gRfd~~i~~~~P~~~~r~~il~~~~~~~~~~~~~~~~~~~~la~~~~~~g~sgadl~~l~~~a~~---~a~~~~~  238 (274)
T 2x8a_A          162 AILRPGRLDKTLFVGLPPPADRLAILKTITKNGTKPPLDADVNLEAIAGDLRCDCYTGADLSALVREASI---CALRQEM  238 (274)
T ss_dssp             HHHSTTSSCEEEECCSCCHHHHHHHHHHHTTTTBTTBBCTTCCHHHHHTCSGGGSCCHHHHHHHHHHHHH---HHHHHHC
T ss_pred             hhcCcccCCeEEEeCCcCHHHHHHHHHHHHhcccCCCCccccCHHHHHHhhccCCcCHHHHHHHHHHHHH---HHHHHHH
Confidence            9999999999999999999999999999986421   22344678898865  49999999999987644   3333322


Q ss_pred             HHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcc
Q 011664          406 TALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD  472 (480)
Q Consensus       406 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~  472 (480)
                      .....                       . .  ..   ....|+++||++|     ++.++||++..
T Consensus       239 ~~~~~-----------------------~-~--~~---~~~~i~~~df~~a-----l~~~~ps~~~~  271 (274)
T 2x8a_A          239 ARQKS-----------------------G-N--EK---GELKVSHKHFEEA-----FKKVRSSISKK  271 (274)
T ss_dssp             ----------------------------------------CCBCHHHHHHH-----HTTCCCCC---
T ss_pred             hhccc-----------------------c-c--cc---cCCeecHHHHHHH-----HHHhcCCCChh
Confidence            11000                       0 0  00   1146999999999     89999998854

>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=100.00  E-value=2e-35  Score=296.11  Aligned_cols=268  Identities=19%  Similarity=0.269  Sum_probs=207.0

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC--
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA--  261 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~--  261 (480)
                      .++.+|++|+|.+++|+.|.+.+..++..++.|...|..+++++|||||||||||++|+++|++++.+++.++++.+.  
T Consensus         9 ~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la~ala~~~~~~~i~v~~~~l~~~   88 (301)
T 3cf0_A            9 VPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTM   88 (301)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHHHHHHHHTTCEEEEECHHHHHHH
T ss_pred             CCCCCHHHhCCHHHHHHHHHHHHHHHhhCHHHHHHcCCCCCceEEEECCCCcCHHHHHHHHHHHhCCCEEEEEhHHHHhh
Confidence            467899999999999999999999999999999999999999999999999999999999999999999999976653  


Q ss_pred             ----ChHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          262 ----DDADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       262 ----~~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                          .+..++.+|..+  ..|+||||||+|.+...++.         ...+++||..||++..   ..+++||+|||+++
T Consensus        89 ~~g~~~~~~~~~f~~a~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~~~~~lL~~l~~~~~---~~~v~vi~atn~~~  165 (301)
T 3cf0_A           89 WFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST---KKNVFIIGATNRPD  165 (301)
T ss_dssp             HHTTCTTHHHHHHHHHHHTCSEEEEECSTTHHHHHHTTTTCCSSCSCCHHHHHHHHHHHSSCT---TSSEEEEEEESCGG
T ss_pred             hcCchHHHHHHHHHHHHhcCCeEEEEEChHHHhhccCCCcCCcchHHHHHHHHHHHHhhcccC---CCCEEEEEecCCcc
Confidence                234467777654  57899999999998764321         2346889999998865   46788999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHH
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT  406 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~  406 (480)
                      .||++++|||||+..|++++|+.++|.+|++.++...+.....+++.++..+.||+++||.++|..+...   ++++.+.
T Consensus       166 ~ld~al~r~gRf~~~i~i~~p~~~~r~~il~~~l~~~~~~~~~~~~~la~~~~g~sg~dl~~l~~~a~~~---a~~~~~~  242 (301)
T 3cf0_A          166 IIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKL---AIRESIE  242 (301)
T ss_dssp             GSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCSSCCHHHHHHTCSSCCHHHHHHHHHHHHHH---HHHHHHH
T ss_pred             ccChHHhcCCccceEEecCCcCHHHHHHHHHHHHccCCCCccchHHHHHHHcCCCCHHHHHHHHHHHHHH---HHHHHHH
Confidence            9999999999999999999999999999999999876554455678899999999999999999876443   3333332


Q ss_pred             HHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcc-ccccc
Q 011664          407 ALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD-LAAAE  477 (480)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~-~~~~~  477 (480)
                      ..........         ...    ...+.  ......++|+++||++|     ++.++||++.+ ...||
T Consensus       243 ~~~~~~~~~~---------~~~----~~~~~--~~~~~~~~v~~~~~~~a-----l~~~~~s~~~~~~~~~~  294 (301)
T 3cf0_A          243 SEIRRERERQ---------TNP----SAMEV--EEDDPVPEIRRDHFEEA-----MRFARRSVSDNDIRKYE  294 (301)
T ss_dssp             HHC-----------------------------------CCCBCHHHHHHH-----HTTCCCSSCHHHHHHHH
T ss_pred             hhhhhhhhcc---------ccc----ccccc--cccccCCccCHHHHHHH-----HHHcCCCCCHHHHHHHH
Confidence            2111000000         000    00000  00011257999999999     99999999953 34443

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=100.00  E-value=8.6e-36  Score=301.36  Aligned_cols=281  Identities=22%  Similarity=0.259  Sum_probs=212.2

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...++++|++|+|.+++|+.|.+.+..++..++.|.. +..+++|+|||||||||||++|+++|++++.+++.++++.+.
T Consensus        10 ~~~~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~-~~~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~v~~~~l~   88 (322)
T 3eie_A           10 SEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLV   88 (322)
T ss_dssp             EECCCCCGGGSCSCHHHHHHHHHHTHHHHHCGGGCCT-TCCCCCEEEEECSSSSCHHHHHHHHHHHHTCEEEEEEHHHHH
T ss_pred             ecCCCCCHHHhcChHHHHHHHHHHHHHHHhCHHHHhc-CCCCCCeEEEECCCCCcHHHHHHHHHHHHCCCEEEEchHHHh
Confidence            3457789999999999999999999999999999887 445678999999999999999999999999999999986543


Q ss_pred             ----C--hHHHHHHHHh--hcCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          262 ----D--DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       262 ----~--~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                          +  +..++.+|..  ...|+||||||||.+...+..      ....++++..|+++...  ..+++||+|||.|+.
T Consensus        89 ~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~--~~~v~vi~atn~~~~  166 (322)
T 3eie_A           89 SKWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGND--SQGVLVLGATNIPWQ  166 (322)
T ss_dssp             TTTGGGHHHHHHHHHHHHHHTSSEEEEEECGGGGSCC------CCTHHHHHHHHHHHGGGGTS--CCCEEEEEEESCGGG
T ss_pred             hcccchHHHHHHHHHHHHHhcCCeEEEechhhhhhccCCCCcchHHHHHHHHHHHHhcccccc--CCceEEEEecCChhh
Confidence                2  2346666644  457899999999999875532      23468899999998642  457888899999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc-hhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHH
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF-PQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT  406 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~-~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~  406 (480)
                      ||++++|  ||+..+++++|+.++|.+|++.++......+. .+++.|+..+.||+++||..+|..+...+.+.+...+ 
T Consensus       167 ld~al~~--Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~l~~la~~t~g~sg~di~~l~~~a~~~a~r~~~~~~-  243 (322)
T 3eie_A          167 LDSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPCVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQPIRKIQSAT-  243 (322)
T ss_dssp             SCHHHHH--HCCEEEECCCCCHHHHHHHHHHHHTTCCCCCCHHHHHHHHHTTTTCCHHHHHHHHHHHTTHHHHHHHHCE-
T ss_pred             CCHHHHc--ccCeEEEeCCCCHHHHHHHHHHHhccCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhh-
Confidence            9999999  99999999999999999999999987665544 4678999999999999999999887765554433221 


Q ss_pred             HHHhcCCCCcccccccccccCCCCCCCC-----CCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc-cccccc
Q 011664          407 ALQTDGEGRGAANAGRRLDKSGSKKSTD-----ADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF-DLAAAE  477 (480)
Q Consensus       407 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~-~~~~~~  477 (480)
                        ... .........+.+..|.+...+.     .+. ..+.+..++|+++||++|     ++.++||++. +...|+
T Consensus       244 --~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~it~~df~~a-----l~~~~ps~~~~~~~~~~  311 (322)
T 3eie_A          244 --HFK-DVSTEDDETRKLTPCSPGDDGAIEMSWTDI-EADELKEPDLTIKDFLKA-----IKSTRPTVNEDDLLKQE  311 (322)
T ss_dssp             --EEE-ECC----CCCCEEECCSSCTTEEEEEGGGS-CSSCBCCCCCCHHHHHHH-----HHHSCCSSCTTHHHHHH
T ss_pred             --hhh-hhcccccccccccccccccccccccccccc-ccccccCCCCCHHHHHHH-----HHhcCCCCCHHHHHHHH
Confidence              111 0111111223344444433221     111 223344588999999999     8999999985 444444

>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=100.00  E-value=1e-34  Score=306.42  Aligned_cols=281  Identities=20%  Similarity=0.228  Sum_probs=209.3

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-CCcEEEEeCCCcC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-SYDVYDVDLSRVA  261 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i~~s~~~  261 (480)
                      ..++++|++|+|++++|+.|.+.+..++..++.|.. +..+++|+|||||||||||++|+++|+++ +.+++.++++.+.
T Consensus       127 ~~~~~~~~di~G~~~~k~~l~~~v~~p~~~~~~~~~-~~~~~~~vLL~GppGtGKT~lA~aia~~~~~~~~~~v~~~~l~  205 (444)
T 2zan_A          127 ERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTG-KRTPWRGILLFGPPGTGKSYLAKAVATEANNSTFFSISSSDLV  205 (444)
T ss_dssp             CCCCCCGGGSCSCHHHHHHHHHHHTHHHHCTTTTSG-GGCCCSEEEEECSTTSSHHHHHHHHHHHCCSSEEEEECCC---
T ss_pred             cCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHhhc-cCCCCceEEEECCCCCCHHHHHHHHHHHcCCCCEEEEeHHHHH
Confidence            456789999999999999999999999999998875 34567899999999999999999999999 8999999988764


Q ss_pred             C------hHHHHHHHHh--hcCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          262 D------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       262 ~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      +      +..++.+|..  ...|+||||||||.+++.+..      ...+++||..|+++...  ..+++||+|||.|+.
T Consensus       206 ~~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~~--~~~v~vI~atn~~~~  283 (444)
T 2zan_A          206 SKWLGESEKLVKNLFQLARENKPSIIFIDEIDSLCGSRSENESEAARRIKTEFLVQMQGVGVD--NDGILVLGATNIPWV  283 (444)
T ss_dssp             ------CCCTHHHHHHHHHHSCSEEEEESCTTTTCCCSSCCCCGGGHHHHHHHHTTTTCSSCC--CSSCEEEEEESCGGG
T ss_pred             hhhcchHHHHHHHHHHHHHHcCCeEEEEechHhhccCCCCccccHHHHHHHHHHHHHhCcccC--CCCEEEEecCCCccc
Confidence            3      2346677754  357999999999999765432      23467899999987542  467889999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCC-chhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHH
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL-FPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT  406 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l-~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~  406 (480)
                      ||++++|  ||+..+++++|+.++|..|++.++...+..+ ..+++.|+..+.|||++||..+|..+...+.+   +++.
T Consensus       284 ld~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~l~~~~l~~la~~t~G~sgadl~~l~~~a~~~a~r---~~~~  358 (444)
T 2zan_A          284 LDSAIRR--RFEKRIYIPLPEAHARAAMFRLHLGSTQNSLTEADFQELGRKTDGYSGADISIIVRDALMQPVR---KVQS  358 (444)
T ss_dssp             SCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCEECCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHH---HHHH
T ss_pred             cCHHHHh--hcceEEEeCCcCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH---HHHh
Confidence            9999999  9999999999999999999999997665543 34678999999999999999999877665544   3332


Q ss_pred             HHH---hcCCCCc--ccccccccccCCCCCCCC-----CCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc-cccc
Q 011664          407 ALQ---TDGEGRG--AANAGRRLDKSGSKKSTD-----ADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF-DLAA  475 (480)
Q Consensus       407 ~~~---~~~~~~~--~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~-~~~~  475 (480)
                      ...   ..+....  .......+.+|.++..++     .+. +.+.+..++|+++||.+|     +++++||||. |+..
T Consensus       359 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~v~~~df~~a-----~~~~~ps~~~~~~~~  432 (444)
T 2zan_A          359 ATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMTWMDV-PGDKLLEPVVSMWDMLRS-----LSSTKPTVNEQDLLK  432 (444)
T ss_dssp             CSEEEEECCBCSSCTTSBCSCEEEEECTTSTTEEECCTTTS-CTTCBCCCCEEHHHHHHH-----HHTCCCSCCHHHHHH
T ss_pred             hhhhhhhccccccccccccccccccCCCCcccchhcccccC-chhhccCCccCHHHHHHH-----HHhCCCCCCHHHHHH
Confidence            100   0000000  001112233444333221     111 233455678999999999     9999999995 3444


Q ss_pred             cc
Q 011664          476 AE  477 (480)
Q Consensus       476 ~~  477 (480)
                      |+
T Consensus       433 ~~  434 (444)
T 2zan_A          433 LK  434 (444)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=100.00  E-value=2.3e-34  Score=295.22  Aligned_cols=280  Identities=22%  Similarity=0.265  Sum_probs=203.8

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-  261 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-  261 (480)
                      ..++.+|++|+|++++|+.|.+.+..++..++.|.. +..+++|+|||||||||||++|+++|++++.+++.++++.+. 
T Consensus        44 ~~~~~~~~di~G~~~~~~~l~~~v~~~~~~~~~~~~-~~~~~~~iLL~GppGtGKT~la~ala~~~~~~~~~v~~~~l~~  122 (355)
T 2qp9_X           44 EKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKG-NRKPTSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS  122 (355)
T ss_dssp             ---CCCGGGSCCGGGHHHHHHHHTHHHHHCGGGGCS-SCCCCCCEEEECSTTSCHHHHHHHHHHHHTCEEEEEEHHHHHS
T ss_pred             cCCCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHhc-CCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEeeHHHHhh
Confidence            346789999999999999999999999999999987 556778999999999999999999999999999999976543 


Q ss_pred             ---C--hHHHHHHHHhh--cCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          262 ---D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       262 ---~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                         +  +..++.+|..+  ..|+||||||||.+.+.+..      ....++|+..|+++...  ..+++||+|||.++.|
T Consensus       123 ~~~g~~~~~~~~~f~~a~~~~~~vl~iDEid~l~~~r~~~~~~~~~~~~~~ll~~l~~~~~~--~~~v~vI~atn~~~~l  200 (355)
T 2qp9_X          123 KWMGESEKLVKQLFAMARENKPSIIFIDQVDALTGTRGEGESEASRRIKTELLVQMNGVGND--SQGVLVLGATNIPWQL  200 (355)
T ss_dssp             CC---CHHHHHHHHHHHHHTSSEEEEEECGGGGTC------CTHHHHHHHHHHHHHHHCC-----CCEEEEEEESCGGGS
T ss_pred             hhcchHHHHHHHHHHHHHHcCCeEEEEechHhhcccCCCCcchHHHHHHHHHHHHhhccccc--CCCeEEEeecCCcccC
Confidence               2  34466777544  48999999999999865432      23468899999987642  4568888999999999


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc-hhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHH
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF-PQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITA  407 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~-~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~  407 (480)
                      |++++|  ||+..+++++|+.++|..|++.++...+..+. .+++.|+..+.||+++||..+|..+...+   +++....
T Consensus       201 d~al~r--Rf~~~i~i~~P~~~~r~~il~~~l~~~~~~~~~~~l~~la~~t~G~sg~dl~~l~~~A~~~a---~~~~~~~  275 (355)
T 2qp9_X          201 DSAIRR--RFERRIYIPLPDLAARTTMFEINVGDTPSVLTKEDYRTLGAMTEGYSGSDIAVVVKDALMQP---IRKIQSA  275 (355)
T ss_dssp             CHHHHH--TCCEEEECCCCCHHHHHHHHHHHHTTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHHHH---HHHHHHC
T ss_pred             CHHHHc--ccCEEEEeCCcCHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH---HHHHHHh
Confidence            999999  99999999999999999999999987665443 46789999999999999999998765544   3333221


Q ss_pred             HHhcCCCCcccccccccccCCCCCCCC-----CCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc-cccccc
Q 011664          408 LQTDGEGRGAANAGRRLDKSGSKKSTD-----ADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF-DLAAAE  477 (480)
Q Consensus       408 ~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~-~~~~~~  477 (480)
                      .... ...+.........+|.+...+.     .+. ..+.+..++|+++||.+|     ++.++||++. ++..|+
T Consensus       276 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~v~~~df~~A-----l~~~~ps~~~~~~~~~~  344 (355)
T 2qp9_X          276 THFK-DVSTEDDETRKLTPSSPGDDGAIEMSWTDI-EADELKEPDLTIKDFLKA-----IKSTRPTVNEDDLLKQE  344 (355)
T ss_dssp             SEEE-ECCC-----CCEEEECTTSSSEEECCGGGS-CGGGBCCCCBCHHHHHHH-----HHHSCCSSCHHHHHHHH
T ss_pred             hhhh-hhccccccccccCcCCccccchhhcccccc-cccccccCCccHHHHHHH-----HHHcCCCCCHHHHHHHH
Confidence            0000 0000000011222333222211     111 122334578999999999     9999999995 444444

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=99.98  E-value=2.2e-31  Score=262.82  Aligned_cols=211  Identities=22%  Similarity=0.251  Sum_probs=180.3

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      ...++.+|++|+|.+++++.|.+.+..++..++.|...|...++++||+||||||||++|+++|++++.+++.++++.+.
T Consensus         9 ~~~~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~   88 (285)
T 3h4m_A            9 DERPNVRYEDIGGLEKQMQEIREVVELPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLAKAVATETNATFIRVVGSELV   88 (285)
T ss_dssp             ESSCCCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHHHHHHHHTTCEEEEEEGGGGC
T ss_pred             cCCCCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEehHHHH
Confidence            34567899999999999999999999999999999999999999999999999999999999999999999999987764


Q ss_pred             C------hHHHHHHHHh--hcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          262 D------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       262 ~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      +      ...+..+|..  ...|+||||||+|.+.+.+..         ...+..+++.+++...   ..+.+||+|||.
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~---~~~~~vI~ttn~  165 (285)
T 3h4m_A           89 KKFIGEGASLVKDIFKLAKEKAPSIIFIDEIDAIAAKRTDALTGGDREVQRTLMQLLAEMDGFDA---RGDVKIIGATNR  165 (285)
T ss_dssp             CCSTTHHHHHHHHHHHHHHHTCSEEEEEETTHHHHBCCSSSCCGGGGHHHHHHHHHHHHHHTTCS---SSSEEEEEECSC
T ss_pred             HhccchHHHHHHHHHHHHHHcCCeEEEEECHHHhcccCccccCCccHHHHHHHHHHHHHhhCCCC---CCCEEEEEeCCC
Confidence            3      2335555643  357899999999999764432         2446677788877655   467889999999


Q ss_pred             CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          325 KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       325 ~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      ++.+|++++|||||+..++++.|+.++|.+|++.++.........++..++..+.|++++||..+|..+..
T Consensus       166 ~~~l~~~l~~~~Rf~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~l~~~~~g~~~~~i~~l~~~a~~  236 (285)
T 3h4m_A          166 PDILDPAILRPGRFDRIIEVPAPDEKGRLEILKIHTRKMNLAEDVNLEEIAKMTEGCVGAELKAICTEAGM  236 (285)
T ss_dssp             GGGBCHHHHSTTSEEEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHHH
T ss_pred             chhcCHHHcCCCcCCeEEEECCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999877665555678999999999999999999876543

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=99.97  E-value=7e-31  Score=256.09  Aligned_cols=207  Identities=23%  Similarity=0.331  Sum_probs=170.4

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      .++.+|++|+|.+++|+.+.+.+. ++..++.|..+|...++|+||+||||||||++|+++|++++.+++.++++.+.. 
T Consensus         6 ~~~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~i~~~~~~~~   84 (257)
T 1lv7_A            6 QIKTTFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM   84 (257)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHHH-HHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTS
T ss_pred             CCCCCHHHhcCcHHHHHHHHHHHH-HHhCHHHHHHcCCCCCCeEEEECcCCCCHHHHHHHHHHHcCCCEEEEeHHHHHHH
Confidence            467899999999999999998664 578888889999989999999999999999999999999999999999887643 


Q ss_pred             -----hHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          263 -----DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 -----~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                           ...++.+|..+  ..|+++||||+|.+...+..         ...+.+++..++++..   ..+++||+|||.++
T Consensus        85 ~~~~~~~~~~~~~~~a~~~~~~il~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~---~~~~~vI~~tn~~~  161 (257)
T 1lv7_A           85 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG---NEGIIVIAATNRPD  161 (257)
T ss_dssp             CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCS---SSCEEEEEEESCTT
T ss_pred             hhhhhHHHHHHHHHHHHHcCCeeehhhhhhhhccCCCCCcCCCchHHHHHHHHHHHHhhCccc---CCCEEEEEeeCCch
Confidence                 34567777654  46899999999998765432         1356778999998765   56788999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      .+|++++|||||+..+++++|+.++|.+|++.++...+.....++..++..+.||+++||..+|..+.
T Consensus       162 ~l~~~l~r~~rf~~~i~i~~P~~~~r~~il~~~~~~~~l~~~~~~~~la~~~~G~~~~dl~~l~~~a~  229 (257)
T 1lv7_A          162 VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAA  229 (257)
T ss_dssp             TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             hCCHHHcCCCcCCeEEEeCCCCHHHHHHHHHHHHhcCCCCccccHHHHHHHcCCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999999999987654433445678888999999999999987653

>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=99.97  E-value=8.4e-31  Score=277.80  Aligned_cols=206  Identities=25%  Similarity=0.335  Sum_probs=177.0

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--  262 (480)
                      +..+|++|+|.+++|+++.+.+. ++..+..|..+|...++|+||+||||||||++|+++|++++.+|+.++++++..  
T Consensus        11 ~~~~f~di~G~~~~~~~l~e~v~-~l~~~~~~~~~g~~~p~gvLL~GppGtGKT~Laraia~~~~~~f~~is~~~~~~~~   89 (476)
T 2ce7_A           11 KRVTFKDVGGAEEAIEELKEVVE-FLKDPSKFNRIGARMPKGILLVGPPGTGKTLLARAVAGEANVPFFHISGSDFVELF   89 (476)
T ss_dssp             CCCCGGGCCSCHHHHHHHHHHHH-HHHCTHHHHTTTCCCCSEEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGTTTCC
T ss_pred             CCCCHHHhCCcHHHHHHHHHHHH-HhhChHHHhhcCCCCCCeEEEECCCCCCHHHHHHHHHHHcCCCeeeCCHHHHHHHH
Confidence            56799999999999999998765 578889999999999999999999999999999999999999999999887642  


Q ss_pred             ----hHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          263 ----DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       263 ----~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                          ...++.+|..+  .+||||||||+|.+...++.         ..++++|++.||++..   ..+++||+|||+++.
T Consensus        90 ~g~~~~~~r~lf~~A~~~~p~ILfIDEid~l~~~r~~~~~g~~~~~~~~l~~LL~~ld~~~~---~~~viVIaaTn~~~~  166 (476)
T 2ce7_A           90 VGVGAARVRDLFAQAKAHAPCIVFIDEIDAVGRHRGAGLGGGHDEREQTLNQLLVEMDGFDS---KEGIIVMAATNRPDI  166 (476)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEETGGGTCCC---------CHHHHHHHHHHHHHHHSCG---GGTEEEEEEESCGGG
T ss_pred             hcccHHHHHHHHHHHHhcCCCEEEEechhhhhhhcccccCcCcHHHHHHHHHHHHHHhccCC---CCCEEEEEecCChhh
Confidence                34577777654  57999999999999875532         2457889999998865   467899999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      ||++++||||||..|.+++|+.++|.+|++.++...+..-..++..++..+.|++++||.++|..+.
T Consensus       167 Ld~allR~gRFd~~i~i~~Pd~~~R~~Il~~~~~~~~l~~~v~l~~la~~t~G~sgadL~~lv~~Aa  233 (476)
T 2ce7_A          167 LDPALLRPGRFDKKIVVDPPDMLGRKKILEIHTRNKPLAEDVNLEIIAKRTPGFVGADLENLVNEAA  233 (476)
T ss_dssp             SCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHH
T ss_pred             hchhhcccCcceeEeecCCCCHHHHHHHHHHHHHhCCCcchhhHHHHHHhcCCCcHHHHHHHHHHHH
Confidence            9999999999999999999999999999999987655443446788999999999999999997654

>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=99.97  E-value=1.4e-31  Score=285.25  Aligned_cols=208  Identities=20%  Similarity=0.266  Sum_probs=181.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      .+.+|++|+|.+.+++.|.+.+..++.+++.|..+|.++++++|||||||||||++|+++|++++.+|+.++++.+.   
T Consensus       199 ~~~~~~~i~G~~~~~~~l~~~i~~~l~~~~~~~~~g~~~~~~vLL~GppGtGKT~lAraia~~~~~~fv~vn~~~l~~~~  278 (489)
T 3hu3_A          199 NEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKL  278 (489)
T ss_dssp             TCCCGGGCCSCHHHHHHHHHHTHHHHHCHHHHHHHTCCCCCEEEEECSTTSSHHHHHHHHHHHCSSEEEEEEHHHHHTSC
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHHHhhCHHHHHhcCCCCCCcEEEECcCCCCHHHHHHHHHHHhCCCEEEEEchHhhhhh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999976543   


Q ss_pred             -C--hHHHHHHHHhh--cCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          262 -D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       262 -~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                       +  ...++.+|..+  ..|+||||||||.+.+.+...      ..++.|+..|++...   ...++||+|||+++.||+
T Consensus       279 ~g~~~~~~~~~f~~A~~~~p~iLfLDEId~l~~~~~~~~~~~~~~~~~~LL~~ld~~~~---~~~v~vIaaTn~~~~Ld~  355 (489)
T 3hu3_A          279 AGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQ---RAHVIVMAATNRPNSIDP  355 (489)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEESHHHHCBCTTSCCCHHHHHHHHHHHHHHHHSCT---TSCEEEEEEESCGGGBCG
T ss_pred             cchhHHHHHHHHHHHHhcCCcEEEecchhhhccccccccchHHHHHHHHHHHHhhcccc---CCceEEEEecCCccccCH
Confidence             3  23466777544  578999999999998755422      456789999998765   567889999999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      +++|+|||+..|++++|+.++|.+|++.++.........++..++..+.||+++||..+|..+..
T Consensus       356 al~r~gRf~~~i~i~~P~~~eR~~IL~~~~~~~~l~~~~~l~~la~~t~g~s~~dL~~L~~~A~~  420 (489)
T 3hu3_A          356 ALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAAL  420 (489)
T ss_dssp             GGGSTTSSCEEEECCCCCHHHHHHHHHHHTTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHHHH
T ss_pred             HHhCCCcCceEEEeCCCCHHHHHHHHHHHHhcCCCcchhhHHHHHHHccCCcHHHHHHHHHHHHH
Confidence            99999999999999999999999999999877665555678999999999999999999976543

>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=99.97  E-value=2.7e-30  Score=251.20  Aligned_cols=209  Identities=21%  Similarity=0.318  Sum_probs=164.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--  262 (480)
                      ++++|++|+|.+++|+.+.+.+. ++..++.|...|...++++|||||||||||++|+++|++++.+++.++++.+.+  
T Consensus         1 ~~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~g~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~~   79 (262)
T 2qz4_A            1 MGVSFKDVAGMHEAKLEVREFVD-YLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGAEFVEVI   79 (262)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHH-HHHCCC------CCCCCEEEEESCTTSSHHHHHHHHHHHHTCCEEEEETTTTSSSS
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH-HHHCHHHHHHcCCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEechHHHHhhc
Confidence            35789999999999999988665 578889999999999999999999999999999999999999999999887643  


Q ss_pred             ----hHHHHHHHHhh--cCCcEEEEecccccccCcc----------cccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          263 ----DADLKSLLLQT--TSKSVILIEDLDRFLVEKP----------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 ----~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~----------~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                          ...++.+|..+  ..|+||||||+|.+...+.          ....+..+++.+++...   ...+++|+|||.++
T Consensus        80 ~~~~~~~~~~~~~~a~~~~~~vl~iDeid~l~~~~~~~~~~~~~~~~~~~l~~ll~~~~~~~~---~~~~~vi~~tn~~~  156 (262)
T 2qz4_A           80 GGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEQTLNQLLVEMDGMGT---TDHVIVLASTNRAD  156 (262)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEECC-------------------CHHHHHHHHHHHTCCT---TCCEEEEEEESCGG
T ss_pred             cChhHHHHHHHHHHHHhcCCeEEEEeCcchhhccccccccCccchhHHHHHHHHHHHhhCcCC---CCCEEEEecCCChh
Confidence                23456666544  4689999999999976442          22456788888888755   46788999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH--HHHHHhCCCCCHHHHHHHHHHhhhcH
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV--EEIFQNGSSLSPAEIGELMIANRNSP  397 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i--~~l~~~~~g~s~adI~~ll~~a~~~~  397 (480)
                      .+|++++|||||+..+++++|+.++|.+|++.++...+.....++  ..++..+.|++++||.++|..+...+
T Consensus       157 ~ld~~l~~~~R~~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~l~~l~~~a~~~a  229 (262)
T 2qz4_A          157 ILDGALMRPGRLDRHVFIDLPTLQERREIFEQHLKSLKLTQSSTFYSQRLAELTPGFSGADIANICNEAALHA  229 (262)
T ss_dssp             GGGSGGGSTTSCCEEEECCSCCHHHHHHHHHHHHHHTTCCBTHHHHHHHHHHTCTTCCHHHHHHHHHHHHTC-
T ss_pred             hcCHHHhcCCcCCeEEEeCCcCHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999987666555443  67888899999999999998765443

>3b9p_A CG5977-PA, isoform A; AAA ATPase, ATP-binding, nucleotide-binding, hydrolase; 2.70A {Drosophila melanogaster}

Probab=99.97  E-value=3e-30  Score=256.40  Aligned_cols=250  Identities=20%  Similarity=0.236  Sum_probs=193.1

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      .++.+|++++|.+++++.+.+.+..+...++.|...+ .+++++||+||||||||++|+++|++++.+++.++++.+.+ 
T Consensus        15 ~~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vll~Gp~GtGKT~la~~la~~~~~~~~~i~~~~l~~~   93 (297)
T 3b9p_A           15 GAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLR-APAKGLLLFGPPGNGKTLLARAVATECSATFLNISAASLTSK   93 (297)
T ss_dssp             SSCCCGGGSCCCHHHHHHHHHHTHHHHHCGGGSCGGG-CCCSEEEEESSSSSCHHHHHHHHHHHTTCEEEEEESTTTSSS
T ss_pred             CCCCCHHHhCChHHHHHHHHHHHHhhhhCHHHHhcCC-CCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEeeHHHHhhc
Confidence            4678999999999999999999999999999888766 35679999999999999999999999999999999887643 


Q ss_pred             -----hHHHHHHHHh--hcCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          263 -----DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       263 -----~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                           ...++.+|..  ...|+||||||+|.+...+..      ....+.++..+++......+..++||+|||.++.+|
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~~~~~~~v~vi~~tn~~~~l~  173 (297)
T 3b9p_A           94 YVGDGEKLVRALFAVARHMQPSIIFIDEVDSLLSERSSSEHEASRRLKTEFLVEFDGLPGNPDGDRIVVLAATNRPQELD  173 (297)
T ss_dssp             SCSCHHHHHHHHHHHHHHTCSEEEEEETGGGTSBCC-----CCSHHHHHHHHHHHHHCC------CEEEEEEESCGGGBC
T ss_pred             ccchHHHHHHHHHHHHHHcCCcEEEeccHHHhccccccCcchHHHHHHHHHHHHHhcccccCCCCcEEEEeecCChhhCC
Confidence                 2335555543  357999999999999875432      233567888888876522235678889999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch-hHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP-QVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITAL  408 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~-~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~  408 (480)
                      ++++|  ||+..+++++|+.++|..|++.++...+..+.+ .++.++..+.|++++||..+|..+...+.+.+....   
T Consensus       174 ~~l~~--R~~~~i~~~~p~~~~r~~il~~~~~~~~~~~~~~~~~~la~~~~g~~~~~l~~l~~~a~~~a~r~~~~~~---  248 (297)
T 3b9p_A          174 EAALR--RFTKRVYVSLPDEQTRELLLNRLLQKQGSPLDTEALRRLAKITDGYSGSDLTALAKDAALEPIRELNVEQ---  248 (297)
T ss_dssp             HHHHH--HCCEEEECCCCCHHHHHHHHHHHHGGGSCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHTCC------
T ss_pred             HHHHh--hCCeEEEeCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHhhhh---
Confidence            99999  999999999999999999999998766655544 567899999999999999999877654433221100   


Q ss_pred             HhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcc
Q 011664          409 QTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD  472 (480)
Q Consensus       409 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~  472 (480)
                      .            +.+           ...     ..+.|+++||.++     ++.++||++.+
T Consensus       249 ~------------~~~-----------~~~-----~~~~i~~~d~~~a-----~~~~~~s~~~~  279 (297)
T 3b9p_A          249 V------------KCL-----------DIS-----AMRAITEQDFHSS-----LKRIRRSVAPQ  279 (297)
T ss_dssp             ----------------------------CC-----CCCCCCHHHHHHH-----TTSCCCSSCHH
T ss_pred             c------------ccc-----------ccc-----ccCCcCHHHHHHH-----HHHcCCCCCHH
Confidence            0            000           000     1257999999999     88899998753

>3d8b_A Fidgetin-like protein 1; AAA+, ATPase, ADP, SGC, structural genomics consortium, ATP- hydrolase, magnesium, metal-binding, nucleotide-binding; HET: ADP; 2.00A {Homo sapiens}

Probab=99.97  E-value=1.4e-30  Score=267.18  Aligned_cols=248  Identities=21%  Similarity=0.286  Sum_probs=193.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--  262 (480)
                      ++.+|++|+|.+++++.|.+.+..++..++.|...+ ..++++||+||||||||++|+++|++++.+++.++++.+.+  
T Consensus        79 ~~~~~~~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~-~~~~~vLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~~  157 (357)
T 3d8b_A           79 PPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLR-GPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKW  157 (357)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGG-SCCSEEEEESSTTSSHHHHHHHHHHHTTCEEEEEEGGGGCCSS
T ss_pred             CCCCHHHhCChHHHHHHHHHHHHHHhhChHhHhhcc-CCCceEEEECCCCCCHHHHHHHHHHHcCCeEEEEehHHhhccc
Confidence            578999999999999999999999999999887765 45779999999999999999999999999999999887643  


Q ss_pred             ----hHHHHHHHHh--hcCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          263 ----DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       263 ----~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                          ...++.+|..  ...|+||||||||.+...+..      ...+++++..+++... .....++||+|||.++.+|+
T Consensus       158 ~g~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~lL~~l~~~~~-~~~~~v~vI~atn~~~~l~~  236 (357)
T 3d8b_A          158 VGEGEKMVRALFAVARCQQPAVIFIDEIDSLLSQRGDGEHESSRRIKTEFLVQLDGATT-SSEDRILVVGATNRPQEIDE  236 (357)
T ss_dssp             TTHHHHHHHHHHHHHHHTCSEEEEEETHHHHTBC------CHHHHHHHHHHHHHHC-----CCCCEEEEEEESCGGGBCH
T ss_pred             cchHHHHHHHHHHHHHhcCCeEEEEeCchhhhccCCCCcchHHHHHHHHHHHHHhcccc-cCCCCEEEEEecCChhhCCH
Confidence                2335566643  357899999999999765432      2346788999998764 22456788899999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch-hHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP-QVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQ  409 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~-~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~  409 (480)
                      +++|  ||+..+++++|+.++|..++..++...+..+.+ .++.++..+.||+++||..+|..+...+.+.++.....  
T Consensus       237 ~l~~--Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~l~~la~~t~G~s~~dl~~l~~~a~~~~ir~l~~~~~~--  312 (357)
T 3d8b_A          237 AARR--RLVKRLYIPLPEASARKQIVINLMSKEQCCLSEEEIEQIVQQSDAFSGADMTQLCREASLGPIRSLQTADIA--  312 (357)
T ss_dssp             HHHT--TCCEEEECCCCCHHHHHHHHHHHHHTSCBCCCHHHHHHHHHHTTTCCHHHHHHHHHHHHTHHHHHCCC------
T ss_pred             HHHh--hCceEEEeCCcCHHHHHHHHHHHHhhcCCCccHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhhhhhhc--
Confidence            9999  999999999999999999999998766655543 56889999999999999999988766554432211000  


Q ss_pred             hcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcc
Q 011664          410 TDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFD  472 (480)
Q Consensus       410 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~  472 (480)
                                   ..        ..+        ..++|+++||.++     ++..+||++.+
T Consensus       313 -------------~~--------~~~--------~~~~i~~~d~~~a-----l~~~~ps~~~~  341 (357)
T 3d8b_A          313 -------------TI--------TPD--------QVRPIAYIDFENA-----FRTVRPSVSPK  341 (357)
T ss_dssp             -----------------------------------CCCBCHHHHHHH-----HHHHGGGCCCC
T ss_pred             -------------cc--------ccc--------ccCCcCHHHHHHH-----HHhcCCCCCHH
Confidence                         00        000        1267999999999     88899998854

>2dhr_A FTSH; AAA+ protein, hexameric Zn metalloprotease, hydrolase; HET: ADP; 3.90A {Thermus thermophilus}

Probab=99.96  E-value=2.2e-29  Score=268.42  Aligned_cols=205  Identities=23%  Similarity=0.308  Sum_probs=174.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--  262 (480)
                      ++.+|++|+|.+++|+++.+.+. ++..+..|..+|...++|+||+||||||||+|++++|++++.+++.++++++..  
T Consensus        26 ~~~~f~dv~G~~~~k~~l~~lv~-~l~~~~~~~~lg~~ip~GvLL~GppGtGKTtLaraIa~~~~~~~i~i~g~~~~~~~  104 (499)
T 2dhr_A           26 PKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEMF  104 (499)
T ss_dssp             CCCCTTSSCSCHHHHHHHHHHHH-HHHCGGGTTTTSCCCCSEEEEECSSSSSHHHHHHHHHHHTTCCEEEEEGGGGTSSC
T ss_pred             CCCCHHHcCCcHHHHHHHHHHHH-HhhchhhhhhccCCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEehhHHHHhh
Confidence            67899999999999999997664 577888899999999999999999999999999999999999999999877643  


Q ss_pred             ----hHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          263 ----DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       263 ----~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                          ...++.+|..+  ..|+|+||||||.+...+..         ...+++++..|+|...   ....+++++||+|+.
T Consensus       105 ~g~~~~~v~~lfq~a~~~~p~il~IDEId~l~~~r~~~~~~~~~e~~~~l~~LL~~Ldg~~~---~~~viviAatn~p~~  181 (499)
T 2dhr_A          105 VGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK---DTAIVVMAATNRPDI  181 (499)
T ss_dssp             TTHHHHHHHHHTTTSSSSSSCEEEEECGGGTCCCSSSSTTTSSHHHHHHHHHHHHHGGGCCS---SCCCEEEECCSCGGG
T ss_pred             hhhHHHHHHHHHHHHHhcCCCEEEEehHHHHHHhhccCcCCCcHHHHHHHHHHHHHhccccc---CccEEEEEecCChhh
Confidence                23466777665  36899999999998764432         2457889999998765   466788999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      ||++++||||||++|++++|+.++|.+|++.++......-..++..++..+.|++++||.++|..+
T Consensus       182 LD~aLlr~gRfdr~i~i~~Pd~~~R~~IL~~~~~~~~l~~dv~l~~lA~~t~G~~gadL~~lv~~A  247 (499)
T 2dhr_A          182 LDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  247 (499)
T ss_dssp             SCTTTSSTTSSCCEEECCCCCHHHHHHHHHHTTSSSCCCCSSTTHHHHTTSCSCCHHHHHHHHHHH
T ss_pred             cCcccccccccceEEecCCCCHHHHHHHHHHHHhcCCCChHHHHHHHHHhcCCCCHHHHHHHHHHH
Confidence            999999999999999999999999999999988654444344578899999999999999999765

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=99.96  E-value=3.8e-29  Score=259.04  Aligned_cols=251  Identities=20%  Similarity=0.246  Sum_probs=193.9

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +...++.+|++|+|.+.+++.|.+.+..+...++.|...+. +++++|||||||||||++|+++|++++.+++.++++.+
T Consensus       106 ~~~~~~~~~~~iiG~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~vLL~GppGtGKT~la~aia~~~~~~~~~v~~~~l  184 (389)
T 3vfd_A          106 VDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRA-PARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASL  184 (389)
T ss_dssp             BCCSCCCCGGGSCSCHHHHHHHHHHTHHHHHCTTTSCGGGC-CCSEEEEESSTTSCHHHHHHHHHHHTTCEEEEECSCCC
T ss_pred             hccCCCCChHHhCCHHHHHHHHHHHHHHhccCHHHhcccCC-CCceEEEECCCCCCHHHHHHHHHHhhcCcEEEeeHHHh
Confidence            44567899999999999999999999999999998888774 46799999999999999999999999999999999886


Q ss_pred             CC------hHHHHHHHHh--hcCCcEEEEecccccccCccc------ccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          261 AD------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPA------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       261 ~~------~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                      .+      +..++.+|..  ...|+||||||||.++..+..      ...+.+|+..|++... .....++||+|||.++
T Consensus       185 ~~~~~g~~~~~~~~~~~~a~~~~~~il~iDEid~l~~~~~~~~~~~~~~~~~~ll~~l~~~~~-~~~~~v~vI~atn~~~  263 (389)
T 3vfd_A          185 TSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQS-AGDDRVLVMGATNRPQ  263 (389)
T ss_dssp             -------CHHHHHHHHHHHHHSSSEEEEEETGGGGC--------CTHHHHHHHHHHHHHHHC------CEEEEEEESCGG
T ss_pred             hccccchHHHHHHHHHHHHHhcCCeEEEEECchhhcccCCCccchHHHHHHHHHHHHhhcccc-cCCCCEEEEEecCCch
Confidence            54      2335666643  457899999999999765432      2345688999998765 2345678889999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch-hHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHH
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP-QVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVI  405 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~-~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i  405 (480)
                      .||++++|  ||+.+|+++.|+.++|..|++.++...+..+.. .+..++..+.|+++++|..+|..+...+.+.+... 
T Consensus       264 ~l~~~l~~--R~~~~i~i~~p~~~~r~~il~~~~~~~~~~l~~~~~~~la~~~~g~~~~~l~~L~~~a~~~~~rel~~~-  340 (389)
T 3vfd_A          264 ELDEAVLR--RFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIRELKPE-  340 (389)
T ss_dssp             GCCHHHHT--TCCEEEECCCCCHHHHHHHHHHHHTTSCCCSCHHHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHTSCCC-
T ss_pred             hcCHHHHc--CcceEEEcCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhhhhh-
Confidence            99999999  999999999999999999999999877666554 56789999999999999999987766543321100 


Q ss_pred             HHHHhcCCCCcccccccccccCCCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCc
Q 011664          406 TALQTDGEGRGAANAGRRLDKSGSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSF  471 (480)
Q Consensus       406 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~  471 (480)
                        .            .+.+           ..     ...+.|+++||.++     ++..+|+++.
T Consensus       341 --~------------~~~~-----------~~-----~~~~~i~~~d~~~a-----l~~~~~s~~~  371 (389)
T 3vfd_A          341 --Q------------VKNM-----------SA-----SEMRNIRLSDFTES-----LKKIKRSVSP  371 (389)
T ss_dssp             -----------------CC-----------SS-----SCCCCCCHHHHHHH-----HHHCCCSSCH
T ss_pred             --h------------hhcc-----------ch-----hhcCCcCHHHHHHH-----HHHcCCCCCH
Confidence              0            0000           00     01256899999999     7788888874

>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=99.96  E-value=5.3e-30  Score=250.97  Aligned_cols=207  Identities=22%  Similarity=0.319  Sum_probs=169.5

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      .++.+|++|+|.+++++.+.+.+. ++..++.|...|...++|+|||||||||||++|+++|++++.+++.++++.+.. 
T Consensus         5 ~~~~~~~~i~G~~~~~~~l~~~~~-~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~~~~~~~~v~~~~~~~~   83 (268)
T 2r62_A            5 KPNVRFKDMAGNEEAKEEVVEIVD-FLKYPERYANLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAHVPFFSMGGSSFIEM   83 (268)
T ss_dssp             CCCCCSTTSSSCTTTHHHHHHHHH-HHHCHHHHHHHSCCCCSCCCCBCSSCSSHHHHHHHHHHHHTCCCCCCCSCTTTTS
T ss_pred             CCCCCHHHhCCcHHHHHHHHHHHH-HHHChHHHHHCCCCCCceEEEECCCCCcHHHHHHHHHHHhCCCEEEechHHHHHh
Confidence            456789999999999999998665 578899999999999999999999999999999999999999999998876542 


Q ss_pred             -----hHHHHHHHHh--hcCCcEEEEecccccccCcc----------cccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          263 -----DADLKSLLLQ--TTSKSVILIEDLDRFLVEKP----------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       263 -----~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~----------~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                           ...++.+|..  ...|+||||||+|.+...+.          ....+++|++.+++....  ...++||+|||.+
T Consensus        84 ~~~~~~~~~~~~~~~a~~~~~~vl~iDEid~l~~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~~--~~~v~vi~ttn~~  161 (268)
T 2r62_A           84 FVGLGASRVRDLFETAKKQAPSIIFIDEIDAIGKSRAAGGVVSGNDEREQTLNQLLAEMDGFGSE--NAPVIVLAATNRP  161 (268)
T ss_dssp             CSSSCSSSSSTTHHHHHHSCSCEEEESCGGGTTC----------CCCSCSSTTTTTTTTTCSSCS--CSCCEEEECBSCC
T ss_pred             hcchHHHHHHHHHHHHHhcCCeEEEEeChhhhcccccccccCCCchhHHHHHHHHHHHhhCcccC--CCCEEEEEecCCc
Confidence                 2223444543  34789999999999976432          124578899999887541  3457889999999


Q ss_pred             ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          326 DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       326 ~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      +.+|++++|+|||+..+++++|+.++|.++++.++.........+++.++..+.|++++||.++|..+
T Consensus       162 ~~ld~~l~r~~Rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~g~~g~dl~~l~~~a  229 (268)
T 2r62_A          162 EILDPALMRPGRFDRQVLVDKPDFNGRVEILKVHIKGVKLANDVNLQEVAKLTAGLAGADLANIINEA  229 (268)
T ss_dssp             TTSCGGGGSSSSSCCCCBCCCCCTTTHHHHHHHHTSSSCCCSSCCTTTTTSSSCSSCHHHHHHHHHHH
T ss_pred             hhcCHhHcCCCCCCeEEEecCcCHHHHHHHHHHHHhcCCCCCccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            99999999999999999999999999999999998765443334567788888999999999998755

>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=99.96  E-value=3.3e-28  Score=236.75  Aligned_cols=209  Identities=22%  Similarity=0.281  Sum_probs=169.5

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      ++..++.+|++++|.++++.++.+.... +..+..+..++...++|++|+||||||||+|++++|+.++..++.++...+
T Consensus         7 ~~~~~~~~~~~i~g~~~~~~~l~~l~~~-~~~~~~~~~~~~~~~~g~ll~G~~G~GKTtl~~~i~~~~~~~~i~~~~~~~   85 (254)
T 1ixz_A            7 LTEAPKVTFKDVAGAEEAKEELKEIVEF-LKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF   85 (254)
T ss_dssp             -CCCCSCCGGGCCSCHHHHHHHHHHHHH-HHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             ccCCCCCCHHHhCCcHHHHHHHHHHHHH-HHCHHHHHHcCCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCEEEeeHHHH
Confidence            3445678999999999999999876654 567788899999999999999999999999999999999999999986543


Q ss_pred             C----C--hHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecC
Q 011664          261 A----D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       261 ~----~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      .    +  ...+..+|...  ..|+++++||+|.+...+..         ...++++++.|+|...   ....+++++||
T Consensus        86 ~~~~~~~~~~~i~~~~~~~~~~~~~i~~~Deid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~g~~~---~~~~i~~a~t~  162 (254)
T 1ixz_A           86 VEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK---DTAIVVMAATN  162 (254)
T ss_dssp             HHSCTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCT---TCCEEEEEEES
T ss_pred             HHHHhhHHHHHHHHHHHHHHhcCCeEEEehhhhhhhcccCccccccchHHHHHHHHHHHHHhCCCC---CCCEEEEEccC
Confidence            2    2  23456667654  36899999999988754321         2346788889988765   45567788999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .|+.||++++|||||+..|+++.|+.++|.+|++.++......-..++..++..+.|++++||.++|..+
T Consensus       163 ~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~~~~~a  232 (254)
T 1ixz_A          163 RPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  232 (254)
T ss_dssp             CGGGSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CchhCCHHHcCCCcCCeEEeeCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999988654443344678899999999999999999755

>1iy2_A ATP-dependent metalloprotease FTSH; AAA domain fold, hydrolase; 3.20A {Thermus thermophilus} SCOP: c.37.1.20

Probab=99.95  E-value=6.1e-27  Score=231.28  Aligned_cols=209  Identities=22%  Similarity=0.296  Sum_probs=169.3

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +...++.+|++++|.+++++++.+... .+..+..+..++...++|++|+||||||||+|++++|+.++..++.++...+
T Consensus        31 ~~~~~~~~~~~i~g~~~~~~~l~~l~~-~~~~~~~l~~~~~~~~~gvll~Gp~GtGKTtl~~~i~~~~~~~~i~~~~~~~  109 (278)
T 1iy2_A           31 LTEAPKVTFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDF  109 (278)
T ss_dssp             BCCCCCCCGGGSSSCHHHHHHHHHHHH-HHHCHHHHHHTTCCCCCEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHH
T ss_pred             ccCCCCCCHHHhCChHHHHHHHHHHHH-HHHCHHHHHHcCCCCCCeEEEECCCcChHHHHHHHHHHHcCCCEEEecHHHH
Confidence            344477899999999999999987655 4567788889999999999999999999999999999999999999986543


Q ss_pred             C----C--hHHHHHHHHhh--cCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecC
Q 011664          261 A----D--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       261 ~----~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      .    +  ...+..+|...  ..|+++++||+|.+...+..         ...+.++++.|+|...   ....+++++||
T Consensus       110 ~~~~~~~~~~~i~~~~~~~~~~~~~i~~iDeid~l~~~~~~~~~~~~~~~~~~~~~ll~~lsgg~~---~~~~i~~a~t~  186 (278)
T 1iy2_A          110 VEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK---DTAIVVMAATN  186 (278)
T ss_dssp             HHSTTTHHHHHHHHHHHHHHTSCSEEEEEETHHHHHCC--------CHHHHHHHHHHHHHHTTCCT---TCCEEEEEEES
T ss_pred             HHHHhhHHHHHHHHHHHHHHhcCCcEEehhhhHhhhcccccccCCcchHHHHHHHHHHHHHhCCCC---CCCEEEEEecC
Confidence            2    1  23355666654  46899999999988654321         2346778888887654   44567788999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .|+.||++++|||||+..|++++|+.++|.+|++.++......-..++..++..+.|++++||..+|..+
T Consensus       187 ~p~~ld~~l~r~~rf~~~i~i~~p~~~~r~~il~~~~~~~~~~~~~~~~~la~~~~G~~~~dl~~l~~~a  256 (278)
T 1iy2_A          187 RPDILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  256 (278)
T ss_dssp             CTTSSCHHHHSTTSSCCEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             CchhCCHhHcCCCcCCeEEEeCCcCHHHHHHHHHHHHccCCCCcccCHHHHHHHcCCCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999988654433344678899999999999999998755

>3t15_A Ribulose bisphosphate carboxylase/oxygenase activ chloroplastic; photosynthesis, rubisco activase, AAA+ protein; 2.95A {Nicotiana tabacum} PDB: 3zw6_A

Probab=99.93  E-value=2.3e-26  Score=229.69  Aligned_cols=165  Identities=13%  Similarity=0.083  Sum_probs=122.3

Q ss_pred             hhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------hHHHHHHHHhh------cCCcEEEEeccc
Q 011664          218 RLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------DADLKSLLLQT------TSKSVILIEDLD  285 (480)
Q Consensus       218 ~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------~~~l~~l~~~~------~~~sII~IDEiD  285 (480)
                      ..+.++|+|+|||||||||||++|+++|++++.+++.++++++.+      ...++.+|..+      ..|+||||||||
T Consensus        30 ~~~~~~p~~lLl~GppGtGKT~la~aiA~~l~~~~i~v~~~~l~~~~~g~~~~~i~~~f~~a~~~~~~~~~~vl~iDEiD  109 (293)
T 3t15_A           30 LPNIKVPLILGIWGGKGQGKSFQCELVFRKMGINPIMMSAGELESGNAGEPAKLIRQRYREAAEIIRKGNMCCLFINDLD  109 (293)
T ss_dssp             CTTCCCCSEEEEEECTTSCHHHHHHHHHHHHTCCCEEEEHHHHHCC---HHHHHHHHHHHHHHHHHTTSSCCCEEEECCC
T ss_pred             cCCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCEEEEeHHHhhhccCchhHHHHHHHHHHHHHHHhcCCCeEEEEechh
Confidence            346778899999999999999999999999999999999876542      23466677544      379999999999


Q ss_pred             ccccCcccc--------cchhhhhhhccccc--------ccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          286 RFLVEKPAA--------VSLSGVLNFMDGVL--------NSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       286 ~l~~~~~~~--------~~ls~lL~~ldg~~--------~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                      .+++...+.        ...+.|++.||+..        ......+++||+|||+++.||++++|||||+..|++  |+.
T Consensus       110 ~~~~~~~~~~~~~~~~~~v~~~Ll~~ld~~~~~~~~~~~~~~~~~~v~vI~ttN~~~~ld~al~R~~R~d~~i~~--P~~  187 (293)
T 3t15_A          110 AGAGRMGGTTQYTVNNQMVNATLMNIADNPTNVQLPGMYNKQENARVPIIVTGNDFSTLYAPLIRDGRMEKFYWA--PTR  187 (293)
T ss_dssp             --------------CHHHHHHHHHHHHHCCC-----------CCCCCCEEEECSSCCC--CHHHHHHHEEEEEEC--CCH
T ss_pred             hhcCCCCCCccccchHHHHHHHHHHHhccccccccccccccccCCCcEEEEecCCcccCCHHHhCCCCCceeEeC--cCH
Confidence            998744321        23477888888553        111245688999999999999999999999998984  699


Q ss_pred             HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHH
Q 011664          350 SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       350 ~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~  388 (480)
                      ++|.+|++.++...+.    +.+.++..+.+|++++|..
T Consensus       188 ~~r~~Il~~~~~~~~~----~~~~l~~~~~~~~~~~l~~  222 (293)
T 3t15_A          188 EDRIGVCTGIFRTDNV----PAEDVVKIVDNFPGQSIDF  222 (293)
T ss_dssp             HHHHHHHHHHHGGGCC----CHHHHHHHHHHSCSCCHHH
T ss_pred             HHHHHHHHHhccCCCC----CHHHHHHHhCCCCcccHHH
Confidence            9999999998865433    3556666677899998864

>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=99.87  E-value=5.4e-24  Score=225.03  Aligned_cols=190  Identities=12%  Similarity=0.082  Sum_probs=125.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC--CcEEEEeCCCcCC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS--YDVYDVDLSRVAD  262 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~--~~~~~i~~s~~~~  262 (480)
                      +...|++++|.+++++.+.+.+..+        ..|..+++++|||||||||||++|+++|++++  .+|+.++++.+.+
T Consensus        32 ~~~~~~~iiG~~~~~~~l~~~~~~~--------~~~~~~~~~iLl~GppGtGKT~la~ala~~l~~~~~~~~~~~~~~~~  103 (456)
T 2c9o_A           32 AKQAASGLVGQENAREACGVIVELI--------KSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPFCPMVGSEVYS  103 (456)
T ss_dssp             BCSEETTEESCHHHHHHHHHHHHHH--------HTTCCTTCEEEEECCTTSSHHHHHHHHHHHHCTTSCEEEEEGGGGCC
T ss_pred             hhhchhhccCHHHHHHHHHHHHHHH--------HhCCCCCCeEEEECCCcCCHHHHHHHHHHHhCCCceEEEEeHHHHHH
Confidence            4557899999999999988766433        23556778999999999999999999999999  8999999876643


Q ss_pred             ----h-HHHHHHHHhh-----cCCcEEEEecccccccCccccc----------ch---------------hhhhhhcccc
Q 011664          263 ----D-ADLKSLLLQT-----TSKSVILIEDLDRFLVEKPAAV----------SL---------------SGVLNFMDGV  307 (480)
Q Consensus       263 ----~-~~l~~l~~~~-----~~~sII~IDEiD~l~~~~~~~~----------~l---------------s~lL~~ldg~  307 (480)
                          + ..++..|..+     ..|+||||||+|.+++.+....          .+               ++++..++..
T Consensus       104 ~~~~~~~~~~~~f~~a~~~~~~~~~il~iDEid~l~~~r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ll~~l~~~  183 (456)
T 2c9o_A          104 TEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLKTAKGTKQLKLDPSIFESLQKE  183 (456)
T ss_dssp             SSSCHHHHHHHHHHHTEEEEEEEEEEEEEEEEEEEEEC--------------CEEEEEEETTEEEEEEECHHHHHHHHHT
T ss_pred             HhhhhhHHHHHHHHHHHhhhhcCCcEEEEechhhcccccCCCCCCCcchHHHHHHHHHhccccchhHhhhHHHHHHHhhc
Confidence                2 2377778665     5799999999999997654321          11               1244444321


Q ss_pred             cccccCCceEEEEecCCCccCcccccCCCceeE--EEEcCCCC--HHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCH
Q 011664          308 LNSCCFEERVMVFTMNSKDHVDQALLRPGRIDV--HIHFPLCD--FSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSP  383 (480)
Q Consensus       308 ~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~--~I~~~~p~--~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~  383 (480)
                      .. ..++.++|++|||+++.+|++++||||||.  .+.+|.|+  .++|++|++.+.       ..+++.++..+.|  +
T Consensus       184 ~~-~~~~~v~i~attn~~~~ld~a~~r~~rfd~~~~~~v~~p~~~~~~R~~il~~~~-------~~dl~~~a~~t~g--g  253 (456)
T 2c9o_A          184 RV-EAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVT-------LHDLDVANARPQG--G  253 (456)
T ss_dssp             TC-CTTEEEEEETTTCCEEEEEEETTSCCTTSCSSSSEECCCCSCSEEEEEEEEEEE-------HHHHHHTC--------
T ss_pred             cC-CCCCEEEEEcCCCCcccCChhhcCCcccCcceeEecCCCchhHHHHHHHHHHHH-------HHHHHHHHHhCCC--h
Confidence            11 113334445699999999999999999998  66777775  466777665443       1367888888888  9


Q ss_pred             HHHHHHHHH
Q 011664          384 AEIGELMIA  392 (480)
Q Consensus       384 adI~~ll~~  392 (480)
                      +|+.++|..
T Consensus       254 adl~~l~~~  262 (456)
T 2c9o_A          254 QDILSMMGQ  262 (456)
T ss_dssp             ---------
T ss_pred             hHHHHHHhh
Confidence            999999853

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=99.84  E-value=7.6e-20  Score=184.61  Aligned_cols=199  Identities=14%  Similarity=0.173  Sum_probs=150.9

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .|.  ....|.+|++++|.+.+++.+...+......        .....++||+||||||||++|+++|+.++.+++.++
T Consensus        18 ~~~--~~~~p~~~~~iiG~~~~~~~l~~~l~~~~~~--------~~~~~~vll~G~~GtGKT~la~~ia~~~~~~~~~~~   87 (338)
T 3pfi_A           18 TYE--TSLRPSNFDGYIGQESIKKNLNVFIAAAKKR--------NECLDHILFSGPAGLGKTTLANIISYEMSANIKTTA   87 (338)
T ss_dssp             -------CCCCSGGGCCSCHHHHHHHHHHHHHHHHT--------TSCCCCEEEECSTTSSHHHHHHHHHHHTTCCEEEEE
T ss_pred             hhh--hccCCCCHHHhCChHHHHHHHHHHHHHHHhc--------CCCCCeEEEECcCCCCHHHHHHHHHHHhCCCeEEec
Confidence            454  2346779999999999999998877655321        124568999999999999999999999999999999


Q ss_pred             CCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccc-------------ccCCceEEEEecC
Q 011664          257 LSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS-------------CCFEERVMVFTMN  323 (480)
Q Consensus       257 ~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~-------------~~~~~~ivI~tTN  323 (480)
                      ++.+.....+...+.....+++|||||||.+..     .....|+..|+...-.             ......++|++||
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~~-----~~~~~Ll~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~atn  162 (338)
T 3pfi_A           88 APMIEKSGDLAAILTNLSEGDILFIDEIHRLSP-----AIEEVLYPAMEDYRLDIIIGSGPAAQTIKIDLPKFTLIGATT  162 (338)
T ss_dssp             GGGCCSHHHHHHHHHTCCTTCEEEEETGGGCCH-----HHHHHHHHHHHTSCC---------CCCCCCCCCCCEEEEEES
T ss_pred             chhccchhHHHHHHHhccCCCEEEEechhhcCH-----HHHHHHHHHHHhccchhhcccCccccceecCCCCeEEEEeCC
Confidence            988887778888888888899999999998842     2345566655432100             0011368899999


Q ss_pred             CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      ....++++|++  ||+.++++++|+.+++..+++.++...+..+.++. +.++... +-.+.++.+++..+
T Consensus       163 ~~~~l~~~L~~--R~~~~i~l~~~~~~e~~~il~~~~~~~~~~~~~~~~~~l~~~~-~G~~r~l~~~l~~~  230 (338)
T 3pfi_A          163 RAGMLSNPLRD--RFGMQFRLEFYKDSELALILQKAALKLNKTCEEKAALEIAKRS-RSTPRIALRLLKRV  230 (338)
T ss_dssp             CGGGSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCEECHHHHHHHHHTT-TTCHHHHHHHHHHH
T ss_pred             CccccCHHHHh--hcCEEeeCCCcCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHH-CcCHHHHHHHHHHH
Confidence            99999999999  99999999999999999999999876665555544 4565543 55667777766553

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=99.83  E-value=4.4e-20  Score=183.68  Aligned_cols=172  Identities=17%  Similarity=0.266  Sum_probs=132.4

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCC---CceEEEEccCCCcHHHHHHHHHHcC-------CCcEEEEeCCCc
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVW---KRSYLLYGPSGTGKSSFAAAMASFM-------SYDVYDVDLSRV  260 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~---~rgiLL~GPpGTGKT~La~aiA~~l-------~~~~~~i~~s~~  260 (480)
                      +|+|++++|+.|.+.+..+.. +..+...|...   ..++||+||||||||++|+++|+.+       ..+++.++++.+
T Consensus        32 ~i~G~~~~~~~l~~~~~~~~~-~~~~~~~g~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~~~~~~~~~~~~~l  110 (309)
T 3syl_A           32 ELIGLKPVKDRIRETAALLLV-ERARQKLGLAHETPTLHMSFTGNPGTGKTTVALKMAGLLHRLGYVRKGHLVSVTRDDL  110 (309)
T ss_dssp             HSSSCHHHHHHHHHHHHHHHH-HHHHHHHTCCSSCCCCEEEEEECTTSSHHHHHHHHHHHHHHTTSSSSCCEEEECGGGT
T ss_pred             HccChHHHHHHHHHHHHHHHh-HHHHHHcCCCCCCCCceEEEECCCCCCHHHHHHHHHHHHHhcCCcCCCcEEEEcHHHh
Confidence            799999999999988887653 56666666543   3469999999999999999999987       338999988766


Q ss_pred             CC------hHHHHHHHHhhcCCcEEEEecccccccCcc----cccchhhhhhhcccccccccCCceEEEEecCCCc----
Q 011664          261 AD------DADLKSLLLQTTSKSVILIEDLDRFLVEKP----AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD----  326 (480)
Q Consensus       261 ~~------~~~l~~l~~~~~~~sII~IDEiD~l~~~~~----~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~----  326 (480)
                      .+      ...+..+|... .++||||||+|.++..+.    ....+..|++.|+..     ....++|+|||.++    
T Consensus       111 ~~~~~g~~~~~~~~~~~~~-~~~vl~iDEid~l~~~~~~~~~~~~~~~~Ll~~l~~~-----~~~~~~i~~~~~~~~~~~  184 (309)
T 3syl_A          111 VGQYIGHTAPKTKEVLKRA-MGGVLFIDEAYYLYRPDNERDYGQEAIEILLQVMENN-----RDDLVVILAGYADRMENF  184 (309)
T ss_dssp             CCSSTTCHHHHHHHHHHHH-TTSEEEEETGGGSCCCC---CCTHHHHHHHHHHHHHC-----TTTCEEEEEECHHHHHHH
T ss_pred             hhhcccccHHHHHHHHHhc-CCCEEEEEChhhhccCCCcccccHHHHHHHHHHHhcC-----CCCEEEEEeCChHHHHHH
Confidence            43      23355566554 678999999999975443    334567788887643     34567888887653    


Q ss_pred             -cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH
Q 011664          327 -HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV  371 (480)
Q Consensus       327 -~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i  371 (480)
                       .++|+|++  ||+.+|+|++|+.+++..|++.++...+..+.++.
T Consensus       185 ~~~~~~l~~--R~~~~i~~~~~~~~~~~~il~~~l~~~~~~~~~~~  228 (309)
T 3syl_A          185 FQSNPGFRS--RIAHHIEFPDYSDEELFEIAGHMLDDQNYQMTPEA  228 (309)
T ss_dssp             HHHSTTHHH--HEEEEEEECCCCHHHHHHHHHHHHHHTTCEECHHH
T ss_pred             HhhCHHHHH--hCCeEEEcCCcCHHHHHHHHHHHHHHcCCCCCHHH
Confidence             35899999  99999999999999999999999987666655544

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=99.81  E-value=5.4e-19  Score=176.80  Aligned_cols=193  Identities=16%  Similarity=0.190  Sum_probs=148.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA  264 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~  264 (480)
                      .|.+|++++|.+..++.+.+.+......       + ..+.++||+||||||||++|+++|+.++.+++.++++.+....
T Consensus         7 ~p~~~~~~ig~~~~~~~l~~~l~~~~~~-------~-~~~~~vll~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~~   78 (324)
T 1hqc_A            7 RPKTLDEYIGQERLKQKLRVYLEAAKAR-------K-EPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPG   78 (324)
T ss_dssp             CCCSTTTCCSCHHHHHHHHHHHHHHHHH-------C-SCCCCCEEECCTTCCCHHHHHHHHHHHTCCEEEECTTTCCSHH
T ss_pred             CcccHHHhhCHHHHHHHHHHHHHHHHcc-------C-CCCCcEEEECCCCCCHHHHHHHHHHHhCCCEEEEeccccCChH
Confidence            5678999999999999988877654321       1 2346899999999999999999999999999999999888777


Q ss_pred             HHHHHHHh-hcCCcEEEEecccccccCcccccchhhhhhhccccc-----cc--------ccCCceEEEEecCCCccCcc
Q 011664          265 DLKSLLLQ-TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----NS--------CCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       265 ~l~~l~~~-~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----~~--------~~~~~~ivI~tTN~~~~LD~  330 (480)
                      ++...+.. ...+++|||||+|.+..     .....|+..++...     ..        ......++|++||.+..+++
T Consensus        79 ~l~~~l~~~~~~~~~l~lDEi~~l~~-----~~~~~L~~~l~~~~~~~v~~~~~~~~~~~~~~~~~~~i~~t~~~~~~~~  153 (324)
T 1hqc_A           79 DLAAILANSLEEGDILFIDEIHRLSR-----QAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITA  153 (324)
T ss_dssp             HHHHHHTTTCCTTCEEEETTTTSCCH-----HHHHHHHHHHHHSEEEECCSSSSSCCCEEEECCCCEEEEEESCCSSCSC
T ss_pred             HHHHHHHHhccCCCEEEEECCccccc-----chHHHHHHHHHhhhhHHhccccccccccccCCCCEEEEEeCCCcccCCH
Confidence            77777766 56789999999998742     22344555554321     00        00124678899999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHHHHh
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      +|++  ||+.++.+++|+.+++..++..++...+..+.++ ++.++..+ +-.+.++.+++..+
T Consensus       154 ~l~~--R~~~~i~l~~~~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~-~G~~r~l~~~l~~~  214 (324)
T 1hqc_A          154 PLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRS-RGTMRVAKRLFRRV  214 (324)
T ss_dssp             STTT--TCSCEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHS-CSCHHHHHHHHHHH
T ss_pred             HHHh--cccEEEecCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHc-cCCHHHHHHHHHHH
Confidence            9999  9988999999999999999999987666666554 35666665 44677777777654

>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=99.79  E-value=2.3e-20  Score=195.63  Aligned_cols=160  Identities=14%  Similarity=0.150  Sum_probs=76.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCC-CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGR-VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~-~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------  262 (480)
                      ++|+|++++|+.+...+..+.+++..+..++. .+++++||+||||||||++|+++|+.++.+++.++++.+.+      
T Consensus        15 ~~IvGqe~ak~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GppGtGKT~lar~lA~~l~~~~~~v~~~~~~~~g~vG~   94 (444)
T 1g41_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (444)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC----CCC
T ss_pred             HHhCCHHHHHHHHHHHHHHHHhhhccccccccccCCceEEEEcCCCCCHHHHHHHHHHHcCCCceeecchhhcccceeec
Confidence            36899999999999999888777776665543 36789999999999999999999999999999999865432      


Q ss_pred             --hHHHHHHHHhhcCCcEEEEecccccccCc---ccccchhhhhhhcccccccccCCceEEEEe-cCCCccCcccccCCC
Q 011664          263 --DADLKSLLLQTTSKSVILIEDLDRFLVEK---PAAVSLSGVLNFMDGVLNSCCFEERVMVFT-MNSKDHVDQALLRPG  336 (480)
Q Consensus       263 --~~~l~~l~~~~~~~sII~IDEiD~l~~~~---~~~~~ls~lL~~ldg~~~~~~~~~~ivI~t-TN~~~~LD~aLlrpG  336 (480)
                        +..++.+|..+.  .++++||+|.+....   .....+++||+.|||+.+   .. .+ +++ ||+|+.||+||+|||
T Consensus        95 d~e~~lr~lf~~a~--~~~~~De~d~~~~~~~~~~e~rvl~~LL~~~dg~~~---~~-~v-~a~~TN~~~~ld~aL~rgg  167 (444)
T 1g41_A           95 EVDSIIRDLTDSAM--KLVRQQEIAKNRARAEDVAEERILDALLPPAKNQWG---EV-EN-HDSHSSTRQAFRKKLREGQ  167 (444)
T ss_dssp             CTHHHHHHHHHHHH--HHHHHHHHHSCC----------------------------------------------------
T ss_pred             cHHHHHHHHHHHHH--hcchhhhhhhhhccchhhHHHHHHHHHHHHhhcccc---cc-cc-ccccccCHHHHHHHHHcCC
Confidence              344666665432  234589988775432   234668999999999976   22 23 444 999999999999999


Q ss_pred             ceeEEEEcCCCCHH-HHHHHH
Q 011664          337 RIDVHIHFPLCDFS-SFKTLA  356 (480)
Q Consensus       337 Rfd~~I~~~~p~~~-~r~~il  356 (480)
                      |||++|++++|+.. .+.+|+
T Consensus       168 r~D~~i~i~lP~~~~~~~ei~  188 (444)
T 1g41_A          168 LDDKEIEIDVSAGVSMGVEIM  188 (444)
T ss_dssp             ---------------------
T ss_pred             CcceEEEEcCCCCccchhhhh
Confidence            99999999999987 566654

>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=99.79  E-value=6.3e-19  Score=174.62  Aligned_cols=213  Identities=15%  Similarity=0.268  Sum_probs=143.9

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhh-CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRL-GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~-g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------  262 (480)
                      ++++|++++++.+...+............. +...+.++||+||||||||++|+++|+.++.+++.++++.+..      
T Consensus        15 ~~i~G~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~vll~G~~GtGKT~la~~la~~l~~~~~~i~~~~~~~~~~~~~   94 (310)
T 1ofh_A           15 QHIIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGK   94 (310)
T ss_dssp             TTCCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGG
T ss_pred             hhcCChHHHHHHHHHHHHHHHhhhhhcccccccCCCceEEEECCCCCCHHHHHHHHHHHhCCCEEEEcchhcccCCccCc
Confidence            358999999999998887654433222111 1124568999999999999999999999999999999876643      


Q ss_pred             --hHHHHHHHHhh-------cCCcEEEEecccccccCcccc-------cchhhhhhhccccccc-----ccCCceEEEEe
Q 011664          263 --DADLKSLLLQT-------TSKSVILIEDLDRFLVEKPAA-------VSLSGVLNFMDGVLNS-----CCFEERVMVFT  321 (480)
Q Consensus       263 --~~~l~~l~~~~-------~~~sII~IDEiD~l~~~~~~~-------~~ls~lL~~ldg~~~~-----~~~~~~ivI~t  321 (480)
                        ...++.++...       ..++||||||+|.+.......       ...+.|+..|++..-.     ......++|++
T Consensus        95 ~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~Ll~~le~~~~~~~~~~~~~~~~~~i~~  174 (310)
T 1ofh_A           95 EVDSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIAS  174 (310)
T ss_dssp             STTHHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEE
T ss_pred             cHHHHHHHHHHHhhHHHhhccCCCEEEEEChhhcCccccccccchhHHHHHHHHHHHhcCCeEecccccccCCcEEEEEc
Confidence              23355555432       357999999999987644211       1145677777753210     01245677777


Q ss_pred             ----cCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCC---CCCHHHHHHHHHHhh
Q 011664          322 ----MNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGS---SLSPAEIGELMIANR  394 (480)
Q Consensus       322 ----TN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~---g~s~adI~~ll~~a~  394 (480)
                          ++.+..++++|++  ||+.+|+|++|+.+++..|++..+.    .+...+........   .+++..+..+...++
T Consensus       175 ~~~~~~~~~~l~~~l~~--R~~~~i~~~~~~~~~~~~il~~~~~----~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~  248 (310)
T 1ofh_A          175 GAFQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEPHA----SLTEQYKALMATEGVNIAFTTDAVKKIAEAAF  248 (310)
T ss_dssp             ECCSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSSTT----CHHHHHHHHHHHTTCEEEECHHHHHHHHHHHH
T ss_pred             CCcccCCcccCCHHHHh--hCCceEEcCCcCHHHHHHHHHhhHH----HHHHHHHHHHHhcCCeeccCHHHHHHHHHHhh
Confidence                5688899999999  9999999999999999999985321    11122222222221   478888877776653


Q ss_pred             h-------cHHHHHHHHHHHH
Q 011664          395 N-------SPSRALKSVITAL  408 (480)
Q Consensus       395 ~-------~~~~al~~~i~~~  408 (480)
                      .       ...+.+..+++.+
T Consensus       249 ~~~~~~~~g~~R~l~~~l~~~  269 (310)
T 1ofh_A          249 RVNEKTENIGARRLHTVMERL  269 (310)
T ss_dssp             HHHHHSCCCTTHHHHHHHHHH
T ss_pred             hhcccccccCcHHHHHHHHHH
Confidence            2       4455555555543

>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=99.77  E-value=2.8e-17  Score=153.17  Aligned_cols=155  Identities=15%  Similarity=0.197  Sum_probs=117.4

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLS  258 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s  258 (480)
                      ..|.+|++++|.++.++.+.+.+..           +  ...+++|+||||||||++++++++.+     ...++.++++
T Consensus        11 ~~p~~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~~ll~G~~G~GKT~l~~~l~~~~~~~~~~~~~~~~~~~   77 (226)
T 2chg_A           11 YRPRTLDEVVGQDEVIQRLKGYVER-----------K--NIPHLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMNAS   77 (226)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHT-----------T--CCCCEEEECSTTSSHHHHHHHHHHHHHGGGGGGGEEEEETT
T ss_pred             cCCCCHHHHcCcHHHHHHHHHHHhC-----------C--CCCeEEEECCCCCCHHHHHHHHHHHHhccccccceEEeccc
Confidence            3678899999999988888765532           1  12359999999999999999999875     4568888887


Q ss_pred             CcCChHHHHHHHHh--------hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          259 RVADDADLKSLLLQ--------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       259 ~~~~~~~l~~l~~~--------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                      ...+...+...+..        ...+.+|+|||+|.+..     .....|+..++..     ..+..+|++||.++.+++
T Consensus        78 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~-----~~~~~l~~~l~~~-----~~~~~~i~~~~~~~~~~~  147 (226)
T 2chg_A           78 DERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA-----DAQAALRRTMEMY-----SKSCRFILSCNYVSRIIE  147 (226)
T ss_dssp             CTTCHHHHHHHHHHHHTSCCSTTCSCEEEEEETGGGSCH-----HHHHHHHHHHHHT-----TTTEEEEEEESCGGGSCH
T ss_pred             cccChHHHHHHHHHHhcccCCCccCceEEEEeChhhcCH-----HHHHHHHHHHHhc-----CCCCeEEEEeCChhhcCH
Confidence            76665554443322        14678999999998743     2234556665542     345678889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCC
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKD  364 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~  364 (480)
                      ++.+  |+. .+++++|+.++...++..++...+
T Consensus       148 ~l~~--r~~-~i~~~~~~~~~~~~~l~~~~~~~~  178 (226)
T 2chg_A          148 PIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEG  178 (226)
T ss_dssp             HHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHT
T ss_pred             HHHH--hCc-eeecCCCCHHHHHHHHHHHHHHcC
Confidence            9999  997 999999999999999988775433

>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=99.76  E-value=7.2e-18  Score=165.38  Aligned_cols=211  Identities=18%  Similarity=0.193  Sum_probs=135.3

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC-cCC------
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR-VAD------  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~-~~~------  262 (480)
                      +.++|.+...+.+.+......   ......+...++++||+||||||||++|+++|+.++.+++.+++++ +.+      
T Consensus        33 ~~~i~~~~~~~~i~~~~~~l~---~~l~~~~~~~~~~vLl~G~~GtGKT~la~~ia~~~~~~~~~i~~~~~~~g~~~~~~  109 (272)
T 1d2n_A           33 NGIIKWGDPVTRVLDDGELLV---QQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAK  109 (272)
T ss_dssp             TCCCCCSHHHHHHHHHHHHHH---HHHHHCSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHH
T ss_pred             cCCCCccHHHHHHHHHHHHHH---HHHhccCCCCCeEEEEECCCCCcHHHHHHHHHHHhCCCEEEEeCHHHhcCCchHHH
Confidence            456777766666665422221   1222334566789999999999999999999999999999998764 222      


Q ss_pred             hHHHHHHHHhh--cCCcEEEEecccccccCcc-----cccchhhhhhhcccccccccCCceEEEEecCCCccCcc-cccC
Q 011664          263 DADLKSLLLQT--TSKSVILIEDLDRFLVEKP-----AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ-ALLR  334 (480)
Q Consensus       263 ~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~-----~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~-aLlr  334 (480)
                      ...++.+|...  ..+++|||||||.+++.+.     ....+..|+..+++...  .....+||+|||.++.+++ ++++
T Consensus       110 ~~~~~~~~~~~~~~~~~vl~iDEid~l~~~~~~~~~~~~~~l~~L~~~~~~~~~--~~~~~~ii~ttn~~~~l~~~~l~~  187 (272)
T 1d2n_A          110 CQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPP--QGRKLLIIGTTSRKDVLQEMEMLN  187 (272)
T ss_dssp             HHHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCS--TTCEEEEEEEESCHHHHHHTTCTT
T ss_pred             HHHHHHHHHHHHhcCCcEEEEEChhhhhccCCCChhHHHHHHHHHHHHhcCccC--CCCCEEEEEecCChhhcchhhhhc
Confidence            13355666543  4689999999999865432     11223444455554432  1345678889999999998 5666


Q ss_pred             CCceeEEEEcCCCCH-HHHHHHHHHHhccCCCCCchhHHHHHHhCCCC----CHHHHHHHHHHhhh-cHHHHHHHHHHHH
Q 011664          335 PGRIDVHIHFPLCDF-SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSL----SPAEIGELMIANRN-SPSRALKSVITAL  408 (480)
Q Consensus       335 pGRfd~~I~~~~p~~-~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~----s~adI~~ll~~a~~-~~~~al~~~i~~~  408 (480)
                        ||+..|++|.++. ++...++....    .--...+..++..+.|+    ...++.+++..+.. .....++.++..+
T Consensus       188 --rf~~~i~~p~l~~r~~i~~i~~~~~----~~~~~~~~~l~~~~~g~~~~g~ir~l~~~l~~a~~~~~~~~~~~~~~~l  261 (272)
T 1d2n_A          188 --AFSTTIHVPNIATGEQLLEALELLG----NFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALL  261 (272)
T ss_dssp             --TSSEEEECCCEEEHHHHHHHHHHHT----CSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTSCGGGHHHHHHHHH
T ss_pred             --ccceEEcCCCccHHHHHHHHHHhcC----CCCHHHHHHHHHHhcCCCccccHHHHHHHHHHHhhhchHHHHHHHHHHH
Confidence              9999999988776 55555554421    11233556777776676    55666666655442 2334455555555


Q ss_pred             Hhc
Q 011664          409 QTD  411 (480)
Q Consensus       409 ~~~  411 (480)
                      +..
T Consensus       262 ~~~  264 (272)
T 1d2n_A          262 REE  264 (272)
T ss_dssp             HHT
T ss_pred             HHc
Confidence            443

>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=99.75  E-value=7.2e-18  Score=181.93  Aligned_cols=205  Identities=19%  Similarity=0.210  Sum_probs=131.8

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHH---
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDAD---  265 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~---  265 (480)
                      .++++|.+++++.+.+.+........      . ....+||+||||||||++|+++|+.++.++..++++.+.....   
T Consensus        80 ~~di~G~~~vk~~i~~~~~l~~~~~~------~-~g~~vll~Gp~GtGKTtlar~ia~~l~~~~~~i~~~~~~~~~~~~g  152 (543)
T 3m6a_A           80 DEEHHGLEKVKERILEYLAVQKLTKS------L-KGPILCLAGPPGVGKTSLAKSIAKSLGRKFVRISLGGVRDESEIRG  152 (543)
T ss_dssp             HHHCSSCHHHHHHHHHHHHHHHHSSS------C-CSCEEEEESSSSSSHHHHHHHHHHHHTCEEEEECCCC---------
T ss_pred             HHHhccHHHHHHHHHHHHHHHHhccc------C-CCCEEEEECCCCCCHHHHHHHHHHhcCCCeEEEEecccchhhhhhh
Confidence            46699999999998765543322111      1 3457999999999999999999999999999999876543221   


Q ss_pred             ------------HHHHHHhhc-CCcEEEEecccccccCcccccchhhhhhhccccccc----------ccCCceEEEEec
Q 011664          266 ------------LKSLLLQTT-SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS----------CCFEERVMVFTM  322 (480)
Q Consensus       266 ------------l~~l~~~~~-~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~----------~~~~~~ivI~tT  322 (480)
                                  +...|..+. ...|+||||||.+..... ....+.|+..||.....          .....++||+||
T Consensus       153 ~~~~~ig~~~~~~~~~~~~a~~~~~vl~lDEid~l~~~~~-~~~~~~LL~~ld~~~~~~~~~~~~~~~~~~~~v~iI~tt  231 (543)
T 3m6a_A          153 HRRTYVGAMPGRIIQGMKKAGKLNPVFLLDEIDKMSSDFR-GDPSSAMLEVLDPEQNSSFSDHYIEETFDLSKVLFIATA  231 (543)
T ss_dssp             -----------CHHHHHHTTCSSSEEEEEEESSSCC----------CCGGGTCTTTTTBCCCSSSCCCCBCSSCEEEEEC
T ss_pred             HHHHHhccCchHHHHHHHHhhccCCEEEEhhhhhhhhhhc-cCHHHHHHHHHhhhhcceeecccCCeeecccceEEEecc
Confidence                        233444432 345999999999976432 22457788888754321          011467899999


Q ss_pred             CCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHH--HHhCCCCCHHHHHHHHHH-hhhcHHH
Q 011664          323 NSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEI--FQNGSSLSPAEIGELMIA-NRNSPSR  399 (480)
Q Consensus       323 N~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l--~~~~~g~s~adI~~ll~~-a~~~~~~  399 (480)
                      |.++.++|+|++  ||+ .|+|+.|+.+++..|++.++-..      .....  ....-.+++..+..++.. .+....+
T Consensus       232 N~~~~l~~aL~~--R~~-vi~~~~~~~~e~~~Il~~~l~~~------~~~~~~~~~~~i~i~~~~l~~l~~~~~~~~~vR  302 (543)
T 3m6a_A          232 NNLATIPGPLRD--RME-IINIAGYTEIEKLEIVKDHLLPK------QIKEHGLKKSNLQLRDQAILDIIRYYTREAGVR  302 (543)
T ss_dssp             SSTTTSCHHHHH--HEE-EEECCCCCHHHHHHHHHHTHHHH------HHHHTTCCGGGCEECHHHHHHHHHHHCCCSSSH
T ss_pred             CccccCCHHHHh--hcc-eeeeCCCCHHHHHHHHHHHHHHH------HHHHcCCCcccccCCHHHHHHHHHhCChhhchh
Confidence            999999999999  996 79999999999999999887210      00000  001123456666665543 3344556


Q ss_pred             HHHHHHHHHHh
Q 011664          400 ALKSVITALQT  410 (480)
Q Consensus       400 al~~~i~~~~~  410 (480)
                      .+++.++.+..
T Consensus       303 ~L~~~i~~~~~  313 (543)
T 3m6a_A          303 SLERQLAAICR  313 (543)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            66655554443

>3uk6_A RUVB-like 2; hexameric AAA+ ATP-ASE, DNA unwinding, hydrolase; HET: ADP; 2.95A {Homo sapiens} PDB: 2xsz_D*

Probab=99.75  E-value=1.1e-17  Score=170.28  Aligned_cols=186  Identities=16%  Similarity=0.161  Sum_probs=124.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCCCcC-
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLSRVA-  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s~~~-  261 (480)
                      +..+|++++|.+.+++.+........        .|..+++++||+||||||||++|+++|+.++.  +++.+++..+. 
T Consensus        39 p~~~~~~ivG~~~~~~~l~~l~~~~~--------~~~~~~~~vLl~GppGtGKT~la~~la~~l~~~~~~~~~~~~~~~~  110 (368)
T 3uk6_A           39 PRQASQGMVGQLAARRAAGVVLEMIR--------EGKIAGRAVLIAGQPGTGKTAIAMGMAQALGPDTPFTAIAGSEIFS  110 (368)
T ss_dssp             BCSEETTEESCHHHHHHHHHHHHHHH--------TTCCTTCEEEEEESTTSSHHHHHHHHHHHHCSSCCEEEEEGGGGSC
T ss_pred             cCcchhhccChHHHHHHHHHHHHHHH--------cCCCCCCEEEEECCCCCCHHHHHHHHHHHhcccCCcccccchhhhh
Confidence            33459999999999988765443321        24445679999999999999999999999875  67777654311 


Q ss_pred             -------------------------------------------------C-----hHHHHHHHHhh-------c----CC
Q 011664          262 -------------------------------------------------D-----DADLKSLLLQT-------T----SK  276 (480)
Q Consensus       262 -------------------------------------------------~-----~~~l~~l~~~~-------~----~~  276 (480)
                                                                       +     ...++..+...       .    .|
T Consensus       111 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~g~~~~~~  190 (368)
T 3uk6_A          111 LEMSKTEALTQAFRRSIGVRIKAGAVHTVSLHEIDVINSRTQGFLALFSGDTGEIKSEVREQINAKVAEWREEGKAEIIP  190 (368)
T ss_dssp             SSSCHHHHHHHHHHHSBEECC------CEEHHHHHHHTC----CCSCC-------CHHHHHHHHHHHHHHHHHTC---CB
T ss_pred             cccchhHHHHHHHHHHHHHHhhhhccccccHhhhhhhhcccccchhhccCcccccHHHHHHHHHHHHHHhhhhccccccC
Confidence                                                             1     12233333221       1    26


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEec------------CCCccCcccccCCCceeEEEEc
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM------------NSKDHVDQALLRPGRIDVHIHF  344 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT------------N~~~~LD~aLlrpGRfd~~I~~  344 (480)
                      +||||||+|.+.     ....+.|+..++...     .. +++++|            |.+..++++|++  ||.. ++|
T Consensus       191 ~vl~IDEi~~l~-----~~~~~~L~~~le~~~-----~~-~~ii~t~~~~~~i~~t~~~~~~~l~~~l~s--R~~~-i~~  256 (368)
T 3uk6_A          191 GVLFIDEVHMLD-----IESFSFLNRALESDM-----AP-VLIMATNRGITRIRGTSYQSPHGIPIDLLD--RLLI-VST  256 (368)
T ss_dssp             CEEEEESGGGSB-----HHHHHHHHHHTTCTT-----CC-EEEEEESCSEEECBTSSCEEETTCCHHHHT--TEEE-EEE
T ss_pred             ceEEEhhccccC-----hHHHHHHHHHhhCcC-----CC-eeeeecccceeeeeccCCCCcccCCHHHHh--hccE-EEe
Confidence            899999999884     233455666554322     12 334333            357889999999  9976 899


Q ss_pred             CCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHH
Q 011664          345 PLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       345 ~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~  392 (480)
                      ++|+.+++..+++.++...+..+.++. +.++..+.+.++.++.++|..
T Consensus       257 ~~~~~~e~~~il~~~~~~~~~~~~~~~l~~l~~~~~~G~~r~~~~ll~~  305 (368)
T 3uk6_A          257 TPYSEKDTKQILRIRCEEEDVEMSEDAYTVLTRIGLETSLRYAIQLITA  305 (368)
T ss_dssp             CCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHHHSCHHHHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence            999999999999998876555555443 445444433566666666544

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=99.75  E-value=2.1e-17  Score=165.80  Aligned_cols=152  Identities=22%  Similarity=0.187  Sum_probs=118.6

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD  263 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~  263 (480)
                      -.|.+|++++|.+++++.+.+.+.            ....+..+|++||||||||++++++|++++.+++.++++... .
T Consensus        20 ~rP~~~~~ivg~~~~~~~l~~~l~------------~~~~~~~~L~~G~~G~GKT~la~~la~~l~~~~~~i~~~~~~-~   86 (324)
T 3u61_B           20 YRPSTIDECILPAFDKETFKSITS------------KGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDCK-I   86 (324)
T ss_dssp             SCCCSTTTSCCCHHHHHHHHHHHH------------TTCCCSEEEECSSTTSSHHHHHHHHHHHTTEEEEEEETTTCC-H
T ss_pred             hCCCCHHHHhCcHHHHHHHHHHHH------------cCCCCeEEEeeCcCCCCHHHHHHHHHHHhCCCEEEEcccccC-H
Confidence            467899999999999888876654            123456789999999999999999999999999999987754 4


Q ss_pred             HHHHHHHHh---h----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCC
Q 011664          264 ADLKSLLLQ---T----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPG  336 (480)
Q Consensus       264 ~~l~~l~~~---~----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpG  336 (480)
                      ..++..+..   .    ..+.||||||+|.+.+    ......|+..++...     ....+|+|||.+..++++|++  
T Consensus        87 ~~i~~~~~~~~~~~~~~~~~~vliiDEi~~l~~----~~~~~~L~~~le~~~-----~~~~iI~~~n~~~~l~~~l~s--  155 (324)
T 3u61_B           87 DFVRGPLTNFASAASFDGRQKVIVIDEFDRSGL----AESQRHLRSFMEAYS-----SNCSIIITANNIDGIIKPLQS--  155 (324)
T ss_dssp             HHHHTHHHHHHHBCCCSSCEEEEEEESCCCGGG----HHHHHHHHHHHHHHG-----GGCEEEEEESSGGGSCTTHHH--
T ss_pred             HHHHHHHHHHHhhcccCCCCeEEEEECCcccCc----HHHHHHHHHHHHhCC-----CCcEEEEEeCCccccCHHHHh--
Confidence            455554432   1    1578999999998841    223456666665432     356788899999999999999  


Q ss_pred             ceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          337 RIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       337 Rfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                      ||. .++|+.|+.+++..++..++
T Consensus       156 R~~-~i~~~~~~~~e~~~il~~~~  178 (324)
T 3u61_B          156 RCR-VITFGQPTDEDKIEMMKQMI  178 (324)
T ss_dssp             HSE-EEECCCCCHHHHHHHHHHHH
T ss_pred             hCc-EEEeCCCCHHHHHHHHHHHH
Confidence            995 79999999999888777664

>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=99.73  E-value=1.3e-17  Score=170.57  Aligned_cols=214  Identities=14%  Similarity=0.228  Sum_probs=140.0

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhh-hC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC------
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHR-LG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD------  262 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~-~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~------  262 (480)
                      .|+|++.+++.+...+............ .+ ...+.++||+||||||||++|+++|+.++.+++.++++.+..      
T Consensus        16 ~i~G~~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~vll~GppGtGKT~la~~ia~~~~~~~~~~~~~~l~~~~~~g~   95 (363)
T 3hws_A           16 YVIGQEQAKKVLAVAVYNHYKRLRNGDTSNGVELGKSNILLIGPTGSGKTLLAETLARLLDVPFTMADATTLTEAGYVGE   95 (363)
T ss_dssp             HCCSCHHHHHHHHHHHHHHHHHHHTTSCSSSCCCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHTTCHHHHH
T ss_pred             hccCHHHHHHHHHHHHHHHHhhhccccccccccCCCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEechHHhcccccccc
Confidence            3699999999999888755543321110 11 124678999999999999999999999999999999876553      


Q ss_pred             --hHHHHHHHHhh------cCCcEEEEecccccccCcccc---------cchhhhhhhccccccc---------------
Q 011664          263 --DADLKSLLLQT------TSKSVILIEDLDRFLVEKPAA---------VSLSGVLNFMDGVLNS---------------  310 (480)
Q Consensus       263 --~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~---------~~ls~lL~~ldg~~~~---------------  310 (480)
                        ...+..++...      ..++||||||||.+...+.+.         ...+.||..|+|....               
T Consensus        96 ~~~~~~~~~~~~~~~~~~~~~~~vl~lDEid~l~~~~~~~~~~~~~~~~~~~~~Ll~~leg~~~~~~~~~~~~~~~~~~~  175 (363)
T 3hws_A           96 DVENIIQKLLQKCDYDVQKAQRGIVYIDQIDKISRKSDNPSITRDVSGEGVQQALLKLIEGTVAAVPPQGGRKHPQQEFL  175 (363)
T ss_dssp             HHTHHHHHHHHHTTTCHHHHHHCEEEEECHHHHCCCSSCC---CHHHHHHHHHHHHHHHHCC----------------CC
T ss_pred             cHHHHHHHHHHHhhhhHHhcCCcEEEEeChhhhcccccccccccccchHHHHHHHHHHhcCceeeccCccccccCCCceE
Confidence              12244555433      467899999999987654332         1578899999854210               


Q ss_pred             -ccCCceEEEEecCCC----------c------------------------------c-----CcccccCCCceeEEEEc
Q 011664          311 -CCFEERVMVFTMNSK----------D------------------------------H-----VDQALLRPGRIDVHIHF  344 (480)
Q Consensus       311 -~~~~~~ivI~tTN~~----------~------------------------------~-----LD~aLlrpGRfd~~I~~  344 (480)
                       ....++++|+|+|..          .                              .     +.|+|+.  ||+..+.+
T Consensus       176 ~i~tsn~~~i~~g~~~~l~~~i~~~~~~~~~~gf~~~~~~~~~~~~~~~l~~~v~~~~l~~~~~~~~l~~--R~~~~~~~  253 (363)
T 3hws_A          176 QVDTSKILFICGGAFAGLDKVISHRVETGSGIGFGATVKAKSDKASEGELLAQVEPEDLIKFGLIPEFIG--RLPVVATL  253 (363)
T ss_dssp             CCCTTSSEEEEEECCTTHHHHHHHHHCCCC------------CCSCHHHHHHTCCHHHHHHHTCCHHHHT--TCCEEEEC
T ss_pred             EEECCCceEEecCCcHHHHHHHHHhhhccccCCccccccccccchhhHHHHHhCCHHHHHHcCCCHHHhc--ccCeeeec
Confidence             012334455554431          1                              1     6788887  99999999


Q ss_pred             CCCCHHHHHHHHHHHhccCCCCCchhHHHHHHh---CCCCCHHHHHHHHHHh--hhcHHHHHHHHHHHHHh
Q 011664          345 PLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQN---GSSLSPAEIGELMIAN--RNSPSRALKSVITALQT  410 (480)
Q Consensus       345 ~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~---~~g~s~adI~~ll~~a--~~~~~~al~~~i~~~~~  410 (480)
                      ++|+.+.+..|+...+.    .+...+......   ...+++..+..++..+  +....|.|+++++..-.
T Consensus       254 ~pl~~~~~~~I~~~~~~----~l~~~~~~~~~~~~~~l~~~~~a~~~L~~~~~~~~~gaR~L~~~ie~~~~  320 (363)
T 3hws_A          254 NELSEEALIQILKEPKN----ALTKQYQALFNLEGVDLEFRDEALDAIAKKAMARKTGARGLRSIVEAALL  320 (363)
T ss_dssp             CCCCHHHHHHHHHSSTT----CHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTTTTHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH----HHHHHHHHHHHhcCceEEECHHHHHHHHHhhcCCccCchHHHHHHHHHHH
Confidence            99999999999876331    111222222221   1246777777777543  23334667776665543

>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=99.73  E-value=1.2e-16  Score=150.55  Aligned_cols=181  Identities=18%  Similarity=0.276  Sum_probs=127.4

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-------------  250 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------  250 (480)
                      ..|.+|++++|.++.++.+.+.+..           + ..++.++|+||||||||++++++++.++.             
T Consensus        17 ~~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~   84 (250)
T 1njg_A           17 WRPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCD   84 (250)
T ss_dssp             TCCCSGGGCCSCHHHHHHHHHHHHH-----------T-CCCSEEEEECSTTSCHHHHHHHHHHHHHCTTCSCSSCCSCSH
T ss_pred             cCCccHHHHhCcHHHHHHHHHHHHc-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhcCCCCCCCCCCcccH
Confidence            3577899999999999888766542           1 12457999999999999999999987643             


Q ss_pred             -----------cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccC
Q 011664          251 -----------DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCF  313 (480)
Q Consensus       251 -----------~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~  313 (480)
                                 +++.++.........++.++...      ..+.+|+|||+|.+.     ......|+..++..     .
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vlviDe~~~l~-----~~~~~~l~~~l~~~-----~  154 (250)
T 1njg_A           85 NCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS-----RHSFNALLKTLEEP-----P  154 (250)
T ss_dssp             HHHHHHTTCCSSEEEEETTCGGGHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC-----HHHHHHHHHHHHSC-----C
T ss_pred             HHHHHhccCCcceEEecCcccccHHHHHHHHHHhhhchhcCCceEEEEECccccc-----HHHHHHHHHHHhcC-----C
Confidence                       34555544333344466666543      257899999999873     23445666666532     3


Q ss_pred             CceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHH
Q 011664          314 EERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       314 ~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll  390 (480)
                      ...++|++||.+..+++++++  |+ ..+++++++.++..+++..++...+..+.++ ++.++..+.| .|.++.+++
T Consensus       155 ~~~~~i~~t~~~~~~~~~l~~--r~-~~i~l~~l~~~e~~~~l~~~~~~~~~~~~~~~~~~l~~~~~G-~~~~~~~~~  228 (250)
T 1njg_A          155 EHVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEG-SLRDALSLT  228 (250)
T ss_dssp             TTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHHHTT-CHHHHHHHH
T ss_pred             CceEEEEEeCChHhCCHHHHH--Hh-hhccCCCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHcCC-CHHHHHHHH
Confidence            467888899999999999998  86 6899999999999999998886544444332 3445555433 555555544

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=99.72  E-value=3.3e-16  Score=165.03  Aligned_cols=187  Identities=14%  Similarity=0.247  Sum_probs=126.4

Q ss_pred             CCCCccccccChHHH---HHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          185 HPSTFDTISMETDLK---NRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k---~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      .|.+|++++|++.++   +.+...+..           |.  ..++|||||||||||++|+++|+.++.+++.+++... 
T Consensus        21 rP~~l~~ivGq~~~~~~~~~L~~~i~~-----------~~--~~~vLL~GppGtGKTtlAr~ia~~~~~~f~~l~a~~~-   86 (447)
T 3pvs_A           21 RPENLAQYIGQQHLLAAGKPLPRAIEA-----------GH--LHSMILWGPPGTGKTTLAEVIARYANADVERISAVTS-   86 (447)
T ss_dssp             CCCSTTTCCSCHHHHSTTSHHHHHHHH-----------TC--CCEEEEECSTTSSHHHHHHHHHHHTTCEEEEEETTTC-
T ss_pred             CCCCHHHhCCcHHHHhchHHHHHHHHc-----------CC--CcEEEEECCCCCcHHHHHHHHHHHhCCCeEEEEeccC-
Confidence            578999999999888   555544431           21  2589999999999999999999999999999997653 


Q ss_pred             ChHHHHHHHHhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEec--CCCccCccccc
Q 011664          262 DDADLKSLLLQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM--NSKDHVDQALL  333 (480)
Q Consensus       262 ~~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT--N~~~~LD~aLl  333 (480)
                      +...++.++..+      ..+.||||||||.+...     ....|+..++.       ..+++|++|  |....++++|+
T Consensus        87 ~~~~ir~~~~~a~~~~~~~~~~iLfIDEI~~l~~~-----~q~~LL~~le~-------~~v~lI~att~n~~~~l~~aL~  154 (447)
T 3pvs_A           87 GVKEIREAIERARQNRNAGRRTILFVDEVHRFNKS-----QQDAFLPHIED-------GTITFIGATTENPSFELNSALL  154 (447)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCEEEEEETTTCC-----------CCHHHHHT-------TSCEEEEEESSCGGGSSCHHHH
T ss_pred             CHHHHHHHHHHHHHhhhcCCCcEEEEeChhhhCHH-----HHHHHHHHHhc-------CceEEEecCCCCcccccCHHHh
Confidence            345566665432      36899999999988432     33557777653       235566654  45568999999


Q ss_pred             CCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHH
Q 011664          334 RPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITAL  408 (480)
Q Consensus       334 rpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~  408 (480)
                      +  |+. ++.++.|+.++...++..++......+.       .....+++..+..++..+.. ..+.+..+++.+
T Consensus       155 s--R~~-v~~l~~l~~edi~~il~~~l~~~~~~~~-------~~~~~i~~~al~~L~~~~~G-d~R~lln~Le~a  218 (447)
T 3pvs_A          155 S--RAR-VYLLKSLSTEDIEQVLTQAMEDKTRGYG-------GQDIVLPDETRRAIAELVNG-DARRALNTLEMM  218 (447)
T ss_dssp             T--TEE-EEECCCCCHHHHHHHHHHHHHCTTTSST-------TSSEECCHHHHHHHHHHHCS-CHHHHHHHHHHH
T ss_pred             C--cee-EEeeCCcCHHHHHHHHHHHHHHHhhhhc-------cccCcCCHHHHHHHHHHCCC-CHHHHHHHHHHH
Confidence            9  986 7889999999999999999865322211       01123566656555554333 333334444433

>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=99.70  E-value=2.7e-16  Score=168.55  Aligned_cols=187  Identities=19%  Similarity=0.298  Sum_probs=129.0

Q ss_pred             cceeCCCCCCCCccccccChHHHHHHHHHHHHHHhh-hhHHhhhCC---CCCceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          177 RWRSVPFTHPSTFDTISMETDLKNRVKSDLESFLKA-KHYYHRLGR---VWKRSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       177 ~w~~v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~-~~~~~~~g~---~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      .|..  .-.|.+|++++|.+++++.+.+.+..+... +..|...|.   +.++++||+||||||||++|+++|++++.++
T Consensus        28 lW~e--kyrP~~~~dliG~~~~~~~L~~~l~~~~~~~~~~~~~~g~~~~~~~~~lLL~GppGtGKTtla~~la~~l~~~~  105 (516)
T 1sxj_A           28 LWTV--KYAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDI  105 (516)
T ss_dssp             CHHH--HTCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEE
T ss_pred             Cccc--ccCCCCHHHhcCCHHHHHHHHHHHHHhHhhchhhccccCccCCCCCcEEEEECCCCCCHHHHHHHHHHHcCCCE
Confidence            5643  346789999999999999999888765433 233444443   2567999999999999999999999999999


Q ss_pred             EEEeCCCcCChHHHHHHHH-------------h-------hcCCcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          253 YDVDLSRVADDADLKSLLL-------------Q-------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       253 ~~i~~s~~~~~~~l~~l~~-------------~-------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                      +.++++.......+...+.             .       ...++||||||+|.+....  ...+..|++.++..     
T Consensus       106 i~in~s~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~vliIDEid~l~~~~--~~~l~~L~~~l~~~-----  178 (516)
T 1sxj_A          106 LEQNASDVRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD--RGGVGQLAQFCRKT-----  178 (516)
T ss_dssp             EEECTTSCCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS--TTHHHHHHHHHHHC-----
T ss_pred             EEEeCCCcchHHHHHHHHHHHhccccHHHHHhhhhhhhhccCCCeEEEEECCCccchhh--HHHHHHHHHHHHhc-----
Confidence            9999988776543333221             1       1467899999999986532  22345555555431     


Q ss_pred             CCceEEEEecC--CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhC
Q 011664          313 FEERVMVFTMN--SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNG  378 (480)
Q Consensus       313 ~~~~ivI~tTN--~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~  378 (480)
                       ... +|+++|  ....+. .+.|  | ...+.|+.|+.+++.+++...+...+..+.++ ++.+++.+
T Consensus       179 -~~~-iIli~~~~~~~~l~-~l~~--r-~~~i~f~~~~~~~~~~~L~~i~~~~~~~i~~~~l~~la~~s  241 (516)
T 1sxj_A          179 -STP-LILICNERNLPKMR-PFDR--V-CLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTT  241 (516)
T ss_dssp             -SSC-EEEEESCTTSSTTG-GGTT--T-SEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHT
T ss_pred             -CCC-EEEEEcCCCCccch-hhHh--c-eEEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc
Confidence             222 333333  333444 3544  4 46999999999999999988876655555554 45666655

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=99.70  E-value=1.2e-17  Score=152.23  Aligned_cols=150  Identities=19%  Similarity=0.246  Sum_probs=105.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|.+|++++|.++..+.+.+.+..             ..+++++|+||||||||++++++|+.+          +.+++.
T Consensus        17 ~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~~ll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~~   83 (195)
T 1jbk_A           17 EQGKLDPVIGRDEEIRRTIQVLQR-------------RTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLA   83 (195)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             hhccccccccchHHHHHHHHHHhc-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhCCCchhhcCCcEEE
Confidence            356789999999888877764421             235689999999999999999999986          788888


Q ss_pred             EeCCCcCC--------hHHHHHHHH---hhcCCcEEEEecccccccCccc--ccchhhhhhhcccccccccCCceEEEEe
Q 011664          255 VDLSRVAD--------DADLKSLLL---QTTSKSVILIEDLDRFLVEKPA--AVSLSGVLNFMDGVLNSCCFEERVMVFT  321 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~---~~~~~sII~IDEiD~l~~~~~~--~~~ls~lL~~ldg~~~~~~~~~~ivI~t  321 (480)
                      ++++.+..        ...+..++.   +...++||+|||+|.+......  ...+..++..+   ..   ..+..+|++
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~l~~~---~~---~~~~~~i~~  157 (195)
T 1jbk_A           84 LDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGAMDAGNMLKPA---LA---RGELHCVGA  157 (195)
T ss_dssp             ECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------CCCCHHHHHHH---HH---TTSCCEEEE
T ss_pred             eeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeEEEEeCHHHHhccCcccchHHHHHHHHHh---hc---cCCeEEEEe
Confidence            88765431        122444443   3456889999999998654321  12222333222   12   245667888


Q ss_pred             cCCCc-----cCcccccCCCceeEEEEcCCCCHHHHHHHH
Q 011664          322 MNSKD-----HVDQALLRPGRIDVHIHFPLCDFSSFKTLA  356 (480)
Q Consensus       322 TN~~~-----~LD~aLlrpGRfd~~I~~~~p~~~~r~~il  356 (480)
                      ||.++     .+++++++  ||+ .|++++|+.+++.+|+
T Consensus       158 ~~~~~~~~~~~~~~~l~~--r~~-~i~~~~p~~~~~~~il  194 (195)
T 1jbk_A          158 TTLDEYRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             ECHHHHHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             CCHHHHHHHHhcCHHHHH--Hhc-eeecCCCCHHHHHHHh
Confidence            88776     78999999  998 7999999999988764

>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=99.69  E-value=2e-16  Score=157.01  Aligned_cols=170  Identities=16%  Similarity=0.193  Sum_probs=123.7

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEe
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVD  256 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~  256 (480)
                      ....|.+|++++|.+++++.+...+..           +. .+ ++|||||||||||++|+++|+.+     +.+++.++
T Consensus         9 ~k~~p~~~~~~~g~~~~~~~l~~~l~~-----------~~-~~-~~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~   75 (319)
T 2chq_A            9 EKYRPRTLDEVVGQDEVIQRLKGYVER-----------KN-IP-HLLFSGPPGTGKTATAIALARDLFGENWRDNFIEMN   75 (319)
T ss_dssp             TTTSCSSGGGSCSCHHHHHHHHTTTTT-----------TC-CC-CEEEESSSSSSHHHHHHHHHHHHHTTCHHHHCEEEE
T ss_pred             HhcCCCCHHHHhCCHHHHHHHHHHHhC-----------CC-CC-eEEEECcCCcCHHHHHHHHHHHhcCCcccCCeEEEe
Confidence            345778999999999998887754421           21 22 49999999999999999999986     34688888


Q ss_pred             CCCcCChHHHHHHH---Hhh-----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          257 LSRVADDADLKSLL---LQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       257 ~s~~~~~~~l~~l~---~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      ++...+...++..+   ...     ..+.||+|||+|.+..     .....|+..++..     ....++|++||.+..+
T Consensus        76 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~-----~~~~~L~~~le~~-----~~~~~~i~~~~~~~~l  145 (319)
T 2chq_A           76 ASDERGIDVVRHKIKEFARTAPIGGAPFKIIFLDEADALTA-----DAQAALRRTMEMY-----SKSCRFILSCNYVSRI  145 (319)
T ss_dssp             TTSTTCTTTSSHHHHHHHHSCCSSSCCCEEEEEETGGGSCH-----HHHHTTGGGTSSS-----SSSEEEEEEESCGGGS
T ss_pred             CccccChHHHHHHHHHHHhcCCCCCCCceEEEEeCCCcCCH-----HHHHHHHHHHHhc-----CCCCeEEEEeCChhhc
Confidence            87654433333222   211     3478999999998742     2345566666542     3467788899999999


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHh
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQN  377 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~  377 (480)
                      ++++.+  |+. .+.+++|+.++...++..++...+..+.++. +.++..
T Consensus       146 ~~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~  192 (319)
T 2chq_A          146 IEPIQS--RCA-VFRFKPVPKEAMKKRLLEICEKEGVKITEDGLEALIYI  192 (319)
T ss_dssp             CHHHHT--TCE-EEECCCCCHHHHHHHHHHHHHTTCCCBCHHHHHHHHHT
T ss_pred             chHHHh--hCe-EEEecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence            999999  886 8999999999999999988876665555433 444443

>4fcw_A Chaperone protein CLPB; AAA domain; HET: ADP; 2.35A {Thermus thermophilus} PDB: 4fcv_A* 4fd2_A* 4fct_A*

Probab=99.69  E-value=2e-16  Score=157.19  Aligned_cols=160  Identities=17%  Similarity=0.291  Sum_probs=115.0

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLK  267 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~  267 (480)
                      +++|.+.+++.+...+......-.   . ...+...+||+||||||||++|+++|+.+   +.+++.++++.+.......
T Consensus        18 ~i~G~~~~~~~l~~~i~~~~~~~~---~-~~~~~~~~ll~G~~GtGKt~la~~la~~~~~~~~~~~~~~~~~~~~~~~~~   93 (311)
T 4fcw_A           18 RVVGQDEAIRAVADAIRRARAGLK---D-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAVS   93 (311)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHTCS---C-TTSCSEEEEEESCSSSSHHHHHHHHHHHHHSCGGGEEEEEGGGCCSTTHHH
T ss_pred             hcCCHHHHHHHHHHHHHHHhcCCC---C-CCCCceEEEEECCCCcCHHHHHHHHHHHHcCCCcceEEeecccccccccHH
Confidence            577899999998887765432110   0 11133479999999999999999999987   5569999988765543322


Q ss_pred             HHH------------------HhhcCCcEEEEecccccccCcccccchhhhhhhccccccc------ccCCceEEEEecC
Q 011664          268 SLL------------------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNS------CCFEERVMVFTMN  323 (480)
Q Consensus       268 ~l~------------------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~------~~~~~~ivI~tTN  323 (480)
                      .++                  ......+||||||+|.+.     ....+.|+..|+.-.-.      ....+.++|+|||
T Consensus        94 ~l~g~~~~~~~~~~~~~~~~~~~~~~~~vl~lDEi~~l~-----~~~~~~Ll~~le~~~~~~~~~~~~~~~~~iiI~ttn  168 (311)
T 4fcw_A           94 RLIGAPPGYVGYEEGGQLTEAVRRRPYSVILFDAIEKAH-----PDVFNILLQMLDDGRLTDSHGRTVDFRNTVIIMTSN  168 (311)
T ss_dssp             HHHCCCTTSTTTTTCCHHHHHHHHCSSEEEEEETGGGSC-----HHHHHHHHHHHHHSEEECTTSCEEECTTEEEEEEES
T ss_pred             HhcCCCCccccccccchHHHHHHhCCCeEEEEeChhhcC-----HHHHHHHHHHHhcCEEEcCCCCEEECCCcEEEEecc
Confidence            222                  112345899999999873     23456677776532210      1123677899999


Q ss_pred             C--------------------------CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          324 S--------------------------KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       324 ~--------------------------~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      .                          ...++|+|++  ||+..+.+++|+.+++..|++.++.
T Consensus       169 ~~~~~i~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~--R~~~~~~~~p~~~~~~~~i~~~~l~  230 (311)
T 4fcw_A          169 LGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQMS  230 (311)
T ss_dssp             TTHHHHHTTTTSCCCSSTHHHHTHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHTH
T ss_pred             cCHHHHHhhhcccccHHHHHHHHHHHHHHhCCHHHHh--cCCeEEEeCCCCHHHHHHHHHHHHH
Confidence            8                          5578899998  9999999999999999999998875

>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=99.68  E-value=1.8e-16  Score=159.32  Aligned_cols=191  Identities=15%  Similarity=0.200  Sum_probs=128.7

Q ss_pred             CCCCCCCccccc-cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          182 PFTHPSTFDTIS-METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       182 ~~~~~~~~~~i~-g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      ++.+..+|++++ |..... .. ..+......+      + ....+++||||||||||++++++++++   +.+++++++
T Consensus         3 ~l~~~~~f~~fv~g~~~~~-a~-~~~~~~~~~~------~-~~~~~lll~G~~GtGKT~la~~i~~~~~~~~~~~~~i~~   73 (324)
T 1l8q_A            3 FLNPKYTLENFIVGEGNRL-AY-EVVKEALENL------G-SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSA   73 (324)
T ss_dssp             CCCTTCCSSSCCCCTTTHH-HH-HHHHHHHHTT------T-TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEH
T ss_pred             CCCCCCCcccCCCCCcHHH-HH-HHHHHHHhCc------C-CCCCeEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEH
Confidence            355677899997 543322 11 2233333332      1 134689999999999999999999988   899999998


Q ss_pred             CCcCChH-------HHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc---c
Q 011664          258 SRVADDA-------DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD---H  327 (480)
Q Consensus       258 s~~~~~~-------~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~---~  327 (480)
                      ..+..+-       ...........+++|||||+|.+...+.   ....++..++....   .+.++|+.+++.+.   .
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~iDEi~~l~~~~~---~~~~l~~~l~~~~~---~~~~iii~~~~~~~~l~~  147 (324)
T 1l8q_A           74 DDFAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKER---TQIEFFHIFNTLYL---LEKQIILASDRHPQKLDG  147 (324)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTTCHH---HHHHHHHHHHHHHH---TTCEEEEEESSCGGGCTT
T ss_pred             HHHHHHHHHHHHcCcHHHHHHHhcCCCEEEEcCcccccCChH---HHHHHHHHHHHHHH---CCCeEEEEecCChHHHHH
Confidence            6653210       0111122234689999999999864322   23445555554433   34456666777776   6


Q ss_pred             CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHH
Q 011664          328 VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       328 LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~  392 (480)
                      ++++|++  ||+  ..+++++ +.+++..+++.++...+..+.+++ +.++...  -...++..++..
T Consensus       148 l~~~L~s--R~~~~~~i~l~~-~~~e~~~il~~~~~~~~~~l~~~~l~~l~~~~--g~~r~l~~~l~~  210 (324)
T 1l8q_A          148 VSDRLVS--RFEGGILVEIEL-DNKTRFKIIKEKLKEFNLELRKEVIDYLLENT--KNVREIEGKIKL  210 (324)
T ss_dssp             SCHHHHH--HHHTSEEEECCC-CHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHC--SSHHHHHHHHHH
T ss_pred             hhhHhhh--cccCceEEEeCC-CHHHHHHHHHHHHHhcCCCCCHHHHHHHHHhC--CCHHHHHHHHHH
Confidence            8999999  996  7899999 999999999999877676676654 5666665  556666666554

>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=99.67  E-value=1.5e-15  Score=155.93  Aligned_cols=213  Identities=15%  Similarity=0.234  Sum_probs=133.8

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhH------------------HhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHY------------------YHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~------------------~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      .|+|++++|+.|...+.........                  +.. ....+.++||+||||||||++|+++|+.++.++
T Consensus        22 ~viGq~~ak~~l~~~~~~~~~~~~~g~~~~~~~~~~~~~p~~~~~~-~~~~~~~ill~Gp~GtGKT~la~~la~~l~~~~  100 (376)
T 1um8_A           22 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEE-VELSKSNILLIGPTGSGKTLMAQTLAKHLDIPI  100 (376)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHH-TTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCE
T ss_pred             HccCcHHHHHHHHHHHHHHHHHHHhhhhhhhccccccccccccccc-cccCCCCEEEECCCCCCHHHHHHHHHHHhCCCE
Confidence            4799999999999888654443321                  111 123456899999999999999999999999999


Q ss_pred             EEEeCCCcCC--------hHHHHHHHHhh------cCCcEEEEecccccccCcccc---------cchhhhhhhcccccc
Q 011664          253 YDVDLSRVAD--------DADLKSLLLQT------TSKSVILIEDLDRFLVEKPAA---------VSLSGVLNFMDGVLN  309 (480)
Q Consensus       253 ~~i~~s~~~~--------~~~l~~l~~~~------~~~sII~IDEiD~l~~~~~~~---------~~ls~lL~~ldg~~~  309 (480)
                      +.++++.+..        ...+..++...      ..++||||||+|.+...+...         ...+.|+..|++..-
T Consensus       101 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~~~~~~~~~~~~~~~~~~~~~Ll~~le~~~~  180 (376)
T 1um8_A          101 AISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLV  180 (376)
T ss_dssp             EEEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHHHHCCEE
T ss_pred             EEecchhhhhcCcCCccHHHHHHHHHhhccchhhhcCCeEEEEcCHHHHhhhcCCCceecccchHHHHHHHHHHhhccce
Confidence            9999876542        12244444322      368999999999987653211         156778888875310


Q ss_pred             c----------------ccCCceEEEEecCC-----------------------------------------CccCcccc
Q 011664          310 S----------------CCFEERVMVFTMNS-----------------------------------------KDHVDQAL  332 (480)
Q Consensus       310 ~----------------~~~~~~ivI~tTN~-----------------------------------------~~~LD~aL  332 (480)
                      .                ....+.++|+|||.                                         ...+.|+|
T Consensus       181 ~~~~~~~~~~~~~~~~~i~t~n~~~I~~~~~~~l~~~l~~R~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~~~p~l  260 (376)
T 1um8_A          181 NIPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPEL  260 (376)
T ss_dssp             C---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHH
T ss_pred             ecccccccccCCcceEEEecCCeEEEecCCHHHHHHHHHHHhcccccCCCchhhhccchhHHHhhcCHHHHhhcCCChHH
Confidence            0                00134567777762                                         11245667


Q ss_pred             cCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHh---CCCCCHHHHHHHHHHhhh--cHHHHHHHHHHH
Q 011664          333 LRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQN---GSSLSPAEIGELMIANRN--SPSRALKSVITA  407 (480)
Q Consensus       333 lrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~---~~g~s~adI~~ll~~a~~--~~~~al~~~i~~  407 (480)
                      ++  |++..+.|++++.++...|+...+.    .+..++......   ...+++..+..++..+..  ...|.++.+++.
T Consensus       261 ~~--R~~~~i~~~~l~~~~l~~i~~~~~~----~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~~~~~~~~~R~L~~~le~  334 (376)
T 1um8_A          261 IG--RLPVLSTLDSISLEAMVDILQKPKN----ALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIED  334 (376)
T ss_dssp             HT--TCCEEEECCCCCHHHHHHHHHSSTT----CHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHH
T ss_pred             hc--CCCceeeccCCCHHHHHHHHhhhHH----HHHHHHHHHHhhcCceEEECHHHHHHHHHHhcccccCcHHHHHHHHH
Confidence            77  9988999999999998888864321    111122211111   124777777777766542  445666666655


Q ss_pred             HHh
Q 011664          408 LQT  410 (480)
Q Consensus       408 ~~~  410 (480)
                      +-.
T Consensus       335 ~~~  337 (376)
T 1um8_A          335 FCL  337 (376)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=99.66  E-value=2.4e-16  Score=149.63  Aligned_cols=189  Identities=13%  Similarity=0.136  Sum_probs=119.7

Q ss_pred             CCCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          181 VPFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       181 v~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      .++.++.+|+++++.+. .+.+.+.+..+...         +..++++|+||||||||++++++|+++   +.+++.+++
T Consensus        19 ~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~~---------~~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~   88 (242)
T 3bos_A           19 VHLPDDETFTSYYPAAG-NDELIGALKSAASG---------DGVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPL   88 (242)
T ss_dssp             CCCCTTCSTTTSCC--C-CHHHHHHHHHHHHT---------CSCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEG
T ss_pred             CCCCCCCChhhccCCCC-CHHHHHHHHHHHhC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEH
Confidence            34455679999988321 12233333333322         135689999999999999999999876   478888888


Q ss_pred             CCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC-CCc---cCccccc
Q 011664          258 SRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SKD---HVDQALL  333 (480)
Q Consensus       258 s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~~---~LD~aLl  333 (480)
                      +.+...  +...+.....+.+|+|||+|.+.....   ....++..++....   .....+|+||| .+.   .+++++.
T Consensus        89 ~~~~~~--~~~~~~~~~~~~vliiDe~~~~~~~~~---~~~~l~~~l~~~~~---~~~~~ii~~~~~~~~~~~~~~~~l~  160 (242)
T 3bos_A           89 GIHASI--STALLEGLEQFDLICIDDVDAVAGHPL---WEEAIFDLYNRVAE---QKRGSLIVSASASPMEAGFVLPDLV  160 (242)
T ss_dssp             GGGGGS--CGGGGTTGGGSSEEEEETGGGGTTCHH---HHHHHHHHHHHHHH---HCSCEEEEEESSCTTTTTCCCHHHH
T ss_pred             HHHHHH--HHHHHHhccCCCEEEEeccccccCCHH---HHHHHHHHHHHHHH---cCCCeEEEEcCCCHHHHHHhhhhhh
Confidence            765432  112233345789999999998854321   13445555554433   12232455444 443   4568888


Q ss_pred             CCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          334 RPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       334 rpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      +  ||.  ..+++++|+.+++.+++..++...+..+.++. +.++..+ +-+..++.+++
T Consensus       161 ~--r~~~~~~i~l~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~-~g~~r~l~~~l  217 (242)
T 3bos_A          161 S--RMHWGLTYQLQPMMDDEKLAALQRRAAMRGLQLPEDVGRFLLNRM-ARDLRTLFDVL  217 (242)
T ss_dssp             H--HHHHSEEEECCCCCGGGHHHHHHHHHHHTTCCCCHHHHHHHHHHT-TTCHHHHHHHH
T ss_pred             h--HhhcCceEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-cCCHHHHHHHH
Confidence            8  886  89999999999999999998875555555443 4455444 33445544444

>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=99.66  E-value=3.3e-16  Score=157.99  Aligned_cols=180  Identities=16%  Similarity=0.180  Sum_probs=128.0

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC------CcEEEEeC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS------YDVYDVDL  257 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~------~~~~~i~~  257 (480)
                      ..|.+|++++|.+++++.+...+.    .       |  ...++||+||||||||++++++|+.++      ..+..+++
T Consensus        31 ~~p~~~~~i~g~~~~~~~l~~~l~----~-------~--~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~   97 (353)
T 1sxj_D           31 YRPKNLDEVTAQDHAVTVLKKTLK----S-------A--NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNA   97 (353)
T ss_dssp             TCCSSTTTCCSCCTTHHHHHHHTT----C-------T--TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECS
T ss_pred             cCCCCHHHhhCCHHHHHHHHHHHh----c-------C--CCCEEEEECCCCCCHHHHHHHHHHHhCCCcccccceEEEcc
Confidence            367899999999999988775442    1       1  112499999999999999999999864      46888888


Q ss_pred             CCcCChHHHHHHH---Hhh---------------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEE
Q 011664          258 SRVADDADLKSLL---LQT---------------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMV  319 (480)
Q Consensus       258 s~~~~~~~l~~l~---~~~---------------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI  319 (480)
                      ++..+...++..+   ...               ..+.||+|||+|.+..     ...+.|+..|+...     ....+|
T Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDE~~~l~~-----~~~~~Ll~~le~~~-----~~~~~i  167 (353)
T 1sxj_D           98 SDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTA-----DAQSALRRTMETYS-----GVTRFC  167 (353)
T ss_dssp             SSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCH-----HHHHHHHHHHHHTT-----TTEEEE
T ss_pred             ccccchHHHHHHHHHHhhhcccccchhhcccCCCCCceEEEEECCCccCH-----HHHHHHHHHHHhcC-----CCceEE
Confidence            7765544443322   211               2456999999998843     23456777765432     345677


Q ss_pred             EecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          320 FTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       320 ~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ++||.+..+++++++  |+. .+.+++|+.++...++...+...+..+.++. +.++..+.| .+..+.+++
T Consensus       168 l~~~~~~~l~~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~~~~~i~~~~l~~l~~~~~G-~~r~~~~~l  235 (353)
T 1sxj_D          168 LICNYVTRIIDPLAS--QCS-KFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDISAG-DLRRGITLL  235 (353)
T ss_dssp             EEESCGGGSCHHHHH--HSE-EEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHHTSS-CHHHHHHHH
T ss_pred             EEeCchhhCcchhhc--cCc-eEEeCCCCHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCC-CHHHHHHHH
Confidence            788999999999999  996 8999999999999999988876665555543 455555433 344444443

>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=99.66  E-value=6.8e-16  Score=153.68  Aligned_cols=180  Identities=14%  Similarity=0.165  Sum_probs=126.3

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEeCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVDLS  258 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~~s  258 (480)
                      ..|.+|++++|.+++++.+...+..           |  ...++||+||||||||++|+++|+.+.     ..++.++++
T Consensus        19 ~~p~~~~~~~g~~~~~~~l~~~l~~-----------~--~~~~~ll~G~~G~GKT~la~~l~~~l~~~~~~~~~~~~~~~   85 (327)
T 1iqp_A           19 YRPQRLDDIVGQEHIVKRLKHYVKT-----------G--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNAS   85 (327)
T ss_dssp             TCCCSTTTCCSCHHHHHHHHHHHHH-----------T--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEETT
T ss_pred             cCCCCHHHhhCCHHHHHHHHHHHHc-----------C--CCCeEEEECcCCCCHHHHHHHHHHHhcCCcccCceEEeecc
Confidence            4678899999999999888765542           2  122599999999999999999999863     347888877


Q ss_pred             CcCChHHHHHHHH---hh-----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          259 RVADDADLKSLLL---QT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       259 ~~~~~~~l~~l~~---~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                      +..+...++..+.   ..     ..+.||+|||+|.+..     ...+.|+..++..     .....+|++||.+..+++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~~~~vliiDe~~~l~~-----~~~~~L~~~le~~-----~~~~~~i~~~~~~~~l~~  155 (327)
T 1iqp_A           86 DERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQ-----DAQQALRRTMEMF-----SSNVRFILSCNYSSKIIE  155 (327)
T ss_dssp             CHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCH-----HHHHHHHHHHHHT-----TTTEEEEEEESCGGGSCH
T ss_pred             ccCchHHHHHHHHHHHhhCCcCCCCCeEEEEeCCCcCCH-----HHHHHHHHHHHhc-----CCCCeEEEEeCCccccCH
Confidence            6443333333221   11     3578999999998742     2345566666542     345678889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      ++.+  |+. .+.|++++.++...++..++...+..+.++. +.++..+ +-++..+.+++
T Consensus       156 ~l~s--r~~-~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~-~g~~r~~~~~l  212 (327)
T 1iqp_A          156 PIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYIA-EGDMRRAINIL  212 (327)
T ss_dssp             HHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHHH-TTCHHHHHHHH
T ss_pred             HHHh--hCc-EEEecCCCHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHC-CCCHHHHHHHH
Confidence            9999  886 8999999999999999988766555444433 4444443 33444444443

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=99.65  E-value=7.5e-16  Score=155.10  Aligned_cols=152  Identities=17%  Similarity=0.140  Sum_probs=107.7

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLK  267 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~  267 (480)
                      .+++++|.+++++.+...+..               .+++||+||||||||++|+++|+.++.+++.++++......++.
T Consensus        25 ~~~~i~g~~~~~~~l~~~l~~---------------~~~vll~G~pGtGKT~la~~la~~~~~~~~~i~~~~~~~~~~l~   89 (331)
T 2r44_A           25 VGKVVVGQKYMINRLLIGICT---------------GGHILLEGVPGLAKTLSVNTLAKTMDLDFHRIQFTPDLLPSDLI   89 (331)
T ss_dssp             HTTTCCSCHHHHHHHHHHHHH---------------TCCEEEESCCCHHHHHHHHHHHHHTTCCEEEEECCTTCCHHHHH
T ss_pred             hccceeCcHHHHHHHHHHHHc---------------CCeEEEECCCCCcHHHHHHHHHHHhCCCeEEEecCCCCChhhcC
Confidence            357789999988877755432               24899999999999999999999999999999986433322221


Q ss_pred             HH--HH-------hhcC---CcEEEEecccccccCcccccchhhhhhhcccc-------cccccCCceEEEEecCCCc--
Q 011664          268 SL--LL-------QTTS---KSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV-------LNSCCFEERVMVFTMNSKD--  326 (480)
Q Consensus       268 ~l--~~-------~~~~---~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~-------~~~~~~~~~ivI~tTN~~~--  326 (480)
                      ..  +.       ....   .+||||||+|.+.+     ...+.|+..|+.-       .. ......++|+|+|..+  
T Consensus        90 g~~~~~~~~~~~~~~~g~l~~~vl~iDEi~~~~~-----~~~~~Ll~~l~~~~~~~~g~~~-~~~~~~~viat~np~~~~  163 (331)
T 2r44_A           90 GTMIYNQHKGNFEVKKGPVFSNFILADEVNRSPA-----KVQSALLECMQEKQVTIGDTTY-PLDNPFLVLATQNPVEQE  163 (331)
T ss_dssp             EEEEEETTTTEEEEEECTTCSSEEEEETGGGSCH-----HHHHHHHHHHHHSEEEETTEEE-ECCSSCEEEEEECTTCCS
T ss_pred             CceeecCCCCceEeccCcccccEEEEEccccCCH-----HHHHHHHHHHhcCceeeCCEEE-ECCCCEEEEEecCCCccc
Confidence            10  00       0112   37999999998732     3345555555421       11 1133456677777443  


Q ss_pred             ---cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhcc
Q 011664          327 ---HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       327 ---~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~  362 (480)
                         .++++|++  ||+.++++++|+.+++.+|++..+..
T Consensus       164 ~~~~l~~~l~~--Rf~~~i~i~~p~~~~~~~il~~~~~~  200 (331)
T 2r44_A          164 GTYPLPEAQVD--RFMMKIHLTYLDKESELEVMRRVSNM  200 (331)
T ss_dssp             CCCCCCHHHHT--TSSEEEECCCCCHHHHHHHHHHHHCT
T ss_pred             CcccCCHHHHh--heeEEEEcCCCCHHHHHHHHHhcccc
Confidence               38999999  99999999999999999999998764

>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=99.65  E-value=6.6e-15  Score=149.11  Aligned_cols=195  Identities=16%  Similarity=0.213  Sum_probs=138.1

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD  262 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~  262 (480)
                      .-.|.+|++++|.+.+++.+...+..-..       .| ..+..++|+||||||||+|++++|++++.++...+.+....
T Consensus        18 ~lr~~~l~~~~g~~~~~~~l~~~i~~~~~-------~~-~~~~~~ll~Gp~G~GKTTLa~~ia~~l~~~~~~~sg~~~~~   89 (334)
T 1in4_A           18 FLRPKSLDEFIGQENVKKKLSLALEAAKM-------RG-EVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVK   89 (334)
T ss_dssp             TTSCSSGGGCCSCHHHHHHHHHHHHHHHH-------HT-CCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCS
T ss_pred             HcCCccHHHccCcHHHHHHHHHHHHHHHh-------cC-CCCCeEEEECCCCCcHHHHHHHHHHHhCCCEEEEechHhcC
Confidence            34677999999998877776654433211       12 23457999999999999999999999999988877766666


Q ss_pred             hHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccc------ccc-------cCCceEEEEecCCCccCc
Q 011664          263 DADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL------NSC-------CFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       263 ~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~------~~~-------~~~~~ivI~tTN~~~~LD  329 (480)
                      ..++..++.....+.|+||||++.+..  .   ....|+..+....      ...       ......++.+||.+..|+
T Consensus        90 ~~~l~~~~~~~~~~~v~~iDE~~~l~~--~---~~e~L~~~~~~~~~~i~~~~~~~~~~i~~~l~~~~li~at~~~~~Ls  164 (334)
T 1in4_A           90 QGDMAAILTSLERGDVLFIDEIHRLNK--A---VEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLS  164 (334)
T ss_dssp             HHHHHHHHHHCCTTCEEEEETGGGCCH--H---HHHHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSC
T ss_pred             HHHHHHHHHHccCCCEEEEcchhhcCH--H---HHHHHHHHHHhcccceeeccCcccccccccCCCeEEEEecCCcccCC
Confidence            666766665556788999999998853  1   1122333332110      000       011245667899999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHHHHh
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      +++++  ||...+.+++++.+++.++++......+..+.++ +..++... +-++.++..++..+
T Consensus       165 ~~l~s--R~~l~~~Ld~~~~~~l~~iL~~~~~~~~~~~~~~~~~~ia~~~-~G~~R~a~~ll~~~  226 (334)
T 1in4_A          165 SPLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRS-RGTPRIAIRLTKRV  226 (334)
T ss_dssp             HHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTS-TTCHHHHHHHHHHH
T ss_pred             HHHHH--hcCceeeCCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhc-CCChHHHHHHHHHH
Confidence            99999  9998999999999999999998876555555554 45676665 44677777777654

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=99.65  E-value=3.1e-16  Score=159.47  Aligned_cols=191  Identities=14%  Similarity=0.117  Sum_probs=125.9

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLS  258 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s  258 (480)
                      .+++++|.++..+.+.+.+...+.         ...+++++|+||||||||++++++++.+         +..++.+++.
T Consensus        17 ~p~~~~gr~~~~~~l~~~l~~~~~---------~~~~~~vll~G~~G~GKT~l~~~~~~~~~~~~~~~~~~~~~~~i~~~   87 (387)
T 2v1u_A           17 VPDVLPHREAELRRLAEVLAPALR---------GEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVKPIYVNAR   87 (387)
T ss_dssp             CCSCCTTCHHHHHHHHHTTGGGTS---------SCCCCCEEECBCTTSSHHHHHHHHHHHHHHHHHHHTCCEEEEEEETT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHc---------CCCCCcEEEECCCCCCHHHHHHHHHHHHHHHHhccCCCeEEEEEECC
Confidence            458899999988888765533211         1245689999999999999999999988         7889999987


Q ss_pred             CcCChH----------------------H-HHHHHHh---hcCCcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          259 RVADDA----------------------D-LKSLLLQ---TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       259 ~~~~~~----------------------~-l~~l~~~---~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                      ...+..                      . +..++..   ...++||+|||+|.+.........+..+++.++....   
T Consensus        88 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDEi~~l~~~~~~~~~l~~l~~~~~~~~~---  164 (387)
T 2v1u_A           88 HRETPYRVASAIAEAVGVRVPFTGLSVGEVYERLVKRLSRLRGIYIIVLDEIDFLPKRPGGQDLLYRITRINQELGD---  164 (387)
T ss_dssp             TSCSHHHHHHHHHHHHSCCCCSSCCCHHHHHHHHHHHHTTSCSEEEEEEETTTHHHHSTTHHHHHHHHHHGGGCC-----
T ss_pred             cCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEccHhhhcccCCCChHHHhHhhchhhcCC---
Confidence            644321                      2 1222221   2347899999999986432123344555555443220   


Q ss_pred             CCceEEEEecCCC---ccCcccccCCCceeE-EEEcCCCCHHHHHHHHHHHhcc--CCCCCchh-HHHHHHhCC--CCCH
Q 011664          313 FEERVMVFTMNSK---DHVDQALLRPGRIDV-HIHFPLCDFSSFKTLASSYLGL--KDHKLFPQ-VEEIFQNGS--SLSP  383 (480)
Q Consensus       313 ~~~~ivI~tTN~~---~~LD~aLlrpGRfd~-~I~~~~p~~~~r~~il~~~l~~--~~~~l~~~-i~~l~~~~~--g~s~  383 (480)
                      ....++|++||.+   +.+++++.+  ||.. .++|++|+.++...+++..+..  .+..+.++ ++.++..+.  .-.+
T Consensus       165 ~~~~~~I~~t~~~~~~~~l~~~l~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~  242 (387)
T 2v1u_A          165 RVWVSLVGITNSLGFVENLEPRVKS--SLGEVELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDA  242 (387)
T ss_dssp             ---CEEEEECSCSTTSSSSCHHHHT--TTTSEECCBCCCCHHHHHHHHHHHHHHHBCTTTBCSSHHHHHHHHHHSSSCCH
T ss_pred             CceEEEEEEECCCchHhhhCHHHHh--cCCCeEEeeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhccCH
Confidence            2456788888877   778999999  9874 8999999999999999988753  23334333 344444432  1345


Q ss_pred             HHHHHHHHH
Q 011664          384 AEIGELMIA  392 (480)
Q Consensus       384 adI~~ll~~  392 (480)
                      ..+.++|..
T Consensus       243 r~~~~~l~~  251 (387)
T 2v1u_A          243 RRALDLLRV  251 (387)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            555555544

>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=99.65  E-value=1.6e-15  Score=150.78  Aligned_cols=180  Identities=12%  Similarity=0.158  Sum_probs=128.8

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLS  258 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s  258 (480)
                      ..|.+|++++|.++.++.+.+.+..           + ..+. +||+||||||||++|+++|+.+     +.+++.++++
T Consensus        15 ~~p~~~~~~~g~~~~~~~l~~~l~~-----------~-~~~~-~ll~G~~G~GKt~la~~l~~~l~~~~~~~~~~~~~~~   81 (323)
T 1sxj_B           15 YRPQVLSDIVGNKETIDRLQQIAKD-----------G-NMPH-MIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNAS   81 (323)
T ss_dssp             TCCSSGGGCCSCTHHHHHHHHHHHS-----------C-CCCC-EEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECTT
T ss_pred             cCCCCHHHHHCCHHHHHHHHHHHHc-----------C-CCCe-EEEECcCCCCHHHHHHHHHHHhcCCcccCCEEEecCc
Confidence            4678899999999999888765431           2 2233 9999999999999999999986     3568888887


Q ss_pred             CcCChHHHHHHHHhh--------c-CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          259 RVADDADLKSLLLQT--------T-SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       259 ~~~~~~~l~~l~~~~--------~-~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                      +..+...++.++...        . .+.||+|||+|.+..     .....|+..++..     ....++|++||.+..++
T Consensus        82 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~viiiDe~~~l~~-----~~~~~L~~~le~~-----~~~~~~il~~~~~~~l~  151 (323)
T 1sxj_B           82 DDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA-----GAQQALRRTMELY-----SNSTRFAFACNQSNKII  151 (323)
T ss_dssp             SCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH-----HHHHTTHHHHHHT-----TTTEEEEEEESCGGGSC
T ss_pred             cccChHHHHHHHHHHHhccccCCCCCceEEEEECcccCCH-----HHHHHHHHHHhcc-----CCCceEEEEeCChhhch
Confidence            765555565554321        2 378999999998742     2234566666432     34567888899999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll  390 (480)
                      +++.+  |+. .+.|++|+.++...++..++...+..+.++ ++.++..+ +-++..+.+++
T Consensus       152 ~~l~s--r~~-~i~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~-~G~~r~a~~~l  209 (323)
T 1sxj_B          152 EPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKLEDVKYTNDGLEAIIFTA-EGDMRQAINNL  209 (323)
T ss_dssp             HHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHH-TTCHHHHHHHH
T ss_pred             hHHHh--hce-EEeecCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHc-CCCHHHHHHHH
Confidence            99999  886 899999999999999998876555444443 34555544 33444444433

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=99.64  E-value=9.1e-17  Score=146.23  Aligned_cols=145  Identities=20%  Similarity=0.245  Sum_probs=99.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|.+|++++|.++..+.+.+.+..             ..++++||+||||||||++|+++|+.+          +.+++.
T Consensus        17 ~~~~~~~~~g~~~~~~~l~~~l~~-------------~~~~~vll~G~~G~GKT~la~~~~~~~~~~~~~~~~~~~~~~~   83 (187)
T 2p65_A           17 RAGKLDPVIGRDTEIRRAIQILSR-------------RTKNNPILLGDPGVGKTAIVEGLAIKIVQGDVPDSLKGRKLVS   83 (187)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHTS-------------SSSCEEEEESCGGGCHHHHHHHHHHHHHTTCSCTTTTTCEEEE
T ss_pred             hccccchhhcchHHHHHHHHHHhC-------------CCCCceEEECCCCCCHHHHHHHHHHHHHhcCCcchhcCCeEEE
Confidence            356799999999877777654421             235689999999999999999999986          778888


Q ss_pred             EeCCCcCC--------hHHHHHHHH---hhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC
Q 011664          255 VDLSRVAD--------DADLKSLLL---QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN  323 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~---~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN  323 (480)
                      ++++.+..        ...+..++.   ....+.+|+|||+|.+.+.+........+++.+..+..   ....++|++||
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDe~~~l~~~~~~~~~~~~~~~~l~~~~~---~~~~~ii~~~~  160 (187)
T 2p65_A           84 LDLSSLIAGAKYRGDFEERLKSILKEVQDAEGQVVMFIDEIHTVVGAGAVAEGALDAGNILKPMLA---RGELRCIGATT  160 (187)
T ss_dssp             ECHHHHHHHCCSHHHHHHHHHHHHHHHHHTTTSEEEEETTGGGGSSSSSSCTTSCCTHHHHHHHHH---TTCSCEEEEEC
T ss_pred             EeHHHhhcCCCchhHHHHHHHHHHHHHHhcCCceEEEEeCHHHhcccccccccchHHHHHHHHHHh---cCCeeEEEecC
Confidence            88655421        112344443   23467899999999987443211111222333322222   34567888888


Q ss_pred             CCc-----cCcccccCCCceeEEEEcCCCC
Q 011664          324 SKD-----HVDQALLRPGRIDVHIHFPLCD  348 (480)
Q Consensus       324 ~~~-----~LD~aLlrpGRfd~~I~~~~p~  348 (480)
                      .++     .+|+++++  ||+ .|+++.|+
T Consensus       161 ~~~~~~~~~~~~~l~~--R~~-~i~i~~p~  187 (187)
T 2p65_A          161 VSEYRQFIEKDKALER--RFQ-QILVEQPS  187 (187)
T ss_dssp             HHHHHHHTTTCHHHHH--HEE-EEECCSCC
T ss_pred             HHHHHHHHhccHHHHH--hcC-cccCCCCC
Confidence            765     68999999  998 59999986

>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=99.64  E-value=2.7e-15  Score=152.44  Aligned_cols=182  Identities=18%  Similarity=0.267  Sum_probs=131.5

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      .|.+|++++|.++.++.+...+..           | ..+..+||+||||||||++++++|+.++.              
T Consensus        11 rp~~~~~~vg~~~~~~~L~~~l~~-----------~-~~~~~~ll~G~~G~GKT~la~~la~~l~~~~~~~~~~~~~~~~   78 (373)
T 1jr3_A           11 RPQTFADVVGQEHVLTALANGLSL-----------G-RIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDN   78 (373)
T ss_dssp             CCCSTTTSCSCHHHHHHHHHHHHH-----------T-CCCSEEEEESCTTSSHHHHHHHHHHHHSCTTCSCSSCCSSSHH
T ss_pred             CCCchhhccCcHHHHHHHHHHHHh-----------C-CCCeEEEEECCCCCCHHHHHHHHHHHhCCCCCCCCCCCcccHH
Confidence            577899999999999888876532           1 23457999999999999999999997754              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhhc------CCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQTT------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~~------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+.-.+...++.++....      .+.||+|||+|.+.     ....+.|+..++..     ..
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~vliiDe~~~l~-----~~~~~~Ll~~le~~-----~~  148 (373)
T 1jr3_A           79 CREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS-----RHSFNALLKTLEEP-----PE  148 (373)
T ss_dssp             HHHHHTSCCSSCEEEETTCSCCSSCHHHHHHHTTSCCSSSSSEEEEEECGGGSC-----HHHHHHHHHHHHSC-----CS
T ss_pred             HHHHhccCCCceEEecccccCCHHHHHHHHHHHhhccccCCeEEEEEECcchhc-----HHHHHHHHHHHhcC-----CC
Confidence                      345555543233344566654432      46899999999873     23446677776542     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHHHH
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      ..++|++||.+..+.+++++  |+ ..+++++|+.++...++..++...+..+.++ ++.++..+ +-++.++.+++..
T Consensus       149 ~~~~Il~~~~~~~l~~~l~s--r~-~~i~~~~l~~~~~~~~l~~~~~~~~~~~~~~a~~~l~~~~-~G~~r~~~~~l~~  223 (373)
T 1jr3_A          149 HVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAA-EGSLRDALSLTDQ  223 (373)
T ss_dssp             SEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCCBCHHHHHHHHHHS-SSCHHHHHHHHHH
T ss_pred             ceEEEEEeCChHhCcHHHHh--he-eEeeCCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence            67888889999999999998  87 6899999999999999998886655555544 35566655 4466666665543

>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=99.64  E-value=9.9e-16  Score=161.12  Aligned_cols=193  Identities=14%  Similarity=0.230  Sum_probs=128.8

Q ss_pred             CCCCCCCccccc-cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEE
Q 011664          182 PFTHPSTFDTIS-METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDV  255 (480)
Q Consensus       182 ~~~~~~~~~~i~-g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i  255 (480)
                      ++.+..+|++++ |.....  ....+..+...+      +.  ..+++||||||||||+|++++|+++     +.+++++
T Consensus        97 ~l~~~~tfd~fv~g~~n~~--a~~~~~~~a~~~------~~--~~~lll~Gp~G~GKTtLa~aia~~l~~~~~~~~v~~v  166 (440)
T 2z4s_A           97 PLNPDYTFENFVVGPGNSF--AYHAALEVAKHP------GR--YNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYI  166 (440)
T ss_dssp             CCCTTCSGGGCCCCTTTHH--HHHHHHHHHHST------TS--SCCEEEECSSSSSHHHHHHHHHHHHHHHCCSSCEEEE
T ss_pred             CCCCCCChhhcCCCCchHH--HHHHHHHHHhCC------CC--CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEe
Confidence            455667899987 654432  222333333322      21  4689999999999999999999988     8889999


Q ss_pred             eCCCcCChH-------HHHHHHHhhc-CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          256 DLSRVADDA-------DLKSLLLQTT-SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       256 ~~s~~~~~~-------~l~~l~~~~~-~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                      ++..+..+-       ....+..... .++||||||+|.+.....   ....|+..++.+..   .+..+||.|.+.+..
T Consensus       167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vL~IDEi~~l~~~~~---~q~~l~~~l~~l~~---~~~~iIitt~~~~~~  240 (440)
T 2z4s_A          167 TSEKFLNDLVDSMKEGKLNEFREKYRKKVDILLIDDVQFLIGKTG---VQTELFHTFNELHD---SGKQIVICSDREPQK  240 (440)
T ss_dssp             EHHHHHHHHHHHHHTTCHHHHHHHHTTTCSEEEEECGGGGSSCHH---HHHHHHHHHHHHHT---TTCEEEEEESSCGGG
T ss_pred             eHHHHHHHHHHHHHcccHHHHHHHhcCCCCEEEEeCcccccCChH---HHHHHHHHHHHHHH---CCCeEEEEECCCHHH
Confidence            876653210       0111122234 789999999999864322   33455555554433   234455545455655


Q ss_pred             ---CcccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHHHHh
Q 011664          328 ---VDQALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       328 ---LD~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll~~a  393 (480)
                         ++++|++  ||+  ..+.+++|+.+++..+++..+...+..+.+++ +.++... +-++.++..++..+
T Consensus       241 l~~l~~~L~s--R~~~g~~i~l~~p~~e~r~~iL~~~~~~~~~~i~~e~l~~la~~~-~gn~R~l~~~L~~~  309 (440)
T 2z4s_A          241 LSEFQDRLVS--RFQMGLVAKLEPPDEETRKSIARKMLEIEHGELPEEVLNFVAENV-DDNLRRLRGAIIKL  309 (440)
T ss_dssp             CSSCCHHHHH--HHHSSBCCBCCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHC-CSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHh--hccCCeEEEeCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhc-CCCHHHHHHHHHHH
Confidence               7899999  996  78999999999999999998876566666554 5666655 45777777766543

>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=99.61  E-value=7.6e-15  Score=143.12  Aligned_cols=199  Identities=14%  Similarity=0.111  Sum_probs=124.3

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEeCCCcCCh
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVDLSRVADD  263 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~~s~~~~~  263 (480)
                      .+|++++|.+...+.+.+.+.....           .+.++||+||||||||++|+++++.+.   .+++.++++.+..+
T Consensus         3 ~~f~~~ig~~~~~~~~~~~~~~~~~-----------~~~~vll~G~~GtGKt~la~~i~~~~~~~~~~~~~v~~~~~~~~   71 (265)
T 2bjv_A            3 EYKDNLLGEANSFLEVLEQVSHLAP-----------LDKPVLIIGERGTGKELIASRLHYLSSRWQGPFISLNCAALNEN   71 (265)
T ss_dssp             -------CCCHHHHHHHHHHHHHTT-----------SCSCEEEECCTTSCHHHHHHHHHHTSTTTTSCEEEEEGGGSCHH
T ss_pred             cccccceeCCHHHHHHHHHHHHHhC-----------CCCCEEEECCCCCcHHHHHHHHHHhcCccCCCeEEEecCCCChh
Confidence            4799999999999988877765432           245899999999999999999999875   68999999887432


Q ss_pred             HHHHHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-cc-----ccCCceEEEE
Q 011664          264 ADLKSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NS-----CCFEERVMVF  320 (480)
Q Consensus       264 ~~l~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~-----~~~~~~ivI~  320 (480)
                      .-...+|.                 ....+++|||||||.+..     .....|+..++.-. ..     .......+|+
T Consensus        72 ~~~~~l~g~~~~~~~g~~~~~~~~l~~a~~~~l~lDEi~~l~~-----~~q~~Ll~~l~~~~~~~~g~~~~~~~~~~iI~  146 (265)
T 2bjv_A           72 LLDSELFGHEAGAFTGAQKRHPGRFERADGGTLFLDELATAPM-----MVQEKLLRVIEYGELERVGGSQPLQVNVRLVC  146 (265)
T ss_dssp             HHHHHHHCCC---------CCCCHHHHTTTSEEEEESGGGSCH-----HHHHHHHHHHHHCEECCCCC--CEECCCEEEE
T ss_pred             HHHHHhcCCcccccccccccccchhhhcCCcEEEEechHhcCH-----HHHHHHHHHHHhCCeecCCCcccccCCeEEEE
Confidence            11112221                 113468999999998843     23345666554211 00     0013456888


Q ss_pred             ecCCC-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhC-CCCCHHHHHHH
Q 011664          321 TMNSK-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNG-SSLSPAEIGEL  389 (480)
Q Consensus       321 tTN~~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~-~g~s~adI~~l  389 (480)
                      |||.+       ..++++|.+  ||. ..|.+|+.+.  ++...+++.++....       ....... ..+++..+..+
T Consensus       147 atn~~~~~~~~~~~~~~~L~~--Rl~~~~i~lp~L~~R~~di~~l~~~~l~~~~-------~~~~~~~~~~~~~~a~~~L  217 (265)
T 2bjv_A          147 ATNADLPAMVNEGTFRADLLD--ALAFDVVQLPPLRERESDIMLMAEYFAIQMC-------REIKLPLFPGFTERARETL  217 (265)
T ss_dssp             EESSCHHHHHHHTSSCHHHHH--HHCSEEEECCCGGGCHHHHHHHHHHHHHHHH-------HHTTCSSCCCBCHHHHHHH
T ss_pred             ecCcCHHHHHHcCCccHHHHH--hhcCcEEeCCChhhhhHHHHHHHHHHHHHHH-------HHhCCCcccCcCHHHHHHH
Confidence            88864       246788988  996 5677776654  455666666553110       0000001 26788777777


Q ss_pred             HHHhhhcHHHHHHHHHHHHHh
Q 011664          390 MIANRNSPSRALKSVITALQT  410 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~  410 (480)
                      +...+....+.++.+++.+..
T Consensus       218 ~~~~~~gn~reL~~~l~~~~~  238 (265)
T 2bjv_A          218 LNYRWPGNIRELKNVVERSVY  238 (265)
T ss_dssp             HHSCCTTHHHHHHHHHHHHHH
T ss_pred             HhCCCCCCHHHHHHHHHHHHH
Confidence            766667778888888776643

>3pxg_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 3.65A {Bacillus subtilis}

Probab=99.60  E-value=8.4e-15  Score=155.18  Aligned_cols=176  Identities=16%  Similarity=0.175  Sum_probs=117.2

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|.+|++++|.++..+.+.+.+..             ..+.++||+||||||||++|+++|+.+          +.+++.
T Consensus       175 r~~~ld~iiGr~~~i~~l~~~l~r-------------~~~~~~LL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~  241 (468)
T 3pxg_A          175 KEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMT  241 (468)
T ss_dssp             TSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEEC
T ss_pred             hcCCCCCccCcHHHHHHHHHHHhc-------------cCCCCeEEECCCCCCHHHHHHHHHHHHHhCCCChhhcCCeEEE
Confidence            466899999999988887765431             235689999999999999999999986          788999


Q ss_pred             EeCCC-cCC--hHHHHHHHHhh--cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc---
Q 011664          255 VDLSR-VAD--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD---  326 (480)
Q Consensus       255 i~~s~-~~~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~---  326 (480)
                      ++++. +.+  +..++.+|...  ..++|||||         ......+.|+..|+       .....+|+|||.++   
T Consensus       242 l~~~~~~~g~~e~~~~~~~~~~~~~~~~iLfiD---------~~~~a~~~L~~~L~-------~g~v~vI~at~~~e~~~  305 (468)
T 3pxg_A          242 LDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID---------AAIDASNILKPSLA-------RGELQCIGATTLDEYRK  305 (468)
T ss_dssp             C----------CTTHHHHHHHHHTCCCCEEEEC---------C--------CCCTT-------SSSCEEEEECCTTTTHH
T ss_pred             eeCCccccchHHHHHHHHHHHHHhcCCeEEEEe---------CchhHHHHHHHhhc-------CCCEEEEecCCHHHHHH
Confidence            88862 222  23456666543  468999999         11112233444332       34577888998876   


Q ss_pred             --cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhcc----CCCCCchhH-HHHHHh-----CCCCCHHHHHHHHHH
Q 011664          327 --HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGL----KDHKLFPQV-EEIFQN-----GSSLSPAEIGELMIA  392 (480)
Q Consensus       327 --~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~----~~~~l~~~i-~~l~~~-----~~g~s~adI~~ll~~  392 (480)
                        .+|++|+|  ||. .|.|+.|+.+++..|++.++..    .+..+.++. ..++..     ...+.|.....++..
T Consensus       306 ~~~~~~al~~--Rf~-~i~v~~p~~e~~~~iL~~~~~~~~~~~~~~i~~~al~~l~~~s~~~~~~~~lp~~ai~ll~~  380 (468)
T 3pxg_A          306 YIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDE  380 (468)
T ss_dssp             HHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHH
T ss_pred             HhhcCHHHHH--hCc-cceeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhccCcCCcHHHHHHHH
Confidence              68999999  998 5999999999999999988765    334444433 333332     223445555555543

>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=99.60  E-value=7.1e-15  Score=149.94  Aligned_cols=152  Identities=18%  Similarity=0.267  Sum_probs=111.3

Q ss_pred             ccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-----------CCcEEEEeC
Q 011664          189 FDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-----------SYDVYDVDL  257 (480)
Q Consensus       189 ~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----------~~~~~~i~~  257 (480)
                      .++++|.++..+.+.+.+...+..         ..+++++|+||||||||++++++++++           +..++.+++
T Consensus        19 p~~l~gr~~~~~~l~~~l~~~~~~---------~~~~~vll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~i~~   89 (384)
T 2qby_B           19 FKEIPFREDILRDAAIAIRYFVKN---------EVKFSNLFLGLTGTGKTFVSKYIFNEIEEVKKEDEEYKDVKQAYVNC   89 (384)
T ss_dssp             CSSCTTCHHHHHHHHHHHHHHHTT---------CCCCEEEEEECTTSSHHHHHHHHHHHHHHHHHHSSSSTTCEEEEEEH
T ss_pred             CCCCCChHHHHHHHHHHHHHHHcC---------CCCCcEEEECCCCCCHHHHHHHHHHHHHHHhhhhcCCCCceEEEEEC
Confidence            388999999999998877665432         235689999999999999999999987           889999987


Q ss_pred             CCcC-Ch-----------------------HH-HHHHHHhhc-CCcEEEEecccccccCcccccc-hhhhhhhccccccc
Q 011664          258 SRVA-DD-----------------------AD-LKSLLLQTT-SKSVILIEDLDRFLVEKPAAVS-LSGVLNFMDGVLNS  310 (480)
Q Consensus       258 s~~~-~~-----------------------~~-l~~l~~~~~-~~sII~IDEiD~l~~~~~~~~~-ls~lL~~ldg~~~~  310 (480)
                      .... +.                       .. +..++.... .+.||+|||+|.+..... ... +..|+...      
T Consensus        90 ~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~l~~~~~vlilDEi~~l~~~~~-~~~~l~~l~~~~------  162 (384)
T 2qby_B           90 REVGGTPQAVLSSLAGKLTGFSVPKHGINLGEYIDKIKNGTRNIRAIIYLDEVDTLVKRRG-GDIVLYQLLRSD------  162 (384)
T ss_dssp             HHHCSCHHHHHHHHHHHHHCSCCCSSSSCTHHHHHHHHHHHSSSCEEEEEETTHHHHHSTT-SHHHHHHHHTSS------
T ss_pred             ccCCCCHHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHHhccCCCEEEEECHHHhccCCC-CceeHHHHhcCC------
Confidence            6543 21                       11 222222222 233999999999864321 222 33333322      


Q ss_pred             ccCCceEEEEecCCC---ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          311 CCFEERVMVFTMNSK---DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       311 ~~~~~~ivI~tTN~~---~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                         .+..+|+|||.+   +.+++++++  ||...++|++++.++...++..++.
T Consensus       163 ---~~~~iI~~t~~~~~~~~l~~~l~s--r~~~~i~l~~l~~~~~~~il~~~~~  211 (384)
T 2qby_B          163 ---ANISVIMISNDINVRDYMEPRVLS--SLGPSVIFKPYDAEQLKFILSKYAE  211 (384)
T ss_dssp             ---SCEEEEEECSSTTTTTTSCHHHHH--TCCCEEEECCCCHHHHHHHHHHHHH
T ss_pred             ---cceEEEEEECCCchHhhhCHHHHh--cCCCeEEECCCCHHHHHHHHHHHHH
Confidence               356788888876   678999998  9877999999999999999998875

>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=99.59  E-value=6.2e-15  Score=164.73  Aligned_cols=158  Identities=20%  Similarity=0.273  Sum_probs=114.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .+.+|++++|.++..+.+.+.+.             ...+.++||+||||||||++|+++|+.+          +..++.
T Consensus       181 ~~~~~d~~iGr~~~i~~l~~~l~-------------~~~~~~vlL~G~~GtGKT~la~~la~~l~~~~v~~~~~~~~~~~  247 (758)
T 1r6b_X          181 RVGGIDPLIGREKELERAIQVLC-------------RRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYS  247 (758)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHT-------------SSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEE
T ss_pred             hcCCCCCccCCHHHHHHHHHHHh-------------ccCCCCeEEEcCCCCCHHHHHHHHHHHHHhCCCChhhcCCEEEE
Confidence            35689999999988887765442             2246689999999999999999999876          677888


Q ss_pred             EeCCCcCC--------hHHHHHHHHhhc--CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCC
Q 011664          255 VDLSRVAD--------DADLKSLLLQTT--SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS  324 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~~~~--~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~  324 (480)
                      ++++.+..        +..++.++....  .++||||||+|.+.+............+.+..+..   ..+..+|++||.
T Consensus       248 ~~~~~l~~~~~~~g~~e~~l~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~~~~~~~~~~L~~~l~---~~~~~~I~at~~  324 (758)
T 1r6b_X          248 LDIGSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS---SGKIRVIGSTTY  324 (758)
T ss_dssp             CCCC---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS---SCCCEEEEEECH
T ss_pred             EcHHHHhccccccchHHHHHHHHHHHHHhcCCeEEEEechHHHhhcCCCCcchHHHHHHHHHHHh---CCCeEEEEEeCc
Confidence            88765442        334666765543  47999999999997654432112233333433333   345677888876


Q ss_pred             Cc-----cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          325 KD-----HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       325 ~~-----~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ++     .+|++|.|  ||+ .+.|+.|+.+++.+|++.++.
T Consensus       325 ~~~~~~~~~d~aL~~--Rf~-~i~v~~p~~~e~~~il~~l~~  363 (758)
T 1r6b_X          325 QEFSNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLKP  363 (758)
T ss_dssp             HHHHCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHHH
T ss_pred             hHHhhhhhcCHHHHh--Cce-EEEcCCCCHHHHHHHHHHHHH
Confidence            43     57899999  998 799999999999999987654

>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=99.58  E-value=1.3e-14  Score=162.01  Aligned_cols=155  Identities=17%  Similarity=0.282  Sum_probs=113.7

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCC----CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh---
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRV----WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD---  263 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~----~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~---  263 (480)
                      .++|.+++++.+...+...        ..|..    +..++||+||||||||++|+++|+.++.+++.++++.+...   
T Consensus       459 ~v~g~~~~~~~l~~~i~~~--------~~g~~~~~~p~~~~ll~G~~GtGKT~la~~la~~l~~~~~~i~~s~~~~~~~~  530 (758)
T 1r6b_X          459 LVFGQDKAIEALTEAIKMA--------RAGLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTV  530 (758)
T ss_dssp             TSCSCHHHHHHHHHHHHHH--------HTTCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCC
T ss_pred             hccCHHHHHHHHHHHHHHH--------hcccCCCCCCceEEEEECCCCCcHHHHHHHHHHHhcCCEEEEechhhcchhhH
Confidence            4778888888777665432        12321    23479999999999999999999999999999998876431   


Q ss_pred             ----------------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccc-cc-----ccCCceEEEEe
Q 011664          264 ----------------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-NS-----CCFEERVMVFT  321 (480)
Q Consensus       264 ----------------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-~~-----~~~~~~ivI~t  321 (480)
                                      ..+...+. ...++||||||||.+.     ...++.|+..||.-. ..     ....+.+||+|
T Consensus       531 ~~l~g~~~g~~g~~~~~~l~~~~~-~~~~~vl~lDEi~~~~-----~~~~~~Ll~~le~~~~~~~~g~~~~~~~~~iI~t  604 (758)
T 1r6b_X          531 SRLIGAPPGYVGFDQGGLLTDAVI-KHPHAVLLLDEIEKAH-----PDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMT  604 (758)
T ss_dssp             SSSCCCCSCSHHHHHTTHHHHHHH-HCSSEEEEEETGGGSC-----HHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEE
T ss_pred             hhhcCCCCCCcCccccchHHHHHH-hCCCcEEEEeCccccC-----HHHHHHHHHHhcCcEEEcCCCCEEecCCeEEEEe
Confidence                            11223332 3457999999999773     345677777776321 10     01145778999


Q ss_pred             cCCCc-------------------------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          322 MNSKD-------------------------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       322 TN~~~-------------------------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ||.+.                         .++|+|++  ||+..|.|++|+.+++..|+..++.
T Consensus       605 sN~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~l~~--R~~~~i~~~~l~~~~~~~i~~~~l~  667 (758)
T 1r6b_X          605 TNAGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  667 (758)
T ss_dssp             ECSSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             cCcchhhhhhcccCccccchHHHHHHHHHHhcCHHHHh--hCCcceeeCCCCHHHHHHHHHHHHH
Confidence            99753                         67889998  9999999999999999999998875

>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=99.58  E-value=8.2e-15  Score=148.29  Aligned_cols=162  Identities=17%  Similarity=0.237  Sum_probs=110.5

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-CC----------
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-SY----------  250 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-~~----------  250 (480)
                      ..-+|.+|++++|++++++.+...+.          ..|. .+. ++|+||||||||++++++|+++ +.          
T Consensus         6 ~kyrP~~~~~~vg~~~~~~~l~~~~~----------~~~~-~~~-~ll~Gp~G~GKTtl~~~la~~l~~~~~g~i~~~~~   73 (354)
T 1sxj_E            6 DKYRPKSLNALSHNEELTNFLKSLSD----------QPRD-LPH-LLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVR   73 (354)
T ss_dssp             TTTCCCSGGGCCSCHHHHHHHHTTTT----------CTTC-CCC-EEEECSTTSSHHHHHHTHHHHHSCTTCCC------
T ss_pred             hccCCCCHHHhcCCHHHHHHHHHHHh----------hCCC-CCe-EEEECCCCCCHHHHHHHHHHHHcCCCCCeEEecce
Confidence            34478899999999998887765431          1122 233 9999999999999999999953 21          


Q ss_pred             ------------------cEEEEeCCCcCChH--HHHHHHHh----------------hcCCcEEEEecccccccCcccc
Q 011664          251 ------------------DVYDVDLSRVADDA--DLKSLLLQ----------------TTSKSVILIEDLDRFLVEKPAA  294 (480)
Q Consensus       251 ------------------~~~~i~~s~~~~~~--~l~~l~~~----------------~~~~sII~IDEiD~l~~~~~~~  294 (480)
                                        +++.++.+......  .++..+..                ...|.||+|||++.+.     .
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~ls~l~~~~~vlilDE~~~L~-----~  148 (354)
T 1sxj_E           74 QFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLT-----K  148 (354)
T ss_dssp             ------------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSC-----H
T ss_pred             eecccccccceeeeecccceEEecHhhcCCcchHHHHHHHHHHHHhccccccccccccCCCCeEEEEeCccccC-----H
Confidence                              13334433221111  24444322                2257799999999852     2


Q ss_pred             cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc
Q 011664          295 VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF  368 (480)
Q Consensus       295 ~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~  368 (480)
                      .....|+..++..     ..+..+|++||.++.+.+++++  |+ ..+.|++|+.++...+++..+...+..+.
T Consensus       149 ~~~~~L~~~le~~-----~~~~~~Il~t~~~~~l~~~l~s--R~-~~~~~~~~~~~~~~~~l~~~~~~~~~~~~  214 (354)
T 1sxj_E          149 DAQAALRRTMEKY-----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNERIQLE  214 (354)
T ss_dssp             HHHHHHHHHHHHS-----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTCEEC
T ss_pred             HHHHHHHHHHHhh-----cCCCEEEEEeCCHHHHHHHHHh--hc-eEEecCCcCHHHHHHHHHHHHHHcCCCCC
Confidence            3345666666543     2356788899999999999999  88 78999999999999999988765444433

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.58  E-value=9.6e-15  Score=163.32  Aligned_cols=160  Identities=16%  Similarity=0.253  Sum_probs=114.0

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChH--
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDA--  264 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~--  264 (480)
                      +.++|.+++++.+.+.+......-.   . ...+..++||+||||||||++|+++|+.+   +.+++.++++.+....  
T Consensus       491 ~~viGq~~a~~~l~~~i~~~~~~~~---~-~~~p~~~~Ll~Gp~GtGKT~lA~ala~~l~~~~~~~i~i~~s~~~~~~~~  566 (758)
T 3pxi_A          491 SRVIGQDEAVVAVAKAVRRARAGLK---D-PKRPIGSFIFLGPTGVGKTELARALAESIFGDEESMIRIDMSEYMEKHST  566 (758)
T ss_dssp             TTSCSCHHHHHHHHHHHHHHTTTCS---C-TTSCSEEEEEESCTTSSHHHHHHHHHHHHHSCTTCEEEEEGGGGCSSCCC
T ss_pred             CcCcChHHHHHHHHHHHHHHHcccC---C-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCcceEEEechhccccccc
Confidence            4688999999988887765422100   0 01122369999999999999999999987   6889999998876532  


Q ss_pred             ---HHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccc------cccCCceEEEEecCCCcc--------
Q 011664          265 ---DLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN------SCCFEERVMVFTMNSKDH--------  327 (480)
Q Consensus       265 ---~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~------~~~~~~~ivI~tTN~~~~--------  327 (480)
                         .+...+ +...++||||||||.+.     ....+.|+..|+.-.-      .....+.+||+|||.+..        
T Consensus       567 ~~~~l~~~~-~~~~~~vl~lDEi~~~~-----~~~~~~Ll~~le~g~~~~~~g~~~~~~~~~iI~ttn~~~~~~~~~~~~  640 (758)
T 3pxi_A          567 SGGQLTEKV-RRKPYSVVLLDAIEKAH-----PDVFNILLQVLEDGRLTDSKGRTVDFRNTILIMTSNVGASEKDKVMGE  640 (758)
T ss_dssp             C---CHHHH-HHCSSSEEEEECGGGSC-----HHHHHHHHHHHHHSBCC-----CCBCTTCEEEEEESSSTTCCHHHHHH
T ss_pred             ccchhhHHH-HhCCCeEEEEeCccccC-----HHHHHHHHHHhccCeEEcCCCCEeccCCeEEEEeCCCChhhHHHHHHH
Confidence               222222 23467899999999773     3455777777764211      011345689999996544        


Q ss_pred             ----CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          328 ----VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       328 ----LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                          +.|+|+.  ||+..|.|++|+.+++..|+..++.
T Consensus       641 ~~~~f~p~l~~--Rl~~~i~~~~l~~~~~~~i~~~~l~  676 (758)
T 3pxi_A          641 LKRAFRPEFIN--RIDEIIVFHSLEKKHLTEIVSLMSD  676 (758)
T ss_dssp             HHHHSCHHHHT--TSSEEEECC--CHHHHHHHHHHHHH
T ss_pred             HHhhCCHHHHh--hCCeEEecCCCCHHHHHHHHHHHHH
Confidence                7888888  9999999999999999999988874

>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=99.57  E-value=7.4e-15  Score=148.06  Aligned_cols=155  Identities=17%  Similarity=0.182  Sum_probs=100.4

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-------------
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-------------  250 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-------------  250 (480)
                      .++.+|++++|.+++++.+.....    .         +...++||+||||||||++|+++|+.++.             
T Consensus        18 ~~~~~f~~i~G~~~~~~~l~~~~~----~---------~~~~~vLl~G~~GtGKT~la~~la~~~~~~~~~~~~~~~~~~   84 (350)
T 1g8p_A           18 RPVFPFSAIVGQEDMKLALLLTAV----D---------PGIGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPN   84 (350)
T ss_dssp             CCCCCGGGSCSCHHHHHHHHHHHH----C---------GGGCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSS
T ss_pred             CCCCCchhccChHHHHHHHHHHhh----C---------CCCceEEEECCCCccHHHHHHHHHHhCccccccccccccccc
Confidence            366789999999987765432211    1         12346999999999999999999998863             


Q ss_pred             --------------------cEEEEeCCCcCChHH------HHHHHHh-----------hcCCcEEEEecccccccCccc
Q 011664          251 --------------------DVYDVDLSRVADDAD------LKSLLLQ-----------TTSKSVILIEDLDRFLVEKPA  293 (480)
Q Consensus       251 --------------------~~~~i~~s~~~~~~~------l~~l~~~-----------~~~~sII~IDEiD~l~~~~~~  293 (480)
                                          +++.+..+.  ....      +...+..           ...++||||||+|.+..    
T Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~g~~~~~~~~~~~~~~~~~g~~~~a~~~vl~iDEi~~l~~----  158 (350)
T 1g8p_A           85 VEMIPDWATVLSTNVIRKPTPVVDLPLGV--SEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLED----  158 (350)
T ss_dssp             GGGSCTTCCCSCCCEEEECCCEEEECTTC--CHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSCH----
T ss_pred             cccccchhhhhccccccCCCcccccCCCc--chhhheeechhhhhhcCCceeecCceeeecCCCEEEEeChhhCCH----
Confidence                                122222111  1111      1222211           12478999999998742    


Q ss_pred             ccchhhhhhhccc----cccc----ccCCceEEEEecCCCc-cCcccccCCCceeEEEEcCCC-CHHHHHHHHHHHh
Q 011664          294 AVSLSGVLNFMDG----VLNS----CCFEERVMVFTMNSKD-HVDQALLRPGRIDVHIHFPLC-DFSSFKTLASSYL  360 (480)
Q Consensus       294 ~~~ls~lL~~ldg----~~~~----~~~~~~ivI~tTN~~~-~LD~aLlrpGRfd~~I~~~~p-~~~~r~~il~~~l  360 (480)
                       .....|+..|+.    +...    ......++|+|||..+ .++++|++  ||+.++++++| +.+.+..|++..+
T Consensus       159 -~~~~~Ll~~le~~~~~~~~~g~~~~~~~~~~li~~~n~~~~~l~~~L~~--R~~~~~~l~~~~~~~~~~~il~~~~  232 (350)
T 1g8p_A          159 -HIVDLLLDVAQSGENVVERDGLSIRHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRRRD  232 (350)
T ss_dssp             -HHHHHHHHHHHHSEEEECCTTCCEEEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHHHH
T ss_pred             -HHHHHHHHHHhcCceEEEecceEEeeCCceEEEEEeCCCCCCCCHHHHh--hcceEEEcCCCCcHHHHHHHHHHHH
Confidence             234555655542    1110    0012567788899644 89999999  99999999999 6777878887754

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=99.57  E-value=1.1e-14  Score=146.72  Aligned_cols=129  Identities=11%  Similarity=0.151  Sum_probs=94.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeCCCcCCh----------------------HHHHHHH
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDLSRVADD----------------------ADLKSLL  270 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~s~~~~~----------------------~~l~~l~  270 (480)
                      .+.+++||||||||||++++++++++          .+.+++++|..+.+.                      ..+..+|
T Consensus        44 ~~~~lli~GpPGTGKT~~v~~v~~~L~~~~~~~~~~~~~~v~INc~~~~t~~~~~~~I~~~L~g~~~~~~~~~~~L~~~f  123 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVNDVMDELITSSARKELPIFDYIHIDALELAGMDALYEKIWFAISKENLCGDISLEALNFYI  123 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHHHHHHHHHHTTTTTSSCCEEEEEEETTCCC--HHHHHHHHHHHSCCC--CCCCHHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHHHhhhccCCceEEEEEeccccCCHHHHHHHHHHHhcCCCCCchHHHHHHHHHH
Confidence            56789999999999999999999988          356888997665432                      2345555


Q ss_pred             Hh----hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCcc----CcccccCCCcee-EE
Q 011664          271 LQ----TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH----VDQALLRPGRID-VH  341 (480)
Q Consensus       271 ~~----~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~----LD~aLlrpGRfd-~~  341 (480)
                      ..    ...+.||+|||+|.+.    .+..+..|++...     ......+||+++|..+.    |++++++  ||. .+
T Consensus       124 ~~~~~~~~~~~ii~lDE~d~l~----~q~~L~~l~~~~~-----~~~s~~~vI~i~n~~d~~~~~L~~~v~S--R~~~~~  192 (318)
T 3te6_A          124 TNVPKAKKRKTLILIQNPENLL----SEKILQYFEKWIS-----SKNSKLSIICVGGHNVTIREQINIMPSL--KAHFTE  192 (318)
T ss_dssp             HHSCGGGSCEEEEEEECCSSSC----CTHHHHHHHHHHH-----CSSCCEEEEEECCSSCCCHHHHHTCHHH--HTTEEE
T ss_pred             HHhhhccCCceEEEEecHHHhh----cchHHHHHHhccc-----ccCCcEEEEEEecCcccchhhcchhhhc--cCCceE
Confidence            54    2457899999999996    2334444444321     11345678888887643    5777888  987 68


Q ss_pred             EEcCCCCHHHHHHHHHHHhcc
Q 011664          342 IHFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       342 I~~~~p~~~~r~~il~~~l~~  362 (480)
                      |.|++++.++...|++..+..
T Consensus       193 i~F~pYt~~el~~Il~~Rl~~  213 (318)
T 3te6_A          193 IKLNKVDKNELQQMIITRLKS  213 (318)
T ss_dssp             EECCCCCHHHHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHh
Confidence            999999999999999988764

>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=99.56  E-value=6e-14  Score=142.96  Aligned_cols=191  Identities=10%  Similarity=0.017  Sum_probs=128.7

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCCcCC
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSRVAD  262 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~~~~  262 (480)
                      ..+++++|.++..+.+.+.+...+...       .+..+.++|+||||||||++++++++.+    +..++.++++...+
T Consensus        14 ~~p~~l~gr~~~~~~l~~~l~~~~~~~-------~~~~~~~li~G~~G~GKTtl~~~l~~~~~~~~~~~~~~i~~~~~~~   86 (389)
T 1fnn_A           14 YVPKRLPHREQQLQQLDILLGNWLRNP-------GHHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRN   86 (389)
T ss_dssp             CCCSCCTTCHHHHHHHHHHHHHHHHST-------TSSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETTTCCS
T ss_pred             cCCCCCCChHHHHHHHHHHHHHHHcCC-------CCCCCeEEEECCCCCCHHHHHHHHHHHHhhhcCeeEEEEeCccCCC
Confidence            344889999999999988777654431       1112379999999999999999999988    67889999766443


Q ss_pred             hHH--------------------------HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCce
Q 011664          263 DAD--------------------------LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEER  316 (480)
Q Consensus       263 ~~~--------------------------l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~  316 (480)
                      ...                          +...+.....|.||+|||+|.+     +...+..|+..++.... ....+.
T Consensus        87 ~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l-----~~~~~~~L~~~~~~~~~-~~~~~~  160 (389)
T 1fnn_A           87 FTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNL-----APDILSTFIRLGQEADK-LGAFRI  160 (389)
T ss_dssp             HHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGS-----CHHHHHHHHHHTTCHHH-HSSCCE
T ss_pred             HHHHHHHHHHHhCccCCCCCCCHHHHHHHHHHHHhhcCCeEEEEEECcccc-----chHHHHHHHHHHHhCCC-CCcCCE
Confidence            211                          1111222345889999999988     23445566666644321 001356


Q ss_pred             EEEEecCCC---ccCcccccCCCceeE-EEEcCCCCHHHHHHHHHHHhcc--CCCCCch-hHHHHHHhCC--------CC
Q 011664          317 VMVFTMNSK---DHVDQALLRPGRIDV-HIHFPLCDFSSFKTLASSYLGL--KDHKLFP-QVEEIFQNGS--------SL  381 (480)
Q Consensus       317 ivI~tTN~~---~~LD~aLlrpGRfd~-~I~~~~p~~~~r~~il~~~l~~--~~~~l~~-~i~~l~~~~~--------g~  381 (480)
                      .+|++||.+   +.+++.+.+  ||.. .++|++++.++...++...+..  ....+.+ .++.++..+.        +-
T Consensus       161 ~iI~~~~~~~~~~~l~~~~~~--r~~~~~i~~~pl~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~G  238 (389)
T 1fnn_A          161 ALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADITGAQTPLDTNRG  238 (389)
T ss_dssp             EEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHHHBCTTSSCHHHHHHHHHHHSBSSTTCTTSC
T ss_pred             EEEEEECCchHHHHhCHHhhh--cCCCceEEeCCCCHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHHhhcccCCCCCC
Confidence            788888877   678888888  8874 8999999999999999887753  1223333 3455655552        23


Q ss_pred             CHHHHHHHHHH
Q 011664          382 SPAEIGELMIA  392 (480)
Q Consensus       382 s~adI~~ll~~  392 (480)
                      .+..+.++|..
T Consensus       239 ~~r~~~~~l~~  249 (389)
T 1fnn_A          239 DARLAIDILYR  249 (389)
T ss_dssp             CHHHHHHHHHH
T ss_pred             cHHHHHHHHHH
Confidence            45555555544

>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=99.56  E-value=4.5e-14  Score=142.91  Aligned_cols=160  Identities=19%  Similarity=0.280  Sum_probs=116.3

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEeCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVDLS  258 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~~s  258 (480)
                      ..|.+|++++|++.+++.|...+.    .       |. .+ .+||+||||||||++++++|+.+.     ..+..++.+
T Consensus        19 ~rp~~~~~~~g~~~~~~~L~~~i~----~-------g~-~~-~~ll~Gp~G~GKTtla~~la~~l~~~~~~~~~~~~~~~   85 (340)
T 1sxj_C           19 YRPETLDEVYGQNEVITTVRKFVD----E-------GK-LP-HLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNAS   85 (340)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHH----T-------TC-CC-CEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTT
T ss_pred             hCCCcHHHhcCcHHHHHHHHHHHh----c-------CC-Cc-eEEEECCCCCCHHHHHHHHHHHHcCCCccceEEEEcCc
Confidence            478899999999988887765443    1       22 23 399999999999999999999863     247778877


Q ss_pred             CcCChHHHHHHH---Hhh-----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          259 RVADDADLKSLL---LQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       259 ~~~~~~~l~~l~---~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                      +..+...++..+   .+.     ..+.|++|||+|.+..     .....|+..++..     .....+|++||.+..+.+
T Consensus        86 ~~~~~~~ir~~i~~~~~~~~~~~~~~~viiiDe~~~l~~-----~~~~~L~~~le~~-----~~~~~~il~~n~~~~i~~  155 (340)
T 1sxj_C           86 DDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN-----AAQNALRRVIERY-----TKNTRFCVLANYAHKLTP  155 (340)
T ss_dssp             SCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH-----HHHHHHHHHHHHT-----TTTEEEEEEESCGGGSCH
T ss_pred             ccccHHHHHHHHHHHHhhcccCCCCceEEEEeCCCCCCH-----HHHHHHHHHHhcC-----CCCeEEEEEecCccccch
Confidence            655544555443   221     2368999999998842     2345566666543     235667888999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCch
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFP  369 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~  369 (480)
                      ++++  |+. .+.|+.++.++....+...+...+..+.+
T Consensus       156 ~i~s--R~~-~~~~~~l~~~~~~~~l~~~~~~~~~~i~~  191 (340)
T 1sxj_C          156 ALLS--QCT-RFRFQPLPQEAIERRIANVLVHEKLKLSP  191 (340)
T ss_dssp             HHHT--TSE-EEECCCCCHHHHHHHHHHHHHTTTCCBCH
T ss_pred             hHHh--hce-eEeccCCCHHHHHHHHHHHHHHcCCCCCH
Confidence            9999  986 78999999998888888777544444443

>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=99.55  E-value=1.2e-14  Score=164.52  Aligned_cols=185  Identities=14%  Similarity=0.150  Sum_probs=116.6

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .|.+|++++|.++..+.+.+.+.    .         ..++++||+||||||||++|+++|+.+          +.+++.
T Consensus       165 r~~~ld~viGr~~~i~~l~~~l~----~---------~~~~~vlL~G~pG~GKT~la~~la~~l~~~~~p~~l~~~~~~~  231 (854)
T 1qvr_A          165 AEGKLDPVIGRDEEIRRVIQILL----R---------RTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVS  231 (854)
T ss_dssp             HTTCSCCCCSCHHHHHHHHHHHH----C---------SSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEE
T ss_pred             hcCCCcccCCcHHHHHHHHHHHh----c---------CCCCceEEEcCCCCCHHHHHHHHHHHHhcCCCchhhcCCeEEE
Confidence            35689999999987777766442    1         235689999999999999999999987          889999


Q ss_pred             EeCCCcCC--------hHHHHHHHHhh---cCCcEEEEecccccccCcccc--cch-hhhhhhcccccccccCCceEEEE
Q 011664          255 VDLSRVAD--------DADLKSLLLQT---TSKSVILIEDLDRFLVEKPAA--VSL-SGVLNFMDGVLNSCCFEERVMVF  320 (480)
Q Consensus       255 i~~s~~~~--------~~~l~~l~~~~---~~~sII~IDEiD~l~~~~~~~--~~l-s~lL~~ldg~~~~~~~~~~ivI~  320 (480)
                      ++++.+..        +..+..++...   ..++||||||+|.+.+.....  ... +.|...+    .   ..+..+|+
T Consensus       232 l~~~~l~~g~~~~g~~~~~l~~~~~~~~~~~~~~iL~IDEi~~l~~~~~~~g~~~~~~~L~~~l----~---~~~i~~I~  304 (854)
T 1qvr_A          232 LQMGSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGAVDAGNMLKPAL----A---RGELRLIG  304 (854)
T ss_dssp             ECC-----------CHHHHHHHHHHHHHTTCSSEEEEECCC-------------------HHHH----H---TTCCCEEE
T ss_pred             eehHHhhccCccchHHHHHHHHHHHHHHhcCCCeEEEEecHHHHhccCCccchHHHHHHHHHHH----h---CCCeEEEE
Confidence            99887642        22355666543   367899999999987543322  111 2222222    2   24566788


Q ss_pred             ecCCCc----cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhcc----CCCCCchh-HHHHHH-----hCCCCCHHHH
Q 011664          321 TMNSKD----HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGL----KDHKLFPQ-VEEIFQ-----NGSSLSPAEI  386 (480)
Q Consensus       321 tTN~~~----~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~----~~~~l~~~-i~~l~~-----~~~g~s~adI  386 (480)
                      +||.++    .+|++|+|  ||+. |.++.|+.+++.+|++.++..    .+..+.++ +..++.     .+..+.|...
T Consensus       305 at~~~~~~~~~~d~aL~r--Rf~~-i~l~~p~~~e~~~iL~~~~~~~~~~~~~~i~~~al~~~~~ls~r~i~~~~lp~ka  381 (854)
T 1qvr_A          305 ATTLDEYREIEKDPALER--RFQP-VYVDEPTVEETISILRGLKEKYEVHHGVRISDSAIIAAATLSHRYITERRLPDKA  381 (854)
T ss_dssp             EECHHHHHHHTTCTTTCS--CCCC-EEECCCCHHHHHHHHHHHHHHHHHHTTCEECHHHHHHHHHHHHHHCCSSCTHHHH
T ss_pred             ecCchHHhhhccCHHHHh--CCce-EEeCCCCHHHHHHHHHhhhhhhhhhcCCCCCHHHHHHHHHHHhhhcccccChHHH
Confidence            888664    47999999  9985 999999999999999876642    23333332 233332     1345667666


Q ss_pred             HHHHHH
Q 011664          387 GELMIA  392 (480)
Q Consensus       387 ~~ll~~  392 (480)
                      ..++..
T Consensus       382 i~llde  387 (854)
T 1qvr_A          382 IDLIDE  387 (854)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            655543

>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=99.54  E-value=1.6e-14  Score=146.49  Aligned_cols=193  Identities=15%  Similarity=0.179  Sum_probs=126.1

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC------CCcEEEEeCC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM------SYDVYDVDLS  258 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l------~~~~~~i~~s  258 (480)
                      +...+++++|.++..+.+.+.+...+..         ..++.++|+||||||||++++++++.+      +..++.+++.
T Consensus        15 ~~~~p~~~~gr~~e~~~l~~~l~~~~~~---------~~~~~vli~G~~G~GKTtl~~~l~~~~~~~~~~~~~~~~i~~~   85 (386)
T 2qby_A           15 PDYIPDELPHREDQIRKIASILAPLYRE---------EKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHVYINTR   85 (386)
T ss_dssp             SSCCCSCCTTCHHHHHHHHHSSGGGGGT---------CCCCCEEEEECTTSSHHHHHHHHHHHHHHHTCSSCEEEEEEHH
T ss_pred             CccCCCCCCChHHHHHHHHHHHHHHHcC---------CCCCeEEEECCCCCCHHHHHHHHHHHHHHHhcCCceEEEEECC
Confidence            3445688999999888887655432211         235689999999999999999999988      8889999864


Q ss_pred             CcCC----------------------hHH-HHH---HHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          259 RVAD----------------------DAD-LKS---LLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       259 ~~~~----------------------~~~-l~~---l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                      ....                      ... +..   .+.....|.||+|||+|.+.... ....+..++..++...    
T Consensus        86 ~~~~~~~~~~~i~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~vlilDE~~~l~~~~-~~~~l~~l~~~~~~~~----  160 (386)
T 2qby_A           86 QIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAFVKKY-NDDILYKLSRINSEVN----  160 (386)
T ss_dssp             HHCSHHHHHHHHTTTTSCCCCSSSCCHHHHHHHHHHHHHTCCSCEEEEEETHHHHHHSS-CSTHHHHHHHHHHSCC----
T ss_pred             CCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHhccCCeEEEEEcChhhhhccC-cCHHHHHHhhchhhcC----
Confidence            3211                      122 122   22222348999999999986432 1344566666665431    


Q ss_pred             CCceEEEEecCCC---ccCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhcc--CCCCCchhH-HHHHHhCC--CCCH
Q 011664          313 FEERVMVFTMNSK---DHVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLGL--KDHKLFPQV-EEIFQNGS--SLSP  383 (480)
Q Consensus       313 ~~~~ivI~tTN~~---~~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~~--~~~~l~~~i-~~l~~~~~--g~s~  383 (480)
                      ..+..+|++||.+   +.+++++.+  ||. ..+++++++.++..+++...+..  ....+.+++ +.++..+.  .-.+
T Consensus       161 ~~~~~~I~~~~~~~~~~~~~~~~~~--r~~~~~i~l~~l~~~~~~~il~~~~~~~~~~~~~~~~~~~~l~~~~~~~~G~~  238 (386)
T 2qby_A          161 KSKISFIGITNDVKFVDLLDPRVKS--SLSEEEIIFPPYNAEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDA  238 (386)
T ss_dssp             C--EEEEEEESCGGGGGGCTTHHHH--TTTTEEEEECCCCHHHHHHHHHHHHHHHBCSSCSCHHHHHHHHHHHHHTTCCH
T ss_pred             CCeEEEEEEECCCChHhhhCHHHhc--cCCCeeEEeCCCCHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHHHHHhcCCH
Confidence            3467788888876   567888888  775 58999999999999999887642  123344433 34444332  1455


Q ss_pred             HHHHHHHHHh
Q 011664          384 AEIGELMIAN  393 (480)
Q Consensus       384 adI~~ll~~a  393 (480)
                      ..+.++|..+
T Consensus       239 r~~~~ll~~a  248 (386)
T 2qby_A          239 RRALDLLRVS  248 (386)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            5555555443

>3pxi_A Negative regulator of genetic competence CLPC/MEC; CLPB, proteolysis, CLPX, HSP100/CLP, AAA+ proteins, PR binding; 6.93A {Bacillus subtilis}

Probab=99.54  E-value=5.9e-14  Score=156.92  Aligned_cols=176  Identities=16%  Similarity=0.186  Sum_probs=118.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEE
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYD  254 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~  254 (480)
                      .+..+++++|.++.++.+.+.+..             ..+.++||+||||||||++|+++|+.+          +..++.
T Consensus       175 ~~~~ld~iiG~~~~i~~l~~~l~~-------------~~~~~vLL~G~pGtGKT~la~~la~~l~~~~~p~~l~~~~~~~  241 (758)
T 3pxi_A          175 KEDSLDPVIGRSKEIQRVIEVLSR-------------RTKNNPVLIGEPGVGKTAIAEGLAQQIINNEVPEILRDKRVMT  241 (758)
T ss_dssp             TSSCSCCCCCCHHHHHHHHHHHHC-------------SSSCEEEEESCTTTTTHHHHHHHHHHHHSSCSCTTTSSCCEEC
T ss_pred             hhCCCCCccCchHHHHHHHHHHhC-------------CCCCCeEEECCCCCCHHHHHHHHHHHHhcCCCChhhcCCeEEE
Confidence            456799999999999888765431             245689999999999999999999986          788888


Q ss_pred             EeCC-CcCC--hHHHHHHHHhh--cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc---
Q 011664          255 VDLS-RVAD--DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD---  326 (480)
Q Consensus       255 i~~s-~~~~--~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~---  326 (480)
                      +++. .+.+  +..++.+|...  ..++|||||         ......+.|+..|+       .....+|+|||..+   
T Consensus       242 ~~~g~~~~G~~e~~l~~~~~~~~~~~~~iLfiD---------~~~~~~~~L~~~l~-------~~~v~~I~at~~~~~~~  305 (758)
T 3pxi_A          242 LDMGTKYRGEFEDRLKKVMDEIRQAGNIILFID---------AAIDASNILKPSLA-------RGELQCIGATTLDEYRK  305 (758)
T ss_dssp             C----------CTTHHHHHHHHHTCCCCEEEEC---------C--------CCCTT-------SSSCEEEEECCTTTTHH
T ss_pred             ecccccccchHHHHHHHHHHHHHhcCCEEEEEc---------CchhHHHHHHHHHh-------cCCEEEEeCCChHHHHH
Confidence            8872 1222  23466776543  478999999         11122233444332       34677888998887   


Q ss_pred             --cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhcc----CCCCCchhH-HHHHH---h--CCCCCHHHHHHHHHH
Q 011664          327 --HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGL----KDHKLFPQV-EEIFQ---N--GSSLSPAEIGELMIA  392 (480)
Q Consensus       327 --~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~----~~~~l~~~i-~~l~~---~--~~g~s~adI~~ll~~  392 (480)
                        .+|++++|  ||. .|.|+.|+.+++..|++.++..    .+..+.++. ..++.   .  +.++.|.....++..
T Consensus       306 ~~~~d~al~r--Rf~-~i~v~~p~~~~~~~il~~~~~~~~~~~~~~i~~~al~~~~~~s~~~i~~~~~p~~ai~ll~~  380 (758)
T 3pxi_A          306 YIEKDAALER--RFQ-PIQVDQPSVDESIQILQGLRDRYEAHHRVSITDDAIEAAVKLSDRYISDRFLPDKAIDLIDE  380 (758)
T ss_dssp             HHTTCSHHHH--SEE-EEECCCCCHHHHHHHHHHTTTTSGGGSSCSCCHHHHHHHHHHHHHSSCCSCTTHHHHHHHHH
T ss_pred             HhhccHHHHh--hCc-EEEeCCCCHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcccccCcCCcHHHHHHHH
Confidence              79999999  995 6999999999999999987765    233444332 33322   1  346667766665544

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=99.49  E-value=9.5e-14  Score=138.99  Aligned_cols=197  Identities=13%  Similarity=0.146  Sum_probs=127.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADL  266 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l  266 (480)
                      ++++|.....+.+.+.+....           ....++||+||||||||++|+++++..   +.+|+.++|+.+..+---
T Consensus         2 ~~iig~s~~~~~~~~~~~~~a-----------~~~~~vLi~Ge~GtGKt~lAr~i~~~~~~~~~~~v~v~~~~~~~~l~~   70 (304)
T 1ojl_A            2 SHMIGSSPAMQHLLNEIAMVA-----------PSDATVLIHGDSGTGKELVARALHACSARSDRPLVTLNCAALNESLLE   70 (304)
T ss_dssp             -CCCCCSHHHHHHHHHHHHHC-----------STTSCEEEESCTTSCHHHHHHHHHHHSSCSSSCCCEEECSSCCHHHHH
T ss_pred             CCcEECCHHHHHHHHHHHHHh-----------CCCCcEEEECCCCchHHHHHHHHHHhCcccCCCeEEEeCCCCChHHHH
Confidence            357888888888887776542           234579999999999999999999965   678999999877532211


Q ss_pred             HHHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhccccc-----cc-ccCCceEEEEecC
Q 011664          267 KSLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----NS-CCFEERVMVFTMN  323 (480)
Q Consensus       267 ~~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----~~-~~~~~~ivI~tTN  323 (480)
                      ..+|.                 ....+++|||||||.+..     .....|+..++...     +. .......||+|||
T Consensus        71 ~~lfg~~~g~~tg~~~~~~g~~~~a~~g~L~LDEi~~l~~-----~~q~~Ll~~l~~~~~~~~g~~~~~~~~~riI~atn  145 (304)
T 1ojl_A           71 SELFGHEKGAFTGADKRREGRFVEADGGTLFLDEIGDISP-----LMQVRLLRAIQEREVQRVGSNQTISVDVRLIAATH  145 (304)
T ss_dssp             HHHTCCCSSCCC---CCCCCHHHHHTTSEEEEESCTTCCH-----HHHHHHHHHHHSSBCCBTTBCCCCBCCCEEEEEES
T ss_pred             HHhcCccccccCchhhhhcCHHHhcCCCEEEEeccccCCH-----HHHHHHHHHHhcCEeeecCCcccccCCeEEEEecC
Confidence            22221                 112458999999998843     23455666665321     00 0023456888888


Q ss_pred             CC-------ccCcccccCCCcee-EEEEcCCCC--HHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SK-------DHVDQALLRPGRID-VHIHFPLCD--FSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~-------~~LD~aLlrpGRfd-~~I~~~~p~--~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .+       ..++++|..  ||. ..|.+|+..  .++...++..++....       .........+++..+..+....
T Consensus       146 ~~l~~~v~~g~fr~~L~~--Rl~~~~i~lPpL~eR~edi~~l~~~~l~~~~-------~~~~~~~~~~s~~a~~~L~~~~  216 (304)
T 1ojl_A          146 RDLAEEVSAGRFRQDLYY--RLNVVAIEMPSLRQRREDIPLLADHFLRRFA-------ERNRKVVKGFTPQAMDLLIHYD  216 (304)
T ss_dssp             SCHHHHHHHTSSCHHHHH--HHSSEEEECCCSGGGGGGHHHHHHHHHHHHH-------HHTTCCCCCBCHHHHHHHHHCC
T ss_pred             ccHHHHHHhCCcHHHHHh--hcCeeEEeccCHHHhHhhHHHHHHHHHHHHH-------HHhccCccCCCHHHHHHHHcCC
Confidence            65       235677777  885 556676665  3455566666653210       0000112468888888777777


Q ss_pred             hhcHHHHHHHHHHHHHhc
Q 011664          394 RNSPSRALKSVITALQTD  411 (480)
Q Consensus       394 ~~~~~~al~~~i~~~~~~  411 (480)
                      +...++.++.+++.+...
T Consensus       217 wpGnvReL~~~l~~~~~~  234 (304)
T 1ojl_A          217 WPGNIRELENAIERAVVL  234 (304)
T ss_dssp             CSSHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            778888888888776554

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=99.48  E-value=7.6e-14  Score=124.24  Aligned_cols=131  Identities=11%  Similarity=0.121  Sum_probs=89.8

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLK  267 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~  267 (480)
                      +++|.....+.+.+.+....           .....+||+||||||||++|+++++..   +.+++ ++++.+.......
T Consensus         2 ~iiG~s~~~~~~~~~~~~~a-----------~~~~~vll~G~~GtGKt~lA~~i~~~~~~~~~~~v-~~~~~~~~~~~~~   69 (145)
T 3n70_A            2 ELIGRSEWINQYRRRLQQLS-----------ETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFV-YRELTPDNAPQLN   69 (145)
T ss_dssp             --CCSSHHHHHHHHHHHHHT-----------TCCSCEEEESSTTSSHHHHHHHHHHSSTTTTSCCE-EEECCTTTSSCHH
T ss_pred             CceeCCHHHHHHHHHHHHHh-----------CCCCCEEEECCCCCCHHHHHHHHHHhCCccCCCEE-EECCCCCcchhhh
Confidence            56788888888887776542           134579999999999999999999987   77899 9999877665555


Q ss_pred             HHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC-------ccCcccccCCCcee-
Q 011664          268 SLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK-------DHVDQALLRPGRID-  339 (480)
Q Consensus       268 ~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~-------~~LD~aLlrpGRfd-  339 (480)
                      ..+..+ .+++|||||||.+..     .....|+..|...     .....+|+|||.+       ..+++.|..  |+. 
T Consensus        70 ~~~~~a-~~g~l~ldei~~l~~-----~~q~~Ll~~l~~~-----~~~~~~I~~t~~~~~~~~~~~~~~~~L~~--rl~~  136 (145)
T 3n70_A           70 DFIALA-QGGTLVLSHPEHLTR-----EQQYHLVQLQSQE-----HRPFRLIGIGDTSLVELAASNHIIAELYY--CFAM  136 (145)
T ss_dssp             HHHHHH-TTSCEEEECGGGSCH-----HHHHHHHHHHHSS-----SCSSCEEEEESSCHHHHHHHSCCCHHHHH--HHHH
T ss_pred             cHHHHc-CCcEEEEcChHHCCH-----HHHHHHHHHHhhc-----CCCEEEEEECCcCHHHHHHcCCCCHHHHH--HhcC
Confidence            556544 568999999998843     2345667766332     2334577788754       134455554  543 


Q ss_pred             EEEEcCC
Q 011664          340 VHIHFPL  346 (480)
Q Consensus       340 ~~I~~~~  346 (480)
                      ..|++|+
T Consensus       137 ~~i~lPp  143 (145)
T 3n70_A          137 TQIACLP  143 (145)
T ss_dssp             HEEECCC
T ss_pred             CEEeCCC
Confidence            3566665

>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=99.46  E-value=1.1e-13  Score=156.63  Aligned_cols=160  Identities=18%  Similarity=0.284  Sum_probs=112.7

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHH-
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDAD-  265 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~-  265 (480)
                      +.|+|.+++++.+...+......-   .. ...+..++||+||||||||++|+++|+.+   +.+++.++++.+..... 
T Consensus       558 ~~viG~~~a~~~l~~~i~~~~~g~---~~-~~~p~~~vLl~Gp~GtGKT~lA~~la~~~~~~~~~~i~i~~~~~~~~~~~  633 (854)
T 1qvr_A          558 KRVVGQDEAIRAVADAIRRARAGL---KD-PNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHAV  633 (854)
T ss_dssp             HHSCSCHHHHHHHHHHHHHHGGGC---SC-SSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGGG
T ss_pred             cccCCcHHHHHHHHHHHHHHhccc---CC-CCCCceEEEEECCCCCCHHHHHHHHHHHhcCCCCcEEEEechhccchhHH
Confidence            567899988888887775432110   00 01123479999999999999999999988   78999999987654211 


Q ss_pred             ------------------HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccc------cccCCceEEEEe
Q 011664          266 ------------------LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLN------SCCFEERVMVFT  321 (480)
Q Consensus       266 ------------------l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~------~~~~~~~ivI~t  321 (480)
                                        +...+ ....++||||||||.+.     ...++.|+..|+.-.-      .....+.+||+|
T Consensus       634 s~l~g~~~~~~G~~~~g~l~~~~-~~~~~~vl~lDEi~~l~-----~~~~~~Ll~~l~~~~~~~~~g~~vd~~~~iiI~t  707 (854)
T 1qvr_A          634 SRLIGAPPGYVGYEEGGQLTEAV-RRRPYSVILFDEIEKAH-----PDVFNILLQILDDGRLTDSHGRTVDFRNTVIILT  707 (854)
T ss_dssp             GGC--------------CHHHHH-HHCSSEEEEESSGGGSC-----HHHHHHHHHHHTTTEECCSSSCCEECTTEEEEEE
T ss_pred             HHHcCCCCCCcCccccchHHHHH-HhCCCeEEEEecccccC-----HHHHHHHHHHhccCceECCCCCEeccCCeEEEEe
Confidence                              11111 22456899999999763     3456777777763211      011246789999


Q ss_pred             cCCC--------------------------ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          322 MNSK--------------------------DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       322 TN~~--------------------------~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ||..                          ..+.|+|+.  ||+..+.+++|+.++...|+..++.
T Consensus       708 sn~~~~~~~~~~~~~~~~~~l~~~v~~~~~~~f~~~l~~--Rl~~~i~~~pl~~edi~~i~~~~l~  771 (854)
T 1qvr_A          708 SNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  771 (854)
T ss_dssp             CCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             cCcChHHHhhhcccccchHHHHHHHHHHHHhhCCHHHHH--hcCeEEeCCCCCHHHHHHHHHHHHH
Confidence            9962                          235677777  9999999999999999999988874

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=99.46  E-value=2.4e-13  Score=144.95  Aligned_cols=146  Identities=12%  Similarity=0.127  Sum_probs=95.2

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCCCcCChHHH--
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLSRVADDADL--  266 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s~~~~~~~l--  266 (480)
                      .++|.+++++.+...+.               ...++||+||||||||++|+++|+.++.  ++..+.+.- ...+++  
T Consensus        23 ~ivGq~~~i~~l~~al~---------------~~~~VLL~GpPGtGKT~LAraLa~~l~~~~~f~~~~~~~-~t~~dL~G   86 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAAL---------------SGESVFLLGPPGIAKSLIARRLKFAFQNARAFEYLMTRF-STPEEVFG   86 (500)
T ss_dssp             TCSSCHHHHHHHHHHHH---------------HTCEEEEECCSSSSHHHHHHHGGGGBSSCCEEEEECCTT-CCHHHHHC
T ss_pred             hhHHHHHHHHHHHHHHh---------------cCCeeEeecCchHHHHHHHHHHHHHHhhhhHHHHHHHhc-CCHHHhcC
Confidence            36788887776654332               1348999999999999999999998854  455555431 111111  


Q ss_pred             ---------HHHHHhh-----cCCcEEEEecccccccCcccccchhhhhhhccc-------ccccccCCceEEEEecCCC
Q 011664          267 ---------KSLLLQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG-------VLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       267 ---------~~l~~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg-------~~~~~~~~~~ivI~tTN~~  325 (480)
                               ...+...     ..++|||||||+.+.     ....+.|+..|+.       ...  ..+.+++|+|||.+
T Consensus        87 ~~~~~~~~~~g~~~~~~~g~l~~~~IL~IDEI~r~~-----~~~q~~LL~~lee~~v~i~G~~~--~~~~~~iI~ATN~l  159 (500)
T 3nbx_X           87 PLSIQALKDEGRYERLTSGYLPEAEIVFLDEIWKAG-----PAILNTLLTAINERQFRNGAHVE--KIPMRLLVAASNEL  159 (500)
T ss_dssp             CBC----------CBCCTTSGGGCSEEEEESGGGCC-----HHHHHHHHHHHHSSEEECSSSEE--ECCCCEEEEEESSC
T ss_pred             cccHHHHhhchhHHhhhccCCCcceeeeHHhHhhhc-----HHHHHHHHHHHHHHhccCCCCcC--CcchhhhhhccccC
Confidence                     1112111     146799999998652     3455677777742       211  12345678888853


Q ss_pred             cc---CcccccCCCceeEEEEcCCCCH-HHHHHHHHHHhc
Q 011664          326 DH---VDQALLRPGRIDVHIHFPLCDF-SSFKTLASSYLG  361 (480)
Q Consensus       326 ~~---LD~aLlrpGRfd~~I~~~~p~~-~~r~~il~~~l~  361 (480)
                      ..   ..+++++  ||..++++|+|+. +++..|++....
T Consensus       160 pe~~~~~~aLld--RF~~~i~v~~p~~~ee~~~IL~~~~~  197 (500)
T 3nbx_X          160 PEADSSLEALYD--RMLIRLWLDKVQDKANFRSMLTSQQD  197 (500)
T ss_dssp             CCTTCTTHHHHT--TCCEEEECCSCCCHHHHHHHHTCCCC
T ss_pred             CCccccHHHHHH--HHHHHHHHHHhhhhhhHHHHHhcccc
Confidence            22   3459999  9999999999997 778888877653

>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=99.46  E-value=2.1e-12  Score=130.63  Aligned_cols=149  Identities=11%  Similarity=0.101  Sum_probs=109.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC------------------------CcEEEEeCC---CcCChHHHHHHHHhh--
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS------------------------YDVYDVDLS---RVADDADLKSLLLQT--  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~------------------------~~~~~i~~s---~~~~~~~l~~l~~~~--  273 (480)
                      .+.++||+||||||||++|+++|+.+.                        .+++.++..   .-.+-..++.++...  
T Consensus        23 ~~~a~L~~G~~G~GKt~~a~~la~~l~~~~~~~~~~c~~c~~c~~~~~~~~~d~~~~~~~~~~~~~~i~~ir~l~~~~~~  102 (334)
T 1a5t_A           23 GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNE  102 (334)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTS
T ss_pred             cceeEEEECCCCchHHHHHHHHHHHHhCCCCCCCCCCCCCHHHHHHhcCCCCCEEEEeccccCCCCCHHHHHHHHHHHhh
Confidence            456899999999999999999998764                        346666653   233445577766543  


Q ss_pred             ----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          274 ----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       274 ----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                          ..+.|++|||+|.+..     ...+.|+..++.-     ....++|++||.++.+.|++++  |+. .++|++|+.
T Consensus       103 ~~~~~~~kvviIdead~l~~-----~a~naLLk~lEep-----~~~~~~Il~t~~~~~l~~ti~S--Rc~-~~~~~~~~~  169 (334)
T 1a5t_A          103 HARLGGAKVVWVTDAALLTD-----AAANALLKTLEEP-----PAETWFFLATREPERLLATLRS--RCR-LHYLAPPPE  169 (334)
T ss_dssp             CCTTSSCEEEEESCGGGBCH-----HHHHHHHHHHTSC-----CTTEEEEEEESCGGGSCHHHHT--TSE-EEECCCCCH
T ss_pred             ccccCCcEEEEECchhhcCH-----HHHHHHHHHhcCC-----CCCeEEEEEeCChHhCcHHHhh--cce-eeeCCCCCH
Confidence                2468999999998842     3356788877642     3567888899999999999999  885 799999999


Q ss_pred             HHHHHHHHHHhccCCCCCch-hHHHHHHhCCCCCHHHHHHHH
Q 011664          350 SSFKTLASSYLGLKDHKLFP-QVEEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       350 ~~r~~il~~~l~~~~~~l~~-~i~~l~~~~~g~s~adI~~ll  390 (480)
                      ++...++....     ...+ .++.++... +-++..+.+++
T Consensus       170 ~~~~~~L~~~~-----~~~~~~~~~l~~~s-~G~~r~a~~~l  205 (334)
T 1a5t_A          170 QYAVTWLSREV-----TMSQDALLAALRLS-AGSPGAALALF  205 (334)
T ss_dssp             HHHHHHHHHHC-----CCCHHHHHHHHHHT-TTCHHHHHHTT
T ss_pred             HHHHHHHHHhc-----CCCHHHHHHHHHHc-CCCHHHHHHHh
Confidence            99998888775     2233 345566555 55666665554

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=99.41  E-value=1.2e-13  Score=122.64  Aligned_cols=132  Identities=11%  Similarity=0.066  Sum_probs=88.1

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLL  270 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~  270 (480)
                      +++|.+...+.+.+.+..+..           ...++||+||||||||++|+++++..+ +++.++++.+... ....++
T Consensus         5 ~~iG~s~~~~~l~~~~~~~~~-----------~~~~vll~G~~GtGKt~lA~~i~~~~~-~~~~~~~~~~~~~-~~~~~~   71 (143)
T 3co5_A            5 DKLGNSAAIQEMNREVEAAAK-----------RTSPVFLTGEAGSPFETVARYFHKNGT-PWVSPARVEYLID-MPMELL   71 (143)
T ss_dssp             ---CCCHHHHHHHHHHHHHHT-----------CSSCEEEEEETTCCHHHHHGGGCCTTS-CEECCSSTTHHHH-CHHHHH
T ss_pred             CceeCCHHHHHHHHHHHHHhC-----------CCCcEEEECCCCccHHHHHHHHHHhCC-CeEEechhhCChH-hhhhHH
Confidence            467888888888887776532           235799999999999999999999888 9999998875432 134444


Q ss_pred             HhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC-cc----CcccccCCCcee-EEEEc
Q 011664          271 LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK-DH----VDQALLRPGRID-VHIHF  344 (480)
Q Consensus       271 ~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~-~~----LD~aLlrpGRfd-~~I~~  344 (480)
                      ..+ .+++|||||+|.+..     .....|+..++...    ..+..+|+|||.+ +.    +++.|..  |+. ..|++
T Consensus        72 ~~a-~~~~l~lDei~~l~~-----~~q~~Ll~~l~~~~----~~~~~iI~~tn~~~~~~~~~~~~~L~~--rl~~~~i~l  139 (143)
T 3co5_A           72 QKA-EGGVLYVGDIAQYSR-----NIQTGITFIIGKAE----RCRVRVIASCSYAAGSDGISCEEKLAG--LFSESVVRI  139 (143)
T ss_dssp             HHT-TTSEEEEEECTTCCH-----HHHHHHHHHHHHHT----TTTCEEEEEEEECTTTC--CHHHHHHH--HSSSEEEEE
T ss_pred             HhC-CCCeEEEeChHHCCH-----HHHHHHHHHHHhCC----CCCEEEEEecCCCHHHHHhCccHHHHH--HhcCcEEeC
Confidence            443 468999999998843     22344666665432    2345677777743 33    3445555  543 56777


Q ss_pred             CCC
Q 011664          345 PLC  347 (480)
Q Consensus       345 ~~p  347 (480)
                      |+.
T Consensus       140 PpL  142 (143)
T 3co5_A          140 PPL  142 (143)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            753

>3f9v_A Minichromosome maintenance protein MCM; replicative helicase, DNA replication, MCM complex, AAA+ Pro ATP-binding, DNA-binding, helicase; 4.35A {Sulfolobus solfataricus}

Probab=99.36  E-value=2.2e-13  Score=148.44  Aligned_cols=184  Identities=15%  Similarity=0.154  Sum_probs=112.6

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC----CCcCC---
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL----SRVAD---  262 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~----s~~~~---  262 (480)
                      ..|.|++++|+.+.-.+..  ..+............++||+||||||||++|+++|+.++..++....    ..+.+   
T Consensus       295 ~~I~G~e~vk~al~~~l~~--g~~~~~~~~~~r~~~~vLL~GppGtGKT~LAr~la~~~~r~~~~~~~~~~~~~l~~~~~  372 (595)
T 3f9v_A          295 PSIYGHWELKEALALALFG--GVPKVLEDTRIRGDIHILIIGDPGTAKSQMLQFISRVAPRAVYTTGKGSTAAGLTAAVV  372 (595)
T ss_dssp             STTSCCHHHHHHHTTTTTC--CCCEETTTTEECCSCCEEEEESSCCTHHHHHHSSSTTCSCEECCCTTCSTTTTSEEECS
T ss_pred             chhcChHHHHHHHHHHHhC--CCcccccCCCcCCCcceEEECCCchHHHHHHHHHHHhCCCceecCCCccccccccceee
Confidence            4578888877766422110  00000000011122279999999999999999999999876655321    11111   


Q ss_pred             -hH-----HHH-HHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccc---------cccccCCceEEEEecCCCc
Q 011664          263 -DA-----DLK-SLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV---------LNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 -~~-----~l~-~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~---------~~~~~~~~~ivI~tTN~~~  326 (480)
                       +.     ... ..+. ...++|+||||||.+..     ...+.|+..|+.-         .. .......||+|||.++
T Consensus       373 ~~~~~g~~~~~~G~l~-~A~~gil~IDEid~l~~-----~~q~~Ll~~le~~~i~i~~~g~~~-~~~~~~~vIaatNp~~  445 (595)
T 3f9v_A          373 REKGTGEYYLEAGALV-LADGGIAVIDEIDKMRD-----EDRVAIHEAMEQQTVSIAKAGIVA-KLNARAAVIAAGNPKF  445 (595)
T ss_dssp             SGGGTSSCSEEECHHH-HHSSSEECCTTTTCCCS-----HHHHHHHHHHHSSSEEEESSSSEE-EECCCCEEEEEECCTT
T ss_pred             eccccccccccCCeeE-ecCCCcEEeehhhhCCH-----hHhhhhHHHHhCCEEEEecCCcEE-EecCceEEEEEcCCcC
Confidence             00     000 0111 12568999999998742     2345666666521         11 1123467889999886


Q ss_pred             -------------cCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHH
Q 011664          327 -------------HVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       327 -------------~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~  392 (480)
                                   .|+++|++  ||| ..+..++|+.+ ...|++..+......         .....+++.++..++..
T Consensus       446 G~~~~~~~~~~ni~l~~aLl~--RFDl~~~~~~~~~~e-~~~i~~~il~~~~~~---------~~~~~l~~~~l~~~i~~  513 (595)
T 3f9v_A          446 GRYISERPVSDNINLPPTILS--RFDLIFILKDQPGEQ-DRELANYILDVHSGK---------STKNIIDIDTLRKYIAY  513 (595)
T ss_dssp             CCSCTTSCSCTTTCSCSSSGG--GCSCCEEECCTTHHH-HHHHHHHHHTTTCCC---------SSSSTTCCTTTHHHHHH
T ss_pred             CccCcccCchhccCCCHHHHh--hCeEEEEeCCCCCHH-HHHHHHHHHHHhhcc---------ccccCCCHHHHHHHHHH
Confidence                         89999999  998 56677788888 888888887654331         12346777777777765


Q ss_pred             hh
Q 011664          393 NR  394 (480)
Q Consensus       393 a~  394 (480)
                      ++
T Consensus       514 ar  515 (595)
T 3f9v_A          514 AR  515 (595)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>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=99.33  E-value=4.3e-12  Score=156.21  Aligned_cols=135  Identities=19%  Similarity=0.264  Sum_probs=101.5

Q ss_pred             CceEEEEccCCCcHHHHH-HHHHHcCCCcEEEEeCCCcCChHHHHHHHHhh-----------------cCCcEEEEeccc
Q 011664          224 KRSYLLYGPSGTGKSSFA-AAMASFMSYDVYDVDLSRVADDADLKSLLLQT-----------------TSKSVILIEDLD  285 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La-~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~-----------------~~~sII~IDEiD  285 (480)
                      .+++||+||||||||++| +++++..+..++.++++...+...+...+...                 ..++||||||||
T Consensus      1267 ~~~vLL~GPpGtGKT~la~~~l~~~~~~~~~~infsa~ts~~~~~~~i~~~~~~~~~~~g~~~~P~~~gk~~VlFiDEin 1346 (2695)
T 4akg_A         1267 KRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKDTTTEHILSALHRHTNYVTTSKGLTLLPKSDIKNLVLFCDEIN 1346 (2695)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHHHSCSSCEEEEEECCTTCCHHHHHHHHHHHBCCEEETTTEEEEEBSSSSCEEEEEETTT
T ss_pred             CCeEEEECCCCCCHHHHHHHHHhcCCCCceEEEEeecCCCHHHHHHHHHHHhhhccccCCccccCCCCCceEEEEecccc
Confidence            468999999999999999 55666668899999999888777776666432                 124799999999


Q ss_pred             ccccCcccccchhhhhhhc---cccccccc-----CCceEEEEecCCCc-----cCcccccCCCceeEEEEcCCCCHHHH
Q 011664          286 RFLVEKPAAVSLSGVLNFM---DGVLNSCC-----FEERVMVFTMNSKD-----HVDQALLRPGRIDVHIHFPLCDFSSF  352 (480)
Q Consensus       286 ~l~~~~~~~~~ls~lL~~l---dg~~~~~~-----~~~~ivI~tTN~~~-----~LD~aLlrpGRfd~~I~~~~p~~~~r  352 (480)
                      ....++.+.+...++|.++   .|++....     -.+..+|+|||+|.     .|+|+++|  || ..++++.|+.+++
T Consensus      1347 mp~~d~yg~q~~lelLRq~le~gg~yd~~~~~~~~~~~i~lIaA~Npp~~gGR~~l~~rllR--rf-~vi~i~~P~~~~l 1423 (2695)
T 4akg_A         1347 LPKLDKYGSQNVVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFTR--HA-AILYLGYPSGKSL 1423 (2695)
T ss_dssp             CSCCCSSSCCHHHHHHHHHHHTSSEECTTTCCEEEEESEEEEEEECCTTSTTCCCCCHHHHT--TE-EEEECCCCTTTHH
T ss_pred             cccccccCchhHHHHHHHHHhcCCEEEcCCCcEEEecCEEEEEecCCCccCCCccCChhhhh--ee-eEEEeCCCCHHHH
Confidence            7655554444445555544   24433100     12467889999994     79999999  99 7899999999999


Q ss_pred             HHHHHHHhc
Q 011664          353 KTLASSYLG  361 (480)
Q Consensus       353 ~~il~~~l~  361 (480)
                      ..|++.++.
T Consensus      1424 ~~I~~~il~ 1432 (2695)
T 4akg_A         1424 SQIYEIYYK 1432 (2695)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999988875

>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=99.31  E-value=2.1e-11  Score=122.20  Aligned_cols=121  Identities=13%  Similarity=0.187  Sum_probs=95.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC------CCcEEEEeCCC-cCChHHHHHHHHhhc------CCcEEEEecccccccCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM------SYDVYDVDLSR-VADDADLKSLLLQTT------SKSVILIEDLDRFLVEK  291 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l------~~~~~~i~~s~-~~~~~~l~~l~~~~~------~~sII~IDEiD~l~~~~  291 (480)
                      ..+|||||||||||++|+++|+.+      +.+++.++.+. -.+-..++.++....      ...|++|||+|.+.   
T Consensus        19 ~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt---   95 (305)
T 2gno_A           19 ISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMT---   95 (305)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBC---
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCCceEEEeccHHHhC---
Confidence            489999999999999999999863      46888888764 445556777665432      34799999999883   


Q ss_pred             ccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          292 PAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       292 ~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                        ....+.||..|+.-     ++..++|++||.+..+.|++++  |   .++|++|+.++....+...+
T Consensus        96 --~~a~naLLk~LEep-----~~~t~fIl~t~~~~kl~~tI~S--R---~~~f~~l~~~~i~~~L~~~~  152 (305)
T 2gno_A           96 --QQAANAFLKALEEP-----PEYAVIVLNTRRWHYLLPTIKS--R---VFRVVVNVPKEFRDLVKEKI  152 (305)
T ss_dssp             --HHHHHHTHHHHHSC-----CTTEEEEEEESCGGGSCHHHHT--T---SEEEECCCCHHHHHHHHHHH
T ss_pred             --HHHHHHHHHHHhCC-----CCCeEEEEEECChHhChHHHHc--e---eEeCCCCCHHHHHHHHHHHh
Confidence              23356788887642     4567888888999999999999  8   89999999999888888776

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=99.28  E-value=2.6e-12  Score=117.74  Aligned_cols=128  Identities=16%  Similarity=0.168  Sum_probs=79.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCCc
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSRV  260 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~~  260 (480)
                      .+.+|+++.+.....+.+.+.+..+...      +......+++|+||||||||+|++++++.+    |..++.+++.++
T Consensus         5 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~------~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~~~~~g~~~~~~~~~~~   78 (180)
T 3ec2_A            5 WNANLDTYHPKNVSQNRALLTIRVFVHN------FNPEEGKGLTFVGSPGVGKTHLAVATLKAIYEKKGIRGYFFDTKDL   78 (180)
T ss_dssp             TTCCSSSCCCCSHHHHHHHHHHHHHHHS------CCGGGCCEEEECCSSSSSHHHHHHHHHHHHHHHSCCCCCEEEHHHH
T ss_pred             hhCccccccCCCHHHHHHHHHHHHHHHh------ccccCCCEEEEECCCCCCHHHHHHHHHHHHHHHcCCeEEEEEHHHH
Confidence            4568999987655455555555555433      333346789999999999999999999876    666777765443


Q ss_pred             CCh-------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          261 ADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       261 ~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ...       .....++.....|.+|+|||++....+....   ..+.+.++....    .+..+|+|||.+
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~llilDE~~~~~~~~~~~---~~l~~ll~~~~~----~~~~ii~tsn~~  143 (180)
T 3ec2_A           79 IFRLKHLMDEGKDTKFLKTVLNSPVLVLDDLGSERLSDWQR---ELISYIITYRYN----NLKSTIITTNYS  143 (180)
T ss_dssp             HHHHHHHHHHTCCSHHHHHHHTCSEEEEETCSSSCCCHHHH---HHHHHHHHHHHH----TTCEEEEECCCC
T ss_pred             HHHHHHHhcCchHHHHHHHhcCCCEEEEeCCCCCcCCHHHH---HHHHHHHHHHHH----cCCCEEEEcCCC
Confidence            211       0011233445588999999998653222222   233344443322    345678888865

>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=99.26  E-value=3e-11  Score=123.99  Aligned_cols=196  Identities=13%  Similarity=0.104  Sum_probs=122.0

Q ss_pred             CCCccccccChHHHHHHHHHH-HHHHhhhhHHhhhCCCCCceEEE--EccCCCcHHHHHHHHHHcC---------CCcEE
Q 011664          186 PSTFDTISMETDLKNRVKSDL-ESFLKAKHYYHRLGRVWKRSYLL--YGPSGTGKSSFAAAMASFM---------SYDVY  253 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l-~~~l~~~~~~~~~g~~~~rgiLL--~GPpGTGKT~La~aiA~~l---------~~~~~  253 (480)
                      ....+.++|.++..+.+.+.+ .......       ...++.+++  +||||||||+|++++++.+         +..++
T Consensus        18 ~~~p~~l~gR~~el~~l~~~l~~~~~~~~-------~~~~~~~li~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~   90 (412)
T 1w5s_A           18 NYIPPELRVRRGEAEALARIYLNRLLSGA-------GLSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQA   90 (412)
T ss_dssp             TCCCSSCSSSCHHHHHHHHHHHHHHHTSS-------CBCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             ccCCCCCCChHHHHHHHHHHHhHHHhcCC-------CCCCCEEEEeCcCcCCCCHHHHHHHHHHHHHHHHhccCCceeEE
Confidence            334578999999888888776 5433220       013457899  9999999999999999876         45677


Q ss_pred             EEeCCCcCCh----------------------HH----HHHHHHhhcCCcEEEEecccccccCc-ccccchhhhhhhccc
Q 011664          254 DVDLSRVADD----------------------AD----LKSLLLQTTSKSVILIEDLDRFLVEK-PAAVSLSGVLNFMDG  306 (480)
Q Consensus       254 ~i~~s~~~~~----------------------~~----l~~l~~~~~~~sII~IDEiD~l~~~~-~~~~~ls~lL~~ldg  306 (480)
                      .+++....+.                      ..    +...+.....|.||+|||+|.+.... .+...+..++..++.
T Consensus        91 ~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~l~~~l~~~~~~~llvlDe~~~l~~~~~~~~~~l~~l~~~~~~  170 (412)
T 1w5s_A           91 YVNAFNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEE  170 (412)
T ss_dssp             EEEGGGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHH
T ss_pred             EEECCCCCCHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHhcCCeEEEEEeCHHHHhhccCcchHHHHHHHHHHHh
Confidence            8886432211                      11    11222223468899999999885421 122334445554443


Q ss_pred             ccccccC--CceEEEEecCCCc---cCc---ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccC--CCCCch-hHHHHH
Q 011664          307 VLNSCCF--EERVMVFTMNSKD---HVD---QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLK--DHKLFP-QVEEIF  375 (480)
Q Consensus       307 ~~~~~~~--~~~ivI~tTN~~~---~LD---~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~--~~~l~~-~i~~l~  375 (480)
                      ...  .+  ....+|++||.++   .++   +.+.+  |+...+.+++++.++..+++...+...  ...+.+ .++.++
T Consensus       171 ~~~--~~~~~~v~lI~~~~~~~~~~~l~~~~~~~~~--~~~~~i~l~~l~~~e~~~ll~~~~~~~~~~~~~~~~~~~~i~  246 (412)
T 1w5s_A          171 IPS--RDGVNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAELGLRDTVWEPRHLELIS  246 (412)
T ss_dssp             SCC--TTSCCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHHHHBCTTSCCHHHHHHHH
T ss_pred             ccc--CCCCceEEEEEEeccccHHHHHhhhcchhhh--hcCCeeeeCCCCHHHHHHHHHHHHHhcCCCCCCChHHHHHHH
Confidence            221  02  3566777887654   345   66777  666569999999999999998765421  122333 345666


Q ss_pred             HhCCC-----CCHHHHHHHHHH
Q 011664          376 QNGSS-----LSPAEIGELMIA  392 (480)
Q Consensus       376 ~~~~g-----~s~adI~~ll~~  392 (480)
                      ..+..     -.|..+.+++..
T Consensus       247 ~~~~~~~~~~G~p~~~~~l~~~  268 (412)
T 1w5s_A          247 DVYGEDKGGDGSARRAIVALKM  268 (412)
T ss_dssp             HHHCGGGTSCCCHHHHHHHHHH
T ss_pred             HHHHHhccCCCcHHHHHHHHHH
Confidence            66540     456666666654

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=99.16  E-value=2.5e-11  Score=144.09  Aligned_cols=137  Identities=13%  Similarity=0.174  Sum_probs=91.3

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhh----------hhHHhh------hC------------CCCCceEEEEccCCCc
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKA----------KHYYHR------LG------------RVWKRSYLLYGPSGTG  236 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~----------~~~~~~------~g------------~~~~rgiLL~GPpGTG  236 (480)
                      ..++|+++.|.+++|+.+.+.+.+++..          ++.|+.      .|            .|..+.+|+|||||||
T Consensus      1015 ~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tG~~glD~~lg~GG~p~g~~~l~~G~~g~G 1094 (1706)
T 3cmw_A         1015 SGSSTGSMSAIDENKQKALAAALGQIEKQFGKGSIMRLGEDRSMDVETISTGSLSLDIALGAGGLPMGRIVEIYGPESSG 1094 (1706)
T ss_dssp             ---------CTTHHHHHHHHHHHHHHHHHHCGGGSEEGGGCGGGSCCEECCSCHHHHHHTSSSSEETTSEEEEECSTTSS
T ss_pred             CCceeeecCCccHHHHHHHHHHHHHHhhccCcccchhchhhhhccccccccCchhHHHHhccCCCCCCCEEEEEcCCCCC
Confidence            3379999999999999999999999954          455655      22            2333449999999999


Q ss_pred             HHHHHHHHHHcC---CCcEEEEeCCCcC----------------------ChHHHHHHHH--hhcCCcEEEEeccccccc
Q 011664          237 KSSFAAAMASFM---SYDVYDVDLSRVA----------------------DDADLKSLLL--QTTSKSVILIEDLDRFLV  289 (480)
Q Consensus       237 KT~La~aiA~~l---~~~~~~i~~s~~~----------------------~~~~l~~l~~--~~~~~sII~IDEiD~l~~  289 (480)
                      ||+||+++|.+.   |.+...|+.....                      ++..++.++.  +...||+||+|++|++++
T Consensus      1095 KT~la~~~~~~~~~~g~~~~fi~~~~~~~~~~~~~~G~d~~~~~~~~~~~~e~~l~~~~~~ar~~~~~~i~~d~~~al~~ 1174 (1706)
T 3cmw_A         1095 KTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTP 1174 (1706)
T ss_dssp             HHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCGGGCCC
T ss_pred             hHHHHHHHHHHhhhcCCceeEEEcccchHHHHHHHhCCCHHHHhhccccchHHHHHHHHHHHHhcCCeEEEeCchHhcCc
Confidence            999999999866   5556666554422                      2334555553  456899999999999987


Q ss_pred             Ccc-----cc-------cchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          290 EKP-----AA-------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       290 ~~~-----~~-------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      .+.     +.       +.++++|..|+++..   ..+++|| +||+.
T Consensus      1175 ~~~~~g~~~~~~~~~~~r~~~q~l~~~~~~~~---~~~v~v~-~~n~~ 1218 (1706)
T 3cmw_A         1175 KAEIEGEIGDSHMGLAARMMSQAMRKLAGNLK---QSNTLLI-FINQI 1218 (1706)
T ss_dssp             HHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHH---HTTCEEE-EEECE
T ss_pred             ccccccccccccccHHHHHHHHHHHHHHhhhc---cCCeEEE-Eeccc
Confidence            632     11       137889999999876   3444444 77754

>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=99.11  E-value=7.3e-11  Score=121.48  Aligned_cols=115  Identities=18%  Similarity=0.249  Sum_probs=83.6

Q ss_pred             hCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEeccccccc-Cccc---c
Q 011664          219 LGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLV-EKPA---A  294 (480)
Q Consensus       219 ~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~-~~~~---~  294 (480)
                      ++.+.++.++|+|||||||||+++++++.++..++.++...    ......+....+..++++||++.+.. .+..   .
T Consensus       164 ~~i~~~~~i~l~G~~GsGKSTl~~~l~~~~~g~~~~~~~~~----~~~~~~lg~~~q~~~~l~dd~~~~~~~~r~l~~~~  239 (377)
T 1svm_A          164 YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPL----DRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQ  239 (377)
T ss_dssp             HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCT----TTHHHHHGGGTTCSCEEETTCCCSTTTTTTCCCCS
T ss_pred             cccCCCCEEEEECCCCCCHHHHHHHHHhhcCCcEEEEeccc----hhHHHHHHHhcchhHHHHHHHHHHHHHHhhccccC
Confidence            36778889999999999999999999998887766543322    11222344455778899999998764 1110   1


Q ss_pred             --cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCC
Q 011664          295 --VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       295 --~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~  346 (480)
                        .+...+.+.+||.        +.++++||+++.+ +++++|||++..++..+
T Consensus       240 ~~~~~~~l~~~ldG~--------v~v~~~tn~~~~l-~alf~pg~ld~~~~~l~  284 (377)
T 1svm_A          240 GINNLDNLRDYLDGS--------VKVNLEKKHLNKR-TQIFPPGIVTMNEYSVP  284 (377)
T ss_dssp             HHHHHHTTHHHHHCS--------SCEEECCSSSCCE-EECCCCEEEEECSCCCC
T ss_pred             cchHHHHHHHHhcCC--------CeEeeccCchhhH-HHhhcCcccChhHHhhc
Confidence              1235567777664        3467889999999 79999999998887766

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=99.10  E-value=1.3e-10  Score=108.02  Aligned_cols=98  Identities=16%  Similarity=0.193  Sum_probs=64.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCC-CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRV-WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV  260 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~-~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~  260 (480)
                      .+.+|+++.+.....+.+.+.+..++...      ... .+++++|+||||||||++++++++++   +.+++.++++.+
T Consensus        20 ~~~~f~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~l~G~~GtGKT~la~~i~~~~~~~~~~~~~~~~~~~   93 (202)
T 2w58_A           20 LRASLSDVDLNDDGRIKAIRFAERFVAEY------EPGKKMKGLYLHGSFGVGKTYLLAAIANELAKRNVSSLIVYVPEL   93 (202)
T ss_dssp             GCCCTTSSCCSSHHHHHHHHHHHHHHHHC------CSSCCCCEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEEHHHH
T ss_pred             HcCCHhhccCCChhHHHHHHHHHHHHHHh------hhccCCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEhHHH
Confidence            35689999887654555555555555432      111 23789999999999999999999977   677888876543


Q ss_pred             CCh-------HHHHHHHHhhcCCcEEEEecccccc
Q 011664          261 ADD-------ADLKSLLLQTTSKSVILIEDLDRFL  288 (480)
Q Consensus       261 ~~~-------~~l~~l~~~~~~~sII~IDEiD~l~  288 (480)
                      ...       ..+..++.....+.+|+|||++...
T Consensus        94 ~~~~~~~~~~~~~~~~~~~~~~~~~lilDei~~~~  128 (202)
T 2w58_A           94 FRELKHSLQDQTMNEKLDYIKKVPVLMLDDLGAEA  128 (202)
T ss_dssp             HHHHHHC---CCCHHHHHHHHHSSEEEEEEECCC-
T ss_pred             HHHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCc
Confidence            210       1112233333456799999998653

>3k1j_A LON protease, ATP-dependent protease LON; ATP-binding, nucleotide-binding, Pro hydrolase; HET: ADP PE8; 2.00A {Thermococcus onnurineus}

Probab=99.07  E-value=3.6e-10  Score=123.27  Aligned_cols=53  Identities=28%  Similarity=0.343  Sum_probs=42.8

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      ..+|.+|++++|.+.+++.+...+.               ....++|+||||||||++|+++|+.+..
T Consensus        34 ~~rp~~l~~i~G~~~~l~~l~~~i~---------------~g~~vll~Gp~GtGKTtlar~ia~~l~~   86 (604)
T 3k1j_A           34 EVPEKLIDQVIGQEHAVEVIKTAAN---------------QKRHVLLIGEPGTGKSMLGQAMAELLPT   86 (604)
T ss_dssp             CCCSSHHHHCCSCHHHHHHHHHHHH---------------TTCCEEEECCTTSSHHHHHHHHHHTSCC
T ss_pred             cccccccceEECchhhHhhcccccc---------------CCCEEEEEeCCCCCHHHHHHHHhccCCc
Confidence            3467889999999988877665443               1247999999999999999999998753

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=99.01  E-value=2.4e-10  Score=114.51  Aligned_cols=97  Identities=19%  Similarity=0.246  Sum_probs=61.3

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCCcC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSRVA  261 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~~~  261 (480)
                      +.+|+++.+...-...+.+.+..++...      +.....+++||||||||||+||+++|+++    |.++..++++.+.
T Consensus       120 ~~tfd~f~~~~~~~~~~~~~~~~~i~~~------~~~~~~~lll~G~~GtGKT~La~aia~~~~~~~g~~v~~~~~~~l~  193 (308)
T 2qgz_A          120 HIHLSDIDVNNASRMEAFSAILDFVEQY------PSAEQKGLYLYGDMGIGKSYLLAAMAHELSEKKGVSTTLLHFPSFA  193 (308)
T ss_dssp             SCCGGGSCCCSHHHHHHHHHHHHHHHHC------SCSSCCEEEEECSTTSSHHHHHHHHHHHHHHHSCCCEEEEEHHHHH
T ss_pred             hCCHhhCcCCChHHHHHHHHHHHHHHhc------cccCCceEEEECCCCCCHHHHHHHHHHHHHHhcCCcEEEEEHHHHH
Confidence            4689999876544444555555555431      11135799999999999999999999865    4777777764332


Q ss_pred             C-------hHHHHHHHHhhcCCcEEEEecccccc
Q 011664          262 D-------DADLKSLLLQTTSKSVILIEDLDRFL  288 (480)
Q Consensus       262 ~-------~~~l~~l~~~~~~~sII~IDEiD~l~  288 (480)
                      .       +..+...+.......+|+|||++...
T Consensus       194 ~~l~~~~~~~~~~~~~~~~~~~~lLiiDdig~~~  227 (308)
T 2qgz_A          194 IDVKNAISNGSVKEEIDAVKNVPVLILDDIGAEQ  227 (308)
T ss_dssp             HHHHCCCC----CCTTHHHHTSSEEEEETCCC--
T ss_pred             HHHHHHhccchHHHHHHHhcCCCEEEEcCCCCCC
Confidence            1       11111222333456899999997653

>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=98.97  E-value=1e-08  Score=102.35  Aligned_cols=178  Identities=13%  Similarity=0.146  Sum_probs=107.3

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc-----
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV-----  260 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~-----  260 (480)
                      +...+.++|-++..+.|.+ +.    .            +.++++||+|+|||+|++.+++.++..++.+++...     
T Consensus         9 ~~~~~~~~gR~~el~~L~~-l~----~------------~~v~i~G~~G~GKT~L~~~~~~~~~~~~~~~~~~~~~~~~~   71 (357)
T 2fna_A            9 KDNRKDFFDREKEIEKLKG-LR----A------------PITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERNY   71 (357)
T ss_dssp             CCSGGGSCCCHHHHHHHHH-TC----S------------SEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCSC
T ss_pred             CCCHHHhcChHHHHHHHHH-hc----C------------CcEEEECCCCCCHHHHHHHHHHhcCCCEEEEEchhhccccC
Confidence            3456778898877776664 32    1            379999999999999999999988777888886542     


Q ss_pred             CCh-----------------------------------------------HHHHHHH---Hhhc-CCcEEEEeccccccc
Q 011664          261 ADD-----------------------------------------------ADLKSLL---LQTT-SKSVILIEDLDRFLV  289 (480)
Q Consensus       261 ~~~-----------------------------------------------~~l~~l~---~~~~-~~sII~IDEiD~l~~  289 (480)
                      .+.                                               ..+..++   .+.. .|.+|+|||++.+..
T Consensus        72 ~~~~~~~~~l~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~vlvlDe~~~~~~  151 (357)
T 2fna_A           72 ISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELVK  151 (357)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGGG
T ss_pred             CCHHHHHHHHHHHHHHHhhhhhHHHHHhcccceEEecceEEEeccCCcchhhHHHHHHHHHhcCCCCeEEEEECHHHhhc
Confidence            110                                               0122222   2222 388999999998753


Q ss_pred             CcccccchhhhhhhcccccccccCCceEEEEecCCCccC---------cccccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          290 EKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV---------DQALLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       290 ~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L---------D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                      .. +    .+++..+..+...  ..+..+|+|+.....+         ...+.  ||+...+.+++.+.++..+++...+
T Consensus       152 ~~-~----~~~~~~l~~~~~~--~~~~~~i~~g~~~~~l~~~l~~~~~~~~l~--~r~~~~i~l~~l~~~e~~~~l~~~~  222 (357)
T 2fna_A          152 LR-G----VNLLPALAYAYDN--LKRIKFIMSGSEMGLLYDYLRVEDPESPLF--GRAFSTVELKPFSREEAIEFLRRGF  222 (357)
T ss_dssp             CT-T----CCCHHHHHHHHHH--CTTEEEEEEESSHHHHHHHTTTTCTTSTTT--TCCCEEEEECCCCHHHHHHHHHHHH
T ss_pred             cC-c----hhHHHHHHHHHHc--CCCeEEEEEcCchHHHHHHHhccCCCCccc--cCccceeecCCCCHHHHHHHHHHHH
Confidence            11 1    1122222222220  1234556655433211         12232  4776799999999999999998776


Q ss_pred             ccCCCCCchhHHHHHHhCCCCCHHHHHHHHH
Q 011664          361 GLKDHKLFPQVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       361 ~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      +..+..... ...+...+.| .|.-+..++.
T Consensus       223 ~~~~~~~~~-~~~i~~~t~G-~P~~l~~~~~  251 (357)
T 2fna_A          223 QEADIDFKD-YEVVYEKIGG-IPGWLTYFGF  251 (357)
T ss_dssp             HHHTCCCCC-HHHHHHHHCS-CHHHHHHHHH
T ss_pred             HHcCCCCCc-HHHHHHHhCC-CHHHHHHHHH
Confidence            432333322 3666677744 4666666554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=98.96  E-value=3.6e-10  Score=101.25  Aligned_cols=99  Identities=11%  Similarity=0.205  Sum_probs=67.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhh
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGV  300 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~l  300 (480)
                      ...++|+||+|+|||+|++++++.+   |..+++++...+....       -..++.+|+|||++.+....     ...+
T Consensus        36 g~~~~l~G~~G~GKTtL~~~i~~~~~~~g~~~~~~~~~~~~~~~-------~~~~~~lLilDE~~~~~~~~-----~~~l  103 (149)
T 2kjq_A           36 GQFIYVWGEEGAGKSHLLQAWVAQALEAGKNAAYIDAASMPLTD-------AAFEAEYLAVDQVEKLGNEE-----QALL  103 (149)
T ss_dssp             CSEEEEESSSTTTTCHHHHHHHHHHHTTTCCEEEEETTTSCCCG-------GGGGCSEEEEESTTCCCSHH-----HHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEcHHHhhHHH-------HHhCCCEEEEeCccccChHH-----HHHH
Confidence            4579999999999999999999977   7778889887766541       13468999999999864322     2334


Q ss_pred             hhhcccccccccCCceEEEEecC-CCccCc--ccccCCCcee
Q 011664          301 LNFMDGVLNSCCFEERVMVFTMN-SKDHVD--QALLRPGRID  339 (480)
Q Consensus       301 L~~ldg~~~~~~~~~~ivI~tTN-~~~~LD--~aLlrpGRfd  339 (480)
                      +..++....   .+..++|+||| .|..+.  ++|.+  |+.
T Consensus       104 ~~li~~~~~---~g~~~iiits~~~p~~l~~~~~L~S--Rl~  140 (149)
T 2kjq_A          104 FSIFNRFRN---SGKGFLLLGSEYTPQQLVIREDLRT--RMA  140 (149)
T ss_dssp             HHHHHHHHH---HTCCEEEEEESSCTTTSSCCHHHHH--HGG
T ss_pred             HHHHHHHHH---cCCcEEEEECCCCHHHccccHHHHH--HHh
Confidence            444444333   12233556666 555443  67777  765

>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=98.92  E-value=1.2e-08  Score=105.17  Aligned_cols=197  Identities=13%  Similarity=0.155  Sum_probs=122.1

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEeCCCcCChHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVDLSRVADDADL  266 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~~s~~~~~~~l  266 (480)
                      +.++|....-+.+.+.+....           .....+|++|++|||||++|++++....   .+|+.++|+.+..+.--
T Consensus       137 ~~~ig~s~~m~~l~~~i~~~a-----------~~~~~vli~Ge~GtGK~~lAr~ih~~s~r~~~~fv~v~~~~~~~~~~~  205 (387)
T 1ny5_A          137 EEYVFESPKMKEILEKIKKIS-----------CAECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFE  205 (387)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHT-----------TCCSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHH
T ss_pred             hhhhhccHHhhHHHHHHHHhc-----------CCCCCeEEecCCCcCHHHHHHHHHHhcCCCCCCeEEEecCCCCHHHHH
Confidence            356666665566655554421           1234689999999999999999998764   68999999987643333


Q ss_pred             HHHHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhccc-----cccc-ccCCceEEEEecC
Q 011664          267 KSLLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG-----VLNS-CCFEERVMVFTMN  323 (480)
Q Consensus       267 ~~l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg-----~~~~-~~~~~~ivI~tTN  323 (480)
                      ..+|..                 ....++||||||+.+..     .....|+..++.     +.+. ...-...+|+|||
T Consensus       206 ~elfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~~-----~~q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~  280 (387)
T 1ny5_A          206 AELFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSL-----EAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATN  280 (387)
T ss_dssp             HHHHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCH-----HHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEES
T ss_pred             HHhcCCCCCCCCCcccccCCceeeCCCcEEEEcChhhCCH-----HHHHHHHHHHhcCcEEeCCCCceeeccEEEEEeCC
Confidence            344421                 12457999999998832     333556655542     1110 0012345788888


Q ss_pred             CC-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          324 SK-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       324 ~~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      ..       ..+.+.|.-  |+. ..|++|+...  ++...|+..++....       ........++|+.-+..+....
T Consensus       281 ~~l~~~~~~g~fr~dl~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~l~~~~  351 (387)
T 1ny5_A          281 RNIKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLKKFS-------RKYAKEVEGFTKSAQELLLSYP  351 (387)
T ss_dssp             SCHHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHHHHH-------HHTTCCCCEECHHHHHHHHHSC
T ss_pred             CCHHHHHHcCCccHHHHH--hhcCCeecCCcchhccccHHHHHHHHHHHHH-------HHcCCCCCCCCHHHHHHHHhCC
Confidence            53       223344443  453 5566666543  555566666653211       0111122468999888888888


Q ss_pred             hhcHHHHHHHHHHHHHhc
Q 011664          394 RNSPSRALKSVITALQTD  411 (480)
Q Consensus       394 ~~~~~~al~~~i~~~~~~  411 (480)
                      +...++.|+++++.....
T Consensus       352 wpGNvreL~~~i~~~~~~  369 (387)
T 1ny5_A          352 WYGNVRELKNVIERAVLF  369 (387)
T ss_dssp             CTTHHHHHHHHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHh
Confidence            999999999998876554

>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=98.92  E-value=1.8e-08  Score=103.33  Aligned_cols=197  Identities=17%  Similarity=0.164  Sum_probs=126.0

Q ss_pred             cccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCc--EEEEeCCCcCChHHHH
Q 011664          190 DTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYD--VYDVDLSRVADDADLK  267 (480)
Q Consensus       190 ~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~--~~~i~~s~~~~~~~l~  267 (480)
                      ..++|.......+.+.+.....           ....+|++|++||||+.+|+++....+..  |+.++|+.+..+....
T Consensus       129 ~~~ig~s~~~~~~~~~~~~~a~-----------~~~~vli~GesGtGKe~lAr~ih~~s~r~~~fv~vnc~~~~~~~~~~  197 (368)
T 3dzd_A          129 IEFVGEHPKILEIKRLIPKIAK-----------SKAPVLITGESGTGKEIVARLIHRYSGRKGAFVDLNCASIPQELAES  197 (368)
T ss_dssp             CCCCCCSHHHHHHHHHHHHHHT-----------SCSCEEEECCTTSSHHHHHHHHHHHHCCCSCEEEEESSSSCTTTHHH
T ss_pred             ccccccchHHHHHHhhhhhhhc-----------cchhheEEeCCCchHHHHHHHHHHhccccCCcEEEEcccCChHHHHH
Confidence            3567777777766655543321           23469999999999999999999876543  9999999886544344


Q ss_pred             HHHH-----------------hhcCCcEEEEecccccccCcccccchhhhhhhcccc-cccccC-----CceEEEEecCC
Q 011664          268 SLLL-----------------QTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV-LNSCCF-----EERVMVFTMNS  324 (480)
Q Consensus       268 ~l~~-----------------~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~-~~~~~~-----~~~ivI~tTN~  324 (480)
                      .+|.                 +......||||||+.+.     ......||..++.- .....+     -..-+|+|||.
T Consensus       198 ~lfg~~~g~~tga~~~~~g~~~~a~~gtlfldei~~l~-----~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~rii~at~~  272 (368)
T 3dzd_A          198 ELFGHEKGAFTGALTRKKGKLELADQGTLFLDEVGELD-----QRVQAKLLRVLETGSFTRLGGNQKIEVDIRVISATNK  272 (368)
T ss_dssp             HHHEECSCSSSSCCCCEECHHHHTTTSEEEEETGGGSC-----HHHHHHHHHHHHHSEECCBTCCCBEECCCEEEEEESS
T ss_pred             HhcCccccccCCcccccCChHhhcCCCeEEecChhhCC-----HHHHHHHHHHHHhCCcccCCCCcceeeeeEEEEecCC
Confidence            4442                 12345789999999883     23345566666421 110001     12346777774


Q ss_pred             C-------ccCcccccCCCcee-EEEEcCCCCH--HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          325 K-------DHVDQALLRPGRID-VHIHFPLCDF--SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       325 ~-------~~LD~aLlrpGRfd-~~I~~~~p~~--~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      .       ..+.+.|..  |+. ..|++|+...  ++...++..++....       ........++|+.-+..++...+
T Consensus       273 ~l~~~v~~g~fr~dL~~--rl~~~~i~lPpLreR~~Di~~l~~~~l~~~~-------~~~~~~~~~~~~~a~~~L~~~~w  343 (368)
T 3dzd_A          273 NLEEEIKKGNFREDLYY--RLSVFQIYLPPLRERGKDVILLAEYFLKKFA-------KEYKKNCFELSEETKEYLMKQEW  343 (368)
T ss_dssp             CHHHHHHTTSSCHHHHH--HHTSEEEECCCGGGSTTHHHHHHHHHHHHHH-------HHTTCCCCCBCHHHHHHHHTCCC
T ss_pred             CHHHHHHcCCccHHHHH--HhCCeEEeCCChhhchhhHHHHHHHHHHHHH-------HHcCCCCCCcCHHHHHHHHhCCC
Confidence            2       123334554  554 4677887766  566677777663211       11112235799999999988888


Q ss_pred             hcHHHHHHHHHHHHHhc
Q 011664          395 NSPSRALKSVITALQTD  411 (480)
Q Consensus       395 ~~~~~al~~~i~~~~~~  411 (480)
                      ...++.|+++++.+...
T Consensus       344 pGNvreL~n~i~~~~~~  360 (368)
T 3dzd_A          344 KGNVRELKNLIERAVIL  360 (368)
T ss_dssp             TTHHHHHHHHHHHHHHT
T ss_pred             CcHHHHHHHHHHHHHHh
Confidence            99999999999877654

>2r2a_A Uncharacterized protein; zonular occludens toxin, structural genomics, APC84050.2, PS protein structure initiative; HET: MSE; 1.82A {Neisseria meningitidis MC58}

Probab=98.92  E-value=2.2e-09  Score=100.89  Aligned_cols=119  Identities=12%  Similarity=0.175  Sum_probs=77.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc--------CC-CcEEEEeCCCcCC---------------------hHHHHHHHH-hhc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF--------MS-YDVYDVDLSRVAD---------------------DADLKSLLL-QTT  274 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~--------l~-~~~~~i~~s~~~~---------------------~~~l~~l~~-~~~  274 (480)
                      -+|++|+||||||++|.+++..        .| .+++..++..+..                     ...+...+. ...
T Consensus         7 i~l~tG~pGsGKT~~a~~~~~~~~~~~~~~~g~r~v~~~~~~gL~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~   86 (199)
T 2r2a_A            7 ICLITGTPGSGKTLKMVSMMANDEMFKPDENGIRRKVFTNIKGLKIPHTYIETDAKKLPKSTDEQLSAHDMYEWIKKPEN   86 (199)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHCGGGSCCTTSCCCCEEECCTTBCSCCEEEECCTTTCSSCCSSCEEGGGHHHHTTSGGG
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhhcccccCceEEEEecCCCccccccccchhhhhccccCcccccHHHHHHHhhcccc
Confidence            5899999999999999886433        34 6666666543321                     122332210 123


Q ss_pred             CCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHH
Q 011664          275 SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFS  350 (480)
Q Consensus       275 ~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~  350 (480)
                      .++||+|||++.+.+.+........++..+..-.    ..+.-||++|+.++.|+.+++.  |++.+++++.|...
T Consensus        87 ~~~vliIDEAq~l~~~~~~~~e~~rll~~l~~~r----~~~~~iil~tq~~~~l~~~lr~--ri~~~~~l~~~~~~  156 (199)
T 2r2a_A           87 IGSIVIVDEAQDVWPARSAGSKIPENVQWLNTHR----HQGIDIFVLTQGPKLLDQNLRT--LVRKHYHIASNKMG  156 (199)
T ss_dssp             TTCEEEETTGGGTSBCCCTTCCCCHHHHGGGGTT----TTTCEEEEEESCGGGBCHHHHT--TEEEEEEEEECSSC
T ss_pred             CceEEEEEChhhhccCccccchhHHHHHHHHhcC----cCCeEEEEECCCHHHHhHHHHH--HhheEEEEcCcccC
Confidence            4899999999998754422211223444443211    3455678888889999999998  99999999986543

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=98.91  E-value=1.3e-09  Score=102.67  Aligned_cols=115  Identities=23%  Similarity=0.207  Sum_probs=67.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSG  299 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~  299 (480)
                      +.|.++++|+|||||||||++|.++|+.+...++...-+.  ..    ..+.......||+|||+|.-+    .......
T Consensus        54 ~iPkkn~ili~GPPGtGKTt~a~ala~~l~g~i~~fans~--s~----f~l~~l~~~kIiiLDEad~~~----~~~~d~~  123 (212)
T 1tue_A           54 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVISFVNST--SH----FWLEPLTDTKVAMLDDATTTC----WTYFDTY  123 (212)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECCCCCSS--SC----GGGGGGTTCSSEEEEEECHHH----HHHHHHH
T ss_pred             cCCcccEEEEECCCCCCHHHHHHHHHHHhCCCeeeEEecc--ch----hhhcccCCCCEEEEECCCchh----HHHHHHH
Confidence            4566778999999999999999999999876544321111  00    011222345699999998431    1111123


Q ss_pred             hhhhcccccc---cccC-----CceEEEEecCCC---ccCcccccCCCceeEEEEcCCC
Q 011664          300 VLNFMDGVLN---SCCF-----EERVMVFTMNSK---DHVDQALLRPGRIDVHIHFPLC  347 (480)
Q Consensus       300 lL~~ldg~~~---~~~~-----~~~ivI~tTN~~---~~LD~aLlrpGRfd~~I~~~~p  347 (480)
                      +-+.+||...   ....     ...-+|+|||..   +.--+.|.+  |+- .+.|+.|
T Consensus       124 lrn~ldG~~~~iD~Khr~~~~~~~~PlIITtN~~~~~~~~~~~L~S--Ri~-~f~F~~~  179 (212)
T 1tue_A          124 MRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLES--RIT-VFEFPNA  179 (212)
T ss_dssp             CHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHT--SCE-EEECCSC
T ss_pred             HHHHhCCCcccHHHhhcCccccCCCCEEEecCCCcccccchhhhhh--hEE-EEEcCCC
Confidence            5566666420   0001     134578899963   222346777  884 7777744

>2vhj_A Ntpase P4, P4; non- hydrolysable ATP analogue, hydrolase, virus dsRNA, molecular motor, packaging ATPase, hexameric helicase; HET: ADP; 1.80A {Pseudomonas phage PHI12} PDB: 2vhq_A* 1w44_A* 1w46_A* 1w47_A* 1w48_A* 1w49_A* 1w4a_A* 1w4b_A* 1w4c_A 2vht_A* 2vhu_A* 2vhc_A*

Probab=98.88  E-value=6.4e-10  Score=111.62  Aligned_cols=109  Identities=13%  Similarity=0.164  Sum_probs=67.4

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC--CC----cC-C-hHHHHHHHHhhcCCcEEEEecccccccCc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL--SR----VA-D-DADLKSLLLQTTSKSVILIEDLDRFLVEK  291 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~--s~----~~-~-~~~l~~l~~~~~~~sII~IDEiD~l~~~~  291 (480)
                      |.+..+.++|+||||||||+||.++|.+.|..+.++++  .+    +. + +..+..+........+||||+++.+....
T Consensus       119 Gi~~gsviLI~GpPGsGKTtLAlqlA~~~G~~VlyIs~~~eE~v~~~~~~le~~l~~i~~~l~~~~LLVIDsI~aL~~~~  198 (331)
T 2vhj_A          119 HRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAA  198 (331)
T ss_dssp             EEEESEEEEEECSCSSSHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEECCTTTC---
T ss_pred             CCCCCcEEEEEcCCCCCHHHHHHHHHHhCCCCEEEEEecchhhhhhhhcCHHHHHHHHHHHHhhCCEEEEeccccccccc
Confidence            44555668999999999999999999875555444443  21    11 1 12222232222222299999999986543


Q ss_pred             cc-------ccchhhhhhhcccccccccCCceEEEEecCCCccCcccc
Q 011664          292 PA-------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQAL  332 (480)
Q Consensus       292 ~~-------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aL  332 (480)
                      ..       ...+.+++..|+++..   ..+..+|++|| +...|+++
T Consensus       199 ~~~s~~G~v~~~lrqlL~~L~~~~k---~~gvtVIlttn-p~s~deal  242 (331)
T 2vhj_A          199 GGNTTSGGISRGAFDLLSDIGAMAA---SRGCVVIASLN-PTSNDDKI  242 (331)
T ss_dssp             --------CCHHHHHHHHHHHHHHH---HHTCEEEEECC-CSSCSSSH
T ss_pred             ccccccchHHHHHHHHHHHHHHHHh---hCCCEEEEEeC-CcccchhH
Confidence            33       3446778888877655   34567788888 66677765

>2qen_A Walker-type ATPase; unknown function; HET: ADP; 2.25A {Pyrococcus abyssi}

Probab=98.83  E-value=2.6e-07  Score=91.98  Aligned_cols=183  Identities=14%  Similarity=0.112  Sum_probs=109.0

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      ++..-+.++|-++..+.|.+.+..           |    +.++++||+|+|||+|++.+++..+  .+.+++....   
T Consensus         7 ~~~~~~~~~gR~~el~~L~~~l~~-----------~----~~v~i~G~~G~GKT~Ll~~~~~~~~--~~~~~~~~~~~~~   69 (350)
T 2qen_A            7 PKTRREDIFDREEESRKLEESLEN-----------Y----PLTLLLGIRRVGKSSLLRAFLNERP--GILIDCRELYAER   69 (350)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHH-----------C----SEEEEECCTTSSHHHHHHHHHHHSS--EEEEEHHHHHHTT
T ss_pred             CCCChHhcCChHHHHHHHHHHHhc-----------C----CeEEEECCCcCCHHHHHHHHHHHcC--cEEEEeecccccc
Confidence            445567789998888887765532           2    4799999999999999999999876  6666653221   


Q ss_pred             ---Ch------------------------------------HHHHHH---HHh---hcCCcEEEEecccccccCcccccc
Q 011664          262 ---DD------------------------------------ADLKSL---LLQ---TTSKSVILIEDLDRFLVEKPAAVS  296 (480)
Q Consensus       262 ---~~------------------------------------~~l~~l---~~~---~~~~sII~IDEiD~l~~~~~~~~~  296 (480)
                         ..                                    ..+..+   +..   ...|.+|+|||++.+.....  ..
T Consensus        70 ~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~vlvlDe~~~~~~~~~--~~  147 (350)
T 2qen_A           70 GHITREELIKELQSTISPFQKFQSKFKISLNLKFLTLEPRKLSLREVFRELNDLGEELGEFIVAFDEAQYLRFYGS--RG  147 (350)
T ss_dssp             TCBCHHHHHHHHHHHSCSHHHHHHHHTCCCCCGGGTSCGGGCCHHHHHHHHHHHHHHHSCEEEEEETGGGGGGBTT--TT
T ss_pred             cCCCHHHHHHHHHHHHHHHHhHhhhceeEEEecceeeccccchHHHHHHHHHHHHhccCCEEEEEeCHHHHhccCc--cc
Confidence               00                                    011222   211   12489999999998753100  00


Q ss_pred             hhhhhhhcccccccccCCceEEEEecCCC---c------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCC
Q 011664          297 LSGVLNFMDGVLNSCCFEERVMVFTMNSK---D------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL  367 (480)
Q Consensus       297 ls~lL~~ldg~~~~~~~~~~ivI~tTN~~---~------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l  367 (480)
                      ..+++..+..+...  ..+..+|+|+...   .      .....+.  ||....+++++.+.++..+++...++..+...
T Consensus       148 ~~~~~~~L~~~~~~--~~~~~~il~g~~~~~l~~~l~~~~~~~~l~--~~~~~~i~l~pl~~~e~~~~l~~~~~~~~~~~  223 (350)
T 2qen_A          148 GKELLALFAYAYDS--LPNLKIILTGSEVGLLHDFLKITDYESPLY--GRIAGEVLVKPFDKDTSVEFLKRGFREVNLDV  223 (350)
T ss_dssp             THHHHHHHHHHHHH--CTTEEEEEEESSHHHHHHHHCTTCTTSTTT--TCCCEEEECCCCCHHHHHHHHHHHHHTTTCCC
T ss_pred             hhhHHHHHHHHHHh--cCCeEEEEECCcHHHHHHHHhhcCCCCccc--cCccceeeCCCCCHHHHHHHHHHHHHHcCCCC
Confidence            11223333222221  1234455554432   1      1122233  47767999999999999999988765444444


Q ss_pred             ch-hHHHHHHhCCCCCHHHHHHHHH
Q 011664          368 FP-QVEEIFQNGSSLSPAEIGELMI  391 (480)
Q Consensus       368 ~~-~i~~l~~~~~g~s~adI~~ll~  391 (480)
                      .+ .+..+...+.| .|.-+..++.
T Consensus       224 ~~~~~~~i~~~tgG-~P~~l~~~~~  247 (350)
T 2qen_A          224 PENEIEEAVELLDG-IPGWLVVFGV  247 (350)
T ss_dssp             CHHHHHHHHHHHTT-CHHHHHHHHH
T ss_pred             CHHHHHHHHHHhCC-CHHHHHHHHH
Confidence            43 45667777745 4655665553

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.80  E-value=2.9e-08  Score=123.53  Aligned_cols=135  Identities=16%  Similarity=0.246  Sum_probs=95.7

Q ss_pred             CceEEEEccCCCcHHHHHHHH-HHcCCCcEEEEeCCCcCChHHHHHHHHh-----h-------------cCCcEEEEecc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAM-ASFMSYDVYDVDLSRVADDADLKSLLLQ-----T-------------TSKSVILIEDL  284 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~ai-A~~l~~~~~~i~~s~~~~~~~l~~l~~~-----~-------------~~~sII~IDEi  284 (480)
                      .+++||+||||||||++++.. ++..+.+++.++++.-.+...+...+..     .             ....|+||||+
T Consensus      1304 ~~pvLL~GptGtGKT~li~~~L~~l~~~~~~~infS~~Tta~~l~~~~e~~~e~~~~~~~G~~~~p~~~Gk~~VlFiDDi 1383 (3245)
T 3vkg_A         1304 HRPLILCGPPGSGKTMTLTSTLRAFPDFEVVSLNFSSATTPELLLKTFDHHCEYKRTPSGETVLRPTQLGKWLVVFCDEI 1383 (3245)
T ss_dssp             TCCCEEESSTTSSHHHHHHHHGGGCTTEEEEEECCCTTCCHHHHHHHHHHHEEEEECTTSCEEEEESSTTCEEEEEETTT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCCCCceEEEEeeCCCCHHHHHHHHhhcceEEeccCCCcccCCCcCCceEEEEeccc
Confidence            457999999999999887654 4445778899999988887777766642     1             11259999999


Q ss_pred             cccccCcccccchhhhhhhc-c--ccccc-----ccCCceEEEEecCCC-----ccCcccccCCCceeEEEEcCCCCHHH
Q 011664          285 DRFLVEKPAAVSLSGVLNFM-D--GVLNS-----CCFEERVMVFTMNSK-----DHVDQALLRPGRIDVHIHFPLCDFSS  351 (480)
Q Consensus       285 D~l~~~~~~~~~ls~lL~~l-d--g~~~~-----~~~~~~ivI~tTN~~-----~~LD~aLlrpGRfd~~I~~~~p~~~~  351 (480)
                      +.-..+..+.+..-++|.++ |  |+...     ..-.+..+|+|+|.|     ..|+++++|  ||- .+.+++|+.++
T Consensus      1384 Nmp~~D~yGtQ~~ielLrqlld~~g~yd~~~~~~~~i~d~~~vaamnPp~~gGr~~l~~Rf~r--~F~-vi~i~~ps~es 1460 (3245)
T 3vkg_A         1384 NLPSTDKYGTQRVITFIRQMVEKGGFWRTSDHTWIKLDKIQFVGACNPPTDAGRVQLTHRFLR--HAP-ILLVDFPSTSS 1460 (3245)
T ss_dssp             TCCCCCTTSCCHHHHHHHHHHHHSEEEETTTTEEEEESSEEEEEEECCTTSTTCCCCCHHHHT--TCC-EEECCCCCHHH
T ss_pred             CCCCccccccccHHHHHHHHHHcCCeEECCCCeEEEecCeEEEEEcCCCCCCCCccCCHHHHh--hce-EEEeCCCCHHH
Confidence            97655544444444555443 3  22221     011345678899987     458999999  996 69999999999


Q ss_pred             HHHHHHHHhc
Q 011664          352 FKTLASSYLG  361 (480)
Q Consensus       352 r~~il~~~l~  361 (480)
                      ...|+..++.
T Consensus      1461 L~~If~til~ 1470 (3245)
T 3vkg_A         1461 LTQIYGTFNR 1470 (3245)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999877654

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=98.67  E-value=1.2e-07  Score=92.70  Aligned_cols=120  Identities=18%  Similarity=0.185  Sum_probs=69.7

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhhhh
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVL  301 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL  301 (480)
                      +++++++||||||||||++|.|+|+.++.. -.++.+.   .   ...+.....+.|++.||....-.      ....+-
T Consensus       102 ~~~n~~~l~GppgtGKt~~a~ala~~~~l~-G~vn~~~---~---~f~l~~~~~k~i~l~Ee~~~~~d------~~~~lr  168 (267)
T 1u0j_A          102 GKRNTIWLFGPATTGKTNIAEAIAHTVPFY-GCVNWTN---E---NFPFNDCVDKMVIWWEEGKMTAK------VVESAK  168 (267)
T ss_dssp             TTCCEEEEECSTTSSHHHHHHHHHHHSSCE-EECCTTC---S---SCTTGGGSSCSEEEECSCCEETT------THHHHH
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHhhhccc-ceeeccc---c---ccccccccccEEEEeccccchhH------HHHHHH
Confidence            456789999999999999999999976552 2223321   1   11234445667777777765421      111222


Q ss_pred             hhccccccc---c-----cCCceEEEEecCC-C----------ccCcccccCCCceeEEEEcC--------CCCHHHHHH
Q 011664          302 NFMDGVLNS---C-----CFEERVMVFTMNS-K----------DHVDQALLRPGRIDVHIHFP--------LCDFSSFKT  354 (480)
Q Consensus       302 ~~ldg~~~~---~-----~~~~~ivI~tTN~-~----------~~LD~aLlrpGRfd~~I~~~--------~p~~~~r~~  354 (480)
                      +.++|-.-.   .     .-....+|+|||. +          +...++|.+  |+ ..+.|+        ..+.++-+.
T Consensus       169 ~i~~G~~~~id~K~k~~~~v~~tPvIitsN~~i~~~~~g~~~s~~~~~~L~s--R~-~~f~F~~~~p~~~~~lt~~~~~~  245 (267)
T 1u0j_A          169 AILGGSKVRVDQKCKSSAQIDPTPVIVTSNTNMCAVIDGNSTTFEHQQPLQD--RM-FKFELTRRLDHDFGKVTKQEVKD  245 (267)
T ss_dssp             HHHTTCCEEC------CCEECCCCEEEEESSCTTCEEETTEEECTTHHHHHT--TE-EEEECCSCCCTTSCCCCHHHHHH
T ss_pred             HHhCCCcEEEecCcCCcccccCCCEEEEecCCcccccccCccchhhhHHHhh--hE-EEEECCCcCCcccCCCCHHHHHH
Confidence            233321110   0     0123357788885 2          245678888  88 578887        455555555


Q ss_pred             HHH
Q 011664          355 LAS  357 (480)
Q Consensus       355 il~  357 (480)
                      .++
T Consensus       246 f~~  248 (267)
T 1u0j_A          246 FFR  248 (267)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            554

>4akg_A Glutathione S-transferase class-MU 26 kDa isozyme heavy chain cytoplasmic; motor protein, AAA+ protein, ASCE protein, P-loop ntpase; HET: ATP ADP; 3.30A {Schistosoma japonicum} PDB: 4ai6_A* 4akh_A* 4aki_A* 3qmz_A

Probab=98.64  E-value=7.8e-08  Score=118.92  Aligned_cols=125  Identities=17%  Similarity=0.188  Sum_probs=92.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhh-cCCcEEEEecccccccCcccccchhhhhh
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLN  302 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~  302 (480)
                      ..|.++.||||||||++++++|+.+|.+++.++|++-.+...+..+|..+ ..++.+++||++.+-.     ..++.+-.
T Consensus       645 ~~~~~l~GpaGtGKTe~vk~LA~~lg~~~v~~nc~e~ld~~~lg~~~~g~~~~Gaw~~~DE~nr~~~-----evLs~l~~  719 (2695)
T 4akg_A          645 KYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSRLLVGITQIGAWGCFDEFNRLDE-----KVLSAVSA  719 (2695)
T ss_dssp             TCEEEEECCTTSCHHHHHHHHHHTTTCCCEEEETTSSCCHHHHHHHHHHHHHHTCEEEEETTTSSCH-----HHHHHHHH
T ss_pred             CCCCcccCCCCCCcHHHHHHHHHHhCCcEEEEECCCCCChhHhhHHHHHHHhcCCEeeehhhhhcCh-----HHHHHHHH
Confidence            45799999999999999999999999999999999988888888888544 4579999999997632     22333211


Q ss_pred             hcc----ccccc-----------ccCCceEEEEecC----CCccCcccccCCCceeEEEEcCCCCHHHHHHHH
Q 011664          303 FMD----GVLNS-----------CCFEERVMVFTMN----SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLA  356 (480)
Q Consensus       303 ~ld----g~~~~-----------~~~~~~ivI~tTN----~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il  356 (480)
                      +++    .+...           .......|++|.|    ....|+++|.+  || +.|.+..||.+...+|.
T Consensus       720 ~l~~i~~al~~~~~~i~~~g~~i~l~~~~~vfiT~NPgy~g~~eLP~~Lk~--~F-r~v~m~~Pd~~~i~ei~  789 (2695)
T 4akg_A          720 NIQQIQNGLQVGKSHITLLEEETPLSPHTAVFITLNPGYNGRSELPENLKK--SF-REFSMKSPQSGTIAEMI  789 (2695)
T ss_dssp             HHHHHHHHHHHTCSEEECSSSEEECCTTCEEEEEECCCSSSSCCCCHHHHT--TE-EEEECCCCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcEEeeCCcEEecCCCceEEEEeCCCccCcccccHHHHh--he-EEEEeeCCCHHHHHHHH
Confidence            111    11000           0112334666777    34578999998  99 68999999998877764

>3aji_B S6C, proteasome (prosome, macropain) 26S subunit, ATPA; gankyrin, S6 ATPase, P-benzoyl-L-phenylalanine, PBPA, amber suppression; HET: PBF; 2.05A {Mus musculus} PDB: 2dwz_B* 2dvw_B*

Probab=98.61  E-value=1.9e-08  Score=80.94  Aligned_cols=81  Identities=15%  Similarity=0.079  Sum_probs=58.2

Q ss_pred             CHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHHHHHHhcCCCCcccccccccccC
Q 011664          348 DFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGEGRGAANAGRRLDKS  427 (480)
Q Consensus       348 ~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i~~~~~~~~~~~~~~~~~~~~~~  427 (480)
                      |.++|.+|++.+++..+.....+++.|++.|.|||||||.++|+.+...+.+.          .                
T Consensus         2 d~~~R~~Il~~~l~~~~~~~~vdl~~la~~t~G~SGADi~~l~~eA~~~a~~~----------~----------------   55 (83)
T 3aji_B            2 DRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQESGMLAVRE----------N----------------   55 (83)
T ss_dssp             CHHHHHHHHHHHHTTSCBCTTCCTHHHHTSSCCCCHHHHHHHHHHHHHGGGTS----------C----------------
T ss_pred             CHHHHHHHHHHHhCCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHh----------c----------------
Confidence            67899999999998776655567899999999999999999998765432210          0                


Q ss_pred             CCCCCCCCCCCCCCCccccCCcHHHHHHhhcccccCcccCCcCcccccc
Q 011664          428 GSKKSTDADSGEHGGVFSRENTVKEFRKLYGLLTLKNSRKSQSFDLAAA  476 (480)
Q Consensus       428 ~~~~~~~~~~~~~~~~~~~~v~~~df~~~~g~~~~~~~~ps~~~~~~~~  476 (480)
                                       .++|+++||.++     +++++||++.++..|
T Consensus        56 -----------------~~~i~~~df~~A-----l~~~~ps~~~~l~~y   82 (83)
T 3aji_B           56 -----------------RYIVLAKDFEKA-----YKTVIKKDEQEHEFY   82 (83)
T ss_dssp             -----------------CSSBCHHHHHHH-----HHHHCC---------
T ss_pred             -----------------cCCcCHHHHHHH-----HHHHccCchHHHHhc
Confidence                             156899999999     899999999555444

>2krk_A 26S protease regulatory subunit 8; structural genomics, northeast structural genomics consortium (NESG), target HR3102A, PSI-2; NMR {Homo sapiens}

Probab=98.56  E-value=4.5e-08  Score=79.53  Aligned_cols=53  Identities=9%  Similarity=-0.108  Sum_probs=45.2

Q ss_pred             EcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          343 HFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       343 ~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      +-.+||.++|.+|++.+++........+++.|++.|.|||||||.++|+.+..
T Consensus         7 ~~~~Pd~~~R~~IL~~~l~~~~l~~dvdl~~LA~~T~G~SGADL~~l~~eAa~   59 (86)
T 2krk_A            7 HHSHPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGM   59 (86)
T ss_dssp             CCCCCCHHHHHHHHHHHTTTSEECTTCCCHHHHHTCSSCCHHHHHHHHHHHHH
T ss_pred             CCCCcCHHHHHHHHHHHHcCCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            34689999999999999987665555678999999999999999999987644

>3kw6_A 26S protease regulatory subunit 8; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 2.10A {Homo sapiens}

Probab=98.50  E-value=1.3e-07  Score=75.11  Aligned_cols=52  Identities=10%  Similarity=-0.117  Sum_probs=45.1

Q ss_pred             CCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhc
Q 011664          345 PLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNS  396 (480)
Q Consensus       345 ~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~  396 (480)
                      |+|+.++|.+|++.++......-..+++.|+..+.|||||||.++|..+...
T Consensus         1 plPd~~~R~~Il~~~l~~~~~~~~~dl~~la~~t~G~SGADi~~l~~eA~~~   52 (78)
T 3kw6_A            1 PPPNEEARLDILKIHSRKMNLTRGINLRKIAELMPGASGAEVKGVCTEAGMY   52 (78)
T ss_dssp             CCCCHHHHHHHHHHHHTTSEECTTCCHHHHHHTCTTCCHHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHhcCCCCCCccCHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence            7899999999999999876655556889999999999999999999876543

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=98.38  E-value=2e-07  Score=112.19  Aligned_cols=102  Identities=19%  Similarity=0.294  Sum_probs=69.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC----------------------hHHHHHH--HHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD----------------------DADLKSL--LLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~----------------------~~~l~~l--~~~  272 (480)
                      |++..++++||||||||||+||.++|.+.   |..+..+++....+                      +..++.+  +.+
T Consensus      1423 Gi~~g~~vll~GppGtGKT~LA~ala~ea~~~G~~v~Fi~~e~~~~~l~a~~~G~dl~~l~v~~~~~~E~~l~~~~~lvr 1502 (2050)
T 3cmu_A         1423 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1502 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEEcccccCHHHHHHcCCCchhceeecCChHHHHHHHHHHHHh
Confidence            37788899999999999999999998754   56777777664321                      1112222  234


Q ss_pred             hcCCcEEEEecccccccCcc------------cccchhhhhhhcccccccccCCceEEEEecCCC
Q 011664          273 TTSKSVILIEDLDRFLVEKP------------AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK  325 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~~~~------------~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~  325 (480)
                      ..+|++||||+++.+.+...            ..+.++++|..|++...   ..+ ++|++||..
T Consensus      1503 ~~~~~lVVIDsi~al~p~~~~~g~~~~~~~~~~~R~lsqlL~~L~~~~~---~~~-v~VI~tNq~ 1563 (2050)
T 3cmu_A         1503 SGAVDVIVVDSVAALTPKAEIEGEIGDSHMGLAARMMSQAMRKLAGNLK---QSN-TLLIFINQI 1563 (2050)
T ss_dssp             HTCCSEEEESCGGGCCCHHHHHSCTTCCCTTHHHHHHHHHHHHHHHHHH---TTT-CEEEEEECE
T ss_pred             cCCCCEEEEcChhHhcccccccccccccccchHHHHHHHHHHHHHHHHH---hCC-cEEEEEccc
Confidence            47899999999998876321            12335788888888765   344 455556643

>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=98.36  E-value=3.9e-07  Score=95.62  Aligned_cols=139  Identities=14%  Similarity=0.106  Sum_probs=80.0

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHH-HHcCCCcEEEEeCCCcCChHHHHHH-
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAM-ASFMSYDVYDVDLSRVADDADLKSL-  269 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~ai-A~~l~~~~~~i~~s~~~~~~~l~~l-  269 (480)
                      |.|++++|..|.-.+..-  .++      ....-++||.|+||| ||++++++ ++.+....+.....  .....+... 
T Consensus       215 I~G~e~vK~aLll~L~GG--~~k------~rgdihVLL~G~PGt-KS~Lar~i~~~i~pR~~ft~g~~--ss~~gLt~s~  283 (506)
T 3f8t_A          215 LPGAEEVGKMLALQLFSC--VGK------NSERLHVLLAGYPVV-CSEILHHVLDHLAPRGVYVDLRR--TELTDLTAVL  283 (506)
T ss_dssp             STTCHHHHHHHHHHHTTC--CSS------GGGCCCEEEESCHHH-HHHHHHHHHHHTCSSEEEEEGGG--CCHHHHSEEE
T ss_pred             cCCCHHHHHHHHHHHcCC--ccc------cCCceeEEEECCCCh-HHHHHHHHHHHhCCCeEEecCCC--CCccCceEEE
Confidence            789999887776332110  000      011226999999999 99999999 77665544432211  011111000 


Q ss_pred             -----H------HhhcCCcEEEEecccccccCcccccchhhhhhhcc-------cccccccCCceEEEEecCCCc-----
Q 011664          270 -----L------LQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMD-------GVLNSCCFEERVMVFTMNSKD-----  326 (480)
Q Consensus       270 -----~------~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ld-------g~~~~~~~~~~ivI~tTN~~~-----  326 (480)
                           +      .......|+|+|||+.+-     ..+++.|+..|+       |. .  -+....||+|+|..+     
T Consensus       284 r~~tG~~~~~G~l~LAdgGvl~lDEIn~~~-----~~~qsaLlEaMEe~~VtI~G~-~--lparf~VIAA~NP~~~yd~~  355 (506)
T 3f8t_A          284 KEDRGWALRAGAAVLADGGILAVDHLEGAP-----EPHRWALMEAMDKGTVTVDGI-A--LNARCAVLAAINPGEQWPSD  355 (506)
T ss_dssp             EESSSEEEEECHHHHTTTSEEEEECCTTCC-----HHHHHHHHHHHHHSEEEETTE-E--EECCCEEEEEECCCC--CCS
T ss_pred             EcCCCcccCCCeeEEcCCCeeehHhhhhCC-----HHHHHHHHHHHhCCcEEECCE-E--cCCCeEEEEEeCcccccCCC
Confidence                 0      011246899999999873     344566666664       22 1  123456888999764     


Q ss_pred             ------cCcccccCCCceeE-EEEcCCCCHHH
Q 011664          327 ------HVDQALLRPGRIDV-HIHFPLCDFSS  351 (480)
Q Consensus       327 ------~LD~aLlrpGRfd~-~I~~~~p~~~~  351 (480)
                            .|.++++.  |||. .+.+++|+.+.
T Consensus       356 ~s~~~~~Lp~alLD--RFDLi~i~~d~pd~e~  385 (506)
T 3f8t_A          356 PPIARIDLDQDFLS--HFDLIAFLGVDPRPGE  385 (506)
T ss_dssp             CGGGGCCSCHHHHT--TCSEEEETTC------
T ss_pred             CCccccCCChHHhh--heeeEEEecCCCChhH
Confidence                  78899999  9985 44567777655

>3vlf_B 26S protease regulatory subunit 7 homolog; heat repeat, chaperone, chaperone-protein binding complex; HET: DNA; 3.80A {Saccharomyces cerevisiae} PDB: 4a3v_B*

Probab=98.33  E-value=4.1e-07  Score=74.04  Aligned_cols=48  Identities=10%  Similarity=-0.103  Sum_probs=41.5

Q ss_pred             CHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          348 DFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       348 ~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |.++|.+|++.+++..+..-..+++.|++.|.|||||||.++|..+..
T Consensus         2 d~~~R~~Il~~~~~~~~~~~dvdl~~lA~~t~G~SGADl~~l~~eAa~   49 (88)
T 3vlf_B            2 DLEGRANIFRIHSKSMSVERGIRWELISRLCPNSTGAELRSVCTEAGM   49 (88)
T ss_dssp             CSSHHHHHHHHHHTTSCBCSCCCHHHHHHTCSSCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCCCccCHHHHHHHcCCCcHHHHHHHHHHHHH
Confidence            567899999999987776656689999999999999999999987644

>3vkg_A Dynein heavy chain, cytoplasmic; AAA+ protein, molecular motor, microtubles, motor protein; HET: ADP SPM; 2.81A {Dictyostelium discoideum} PDB: 3vkh_A*

Probab=98.25  E-value=3e-06  Score=105.80  Aligned_cols=123  Identities=16%  Similarity=0.153  Sum_probs=90.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhh-cCCcEEEEecccccccCcccccchhhhhhh
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLNF  303 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~~  303 (480)
                      .|..+.||+|||||.+++.+|+.+|..++.++|++-.+...+.++|... ...+..++||++.+-     ...++.+..+
T Consensus       605 ~gg~~~GPaGtGKTet~k~La~~lgr~~~vfnC~~~~d~~~~g~i~~G~~~~GaW~cfDEfNrl~-----~~vLSvv~~q  679 (3245)
T 3vkg_A          605 MGGNPFGPAGTGKTETVKALGSQLGRFVLVFCCDEGFDLQAMSRIFVGLCQCGAWGCFDEFNRLE-----ERILSAVSQQ  679 (3245)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHTTCCEEEEECSSCCCHHHHHHHHHHHHHHTCEEEEETTTSSC-----HHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhCCeEEEEeCCCCCCHHHHHHHHhhHhhcCcEEEehhhhcCC-----HHHHHHHHHH
Confidence            4678999999999999999999999999999999988887777777544 467889999999873     2223332222


Q ss_pred             cc-----------------cccccccCCceEEEEecCC----CccCcccccCCCceeEEEEcCCCCHHHHHHHH
Q 011664          304 MD-----------------GVLNSCCFEERVMVFTMNS----KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLA  356 (480)
Q Consensus       304 ld-----------------g~~~~~~~~~~ivI~tTN~----~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il  356 (480)
                      +.                 |-.- .-..+.-|++|.|.    ...|+++|..  || +.|.++.||.+...+|+
T Consensus       680 i~~I~~a~~~~~~~~~~~~G~~i-~l~~~~~vfiTmNpgY~gr~eLP~nLk~--lF-r~v~m~~Pd~~~i~ei~  749 (3245)
T 3vkg_A          680 IQTIQVALKENSKEVELLGGKNI-SLHQDMGIFVTMNPGYAGRSNLPDNLKK--LF-RSMAMIKPDREMIAQVM  749 (3245)
T ss_dssp             HHHHHHHHHHTCSEECCC---CE-ECCTTCEEEECBCCCGGGCCCSCHHHHT--TE-EEEECCSCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCeEEecCCCEE-eecCCeEEEEEeCCCccCcccChHHHHh--hc-EEEEEeCCCHHHHHHHH
Confidence            21                 2100 01223456778773    4678999999  98 57999999998877765

>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=98.21  E-value=1.2e-05  Score=80.79  Aligned_cols=133  Identities=12%  Similarity=0.112  Sum_probs=88.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CC-cEEEEeCCCcCChHHHHHHHHhh------cCCcEEEEecccc-cccCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SY-DVYDVDLSRVADDADLKSLLLQT------TSKSVILIEDLDR-FLVEK  291 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~-~~~~i~~s~~~~~~~l~~l~~~~------~~~sII~IDEiD~-l~~~~  291 (480)
                      ....||||||+|+||++.++++++.+   +. ++..+....   +.+++.++...      ....|++|||++. +.   
T Consensus        17 ~~~~yl~~G~e~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~~~~~plf~~~kvvii~~~~~kl~---   90 (343)
T 1jr3_D           17 LRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDP---NTDWNAIFSLCQAMSLFASRQTLLLLLPENGPN---   90 (343)
T ss_dssp             CCSEEEEEESCHHHHHHHHHHHHHHHHHHTCCEEEEEECCT---TCCHHHHHHHHHHHHHCCSCEEEEEECCSSCCC---
T ss_pred             CCcEEEEECCcHHHHHHHHHHHHHHHHhCCCCeeEEEEecC---CCCHHHHHHHhcCcCCccCCeEEEEECCCCCCC---
Confidence            45589999999999999999998865   32 222333322   23455554332      3578999999997 52   


Q ss_pred             ccccchhhhhhhcccccccccCCceEEEEecCCC------ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCC
Q 011664          292 PAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSK------DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDH  365 (480)
Q Consensus       292 ~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~------~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~  365 (480)
                        ....+.|+..++..     +++.++|++|+.+      ..+-+++.+  |. .++++..++.++....++..+...+.
T Consensus        91 --~~~~~aLl~~le~p-----~~~~~~il~~~~~~~~~~~~k~~~~i~s--r~-~~~~~~~l~~~~l~~~l~~~~~~~g~  160 (343)
T 1jr3_D           91 --AAINEQLLTLTGLL-----HDDLLLIVRGNKLSKAQENAAWFTALAN--RS-VQVTCQTPEQAQLPRWVAARAKQLNL  160 (343)
T ss_dssp             --TTHHHHHHHHHTTC-----BTTEEEEEEESCCCTTTTTSHHHHHHTT--TC-EEEEECCCCTTHHHHHHHHHHHHTTC
T ss_pred             --hHHHHHHHHHHhcC-----CCCeEEEEEcCCCChhhHhhHHHHHHHh--Cc-eEEEeeCCCHHHHHHHHHHHHHHcCC
Confidence              22345567666532     3355666655543      346678887  66 48899999999888888888876665


Q ss_pred             CCchhH
Q 011664          366 KLFPQV  371 (480)
Q Consensus       366 ~l~~~i  371 (480)
                      .+.++.
T Consensus       161 ~i~~~a  166 (343)
T 1jr3_D          161 ELDDAA  166 (343)
T ss_dssp             EECHHH
T ss_pred             CCCHHH
Confidence            555443

>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=98.04  E-value=9.2e-06  Score=74.53  Aligned_cols=27  Identities=15%  Similarity=0.381  Sum_probs=23.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      .+.|.||+|+|||||++.+++.++..+
T Consensus         2 ~i~l~G~nGsGKTTLl~~l~g~l~i~~   28 (178)
T 1ye8_A            2 KIIITGEPGVGKTTLVKKIVERLGKRA   28 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHGGGE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcC
Confidence            378999999999999999999875443

>1z6t_A APAF-1, apoptotic protease activating factor 1; caspase activation, ADP, nucleotide binding, CARD, apoptosis; HET: ADP; 2.21A {Homo sapiens}

Probab=98.03  E-value=0.00011  Score=79.07  Aligned_cols=170  Identities=18%  Similarity=0.196  Sum_probs=95.1

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-------CCcEEEEeCC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-------SYDVYDVDLS  258 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-------~~~~~~i~~s  258 (480)
                      |.....++|-+...+.|.+.+...           ....+-++++||+|+|||+||+.+++..       ...++.++++
T Consensus       120 P~~~~~~vGR~~~l~~L~~~L~~~-----------~~~~~~v~I~G~~GiGKTtLa~~~~~~~~~~~~~f~~~v~wv~~~  188 (591)
T 1z6t_A          120 PQRPVVFVTRKKLVNAIQQKLSKL-----------KGEPGWVTIHGMAGCGKSVLAAEAVRDHSLLEGCFPGGVHWVSVG  188 (591)
T ss_dssp             CCCCSSCCCCHHHHHHHHHHHTTS-----------TTSCEEEEEECCTTSSHHHHHHHHHCCHHHHHHHCTTCEEEEEEE
T ss_pred             CCCCCeecccHHHHHHHHHHHhcc-----------cCCCceEEEEcCCCCCHHHHHHHHHhchhHHHhhCCCceEEEECC
Confidence            445567899988888887655310           1124578999999999999999997532       1234555443


Q ss_pred             CcCCh---------------------------HH----HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccc
Q 011664          259 RVADD---------------------------AD----LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV  307 (480)
Q Consensus       259 ~~~~~---------------------------~~----l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~  307 (480)
                      .....                           ..    ++..+.....|.+|+|||++..           ..+..+   
T Consensus       189 ~~~~~~~~~~l~~l~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LLVLDdv~~~-----------~~l~~l---  254 (591)
T 1z6t_A          189 KQDKSGLLMKLQNLCTRLDQDESFSQRLPLNIEEAKDRLRILMLRKHPRSLLILDDVWDS-----------WVLKAF---  254 (591)
T ss_dssp             SCCHHHHHHHHHHHHHHHCSSCCSCSSCCCSHHHHHHHHHHHHHHTCTTCEEEEEEECCH-----------HHHHTT---
T ss_pred             CCchHHHHHHHHHHHHHhccccccccCCCCCHHHHHHHHHHHHccCCCCeEEEEeCCCCH-----------HHHHHh---
Confidence            22100                           11    1222222236899999999842           112221   


Q ss_pred             cccccCCceEEEEecCCCccCcccccCCCceeEEEEc-CCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHH
Q 011664          308 LNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHF-PLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEI  386 (480)
Q Consensus       308 ~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~-~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI  386 (480)
                           ..+..||+||..+..... . . |.. ..+.. ...+.++-.+++..+++.......+.+..+++.+.| -|.-|
T Consensus       255 -----~~~~~ilvTsR~~~~~~~-~-~-~~~-~~v~~l~~L~~~ea~~L~~~~~~~~~~~~~~~~~~i~~~~~G-~PLal  324 (591)
T 1z6t_A          255 -----DSQCQILLTTRDKSVTDS-V-M-GPK-YVVPVESSLGKEKGLEILSLFVNMKKADLPEQAHSIIKECKG-SPLVV  324 (591)
T ss_dssp             -----CSSCEEEEEESCGGGGTT-C-C-SCE-EEEECCSSCCHHHHHHHHHHHHTSCGGGSCTHHHHHHHHHTT-CHHHH
T ss_pred             -----cCCCeEEEECCCcHHHHh-c-C-CCc-eEeecCCCCCHHHHHHHHHHHhCCCcccccHHHHHHHHHhCC-CcHHH
Confidence                 123346667765432211 1 1 222 22322 467788888888888764222233456777777744 45555


Q ss_pred             HHHH
Q 011664          387 GELM  390 (480)
Q Consensus       387 ~~ll  390 (480)
                      ..+.
T Consensus       325 ~~~a  328 (591)
T 1z6t_A          325 SLIG  328 (591)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            5443

>2cvh_A DNA repair and recombination protein RADB; filament formation, homologous recombination, ATPase domain, hyperthermophIle; HET: DNA; 2.20A {Thermococcus kodakarensis} PDB: 2cvf_A*

Probab=97.87  E-value=3.5e-05  Score=71.57  Aligned_cols=40  Identities=25%  Similarity=0.261  Sum_probs=32.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~  259 (480)
                      |++...-++|+||||+|||+++..+|...+..+++++...
T Consensus        16 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~v~~i~~~~   55 (220)
T 2cvh_A           16 GFAPGVLTQVYGPYASGKTTLALQTGLLSGKKVAYVDTEG   55 (220)
T ss_dssp             SBCTTSEEEEECSTTSSHHHHHHHHHHHHCSEEEEEESSC
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHHcCCcEEEEECCC
Confidence            4556667899999999999999999985567788787654

>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=97.83  E-value=0.001  Score=76.90  Aligned_cols=169  Identities=15%  Similarity=0.148  Sum_probs=100.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC-------CCcEEEEeC
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM-------SYDVYDVDL  257 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l-------~~~~~~i~~  257 (480)
                      .|.....++|-++..++|.+.+...           ....+-+.|+|++|+|||+||+.+++..       ...++.+++
T Consensus       119 ~p~~~~~~vgR~~~~~~l~~~l~~~-----------~~~~~~v~i~G~gG~GKTtLa~~~~~~~~~~~~~~~~~~~~v~~  187 (1249)
T 3sfz_A          119 VPQRPVIFVTRKKLVHAIQQKLWKL-----------NGEPGWVTIYGMAGCGKSVLAAEAVRDHSLLEGCFSGGVHWVSI  187 (1249)
T ss_dssp             CCCCCSSCCCCHHHHHHHHHHHHTT-----------TTSCEEEEEECSTTSSHHHHHHHHTCCHHHHTTTSTTCEEEEEC
T ss_pred             CCCCCceeccHHHHHHHHHHHHhhc-----------cCCCCEEEEEeCCCCCHHHHHHHHhcChhHHHhhCCCeEEEEEE
Confidence            4455667899999888888765321           1134568899999999999999998752       233556766


Q ss_pred             CCcCCh---------------------------HHHHHHHHh----hcCCcEEEEecccccccCcccccchhhhhhhccc
Q 011664          258 SRVADD---------------------------ADLKSLLLQ----TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG  306 (480)
Q Consensus       258 s~~~~~---------------------------~~l~~l~~~----~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg  306 (480)
                      +.....                           ..+...+..    ...+.+|+|||++..          .    .++.
T Consensus       188 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~LlvlDd~~~~----------~----~~~~  253 (1249)
T 3sfz_A          188 GKQDKSGLLMKLQNLCMRLDQEESFSQRLPLNIEEAKDRLRVLMLRKHPRSLLILDDVWDP----------W----VLKA  253 (1249)
T ss_dssp             CSCCHHHHHHHHHHHHHHHTTTCTTCSSCCSSHHHHHHHHHHHTSSSSCSCEEEEESCCCH----------H----HHTT
T ss_pred             CCcCchHHHHHHHHHHHHhhhhcccccCCCCCHHHHHHHHHHHHhccCCCEEEEEecCCCH----------H----HHHh
Confidence            552110                           111111211    134789999999853          1    1222


Q ss_pred             ccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCC-CCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHH
Q 011664          307 VLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPL-CDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAE  385 (480)
Q Consensus       307 ~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~-p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~ad  385 (480)
                      +.     .+.-||+||..+..... +.   .....+.++. .+.++-.+++..+.......+.+...++++...|+ |--
T Consensus       254 ~~-----~~~~ilvTtR~~~~~~~-~~---~~~~~~~~~~~l~~~~a~~l~~~~~~~~~~~~~~~~~~i~~~~~gl-PLa  323 (1249)
T 3sfz_A          254 FD-----NQCQILLTTRDKSVTDS-VM---GPKHVVPVESGLGREKGLEILSLFVNMKKEDLPAEAHSIIKECKGS-PLV  323 (1249)
T ss_dssp             TC-----SSCEEEEEESSTTTTTT-CC---SCBCCEECCSSCCHHHHHHHHHHHHTSCSTTCCTHHHHHHHHTTTC-HHH
T ss_pred             hc-----CCCEEEEEcCCHHHHHh-hc---CCceEEEecCCCCHHHHHHHHHHhhCCChhhCcHHHHHHHHHhCCC-HHH
Confidence            21     22346677765433211 11   2234677775 78888888888877554444445567787777444 544


Q ss_pred             HHH
Q 011664          386 IGE  388 (480)
Q Consensus       386 I~~  388 (480)
                      |..
T Consensus       324 l~~  326 (1249)
T 3sfz_A          324 VSL  326 (1249)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            543

>2dzn_B 26S protease regulatory subunit 6B homolog; ankyrin repeats, A-helical domain, structural genomics, NPPSFA; 2.20A {Saccharomyces cerevisiae} PDB: 2dzo_B

Probab=97.80  E-value=2.5e-06  Score=68.31  Aligned_cols=46  Identities=13%  Similarity=0.061  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          350 SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       350 ~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      ++|.+|++.+++..+.....+++.|+..+.|||||||.++|..+..
T Consensus         1 ~~R~~Il~~~l~~~~~~~~vdl~~lA~~t~G~SGADi~~l~~eAa~   46 (82)
T 2dzn_B            1 MERRLIFGTIASKMSLAPEADLDSLIIRNDSLSGAVIAAIMQEAGL   46 (82)
T ss_dssp             -------------CEECTTCCSTTTTTSSCCCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHcCCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            4688999999876554445577899999999999999999986644

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=97.74  E-value=4.5e-05  Score=71.89  Aligned_cols=40  Identities=18%  Similarity=0.175  Sum_probs=31.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc--C-------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF--M-------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~--l-------~~~~~~i~~s~  259 (480)
                      |++...-++|+||||+|||+|+..+|..  +       +...++++...
T Consensus        20 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~g~~~~~~~~i~~~~   68 (243)
T 1n0w_A           20 GIETGSITEMFGEFRTGKTQICHTLAVTCQLPIDRGGGEGKAMYIDTEG   68 (243)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CCcCCeEEEEECCCCCcHHHHHHHHHHHHhCchhcCCCCCeEEEEECCC
Confidence            4556667899999999999999999984  3       45677777654

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=97.74  E-value=4.1e-05  Score=77.72  Aligned_cols=70  Identities=19%  Similarity=0.292  Sum_probs=48.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC---------------------hHHHHHH---HHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD---------------------DADLKSL---LLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~---------------------~~~l~~l---~~~  272 (480)
                      |++..+-++++||||+|||+|+..+|..+   +..+.+++...-..                     ..++..+   +.+
T Consensus        57 Gl~~G~iv~I~G~pGsGKTtLal~la~~~~~~g~~vlyi~~E~~~~~~~a~~lG~~~~~l~i~~~~~~e~~l~~~~~l~~  136 (349)
T 2zr9_A           57 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGIAAFIDAEHALDPEYAKKLGVDTDSLLVSQPDTGEQALEIADMLVR  136 (349)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEECCCCcCHHHHHHcCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            55566679999999999999999998653   56777777553211                     1111122   122


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|+||++..+..
T Consensus       137 ~~~~~lIVIDsl~~l~~  153 (349)
T 2zr9_A          137 SGALDIIVIDSVAALVP  153 (349)
T ss_dssp             TTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEcChHhhcc
Confidence            34689999999999874

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=97.74  E-value=6.8e-05  Score=69.87  Aligned_cols=37  Identities=24%  Similarity=0.145  Sum_probs=27.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      |++....++|+||||+|||+|++.+|..+   +..++.++
T Consensus        19 gi~~G~~~~i~G~~GsGKTtl~~~l~~~~~~~~~~v~~~~   58 (235)
T 2w0m_A           19 GIPQGFFIALTGEPGTGKTIFSLHFIAKGLRDGDPCIYVT   58 (235)
T ss_dssp             SEETTCEEEEECSTTSSHHHHHHHHHHHHHHHTCCEEEEE
T ss_pred             CCcCCCEEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEEE
Confidence            44555678999999999999999999643   44555554

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=97.69  E-value=4.9e-05  Score=91.85  Aligned_cols=70  Identities=17%  Similarity=0.292  Sum_probs=53.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCCcCChH------------------------HHHHHHHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSRVADDA------------------------DLKSLLLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~~~~~~------------------------~l~~l~~~  272 (480)
                      |++..+.++|+||||||||+|+.+++.+   .|.+..++++.+...+-                        .+...+.+
T Consensus      1077 gi~~g~~vll~G~~GtGKT~la~~~~~ea~k~Ge~~~Fit~ee~~~~L~a~~~G~dl~~l~~~~pd~~e~~~~i~~~l~~ 1156 (2050)
T 3cmu_A         1077 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR 1156 (2050)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEECTTSCCCHHHHHHTTCCTTTCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCcEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEccccHHHHHHHHcCCChhHheeecCcchHHHHHHHHHHHH
Confidence            4677788999999999999999999864   37888888877643311                        12233455


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...|++|+||++..+.+
T Consensus      1157 ~~~~dlvVIDsl~~L~~ 1173 (2050)
T 3cmu_A         1157 SGAVDVIVVDSVAALTP 1173 (2050)
T ss_dssp             HTCCSEEEESCGGGCCC
T ss_pred             hCCCCEEEECCcccccc
Confidence            67899999999999855

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=97.67  E-value=0.00012  Score=74.50  Aligned_cols=70  Identities=13%  Similarity=0.214  Sum_probs=48.4

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC---------------------hHHHHHHH---Hh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD---------------------DADLKSLL---LQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~---------------------~~~l~~l~---~~  272 (480)
                      |++...-++|+||||+|||+|+..+|..+   +..+++++......                     ..++...+   .+
T Consensus        57 Gi~~G~i~~I~GppGsGKSTLal~la~~~~~~gg~VlyId~E~s~~~~ra~rlgv~~~~l~i~~~~~~e~~l~~~~~l~~  136 (356)
T 3hr8_A           57 GYPRGRIVEIFGQESSGKTTLALHAIAEAQKMGGVAAFIDAEHALDPVYAKNLGVDLKSLLISQPDHGEQALEIVDELVR  136 (356)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEecccccchHHHHHcCCchhhhhhhhccCHHHHHHHHHHHhh
Confidence            45556678999999999999999998764   66777787654221                     11111111   22


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+++||.+..+.+
T Consensus       137 ~~~~dlvVIDSi~~l~~  153 (356)
T 3hr8_A          137 SGVVDLIVVDSVAALVP  153 (356)
T ss_dssp             TSCCSEEEEECTTTCCC
T ss_pred             hcCCCeEEehHhhhhcC
Confidence            35789999999988775

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=97.67  E-value=3.2e-05  Score=77.50  Aligned_cols=40  Identities=18%  Similarity=0.241  Sum_probs=32.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~  259 (480)
                      |++...-++++||||+|||+++..+|...         +..+++++...
T Consensus       103 Gl~~G~i~~i~G~~GsGKT~la~~la~~~~~~~~~gg~~~~vlyi~~e~  151 (324)
T 2z43_A          103 GIETRTMTEFFGEFGSGKTQLCHQLSVNVQLPPEKGGLSGKAVYIDTEG  151 (324)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSCEEEEEESSS
T ss_pred             CCCCCcEEEEECCCCCCHhHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            56666678999999999999999999764         56788888765

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=97.66  E-value=0.00013  Score=74.64  Aligned_cols=70  Identities=17%  Similarity=0.279  Sum_probs=49.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC---------------------hHHHHHHHH---h
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD---------------------DADLKSLLL---Q  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~---------------------~~~l~~l~~---~  272 (480)
                      |++...-++++||||+|||+|+..+|..+   +.++.++++..-..                     ...+...+.   +
T Consensus        70 Gl~~G~li~I~G~pGsGKTtlal~la~~~~~~g~~vlyi~~E~s~~~~~a~~~g~d~~~l~i~~~~~~e~~l~~l~~l~~  149 (366)
T 1xp8_A           70 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  149 (366)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCCcEEEEEcCCCCChHHHHHHHHHHHHHCCCeEEEEECCCChhHHHHHHcCCCHHHceeecCCcHHHHHHHHHHHHh
Confidence            56666779999999999999999888653   66788887654211                     112222222   2


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+||||.+..+.+
T Consensus       150 ~~~~~lVVIDsl~~l~~  166 (366)
T 1xp8_A          150 SGAIDVVVVDSVAALTP  166 (366)
T ss_dssp             TTCCSEEEEECTTTCCC
T ss_pred             cCCCCEEEEeChHHhcc
Confidence            35689999999999874

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=97.65  E-value=1.7e-05  Score=73.15  Aligned_cols=107  Identities=12%  Similarity=0.112  Sum_probs=55.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCC--C------cCC----------hHHHHHHHHhhc-CCcEEEEec
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLS--R------VAD----------DADLKSLLLQTT-SKSVILIED  283 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s--~------~~~----------~~~l~~l~~~~~-~~sII~IDE  283 (480)
                      -++++||||+|||+++..++..   .+..++.+...  .      +.+          -.....++.... .+.+|+|||
T Consensus         5 i~vi~G~~gsGKTT~ll~~~~~~~~~g~~v~~~~~~~d~r~~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~dvviIDE   84 (184)
T 2orw_A            5 LTVITGPMYSGKTTELLSFVEIYKLGKKKVAVFKPKIDSRYHSTMIVSHSGNGVEAHVIERPEEMRKYIEEDTRGVFIDE   84 (184)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHHHHTTCEEEEEEEC-----CCCEECC----CEECEEESSGGGGGGGCCTTEEEEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeeccccccCcccEEecCCCceeeEEECCHHHHHHHhcCCCCEEEEEC
Confidence            5789999999999998666643   35555443211  0      000          001112222222 467999999


Q ss_pred             ccccccCcccccchhhhhhhcccccccccCCceEEEE--ecC---CCccCcccccCCCceeEEEEcCC
Q 011664          284 LDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF--TMN---SKDHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       284 iD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~--tTN---~~~~LD~aLlrpGRfd~~I~~~~  346 (480)
                      +..+.+         +++..+..+..   .+..+++.  ++|   .+....++|+.  +.|...++..
T Consensus        85 ~Q~~~~---------~~~~~l~~l~~---~~~~Vi~~Gl~~~f~~~~f~~~~~ll~--~ad~v~~l~~  138 (184)
T 2orw_A           85 VQFFNP---------SLFEVVKDLLD---RGIDVFCAGLDLTHKQNPFETTALLLS--LADTVIKKKA  138 (184)
T ss_dssp             GGGSCT---------THHHHHHHHHH---TTCEEEEEEESBCTTSCBCHHHHHHHH--HCSEEEECCB
T ss_pred             cccCCH---------HHHHHHHHHHH---CCCCEEEEeeccccccCCccchHHHHH--HhhheEEeee
Confidence            997521         12222222222   12233433  344   44455667776  7776666543

>1u94_A RECA protein, recombinase A; homologous recombination, ATPase, DNA repair, DNA binding protein; 1.90A {Escherichia coli} SCOP: c.37.1.11 d.48.1.1 PDB: 1u98_A 1u99_A 1xms_A* 1xmv_A* 2rec_A 2reb_A 1n03_A* 1rea_A 1aa3_A

Probab=97.65  E-value=6.2e-05  Score=76.65  Aligned_cols=70  Identities=16%  Similarity=0.273  Sum_probs=50.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC---------------------hHHHHHHH---Hh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD---------------------DADLKSLL---LQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~---------------------~~~l~~l~---~~  272 (480)
                      |++..+-++++||||+|||+||..+|..+   +..+.++++..-..                     ...+..++   .+
T Consensus        59 Gl~~G~ii~I~G~pGsGKTtLal~la~~~~~~g~~vlyid~E~s~~~~~a~~~g~~~~~l~i~~~~~~e~~~~~~~~l~~  138 (356)
T 1u94_A           59 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  138 (356)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCCCCccHHHHHHcCCChhheeeeCCCCHHHHHHHHHHHHh
Confidence            56667789999999999999999988653   66788888743221                     12222222   23


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|+||.+..+..
T Consensus       139 ~~~~~lVVIDsl~~l~~  155 (356)
T 1u94_A          139 SGAVDVIVVDSVAALTP  155 (356)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             ccCCCEEEEcCHHHhcc
Confidence            45789999999998874

>1qhx_A CPT, protein (chloramphenicol phosphotransferase); kinase, antibiotic resistance, phosphorylation, mononucleoti binding fold; HET: ATP; 2.50A {Streptomyces venezuelae} SCOP: c.37.1.3 PDB: 1grr_A* 1grq_A 1qhs_A* 1qhn_A* 1qhy_A*

Probab=97.61  E-value=4.7e-05  Score=68.50  Aligned_cols=33  Identities=24%  Similarity=0.339  Sum_probs=29.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      .-|+|.||||+||||+++++|..++.+++.++.
T Consensus         4 ~~i~l~G~~GsGKST~a~~La~~l~~~~~~~~~   36 (178)
T 1qhx_A            4 RMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCeEEecc
Confidence            468999999999999999999999988887765

>3trf_A Shikimate kinase, SK; amino acid biosynthesis, transferase; 2.60A {Coxiella burnetii}

Probab=97.60  E-value=2.7e-05  Score=70.64  Aligned_cols=33  Identities=30%  Similarity=0.461  Sum_probs=29.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ++.++|.||||||||++++.+|..++..+++.+
T Consensus         5 ~~~i~l~G~~GsGKst~a~~La~~l~~~~i~~d   37 (185)
T 3trf_A            5 LTNIYLIGLMGAGKTSVGSQLAKLTKRILYDSD   37 (185)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHHCCCEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            457999999999999999999999999988764

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=97.58  E-value=0.00011  Score=74.38  Aligned_cols=40  Identities=15%  Similarity=0.111  Sum_probs=32.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---------CCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---------MSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---------l~~~~~~i~~s~  259 (480)
                      |++...-++++||||+|||+|+..+|..         .+..+++++...
T Consensus       118 Gl~~G~i~~I~G~~GsGKTtla~~la~~~~~~~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          118 GIESMAITEAFGEFRTGKTQLSHTLCVTAQLPGAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHHTTSCBTTTBCCCEEEEEESSS
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHHhcccccCCCCCeEEEEECCC
Confidence            5555566899999999999999999885         256788888655

>3vaa_A Shikimate kinase, SK; structural genomics, center for structural genomics of infec diseases, csgid, metal binding, transferase; 1.70A {Bacteroides thetaiotaomicron}

Probab=97.52  E-value=4e-05  Score=70.83  Aligned_cols=34  Identities=26%  Similarity=0.352  Sum_probs=29.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ....++|.|||||||||+++++|..++..++..+
T Consensus        24 ~~~~i~l~G~~GsGKsTl~~~La~~l~~~~i~~d   57 (199)
T 3vaa_A           24 AMVRIFLTGYMGAGKTTLGKAFARKLNVPFIDLD   57 (199)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHcCCCEEcch
Confidence            3457999999999999999999999999887654

>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=97.52  E-value=9.5e-05  Score=74.97  Aligned_cols=40  Identities=23%  Similarity=0.306  Sum_probs=31.3

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~  259 (480)
                      |++...-+.|+||||+|||+|++.+|...         +-.+++++...
T Consensus       127 gi~~G~i~~I~G~~GsGKTTL~~~l~~~~~~~~~~Gg~~G~vi~i~~e~  175 (349)
T 1pzn_A          127 GIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTEN  175 (349)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSS
T ss_pred             CCCCCeEEEEECCCCCCHHHHHHHHHHHhccchhcCCCCCeEEEEeCCC
Confidence            56666678999999999999999999876         23557776543

>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=97.51  E-value=4.5e-05  Score=69.36  Aligned_cols=34  Identities=18%  Similarity=0.244  Sum_probs=29.1

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ..+.-|+|.|+||+||||+++.++..++..++..
T Consensus         3 ~~~~~I~l~G~~GsGKST~~~~L~~~l~~~~i~~   36 (193)
T 2rhm_A            3 QTPALIIVTGHPATGKTTLSQALATGLRLPLLSK   36 (193)
T ss_dssp             SCCEEEEEEESTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CCCeEEEEECCCCCCHHHHHHHHHHHcCCeEecH
Confidence            3455789999999999999999999999877663

>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=97.50  E-value=0.0016  Score=69.63  Aligned_cols=163  Identities=14%  Similarity=0.106  Sum_probs=91.1

Q ss_pred             ccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHH----cCCCc---EEEEeCCCcC--C-
Q 011664          193 SMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMAS----FMSYD---VYDVDLSRVA--D-  262 (480)
Q Consensus       193 ~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~----~l~~~---~~~i~~s~~~--~-  262 (480)
                      +|-++.+++|.+.+..-          +....+.+.++|++|+|||+||+.+++    .....   .+.++++...  + 
T Consensus       131 ~GR~~~~~~l~~~L~~~----------~~~~~~vv~I~G~gGvGKTtLA~~v~~~~~~~~~~~F~~~~wv~vs~~~~~~~  200 (549)
T 2a5y_B          131 YIREYHVDRVIKKLDEM----------CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKST  200 (549)
T ss_dssp             CCCHHHHHHHHHHHHHH----------TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTHH
T ss_pred             CCchHHHHHHHHHHhcc----------cCCCceEEEEEcCCCCCHHHHHHHHHHhhhHHHhccCCcEEEEEECCCCCCCH
Confidence            48888888888776321          112245788999999999999999997    33222   3444554421  0 


Q ss_pred             ---------------------------hHHHHHHHHhh--cC-CcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          263 ---------------------------DADLKSLLLQT--TS-KSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       263 ---------------------------~~~l~~l~~~~--~~-~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                                                 ...+...+.+.  .. +.+|+|||++..          .++  .+.+.     
T Consensus       201 ~~~~~~il~~l~~~~~~~~~~~~~~~~~~~l~~~l~~~L~~~kr~LlVLDdv~~~----------~~~--~~~~~-----  263 (549)
T 2a5y_B          201 FDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQE----------ETI--RWAQE-----  263 (549)
T ss_dssp             HHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCH----------HHH--HHHHH-----
T ss_pred             HHHHHHHHHHHhcCcccccccccccccHHHHHHHHHHHHcCCCcEEEEEECCCCc----------hhh--ccccc-----
Confidence                                       01122222221  23 789999999853          111  11111     


Q ss_pred             CCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCC-C-CchhHHHHHHhCCCCCHHHHHH
Q 011664          313 FEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDH-K-LFPQVEEIFQNGSSLSPAEIGE  388 (480)
Q Consensus       313 ~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~-~-l~~~i~~l~~~~~g~s~adI~~  388 (480)
                       .+..||+||....... . .  +-.+..+.++..+.++-.+++..+...... . +.+...++++.. |..|--|..
T Consensus       264 -~gs~ilvTTR~~~v~~-~-~--~~~~~~~~l~~L~~~ea~~Lf~~~a~~~~~~~~~~~~~~~I~~~c-~GlPLAl~~  335 (549)
T 2a5y_B          264 -LRLRCLVTTRDVEISN-A-A--SQTCEFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELS-SGNPATLMM  335 (549)
T ss_dssp             -TTCEEEEEESBGGGGG-G-C--CSCEEEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHH-TTCHHHHHH
T ss_pred             -CCCEEEEEcCCHHHHH-H-c--CCCCeEEECCCCCHHHHHHHHHHHhcCCCCchhHHHHHHHHHHHh-CCChHHHHH
Confidence             2334667776433211 1 1  123457899999999999999988533221 1 111234566655 444544443

>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=97.43  E-value=6.8e-05  Score=66.68  Aligned_cols=31  Identities=26%  Similarity=0.323  Sum_probs=28.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -|+|.|||||||||+++.+|..+++.++..+
T Consensus         3 ~i~l~G~~GsGKsT~~~~L~~~l~~~~i~~d   33 (173)
T 3kb2_A            3 LIILEGPDCCFKSTVAAKLSKELKYPIIKGS   33 (173)
T ss_dssp             EEEEECSSSSSHHHHHHHHHHHHCCCEEECC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeeecCc
Confidence            4789999999999999999999998887665

>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=97.42  E-value=0.00026  Score=68.93  Aligned_cols=28  Identities=32%  Similarity=0.321  Sum_probs=23.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      |++...-++|+||||+|||+|+..+|..
T Consensus        26 gl~~G~i~~i~G~~GsGKTtl~~~l~~~   53 (279)
T 1nlf_A           26 NMVAGTVGALVSPGGAGKSMLALQLAAQ   53 (279)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCCEEEEEcCCCCCHHHHHHHHHHH
Confidence            3445567899999999999999999864

>1via_A Shikimate kinase; structural genomics, transferase; HET: MSE; 1.57A {Campylobacter jejuni} SCOP: c.37.1.2

Probab=97.38  E-value=6.6e-05  Score=67.69  Aligned_cols=31  Identities=32%  Similarity=0.455  Sum_probs=27.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .++|.||||||||++++++|..++.++++.+
T Consensus         6 ~i~i~G~~GsGKsTla~~La~~l~~~~~d~d   36 (175)
T 1via_A            6 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   36 (175)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHcCCCEEccc
Confidence            5899999999999999999999998877643

>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=97.37  E-value=7.5e-05  Score=67.53  Aligned_cols=32  Identities=28%  Similarity=0.410  Sum_probs=28.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ++.++|.||||+|||++++++|..++..++..
T Consensus        11 ~~~i~i~G~~GsGKst~~~~l~~~~~~~~~~~   42 (180)
T 3iij_A           11 LPNILLTGTPGVGKTTLGKELASKSGLKYINV   42 (180)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHHHhCCeEEEH
Confidence            34699999999999999999999999887765

>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=97.36  E-value=0.00014  Score=72.34  Aligned_cols=40  Identities=15%  Similarity=0.111  Sum_probs=31.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------------C----CcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------------S----YDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------------~----~~~~~i~~s~  259 (480)
                      |++...-++++||||+|||+++..+|...               |    ..+++++...
T Consensus        94 Gl~~g~i~~i~G~~gsGKT~la~~la~~~~l~~~~~~~~~~~~~gg~~~~~v~yi~~e~  152 (322)
T 2i1q_A           94 GLESQSVTEFAGVFGSGKTQIMHQSCVNLQNPEFLFYDEEAVSKGEVAQPKAVYIDTEG  152 (322)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHTTCGGGEECCTTTSCTTTTSSEEEEEEESSS
T ss_pred             CccCCeEEEEECCCCCCHHHHHHHHHHHHhccccccccccccccCCCCCceEEEEECCC
Confidence            55666678999999999999999998642               3    5778888765

>1gvn_B Zeta; postsegregational killing system, plasmid; 1.95A {Streptococcus pyogenes} SCOP: c.37.1.21 PDB: 3q8x_B*

Probab=97.36  E-value=0.00024  Score=69.97  Aligned_cols=57  Identities=26%  Similarity=0.402  Sum_probs=37.5

Q ss_pred             hHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          196 TDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      +++.+.+.+.+...+...     .....+.-++|.||||+||||++++++..++...+.++.
T Consensus        10 ~~~~~~~~~~~~~~l~~~-----~~~~~~~livl~G~sGsGKSTla~~L~~~~~~~~~~Is~   66 (287)
T 1gvn_B           10 KQFENRLNDNLEELIQGK-----KAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDN   66 (287)
T ss_dssp             HHHHHHHHHHHHHHHTTC-----CCCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECT
T ss_pred             HHHHHHHHHHHHHHhccc-----cCCCCCeEEEEECCCCCCHHHHHHHHHHHhCCCeEEEec
Confidence            344444444444444321     122345678999999999999999999988555566664

>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=97.34  E-value=0.0001  Score=67.32  Aligned_cols=33  Identities=30%  Similarity=0.448  Sum_probs=28.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc-CCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF-MSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~-l~~~~~~i~  256 (480)
                      +..++|.|+||||||++++.+|.. +|+++++.+
T Consensus        10 ~~~I~l~G~~GsGKSTv~~~La~~l~g~~~id~d   43 (184)
T 1y63_A           10 GINILITGTPGTGKTSMAEMIAAELDGFQHLEVG   43 (184)
T ss_dssp             SCEEEEECSTTSSHHHHHHHHHHHSTTEEEEEHH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhcCCCEEeeHH
Confidence            346999999999999999999999 787777653

>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=97.34  E-value=8.2e-05  Score=67.44  Aligned_cols=31  Identities=29%  Similarity=0.491  Sum_probs=28.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -|+|.|+||||||++++.+|..+|.++++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id~D   34 (184)
T 2iyv_A            4 KAVLVGLPGSGKSTIGRRLAKALGVGLLDTD   34 (184)
T ss_dssp             SEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHcCCCEEeCc
Confidence            4899999999999999999999999887654

>2r8r_A Sensor protein; KDPD, PFAM02702, MCSG, structural genomics, protein structure initiative, midwest center for structural genomics, kinase; 2.30A {Pseudomonas syringae PV}

Probab=97.34  E-value=0.00034  Score=66.66  Aligned_cols=61  Identities=21%  Similarity=0.268  Sum_probs=42.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc---------C-----------------ChHHHHHHHHhhcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV---------A-----------------DDADLKSLLLQTTS  275 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~---------~-----------------~~~~l~~l~~~~~~  275 (480)
                      -.+++.|+||+|||+++-.+|..+   |.++..+++..-         .                 .+..+...+.  ..
T Consensus         7 l~I~~~~kgGvGKTt~a~~la~~l~~~G~~V~v~d~D~q~~~~~~al~~gl~~~~~~~~~~~~~~~~e~~l~~~L~--~~   84 (228)
T 2r8r_A            7 LKVFLGAAPGVGKTYAMLQAAHAQLRQGVRVMAGVVETHGRAETEALLNGLPQQPLLRTEYRGMTLEEMDLDALLK--AA   84 (228)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECCCTTCHHHHHHHTTSCBCCCEEEEETTEEEEECCHHHHHH--HC
T ss_pred             EEEEEECCCCCcHHHHHHHHHHHHHHCCCCEEEEEeCCCCChhHHHHhcCccccCcceeecCCcccccccHHHHHh--cC
Confidence            468999999999999999998765   777766655320         0                 0122333333  36


Q ss_pred             CcEEEEeccccc
Q 011664          276 KSVILIEDLDRF  287 (480)
Q Consensus       276 ~sII~IDEiD~l  287 (480)
                      |.+++|||+-..
T Consensus        85 pdlvIVDElG~~   96 (228)
T 2r8r_A           85 PSLVLVDELAHT   96 (228)
T ss_dssp             CSEEEESCTTCB
T ss_pred             CCEEEEeCCCCC
Confidence            899999998764

>1kag_A SKI, shikimate kinase I; transferase, structural genomics, PSI, protein structure initiative; 2.05A {Escherichia coli} SCOP: c.37.1.2

Probab=97.34  E-value=0.00014  Score=65.03  Aligned_cols=31  Identities=35%  Similarity=0.695  Sum_probs=27.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ..+.|.|||||||||+++.+|..++..++..
T Consensus         5 ~~i~l~G~~GsGKSTl~~~La~~l~~~~id~   35 (173)
T 1kag_A            5 RNIFLVGPMGAGKSTIGRQLAQQLNMEFYDS   35 (173)
T ss_dssp             CCEEEECCTTSCHHHHHHHHHHHTTCEEEEH
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHhCCCEEec
Confidence            4589999999999999999999999866653

>1zuh_A Shikimate kinase; alpha-beta protein, transferase; 1.80A {Helicobacter pylori} PDB: 1zui_A* 3hr7_A 3muf_A* 3mrs_A 3n2e_A*

Probab=97.31  E-value=0.0001  Score=65.90  Aligned_cols=32  Identities=34%  Similarity=0.538  Sum_probs=29.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ..++|.|+||||||++++.+|..+|.++++.+
T Consensus         8 ~~i~l~G~~GsGKSTva~~La~~lg~~~id~D   39 (168)
T 1zuh_A            8 QHLVLIGFMGSGKSSLAQELGLALKLEVLDTD   39 (168)
T ss_dssp             CEEEEESCTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHhCCCEEECh
Confidence            47899999999999999999999999988754

>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=97.28  E-value=0.00041  Score=71.68  Aligned_cols=40  Identities=23%  Similarity=0.173  Sum_probs=29.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~  259 (480)
                      |++...-++|+||||||||+|+..+|-..         +...++++...
T Consensus       174 GI~~Gei~~I~G~sGsGKTTLl~~la~~~~~p~~~Gg~~~~viyid~E~  222 (400)
T 3lda_A          174 GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEG  222 (400)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHTTSCGGGTCCSSEEEEEESSS
T ss_pred             CcCCCcEEEEEcCCCCChHHHHHHHHHHhccCcccCCCCCcEEEEeCCC
Confidence            56666678999999999999999776322         34577777654

>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=97.27  E-value=0.00012  Score=64.84  Aligned_cols=29  Identities=31%  Similarity=0.384  Sum_probs=26.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -|+|.|||||||||+++.+ ..+|.+++.+
T Consensus         3 ~I~l~G~~GsGKsT~a~~L-~~~g~~~i~~   31 (179)
T 3lw7_A            3 VILITGMPGSGKSEFAKLL-KERGAKVIVM   31 (179)
T ss_dssp             EEEEECCTTSCHHHHHHHH-HHTTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHH-HHCCCcEEEH
Confidence            4889999999999999999 8899887764

>2ze6_A Isopentenyl transferase; crown GALL tumor, cytokinin biosynthesis; HET: DST AMP; 2.10A {Agrobacterium tumefaciens} PDB: 2ze5_A* 2ze7_A* 2ze8_A

Probab=97.27  E-value=0.00013  Score=70.53  Aligned_cols=32  Identities=31%  Similarity=0.532  Sum_probs=28.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      -++|.||||||||++++++|..++..++..|.
T Consensus         3 li~I~G~~GSGKSTla~~La~~~~~~~i~~D~   34 (253)
T 2ze6_A            3 LHLIYGPTCSGKTDMAIQIAQETGWPVVALDR   34 (253)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCCEEECCS
T ss_pred             EEEEECCCCcCHHHHHHHHHhcCCCeEEeccH
Confidence            47899999999999999999999998887764

>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=97.27  E-value=0.0006  Score=68.22  Aligned_cols=69  Identities=23%  Similarity=0.189  Sum_probs=45.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC-----CCcEEEEeCCCcCC---------------------hHHH-HHHHH-
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM-----SYDVYDVDLSRVAD---------------------DADL-KSLLL-  271 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l-----~~~~~~i~~s~~~~---------------------~~~l-~~l~~-  271 (480)
                      |++.. -++++||||||||+|+..++..+     +..+.+++...-..                     ..++ ..+.. 
T Consensus        25 Gl~~G-iteI~G~pGsGKTtL~Lq~~~~~~~~g~g~~vlyId~E~s~~~~ra~~lGvd~d~llv~~~~~~E~~~l~i~~~  103 (333)
T 3io5_A           25 GMQSG-LLILAGPSKSFKSNFGLTMVSSYMRQYPDAVCLFYDSEFGITPAYLRSMGVDPERVIHTPVQSLEQLRIDMVNQ  103 (333)
T ss_dssp             CBCSE-EEEEEESSSSSHHHHHHHHHHHHHHHCTTCEEEEEESSCCCCHHHHHHTTCCGGGEEEEECSBHHHHHHHHHHH
T ss_pred             CCcCC-eEEEECCCCCCHHHHHHHHHHHHHhcCCCceEEEEeccchhhHHHHHHhCCCHHHeEEEcCCCHHHHHHHHHHH
Confidence            34443 57899999999999987766533     66788887643211                     1112 11211 


Q ss_pred             ----hhcCCcEEEEeccccccc
Q 011664          272 ----QTTSKSVILIEDLDRFLV  289 (480)
Q Consensus       272 ----~~~~~sII~IDEiD~l~~  289 (480)
                          +...|.+|+||-|..+.+
T Consensus       104 l~~i~~~~~~lvVIDSI~aL~~  125 (333)
T 3io5_A          104 LDAIERGEKVVVFIDSLGNLAS  125 (333)
T ss_dssp             HHTCCTTCCEEEEEECSTTCBC
T ss_pred             HHHhhccCceEEEEeccccccc
Confidence                234789999999999874

>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=97.24  E-value=0.00019  Score=65.20  Aligned_cols=35  Identities=29%  Similarity=0.317  Sum_probs=29.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      ...-+.|.||||+||||+++.+|+..+...+.++.
T Consensus         8 ~g~~i~l~G~~GsGKSTl~~~La~~~~~g~i~i~~   42 (191)
T 1zp6_A            8 GGNILLLSGHPGSGKSTIAEALANLPGVPKVHFHS   42 (191)
T ss_dssp             TTEEEEEEECTTSCHHHHHHHHHTCSSSCEEEECT
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHhccCCCeEEEcc
Confidence            44568899999999999999999987776666654

>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=97.24  E-value=0.00012  Score=65.39  Aligned_cols=31  Identities=23%  Similarity=0.530  Sum_probs=27.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -|+|.|+||||||++++.+|..++.++++.+
T Consensus         4 ~I~l~G~~GsGKsT~a~~La~~lg~~~id~d   34 (173)
T 1e6c_A            4 PIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (173)
T ss_dssp             CEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCcEEccc
Confidence            5899999999999999999999998877643

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=97.22  E-value=0.00049  Score=64.78  Aligned_cols=39  Identities=33%  Similarity=0.289  Sum_probs=29.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc----CCCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF----MSYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~----l~~~~~~i~~s  258 (480)
                      |++...-++++|+||+|||+++..+|..    .+.+++++++.
T Consensus        26 Gl~~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~~~~v~~~s~E   68 (251)
T 2zts_A           26 GFPEGTTVLLTGGTGTGKTTFAAQFIYKGAEEYGEPGVFVTLE   68 (251)
T ss_dssp             SEETTCEEEEECCTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCceeeccc
Confidence            4556667899999999999999877643    35667776643

>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=97.22  E-value=0.00016  Score=66.62  Aligned_cols=32  Identities=28%  Similarity=0.426  Sum_probs=28.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +.-|+|.|||||||||+++.+|..++..++..
T Consensus        20 ~~~I~l~G~~GsGKST~a~~La~~l~~~~i~~   51 (201)
T 2cdn_A           20 HMRVLLLGPPGAGKGTQAVKLAEKLGIPQIST   51 (201)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCcEEeh
Confidence            34589999999999999999999999887765

>1tev_A UMP-CMP kinase; ploop, NMP binding region, LID region, conformational changes, transferase; 2.10A {Homo sapiens} SCOP: c.37.1.1

Probab=97.21  E-value=0.00014  Score=65.84  Aligned_cols=31  Identities=19%  Similarity=0.320  Sum_probs=27.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-|+|.|+|||||||+++.+|..++..++..
T Consensus         4 ~~I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   34 (196)
T 1tev_A            4 LVVFVLGGPGAGKGTQCARIVEKYGYTHLSA   34 (196)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            4689999999999999999999999876654

>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=97.21  E-value=0.00017  Score=65.29  Aligned_cols=33  Identities=15%  Similarity=0.232  Sum_probs=28.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .+.-|+|.|+|||||||+++.+|..++..+++.
T Consensus         5 ~~~~I~l~G~~GsGKsT~~~~L~~~l~~~~i~~   37 (194)
T 1qf9_A            5 KPNVVFVLGGPGSGKGTQCANIVRDFGWVHLSA   37 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cCcEEEEECCCCCCHHHHHHHHHHHhCCeEeeH
Confidence            345689999999999999999999999877765

>1ly1_A Polynucleotide kinase; PNK, phosphatase, transferase; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1

Probab=97.19  E-value=0.00018  Score=64.43  Aligned_cols=30  Identities=27%  Similarity=0.362  Sum_probs=24.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH-cCCCcEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS-FMSYDVY  253 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~-~l~~~~~  253 (480)
                      +.-|+|.||||+||||+++.++. .++..++
T Consensus         2 ~~~I~i~G~~GsGKST~a~~L~~~~~~~~~i   32 (181)
T 1ly1_A            2 KKIILTIGCPGSGKSTWAREFIAKNPGFYNI   32 (181)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHSTTEEEE
T ss_pred             CeEEEEecCCCCCHHHHHHHHHhhcCCcEEe
Confidence            34689999999999999999998 5664443

>2p5t_B PEZT; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=97.19  E-value=0.00027  Score=67.98  Aligned_cols=38  Identities=21%  Similarity=0.201  Sum_probs=30.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      .+..++|.||||+||||+++.++..++...+.++...+
T Consensus        31 ~~~~i~l~G~~GsGKSTla~~L~~~l~~~~~~~~~D~~   68 (253)
T 2p5t_B           31 QPIAILLGGQSGAGKTTIHRIKQKEFQGNIVIIDGDSF   68 (253)
T ss_dssp             SCEEEEEESCGGGTTHHHHHHHHHHTTTCCEEECGGGG
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHhcCCCcEEEecHHH
Confidence            45678999999999999999999999866666665443

>2c95_A Adenylate kinase 1; transferase, AP4A, nucleotide kinase, transferase ATP-bindi; HET: B4P; 1.71A {Homo sapiens} PDB: 1z83_A* 3adk_A

Probab=97.19  E-value=0.00017  Score=65.60  Aligned_cols=32  Identities=16%  Similarity=0.307  Sum_probs=28.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-|+|.|||||||||+++.+|..++..+++.+
T Consensus        10 ~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~d   41 (196)
T 2c95_A           10 NIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTG   41 (196)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHhCCeEEcHH
Confidence            46899999999999999999999998877654

>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=97.18  E-value=0.00029  Score=84.25  Aligned_cols=71  Identities=15%  Similarity=0.269  Sum_probs=52.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCCcCC---------------------hHHHHHHH---Hh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSRVAD---------------------DADLKSLL---LQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~~~~---------------------~~~l~~l~---~~  272 (480)
                      |++..+.++|+||||||||+||.+++..   .|..+++++......                     ...+..++   .+
T Consensus        30 Gi~~G~i~lI~G~pGsGKT~LAlqla~~~~~~G~~vlYI~te~~~~~l~~~~lg~dl~~i~i~~p~t~e~l~~ll~~L~~  109 (1706)
T 3cmw_A           30 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  109 (1706)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEECTTSCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcCCCeEEEEECCCCCCHHHHHHHHHHHHhhCCCceEEEEecCccHHHHHHhhccCccceeeeccCcHHHHHHHHHHHHh
Confidence            6777889999999999999999998864   477888888765432                     12223333   23


Q ss_pred             hcCCcEEEEecccccccC
Q 011664          273 TTSKSVILIEDLDRFLVE  290 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~~  290 (480)
                      ...+.+|+||++..+...
T Consensus       110 ~~~~~LVVIDSLt~L~~~  127 (1706)
T 3cmw_A          110 SGAVDVIVVDSVAALTPK  127 (1706)
T ss_dssp             HTCCSEEEESCSTTCCCH
T ss_pred             ccCCCEEEEcchhhhccc
Confidence            357899999999988753

>1zd8_A GTP:AMP phosphotransferase mitochondrial; ATP:AMP phosphotransferase, myokinase, structural genomics, structural genomics consortium, SGC; 1.48A {Homo sapiens} PDB: 2ak3_A*

Probab=97.16  E-value=0.0002  Score=67.42  Aligned_cols=32  Identities=13%  Similarity=0.322  Sum_probs=28.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +.-|+|.|||||||||+++.+|..++..+++.
T Consensus         7 ~~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   38 (227)
T 1zd8_A            7 LLRAVIMGAPGSGKGTVSSRITTHFELKHLSS   38 (227)
T ss_dssp             CCEEEEEECTTSSHHHHHHHHHHHSSSEEEEH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCeEEec
Confidence            35689999999999999999999999877654

>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=97.15  E-value=0.0013  Score=66.79  Aligned_cols=61  Identities=23%  Similarity=0.429  Sum_probs=39.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCC-CcC---------------ChHHHHHHHHhh--cCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLS-RVA---------------DDADLKSLLLQT--TSKSVILIE  282 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s-~~~---------------~~~~l~~l~~~~--~~~sII~ID  282 (480)
                      .-+++.||+|+||||+++++++.+    +..++.+.-. ++.               ....+...++.+  ..|.+|++|
T Consensus       124 g~i~I~GptGSGKTTlL~~l~g~~~~~~~~~i~t~ed~~e~~~~~~~~~v~q~~~~~~~~~~~~~La~aL~~~PdvillD  203 (356)
T 3jvv_A          124 GLVLVTGPTGSGKSTTLAAMLDYLNNTKYHHILTIEDPIEFVHESKKCLVNQREVHRDTLGFSEALRSALREDPDIILVG  203 (356)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHTTSCCSEEEES
T ss_pred             CEEEEECCCCCCHHHHHHHHHhcccCCCCcEEEEccCcHHhhhhccccceeeeeeccccCCHHHHHHHHhhhCcCEEecC
Confidence            357899999999999999999865    3444443210 000               011233344433  589999999


Q ss_pred             ccc
Q 011664          283 DLD  285 (480)
Q Consensus       283 EiD  285 (480)
                      |+-
T Consensus       204 Ep~  206 (356)
T 3jvv_A          204 EMR  206 (356)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            995

>3t61_A Gluconokinase; PSI-biology, structural genomics, protein structure initiati YORK structural genomics research consortium, nysgrc; 2.20A {Sinorhizobium meliloti}

Probab=97.15  E-value=0.0002  Score=66.08  Aligned_cols=33  Identities=36%  Similarity=0.491  Sum_probs=28.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.-|+|.||||+||||+++.++..+|..++..+
T Consensus        18 ~~~I~l~G~~GsGKSTla~~L~~~lg~~~i~~d   50 (202)
T 3t61_A           18 PGSIVVMGVSGSGKSSVGEAIAEACGYPFIEGD   50 (202)
T ss_dssp             SSCEEEECSTTSCHHHHHHHHHHHHTCCEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCEEEeCC
Confidence            346999999999999999999999987766543

>3cm0_A Adenylate kinase; ATP-binding, cytoplasm, nucleotide biosynthesis, nucleotide-binding, transferase, structural genomics; 1.80A {Thermus thermophilus}

Probab=97.14  E-value=0.00014  Score=65.80  Aligned_cols=30  Identities=23%  Similarity=0.531  Sum_probs=26.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -++|.|||||||||+++.+|..++..++..
T Consensus         6 ~I~l~G~~GsGKST~~~~La~~l~~~~i~~   35 (186)
T 3cm0_A            6 AVIFLGPPGAGKGTQASRLAQELGFKKLST   35 (186)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCEEECH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEecH
Confidence            588999999999999999999998776654

>2bwj_A Adenylate kinase 5; phosphoryl transfer reaction, transferase; HET: AMP; 2.3A {Homo sapiens}

Probab=97.14  E-value=0.00019  Score=65.48  Aligned_cols=32  Identities=13%  Similarity=0.291  Sum_probs=27.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +.-|.|.|||||||||+++.+|..++..+++.
T Consensus        12 ~~~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~   43 (199)
T 2bwj_A           12 CKIIFIIGGPGSGKGTQCEKLVEKYGFTHLST   43 (199)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHhCCeEEcH
Confidence            34689999999999999999999999776654

>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=97.14  E-value=0.0011  Score=69.28  Aligned_cols=146  Identities=14%  Similarity=0.263  Sum_probs=93.4

Q ss_pred             cCChHHH-HHHHHhhcCCcEEEEecccccccCcc---ccc----chhhhhhhccccccc-----ccCCceEEEEec----
Q 011664          260 VADDADL-KSLLLQTTSKSVILIEDLDRFLVEKP---AAV----SLSGVLNFMDGVLNS-----CCFEERVMVFTM----  322 (480)
Q Consensus       260 ~~~~~~l-~~l~~~~~~~sII~IDEiD~l~~~~~---~~~----~ls~lL~~ldg~~~~-----~~~~~~ivI~tT----  322 (480)
                      +.+...+ +..+.++....|+++||||.++...+   ...    ....||..|||-...     ...+++++|+|.    
T Consensus       234 l~~~~~~~~~ai~~ae~~~il~~DEidki~~~~~~~~~D~s~egvq~aLL~~le~~~~~~~~~~~d~~~ilfI~~gaf~~  313 (444)
T 1g41_A          234 LINPEELKQKAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGAFQV  313 (444)
T ss_dssp             SCCHHHHHHHHHHHHHHHCEEEEETGGGGSCCSSCSSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEECCSS
T ss_pred             ccCHHHHHHHHHHHhccCCeeeHHHHHHHhhccCCCCCCchHHHHHHHHHHHhcccccccccceecCCcEEEEecccccc
Confidence            3343443 34445555667999999999986422   111    234789999885321     124567888875    


Q ss_pred             CCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHh-C--CCCCHHHHHHHHHHh------
Q 011664          323 NSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQN-G--SSLSPAEIGELMIAN------  393 (480)
Q Consensus       323 N~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~-~--~g~s~adI~~ll~~a------  393 (480)
                      +.|.++-|.|+.  ||+.+|.++.++.+++..|+..-    ...+..+...+... .  -.||+..+..+...+      
T Consensus       314 ~~~~dlipel~~--R~~i~i~l~~lt~~e~~~Il~~~----~~~l~~q~~~~~~~~~~~l~~~~~al~~i~~~a~~~~~~  387 (444)
T 1g41_A          314 ARPSDLIPELQG--RLPIRVELTALSAADFERILTEP----HASLTEQYKALMATEGVNIAFTTDAVKKIAEAAFRVNEK  387 (444)
T ss_dssp             CCGGGSCHHHHT--TCCEEEECCCCCHHHHHHHHHSS----TTCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHHHHH
T ss_pred             CChhhcchHHhc--ccceeeeCCCCCHHHHHHHHHHH----HHhHHHHHHHHhcccCceEEECHHHHHHHHHHHHHhccC
Confidence            345556688888  99999999999999999998410    11122333333221 1  147888888777653      


Q ss_pred             -hhcHHHHHHHHHHHHHhc
Q 011664          394 -RNSPSRALKSVITALQTD  411 (480)
Q Consensus       394 -~~~~~~al~~~i~~~~~~  411 (480)
                       +....|.|+.+++.+-.+
T Consensus       388 t~~~GaR~L~~~ie~~~~~  406 (444)
T 1g41_A          388 TENIGARRLHTVMERLMDK  406 (444)
T ss_dssp             SCCCGGGHHHHHHHHHHHH
T ss_pred             CccCCchHHHHHHHHHHHH
Confidence             356778888888877655

>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=97.14  E-value=0.0002  Score=66.65  Aligned_cols=29  Identities=17%  Similarity=0.261  Sum_probs=26.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+|.|||||||||+++.+|..++..++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3dl0_A            3 LVLMGLPGAGKGTQGERIVEKYGIPHIST   31 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHSSCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEeH
Confidence            78999999999999999999999887766

>3be4_A Adenylate kinase; malaria, cryptosporidium parvum nonprotein inhibitors, nucleotide-binding, transferase; HET: AP5; 1.60A {Cryptosporidium parvum iowa II}

Probab=97.13  E-value=0.00019  Score=67.22  Aligned_cols=31  Identities=16%  Similarity=0.292  Sum_probs=27.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-|+|.|||||||||+++.+|..++..++..
T Consensus         6 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   36 (217)
T 3be4_A            6 HNLILIGAPGSGKGTQCEFIKKEYGLAHLST   36 (217)
T ss_dssp             CEEEEEECTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCceEEeh
Confidence            3589999999999999999999999877765

>2pt5_A Shikimate kinase, SK; aromatic amino acid biosynthesis, P-loop kinase, SHI kinase, shikimate pathway; 2.10A {Aquifex aeolicus}

Probab=97.13  E-value=0.00018  Score=63.88  Aligned_cols=31  Identities=29%  Similarity=0.444  Sum_probs=27.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .|+|.|+||||||++++.++..++.+++..+
T Consensus         2 ~I~l~G~~GsGKsT~a~~L~~~l~~~~i~~d   32 (168)
T 2pt5_A            2 RIYLIGFMCSGKSTVGSLLSRSLNIPFYDVD   32 (168)
T ss_dssp             EEEEESCTTSCHHHHHHHHHHHHTCCEEEHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHhCCCEEECc
Confidence            3789999999999999999999998887643

>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=97.11  E-value=0.00015  Score=65.59  Aligned_cols=25  Identities=12%  Similarity=0.259  Sum_probs=22.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-|+|.|||||||||+++.+|..++
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            3589999999999999999999887

>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=97.10  E-value=0.00023  Score=66.55  Aligned_cols=31  Identities=23%  Similarity=0.343  Sum_probs=27.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-|+|.|||||||||+++.+|..++..++..
T Consensus         5 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   35 (220)
T 1aky_A            5 IRMVLIGPPGAGKGTQAPNLQERFHAAHLAT   35 (220)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeh
Confidence            4689999999999999999999999877664

>3fb4_A Adenylate kinase; psychrophIle, phosphotransferase, ATP-binding, nucleotide-binding, transferase; HET: AP5; 2.00A {Marinibacillus marinus}

Probab=97.07  E-value=0.00022  Score=66.31  Aligned_cols=29  Identities=21%  Similarity=0.267  Sum_probs=26.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+|.|||||||||+++.+|..++..++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~~~~~i~~   31 (216)
T 3fb4_A            3 IVLMGLPGAGKGTQAEQIIEKYEIPHIST   31 (216)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEeeH
Confidence            78999999999999999999999877765

>1ukz_A Uridylate kinase; transferase; HET: ADP AMP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1uky_A*

Probab=97.06  E-value=0.00031  Score=64.55  Aligned_cols=32  Identities=16%  Similarity=0.263  Sum_probs=28.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-|+|.|||||||||+++.+|..+|..+++.+
T Consensus        16 ~~I~l~G~~GsGKsT~~~~L~~~~g~~~i~~d   47 (203)
T 1ukz_A           16 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSAG   47 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEHH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCceEEeHH
Confidence            46889999999999999999999998776654

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=97.06  E-value=0.0013  Score=62.50  Aligned_cols=62  Identities=13%  Similarity=0.186  Sum_probs=39.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC-------cC-------------ChHHHHHHHHhh---cCCcEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR-------VA-------------DDADLKSLLLQT---TSKSVI  279 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~-------~~-------------~~~~l~~l~~~~---~~~sII  279 (480)
                      -++++||||+|||+++..++..+   |..++.+....       +.             ...++...+.+.   ..+.+|
T Consensus        14 i~litG~mGsGKTT~ll~~~~r~~~~g~kVli~~~~~d~r~~~~i~srlG~~~~~~~~~~~~~i~~~i~~~~~~~~~dvV   93 (223)
T 2b8t_A           14 IEFITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVI   93 (223)
T ss_dssp             EEEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEE
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHhcCCEEEEEEeccCchHHHHHHHhcCCCccccccCCHHHHHHHHHHHhhCCCCCEE
Confidence            46788999999999988887654   55666653211       11             012333333322   247899


Q ss_pred             EEeccccc
Q 011664          280 LIEDLDRF  287 (480)
Q Consensus       280 ~IDEiD~l  287 (480)
                      +|||+..+
T Consensus        94 iIDEaQ~l  101 (223)
T 2b8t_A           94 GIDEVQFF  101 (223)
T ss_dssp             EECSGGGS
T ss_pred             EEecCccC
Confidence            99999865

>2vli_A Antibiotic resistance protein; transferase, tunicamycin, phosphotransferase; 1.95A {Deinococcus radiodurans}

Probab=97.05  E-value=0.00028  Score=63.57  Aligned_cols=29  Identities=21%  Similarity=0.279  Sum_probs=22.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      .-|+|.|+|||||||+++.+|..++.+++
T Consensus         6 ~~I~l~G~~GsGKST~a~~La~~l~~~~i   34 (183)
T 2vli_A            6 PIIWINGPFGVGKTHTAHTLHERLPGSFV   34 (183)
T ss_dssp             CEEEEECCC----CHHHHHHHHHSTTCEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCCEE
Confidence            46899999999999999999999999877

>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=97.04  E-value=0.00027  Score=63.44  Aligned_cols=31  Identities=35%  Similarity=0.504  Sum_probs=26.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-+.|.||||+||||+++.++..+|..++..
T Consensus         9 ~~i~l~G~~GsGKSTl~~~l~~~~g~~~i~~   39 (175)
T 1knq_A            9 HIYVLMGVSGSGKSAVASEVAHQLHAAFLDG   39 (175)
T ss_dssp             EEEEEECSTTSCHHHHHHHHHHHHTCEEEEG
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHhhCcEEEeC
Confidence            4588999999999999999999888665543

>2c9o_A RUVB-like 1; hexameric helicase, AAA+-ATPase, ATP-binding, chromatin regulator, growth regulation, hydrolase, nuclear protein, DNA recombination; HET: ADP; 2.2A {Homo sapiens} PDB: 2xsz_A*

Probab=97.02  E-value=0.00079  Score=70.46  Aligned_cols=73  Identities=12%  Similarity=0.217  Sum_probs=55.4

Q ss_pred             CcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCC-------------CccCcccccCCCceeEEE
Q 011664          276 KSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNS-------------KDHVDQALLRPGRIDVHI  342 (480)
Q Consensus       276 ~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~-------------~~~LD~aLlrpGRfd~~I  342 (480)
                      |.|+||||+|.+.     ....+.|+..|+.-     ... ++|++||.             |..|+|.+++  ||.. +
T Consensus       296 ~~VliIDEa~~l~-----~~a~~aLlk~lEe~-----~~~-~~il~tn~~~~~i~~~~~~~~~~~l~~~i~s--R~~~-~  361 (456)
T 2c9o_A          296 PGVLFVDEVHMLD-----IECFTYLHRALESS-----IAP-IVIFASNRGNCVIRGTEDITSPHGIPLDLLD--RVMI-I  361 (456)
T ss_dssp             ECEEEEESGGGCB-----HHHHHHHHHHTTST-----TCC-EEEEEECCSEEECBTTSSCEEETTCCHHHHT--TEEE-E
T ss_pred             ceEEEEechhhcC-----HHHHHHHHHHhhcc-----CCC-EEEEecCCccccccccccccccccCChhHHh--hcce-e
Confidence            4799999999883     34567777777532     223 56655533             7789999999  9976 6


Q ss_pred             EcCCCCHHHHHHHHHHHhcc
Q 011664          343 HFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       343 ~~~~p~~~~r~~il~~~l~~  362 (480)
                      .|++|+.++..++++..+..
T Consensus       362 ~~~~~~~~e~~~iL~~~~~~  381 (456)
T 2c9o_A          362 RTMLYTPQEMKQIIKIRAQT  381 (456)
T ss_dssp             ECCCCCHHHHHHHHHHHHHH
T ss_pred             eCCCCCHHHHHHHHHHHHHH
Confidence            99999999999999887643

>1zak_A Adenylate kinase; ATP:AMP-phosphotransferase, transferase; HET: AP5; 3.50A {Zea mays} SCOP: c.37.1.1 g.41.2.1

Probab=97.00  E-value=0.00021  Score=66.93  Aligned_cols=32  Identities=9%  Similarity=0.163  Sum_probs=27.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      +.-|+|.||||+||||+++.+|..++..++.+
T Consensus         5 ~~~I~l~G~~GsGKsT~~~~La~~l~~~~i~~   36 (222)
T 1zak_A            5 PLKVMISGAPASGKGTQCELIKTKYQLAHISA   36 (222)
T ss_dssp             SCCEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            34689999999999999999999999765543

>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=96.99  E-value=0.00034  Score=66.22  Aligned_cols=31  Identities=26%  Similarity=0.344  Sum_probs=27.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ..|+|.|+|||||||+++.+|..++..++..
T Consensus        17 ~~I~l~G~~GsGKsT~a~~La~~l~~~~i~~   47 (233)
T 1ak2_A           17 VRAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   47 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCceecH
Confidence            4689999999999999999999999877664

>3crm_A TRNA delta(2)-isopentenylpyrophosphate transferase; ATP-binding, nucleotide-binding, nucleotidyltransferase, tRNA processing; 1.90A {Pseudomonas aeruginosa} PDB: 3crq_A 3crr_A

Probab=96.97  E-value=0.00047  Score=69.16  Aligned_cols=34  Identities=29%  Similarity=0.548  Sum_probs=30.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      ++.++|.||+|||||+++.++|..++..++++|.
T Consensus         5 ~~~i~i~GptGsGKTtla~~La~~l~~~iis~Ds   38 (323)
T 3crm_A            5 PPAIFLMGPTAAGKTDLAMALADALPCELISVDS   38 (323)
T ss_dssp             CEEEEEECCTTSCHHHHHHHHHHHSCEEEEEECT
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHcCCcEEeccc
Confidence            4578999999999999999999999988888863

>4eun_A Thermoresistant glucokinase; putative sugar kinase, enzyme function initiative, EFI, STRU genomics, transferase; 1.60A {Janibacter SP}

Probab=96.97  E-value=0.0005  Score=63.38  Aligned_cols=31  Identities=26%  Similarity=0.448  Sum_probs=26.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      +.-+.|.||||+||||+++.+++.+|..++.
T Consensus        29 g~~i~l~G~~GsGKSTl~~~L~~~~g~~~i~   59 (200)
T 4eun_A           29 TRHVVVMGVSGSGKTTIAHGVADETGLEFAE   59 (200)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHHHCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhhCCeEEc
Confidence            4468899999999999999999998765543

>2pez_A Bifunctional 3'-phosphoadenosine 5'- phosphosulfate synthetase 1 (PAPS synthetase...; NMP-kinase fold, protein in complex with nucleic acid; HET: GGZ DAT; 1.40A {Homo sapiens} PDB: 2pey_A* 2ax4_A*

Probab=96.96  E-value=0.00059  Score=61.53  Aligned_cols=33  Identities=27%  Similarity=0.527  Sum_probs=29.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      ..-+.|.|++||||||+++.++..+   |.+++.++
T Consensus         5 g~~i~l~G~~GsGKST~~~~L~~~l~~~g~~~i~~d   40 (179)
T 2pez_A            5 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   40 (179)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHhhCCCcEEEEC
Confidence            3457899999999999999999987   88888776

>2pbr_A DTMP kinase, thymidylate kinase; transferase, nucleotide biosynthesis, TMP-binding, A binding, structural genomics, NPPSFA; 1.96A {Aquifex aeolicus}

Probab=96.94  E-value=0.00055  Score=61.95  Aligned_cols=31  Identities=23%  Similarity=0.297  Sum_probs=27.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      +.|.|+|||||||+++.++..+   |.+++..+-
T Consensus         3 I~l~G~~GsGKsT~~~~L~~~l~~~g~~~i~~d~   36 (195)
T 2pbr_A            3 IAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYRE   36 (195)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeC
Confidence            7899999999999999999987   888888763

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=96.93  E-value=0.0003  Score=63.54  Aligned_cols=20  Identities=45%  Similarity=0.650  Sum_probs=17.2

Q ss_pred             CceEEEEccCCCcHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAA  243 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~a  243 (480)
                      ..-+.|.||+|+|||||+++
T Consensus         9 gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            9 LSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SEEEEEECCTTSCHHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHHH
Confidence            34578999999999999994

>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=96.93  E-value=0.0045  Score=61.12  Aligned_cols=84  Identities=11%  Similarity=0.224  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCCcCC----------
Q 011664          197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSRVAD----------  262 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~~~~----------  262 (480)
                      .+++.+.+.+...+...... .+ ...++-+++.||+|+||||++..+|..+    |..+..++......          
T Consensus        80 ~~~~~~~~~l~~~l~~~~~~-~~-~~~g~vi~lvG~~GsGKTTl~~~LA~~l~~~~G~~V~lv~~D~~r~~a~eqL~~~~  157 (296)
T 2px0_A           80 NVVGKLQEILCDMLPSADKW-QE-PIHSKYIVLFGSTGAGKTTTLAKLAAISMLEKHKKIAFITTDTYRIAAVEQLKTYA  157 (296)
T ss_dssp             THHHHHHHHHHTTSCCGGGS-CC-CCCSSEEEEEESTTSSHHHHHHHHHHHHHHTTCCCEEEEECCCSSTTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCcccc-cc-cCCCcEEEEECCCCCCHHHHHHHHHHHHHHhcCCEEEEEecCcccchHHHHHHHHH
Confidence            45566666555544322110 01 1234578899999999999999999754    55676666543221          


Q ss_pred             ------------hHHHHHHHHhhcCCcEEEEe
Q 011664          263 ------------DADLKSLLLQTTSKSVILIE  282 (480)
Q Consensus       263 ------------~~~l~~l~~~~~~~sII~ID  282 (480)
                                  ...++..+.....+.+|+||
T Consensus       158 ~~~gl~~~~~~~~~~l~~al~~~~~~dlvIiD  189 (296)
T 2px0_A          158 ELLQAPLEVCYTKEEFQQAKELFSEYDHVFVD  189 (296)
T ss_dssp             TTTTCCCCBCSSHHHHHHHHHHGGGSSEEEEE
T ss_pred             HhcCCCeEecCCHHHHHHHHHHhcCCCEEEEe
Confidence                        12233344445677888888

>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=96.92  E-value=0.00036  Score=65.04  Aligned_cols=29  Identities=17%  Similarity=0.180  Sum_probs=26.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+|.||||+||||+++.+|..++..++..
T Consensus         3 I~l~G~~GsGKsT~a~~L~~~~g~~~i~~   31 (214)
T 1e4v_A            3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            78999999999999999999998877665

>3umf_A Adenylate kinase; rossmann fold, transferase; 2.05A {Schistosoma mansoni}

Probab=96.91  E-value=0.00051  Score=65.00  Aligned_cols=32  Identities=13%  Similarity=0.316  Sum_probs=27.1

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      ..++-|+|.||||+||+|.|+.+|..+|...+
T Consensus        27 ~k~kiI~llGpPGsGKgTqa~~L~~~~g~~hI   58 (217)
T 3umf_A           27 AKAKVIFVLGGPGSGKGTQCEKLVQKFHFNHL   58 (217)
T ss_dssp             TSCEEEEEECCTTCCHHHHHHHHHHHHCCEEE
T ss_pred             cCCcEEEEECCCCCCHHHHHHHHHHHHCCceE
Confidence            34567889999999999999999999886544

>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=96.91  E-value=0.00043  Score=66.22  Aligned_cols=34  Identities=18%  Similarity=0.322  Sum_probs=29.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .+.-|+|.||||+||||+++.++..++...++.+
T Consensus        28 ~~~~I~l~G~~GsGKsT~a~~L~~~~g~~~is~~   61 (243)
T 3tlx_A           28 PDGRYIFLGAPGSGKGTQSLNLKKSHCYCHLSTG   61 (243)
T ss_dssp             CCEEEEEECCTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHhCCeEEecH
Confidence            3456999999999999999999999988777653

>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=96.89  E-value=0.00045  Score=63.52  Aligned_cols=30  Identities=33%  Similarity=0.381  Sum_probs=26.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -+.|.||+||||||+++.+|+ +|..+++.+
T Consensus         3 ~i~i~G~~GsGKSTl~~~L~~-~g~~~i~~d   32 (204)
T 2if2_A            3 RIGLTGNIGCGKSTVAQMFRE-LGAYVLDAD   32 (204)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH-TTCEEEEHH
T ss_pred             EEEEECCCCcCHHHHHHHHHH-CCCEEEEcc
Confidence            478999999999999999999 888777665

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A*

Probab=96.88  E-value=0.0058  Score=69.97  Aligned_cols=55  Identities=15%  Similarity=0.208  Sum_probs=38.8

Q ss_pred             ccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC------CCcEEEEeCCC
Q 011664          193 SMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM------SYDVYDVDLSR  259 (480)
Q Consensus       193 ~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l------~~~~~~i~~s~  259 (480)
                      +|-++..++|.+.+...            ...+-+.++||+|.|||+||+.+++..      ...++.++++.
T Consensus       131 VGRe~eLeeL~elL~~~------------d~~RVV~IvGmGGIGKTTLAk~Vy~d~rV~~~Fd~gV~WVsVs~  191 (1221)
T 1vt4_I          131 VSRLQPYLKLRQALLEL------------RPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKN  191 (1221)
T ss_dssp             CCCHHHHHHHHHHHHHC------------CSSCEEEECCSTTSSHHHHHHHHHHHCHHHHHHSSCEEEEECCC
T ss_pred             CCcHHHHHHHHHHHhcc------------CCCeEEEEEcCCCccHHHHHHHHHHhhHHHHhCCCcEEEEEeCC
Confidence            78888888877665420            124578899999999999999998632      33456666554

>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=96.84  E-value=0.00062  Score=64.91  Aligned_cols=31  Identities=19%  Similarity=0.383  Sum_probs=26.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      +.-+.|.||||+||||+++.+|..+|...+.
T Consensus        27 ~~~i~l~G~~GsGKSTl~k~La~~lg~~~~~   57 (246)
T 2bbw_A           27 LLRAVILGPPGSGKGTVCQRIAQNFGLQHLS   57 (246)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHHCCCCEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeEec
Confidence            4568999999999999999999888765443

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=96.82  E-value=0.0017  Score=70.04  Aligned_cols=63  Identities=22%  Similarity=0.307  Sum_probs=41.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC----------hHHHHHHHHhh-----------cCCcEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD----------DADLKSLLLQT-----------TSKSVIL  280 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~----------~~~l~~l~~~~-----------~~~sII~  280 (480)
                      +.+++.||||||||+++.+++..+   +..+..+..+.-..          ...+..++...           ....+|+
T Consensus       205 ~~~~I~G~pGTGKTt~i~~l~~~l~~~g~~Vl~~ApT~~Aa~~L~e~~~~~a~Tih~ll~~~~~~~~~~~~~~~~~dvlI  284 (574)
T 3e1s_A          205 RLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLI  284 (574)
T ss_dssp             SEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSHHHHHHHHHHHTSCEEEHHHHTTEETTEESCSSSSCCSCSEEE
T ss_pred             CEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEecCcHHHHHHhHhhhcccHHHHHHHHcCCcchhhhhhcccccCCEEE
Confidence            468899999999999999998754   66676664432110          11133333111           1348999


Q ss_pred             Eeccccc
Q 011664          281 IEDLDRF  287 (480)
Q Consensus       281 IDEiD~l  287 (480)
                      |||+..+
T Consensus       285 IDEasml  291 (574)
T 3e1s_A          285 VDEVSMM  291 (574)
T ss_dssp             ECCGGGC
T ss_pred             EcCccCC
Confidence            9999866

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=96.81  E-value=0.0015  Score=68.35  Aligned_cols=38  Identities=21%  Similarity=0.233  Sum_probs=29.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~  257 (480)
                      |+++..-+++.||||+|||+++..+|..+    |.++..+++
T Consensus       199 Gl~~G~liiI~G~pG~GKTtl~l~ia~~~~~~~g~~Vl~~s~  240 (454)
T 2r6a_A          199 GFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSL  240 (454)
T ss_dssp             SBCTTCEEEEECCTTSCHHHHHHHHHHHHHHHSSCCEEEEES
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHHhCCCcEEEEEC
Confidence            56666678999999999999999988743    557777764

>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=96.81  E-value=0.0009  Score=61.22  Aligned_cols=33  Identities=9%  Similarity=0.186  Sum_probs=28.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-CCcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-SYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i~~  257 (480)
                      .-|.|.|||||||||+++.+|..+ |.+++.++.
T Consensus         5 ~~I~l~G~~GsGKsT~~~~L~~~l~g~~~~~~~~   38 (204)
T 2v54_A            5 ALIVFEGLDKSGKTTQCMNIMESIPANTIKYLNF   38 (204)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHTSCGGGEEEEES
T ss_pred             cEEEEEcCCCCCHHHHHHHHHHHHCCCceEEEec
Confidence            458899999999999999999998 578887764

>2jaq_A Deoxyguanosine kinase; transferase, deoxyribonucleoside kinase; HET: DCP; 2.3A {Mycoplasma mycoides subsp} PDB: 2jat_A* 2jas_A*

Probab=96.80  E-value=0.00065  Score=61.98  Aligned_cols=29  Identities=24%  Similarity=0.688  Sum_probs=25.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      -|.|.|+|||||||+++.+|..++..++.
T Consensus         2 ~I~i~G~~GsGKsT~~~~L~~~l~~~~~~   30 (205)
T 2jaq_A            2 KIAIFGTVGAGKSTISAEISKKLGYEIFK   30 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHCCEEEC
T ss_pred             EEEEECCCccCHHHHHHHHHHhcCCcEEc
Confidence            37899999999999999999999986653

>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=96.79  E-value=0.0007  Score=63.17  Aligned_cols=30  Identities=33%  Similarity=0.606  Sum_probs=26.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      .-+.|.|||||||||+++.+++.+|+++++
T Consensus         6 ~~i~i~G~~GsGKSTl~~~L~~~~g~~~~d   35 (227)
T 1cke_A            6 PVITIDGPSGAGKGTLCKAMAEALQWHLLD   35 (227)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCccc
Confidence            358899999999999999999999976665

>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=96.79  E-value=0.00071  Score=63.39  Aligned_cols=28  Identities=25%  Similarity=0.436  Sum_probs=24.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ++|.||||+||+|.|+.+|..+|...++
T Consensus         3 Iil~GpPGsGKgTqa~~La~~~g~~~is   30 (206)
T 3sr0_A            3 LVFLGPPGAGKGTQAKRLAKEKGFVHIS   30 (206)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCeEEc
Confidence            7889999999999999999998876544

>2xb4_A Adenylate kinase; ATP-binding, nucleotide-binding, transferase; HET: SRT; 1.80A {Desulfovibrio gigas} PDB: 3l0s_A* 3l0p_A*

Probab=96.77  E-value=0.00073  Score=63.59  Aligned_cols=29  Identities=24%  Similarity=0.479  Sum_probs=25.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+|.|||||||||+++.+|..++..++..
T Consensus         3 I~l~G~~GsGKsT~a~~La~~lg~~~i~~   31 (223)
T 2xb4_A            3 ILIFGPNGSGKGTQGNLVKDKYSLAHIES   31 (223)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCeEEch
Confidence            78999999999999999999998766554

>1nks_A Adenylate kinase; thermophilic, transferase; HET: AMP ADP; 2.57A {Sulfolobus acidocaldarius} SCOP: c.37.1.1

Probab=96.76  E-value=0.00047  Score=62.27  Aligned_cols=31  Identities=19%  Similarity=0.289  Sum_probs=25.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC---CcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS---YDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~---~~~~~i~  256 (480)
                      -|+|.|||||||||+++.++..++   .++..++
T Consensus         3 ~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~~   36 (194)
T 1nks_A            3 IGIVTGIPGVGKSTVLAKVKEILDNQGINNKIIN   36 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhcCceEEEEE
Confidence            478999999999999999999775   3355554

>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=96.76  E-value=0.00062  Score=62.79  Aligned_cols=30  Identities=27%  Similarity=0.391  Sum_probs=26.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -+.|.||+||||||+++.+|. +|..+++.+
T Consensus         4 ~i~l~G~~GsGKST~~~~La~-lg~~~id~d   33 (206)
T 1jjv_A            4 IVGLTGGIGSGKTTIANLFTD-LGVPLVDAD   33 (206)
T ss_dssp             EEEEECSTTSCHHHHHHHHHT-TTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcccchH
Confidence            478999999999999999998 888877653

>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=96.74  E-value=0.0011  Score=60.94  Aligned_cols=33  Identities=30%  Similarity=0.420  Sum_probs=26.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      +.-+.|.||+||||||+++++|..+   |...+.++
T Consensus        25 g~~i~l~G~sGsGKSTl~~~La~~l~~~G~~~~~~d   60 (200)
T 3uie_A           25 GCVIWVTGLSGSGKSTLACALNQMLYQKGKLCYILD   60 (200)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHhcCceEEEec
Confidence            4568899999999999999999987   55444554

>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=96.74  E-value=0.0014  Score=68.51  Aligned_cols=64  Identities=20%  Similarity=0.290  Sum_probs=38.0

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CC-cEEEEeC
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SY-DVYDVDL  257 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~-~~~~i~~  257 (480)
                      +...|.+|+++  .+++++.+...+ .++..          ..+.+++.||||||||+++.+++..+   +. .++.+..
T Consensus        16 ~~~~p~~~~~L--n~~Q~~av~~~~-~~i~~----------~~~~~li~G~aGTGKT~ll~~~~~~l~~~~~~~il~~a~   82 (459)
T 3upu_A           16 PRGSHMTFDDL--TEGQKNAFNIVM-KAIKE----------KKHHVTINGPAGTGATTLTKFIIEALISTGETGIILAAP   82 (459)
T ss_dssp             -----CCSSCC--CHHHHHHHHHHH-HHHHS----------SSCEEEEECCTTSCHHHHHHHHHHHHHHTTCCCEEEEES
T ss_pred             cccCCCccccC--CHHHHHHHHHHH-HHHhc----------CCCEEEEEeCCCCCHHHHHHHHHHHHHhcCCceEEEecC
Confidence            55567788876  444555444322 22222          12379999999999999999999866   33 4555544


Q ss_pred             C
Q 011664          258 S  258 (480)
Q Consensus       258 s  258 (480)
                      +
T Consensus        83 T   83 (459)
T 3upu_A           83 T   83 (459)
T ss_dssp             S
T ss_pred             c
Confidence            3

>3a4m_A L-seryl-tRNA(SEC) kinase; P-loop motif, walker A motif, ATP binding motif, ATP- binding, nucleotide-binding, transferase; HET: ADP; 1.79A {Methanocaldococcus jannaschii} PDB: 3a4l_A* 3a4n_A 3am1_A* 3add_A* 3adc_A* 3adb_A*

Probab=96.70  E-value=0.0011  Score=64.04  Aligned_cols=33  Identities=30%  Similarity=0.417  Sum_probs=28.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~  257 (480)
                      .-|+|.|+||+||||+++.++..   .|..++.++.
T Consensus         5 ~lIvl~G~pGSGKSTla~~La~~L~~~g~~~i~~~~   40 (260)
T 3a4m_A            5 MLIILTGLPGVGKSTFSKNLAKILSKNNIDVIVLGS   40 (260)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEECT
T ss_pred             EEEEEEcCCCCCHHHHHHHHHHHHHhCCCEEEEECc
Confidence            35889999999999999999997   7888875543

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=96.66  E-value=0.0044  Score=64.53  Aligned_cols=61  Identities=21%  Similarity=0.204  Sum_probs=38.3

Q ss_pred             hHHHHHHHHHHHHHHhhhh-HHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          196 TDLKNRVKSDLESFLKAKH-YYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~-~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      +.+.+.+.+.+...+.... ..... ...++-+++.||+|+||||++..+|..+   |..+..+++
T Consensus        69 ~~v~~~v~~eL~~~L~~~~~~~~~~-~~~~~vI~lvG~~GsGKTTt~~kLA~~l~~~G~kVllv~~  133 (433)
T 3kl4_A           69 EWFISIVYDELSKLFGGDKEPNVNP-TKLPFIIMLVGVQGSGKTTTAGKLAYFYKKRGYKVGLVAA  133 (433)
T ss_dssp             HHHHHHHHHHHHHHHCSSSCCCCSC-CSSSEEEEECCCTTSCHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHHhcCccccccccc-cCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEec
Confidence            3455666666666554321 11111 1235678899999999999999999755   566655554

>1uf9_A TT1252 protein; P-loop, nucleotide binding domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; HET: ATP; 2.80A {Thermus thermophilus} SCOP: c.37.1.1

Probab=96.65  E-value=0.001  Score=60.69  Aligned_cols=32  Identities=38%  Similarity=0.525  Sum_probs=27.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.-|.|.|++|||||++++.+|.. |..+++.+
T Consensus         8 ~~~I~i~G~~GsGKST~~~~La~~-g~~~id~d   39 (203)
T 1uf9_A            8 PIIIGITGNIGSGKSTVAALLRSW-GYPVLDLD   39 (203)
T ss_dssp             CEEEEEEECTTSCHHHHHHHHHHT-TCCEEEHH
T ss_pred             ceEEEEECCCCCCHHHHHHHHHHC-CCEEEccc
Confidence            346889999999999999999998 87777654

>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=96.64  E-value=0.0011  Score=60.80  Aligned_cols=31  Identities=29%  Similarity=0.350  Sum_probs=28.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -+.|.||+|||||++++.+|..+|.+++..+
T Consensus         4 ~i~i~G~~GsGKst~~~~la~~lg~~~~d~d   34 (208)
T 3ake_A            4 IVTIDGPSASGKSSVARRVAAALGVPYLSSG   34 (208)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCceeccc
Confidence            5889999999999999999999998887754

>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=96.63  E-value=0.0049  Score=64.36  Aligned_cols=62  Identities=23%  Similarity=0.298  Sum_probs=40.4

Q ss_pred             hHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          196 TDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      +.+++.+.+.+...+..+...... ...+.-+++.||||+||||++..+|..+   |..+..+++.
T Consensus        73 ~~v~~~l~~eL~~~L~~~~~~~~~-~~~p~vIlivG~~G~GKTTt~~kLA~~l~~~G~kVllv~~D  137 (443)
T 3dm5_A           73 EHIIKIVYEELTKFLGTEAKPIEI-KEKPTILLMVGIQGSGKTTTVAKLARYFQKRGYKVGVVCSD  137 (443)
T ss_dssp             HHHHHHHHHHHHHHTTSSCCCCCC-CSSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHHHhcCccccccc-CCCCeEEEEECcCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            445666666666665432111111 1135678999999999999999999755   6666666654

>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=96.63  E-value=0.0082  Score=59.60  Aligned_cols=59  Identities=15%  Similarity=0.120  Sum_probs=38.8

Q ss_pred             HHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          198 LKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       198 ~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      +++.+.+.+...+.....+ .+....+.-+++.||+|+||||++..+|..+   +..+..+++
T Consensus        79 ~~~~~~~~l~~~l~~~~~~-~~~~~~~~vi~ivG~~GsGKTTl~~~LA~~l~~~g~kV~lv~~  140 (306)
T 1vma_A           79 ALESLKEIILEILNFDTKL-NVPPEPPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAA  140 (306)
T ss_dssp             HHHHHHHHHHHHTCSCCCC-CCCSSSCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHhCCCCCC-cccCCCCeEEEEEcCCCChHHHHHHHHHHHHHhcCCEEEEEcc
Confidence            5666777666666432210 1112345568899999999999999999865   555655554

>3nwj_A ATSK2; P loop, shikimate, nucleoside monophosphate kinase, shikimat ATP binding, chloroplast, transferase; 2.35A {Arabidopsis thaliana}

Probab=96.62  E-value=0.00084  Score=64.85  Aligned_cols=32  Identities=38%  Similarity=0.646  Sum_probs=29.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ..+.|.||||+||||+++.+|..+|.++++.+
T Consensus        49 ~~i~l~G~~GsGKSTl~~~La~~lg~~~~d~d   80 (250)
T 3nwj_A           49 RSMYLVGMMGSGKTTVGKIMARSLGYTFFDCD   80 (250)
T ss_dssp             CCEEEECSTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhcCCcEEeCc
Confidence            46999999999999999999999999888764

>2plr_A DTMP kinase, probable thymidylate kinase; TMP-binding, ATP-binding, structural GEN NPPSFA; HET: 1PE PGE EPE PG4; 1.60A {Sulfolobus tokodaii}

Probab=96.62  E-value=0.0013  Score=60.32  Aligned_cols=32  Identities=31%  Similarity=0.450  Sum_probs=26.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~  256 (480)
                      .-|+|.|||||||||+++.+|..++.  +++...
T Consensus         5 ~~I~i~G~~GsGKsT~~~~L~~~l~~~g~~~~~~   38 (213)
T 2plr_A            5 VLIAFEGIDGSGKSSQATLLKDWIELKRDVYLTE   38 (213)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHHhhcCCEEEec
Confidence            35889999999999999999998876  354443

>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=96.61  E-value=0.0031  Score=58.55  Aligned_cols=29  Identities=24%  Similarity=0.399  Sum_probs=24.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      |++...-+.|.||+|+|||+|++.++..+
T Consensus        21 gi~~G~~~~l~G~nGsGKSTll~~l~g~~   49 (231)
T 4a74_A           21 GIETQAITEVFGEFGSGKTQLAHTLAVMV   49 (231)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            45555568899999999999999999843

>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=96.60  E-value=0.0013  Score=62.93  Aligned_cols=31  Identities=32%  Similarity=0.433  Sum_probs=27.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-+.|.||||||||++++.+|..+|+.++..
T Consensus        10 ~~i~i~G~~GsGKsTla~~la~~lg~~~~d~   40 (233)
T 3r20_A           10 LVVAVDGPAGTGKSSVSRGLARALGARYLDT   40 (233)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCcccC
Confidence            4688999999999999999999999877654

>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=96.59  E-value=0.0053  Score=58.32  Aligned_cols=32  Identities=25%  Similarity=0.173  Sum_probs=27.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      .++++||+|+|||.++.+++..++..++.+-.
T Consensus       110 ~~ll~~~tG~GKT~~a~~~~~~~~~~~liv~P  141 (237)
T 2fz4_A          110 RGCIVLPTGSGKTHVAMAAINELSTPTLIVVP  141 (237)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEES
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHcCCCEEEEeC
Confidence            48999999999999999999888776666643

>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=96.58  E-value=0.00091  Score=61.95  Aligned_cols=31  Identities=29%  Similarity=0.339  Sum_probs=27.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      -+.|.|++||||||+++.++..+|+++++.|
T Consensus        14 iIgltG~~GSGKSTva~~L~~~lg~~vid~D   44 (192)
T 2grj_A           14 VIGVTGKIGTGKSTVCEILKNKYGAHVVNVD   44 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHCCEEEEHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCEEEECc
Confidence            5779999999999999999999898877754

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.53  E-value=0.01  Score=55.06  Aligned_cols=105  Identities=16%  Similarity=0.201  Sum_probs=60.3

Q ss_pred             eEEEEccCCCcHH-HHHHHHHHcC--CCcEEEEeCC---C----cCCh----------HHHHHHHHhhcCCcEEEEeccc
Q 011664          226 SYLLYGPSGTGKS-SFAAAMASFM--SYDVYDVDLS---R----VADD----------ADLKSLLLQTTSKSVILIEDLD  285 (480)
Q Consensus       226 giLL~GPpGTGKT-~La~aiA~~l--~~~~~~i~~s---~----~~~~----------~~l~~l~~~~~~~sII~IDEiD  285 (480)
                      =+++|||.|+||| .|++++.+..  +..++.+...   .    +.+.          .....++.......+|+|||+.
T Consensus        22 l~fiyG~MgsGKTt~Ll~~i~n~~~~~~kvl~~kp~~D~R~~~~i~S~~g~~~~A~~~~~~~d~~~~~~~~DvIlIDEaQ  101 (195)
T 1w4r_A           22 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYSSSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEGQ  101 (195)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEETTCCCGGGSCCHHHHHHSEEEEESSGGGGHHHHHTCSEEEESSGG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEccccCccchhhhhhccCCcccceecCCHHHHHHhccCCCEEEEEchh
Confidence            4789999999999 9999998754  6677777533   1    1110          0011122233456899999999


Q ss_pred             ccccCcccccchhhhhhhcccccccccCCceEEEEe--cC---CCccCcccccCCCceeEEEEcC
Q 011664          286 RFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFT--MN---SKDHVDQALLRPGRIDVHIHFP  345 (480)
Q Consensus       286 ~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~t--TN---~~~~LD~aLlrpGRfd~~I~~~  345 (480)
                      -+ .+      +.++++.+..      .+..||++.  ++   .|..--+.|+-  .-|.+.++.
T Consensus       102 Ff-k~------~ve~~~~L~~------~gk~VI~~GL~~DF~~~~F~~~~~Ll~--~Ad~v~kl~  151 (195)
T 1w4r_A          102 FF-PD------IVEFCEAMAN------AGKTVIVAALDGTFQRKPFGAILNLVP--LAESVVKLT  151 (195)
T ss_dssp             GC-TT------HHHHHHHHHH------TTCEEEEEEESBCTTSSBCTTGGGGGG--GCSEEEECC
T ss_pred             hh-HH------HHHHHHHHHH------CCCeEEEEecccccccccchhHHHHHH--hcCeEEEee
Confidence            76 21      3455555531      233444442  32   34444456664  556555554

>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=96.52  E-value=0.0075  Score=56.06  Aligned_cols=109  Identities=13%  Similarity=0.171  Sum_probs=65.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc--C-Ch-----------------------------HHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV--A-DD-----------------------------ADLKSL  269 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~--~-~~-----------------------------~~l~~l  269 (480)
                      ..+++|+++|.|||++|-++|-.+   |..+..+.+.+-  . ++                             ......
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~G~rV~~vQF~Kg~~~~gE~~~l~~L~v~~~~~g~gf~~~~~~~~~~~~~a~~~  108 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGHGKNVGVVQFIKGTWPNGERNLLEPHGVEFQVMATGFTWETQNREADTAACMAV  108 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHTTCCEEEEESSCCSSCCHHHHHHGGGTCEEEECCTTCCCCGGGHHHHHHHHHHH
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEEeeCCCCCccHHHHHHhCCcEEEEcccccccCCCCcHHHHHHHHHH
Confidence            358899999999999999998643   778887754331  0 00                             011112


Q ss_pred             HH----hh--cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEE
Q 011664          270 LL----QT--TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIH  343 (480)
Q Consensus       270 ~~----~~--~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~  343 (480)
                      +.    ..  ....+|++||+-....  -+-....+++..+..-     .+..-||+|+|.+   +++|+.  .-|.+-+
T Consensus       109 l~~a~~~l~~~~yDlvILDEi~~al~--~g~l~~~ev~~~l~~R-----p~~~~vIlTGr~a---p~~l~e--~AD~VTe  176 (196)
T 1g5t_A          109 WQHGKRMLADPLLDMVVLDELTYMVA--YDYLPLEEVISALNAR-----PGHQTVIITGRGC---HRDILD--LADTVSE  176 (196)
T ss_dssp             HHHHHHHTTCTTCSEEEEETHHHHHH--TTSSCHHHHHHHHHTS-----CTTCEEEEECSSC---CHHHHH--HCSEEEE
T ss_pred             HHHHHHHHhcCCCCEEEEeCCCcccc--CCCCCHHHHHHHHHhC-----cCCCEEEEECCCC---cHHHHH--hCcceee
Confidence            21    12  3568999999965321  1123345566666422     4556788888854   455555  5555555


Q ss_pred             cC
Q 011664          344 FP  345 (480)
Q Consensus       344 ~~  345 (480)
                      +.
T Consensus       177 m~  178 (196)
T 1g5t_A          177 LR  178 (196)
T ss_dssp             CC
T ss_pred             ec
Confidence            43

>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=96.51  E-value=0.0072  Score=64.92  Aligned_cols=74  Identities=7%  Similarity=0.146  Sum_probs=50.6

Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc--cCcccccCCCceeEEEEcCCCCHHHHHH
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD--HVDQALLRPGRIDVHIHFPLCDFSSFKT  354 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~--~LD~aLlrpGRfd~~I~~~~p~~~~r~~  354 (480)
                      -+|+|||+..+.....  ....+.+..+-....   .-++-+|++|.+|.  .|+..++.  -|..+|.+...+..+-..
T Consensus       345 ivvVIDE~~~L~~~~~--~~~~~~L~~Iar~GR---a~GIhLIlaTQRPs~d~I~~~Ira--n~~~RI~lrv~s~~Dsr~  417 (574)
T 2iut_A          345 IVVVVDEFADMMMIVG--KKVEELIARIAQKAR---AAGIHLILATQRPSVDVITGLIKA--NIPTRIAFQVSSKIDSRT  417 (574)
T ss_dssp             EEEEESCCTTHHHHTC--HHHHHHHHHHHHHCT---TTTEEEEEEESCCCTTTSCHHHHH--TCCEEEEECCSCHHHHHH
T ss_pred             EEEEEeCHHHHhhhhh--HHHHHHHHHHHHHHh---hCCeEEEEEecCcccccccHHHHh--hhccEEEEEcCCHHHHHH
Confidence            5899999998764221  122233333322222   45778888999887  78888777  788899999999888777


Q ss_pred             HHH
Q 011664          355 LAS  357 (480)
Q Consensus       355 il~  357 (480)
                      ++.
T Consensus       418 ILd  420 (574)
T 2iut_A          418 ILD  420 (574)
T ss_dssp             HHS
T ss_pred             hcC
Confidence            763

>2wwf_A Thymidilate kinase, putative; transferase, malaria; HET: TMP ADP; 1.89A {Plasmodium falciparum} PDB: 2wwg_A* 2wwh_A* 2wwi_A*

Probab=96.51  E-value=0.00065  Score=62.59  Aligned_cols=28  Identities=14%  Similarity=0.321  Sum_probs=23.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      +.-|.|.|+|||||||+++.++..++..
T Consensus        10 ~~~I~l~G~~GsGKST~~~~L~~~l~~~   37 (212)
T 2wwf_A           10 GKFIVFEGLDRSGKSTQSKLLVEYLKNN   37 (212)
T ss_dssp             SCEEEEEESTTSSHHHHHHHHHHHHHHT
T ss_pred             CCEEEEEcCCCCCHHHHHHHHHHHHHHc
Confidence            3468899999999999999999876543

>2ga8_A Hypothetical 39.9 kDa protein; YFR007W, YFH7, unknown function; HET: CME; 1.77A {Saccharomyces cerevisiae} PDB: 2gaa_A*

Probab=96.50  E-value=0.00091  Score=67.85  Aligned_cols=30  Identities=23%  Similarity=0.418  Sum_probs=26.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ..++|.||||+|||++++++|+.++.+|+.
T Consensus        25 ~~i~l~G~~G~GKTTl~~~la~~l~~~f~~   54 (359)
T 2ga8_A           25 VCVILVGSPGSGKSTIAEELCQIINEKYHT   54 (359)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHHHhCCCeee
Confidence            369999999999999999999999887744

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=96.50  E-value=0.0032  Score=65.67  Aligned_cols=38  Identities=18%  Similarity=0.071  Sum_probs=29.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~  257 (480)
                      |+++..-+++.|+||+|||+++..+|...    |.++..+++
T Consensus       196 Gl~~G~l~ii~G~pg~GKT~lal~ia~~~a~~~g~~vl~~sl  237 (444)
T 2q6t_A          196 TLGPGSLNIIAARPAMGKTAFALTIAQNAALKEGVGVGIYSL  237 (444)
T ss_dssp             CCCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCCCEEEEES
T ss_pred             CcCCCcEEEEEeCCCCCHHHHHHHHHHHHHHhCCCeEEEEEC
Confidence            56666678999999999999999888642    566777665

>3a8t_A Adenylate isopentenyltransferase; rossmann fold protein; HET: ATP; 2.37A {Humulus lupulus}

Probab=96.48  E-value=0.0015  Score=65.93  Aligned_cols=35  Identities=29%  Similarity=0.525  Sum_probs=30.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR  259 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~  259 (480)
                      +-++|.||+|||||+|+..+|..++..|++.|.-.
T Consensus        41 ~lIvI~GPTgsGKTtLa~~LA~~l~~eiIs~Ds~q   75 (339)
T 3a8t_A           41 KLLVLMGATGTGKSRLSIDLAAHFPLEVINSDKMQ   75 (339)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTTSCEEEEECCSST
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHCCCcEEcccccc
Confidence            46889999999999999999999998888877543

>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=96.43  E-value=0.0048  Score=61.85  Aligned_cols=62  Identities=13%  Similarity=0.365  Sum_probs=41.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC--cEEEEeCCC-c-----------C--ChHHHHHHHHhh--cCCcEEEEecccc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY--DVYDVDLSR-V-----------A--DDADLKSLLLQT--TSKSVILIEDLDR  286 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~--~~~~i~~s~-~-----------~--~~~~l~~l~~~~--~~~sII~IDEiD~  286 (480)
                      ..+++.||+|+|||||++++++....  ..+.++-.. +           .  +....+..++.+  ..|.+|++||.-.
T Consensus       172 ~~v~i~G~~GsGKTTll~~l~g~~~~~~g~i~i~~~~e~~~~~~~~~i~~~~ggg~~~r~~la~aL~~~p~ilildE~~~  251 (330)
T 2pt7_A          172 KNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELRS  251 (330)
T ss_dssp             CCEEEEESTTSCHHHHHHHGGGGSCTTSCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEECCCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCcCCCcEEEECCeeccccccchhEEEEEeCCChhHHHHHHHHhhhCCCEEEEcCCCh
Confidence            46999999999999999999998743  344443211 0           0  122234444433  5899999999874

>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A {Staphylococcus aureus}

Probab=96.43  E-value=0.0016  Score=60.53  Aligned_cols=32  Identities=34%  Similarity=0.376  Sum_probs=28.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ..+.|.|+||||||++++.+|..+|.++++.+
T Consensus         4 ~~i~i~G~~gsGkst~~~~l~~~~g~~~~~~d   35 (219)
T 2h92_A            4 INIALDGPAAAGKSTIAKRVASELSMIYVDTG   35 (219)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHTTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCceecCC
Confidence            35889999999999999999999998877653

>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=96.43  E-value=0.0017  Score=60.48  Aligned_cols=31  Identities=39%  Similarity=0.506  Sum_probs=26.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-+.|.|++||||||+++.++. +|.++++.|
T Consensus         5 ~~I~i~G~~GSGKST~~~~L~~-lg~~~id~D   35 (218)
T 1vht_A            5 YIVALTGGIGSGKSTVANAFAD-LGINVIDAD   35 (218)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHH-TTCEEEEHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHH-cCCEEEEcc
Confidence            4588999999999999999998 888777654

>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=96.42  E-value=0.0016  Score=60.10  Aligned_cols=31  Identities=16%  Similarity=0.254  Sum_probs=25.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-CCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-SYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~i  255 (480)
                      .-+.|.||||+||||+++.+++.+ +..++..
T Consensus        22 ~~i~i~G~~GsGKSTl~~~L~~~~~~~~~i~~   53 (207)
T 2qt1_A           22 FIIGISGVTNSGKTTLAKNLQKHLPNCSVISQ   53 (207)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHTTSTTEEEEEG
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcCCcEEEeC
Confidence            357799999999999999999987 5544443

>2ius_A DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA- binding, cell division, transmembrane, inner membrane; HET: DNA; 2.7A {Escherichia coli} PDB: 2j5p_A*

Probab=96.41  E-value=0.0071  Score=64.26  Aligned_cols=73  Identities=10%  Similarity=0.194  Sum_probs=48.5

Q ss_pred             EEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc--cCcccccCCCceeEEEEcCCCCHHHHHHH
Q 011664          278 VILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD--HVDQALLRPGRIDVHIHFPLCDFSSFKTL  355 (480)
Q Consensus       278 II~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~--~LD~aLlrpGRfd~~I~~~~p~~~~r~~i  355 (480)
                      +|+|||...+....  .....+++..+-....   .-++-+|++|.+|.  .++..++.  -+..+|.|...+..+.+.+
T Consensus       300 vlvIDE~~~ll~~~--~~~~~~~l~~Lar~gR---a~GI~LIlaTQrp~~dvl~~~i~~--n~~~RI~lrv~s~~dsr~i  372 (512)
T 2ius_A          300 VVLVDEFADLMMTV--GKKVEELIARLAQKAR---AAGIHLVLATQRPSVDVITGLIKA--NIPTRIAFTVSSKIDSRTI  372 (512)
T ss_dssp             EEEEETHHHHHHHH--HHHHHHHHHHHHHHCG---GGTEEEEEEESCCCTTTSCHHHHH--HCCEEEEECCSSHHHHHHH
T ss_pred             EEEEeCHHHHHhhh--hHHHHHHHHHHHHHhh---hCCcEEEEEecCCccccccHHHHh--hcCCeEEEEcCCHHHHHHh
Confidence            89999998775411  1122333333322211   23567788888886  57777777  7888999999999888877


Q ss_pred             HH
Q 011664          356 AS  357 (480)
Q Consensus       356 l~  357 (480)
                      +.
T Consensus       373 lg  374 (512)
T 2ius_A          373 LD  374 (512)
T ss_dssp             HS
T ss_pred             cC
Confidence            64

>4e22_A Cytidylate kinase; P-loop, CMP/ATP binding, transferase; 2.32A {Yersinia pseudotuberculosis}

Probab=96.39  E-value=0.0026  Score=61.11  Aligned_cols=30  Identities=30%  Similarity=0.573  Sum_probs=26.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      .-+.|.||+||||||+++.+|..+|..+++
T Consensus        28 ~~I~I~G~~GsGKSTl~k~La~~Lg~~~~d   57 (252)
T 4e22_A           28 PVITVDGPSGAGKGTLCKALAESLNWRLLD   57 (252)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHTTCEEEE
T ss_pred             cEEEEECCCCCCHHHHHHHHHHhcCCCcCC
Confidence            357899999999999999999999987664

>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=96.39  E-value=0.0021  Score=58.36  Aligned_cols=25  Identities=32%  Similarity=0.636  Sum_probs=21.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -+.|.||||+||||+++.++...+.
T Consensus         4 ii~l~G~~GaGKSTl~~~L~~~~~g   28 (189)
T 2bdt_A            4 LYIITGPAGVGKSTTCKRLAAQLDN   28 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHSSS
T ss_pred             EEEEECCCCCcHHHHHHHHhcccCC
Confidence            4789999999999999999986654

>2qor_A Guanylate kinase; phosphotransferase, purine metabolism, structural genomics, structural genomics of pathogenic protozoa consortium; HET: 5GP POP; 1.80A {Plasmodium vivax}

Probab=96.39  E-value=0.0019  Score=59.58  Aligned_cols=28  Identities=25%  Similarity=0.415  Sum_probs=24.4

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ..++-++|.||||+||||+++.++..++
T Consensus        10 ~~~~~i~l~G~sGsGKsTl~~~L~~~~~   37 (204)
T 2qor_A           10 ARIPPLVVCGPSGVGKGTLIKKVLSEFP   37 (204)
T ss_dssp             CCCCCEEEECCTTSCHHHHHHHHHHHCT
T ss_pred             ccCCEEEEECCCCCCHHHHHHHHHHhCc
Confidence            3455789999999999999999999875

>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=96.38  E-value=0.0009  Score=61.68  Aligned_cols=26  Identities=19%  Similarity=0.235  Sum_probs=22.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +.-|.|.|+|||||||+++.++..++
T Consensus         9 ~~~I~l~G~~GsGKsT~~~~L~~~l~   34 (215)
T 1nn5_A            9 GALIVLEGVDRAGKSTQSRKLVEALC   34 (215)
T ss_dssp             CCEEEEEESTTSSHHHHHHHHHHHHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHH
Confidence            34588999999999999999998764

>1ltq_A Polynucleotide kinase; phosphatase, alpha/beta, P-loop, transferase; HET: ADP; 2.33A {Enterobacteria phage T4} SCOP: c.108.1.9 c.37.1.1 PDB: 1rc8_A* 1rpz_A* 1rrc_A* 2ia5_A

Probab=96.37  E-value=0.0013  Score=64.37  Aligned_cols=30  Identities=23%  Similarity=0.351  Sum_probs=24.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC-CCcEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM-SYDVYD  254 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l-~~~~~~  254 (480)
                      .-|+|.||||+||||+++.++..+ +..++.
T Consensus         3 ~~I~l~G~~GsGKST~a~~L~~~~~~~~~i~   33 (301)
T 1ltq_A            3 KIILTIGCPGSGKSTWAREFIAKNPGFYNIN   33 (301)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHSTTEEEEC
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhCCCcEEec
Confidence            468999999999999999999864 655443

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=96.37  E-value=0.0026  Score=59.69  Aligned_cols=40  Identities=30%  Similarity=0.277  Sum_probs=30.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLSR  259 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s~  259 (480)
                      |++...-++|+||||+|||+++..+|..   .+..+++++...
T Consensus        19 Gl~~G~~~~i~G~~GsGKTtl~~~~~~~~~~~~~~v~~~~~e~   61 (247)
T 2dr3_A           19 GIPERNVVLLSGGPGTGKTIFSQQFLWNGLKMGEPGIYVALEE   61 (247)
T ss_dssp             SEETTCEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEESSS
T ss_pred             CCCCCcEEEEECCCCCCHHHHHHHHHHHHHhcCCeEEEEEccC
Confidence            5556667899999999999998888753   366777777543

>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=96.35  E-value=0.0024  Score=63.60  Aligned_cols=35  Identities=23%  Similarity=0.543  Sum_probs=30.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      .++-+++.||+|+|||+|+..+|..++..++..|.
T Consensus         9 ~~~~i~i~GptgsGKt~la~~La~~~~~~iis~Ds   43 (316)
T 3foz_A            9 LPKAIFLMGPTASGKTALAIELRKILPVELISVDS   43 (316)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHSCEEEEECCT
T ss_pred             CCcEEEEECCCccCHHHHHHHHHHhCCCcEEeccc
Confidence            34568899999999999999999999988877764

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=96.34  E-value=0.0061  Score=66.57  Aligned_cols=59  Identities=27%  Similarity=0.327  Sum_probs=37.4

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      +..|-+-...+++++.+...+.    .           +.-.|+.||||||||+++..+...+   +..+..+..+.
T Consensus       182 ~~~~~~~~LN~~Q~~AV~~al~----~-----------~~~~lI~GPPGTGKT~ti~~~I~~l~~~~~~ILv~a~TN  243 (646)
T 4b3f_X          182 PLTFFNTCLDTSQKEAVLFALS----Q-----------KELAIIHGPPGTGKTTTVVEIILQAVKQGLKVLCCAPSN  243 (646)
T ss_dssp             CCCCSSTTCCHHHHHHHHHHHH----C-----------SSEEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEESSH
T ss_pred             cccccCCCCCHHHHHHHHHHhc----C-----------CCceEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEcCch
Confidence            3444444567888888775442    1           1246899999999997655544332   66677666653

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=96.32  E-value=0.0023  Score=57.96  Aligned_cols=25  Identities=16%  Similarity=0.433  Sum_probs=22.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +-+.|.||+|+|||||++.++....
T Consensus         6 ~~i~i~GpsGsGKSTL~~~L~~~~~   30 (180)
T 1kgd_A            6 KTLVLLGAHGVGRRHIKNTLITKHP   30 (180)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CEEEEECCCCCCHHHHHHHHHhhCC
Confidence            4588999999999999999998764

>2j41_A Guanylate kinase; GMP, GMK, transferase, ATP-binding, nucleotide- binding; HET: 5GP; 1.9A {Staphylococcus aureus}

Probab=96.29  E-value=0.0025  Score=58.27  Aligned_cols=25  Identities=28%  Similarity=0.328  Sum_probs=22.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||+|+||||+++.++..+
T Consensus         6 g~~i~l~G~~GsGKSTl~~~L~~~~   30 (207)
T 2j41_A            6 GLLIVLSGPSGVGKGTVRKRIFEDP   30 (207)
T ss_dssp             CCEEEEECSTTSCHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHhh
Confidence            3468899999999999999999987

>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase, transferase; NMR {Streptococcus pneumoniae} SCOP: c.37.1.1

Probab=96.28  E-value=0.0029  Score=59.83  Aligned_cols=31  Identities=26%  Similarity=0.421  Sum_probs=27.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ..+.|.|++|||||++++.+|..+|.++++.
T Consensus        17 ~~i~i~G~~gsGKst~~~~l~~~lg~~~~d~   47 (236)
T 1q3t_A           17 IQIAIDGPASSGKSTVAKIIAKDFGFTYLDT   47 (236)
T ss_dssp             CEEEEECSSCSSHHHHHHHHHHHHCCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHcCCceecC
Confidence            3578999999999999999999999877664

>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=96.26  E-value=0.0023  Score=61.18  Aligned_cols=38  Identities=18%  Similarity=0.178  Sum_probs=30.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc--------EEEEeCCCcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD--------VYDVDLSRVA  261 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~--------~~~i~~s~~~  261 (480)
                      +.-|.|.||||||||++++.+|..++.+        +..+++..+.
T Consensus        22 ~~iI~I~G~~GSGKST~a~~L~~~lg~~~~d~~~~~~~~i~~D~~~   67 (252)
T 1uj2_A           22 PFLIGVSGGTASGKSSVCAKIVQLLGQNEVDYRQKQVVILSQDSFY   67 (252)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHTTGGGSCGGGCSEEEEEGGGGB
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHhhhhcccccCCceEEEecCccc
Confidence            3468899999999999999999999876        3356655543

>2yvu_A Probable adenylyl-sulfate kinase; transferase, structural genomics, NPPSFA, national P protein structural and functional analyses; 2.10A {Aeropyrum pernix}

Probab=96.24  E-value=0.0039  Score=56.41  Aligned_cols=33  Identities=30%  Similarity=0.481  Sum_probs=26.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      +.-++|.|+||+||||+++.+|..+   +.++..++
T Consensus        13 ~~~i~l~G~~GsGKsT~~~~L~~~l~~~~~~~~~~~   48 (186)
T 2yvu_A           13 GIVVWLTGLPGSGKTTIATRLADLLQKEGYRVEVLD   48 (186)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CcEEEEEcCCCCCHHHHHHHHHHHHHhcCCeEEEee
Confidence            3468899999999999999999876   34455554

>1rz3_A Hypothetical protein rbstp0775; MCSG, structural genomics, PSI, protein structure initiative; 1.90A {Geobacillus stearothermophilus} SCOP: c.37.1.6

Probab=96.16  E-value=0.0083  Score=55.21  Aligned_cols=35  Identities=17%  Similarity=0.263  Sum_probs=27.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      +.-+.|.||+|+||||+++.++..+   +.+++.++..
T Consensus        22 ~~~i~i~G~~GsGKstl~~~l~~~~~~~~~~v~~~~~d   59 (201)
T 1rz3_A           22 RLVLGIDGLSRSGKTTLANQLSQTLREQGISVCVFHMD   59 (201)
T ss_dssp             SEEEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCeEEEeccC
Confidence            3457899999999999999999865   6667666543

>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=96.16  E-value=0.0028  Score=59.24  Aligned_cols=32  Identities=28%  Similarity=0.265  Sum_probs=26.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .++++|.||+|+|||+||.+++...+ .++..|
T Consensus        34 g~~ilI~GpsGsGKStLA~~La~~g~-~iIsdD   65 (205)
T 2qmh_A           34 GLGVLITGDSGVGKSETALELVQRGH-RLIADD   65 (205)
T ss_dssp             TEEEEEECCCTTTTHHHHHHHHTTTC-EEEESS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhCC-eEEecc
Confidence            46899999999999999999998876 555543

>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=96.15  E-value=0.0018  Score=66.98  Aligned_cols=31  Identities=23%  Similarity=0.265  Sum_probs=26.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      +.-|+|.||||+||||+++.++..+++.++.
T Consensus       258 ~~lIil~G~pGSGKSTla~~L~~~~~~~~i~  288 (416)
T 3zvl_A          258 PEVVVAVGFPGAGKSTFIQEHLVSAGYVHVN  288 (416)
T ss_dssp             CCEEEEESCTTSSHHHHHHHHTGGGTCEECC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhcCcEEEc
Confidence            4568899999999999999999998765544

>3d3q_A TRNA delta(2)-isopentenylpyrophosphate transferase; alpha-beta protein, structural genomics, PSI-2; 2.70A {Staphylococcus epidermidis atcc 12228}

Probab=96.15  E-value=0.0026  Score=64.22  Aligned_cols=32  Identities=19%  Similarity=0.369  Sum_probs=27.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-+.+.||+|+|||+++..+|..++..++..|
T Consensus         8 ~lI~I~GptgSGKTtla~~La~~l~~~iis~D   39 (340)
T 3d3q_A            8 FLIVIVGPTASGKTELSIEVAKKFNGEIISGD   39 (340)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHTTEEEEECC
T ss_pred             ceEEEECCCcCcHHHHHHHHHHHcCCceeccc
Confidence            46889999999999999999999987666655

>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=96.14  E-value=0.0032  Score=58.41  Aligned_cols=27  Identities=30%  Similarity=0.312  Sum_probs=23.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      +.-+.|.||+|+||||+++.++..+..
T Consensus         8 g~~i~l~GpsGsGKsTl~~~L~~~~~~   34 (208)
T 3tau_A            8 GLLIVLSGPSGVGKGTVREAVFKDPET   34 (208)
T ss_dssp             CCEEEEECCTTSCHHHHHHHHHHSTTC
T ss_pred             CcEEEEECcCCCCHHHHHHHHHhhCCC
Confidence            345889999999999999999998753

>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=96.10  E-value=0.0026  Score=62.24  Aligned_cols=31  Identities=35%  Similarity=0.360  Sum_probs=26.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-|.|.|+|||||||+++.++ .+|+++++.+
T Consensus        76 ~iI~I~G~~GSGKSTva~~La-~lg~~~id~D  106 (281)
T 2f6r_A           76 YVLGLTGISGSGKSSVAQRLK-NLGAYIIDSD  106 (281)
T ss_dssp             EEEEEEECTTSCHHHHHHHHH-HHTCEEEEHH
T ss_pred             EEEEEECCCCCCHHHHHHHHH-HCCCcEEehh
Confidence            458899999999999999999 5787766543

>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=96.04  E-value=0.0035  Score=62.53  Aligned_cols=32  Identities=22%  Similarity=0.366  Sum_probs=27.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +-+++.||+|+|||+|+..+|..++..+++.|
T Consensus         4 ~~i~i~GptgsGKt~la~~La~~~~~~iis~D   35 (322)
T 3exa_A            4 KLVAIVGPTAVGKTKTSVMLAKRLNGEVISGD   35 (322)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHTTTEEEEECC
T ss_pred             cEEEEECCCcCCHHHHHHHHHHhCccceeecC
Confidence            35789999999999999999999987776655

>1m7g_A Adenylylsulfate kinase; APS kinase, transferase, sulfate Met nucleotide 2 kinase; HET: AV2 ADX ADP; 1.43A {Penicillium chrysogenum} SCOP: c.37.1.4 PDB: 1d6j_A* 1m7h_A* 3cr7_A*

Probab=96.04  E-value=0.0039  Score=57.81  Aligned_cols=34  Identities=26%  Similarity=0.384  Sum_probs=27.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC----CcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS----YDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~----~~~~~i~  256 (480)
                      .+.-++|.|+||+||||+++.++..++    .+++.++
T Consensus        24 ~~~~i~~~G~~GsGKsT~~~~l~~~l~~~~g~~~~~~~   61 (211)
T 1m7g_A           24 RGLTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLD   61 (211)
T ss_dssp             SCEEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHhccccCCcEEEEC
Confidence            345688999999999999999998764    4566665

>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=96.02  E-value=0.0079  Score=62.64  Aligned_cols=64  Identities=20%  Similarity=0.293  Sum_probs=43.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC------------------------C-h--HHHHHHHHhh
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA------------------------D-D--ADLKSLLLQT  273 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~------------------------~-~--~~l~~l~~~~  273 (480)
                      ++.+++.||||+||||++..+|..+   |..+..+++....                        + +  .-+...+...
T Consensus        99 ~~vI~ivG~~GvGKTTla~~La~~l~~~G~kVllv~~D~~r~~a~~qL~~~~~~~gv~v~~~~~~~~dp~~i~~~~l~~~  178 (432)
T 2v3c_C           99 QNVILLVGIQGSGKTTTAAKLARYIQKRGLKPALIAADTYRPAAYEQLKQLAEKIHVPIYGDETRTKSPVDIVKEGMEKF  178 (432)
T ss_dssp             CCCEEEECCSSSSTTHHHHHHHHHHHHHHCCEEEECCSCCCTTGGGSSHHHHHHSSCCEECCSSSCCSSSTTHHHHHHTT
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEeccccCchHHHHHHHhhhccCcceEecCCCCCCHHHHHHHHHHHh
Confidence            4579999999999999999999866   4566666543210                        0 0  1123445445


Q ss_pred             cCCcEEEEeccccc
Q 011664          274 TSKSVILIEDLDRF  287 (480)
Q Consensus       274 ~~~sII~IDEiD~l  287 (480)
                      ....+++||....+
T Consensus       179 ~~~D~vIIDT~G~~  192 (432)
T 2v3c_C          179 KKADVLIIDTAGRH  192 (432)
T ss_dssp             SSCSEEEEECCCSC
T ss_pred             hCCCEEEEcCCCCc
Confidence            66789999988754

>3c8u_A Fructokinase; YP_612366.1, putative fructose transport system kinase, STRU genomics, joint center for structural genomics, JCSG; 1.95A {Silicibacter SP}

Probab=96.02  E-value=0.0049  Score=57.05  Aligned_cols=34  Identities=26%  Similarity=0.415  Sum_probs=26.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~~  257 (480)
                      ..-+.|.||+|+|||||++.++..+.   ...-.+..
T Consensus        22 g~~v~I~G~sGsGKSTl~~~l~~~~~~~g~~~g~v~~   58 (208)
T 3c8u_A           22 RQLVALSGAPGSGKSTLSNPLAAALSAQGLPAEVVPM   58 (208)
T ss_dssp             CEEEEEECCTTSCTHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCceEEEec
Confidence            34577999999999999999999875   33445544

>1ex7_A Guanylate kinase; substrate-induced FIT, domain movement, GMP, ATP, substrate specificity, X-RAY diffraction, transferase; HET: 5GP; 1.90A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 1ex6_A* 1gky_A* 3sqk_A 4f4j_A

Probab=96.00  E-value=0.0048  Score=56.84  Aligned_cols=28  Identities=32%  Similarity=0.498  Sum_probs=23.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      |.|+|.||+|+|||+|++.+.......+
T Consensus         2 RpIVi~GPSG~GK~Tl~~~L~~~~~~~~   29 (186)
T 1ex7_A            2 RPIVISGPSGTGKSTLLKKLFAEYPDSF   29 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CEEEEECCCCCCHHHHHHHHHHhCCCCe
Confidence            4589999999999999999987764333

>3tr0_A Guanylate kinase, GMP kinase; purines, pyrimidines, nucleosides, nucleotides, transferase; HET: 5GP; 1.85A {Coxiella burnetii}

Probab=95.98  E-value=0.0043  Score=56.68  Aligned_cols=25  Identities=28%  Similarity=0.620  Sum_probs=22.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||+|+||||+++.+++.+.
T Consensus         8 ~ii~l~Gp~GsGKSTl~~~L~~~~~   32 (205)
T 3tr0_A            8 NLFIISAPSGAGKTSLVRALVKALA   32 (205)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHSS
T ss_pred             cEEEEECcCCCCHHHHHHHHHhhCC
Confidence            3577999999999999999999863

>3fdi_A Uncharacterized protein; cytidylate kinase like protein, PSI, MCSG, PRK04182 class ME structural genomics, protein structure initiative; 2.20A {Eubacterium ventriosum}

Probab=95.98  E-value=0.0038  Score=57.96  Aligned_cols=29  Identities=17%  Similarity=0.214  Sum_probs=27.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      -|.+.||+|||||++++.+|..+|+++++
T Consensus         8 iI~i~g~~GsGk~ti~~~la~~lg~~~~D   36 (201)
T 3fdi_A            8 IIAIGREFGSGGHLVAKKLAEHYNIPLYS   36 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTTCCEEC
T ss_pred             EEEEeCCCCCCHHHHHHHHHHHhCcCEEC
Confidence            58899999999999999999999999886

>3thx_B DNA mismatch repair protein MSH3; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 3thw_B* 3thy_B* 3thz_B*

Probab=95.93  E-value=0.011  Score=66.93  Aligned_cols=24  Identities=33%  Similarity=0.492  Sum_probs=20.5

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ...-+.|.||.|+||||+.+.+|.
T Consensus       672 ~g~i~~ItGPNGaGKSTlLr~i~~  695 (918)
T 3thx_B          672 SERVMIITGPNMGGKSSYIKQVAL  695 (918)
T ss_dssp             SCCEEEEESCCCHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCchHHHHHHHHH
Confidence            345688999999999999999874

>3b9q_A Chloroplast SRP receptor homolog, alpha subunit CPFTSY; protein translocation, GTP-binding, nucleotide-binding, protein transport; 1.75A {Arabidopsis thaliana}

Probab=95.92  E-value=0.0057  Score=60.61  Aligned_cols=53  Identities=19%  Similarity=0.270  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHHHHHHhhhhHHhhhC--CCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          196 TDLKNRVKSDLESFLKAKHYYHRLG--RVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~~~~~~g--~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||+|+||||+++.+|+.+
T Consensus        70 ~~~~~~~~~~l~~~l~~~~~~~~l~~~~~~g~vi~lvG~nGsGKTTll~~Lag~l  124 (302)
T 3b9q_A           70 SEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL  124 (302)
T ss_dssp             HHHHHHHHHHHHHHHCC--CCCSCCCCSSSCEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcccccccccccCCCcEEEEEcCCCCCHHHHHHHHHHHH
Confidence            4566777777776664322001122  2344567899999999999999999865

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=95.88  E-value=0.023  Score=60.46  Aligned_cols=37  Identities=19%  Similarity=0.168  Sum_probs=27.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      |++...-++|.||||+|||+|++.++...   |..++++.
T Consensus       277 ~i~~G~i~~i~G~~GsGKSTLl~~l~g~~~~~G~~vi~~~  316 (525)
T 1tf7_A          277 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFA  316 (525)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHhCCCCEEEEE
Confidence            45555668999999999999999998753   44454443

>1c9k_A COBU, adenosylcobinamide kinase; alpha/beta structure rossmann fold P-loop, transferase; HET: 5GP; 2.20A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1cbu_A

Probab=95.82  E-value=0.012  Score=53.85  Aligned_cols=33  Identities=27%  Similarity=0.325  Sum_probs=29.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRV  260 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~  260 (480)
                      +|++|++|+|||++|..+|.. +.+.+++.....
T Consensus         2 ilV~Gg~~SGKS~~A~~la~~-~~~~~yiaT~~~   34 (180)
T 1c9k_A            2 ILVTGGARSGKSRHAEALIGD-APQVLYIATSQI   34 (180)
T ss_dssp             EEEEECTTSSHHHHHHHHHCS-CSSEEEEECCCC
T ss_pred             EEEECCCCCcHHHHHHHHHhc-CCCeEEEecCCC
Confidence            689999999999999999988 888888887654

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=95.81  E-value=0.014  Score=62.01  Aligned_cols=62  Identities=21%  Similarity=0.392  Sum_probs=40.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC--CcEEEEeCCC-cC-----------------ChHHHHHHHHhh--cCCcEEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS--YDVYDVDLSR-VA-----------------DDADLKSLLLQT--TSKSVILI  281 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~--~~~~~i~~s~-~~-----------------~~~~l~~l~~~~--~~~sII~I  281 (480)
                      ..++++.||+|+||||+++++++.+.  ..++.+.-.. +.                 +...+..++...  ..|.++++
T Consensus       260 g~~i~I~GptGSGKTTlL~aL~~~i~~~~giitied~~E~~~~~~~~v~~~~r~~~~~~~~~~~~~l~~~LR~~PD~iiv  339 (511)
T 2oap_1          260 KFSAIVVGETASGKTTTLNAIMMFIPPDAKVVSIEDTREIKLYHENWIAEVTRTGMGEGEIDMYDLLRAALRQRPDYIIV  339 (511)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCCCSSEEEEECBCCSSSCCBCHHHHHHTTGGGCCSEEEE
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCCCCCCEEEEcCcccccCCCCCeEEEEeecccccCCcCHHHHHHHhhccCCCeEEe
Confidence            34699999999999999999999874  3455553211 11                 011233333322  47999999


Q ss_pred             eccc
Q 011664          282 EDLD  285 (480)
Q Consensus       282 DEiD  285 (480)
                      .|+-
T Consensus       340 gEir  343 (511)
T 2oap_1          340 GEVR  343 (511)
T ss_dssp             SCCC
T ss_pred             CCcC
Confidence            9974

>3asz_A Uridine kinase; cytidine phosphorylation, transferase; HET: C5P; 2.25A {Thermus thermophilus} PDB: 3asy_A*

Probab=95.73  E-value=0.0051  Score=56.66  Aligned_cols=32  Identities=22%  Similarity=0.215  Sum_probs=25.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-+.|.||+|+||||+++.+++.++..+..++
T Consensus         7 ~~i~i~G~~GsGKSTl~~~l~~~~~~~i~~v~   38 (211)
T 3asz_A            7 FVIGIAGGTASGKTTLAQALARTLGERVALLP   38 (211)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHHHGGGEEEEE
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhCCCeEEEe
Confidence            35779999999999999999998773344444

>2og2_A Putative signal recognition particle receptor; nucleotide-binding, protein transport; 2.00A {Arabidopsis thaliana}

Probab=95.67  E-value=0.0075  Score=61.28  Aligned_cols=53  Identities=19%  Similarity=0.270  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHHHHHHhhhhHHhhhC--CCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          196 TDLKNRVKSDLESFLKAKHYYHRLG--RVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       196 ~~~k~~l~e~l~~~l~~~~~~~~~g--~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +.+++.+.+.+...+........+.  ...+.-+.|.||+|+||||+++.+|+.+
T Consensus       127 ~~~~~~l~~~l~~~l~~~~~~~~l~l~~~~g~vi~lvG~nGsGKTTll~~Lag~l  181 (359)
T 2og2_A          127 SEIKDALKESVLEMLAKKNSKTELQLGFRKPAVIMIVGVNGGGKTTSLGKLAHRL  181 (359)
T ss_dssp             HHHHHHHHHHHHHHHCCC---CSCCCCSSSSEEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCcccCCCcceecCCCeEEEEEcCCCChHHHHHHHHHhhc
Confidence            4566677777766664322101222  3345568899999999999999999865

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=95.67  E-value=0.0055  Score=56.47  Aligned_cols=25  Identities=36%  Similarity=0.533  Sum_probs=21.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .+-+.|.||+|+|||||++.+++..
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            3468999999999999999999865

>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=95.65  E-value=0.008  Score=53.75  Aligned_cols=27  Identities=22%  Similarity=0.234  Sum_probs=23.2

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +...-+.|.||.|+|||||++++++.+
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            344457899999999999999999987

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=95.64  E-value=0.022  Score=57.97  Aligned_cols=24  Identities=29%  Similarity=0.477  Sum_probs=21.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+-|.||+|+|||||+++|+...
T Consensus        55 ei~~IiGpnGaGKSTLlr~i~GL~   78 (366)
T 3tui_C           55 QIYGVIGASGAGKSTLIRCVNLLE   78 (366)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEEcCCCchHHHHHHHHhcCC
Confidence            347799999999999999999865

>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=95.62  E-value=0.0054  Score=63.18  Aligned_cols=33  Identities=27%  Similarity=0.482  Sum_probs=28.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.-+++.||+|+|||+|+..+|..++..++..|
T Consensus         2 ~~~i~i~GptgsGKttla~~La~~~~~~iis~D   34 (409)
T 3eph_A            2 KKVIVIAGTTGVGKSQLSIQLAQKFNGEVINSD   34 (409)
T ss_dssp             CEEEEEEECSSSSHHHHHHHHHHHHTEEEEECC
T ss_pred             CcEEEEECcchhhHHHHHHHHHHHCCCeEeecC
Confidence            345789999999999999999999887776654

>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=95.61  E-value=0.0029  Score=58.27  Aligned_cols=25  Identities=16%  Similarity=0.303  Sum_probs=22.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -|.+.||+|+||||+++.++..++.
T Consensus         2 ~I~i~G~~GsGKsTl~~~L~~~l~~   26 (214)
T 1gtv_A            2 LIAIEGVDGAGKRTLVEKLSGAFRA   26 (214)
T ss_dssp             EEEEEEEEEEEHHHHHHHHHHHHHE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHh
Confidence            3789999999999999999998753

>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=95.58  E-value=0.0089  Score=63.17  Aligned_cols=26  Identities=23%  Similarity=0.294  Sum_probs=22.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .+.-+.|.||+|+||||+++.||+.+
T Consensus       292 ~GeVI~LVGpNGSGKTTLl~~LAgll  317 (503)
T 2yhs_A          292 APFVILMVGVNGVGKTTTIGKLARQF  317 (503)
T ss_dssp             TTEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCcccHHHHHHHHHHHh
Confidence            34457899999999999999999865

>2ce2_X GTPase HRAS; signaling protein, guanine nucleotide binding protein, fluor membrane, lipoprotein, palmitate, prenylation; HET: GDP XY2; 1.0A {Homo sapiens} PDB: 2cl0_X* 2cl6_X* 2cl7_X* 2clc_X* 2evw_X* 2cld_X* 1aa9_A* 1ioz_A* 1q21_A* 6q21_A* 3k9l_A* 3k9n_A* 1ctq_A* 1bkd_R 1crp_A* 1crq_A* 1crr_A* 121p_A* 1gnp_A* 1gnq_A* ...

Probab=95.54  E-value=0.022  Score=48.94  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         5 ~i~v~G~~~~GKssl~~~l~~~   26 (166)
T 2ce2_X            5 KLVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999999864

>2j37_W Signal recognition particle 54 kDa protein (SRP54); ribosome, SRP, translation/RNA; 8.00A {Canis SP} PDB: 1wgw_A

Probab=95.54  E-value=0.027  Score=59.72  Aligned_cols=59  Identities=12%  Similarity=0.182  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHHHHHhhhhHHhhhCC--CCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          197 DLKNRVKSDLESFLKAKHYYHRLGR--VWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~~~~~~g~--~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      .+.+.+.+.+...+.....  .+..  ..++.|++.|+||+||||++..+|..+   |..+..+++
T Consensus        74 ~~~~~v~~eL~~ll~~~~~--~~~~~~~~~~vI~ivG~~GvGKTTl~~kLA~~l~~~G~kVllVd~  137 (504)
T 2j37_W           74 MIQHAVFKELVKLVDPGVK--AWTPTKGKQNVIMFVGLQGSGKTTTCSKLAYYYQRKGWKTCLICA  137 (504)
T ss_dssp             HHHHHHHHHHHHHHCCCCC--CCCCCSS--EEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEE
T ss_pred             HHHHHHHHHHHHHhccccc--hhccccCCCeEEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEec
Confidence            3455556656555543210  1111  235578999999999999999999765   666666655

>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=95.54  E-value=0.0093  Score=58.70  Aligned_cols=27  Identities=22%  Similarity=0.333  Sum_probs=23.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .+.-+.+.||+|+||||+++.++..++
T Consensus        30 ~~~ii~I~G~sGsGKSTla~~L~~~l~   56 (290)
T 1odf_A           30 CPLFIFFSGPQGSGKSFTSIQIYNHLM   56 (290)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHhh
Confidence            344578999999999999999998875

>1z6g_A Guanylate kinase; structural genomics, SGC, structural genom consortium, transferase; HET: EPE; 2.18A {Plasmodium falciparum}

Probab=95.51  E-value=0.0075  Score=56.48  Aligned_cols=25  Identities=24%  Similarity=0.479  Sum_probs=22.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||+|+|||||++.+++..
T Consensus        23 G~~~~lvGpsGsGKSTLl~~L~g~~   47 (218)
T 1z6g_A           23 IYPLVICGPSGVGKGTLIKKLLNEF   47 (218)
T ss_dssp             CCCEEEECSTTSSHHHHHHHHHHHS
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhC
Confidence            3458899999999999999999976

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=95.51  E-value=0.019  Score=64.36  Aligned_cols=23  Identities=30%  Similarity=0.537  Sum_probs=20.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      .+-+.|.||.|+|||++.+.+|.
T Consensus       607 g~i~~ItGpNGsGKSTlLr~iag  629 (800)
T 1wb9_A          607 RRMLIITGPNMGGKSTYMRQTAL  629 (800)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHHH
Confidence            34688999999999999999986

>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=95.50  E-value=0.0082  Score=55.46  Aligned_cols=26  Identities=31%  Similarity=0.488  Sum_probs=22.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ..-+.|.||+|+|||||+++|++.+.
T Consensus        20 Gei~~l~GpnGsGKSTLl~~l~gl~~   45 (207)
T 1znw_A           20 GRVVVLSGPSAVGKSTVVRCLRERIP   45 (207)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhhCC
Confidence            34577999999999999999999874

>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=95.50  E-value=0.009  Score=55.56  Aligned_cols=26  Identities=31%  Similarity=0.528  Sum_probs=22.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .+-+.|.||+|+|||+|+++++....
T Consensus        19 g~~ivl~GPSGaGKsTL~~~L~~~~~   44 (197)
T 3ney_A           19 RKTLVLIGASGVGRSHIKNALLSQNP   44 (197)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCEEEEECcCCCCHHHHHHHHHhhCC
Confidence            44688999999999999999998764

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens}

Probab=95.49  E-value=0.0079  Score=54.98  Aligned_cols=23  Identities=26%  Similarity=0.476  Sum_probs=19.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      +.+++.+|+|+|||.++...+..
T Consensus        49 ~~~li~~~tGsGKT~~~~~~~~~   71 (216)
T 3b6e_A           49 KNIIICLPTGSGKTRVAVYIAKD   71 (216)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHH
T ss_pred             CCEEEEcCCCCCHHHHHHHHHHH
Confidence            46999999999999988877654

>1zu4_A FTSY; GTPase, signal recognition particle, SRP, receptor, protein transport; 1.95A {Mycoplasma mycoides} PDB: 1zu5_A

Probab=95.49  E-value=0.016  Score=57.87  Aligned_cols=61  Identities=23%  Similarity=0.359  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHHhhhhHH---hhhC--CCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          198 LKNRVKSDLESFLKAKHYY---HRLG--RVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       198 ~k~~l~e~l~~~l~~~~~~---~~~g--~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      +++.+.+.+...+.....-   ..+.  ...++-+++.||+|+||||++..+|..+   +..+..+++.
T Consensus        74 ~~~~~~~~l~~~l~~~~~~~~~~~l~~~~~~~~vI~ivG~~G~GKTT~~~~LA~~l~~~g~kVllid~D  142 (320)
T 1zu4_A           74 IKDALVESLYQAYTDNDWTNKKYRIDFKENRLNIFMLVGVNGTGKTTSLAKMANYYAELGYKVLIAAAD  142 (320)
T ss_dssp             HHHHHHHHHHHHHHCSCC----CCCCCCTTSCEEEEEESSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHhCcccccccccCccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            5666666666666533200   1122  2345678899999999999999999754   5666666654

>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=95.48  E-value=0.0072  Score=58.97  Aligned_cols=39  Identities=26%  Similarity=0.158  Sum_probs=30.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s  258 (480)
                      |++...-++|.||||+|||+|++.+|..+    |.++..++..
T Consensus        31 ~l~~G~~~~i~G~~G~GKTTl~~~ia~~~~~~~G~~v~~~~~e   73 (296)
T 1cr0_A           31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (296)
T ss_dssp             SBCTTCEEEEEESTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHHHHHHcCCeEEEEeCc
Confidence            55556678899999999999999998754    4466666543

>2v9p_A Replication protein E1; AAA+ molecular motor, DNA replication, DNA translocation, nucleotide-binding, DNA-binding; 3.00A {Bovine papillomavirus type 1} PDB: 2gxa_A*

Probab=95.43  E-value=0.0095  Score=59.16  Aligned_cols=33  Identities=30%  Similarity=0.465  Sum_probs=27.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      .++....+.|.||+|+|||||++.|++.+.-.+
T Consensus       122 ~i~~Ge~vaIvGpsGsGKSTLl~lL~gl~~G~I  154 (305)
T 2v9p_A          122 GIPKKNCLAFIGPPNTGKSMLCNSLIHFLGGSV  154 (305)
T ss_dssp             TCTTCSEEEEECSSSSSHHHHHHHHHHHHTCEE
T ss_pred             EecCCCEEEEECCCCCcHHHHHHHHhhhcCceE
Confidence            455666789999999999999999999873333

>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=95.36  E-value=0.011  Score=64.34  Aligned_cols=33  Identities=27%  Similarity=0.527  Sum_probs=29.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      +.-|+|.|+||+||||++++++..+   |.+++.++
T Consensus        52 g~lIvLtGlsGSGKSTlAr~La~~L~~~G~~~v~lD   87 (630)
T 1x6v_B           52 GCTVWLTGLSGAGKTTVSMALEEYLVCHGIPCYTLD   87 (630)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEES
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHHHHHhcCCeEEEec
Confidence            3458899999999999999999998   99999886

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=95.29  E-value=0.024  Score=52.26  Aligned_cols=62  Identities=18%  Similarity=0.156  Sum_probs=37.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC--------cC---C-------hHHHHHHHHhhc-CCcEEEEec
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR--------VA---D-------DADLKSLLLQTT-SKSVILIED  283 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~--------~~---~-------~~~l~~l~~~~~-~~sII~IDE  283 (480)
                      -++++||+|+|||+.+-.+|..+   |..+..+....        +.   +       -.....++.... ...+|+|||
T Consensus        10 i~v~~G~mgsGKTT~ll~~a~r~~~~g~kV~v~k~~~d~r~~~~~i~s~~g~~~~a~~~~~~~~i~~~~~~~~dvViIDE   89 (191)
T 1xx6_A           10 VEVIVGPMYSGKSEELIRRIRRAKIAKQKIQVFKPEIDNRYSKEDVVSHMGEKEQAVAIKNSREILKYFEEDTEVIAIDE   89 (191)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEEC-------CEEECTTSCEEECEEESSSTHHHHHCCTTCSEEEECS
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEEeccCccchHHHHHhhcCCceeeEeeCCHHHHHHHHhccCCEEEEEC
Confidence            46789999999998888877654   66655553110        00   0       000123343333 358999999


Q ss_pred             cccc
Q 011664          284 LDRF  287 (480)
Q Consensus       284 iD~l  287 (480)
                      +.-+
T Consensus        90 aqfl   93 (191)
T 1xx6_A           90 VQFF   93 (191)
T ss_dssp             GGGS
T ss_pred             CCCC
Confidence            9865

>3gmt_A Adenylate kinase; ssgcid, ATP-BIN cytoplasm, nucleotide biosynthesis, nucleotide-BIND transferase, structural genomics; 2.10A {Burkholderia pseudomallei 1710B}

Probab=95.28  E-value=0.0075  Score=57.48  Aligned_cols=30  Identities=20%  Similarity=0.311  Sum_probs=25.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -+-|.||||+||||+++.+|..++...++.
T Consensus        10 ~~~~~G~pGsGKsT~a~~L~~~~g~~~is~   39 (230)
T 3gmt_A           10 RLILLGAPGAGKGTQANFIKEKFGIPQIST   39 (230)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTCCEECH
T ss_pred             ceeeECCCCCCHHHHHHHHHHHhCCCeeec
Confidence            356889999999999999999998776654

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=95.27  E-value=0.017  Score=57.37  Aligned_cols=39  Identities=26%  Similarity=0.202  Sum_probs=31.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      |+++..-++|.|+||+|||+++..+|...   +.++..+++.
T Consensus        64 Gl~~G~l~li~G~pG~GKTtl~l~ia~~~a~~g~~vl~~slE  105 (315)
T 3bh0_A           64 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  105 (315)
T ss_dssp             SBCTTCEEEEECCTTSSHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEECC
Confidence            56666679999999999999999998643   4677777765

>2eyu_A Twitching motility protein PILT; pilus retraction motor, C-terminal domain PILT, protein transport; 1.87A {Aquifex aeolicus}

Probab=95.26  E-value=0.01  Score=57.49  Aligned_cols=63  Identities=24%  Similarity=0.473  Sum_probs=39.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC----CcEEEEe--CCCcC--------------ChHHHHHHHHhh--cCCcEEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS----YDVYDVD--LSRVA--------------DDADLKSLLLQT--TSKSVIL  280 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~----~~~~~i~--~s~~~--------------~~~~l~~l~~~~--~~~sII~  280 (480)
                      ...-+++.||+|+||||+++++++.+.    ..++...  ...+.              ....++..++.+  ..|.+|+
T Consensus        24 ~g~~v~i~Gp~GsGKSTll~~l~g~~~~~~~G~I~~~g~~i~~~~~~~~~~v~q~~~gl~~~~l~~~la~aL~~~p~ill  103 (261)
T 2eyu_A           24 KMGLILVTGPTGSGKSTTIASMIDYINQTKSYHIITIEDPIEYVFKHKKSIVNQREVGEDTKSFADALRAALREDPDVIF  103 (261)
T ss_dssp             SSEEEEEECSTTCSHHHHHHHHHHHHHHHCCCEEEEEESSCCSCCCCSSSEEEEEEBTTTBSCHHHHHHHHHHHCCSEEE
T ss_pred             CCCEEEEECCCCccHHHHHHHHHHhCCCCCCCEEEEcCCcceeecCCcceeeeHHHhCCCHHHHHHHHHHHHhhCCCEEE
Confidence            344578999999999999999998652    2333222  11100              011233334332  4899999


Q ss_pred             Eeccc
Q 011664          281 IEDLD  285 (480)
Q Consensus       281 IDEiD  285 (480)
                      +||.-
T Consensus       104 lDEp~  108 (261)
T 2eyu_A          104 VGEMR  108 (261)
T ss_dssp             ESCCC
T ss_pred             eCCCC
Confidence            99984

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=95.25  E-value=0.047  Score=64.45  Aligned_cols=30  Identities=23%  Similarity=0.327  Sum_probs=24.8

Q ss_pred             CCCCceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          221 RVWKRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       221 ~~~~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      +++..-+.+.||+|+|||||++++.++...
T Consensus       441 i~~G~~vaivG~sGsGKSTll~ll~~~~~~  470 (1321)
T 4f4c_A          441 VNAGQTVALVGSSGCGKSTIISLLLRYYDV  470 (1321)
T ss_dssp             ECTTCEEEEEECSSSCHHHHHHHHTTSSCC
T ss_pred             ecCCcEEEEEecCCCcHHHHHHHhcccccc
Confidence            334456889999999999999999998754

>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=95.24  E-value=0.047  Score=53.79  Aligned_cols=37  Identities=30%  Similarity=0.362  Sum_probs=29.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV  260 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~  260 (480)
                      +.-+.+.||+|+|||+++..+|..+   +..+..+++.-.
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            4567889999999999999999765   667777776543

>1s96_A Guanylate kinase, GMP kinase; E.coli, dimer, SAD, transferase; 2.00A {Escherichia coli} SCOP: c.37.1.1 PDB: 2an9_A* 2anb_A* 2anc_A 2f3r_A* 2f3t_A*

Probab=95.24  E-value=0.011  Score=55.66  Aligned_cols=27  Identities=33%  Similarity=0.475  Sum_probs=23.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+.|.||+|+|||||++++++...
T Consensus        15 ~G~ii~l~GpsGsGKSTLlk~L~g~~~   41 (219)
T 1s96_A           15 QGTLYIVSAPSGAGKSSLIQALLKTQP   41 (219)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             CCcEEEEECCCCCCHHHHHHHHhccCC
Confidence            345678999999999999999999775

>3tqf_A HPR(Ser) kinase; transferase, hydrolase; 2.80A {Coxiella burnetii}

Probab=95.22  E-value=0.014  Score=53.23  Aligned_cols=24  Identities=29%  Similarity=0.397  Sum_probs=21.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+|+||.||+|+|||++|.++...
T Consensus        16 G~gvli~G~SGaGKStlal~L~~r   39 (181)
T 3tqf_A           16 KMGVLITGEANIGKSELSLALIDR   39 (181)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHHT
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc
Confidence            469999999999999999999874

>1kao_A RAP2A; GTP-binding protein, small G protein, GDP, RAS; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2rap_A* 3rap_R*

Probab=95.20  E-value=0.05  Score=46.76  Aligned_cols=22  Identities=23%  Similarity=0.459  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|+||+|||+|+.++.+.
T Consensus         5 ~i~v~G~~~~GKSsli~~l~~~   26 (167)
T 1kao_A            5 KVVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>3hdt_A Putative kinase; structura genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; 2.79A {Clostridium symbiosum atcc 14940}

Probab=95.19  E-value=0.0094  Score=56.42  Aligned_cols=31  Identities=16%  Similarity=0.176  Sum_probs=27.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-|.+.|++|||||++++.+|..+|+++++-
T Consensus        15 ~iI~i~g~~gsGk~~i~~~la~~lg~~~~d~   45 (223)
T 3hdt_A           15 LIITIEREYGSGGRIVGKKLAEELGIHFYDD   45 (223)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHTCEEECH
T ss_pred             eEEEEeCCCCCCHHHHHHHHHHHcCCcEEcH
Confidence            3578999999999999999999999998763

>1nrj_B SR-beta, signal recognition particle receptor beta subunit; transmembrane, endoplasmic reticulum, GTP-binding; HET: GTP; 1.70A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=95.16  E-value=0.033  Score=51.02  Aligned_cols=25  Identities=24%  Similarity=0.461  Sum_probs=21.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...+++.|++|+|||+|+.++++..
T Consensus        12 ~~~i~~~G~~g~GKTsl~~~l~~~~   36 (218)
T 1nrj_B           12 QPSIIIAGPQNSGKTSLLTLLTTDS   36 (218)
T ss_dssp             CCEEEEECSTTSSHHHHHHHHHHSS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCC
Confidence            3469999999999999999999854

>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=95.12  E-value=0.02  Score=57.30  Aligned_cols=52  Identities=17%  Similarity=0.261  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHhhhh---HH-hhhCCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          197 DLKNRVKSDLESFLKAKH---YY-HRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~---~~-~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .+++.+.+.+...+....   .. .......+.-+.|.||+|+||||+++.+|..+
T Consensus        98 ~~~~~l~~~l~~~l~~~~~~~~~~~~~~~~~g~vi~lvG~nGaGKTTll~~Lag~l  153 (328)
T 3e70_C           98 IIEEAVKEAVSEILETSRRIDLIEEIRKAEKPYVIMFVGFNGSGKTTTIAKLANWL  153 (328)
T ss_dssp             HHHHHHHHHHHHHSCCSSCCCHHHHHHSSCSSEEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCccccchhhhcccCCCCeEEEEECCCCCCHHHHHHHHHHHH
Confidence            445556666655554321   00 01122345568899999999999999999865

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=95.11  E-value=0.033  Score=54.82  Aligned_cols=56  Identities=11%  Similarity=0.119  Sum_probs=32.2

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhC----CCCCceEEEEccCCCcHHHHHHHHH
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLG----RVWKRSYLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g----~~~~rgiLL~GPpGTGKT~La~aiA  245 (480)
                      .+|+++...+.+.+.+.+.-   ...+..+....    ..-.+.+++.+|+|+|||..+-..+
T Consensus         6 ~~f~~~~l~~~~~~~l~~~g---~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~   65 (367)
T 1hv8_A            6 MNFNELNLSDNILNAIRNKG---FEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPL   65 (367)
T ss_dssp             CCGGGSSCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHH
T ss_pred             CchhhcCCCHHHHHHHHHcC---CCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHH
Confidence            46788877777776665421   01111111110    0113579999999999998765444

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=95.11  E-value=0.048  Score=62.02  Aligned_cols=21  Identities=24%  Similarity=0.388  Sum_probs=19.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA  245 (480)
                      .-++|.||.|+||||+++.+|
T Consensus       663 ~i~~ItGpNGsGKSTlLr~ia  683 (934)
T 3thx_A          663 MFHIITGPNMGGKSTYIRQTG  683 (934)
T ss_dssp             CEEEEECCTTSSHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHH
Confidence            458899999999999999995

>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=95.08  E-value=0.0098  Score=56.30  Aligned_cols=30  Identities=27%  Similarity=0.432  Sum_probs=24.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC--CcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS--YDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~--~~~~~i  255 (480)
                      -+.|.||||+||||+++.++..++  .+++..
T Consensus        28 ~i~i~G~~GsGKsT~~~~l~~~l~~~~~~~~~   59 (229)
T 4eaq_A           28 FITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   59 (229)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHhcCCCceee
Confidence            477889999999999999999886  455443

>2jeo_A Uridine-cytidine kinase 1; UCK, transferase, ATP-binding, nucleoside kinase, nucleotide-binding; 2.50A {Homo sapiens} PDB: 2uvq_A*

Probab=95.06  E-value=0.012  Score=56.00  Aligned_cols=26  Identities=15%  Similarity=0.291  Sum_probs=22.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      -+-|.||+|+||||+++.+++.+|..
T Consensus        27 iigI~G~~GsGKSTl~k~L~~~lG~~   52 (245)
T 2jeo_A           27 LIGVSGGTASGKSTVCEKIMELLGQN   52 (245)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHTGG
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhchh
Confidence            46799999999999999999987753

>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=95.05  E-value=0.01  Score=60.41  Aligned_cols=28  Identities=32%  Similarity=0.515  Sum_probs=23.4

Q ss_pred             CCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          221 RVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       221 ~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ......+++.||+|+||||+++++++.+
T Consensus       133 ~~~g~~i~ivG~~GsGKTTll~~l~~~~  160 (372)
T 2ewv_A          133 HRKMGLILVTGPTGSGKSTTIASMIDYI  160 (372)
T ss_dssp             TSSSEEEEEECSSSSSHHHHHHHHHHHH
T ss_pred             hcCCCEEEEECCCCCCHHHHHHHHHhhc
Confidence            3344568899999999999999999865

>2p5s_A RAS and EF-hand domain containing; G-protein, RAB, GDP, structural genomics, SGC, structural genomics consortium, signaling protein; HET: GDP; 2.15A {Homo sapiens}

Probab=94.99  E-value=0.05  Score=49.17  Aligned_cols=24  Identities=29%  Similarity=0.380  Sum_probs=21.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ...+++.|++|+|||+|+.++.+.
T Consensus        28 ~~ki~v~G~~~~GKSsli~~l~~~   51 (199)
T 2p5s_A           28 AYKIVLAGDAAVGKSSFLMRLCKN   51 (199)
T ss_dssp             CEEEEEESSTTSSHHHHHHHHHHC
T ss_pred             CeEEEEECcCCCCHHHHHHHHHhC
Confidence            346999999999999999999863

>2i3b_A HCR-ntpase, human cancer-related ntpase; AAA, rossmann, hydrolase; NMR {Homo sapiens} SCOP: c.37.1.11

Probab=94.96  E-value=0.011  Score=54.44  Aligned_cols=23  Identities=26%  Similarity=0.585  Sum_probs=20.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+.|.||+|+||||+++.+++.+
T Consensus         3 ~i~i~G~nG~GKTTll~~l~g~~   25 (189)
T 2i3b_A            3 HVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CEEEESCCSSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCChHHHHHHHHHhhc
Confidence            37899999999999999999865

>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=94.90  E-value=0.031  Score=57.91  Aligned_cols=57  Identities=19%  Similarity=0.276  Sum_probs=37.3

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEe
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVD  256 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~  256 (480)
                      ..+++++....+.+..+.+.    +.          ....-+++.||+|+||||+++++++.+.   .+++.+.
T Consensus       143 ~~~l~~Lg~~~~~~~~L~~l----~~----------~~ggii~I~GpnGSGKTTlL~allg~l~~~~g~I~~~e  202 (418)
T 1p9r_A          143 RLDLHSLGMTAHNHDNFRRL----IK----------RPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVE  202 (418)
T ss_dssp             CCCGGGSCCCHHHHHHHHHH----HT----------SSSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEE
T ss_pred             CCCHHHcCCCHHHHHHHHHH----HH----------hcCCeEEEECCCCCCHHHHHHHHHhhcCCCCCEEEEec
Confidence            45788887766554433321    11          1223478999999999999999999774   2455443

>1r8s_A ADP-ribosylation factor 1; protein transport/exchange factor, protein transport-exchang complex; HET: GDP; 1.46A {Bos taurus} SCOP: c.37.1.8 PDB: 1re0_A* 1s9d_A* 1u81_A* 1r8q_A* 1rrf_A* 1rrg_A* 1hur_A* 1o3y_A* 1j2j_A* 2j59_A* 1mr3_F* 2k5u_A* 3lrp_A* 3tjz_A* 3rd1_A* 2ksq_A* 2a5d_A* 2a5f_A* 2j5x_A* 1e0s_A* ...

Probab=94.83  E-value=0.11  Score=44.72  Aligned_cols=20  Identities=20%  Similarity=0.355  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|++|+|||+|+.++.+
T Consensus         3 i~~~G~~~~GKssl~~~l~~   22 (164)
T 1r8s_A            3 ILMVGLDAAGKTTILYKLKL   22 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            78999999999999999975

>3lnc_A Guanylate kinase, GMP kinase; ALS collaborative crystallography, emerald biostructures, ATP-binding, cytoplasm, nucleotide-binding; HET: 5GP; 1.95A {Anaplasma phagocytophilum}

Probab=94.80  E-value=0.0094  Score=55.92  Aligned_cols=25  Identities=28%  Similarity=0.369  Sum_probs=15.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHH-HcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMA-SFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA-~~l  248 (480)
                      ..-+.|.||+|+||||+++.++ +.+
T Consensus        27 G~ii~l~Gp~GsGKSTl~~~L~~~~~   52 (231)
T 3lnc_A           27 GVILVLSSPSGCGKTTVANKLLEKQK   52 (231)
T ss_dssp             CCEEEEECSCC----CHHHHHHC---
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            3457899999999999999999 765

>1u8z_A RAS-related protein RAL-A; GNP, GTP, GMPPNP, GPPNHP, GDP, GTPase, signaling protein; HET: GDP; 1.50A {Saguinus oedipus} SCOP: c.37.1.8 PDB: 1u8y_A* 1u90_A* 1uad_A* 1zc3_A* 1zc4_A* 2kwi_A* 2ke5_A*

Probab=94.80  E-value=0.047  Score=47.00  Aligned_cols=23  Identities=22%  Similarity=0.391  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         5 ~~i~v~G~~~~GKssl~~~l~~~   27 (168)
T 1u8z_A            5 HKVIMVGSGGVGKSALTLQFMYD   27 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999999863

>2ged_A SR-beta, signal recognition particle receptor beta subunit; protein transport, G protein, proline isomerization, circular permutation; 2.20A {Saccharomyces cerevisiae}

Probab=94.79  E-value=0.014  Score=52.35  Aligned_cols=26  Identities=23%  Similarity=0.496  Sum_probs=22.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ....+++.|++|+|||+|+.++.+.-
T Consensus        47 ~~~~i~vvG~~g~GKSsll~~l~~~~   72 (193)
T 2ged_A           47 YQPSIIIAGPQNSGKTSLLTLLTTDS   72 (193)
T ss_dssp             CCCEEEEECCTTSSHHHHHHHHHHSS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            34579999999999999999998753

>1np6_A Molybdopterin-guanine dinucleotide biosynthesis protein B; mixed alpha-beta fold, elongated beta-sheet, walker A motif, P-loop structural motif; 1.90A {Escherichia coli} SCOP: c.37.1.10 PDB: 1p9n_A

Probab=94.73  E-value=0.016  Score=52.57  Aligned_cols=26  Identities=19%  Similarity=0.194  Sum_probs=22.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...-+.+.||+|+|||++++.++..+
T Consensus         5 ~~~~i~i~G~sGsGKTTl~~~l~~~l   30 (174)
T 1np6_A            5 MIPLLAFAAWSGTGKTTLLKKLIPAL   30 (174)
T ss_dssp             CCCEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             cceEEEEEeCCCCCHHHHHHHHHHhc
Confidence            34568899999999999999998764

>2erx_A GTP-binding protein DI-RAS2; GTP hydrolysis, transport protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8

Probab=94.72  E-value=0.051  Score=47.05  Aligned_cols=21  Identities=29%  Similarity=0.550  Sum_probs=19.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus         5 ~i~v~G~~~~GKssli~~l~~   25 (172)
T 2erx_A            5 RVAVFGAGGVGKSSLVLRFVK   25 (172)
T ss_dssp             EEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            489999999999999999986

>3kta_A Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xex_A* 1xew_X*

Probab=94.71  E-value=0.019  Score=51.44  Aligned_cols=24  Identities=25%  Similarity=0.418  Sum_probs=21.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -.+|+||.|+|||+++.||+..++
T Consensus        28 ~~~i~G~NGsGKStll~ai~~~l~   51 (182)
T 3kta_A           28 FTAIVGANGSGKSNIGDAILFVLG   51 (182)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHTT
T ss_pred             cEEEECCCCCCHHHHHHHHHHHHc
Confidence            467999999999999999998775

>1a7j_A Phosphoribulokinase; transferase, calvin cycle; 2.50A {Rhodobacter sphaeroides} SCOP: c.37.1.6

Probab=94.70  E-value=0.0082  Score=59.01  Aligned_cols=36  Identities=14%  Similarity=0.233  Sum_probs=26.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC---CcEEEEeCCCcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS---YDVYDVDLSRVA  261 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~---~~~~~i~~s~~~  261 (480)
                      -|.|.||+|+||||+++.++..++   ..+..+++..+.
T Consensus         7 iIgItG~sGSGKSTva~~L~~~lg~~~~~~~vI~~D~~~   45 (290)
T 1a7j_A            7 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFH   45 (290)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGB
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhhcCCCeeEeecchhh
Confidence            478999999999999999998775   456667766655

>3tkl_A RAS-related protein RAB-1A; vesicle trafficking, protein transport-protein binding compl; HET: GTP; 2.18A {Homo sapiens}

Probab=94.68  E-value=0.044  Score=48.95  Aligned_cols=23  Identities=39%  Similarity=0.436  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      --+++.|++|+|||+|+.++.+.
T Consensus        17 ~ki~v~G~~~~GKSsli~~l~~~   39 (196)
T 3tkl_A           17 FKLLLIGDSGVGKSCLLLRFADD   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999873

>2fg5_A RAB-22B, RAS-related protein RAB-31; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.80A {Homo sapiens} SCOP: c.37.1.8

Probab=94.68  E-value=0.046  Score=49.11  Aligned_cols=22  Identities=32%  Similarity=0.427  Sum_probs=20.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        25 ki~vvG~~~~GKSsli~~l~~~   46 (192)
T 2fg5_A           25 KVCLLGDTGVGKSSIVCRFVQD   46 (192)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999864

>1c1y_A RAS-related protein RAP-1A; GTP-binding proteins, protein-protein complex, effectors, signaling protein; HET: GTP; 1.90A {Homo sapiens} SCOP: c.37.1.8 PDB: 3kuc_A* 1gua_A* 3cf6_R* 3brw_D*

Probab=94.68  E-value=0.045  Score=47.23  Aligned_cols=22  Identities=23%  Similarity=0.456  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         5 ki~v~G~~~~GKssli~~l~~~   26 (167)
T 1c1y_A            5 KLVVLGSGGVGKSALTVQFVQG   26 (167)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>1x3s_A RAS-related protein RAB-18; GTPase, GNP, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GNP; 1.32A {Homo sapiens} SCOP: c.37.1.8

Probab=94.62  E-value=0.062  Score=47.82  Aligned_cols=22  Identities=36%  Similarity=0.483  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        17 ~i~v~G~~~~GKssli~~l~~~   38 (195)
T 1x3s_A           17 KILIIGESGVGKSSLLLRFTDD   38 (195)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6899999999999999999864

>4a82_A Cystic fibrosis transmembrane conductance regulat; CFTR, ION channel, transport protein, casse protein; 2.00A {Homo sapiens} PDB: 2onj_A* 2hyd_A

Probab=94.62  E-value=0.048  Score=58.65  Aligned_cols=27  Identities=26%  Similarity=0.383  Sum_probs=22.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+.+.||+|+|||||++.+++...
T Consensus       366 ~G~~~~ivG~sGsGKSTll~~l~g~~~  392 (578)
T 4a82_A          366 KGETVAFVGMSGGGKSTLINLIPRFYD  392 (578)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCCC
Confidence            334578999999999999999998764

>3tqc_A Pantothenate kinase; biosynthesis of cofactors, prosthetic groups, carriers, TRAN; HET: ADP; 2.30A {Coxiella burnetii}

Probab=94.55  E-value=0.038  Score=55.19  Aligned_cols=35  Identities=17%  Similarity=0.195  Sum_probs=26.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC-----cEEEEeCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY-----DVYDVDLSR  259 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~-----~~~~i~~s~  259 (480)
                      .-+-|.||+||||||+++.++..++.     .+..+....
T Consensus        93 ~iigI~GpsGSGKSTl~~~L~~ll~~~~~~~~v~~i~~D~  132 (321)
T 3tqc_A           93 YIIGIAGSVAVGKSTTSRVLKALLSRWPDHPNVEVITTDG  132 (321)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGG
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHhcccCCCCeEEEEeecc
Confidence            35779999999999999999987752     355555444

>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=94.53  E-value=0.026  Score=60.11  Aligned_cols=33  Identities=9%  Similarity=0.241  Sum_probs=26.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      +.-|+|.|+||+|||++++.+|..+   +.+...++
T Consensus        35 ~~lIvlvGlpGSGKSTia~~La~~L~~~~~d~~v~s   70 (520)
T 2axn_A           35 PTVIVMVGLPARGKTYISKKLTRYLNWIGVPTKVFN   70 (520)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHhhcCCCeEEec
Confidence            4468999999999999999999987   44444443

>2a9k_A RAS-related protein RAL-A; bacterial ADP-ribosyltransferase, RAL, RHO, GD binding; HET: GDP NAD; 1.73A {Homo sapiens} SCOP: c.37.1.8 PDB: 2a78_A*

Probab=94.48  E-value=0.066  Score=47.11  Aligned_cols=23  Identities=22%  Similarity=0.391  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        19 ~ki~v~G~~~~GKSsli~~l~~~   41 (187)
T 2a9k_A           19 HKVIMVGSGGVGKSALTLQFMYD   41 (187)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHhhC
Confidence            36999999999999999999863

>2xxa_A Signal recognition particle protein; protein transport, RNA/RNA binding protein, hydrolase, gtpas; HET: GCP; 3.94A {Escherichia coli} PDB: 2j28_9

Probab=94.44  E-value=0.036  Score=57.68  Aligned_cols=62  Identities=18%  Similarity=0.229  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCCC
Q 011664          198 LKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLSR  259 (480)
Q Consensus       198 ~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s~  259 (480)
                      +.+.+.+.+...+.....--......++.+++.|++|+||||++..+|..+    |..+.-+++..
T Consensus        74 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~vI~ivG~~GvGKTT~a~~LA~~l~~~~G~kVllvd~D~  139 (433)
T 2xxa_A           74 FVKIVRNELVAAMGEENQTLNLAAQPPAVVLMAGLQGAGKTTSVGKLGKFLREKHKKKVLVVSADV  139 (433)
T ss_dssp             THHHHHHHHHHHHCSSSCCCCCCSSSSEEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEECCC
T ss_pred             HHHHHHHHHHHHhccccccccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHhcCCeEEEEecCC
Confidence            345555555555543210000111345678899999999999999999654    77777777654

>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=94.44  E-value=0.011  Score=56.62  Aligned_cols=25  Identities=20%  Similarity=0.381  Sum_probs=22.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-|.|.|++|+||||+++.++..++
T Consensus        25 ~~I~ieG~~GsGKST~~~~L~~~l~   49 (263)
T 1p5z_B           25 KKISIEGNIAAGKSTFVNILKQLCE   49 (263)
T ss_dssp             EEEEEECSTTSSHHHHHTTTGGGCT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhcC
Confidence            3578999999999999999999983

>3t1o_A Gliding protein MGLA; G domain containing protein, bacterial GTPase, bacterial POL motility, POLE localisation, alpha/beta protein; HET: GDP; 1.90A {Thermus thermophilus} PDB: 3t12_A* 3t1q_A* 3t1t_A* 3t1v_A*

Probab=94.39  E-value=0.067  Score=47.53  Aligned_cols=23  Identities=26%  Similarity=0.378  Sum_probs=20.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+++.|+||+|||+|++.+.+..
T Consensus        16 ki~vvG~~~~GKssL~~~l~~~~   38 (198)
T 3t1o_A           16 KIVYYGPGLSGKTTNLKWIYSKV   38 (198)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHhhc
Confidence            58999999999999999998754

>2ocp_A DGK, deoxyguanosine kinase; protein-nucleotide complex, transferase; HET: DTP; 2.80A {Homo sapiens} SCOP: c.37.1.1

Probab=94.36  E-value=0.028  Score=52.98  Aligned_cols=25  Identities=24%  Similarity=0.367  Sum_probs=22.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-|.+.|++|+||||+++.++..+.
T Consensus         3 ~~i~~~G~~g~GKtt~~~~l~~~l~   27 (241)
T 2ocp_A            3 RRLSIEGNIAVGKSTFVKLLTKTYP   27 (241)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHCT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHcC
Confidence            3588999999999999999999984

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=94.35  E-value=0.016  Score=54.56  Aligned_cols=27  Identities=22%  Similarity=0.288  Sum_probs=22.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .-+.|.||+|+|||||++++++.+...
T Consensus        31 e~~~iiG~nGsGKSTLl~~l~Gl~~p~   57 (224)
T 2pcj_A           31 EFVSIIGASGSGKSTLLYILGLLDAPT   57 (224)
T ss_dssp             CEEEEEECTTSCHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            347799999999999999999877543

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=94.34  E-value=0.02  Score=54.71  Aligned_cols=26  Identities=35%  Similarity=0.597  Sum_probs=22.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-+.|.||+|+|||||++++++.+..
T Consensus        25 e~~~liG~nGsGKSTLl~~l~Gl~~p   50 (240)
T 2onk_A           25 DYCVLLGPTGAGKSVFLELIAGIVKP   50 (240)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            56789999999999999999987653

>2cbz_A Multidrug resistance-associated protein 1; ABC proteins, MRP1/ABCC1, nucleotide-binding domain, ATP- binding, hydrolysis, transport; HET: ATP; 1.5A {Homo sapiens}

Probab=94.34  E-value=0.019  Score=54.64  Aligned_cols=26  Identities=31%  Similarity=0.302  Sum_probs=22.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...-+.|.||+|+|||||++++++.+
T Consensus        30 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~   55 (237)
T 2cbz_A           30 EGALVAVVGQVGCGKSSLLSALLAEM   55 (237)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTCS
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhcCC
Confidence            33458899999999999999999865

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=94.34  E-value=0.055  Score=53.79  Aligned_cols=56  Identities=20%  Similarity=0.171  Sum_probs=31.3

Q ss_pred             CCccccccChHHHHHHHHHHH-HHHh-hhhHHhhhCCCCCceEEEEccCCCcHHHHHH
Q 011664          187 STFDTISMETDLKNRVKSDLE-SFLK-AKHYYHRLGRVWKRSYLLYGPSGTGKSSFAA  242 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~-~~l~-~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~  242 (480)
                      .+|+++...+.+.+.+.+.-. .+.. ..+.+..+-...++.+++.+|+|+|||..+-
T Consensus         5 ~~f~~~~l~~~l~~~l~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~   62 (395)
T 3pey_A            5 KSFDELGLAPELLKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFS   62 (395)
T ss_dssp             CSSTTSCCCHHHHHHHHHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHH
T ss_pred             cCHhhCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHH
Confidence            467777777777776654110 0000 0111111111133689999999999997654

>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=94.32  E-value=0.019  Score=54.54  Aligned_cols=28  Identities=25%  Similarity=0.386  Sum_probs=23.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ..-+.|.||+|+|||||++++++.+...
T Consensus        31 Ge~~~iiG~nGsGKSTLl~~l~Gl~~p~   58 (235)
T 3tif_A           31 GEFVSIMGPSGSGKSTMLNIIGCLDKPT   58 (235)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCCCCC
Confidence            3457899999999999999999877544

>1sq5_A Pantothenate kinase; P-loop, transferase; HET: PAU ADP; 2.20A {Escherichia coli} SCOP: c.37.1.6 PDB: 1esm_A* 1esn_A*

Probab=94.31  E-value=0.017  Score=57.06  Aligned_cols=25  Identities=24%  Similarity=0.329  Sum_probs=22.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+-|.||+|+||||+++.+++.++
T Consensus        81 ~iigI~G~~GsGKSTl~~~L~~~l~  105 (308)
T 1sq5_A           81 YIISIAGSVAVGKSTTARVLQALLS  105 (308)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHT
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHh
Confidence            3467999999999999999999765

>1m8p_A Sulfate adenylyltransferase; rossmann fold, phosphosulfate binding, T-state; HET: PPS; 2.60A {Penicillium chrysogenum} SCOP: b.122.1.3 c.26.1.5 c.37.1.15 PDB: 1i2d_A*

Probab=94.30  E-value=0.021  Score=61.52  Aligned_cols=33  Identities=21%  Similarity=0.153  Sum_probs=28.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC----CcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS----YDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~----~~~~~i~~  257 (480)
                      .-|+|.|+||+||||++++++..++    .+++.++.
T Consensus       397 ~~I~l~GlsGSGKSTiA~~La~~L~~~G~~~~~~lD~  433 (573)
T 1m8p_A          397 FTIFLTGYMNSGKDAIARALQVTLNQQGGRSVSLLLG  433 (573)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHCSSCEEEEEH
T ss_pred             eEEEeecCCCCCHHHHHHHHHHHhcccCCceEEEECc
Confidence            3578999999999999999999886    67777763

>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=94.28  E-value=0.023  Score=56.48  Aligned_cols=60  Identities=12%  Similarity=0.060  Sum_probs=34.9

Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHH
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      +.+..  .||..|.+..+.......++++.....+.. ..+.+.......|+|..++.+.+..
T Consensus       212 ~~l~~--~~D~~I~V~a~~~~~~~R~i~R~~~~rd~~-~r~~~~~~~~~~g~s~e~a~~~v~~  271 (312)
T 3aez_A          212 LMVSD--LFDFSLYVDARIEDIEQWYVSRFLAMRTTA-FADPESHFHHYAAFSDSQAVVAARE  271 (312)
T ss_dssp             CCGGG--GCSEEEEEEECHHHHHHHHHHHHHHHTTTG-GGSTTSTTGGGTTCCHHHHHHHHHH
T ss_pred             HHHHH--hcCcEEEEECCHHHHHHHHHHHHHHHHhcc-ccCcchhhhcccCCCHHHHHHHHHH
Confidence            44555  789999999887666666666654311111 0111122233358899998877654

>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=94.28  E-value=0.024  Score=56.07  Aligned_cols=25  Identities=28%  Similarity=0.511  Sum_probs=22.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +.-+.|.||+|+||||+++.+|..+
T Consensus       102 g~vi~lvG~nGsGKTTll~~Lagll  126 (304)
T 1rj9_A          102 GRVVLVVGVNGVGKTTTIAKLGRYY  126 (304)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHH
Confidence            4568899999999999999999865

>1fzq_A ADP-ribosylation factor-like protein 3; protein-GDP complex without magnesium, ARF family, RAS superfamily, G-domain, signaling protein; HET: MES GDP; 1.70A {Mus musculus} SCOP: c.37.1.8 PDB: 3bh7_A* 3bh6_A*

Probab=94.23  E-value=0.087  Score=46.93  Aligned_cols=24  Identities=29%  Similarity=0.398  Sum_probs=21.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..-+++.|++|+|||+|+.++.+.
T Consensus        16 ~~ki~ivG~~~vGKSsL~~~l~~~   39 (181)
T 1fzq_A           16 EVRILLLGLDNAGKTTLLKQLASE   39 (181)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCCS
T ss_pred             ceEEEEECCCCCCHHHHHHHHhcC
Confidence            346899999999999999999864

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*

Probab=94.21  E-value=0.088  Score=60.47  Aligned_cols=22  Identities=27%  Similarity=0.380  Sum_probs=19.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA  245 (480)
                      .+-++|.||.|+|||++++.++
T Consensus       789 g~i~~ItGpNgsGKSTlLr~iG  810 (1022)
T 2o8b_B          789 AYCVLVTGPNMGGKSTLMRQAG  810 (1022)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHH
T ss_pred             CcEEEEECCCCCChHHHHHHHH
Confidence            3568899999999999999984

>1xjc_A MOBB protein homolog; structural genomics, midwest center for structural GEN PSI, protein structure initiative, MCSG; 2.10A {Geobacillus stearothermophilus} SCOP: c.37.1.10

Probab=94.20  E-value=0.039  Score=49.96  Aligned_cols=33  Identities=15%  Similarity=0.231  Sum_probs=26.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      .-+.+.|++|+|||+++..++..+   |..+..+..
T Consensus         5 ~~i~i~G~sGsGKTTl~~~L~~~l~~~g~~v~~ik~   40 (169)
T 1xjc_A            5 NVWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVKH   40 (169)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEEEEECCCCCCHHHHHHHHHHhhHhcCCeeeEEEe
Confidence            358899999999999999999865   555555553

>2bov_A RAla, RAS-related protein RAL-A; C3BOT, exoenzyme, RAla, GTPase, ribosylating toxin, GTP-binding, lipoprotein, prenylation; HET: GDP; 2.66A {Homo sapiens}

Probab=94.20  E-value=0.079  Score=47.64  Aligned_cols=23  Identities=22%  Similarity=0.391  Sum_probs=20.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        15 ~ki~v~G~~~~GKSsli~~l~~~   37 (206)
T 2bov_A           15 HKVIMVGSGGVGKSALTLQFMYD   37 (206)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            36899999999999999999863

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=94.18  E-value=0.018  Score=53.72  Aligned_cols=23  Identities=35%  Similarity=0.447  Sum_probs=20.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-+.|.||+|+|||||+++++..
T Consensus        23 e~~~liG~nGsGKSTLl~~l~Gl   45 (208)
T 3b85_A           23 TIVFGLGPAGSGKTYLAMAKAVQ   45 (208)
T ss_dssp             SEEEEECCTTSSTTHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHhcC
Confidence            35789999999999999999975

>4i1u_A Dephospho-COA kinase; structural genomics, niaid, national institute of allergy AN infectious diseases; 2.05A {Burkholderia vietnamiensis} PDB: 4i1v_A*

Probab=94.16  E-value=0.028  Score=52.74  Aligned_cols=31  Identities=32%  Similarity=0.425  Sum_probs=28.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      .+-|.|..|||||++++.++. +|+++++.|.
T Consensus        11 ~iglTGgigsGKStv~~~l~~-~g~~vidaD~   41 (210)
T 4i1u_A           11 AIGLTGGIGSGKTTVADLFAA-RGASLVDTDL   41 (210)
T ss_dssp             EEEEECCTTSCHHHHHHHHHH-TTCEEEEHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHH-CCCcEEECcH
Confidence            578999999999999999998 9999988763

>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=94.12  E-value=0.025  Score=51.13  Aligned_cols=23  Identities=30%  Similarity=0.434  Sum_probs=20.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+.|.||+|+|||+|++.+++..
T Consensus        31 kv~lvG~~g~GKSTLl~~l~~~~   53 (191)
T 1oix_A           31 KVVLIGDSGVGKSNLLSRFTRNE   53 (191)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHhcCC
Confidence            47899999999999999999854

>2f9l_A RAB11B, member RAS oncogene family; RAB11B GTPase, vesicle transport, hydrolase; HET: GDP; 1.55A {Homo sapiens} SCOP: c.37.1.8 PDB: 2f9m_A* 1yzk_A* 2hv8_A* 2gzd_A* 2gzh_A* 2d7c_A* 3bfk_A*

Probab=94.11  E-value=0.026  Score=51.21  Aligned_cols=22  Identities=32%  Similarity=0.484  Sum_probs=20.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+.|.||+|+|||+|++.+++.
T Consensus         7 kv~lvG~~g~GKSTLl~~l~~~   28 (199)
T 2f9l_A            7 KVVLIGDSGVGKSNLLSRFTRN   28 (199)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            4889999999999999999985

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=94.11  E-value=0.054  Score=54.48  Aligned_cols=39  Identities=18%  Similarity=0.060  Sum_probs=31.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s  258 (480)
                      |+.+..-++|.|+||+|||+++..+|..   .+.++..+++.
T Consensus        42 Gl~~G~LiiIaG~pG~GKTt~al~ia~~~a~~g~~Vl~fSlE   83 (338)
T 4a1f_A           42 GFNKGSLVIIGARPSMGKTSLMMNMVLSALNDDRGVAVFSLE   83 (338)
T ss_dssp             SBCTTCEEEEEECTTSCHHHHHHHHHHHHHHTTCEEEEEESS
T ss_pred             CCCCCcEEEEEeCCCCCHHHHHHHHHHHHHHcCCeEEEEeCC
Confidence            5556666899999999999999999875   36777777653

>2f7s_A C25KG, RAS-related protein RAB-27B; G-protein, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2iez_A*

Probab=94.11  E-value=0.065  Score=48.98  Aligned_cols=22  Identities=32%  Similarity=0.474  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        27 ki~vvG~~~~GKSsLi~~l~~~   48 (217)
T 2f7s_A           27 KLLALGDSGVGKTTFLYRYTDN   48 (217)
T ss_dssp             EEEEESCTTSSHHHHHHHHHCS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999863

>1q57_A DNA primase/helicase; dntpase, DNA replication, transferase; HET: DNA; 3.45A {Enterobacteria phage T7} SCOP: c.37.1.11 e.13.1.2

Probab=94.03  E-value=0.036  Score=58.45  Aligned_cols=39  Identities=21%  Similarity=0.035  Sum_probs=30.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s  258 (480)
                      |+++..-++|.|+||+|||+++..+|..+    |.++..+++.
T Consensus       238 Gl~~G~l~li~G~pG~GKT~lal~~a~~~a~~~g~~vl~~s~E  280 (503)
T 1q57_A          238 GARGGEVIMVTSGSGMVMSTFVRQQALQWGTAMGKKVGLAMLE  280 (503)
T ss_dssp             CCCTTCEEEEEESSCHHHHHHHHHHHHHHTTTSCCCEEEEESS
T ss_pred             ccCCCeEEEEeecCCCCchHHHHHHHHHHHHhcCCcEEEEecc
Confidence            45555668999999999999999988643    5678888764

>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=94.03  E-value=0.026  Score=56.97  Aligned_cols=28  Identities=18%  Similarity=0.368  Sum_probs=24.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ..-+.|.||+|+|||||++.+++.+..+
T Consensus       170 g~k~~IvG~nGsGKSTLlk~L~gl~~~~  197 (365)
T 1lw7_A          170 AKTVAILGGESSGKSVLVNKLAAVFNTT  197 (365)
T ss_dssp             CEEEEEECCTTSHHHHHHHHHHHHTTCE
T ss_pred             hCeEEEECCCCCCHHHHHHHHHHHhCCC
Confidence            4568899999999999999999987654

>3bgw_A DNAB-like replicative helicase; ATPase, replication; 3.91A {Bacillus phage SPP1}

Probab=93.99  E-value=0.043  Score=57.17  Aligned_cols=39  Identities=26%  Similarity=0.202  Sum_probs=31.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      |+.+..-+++.|+||+|||+++..+|...   |.++..+++.
T Consensus       193 Gl~~G~liiIaG~pG~GKTtlal~ia~~~a~~g~~vl~fSlE  234 (444)
T 3bgw_A          193 GYKRRNFVLIAARPSMGKTAFALKQAKNMSDNDDVVNLHSLE  234 (444)
T ss_dssp             SBCSSCEEEEEECSSSSHHHHHHHHHHHHHHTTCEEEEECSS
T ss_pred             CCCCCcEEEEEeCCCCChHHHHHHHHHHHHHcCCEEEEEECC
Confidence            55555668999999999999999888644   6778887765

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=93.99  E-value=0.024  Score=61.59  Aligned_cols=33  Identities=30%  Similarity=0.372  Sum_probs=24.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLS  258 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s  258 (480)
                      ..++.||||||||+++..++..+    +..+..+..+
T Consensus       197 ~~li~GppGTGKT~~~~~~i~~l~~~~~~~ilv~a~t  233 (624)
T 2gk6_A          197 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAPS  233 (624)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTSSSCCEEEEESS
T ss_pred             CeEEECCCCCCHHHHHHHHHHHHHHcCCCeEEEEeCc
Confidence            57899999999999887776543    4456555544

>1sgw_A Putative ABC transporter; structural genomics, P protein structure initiative, southeast collaboratory for S genomics, secsg; 1.70A {Pyrococcus furiosus} SCOP: c.37.1.12

Probab=93.96  E-value=0.037  Score=51.89  Aligned_cols=27  Identities=19%  Similarity=0.444  Sum_probs=23.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .-+.|.||.|+|||||++++++.+...
T Consensus        36 e~~~iiG~NGsGKSTLlk~l~Gl~~p~   62 (214)
T 1sgw_A           36 NVVNFHGPNGIGKTTLLKTISTYLKPL   62 (214)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            357899999999999999999876543

>2dyk_A GTP-binding protein; GTPase, ribosome-binding protein, structural genomics; HET: GDP; 1.96A {Thermus thermophilus}

Probab=93.96  E-value=0.03  Score=48.16  Aligned_cols=22  Identities=23%  Similarity=0.311  Sum_probs=20.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (161)
T 2dyk_A            3 KVVIVGRPNVGKSSLFNRLLKK   24 (161)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999874

>1g6h_A High-affinity branched-chain amino acid transport ATP-binding protein; beta-core domain; HET: ADP; 1.60A {Methanocaldococcus jannaschii} SCOP: c.37.1.12 PDB: 1gaj_A 1g9x_A*

Probab=93.94  E-value=0.022  Score=54.78  Aligned_cols=26  Identities=31%  Similarity=0.664  Sum_probs=22.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-+.|.||+|+|||||++++++.+..
T Consensus        34 e~~~liG~nGsGKSTLlk~l~Gl~~p   59 (257)
T 1g6h_A           34 DVTLIIGPNGSGKSTLINVITGFLKA   59 (257)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCC
Confidence            34779999999999999999987754

>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=93.93  E-value=0.074  Score=55.14  Aligned_cols=60  Identities=20%  Similarity=0.166  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .+++.+.+.+...+....  ..+....+..+++.||+|+||||++..+|..+   +..+..+++.
T Consensus        73 ~~~~~v~~~L~~~~~~~~--~~i~l~~~~vi~i~G~~GsGKTT~~~~LA~~l~~~g~~Vllvd~D  135 (425)
T 2ffh_A           73 VILATVYEALKEALGGEA--RLPVLKDRNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD  135 (425)
T ss_dssp             HHHHHHHHHHHHHTTSSC--CCCCCCSSEEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEECC
T ss_pred             HHHHHHHHHHHHHhCCCc--ccccCCCCeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEeecc
Confidence            344555555554443211  11222235568889999999999999999765   5566666553

>1b0u_A Histidine permease; ABC transporter, transport protein; HET: ATP; 1.50A {Salmonella typhimurium} SCOP: c.37.1.12

Probab=93.93  E-value=0.025  Score=54.64  Aligned_cols=27  Identities=26%  Similarity=0.389  Sum_probs=22.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .-+.|.||+|+|||||++++++.+...
T Consensus        33 e~~~liG~nGsGKSTLlk~l~Gl~~p~   59 (262)
T 1b0u_A           33 DVISIIGSSGSGKSTFLRCINFLEKPS   59 (262)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            347799999999999999999977543

>2gf0_A GTP-binding protein DI-RAS1; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, transport protein; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=93.93  E-value=0.12  Score=46.03  Aligned_cols=22  Identities=27%  Similarity=0.543  Sum_probs=20.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      -.+++.|++|+|||+|+.++.+
T Consensus         9 ~ki~vvG~~~~GKSsli~~l~~   30 (199)
T 2gf0_A            9 YRVVVFGAGGVGKSSLVLRFVK   30 (199)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHH
T ss_pred             eEEEEECCCCCcHHHHHHHHHc
Confidence            3689999999999999999986

>1mv5_A LMRA, multidrug resistance ABC transporter ATP-binding and permease protein; asymmetric dimer, tetramer, P-glycoprotein; HET: ATP ADP; 3.10A {Lactococcus lactis} SCOP: c.37.1.12

Probab=93.90  E-value=0.025  Score=53.95  Aligned_cols=26  Identities=31%  Similarity=0.517  Sum_probs=22.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ..-+.|.||+|+|||||++++++.+.
T Consensus        28 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   53 (243)
T 1mv5_A           28 NSIIAFAGPSGGGKSTIFSLLERFYQ   53 (243)
T ss_dssp             TEEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCC
Confidence            34578999999999999999998653

>3sop_A Neuronal-specific septin-3; hydrolase; HET: GDP; 2.88A {Homo sapiens}

Probab=93.90  E-value=0.029  Score=54.46  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=20.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .+.|.||+|+|||||++++++..
T Consensus         4 ~v~lvG~nGaGKSTLln~L~g~~   26 (270)
T 3sop_A            4 NIMVVGQSGLGKSTLVNTLFKSQ   26 (270)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhCCC
Confidence            57899999999999999999865

>2pze_A Cystic fibrosis transmembrane conductance regulat; NBD, ABC transporter, CFTR, hydrolase; HET: ATP; 1.70A {Homo sapiens} PDB: 2pzg_A* 2pzf_A* 1ckx_A 1cky_A 1ckw_A 1ckz_A

Probab=93.85  E-value=0.024  Score=53.61  Aligned_cols=26  Identities=19%  Similarity=0.342  Sum_probs=22.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ..-+.|.||.|+|||||++++++.+.
T Consensus        34 Ge~~~i~G~nGsGKSTLl~~l~Gl~~   59 (229)
T 2pze_A           34 GQLLAVAGSTGAGKTSLLMMIMGELE   59 (229)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCCc
Confidence            34578999999999999999998764

>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=93.85  E-value=0.027  Score=57.19  Aligned_cols=23  Identities=30%  Similarity=0.603  Sum_probs=20.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+.|.||+|||||||.++||+..
T Consensus        32 ~~~llGpsGsGKSTLLr~iaGl~   54 (359)
T 3fvq_A           32 ILFIIGASGCGKTTLLRCLAGFE   54 (359)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTSS
T ss_pred             EEEEECCCCchHHHHHHHHhcCC
Confidence            47799999999999999999865

>1z2a_A RAS-related protein RAB-23; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 1.90A {Mus musculus} SCOP: c.37.1.8 PDB: 1z22_A*

Probab=93.84  E-value=0.031  Score=48.33  Aligned_cols=23  Identities=22%  Similarity=0.234  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         6 ~~i~v~G~~~~GKssl~~~l~~~   28 (168)
T 1z2a_A            6 IKMVVVGNGAVGKSSMIQRYCKG   28 (168)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             EEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999874

>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=93.82  E-value=0.015  Score=60.87  Aligned_cols=26  Identities=12%  Similarity=0.355  Sum_probs=23.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +.-|+|.|.||+|||++++.+|..++
T Consensus        39 ~~~IvlvGlpGsGKSTia~~La~~l~   64 (469)
T 1bif_A           39 PTLIVMVGLPARGKTYISKKLTRYLN   64 (469)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHH
T ss_pred             cEEEEEECCCCCCHHHHHHHHHHHHh
Confidence            44689999999999999999998764

>1ji0_A ABC transporter; ATP binding protein, structural genomics, PSI, protein structure initiative, midwest center for structural genomics, MCSG; HET: ATP; 2.00A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.78  E-value=0.025  Score=53.85  Aligned_cols=27  Identities=26%  Similarity=0.444  Sum_probs=23.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .-+.|.||.|+|||||++.+++.+...
T Consensus        33 e~~~l~G~nGsGKSTLl~~l~Gl~~p~   59 (240)
T 1ji0_A           33 QIVTLIGANGAGKTTTLSAIAGLVRAQ   59 (240)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCCCC
Confidence            347799999999999999999977543

>2ghi_A Transport protein; multidrug resistance protein, MDR, structural genomics, structural genomics consortium, SGC; 2.20A {Plasmodium yoelii yoelii str}

Probab=93.77  E-value=0.028  Score=54.25  Aligned_cols=27  Identities=30%  Similarity=0.448  Sum_probs=23.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+.|.||+|+|||||+++|++.+.
T Consensus        45 ~Ge~~~i~G~nGsGKSTLl~~l~Gl~~   71 (260)
T 2ghi_A           45 SGTTCALVGHTGSGKSTIAKLLYRFYD   71 (260)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhccCC
Confidence            334588999999999999999998764

>2d2e_A SUFC protein; ABC-ATPase, SUF protein, 310-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics, binding; 1.70A {Thermus thermophilus} PDB: 2d2f_A*

Probab=93.76  E-value=0.029  Score=53.81  Aligned_cols=23  Identities=35%  Similarity=0.551  Sum_probs=20.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-+.|.||+|+|||||++++++.
T Consensus        30 e~~~l~G~nGsGKSTLlk~l~Gl   52 (250)
T 2d2e_A           30 EVHALMGPNGAGKSTLGKILAGD   52 (250)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            35779999999999999999986

>2h57_A ADP-ribosylation factor-like protein 6; GTP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GTP; 2.00A {Homo sapiens}

Probab=93.76  E-value=0.032  Score=49.94  Aligned_cols=22  Identities=18%  Similarity=0.308  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~   44 (190)
T 2h57_A           23 HVLCLGLDNSGKTTIINKLKPS   44 (190)
T ss_dssp             EEEEEECTTSSHHHHHHHTSCG
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5999999999999999999754

>2ff7_A Alpha-hemolysin translocation ATP-binding protein HLYB; ABC-transporter, transport protein; HET: ADP; 1.60A {Escherichia coli} SCOP: c.37.1.12 PDB: 2ffb_A* 2fgk_A* 2ffa_A* 2fgj_A* 2pmk_A* 3b5j_A* 1mt0_A 1xef_A*

Probab=93.76  E-value=0.025  Score=54.13  Aligned_cols=28  Identities=25%  Similarity=0.383  Sum_probs=23.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ..-+.|.||+|+|||||++.|++.+...
T Consensus        35 Ge~~~i~G~nGsGKSTLl~~l~Gl~~p~   62 (247)
T 2ff7_A           35 GEVIGIVGRSGSGKSTLTKLIQRFYIPE   62 (247)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            3457899999999999999999977543

>2qi9_C Vitamin B12 import ATP-binding protein BTUD; inner membrane, membrane, transmembrane, transport, ATP- binding, hydrolase, nucleotide-binding, periplasm; HET: 1PE; 2.60A {Escherichia coli} PDB: 1l7v_C* 4dbl_C

Probab=93.75  E-value=0.038  Score=53.01  Aligned_cols=31  Identities=35%  Similarity=0.488  Sum_probs=25.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      .-+.|.||.|+|||||++++++.+... =.+.
T Consensus        27 e~~~liG~NGsGKSTLlk~l~Gl~~p~-G~i~   57 (249)
T 2qi9_C           27 EILHLVGPNGAGKSTLLARMAGMTSGK-GSIQ   57 (249)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCCE-EEEE
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCCCC-eEEE
Confidence            357899999999999999999987654 4443

>3gfo_A Cobalt import ATP-binding protein CBIO 1; structural genomics, cell membrane, cobalt transport, hydrolase, ION transport; 2.30A {Clostridium perfringens atcc 13124}

Probab=93.75  E-value=0.025  Score=55.18  Aligned_cols=25  Identities=20%  Similarity=0.400  Sum_probs=21.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||+|+|||||++++++.+.
T Consensus        35 e~~~iiGpnGsGKSTLl~~l~Gl~~   59 (275)
T 3gfo_A           35 EVTAILGGNGVGKSTLFQNFNGILK   59 (275)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHHcCCC
Confidence            3478999999999999999998663

>2fh5_B SR-beta, signal recognition particle receptor beta subunit; endomembrane targeting, GTPase, GAP, longin domain, SEDL, transport protein; HET: GTP; 2.45A {Mus musculus} SCOP: c.37.1.8 PDB: 2go5_2

Probab=93.74  E-value=0.085  Score=48.06  Aligned_cols=23  Identities=22%  Similarity=0.319  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         8 ~ki~vvG~~~~GKTsli~~l~~~   30 (214)
T 2fh5_B            8 RAVLFVGLCDSGKTLLFVRLLTG   30 (214)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             CEEEEECCCCCCHHHHHHHHhCC
Confidence            46999999999999999999863

>2olj_A Amino acid ABC transporter; ABC domain, ATPase, hydrolase; HET: ADP; 2.05A {Geobacillus stearothermophilus} PDB: 2olk_A* 2ouk_A 2q0h_A* 3c4j_A* 3c41_J*

Probab=93.73  E-value=0.029  Score=54.38  Aligned_cols=27  Identities=30%  Similarity=0.615  Sum_probs=23.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      ..-+.|.||+|+|||||++++++.+..
T Consensus        50 Gei~~liG~NGsGKSTLlk~l~Gl~~p   76 (263)
T 2olj_A           50 GEVVVVIGPSGSGKSTFLRCLNLLEDF   76 (263)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEEcCCCCcHHHHHHHHHcCCCC
Confidence            335779999999999999999987754

>4edh_A DTMP kinase, thymidylate kinase; structural genomics, PSI-biology; HET: TMP ADP; 1.32A {Pseudomonas aeruginosa PAO1} PDB: 4e5u_A* 4esh_A* 4gmd_A* 3uwk_A* 3uwo_A* 3uxm_A*

Probab=93.72  E-value=0.024  Score=53.09  Aligned_cols=31  Identities=29%  Similarity=0.322  Sum_probs=24.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      -|.|.||+|+||||+++.++..+   |.+++...
T Consensus         8 ~i~~eG~~gsGKsT~~~~l~~~l~~~~~~v~~~~   41 (213)
T 4edh_A            8 FVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTR   41 (213)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHcCCCccccc
Confidence            46788999999999999999876   45555443

>2ixe_A Antigen peptide transporter 1; ABC ATPase, hydrolase; HET: ATP; 2.0A {Rattus norvegicus} PDB: 2ixg_A* 2ixf_A* 1jj7_A*

Probab=93.72  E-value=0.029  Score=54.53  Aligned_cols=27  Identities=33%  Similarity=0.534  Sum_probs=23.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      ..-+.|.||+|+|||||++.|++.+..
T Consensus        45 Ge~~~i~G~nGsGKSTLlk~l~Gl~~p   71 (271)
T 2ixe_A           45 GKVTALVGPNGSGKSTVAALLQNLYQP   71 (271)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSCC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            345789999999999999999987643

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=93.62  E-value=0.037  Score=56.01  Aligned_cols=26  Identities=23%  Similarity=0.497  Sum_probs=23.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...++|.||+|+|||||++++++...
T Consensus       175 G~~i~ivG~sGsGKSTll~~l~~~~~  200 (361)
T 2gza_A          175 ERVIVVAGETGSGKTTLMKALMQEIP  200 (361)
T ss_dssp             TCCEEEEESSSSCHHHHHHHHHTTSC
T ss_pred             CCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            44689999999999999999998764

>1ek0_A Protein (GTP-binding protein YPT51); vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase; HET: MHO GNP GDP; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=93.61  E-value=0.038  Score=47.79  Aligned_cols=22  Identities=32%  Similarity=0.424  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1ek0_A            5 KLVLLGEAAVGKSSIVLRFVSN   26 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999863

>2zu0_C Probable ATP-dependent transporter SUFC; iron-sulfur cluster, ABC-ATPase, ATP-binding, cytoplasm, nucleotide-binding; HET: MES; 2.20A {Escherichia coli} PDB: 2d3w_A

Probab=93.60  E-value=0.035  Score=53.77  Aligned_cols=25  Identities=32%  Similarity=0.543  Sum_probs=21.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||.|+|||||++.|++..
T Consensus        46 Ge~~~l~G~NGsGKSTLlk~l~Gl~   70 (267)
T 2zu0_C           46 GEVHAIMGPNGSGKSTLSATLAGRE   70 (267)
T ss_dssp             TCEEEEECCTTSSHHHHHHHHHTCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCCC
Confidence            3457899999999999999999964

>2wji_A Ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GNP; 1.90A {Methanocaldococcus jannaschii} PDB: 2wjj_A* 2wjh_A*

Probab=93.60  E-value=0.032  Score=49.00  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+.|.|+||+|||+|+.++++.
T Consensus         5 ~v~lvG~~gvGKStL~~~l~~~   26 (165)
T 2wji_A            5 EIALIGNPNVGKSTIFNALTGE   26 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999863

>2ihy_A ABC transporter, ATP-binding protein; ATPase, ABC cassette, hydrolase; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=93.58  E-value=0.028  Score=54.91  Aligned_cols=27  Identities=22%  Similarity=0.597  Sum_probs=23.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .-+.|.||.|+|||||++++++.+...
T Consensus        48 e~~~liG~NGsGKSTLlk~l~Gl~~p~   74 (279)
T 2ihy_A           48 DKWILYGLNGAGKTTLLNILNAYEPAT   74 (279)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCCCC
Confidence            347899999999999999999977543

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=93.57  E-value=0.032  Score=56.47  Aligned_cols=25  Identities=32%  Similarity=0.506  Sum_probs=21.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||+|||||||.++||+...
T Consensus        42 e~~~llGpnGsGKSTLLr~iaGl~~   66 (355)
T 1z47_A           42 EMVGLLGPSGSGKTTILRLIAGLER   66 (355)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCCC
Confidence            3477999999999999999998663

>4g1u_C Hemin import ATP-binding protein HMUV; membrane transporter, type II ABC importer, HMUT, plasma MEM transport protein-hydrolase complex; 3.01A {Yersinia pestis}

Probab=93.52  E-value=0.028  Score=54.51  Aligned_cols=26  Identities=27%  Similarity=0.570  Sum_probs=22.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-+.|.||+|+|||||++++++.+..
T Consensus        38 e~~~liG~nGsGKSTLl~~l~Gl~~p   63 (266)
T 4g1u_C           38 EMVAIIGPNGAGKSTLLRLLTGYLSP   63 (266)
T ss_dssp             CEEEEECCTTSCHHHHHHHHTSSSCC
T ss_pred             CEEEEECCCCCcHHHHHHHHhcCCCC
Confidence            35779999999999999999987643

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=93.50  E-value=0.034  Score=56.49  Aligned_cols=24  Identities=38%  Similarity=0.600  Sum_probs=21.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -+.|.||+|||||||.++||+...
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (362)
T 2it1_A           31 FMALLGPSGSGKSTLLYTIAGIYK   54 (362)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCchHHHHHHHHhcCCC
Confidence            477999999999999999998663

>2nq2_C Hypothetical ABC transporter ATP-binding protein HI1470; putative iron chelatin ABC transporter, nucleotide binding domain; 2.40A {Haemophilus influenzae}

Probab=93.48  E-value=0.03  Score=53.89  Aligned_cols=25  Identities=20%  Similarity=0.351  Sum_probs=22.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||+|+|||||++++++.+.
T Consensus        32 e~~~l~G~nGsGKSTLl~~l~Gl~~   56 (253)
T 2nq2_C           32 DILAVLGQNGCGKSTLLDLLLGIHR   56 (253)
T ss_dssp             CEEEEECCSSSSHHHHHHHHTTSSC
T ss_pred             CEEEEECCCCCCHHHHHHHHhCCCC
Confidence            3578999999999999999998764

>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=93.48  E-value=0.038  Score=56.51  Aligned_cols=24  Identities=33%  Similarity=0.571  Sum_probs=21.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -+.|.||+|||||||+++||+...
T Consensus        31 ~~~llGpsGsGKSTLLr~iaGl~~   54 (381)
T 3rlf_A           31 FVVFVGPSGCGKSTLLRMIAGLET   54 (381)
T ss_dssp             EEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEcCCCchHHHHHHHHHcCCC
Confidence            477999999999999999998663

>1g16_A RAS-related protein SEC4; G protein RAB, signaling protein, endocytosis/exocytosis complex; HET: GDP; 1.80A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1g17_A* 2ocy_C 2eqb_A

Probab=93.48  E-value=0.04  Score=47.71  Aligned_cols=22  Identities=36%  Similarity=0.474  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         5 ~i~v~G~~~~GKssli~~l~~~   26 (170)
T 1g16_A            5 KILLIGDSGVGKSCLLVRFVED   26 (170)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5899999999999999999863

>1z0j_A RAB-22, RAS-related protein RAB-22A; RAB GTPase, RAB22 GTPase, rabenosyn, endosomal trafficking; HET: GTP; 1.32A {Mus musculus} SCOP: c.37.1.8 PDB: 1yvd_A*

Probab=93.48  E-value=0.041  Score=47.67  Aligned_cols=23  Identities=30%  Similarity=0.317  Sum_probs=20.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .+++.|++|+|||+|+.++.+.-
T Consensus         8 ~i~v~G~~~~GKSsli~~l~~~~   30 (170)
T 1z0j_A            8 KVCLLGDTGVGKSSIMWRFVEDS   30 (170)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHSC
T ss_pred             EEEEECcCCCCHHHHHHHHHcCC
Confidence            58999999999999999998743

>1vpl_A ABC transporter, ATP-binding protein; TM0544, structural GENO joint center for structural genomics, JCSG, protein structu initiative, PSI; 2.10A {Thermotoga maritima} SCOP: c.37.1.12

Probab=93.48  E-value=0.034  Score=53.62  Aligned_cols=26  Identities=23%  Similarity=0.507  Sum_probs=22.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-+.|.||.|+|||||++++++.+..
T Consensus        42 ei~~l~G~NGsGKSTLlk~l~Gl~~p   67 (256)
T 1vpl_A           42 EIFGLIGPNGAGKTTTLRIISTLIKP   67 (256)
T ss_dssp             CEEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             cEEEEECCCCCCHHHHHHHHhcCCCC
Confidence            35789999999999999999987643

>2yyz_A Sugar ABC transporter, ATP-binding protein; sugar transport, alpha and beta proteins (A/B) TM0421, structural genomics, NPPSFA; 2.11A {Thermotoga maritima}

Probab=93.48  E-value=0.038  Score=56.04  Aligned_cols=24  Identities=33%  Similarity=0.492  Sum_probs=21.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -+.|.||+|||||||.++||+...
T Consensus        31 ~~~llGpnGsGKSTLLr~iaGl~~   54 (359)
T 2yyz_A           31 FVALLGPSGCGKTTTLLMLAGIYK   54 (359)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEEcCCCchHHHHHHHHHCCCC
Confidence            477999999999999999998653

>3v9p_A DTMP kinase, thymidylate kinase; ssgcid, STRU genomics, seattle structural genomics center for infectious transferase; 1.90A {Burkholderia thailandensis}

Probab=93.47  E-value=0.04  Score=52.25  Aligned_cols=30  Identities=17%  Similarity=0.163  Sum_probs=21.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC-------CCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM-------SYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l-------~~~~~~i  255 (480)
                      -|.|.||+|+||||+++.++..+       |.+++..
T Consensus        27 ~I~~eG~~GsGKsT~~~~l~~~l~~~~~~~g~~v~~~   63 (227)
T 3v9p_A           27 FITFEGIDGAGKTTHLQWFCDRLQERLGPAGRHVVVT   63 (227)
T ss_dssp             EEEEECCC---CHHHHHHHHHHHHHHHGGGTCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhhccccceeeeee
Confidence            37788999999999999999877       5555544

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=93.44  E-value=0.034  Score=53.77  Aligned_cols=26  Identities=27%  Similarity=0.523  Sum_probs=22.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ..-+.|.||.|+|||||+++|++.+.
T Consensus        33 Ge~~~liG~nGsGKSTLl~~i~Gl~~   58 (266)
T 2yz2_A           33 GECLLVAGNTGSGKSTLLQIVAGLIE   58 (266)
T ss_dssp             TCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCEEEEECCCCCcHHHHHHHHhCCCC
Confidence            33577999999999999999998664

>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport; HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB: 1s8f_A* 1yzl_A* 2ocb_A*

Probab=93.43  E-value=0.042  Score=48.14  Aligned_cols=22  Identities=32%  Similarity=0.480  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         9 ~i~v~G~~~~GKSsli~~l~~~   30 (177)
T 1wms_A            9 KVILLGDGGVGKSSLMNRYVTN   30 (177)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>2nzj_A GTP-binding protein REM 1; GDP/GTP binding, GTP hydrolysis, RAD and GEM like GTP protein 1, structural genomics; HET: GDP; 2.50A {Homo sapiens}

Probab=93.42  E-value=0.035  Score=48.45  Aligned_cols=22  Identities=36%  Similarity=0.551  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|+||+|||+|+.++.+.
T Consensus         6 ki~i~G~~~vGKSsl~~~l~~~   27 (175)
T 2nzj_A            6 RVVLLGDPGVGKTSLASLFAGK   27 (175)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCccHHHHHHHHhcC
Confidence            5899999999999999999753

>2zej_A Dardarin, leucine-rich repeat kinase 2; parkinson'S disease, LRRK2, ROC, GTPase, ROCO, ATP-B disease mutation, GTP-binding, GTPase activation; HET: GDP; 2.00A {Homo sapiens} PDB: 3d6t_B*

Probab=93.41  E-value=0.029  Score=50.18  Aligned_cols=22  Identities=18%  Similarity=0.502  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|+||+|||+|++.+++.
T Consensus         4 kv~ivG~~gvGKStLl~~l~~~   25 (184)
T 2zej_A            4 KLMIVGNTGSGKTTLLQQLMKT   25 (184)
T ss_dssp             EEEEESCTTSSHHHHHHHHTCC
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            4889999999999999999873

>1v43_A Sugar-binding transport ATP-binding protein; ATPase, active transport, sugar uptake and regulation, transport protein; 2.20A {Pyrococcus horikoshii} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 1vci_A*

Probab=93.41  E-value=0.036  Score=56.53  Aligned_cols=24  Identities=33%  Similarity=0.546  Sum_probs=21.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.|.||+|||||||.++||+..
T Consensus        38 e~~~llGpnGsGKSTLLr~iaGl~   61 (372)
T 1v43_A           38 EFLVLLGPSGCGKTTTLRMIAGLE   61 (372)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHHcCC
Confidence            347799999999999999999865

>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport, maltose uptake and regulation, sugar binding protein; 1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3 c.37.1.12 PDB: 2d62_A

Probab=93.37  E-value=0.036  Score=56.45  Aligned_cols=24  Identities=33%  Similarity=0.558  Sum_probs=21.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.|.||+|||||||.++||+..
T Consensus        30 e~~~llGpnGsGKSTLLr~iaGl~   53 (372)
T 1g29_1           30 EFMILLGPSGCGKTTTLRMIAGLE   53 (372)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCcHHHHHHHHHHcCC
Confidence            347799999999999999999865

>2www_A Methylmalonic aciduria type A protein, mitochondrial; transport protein, nucleotide-binding; HET: GDP 2PE; 2.64A {Homo sapiens}

Probab=93.37  E-value=0.15  Score=51.29  Aligned_cols=24  Identities=33%  Similarity=0.544  Sum_probs=20.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.|.|+||+|||||+.++++.+
T Consensus        75 ~~v~lvG~pgaGKSTLln~L~~~~   98 (349)
T 2www_A           75 FRVGLSGPPGAGKSTFIEYFGKML   98 (349)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHh
Confidence            357799999999999999999753

>1z08_A RAS-related protein RAB-21; RAB GTPase, vesicular trafficking, protein transport; HET: GNP; 1.80A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ot3_B 1yzu_A* 1z0i_A 1yzt_A*

Probab=93.36  E-value=0.044  Score=47.56  Aligned_cols=22  Identities=23%  Similarity=0.312  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         8 ~i~v~G~~~~GKssli~~l~~~   29 (170)
T 1z08_A            8 KVVLLGEGCVGKTSLVLRYCEN   29 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHC
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>3tmk_A Thymidylate kinase; phosphotransferase; HET: T5A; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.1 PDB: 2tmk_A* 1tmk_A*

Probab=93.35  E-value=0.053  Score=50.98  Aligned_cols=28  Identities=18%  Similarity=0.176  Sum_probs=24.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      -|.+.||+|+||||+++.++..++.+..
T Consensus         7 ~i~~eG~~g~GKst~~~~l~~~l~~~~~   34 (216)
T 3tmk_A            7 LILIEGLDRTGKTTQCNILYKKLQPNCK   34 (216)
T ss_dssp             EEEEEECSSSSHHHHHHHHHHHHCSSEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhcccce
Confidence            4778899999999999999999986443

>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis, YPT/RAB protein, endocytosis, hydrolase, endocytosis/exocytosis complex; HET: GDP; 1.35A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*

Probab=93.32  E-value=0.045  Score=48.02  Aligned_cols=23  Identities=26%  Similarity=0.390  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         9 ~~i~v~G~~~~GKSsli~~l~~~   31 (182)
T 1ky3_A            9 LKVIILGDSGVGKTSLMHRYVND   31 (182)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHHhC
Confidence            36899999999999999999864

>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=93.32  E-value=0.12  Score=50.73  Aligned_cols=35  Identities=26%  Similarity=0.386  Sum_probs=27.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      ++.+.+.||+|+|||+++..+|..+   +..+..+++.
T Consensus        98 ~~~i~i~g~~G~GKTT~~~~la~~~~~~~~~v~l~~~d  135 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAAD  135 (295)
T ss_dssp             SEEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEecCC
Confidence            4567788999999999999999754   5566666553

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=93.28  E-value=0.034  Score=53.88  Aligned_cols=24  Identities=25%  Similarity=0.728  Sum_probs=21.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.|.||+|+|||||++++++.+
T Consensus        31 e~~~i~G~NGsGKSTLlk~l~Gl~   54 (263)
T 2pjz_A           31 EKVIILGPNGSGKTTLLRAISGLL   54 (263)
T ss_dssp             SEEEEECCTTSSHHHHHHHHTTSS
T ss_pred             EEEEEECCCCCCHHHHHHHHhCCC
Confidence            357899999999999999999876

>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=93.27  E-value=0.14  Score=48.02  Aligned_cols=30  Identities=13%  Similarity=-0.006  Sum_probs=22.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHc---CCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASF---MSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~---l~~~~~~i~  256 (480)
                      ++++||.|+|||+.+-.+|..   .|..++.+.
T Consensus        31 ~vitG~MgsGKTT~lL~~a~r~~~~g~kVli~k   63 (214)
T 2j9r_A           31 EVICGSMFSGKSEELIRRVRRTQFAKQHAIVFK   63 (214)
T ss_dssp             EEEECSTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHCCCEEEEEE
Confidence            458999999999888777653   366666665

>1r2q_A RAS-related protein RAB-5A; GTPase, GNP, atomic resolution, protein transport; HET: GNP; 1.05A {Homo sapiens} SCOP: c.37.1.8 PDB: 1n6h_A* 1tu4_A* 1tu3_A* 1n6k_A* 1n6i_A* 1n6l_A* 1n6o_A* 1n6p_A* 1n6n_A* 1n6r_A* 3mjh_A* 1z0d_A* 1huq_A* 2hei_A* 1z07_A*

Probab=93.27  E-value=0.047  Score=47.21  Aligned_cols=21  Identities=33%  Similarity=0.493  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus         8 ~i~v~G~~~~GKssli~~l~~   28 (170)
T 1r2q_A            8 KLVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999986

>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=93.25  E-value=0.043  Score=58.23  Aligned_cols=26  Identities=15%  Similarity=0.070  Sum_probs=23.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      ..|.|.|++||||||+++++|..++.
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            46889999999999999999999875

>2f1r_A Molybdopterin-guanine dinucleotide biosynthesis protein B (MOBB); structural genomics, PSI, protein structure initiative; 2.10A {Archaeoglobus fulgidus}

Probab=93.21  E-value=0.026  Score=51.10  Aligned_cols=24  Identities=21%  Similarity=0.416  Sum_probs=21.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .+.+.||+|+|||||++.+++.+.
T Consensus         4 ~v~IvG~SGsGKSTL~~~L~~~~~   27 (171)
T 2f1r_A            4 ILSIVGTSDSGKTTLITRMMPILR   27 (171)
T ss_dssp             EEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhh
Confidence            578999999999999999998763

>2wjg_A FEOB, ferrous iron transport protein B homolog; membrane G-proteins, cell membrane, ION transport, transmembrane; HET: GDP; 2.20A {Methanocaldococcus jannaschii}

Probab=93.19  E-value=0.043  Score=48.78  Aligned_cols=22  Identities=27%  Similarity=0.339  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+.|.|++|+|||+|+.++++.
T Consensus         9 ~i~lvG~~gvGKStL~~~l~~~   30 (188)
T 2wjg_A            9 EIALIGNPNVGKSTIFNALTGE   30 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5899999999999999999873

>3d31_A Sulfate/molybdate ABC transporter, ATP-binding protein; ATP-binding, nucleotide-binding, membrane, transmembrane, transport protein; 3.00A {Methanosarcina acetivorans} SCOP: b.40.6.3 c.37.1.12

Probab=93.17  E-value=0.035  Score=56.07  Aligned_cols=25  Identities=32%  Similarity=0.732  Sum_probs=21.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||+|||||||.+.||+...
T Consensus        27 e~~~llGpnGsGKSTLLr~iaGl~~   51 (348)
T 3d31_A           27 EYFVILGPTGAGKTLFLELIAGFHV   51 (348)
T ss_dssp             CEEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCccHHHHHHHHHcCCC
Confidence            3477999999999999999998663

>3cr8_A Sulfate adenylyltranferase, adenylylsulfate kinase; APS kinase, transferase, sulfate metabolism, nucleotide 2 kinase; 2.95A {Thiobacillus denitrificans}

Probab=93.17  E-value=0.034  Score=59.65  Aligned_cols=33  Identities=33%  Similarity=0.323  Sum_probs=26.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC----CcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS----YDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~----~~~~~i~~  257 (480)
                      ..+.|.||+||||||+++++|..++    ..+..++.
T Consensus       370 ~iI~LiG~sGSGKSTLar~La~~L~~~~G~~i~~lDg  406 (552)
T 3cr8_A          370 FTVFFTGLSGAGKSTLARALAARLMEMGGRCVTLLDG  406 (552)
T ss_dssp             EEEEEEESSCHHHHHHHHHHHHHHHTTCSSCEEEESS
T ss_pred             eEEEEECCCCChHHHHHHHHHHhhcccCCceEEEECC
Confidence            4578999999999999999999874    24544543

>2obl_A ESCN; ATPase, hydrolase; 1.80A {Escherichia coli O127} PDB: 2obm_A*

Probab=93.15  E-value=0.065  Score=53.99  Aligned_cols=28  Identities=25%  Similarity=0.352  Sum_probs=24.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      -+.|.||+|+|||+|++.|++....+..
T Consensus        73 ~~gIiG~nGaGKTTLl~~I~g~~~~~~g  100 (347)
T 2obl_A           73 RIGIFAGSGVGKSTLLGMICNGASADII  100 (347)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSCCSEE
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCCEE
Confidence            4789999999999999999998876543

>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=93.14  E-value=0.039  Score=59.79  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=19.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      +-+++.||||||||+++.++...
T Consensus       165 ~~~vi~G~pGTGKTt~l~~ll~~  187 (608)
T 1w36_D          165 RISVISGGPGTGKTTTVAKLLAA  187 (608)
T ss_dssp             SEEEEECCTTSTHHHHHHHHHHH
T ss_pred             CCEEEEeCCCCCHHHHHHHHHHH
Confidence            46899999999999998877654

>2hxs_A RAB-26, RAS-related protein RAB-28; GTPase, signaling protein; HET: G3D; 1.10A {Homo sapiens} PDB: 2hy4_A* 3e5h_A*

Probab=93.10  E-value=0.05  Score=47.68  Aligned_cols=21  Identities=24%  Similarity=0.520  Sum_probs=19.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|+||+|||+|+.++.+
T Consensus         8 ki~v~G~~~~GKssl~~~l~~   28 (178)
T 2hxs_A            8 KIVVLGDGASGKTSLTTCFAQ   28 (178)
T ss_dssp             EEEEECCTTSSHHHHHHHHHG
T ss_pred             EEEEECcCCCCHHHHHHHHHh
Confidence            589999999999999999975

>2y8e_A RAB-protein 6, GH09086P, RAB6; hydrolase, nucleotide binding, GTP binding; HET: GNP; 1.39A {Drosophila melanogaster} PDB: 3cwz_A* 1yzq_A* 2gil_A* 2e9s_A* 2fe4_A* 2ffq_A* 1d5c_A*

Probab=93.10  E-value=0.05  Score=47.56  Aligned_cols=21  Identities=19%  Similarity=0.387  Sum_probs=19.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus        16 ~i~v~G~~~~GKssli~~l~~   36 (179)
T 2y8e_A           16 KLVFLGEQSVGKTSLITRFMY   36 (179)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999985

>3bc1_A RAS-related protein RAB-27A; RAB27, GTPase, RAB, signaling protein, GDPNP, SLP2A, exophil GTP-binding, lipoprotein, membrane, methylation; HET: GNP; 1.80A {Mus musculus} PDB: 2iey_A* 2if0_A* 2zet_A*

Probab=93.10  E-value=0.05  Score=48.17  Aligned_cols=22  Identities=32%  Similarity=0.474  Sum_probs=20.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      -.+++.|++|+|||+|+.++.+
T Consensus        12 ~ki~v~G~~~~GKSsli~~l~~   33 (195)
T 3bc1_A           12 IKFLALGDSGVGKTSVLYQYTD   33 (195)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEEECCCCCCHHHHHHHHhc
Confidence            3689999999999999999986

>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=93.07  E-value=0.046  Score=48.06  Aligned_cols=23  Identities=35%  Similarity=0.483  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -.+++||.|+|||+++.||.-.+
T Consensus        25 ~~~I~G~NGsGKStil~Ai~~~l   47 (149)
T 1f2t_A           25 INLIIGQNGSGKSSLLDAILVGL   47 (149)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH
Confidence            46899999999999999998644

>3q85_A GTP-binding protein REM 2; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.76A {Mus musculus} SCOP: c.37.1.8 PDB: 4aii_A*

Probab=93.05  E-value=0.05  Score=47.25  Aligned_cols=21  Identities=38%  Similarity=0.653  Sum_probs=19.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|+||+|||+|+.++.+
T Consensus         4 ki~ivG~~~~GKSsli~~l~~   24 (169)
T 3q85_A            4 KVMLVGESGVGKSTLAGTFGG   24 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            388999999999999999974

>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=93.02  E-value=0.064  Score=53.97  Aligned_cols=32  Identities=22%  Similarity=0.238  Sum_probs=25.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      .-+.|.|+||+|||+++.+++..+   |..+..++
T Consensus        80 ~~I~i~G~~G~GKSTl~~~L~~~l~~~g~kV~vi~  114 (355)
T 3p32_A           80 HRVGITGVPGVGKSTAIEALGMHLIERGHRVAVLA  114 (355)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhCCCceEEEe
Confidence            468899999999999999998765   55554444

>3q72_A GTP-binding protein RAD; G-domain, CAV2 beta, signaling protein; HET: GNP; 1.66A {Homo sapiens} SCOP: c.37.1.8 PDB: 3q7p_A* 3q7q_A* 2gjs_A* 2dpx_A*

Probab=93.00  E-value=0.047  Score=47.25  Aligned_cols=21  Identities=38%  Similarity=0.627  Sum_probs=19.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|+||+|||+|+.++.+
T Consensus         4 ki~~vG~~~~GKSsli~~l~~   24 (166)
T 3q72_A            4 KVLLLGAPGVGKSALARIFGG   24 (166)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHcC
Confidence            489999999999999999964

>1upt_A ARL1, ADP-ribosylation factor-like protein 1; hydrolase/protein-binding, complex (GTPase/golgin), golgin-245, GRIP, golgin, GTPase, G-protein; HET: GTP; 1.7A {Homo sapiens} SCOP: c.37.1.8 PDB: 1r4a_A*

Probab=92.91  E-value=0.071  Score=46.23  Aligned_cols=23  Identities=22%  Similarity=0.418  Sum_probs=20.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ...+++.|++|+|||+|+.++.+
T Consensus         7 ~~~i~v~G~~~~GKssl~~~l~~   29 (171)
T 1upt_A            7 EMRILILGLDGAGKTTILYRLQV   29 (171)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHH
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            34689999999999999999976

>2atv_A RERG, RAS-like estrogen-regulated growth inhibitor; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.88  E-value=0.063  Score=48.30  Aligned_cols=24  Identities=21%  Similarity=0.455  Sum_probs=21.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-.+++.|++|+|||+|+.++.+.
T Consensus        28 ~~ki~v~G~~~vGKSsli~~l~~~   51 (196)
T 2atv_A           28 EVKLAIFGRAGVGKSALVVRFLTK   51 (196)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHS
T ss_pred             ceEEEEECCCCCCHHHHHHHHHhC
Confidence            446999999999999999999864

>3gd7_A Fusion complex of cystic fibrosis transmembrane conductance regulator, residues 1193-1427...; CFTR, ABC transporter, nucleotide binding domain, NBD; HET: B44; 2.70A {Homo sapiens}

Probab=92.88  E-value=0.047  Score=56.00  Aligned_cols=25  Identities=28%  Similarity=0.492  Sum_probs=21.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||+|||||||+++||+..
T Consensus        47 Ge~~~llGpsGsGKSTLLr~iaGl~   71 (390)
T 3gd7_A           47 GQRVGLLGRTGSGKSTLLSAFLRLL   71 (390)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHHTCS
T ss_pred             CCEEEEECCCCChHHHHHHHHhCCC
Confidence            3457899999999999999999854

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=92.88  E-value=0.041  Score=61.59  Aligned_cols=32  Identities=28%  Similarity=0.361  Sum_probs=22.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDL  257 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~  257 (480)
                      -.++.||||||||+++..++..+    +..+..+..
T Consensus       373 ~~lI~GppGTGKT~ti~~~i~~l~~~~~~~ilv~a~  408 (800)
T 2wjy_A          373 LSLIQGPPGTGKTVTSATIVYHLARQGNGPVLVCAP  408 (800)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTCSSCEEEEES
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHHHHcCCCcEEEEcC
Confidence            57899999999999887776543    344544443

>4dsu_A GTPase KRAS, isoform 2B; small G-protein, signaling, hydrolase; HET: GDP; 1.70A {Homo sapiens} PDB: 4dsn_A* 4dst_A* 4dso_A*

Probab=92.88  E-value=0.056  Score=47.75  Aligned_cols=22  Identities=23%  Similarity=0.462  Sum_probs=20.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+.++.+.
T Consensus         6 ki~v~G~~~~GKSsli~~l~~~   27 (189)
T 4dsu_A            6 KLVVVGADGVGKSALTIQLIQN   27 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999864

>1z0f_A RAB14, member RAS oncogene family; RAB GTPase, vesicular trafficking, protein transport; HET: GDP; 2.15A {Homo sapiens} SCOP: c.37.1.8 PDB: 2aed_A* 4drz_A*

Probab=92.88  E-value=0.057  Score=47.16  Aligned_cols=23  Identities=26%  Similarity=0.460  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        16 ~~i~v~G~~~~GKSsli~~l~~~   38 (179)
T 1z0f_A           16 FKYIIIGDMGVGKSCLLHQFTEK   38 (179)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            36999999999999999999864

>3clv_A RAB5 protein, putative; malaria, GTPase, structural genomics, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.89A {Plasmodium falciparum}

Probab=92.87  E-value=0.056  Score=48.09  Aligned_cols=23  Identities=30%  Similarity=0.340  Sum_probs=20.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      --+++.|++|+|||+|+.++.+.
T Consensus         8 ~ki~v~G~~~~GKSsli~~l~~~   30 (208)
T 3clv_A            8 YKTVLLGESSVGKSSIVLRLTKD   30 (208)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            35899999999999999999875

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=92.87  E-value=0.097  Score=54.51  Aligned_cols=24  Identities=25%  Similarity=0.382  Sum_probs=20.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+-.++.|+||||||+++..+++.
T Consensus       161 ~~v~~I~G~aGsGKTt~I~~~~~~  184 (446)
T 3vkw_A          161 AKVVLVDGVPGCGKTKEILSRVNF  184 (446)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHCCT
T ss_pred             ccEEEEEcCCCCCHHHHHHHHhcc
Confidence            345689999999999999888753

>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=92.85  E-value=0.074  Score=47.49  Aligned_cols=24  Identities=33%  Similarity=0.367  Sum_probs=21.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ...+++.|++|+|||+|+.++.+.
T Consensus        23 ~~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 1svi_A           23 LPEIALAGRSNVGKSSFINSLINR   46 (195)
T ss_dssp             CCEEEEEEBTTSSHHHHHHHHHTC
T ss_pred             CCEEEEECCCCCCHHHHHHHHhCC
Confidence            346999999999999999999864

>2fn4_A P23, RAS-related protein R-RAS; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 1.65A {Homo sapiens} SCOP: c.37.1.8 PDB: 2ery_A*

Probab=92.84  E-value=0.057  Score=47.27  Aligned_cols=23  Identities=22%  Similarity=0.408  Sum_probs=20.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        10 ~~i~v~G~~~~GKssli~~l~~~   32 (181)
T 2fn4_A           10 HKLVVVGGGGVGKSALTIQFIQS   32 (181)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            36899999999999999999874

>1tf7_A KAIC; homohexamer, hexamer, circadian clock protein; HET: ATP; 2.80A {Synechococcus SP} SCOP: c.37.1.11 c.37.1.11 PDB: 3s1a_A* 1u9i_A* 2gbl_A* 3dvl_A* 3k0a_A* 3k09_A* 3jzm_A* 3k0e_A* 4dug_A* 3ua2_A* 3k0c_A* 3k0f_A*

Probab=92.84  E-value=0.051  Score=57.73  Aligned_cols=25  Identities=44%  Similarity=0.594  Sum_probs=20.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHH
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAM  244 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~ai  244 (480)
                      +++...-++|.||+|||||+|++.+
T Consensus        35 ~i~~Ge~~~l~G~nGsGKSTL~~~~   59 (525)
T 1tf7_A           35 GLPIGRSTLVSGTSGTGKTLFSIQF   59 (525)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHH
T ss_pred             CCCCCeEEEEEcCCCCCHHHHHHHH
Confidence            3445567899999999999999994

>2gj8_A MNME, tRNA modification GTPase TRME; G-domain dimer, alpha-beta-sandwich, hydrolase; HET: GDP; 1.70A {Escherichia coli BL21} SCOP: c.37.1.8 PDB: 2gj9_A* 2gja_A* 1rfl_A

Probab=92.83  E-value=0.051  Score=48.18  Aligned_cols=22  Identities=32%  Similarity=0.425  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+.|.|+||+|||+|+.++++.
T Consensus         6 ki~ivG~~g~GKStLl~~l~~~   27 (172)
T 2gj8_A            6 KVVIAGRPNAGKSSLLNALAGR   27 (172)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            5889999999999999999974

>2lkc_A Translation initiation factor IF-2; NMR {Geobacillus stearothermophilus} PDB: 2lkd_A*

Probab=92.83  E-value=0.066  Score=46.90  Aligned_cols=23  Identities=17%  Similarity=0.283  Sum_probs=20.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ..-+++.|++|+|||+|+.++.+
T Consensus         8 ~~~i~v~G~~~~GKssl~~~l~~   30 (178)
T 2lkc_A            8 PPVVTIMGHVDHGKTTLLDAIRH   30 (178)
T ss_dssp             CCEEEEESCTTTTHHHHHHHHHT
T ss_pred             CCEEEEECCCCCCHHHHHHHHhC
Confidence            34689999999999999999976

>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=92.83  E-value=0.047  Score=52.03  Aligned_cols=24  Identities=21%  Similarity=0.357  Sum_probs=21.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-|.+.||+|+||||+++.++..+
T Consensus        28 ~~i~~eG~~GsGKsT~~~~l~~~l   51 (236)
T 3lv8_A           28 KFIVIEGLEGAGKSTAIQVVVETL   51 (236)
T ss_dssp             CEEEEEESTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHH
Confidence            357889999999999999999866

>1tq4_A IIGP1, interferon-inducible GTPase; interferon gamma, dimer, immunology, signaling protein; HET: GDP; 1.95A {Mus musculus} SCOP: c.37.1.8 PDB: 1tqd_A* 1tq6_A* 1tpz_A* 1tq2_A*

Probab=92.83  E-value=0.076  Score=54.86  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=20.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+.|.||+|+|||||++++++..
T Consensus        71 ~valvG~nGaGKSTLln~L~Gl~   93 (413)
T 1tq4_A           71 NVAVTGETGSGKSSFINTLRGIG   93 (413)
T ss_dssp             EEEEEECTTSSHHHHHHHHHTCC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            46799999999999999999843

>2bbs_A Cystic fibrosis transmembrane conductance regulator; ATP binding cassette, transport protein; HET: ATP; 2.05A {Homo sapiens} PDB: 2bbt_A* 1xmi_A* 1xmj_A* 2bbo_A* 3si7_A* 1r0w_A 1q3h_A 1r0x_A* 1r0y_A* 1r0z_A* 1r10_A* 1xf9_A* 1xfa_A*

Probab=92.82  E-value=0.047  Score=53.63  Aligned_cols=25  Identities=20%  Similarity=0.353  Sum_probs=21.8

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.||.|+|||||+++|++.+
T Consensus        64 Ge~~~i~G~NGsGKSTLlk~l~Gl~   88 (290)
T 2bbs_A           64 GQLLAVAGSTGAGKTSLLMMIMGEL   88 (290)
T ss_dssp             TCEEEEEESTTSSHHHHHHHHTTSS
T ss_pred             CCEEEEECCCCCcHHHHHHHHhcCC
Confidence            3357899999999999999999866

>1moz_A ARL1, ADP-ribosylation factor-like protein 1; GTP-binding, protein binding; HET: GDP; 3.17A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=92.81  E-value=0.072  Score=46.94  Aligned_cols=24  Identities=21%  Similarity=0.335  Sum_probs=20.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ....+++.|++|+|||+|+.++.+
T Consensus        17 ~~~~i~v~G~~~~GKssli~~l~~   40 (183)
T 1moz_A           17 KELRILILGLDGAGKTTILYRLQI   40 (183)
T ss_dssp             SCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CccEEEEECCCCCCHHHHHHHHhc
Confidence            345799999999999999998873

>1oxx_K GLCV, glucose, ABC transporter, ATP binding protein; ABC-ATPase, ATP-binding cassette, ATPase, transport protein; 1.45A {Sulfolobus solfataricus} SCOP: b.40.6.3 c.37.1.12 PDB: 1oxs_C 1oxt_A 1oxu_A* 1oxv_A*

Probab=92.80  E-value=0.034  Score=56.24  Aligned_cols=24  Identities=33%  Similarity=0.685  Sum_probs=21.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.|.||+|||||||.++||+..
T Consensus        32 e~~~llGpnGsGKSTLLr~iaGl~   55 (353)
T 1oxx_K           32 ERFGILGPSGAGKTTFMRIIAGLD   55 (353)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHhCCC
Confidence            347799999999999999999865

>1m7b_A RND3/RHOE small GTP-binding protein; small GTPase, signaling protein; HET: GTP; 2.00A {Homo sapiens} SCOP: c.37.1.8 PDB: 2v55_B*

Probab=92.80  E-value=0.058  Score=48.05  Aligned_cols=23  Identities=22%  Similarity=0.268  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      --+++.|++|+|||+|+.++.+.
T Consensus         8 ~ki~v~G~~~vGKSsli~~l~~~   30 (184)
T 1m7b_A            8 CKIVVVGDSQCGKTALLHVFAKD   30 (184)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999999874

>2bme_A RAB4A, RAS-related protein RAB4A; GTP-binding protein, vesicular transport, endocytosis, prenylation, protein transport, transport; HET: GNP; 1.57A {Homo sapiens} SCOP: c.37.1.8 PDB: 2bmd_A* 1yu9_A* 1z0k_A*

Probab=92.80  E-value=0.058  Score=47.72  Aligned_cols=23  Identities=30%  Similarity=0.473  Sum_probs=20.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      --+++.|++|+|||+|+.++.+.
T Consensus        11 ~ki~v~G~~~~GKSsli~~l~~~   33 (186)
T 2bme_A           11 FKFLVIGNAGTGKSCLLHQFIEK   33 (186)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            35899999999999999999863

>2oil_A CATX-8, RAS-related protein RAB-25; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.30A {Homo sapiens}

Probab=92.77  E-value=0.059  Score=48.22  Aligned_cols=23  Identities=26%  Similarity=0.410  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      -.+++.|++|+|||+|+.++.+.
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~~   48 (193)
T 2oil_A           26 FKVVLIGESGVGKTNLLSRFTRN   48 (193)
T ss_dssp             EEEEEESSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHhcC
Confidence            36899999999999999999873

>2efe_B Small GTP-binding protein-like; GEF, GTPase, VPS9, nucleotide, transport protein; HET: GNH; 2.08A {Arabidopsis thaliana} PDB: 2efd_B 2efc_B* 2efh_B*

Probab=92.75  E-value=0.061  Score=47.27  Aligned_cols=23  Identities=30%  Similarity=0.424  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        13 ~ki~v~G~~~~GKSsli~~l~~~   35 (181)
T 2efe_B           13 AKLVLLGDVGAGKSSLVLRFVKD   35 (181)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            35899999999999999999863

>2dpy_A FLII, flagellum-specific ATP synthase; beta barrel, alpha-beta structure, hydrolase; HET: ADP; 2.40A {Salmonella typhimurium}

Probab=92.72  E-value=0.079  Score=55.12  Aligned_cols=27  Identities=37%  Similarity=0.498  Sum_probs=23.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      -+.|.||+|||||+|++.||+....+.
T Consensus       159 ~~~IvG~sGsGKSTLl~~Iag~~~~~~  185 (438)
T 2dpy_A          159 RMGLFAGSGVGKSVLLGMMARYTRADV  185 (438)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHSCCSE
T ss_pred             EEEEECCCCCCHHHHHHHHhcccCCCe
Confidence            478999999999999999999886553

>3con_A GTPase NRAS; structural genomics consortium, SGC, GDP, oncogene, disease mutation, golgi apparatus, GTP-binding, lipoprotein membrane, methylation; HET: GDP; 1.65A {Homo sapiens} PDB: 2pmx_A* 3gft_A* 4q21_A*

Probab=92.69  E-value=0.062  Score=47.87  Aligned_cols=22  Identities=23%  Similarity=0.460  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++++.
T Consensus        23 ki~vvG~~~~GKSsli~~l~~~   44 (190)
T 3con_A           23 KLVVVGAGGVGKSALTIQLIQN   44 (190)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHcC
Confidence            5899999999999999999864

>2cxx_A Probable GTP-binding protein ENGB; structural genomics, NPPSFA, national P protein structural and functional analyses; HET: GDP; 1.70A {Pyrococcus horikoshii} SCOP: c.37.1.8

Probab=92.61  E-value=0.054  Score=48.01  Aligned_cols=22  Identities=23%  Similarity=0.366  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         3 ki~v~G~~~~GKSsli~~l~~~   24 (190)
T 2cxx_A            3 TIIFAGRSNVGKSTLIYRLTGK   24 (190)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCc
Confidence            4889999999999999999863

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=92.57  E-value=0.59  Score=44.37  Aligned_cols=103  Identities=12%  Similarity=0.153  Sum_probs=56.5

Q ss_pred             eEEEEccCCCcHHHHHHHHH-H--cCCCcEEEEeCCC--cCChHHH----------------HHHHHhhcCCcEEEEecc
Q 011664          226 SYLLYGPSGTGKSSFAAAMA-S--FMSYDVYDVDLSR--VADDADL----------------KSLLLQTTSKSVILIEDL  284 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA-~--~l~~~~~~i~~s~--~~~~~~l----------------~~l~~~~~~~sII~IDEi  284 (480)
                      -.++|||.|+|||+.+-..+ +  ..|..++.+....  -.+ ..+                ..++.......+|+|||+
T Consensus        21 l~v~~G~MgsGKTT~lL~~~~r~~~~g~kvli~kp~~D~Ryg-~~i~sr~G~~~~a~~i~~~~di~~~~~~~dvViIDEa   99 (234)
T 2orv_A           21 IQVILGPMFSGKSTELMRRVRRFQIAQYKCLVIKYAKDTRYS-SSFCTHDRNTMEALPACLLRDVAQEALGVAVIGIDEG   99 (234)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEEEETTCCCC------------CEEEEESSGGGGHHHHTTCSEEEESSG
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEeecCCccch-HHHHhhcCCeeEEEecCCHHHHHHHhccCCEEEEEch
Confidence            46788999999996555444 3  3355555554211  001 111                112223345689999999


Q ss_pred             cccccCcccccchhhhhhhcccccccccCCceEEEEec------CCCccCcccccCCCceeEEEEcC
Q 011664          285 DRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTM------NSKDHVDQALLRPGRIDVHIHFP  345 (480)
Q Consensus       285 D~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tT------N~~~~LD~aLlrpGRfd~~I~~~  345 (480)
                      .-+.     .  +.++++.++.       .+.-||+|.      +.|..-.+.|+-  .-|.+.++.
T Consensus       100 QF~~-----~--v~el~~~l~~-------~gi~VI~~GL~~DF~~~~F~~~~~Ll~--~AD~Vtelk  150 (234)
T 2orv_A          100 QFFP-----D--IVEFCEAMAN-------AGKTVIVAALDGTFQRKPFGAILNLVP--LAESVVKLT  150 (234)
T ss_dssp             GGCT-----T--HHHHHHHHHH-------TTCEEEEECCSBCTTSSBCTTGGGGGG--GCSEEEECC
T ss_pred             hhhh-----h--HHHHHHHHHh-------CCCEEEEEecccccccCCcccHHHHHH--hcccEEeee
Confidence            9762     1  5667776654       123344442      234445666765  666666654

>3b1v_A Ferrous iron uptake transporter protein B; G protein, iron transport, GTPase, transmembrane, potassium; HET: GGM; 1.85A {Streptococcus thermophilus} PDB: 3b1w_A* 3lx5_A* 3lx8_A* 3ss8_A* 3b1z_A 3b1y_A* 3b1x_A* 3tah_A*

Probab=92.56  E-value=0.23  Score=48.03  Aligned_cols=22  Identities=23%  Similarity=0.375  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+.|.|+||+|||+|..++.+.
T Consensus         5 kI~lvG~~nvGKSTL~n~L~g~   26 (272)
T 3b1v_A            5 EIALIGNPNSGKTSLFNLITGH   26 (272)
T ss_dssp             EEEEECCTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            5889999999999999999863

>3tw8_B RAS-related protein RAB-35; longin domain, RAB GTPase, guanine exchange factor; 2.10A {Homo sapiens}

Probab=92.56  E-value=0.06  Score=47.14  Aligned_cols=21  Identities=43%  Similarity=0.613  Sum_probs=19.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus        11 ~i~v~G~~~~GKssl~~~l~~   31 (181)
T 3tw8_B           11 KLLIIGDSGVGKSSLLLRFAD   31 (181)
T ss_dssp             EEEEECCTTSCHHHHHHHHCS
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999975

>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=92.48  E-value=0.097  Score=49.45  Aligned_cols=34  Identities=24%  Similarity=0.563  Sum_probs=26.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC--CCcEEEEeCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM--SYDVYDVDLS  258 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l--~~~~~~i~~s  258 (480)
                      ..+++.|++|+||||++..+|..+  |..+..+++.
T Consensus        15 ~i~~~~GkgGvGKTTl~~~La~~l~~g~~v~vvd~D   50 (262)
T 1yrb_A           15 MIVVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVNLD   50 (262)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHTTTSCEEEEECC
T ss_pred             EEEEEeCCCCCCHHHHHHHHHHHHHCCCeEEEEeCC
Confidence            357789999999999999999765  5666666543

>2npi_A Protein CLP1; CLP1-PCF11 complex, ATP binding, ternary complex, transcript; HET: ATP; 2.95A {Saccharomyces cerevisiae}

Probab=92.43  E-value=0.063  Score=56.25  Aligned_cols=26  Identities=27%  Similarity=0.400  Sum_probs=22.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ...-+.|.||.|+|||||++.+++.+
T Consensus       137 ~Ge~v~IvGpnGsGKSTLlr~L~Gl~  162 (460)
T 2npi_A          137 EGPRVVIVGGSQTGKTSLSRTLCSYA  162 (460)
T ss_dssp             SCCCEEEEESTTSSHHHHHHHHHHTT
T ss_pred             CCCEEEEECCCCCCHHHHHHHHhCcc
Confidence            33458899999999999999999865

>2g6b_A RAS-related protein RAB-26; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, unknown function; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=92.43  E-value=0.071  Score=46.77  Aligned_cols=23  Identities=26%  Similarity=0.355  Sum_probs=20.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      -.+++.|++|+|||+|+.++.+.
T Consensus        11 ~~i~v~G~~~~GKssli~~l~~~   33 (180)
T 2g6b_A           11 FKVMLVGDSGVGKTCLLVRFKDG   33 (180)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHhC
Confidence            35899999999999999999863

>1mh1_A RAC1; GTP-binding, GTPase, small G-protein, RHO family, RAS super family; HET: GNP; 1.38A {Homo sapiens} SCOP: c.37.1.8 PDB: 1hh4_A* 2p2l_A* 2h7v_A* 1g4u_R* 1i4d_D* 1i4l_D* 2vrw_A 1e96_A* 1i4t_D* 2rmk_A* 2yin_C 1ryf_A* 1ryh_A* 3su8_A* 3sua_A* 2fju_A* 1he1_C* 2nz8_A 1foe_B 3bji_C ...

Probab=92.42  E-value=0.071  Score=46.95  Aligned_cols=22  Identities=14%  Similarity=0.308  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus         7 ~i~~~G~~~~GKssl~~~l~~~   28 (186)
T 1mh1_A            7 KCVVVGDGAVGKTCLLISYTTN   28 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            5899999999999999999863

>2gf9_A RAS-related protein RAB-3D; G-protein, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.53A {Homo sapiens} PDB: 3rab_A*

Probab=92.41  E-value=0.07  Score=47.60  Aligned_cols=22  Identities=41%  Similarity=0.460  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        24 ki~vvG~~~~GKSsli~~l~~~   45 (189)
T 2gf9_A           24 KLLLIGNSSVGKTSFLFRYADD   45 (189)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHcC
Confidence            6899999999999999999864

>3kkq_A RAS-related protein M-RAS; GTP-binding, GTPase, signaling protein; HET: GDP; 1.20A {Mus musculus} SCOP: c.37.1.8 PDB: 3kkp_A* 3kko_A* 3pit_A* 3pir_A* 1x1r_A* 1x1s_A*

Probab=92.41  E-value=0.071  Score=47.06  Aligned_cols=23  Identities=22%  Similarity=0.358  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      -.+++.|++|+|||+|+.++.+.
T Consensus        19 ~ki~v~G~~~~GKSsl~~~l~~~   41 (183)
T 3kkq_A           19 YKLVVVGDGGVGKSALTIQFFQK   41 (183)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHS
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            36899999999999999999864

>1m2o_B GTP-binding protein SAR1, GTP binding protein; zinc-finger, beta barrel, VWA domain, gelsolin domain,; HET: GNP; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 2qtv_B*

Probab=92.35  E-value=0.071  Score=48.00  Aligned_cols=21  Identities=19%  Similarity=0.434  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|+||+|||+|+.++.+
T Consensus        25 ki~~vG~~~vGKSsli~~l~~   45 (190)
T 1m2o_B           25 KLLFLGLDNAGKTTLLHMLKN   45 (190)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999997

>1ko7_A HPR kinase/phosphatase; protein kinase, phosphotransfer, protein phosphatase, dual activity, product, substrate, transferase, hydrolase; 1.95A {Staphylococcus xylosus} SCOP: c.98.2.1 c.91.1.2

Probab=92.32  E-value=0.097  Score=52.06  Aligned_cols=28  Identities=29%  Similarity=0.299  Sum_probs=23.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      .+|++|.|++|+|||++|.++... |..+
T Consensus       144 g~~vl~~G~sG~GKSt~a~~l~~~-g~~l  171 (314)
T 1ko7_A          144 GVGVLITGDSGIGKSETALELIKR-GHRL  171 (314)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHhc-CCce
Confidence            468999999999999999999875 4433

>1pui_A ENGB, probable GTP-binding protein ENGB; structural genomics, nysgxrc T16, GTPase, PSI, protein structure initiative; 2.00A {Escherichia coli} SCOP: c.37.1.8

Probab=92.31  E-value=0.035  Score=50.51  Aligned_cols=25  Identities=24%  Similarity=0.194  Sum_probs=20.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.|.|++|+|||+|++++++..
T Consensus        26 ~~~v~lvG~~g~GKSTLl~~l~g~~   50 (210)
T 1pui_A           26 GIEVAFAGRSNAGKSSALNTLTNQK   50 (210)
T ss_dssp             SEEEEEEECTTSSHHHHHTTTCCC-
T ss_pred             CcEEEEECCCCCCHHHHHHHHhCCC
Confidence            3358899999999999999987643

>4tmk_A Protein (thymidylate kinase); ATP:DTMP phosphotransferase, transferase; HET: T5A; 1.98A {Escherichia coli} SCOP: c.37.1.1 PDB: 5tmp_A*

Probab=92.31  E-value=0.061  Score=50.36  Aligned_cols=23  Identities=17%  Similarity=0.338  Sum_probs=20.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      =|.|.|++|+||||+++.++..+
T Consensus         5 ~i~~eG~~gsGKsT~~~~l~~~l   27 (213)
T 4tmk_A            5 YIVIEGLEGAGKTTARNVVVETL   27 (213)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Confidence            47788999999999999999876

>3k53_A Ferrous iron transport protein B; GTPase fold, helical bundle, G-protein, prokaryote, GTP-BIND nucleotide-binding, metal transport; 2.70A {Pyrococcus furiosus}

Probab=92.27  E-value=0.069  Score=51.32  Aligned_cols=23  Identities=22%  Similarity=0.446  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+.|.|+||+|||+|+.++.+.
T Consensus         4 ~~i~lvG~~g~GKTTL~n~l~g~   26 (271)
T 3k53_A            4 KTVALVGNPNVGKTTIFNALTGL   26 (271)
T ss_dssp             EEEEEEECSSSSHHHHHHHHHTT
T ss_pred             eEEEEECCCCCCHHHHHHHHhCC
Confidence            46899999999999999999864

>3pqc_A Probable GTP-binding protein ENGB; rossmann fold, GTPase, cell cycle, hydrolase; HET: GDP; 1.90A {Thermotoga maritima} PDB: 3pr1_A

Probab=92.26  E-value=0.083  Score=46.88  Aligned_cols=23  Identities=30%  Similarity=0.312  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-+++.|++|+|||+|+.++.+.
T Consensus        24 ~~i~v~G~~~~GKSsli~~l~~~   46 (195)
T 3pqc_A           24 GEVAFVGRSNVGKSSLLNALFNR   46 (195)
T ss_dssp             CEEEEEEBTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHHcC
Confidence            36999999999999999999864

>2wsm_A Hydrogenase expression/formation protein (HYPB); metal binding protein; 2.30A {Archaeoglobus fulgidus}

Probab=92.26  E-value=0.071  Score=48.97  Aligned_cols=25  Identities=16%  Similarity=0.256  Sum_probs=22.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ..+.+.|++|+|||+|+..++..+.
T Consensus        31 ~~i~i~G~~g~GKTTl~~~l~~~~~   55 (221)
T 2wsm_A           31 VAVNIMGAIGSGKTLLIERTIERIG   55 (221)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHHHHT
T ss_pred             eEEEEEcCCCCCHHHHHHHHHHHhc
Confidence            4689999999999999999998753

>2qm8_A GTPase/ATPase; G protein, G3E, metallochaperone, chaperone; HET: MSE; 1.70A {Methylobacterium extorquens} SCOP: c.37.1.10 PDB: 2qm7_A*

Probab=92.24  E-value=0.06  Score=53.91  Aligned_cols=24  Identities=29%  Similarity=0.383  Sum_probs=20.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+.|.||||+|||||++++++.+
T Consensus        56 ~~v~i~G~~GaGKSTLl~~l~g~~   79 (337)
T 2qm8_A           56 IRVGITGVPGVGKSTTIDALGSLL   79 (337)
T ss_dssp             EEEEEECCTTSCHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHhh
Confidence            347799999999999999999754

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=92.24  E-value=0.063  Score=60.14  Aligned_cols=33  Identities=27%  Similarity=0.377  Sum_probs=23.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLS  258 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s  258 (480)
                      -+++.||||||||+++..++..+    +..+..+..+
T Consensus       377 ~~lI~GppGTGKT~~i~~~i~~l~~~~~~~ILv~a~t  413 (802)
T 2xzl_A          377 LSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPS  413 (802)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEEESS
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHhCCCCeEEEEcCc
Confidence            47899999999998877665433    4556665544

>3nh6_A ATP-binding cassette SUB-family B member 6, mitoc; ABC-transporter, ABCB6, nucleotide binding domain, heme BIOS transport protein; 2.00A {Homo sapiens} PDB: 3nh9_A* 3nha_A* 3nhb_A*

Probab=92.24  E-value=0.048  Score=54.06  Aligned_cols=28  Identities=32%  Similarity=0.511  Sum_probs=23.6

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +...-+.|.||+|+|||||++.+++.+.
T Consensus        78 ~~Ge~vaivG~sGsGKSTLl~ll~gl~~  105 (306)
T 3nh6_A           78 MPGQTLALVGPSGAGKSTILRLLFRFYD  105 (306)
T ss_dssp             CTTCEEEEESSSCHHHHHHHHHHTTSSC
T ss_pred             cCCCEEEEECCCCchHHHHHHHHHcCCC
Confidence            3445688999999999999999998764

>2b6h_A ADP-ribosylation factor 5; membrane trafficking, GDP, structural genomics, structural G consortium, SGC, protein transport; HET: GDP; 1.76A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z6x_A* 3aq4_A*

Probab=92.24  E-value=0.095  Score=47.20  Aligned_cols=23  Identities=17%  Similarity=0.303  Sum_probs=20.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      .--+++.|++|+|||+|+.++..
T Consensus        29 ~~ki~v~G~~~vGKSsLi~~l~~   51 (192)
T 2b6h_A           29 QMRILMVGLDAAGKTTILYKLKL   51 (192)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHCS
T ss_pred             ccEEEEECCCCCCHHHHHHHHHh
Confidence            34699999999999999999964

>3bwd_D RAC-like GTP-binding protein ARAC6; G domain, cytoplasm, lipoprotein, membrane, methylation, nucleotide-binding, prenylation, ----; HET: GDP; 1.53A {Arabidopsis thaliana} PDB: 2nty_C* 2wbl_C

Probab=92.19  E-value=0.079  Score=46.55  Aligned_cols=23  Identities=17%  Similarity=0.225  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKssl~~~~~~~   31 (182)
T 3bwd_D            9 IKCVTVGDGAVGKTCLLISYTSN   31 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCCCHHHHHHHHhcC
Confidence            46999999999999999999864

>3ld9_A DTMP kinase, thymidylate kinase; ssgcid, NIH, niaid, SBRI, UW, emerald biostructures, ehrlich chaffeensis; 2.15A {Ehrlichia chaffeensis}

Probab=92.16  E-value=0.066  Score=50.58  Aligned_cols=26  Identities=23%  Similarity=0.354  Sum_probs=22.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-|.+.|++|+|||++++.++..++.
T Consensus        22 ~~i~~~G~~g~GKst~~~~l~~~l~~   47 (223)
T 3ld9_A           22 MFITFEGIDGSGKTTQSHLLAEYLSE   47 (223)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHhh
Confidence            34678899999999999999987654

>3dz8_A RAS-related protein RAB-3B; GDP, GTPase, structural genomics consortium, SGC, cell GTP-binding, lipoprotein, membrane, methylation; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=92.14  E-value=0.078  Score=47.47  Aligned_cols=23  Identities=35%  Similarity=0.414  Sum_probs=20.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+++.|++|+|||+|+.++.+.-
T Consensus        25 ki~v~G~~~~GKSsli~~l~~~~   47 (191)
T 3dz8_A           25 KLLIIGNSSVGKTSFLFRYADDT   47 (191)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHHT
T ss_pred             EEEEECCCCcCHHHHHHHHhcCC
Confidence            59999999999999999998743

>3c5c_A RAS-like protein 12; GDP, GTPase, structural genomics consortium, SGC, limited proteolysis, GTP-binding, nucleotide-binding, signaling protein; HET: GDP; 1.85A {Homo sapiens}

Probab=92.06  E-value=0.082  Score=47.36  Aligned_cols=22  Identities=23%  Similarity=0.443  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus        23 ki~vvG~~~vGKTsLi~~l~~~   44 (187)
T 3c5c_A           23 NLAILGRRGAGKSALTVKFLTK   44 (187)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCcHHHHHHHHHhC
Confidence            5899999999999999999863

>1knx_A Probable HPR(Ser) kinase/phosphatase; HPR kinase, HPR kinase/phosphatase, HPRK/P, P-loop, walker A BOX, catabolite repression; 2.50A {Mycoplasma pneumoniae} SCOP: c.98.2.1 c.91.1.2

Probab=92.05  E-value=0.099  Score=51.94  Aligned_cols=29  Identities=31%  Similarity=0.274  Sum_probs=23.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      .+|+||.||+|+|||++|.++.. -|..++
T Consensus       147 g~gvli~G~sG~GKStlal~l~~-~G~~lv  175 (312)
T 1knx_A          147 GVGVLLTGRSGIGKSECALDLIN-KNHLFV  175 (312)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHT-TTCEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHH-cCCEEE
Confidence            56899999999999999998865 344443

>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport; HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB: 1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*

Probab=92.05  E-value=0.082  Score=47.68  Aligned_cols=23  Identities=26%  Similarity=0.420  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (207)
T 1vg8_A            9 LKVIILGDSGVGKTSLMNQYVNK   31 (207)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHHS
T ss_pred             eEEEEECcCCCCHHHHHHHHHcC
Confidence            36899999999999999999874

>3t5g_A GTP-binding protein RHEB; immunoglobulin-like beta sandwitch, PDE delta, RHEB; HET: GDP FAR; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 1xtq_A* 1xtr_A* 1xts_A* 2l0x_A* 3sea_A*

Probab=92.04  E-value=0.082  Score=46.55  Aligned_cols=22  Identities=27%  Similarity=0.412  Sum_probs=19.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      .-+++.|++|+|||+|+.++.+
T Consensus         7 ~ki~~~G~~~~GKSsli~~l~~   28 (181)
T 3t5g_A            7 RKIAILGYRSVGKSSLTIQFVE   28 (181)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEEECcCCCCHHHHHHHHHc
Confidence            3589999999999999999985

>1z06_A RAS-related protein RAB-33B; RAB GTPase, RAB33B GTPase, vesicular trafficking, protein transport; HET: GNP; 1.81A {Mus musculus} SCOP: c.37.1.8 PDB: 2g77_B*

Probab=92.02  E-value=0.084  Score=47.10  Aligned_cols=21  Identities=19%  Similarity=0.417  Sum_probs=19.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus        22 ki~v~G~~~~GKSsli~~l~~   42 (189)
T 1z06_A           22 KIIVIGDSNVGKTCLTYRFCA   42 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            699999999999999999985

>1zd9_A ADP-ribosylation factor-like 10B; transport protein, GDP-binding, membrane trafficking, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.70A {Homo sapiens} SCOP: c.37.1.8 PDB: 2al7_A* 2h18_A*

Probab=92.01  E-value=0.084  Score=47.19  Aligned_cols=21  Identities=33%  Similarity=0.487  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus        24 ki~v~G~~~~GKSsli~~l~~   44 (188)
T 1zd9_A           24 ELTLVGLQYSGKTTFVNVIAS   44 (188)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHc
Confidence            589999999999999999986

>1zbd_A Rabphilin-3A; G protein, effector, RABCDR, synaptic exocytosis, RAB protein, RAB3A; HET: GTP; 2.60A {Rattus norvegicus} SCOP: c.37.1.8

Probab=91.98  E-value=0.076  Score=47.91  Aligned_cols=23  Identities=35%  Similarity=0.366  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      -.+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (203)
T 1zbd_A            9 FKILIIGNSSVGKTSFLFRYADD   31 (203)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHTC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            36899999999999999999863

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=91.97  E-value=0.14  Score=51.91  Aligned_cols=34  Identities=21%  Similarity=0.196  Sum_probs=25.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      ..++++.||+|+|||++++.++..+   +..++.+|.
T Consensus        35 ~~~~~i~G~~G~GKs~~~~~~~~~~~~~~~~~~~~D~   71 (392)
T 4ag6_A           35 NSNWTILAKPGAGKSFTAKMLLLREYMQGSRVIIIDP   71 (392)
T ss_dssp             CCCEEEECCTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             cCceEEEcCCCCCHHHHHHHHHHHHHHCCCEEEEEeC
Confidence            4578999999999999999988642   444444443

>2bcg_Y Protein YP2, GTP-binding protein YPT1; RABGTPase, geranylgeranylation, vesicular transport, protein transport; HET: GDP GER; 1.48A {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ukv_Y* 3cue_F* 1yzn_A* 3sfv_A* 2wwx_A 2fol_A* 3nkv_A* 3jza_A* 2rhd_A*

Probab=91.97  E-value=0.083  Score=47.84  Aligned_cols=23  Identities=35%  Similarity=0.414  Sum_probs=20.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-+++.|++|+|||+|+.++.+.
T Consensus         9 ~ki~v~G~~~~GKSsli~~l~~~   31 (206)
T 2bcg_Y            9 FKLLLIGNSGVGKSCLLLRFSDD   31 (206)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHhcC
Confidence            35899999999999999999863

>3ihw_A Centg3; RAS, centaurin, GTPase, structural genomics, structural genomics consortium, SGC, alternative splicing, ANK repeat, cytoplasm, GTP-binding; 1.92A {Homo sapiens} SCOP: c.37.1.0

Probab=91.96  E-value=0.086  Score=47.24  Aligned_cols=22  Identities=18%  Similarity=0.161  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus        22 ki~ivG~~~vGKSsL~~~~~~~   43 (184)
T 3ihw_A           22 KVGIVGNLSSGKSALVHRYLTG   43 (184)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999888764

>2vp4_A Deoxynucleoside kinase; ATP-binding, DNA synthesis, phosphoprotein, feedback inhibition, deoxyribonucleoside kinase, salvage pathway; HET: DCP; 2.20A {Drosophila melanogaster} SCOP: c.37.1.1 PDB: 1j90_A* 2jj8_A* 2vp2_A* 1oe0_A* 2vp5_A* 2vp6_A* 2vp9_A* 2vpp_A* 2vqs_A* 2vp0_A* 1ot3_A* 2jcs_A* 1zm7_A* 1zmx_A*

Probab=91.95  E-value=0.096  Score=49.07  Aligned_cols=29  Identities=21%  Similarity=0.492  Sum_probs=23.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -+.|.||.|+||||+++.+++. +..+...
T Consensus        22 ~i~i~G~~GsGKSTl~~~L~~~-~g~v~~~   50 (230)
T 2vp4_A           22 TVLIEGNIGSGKTTYLNHFEKY-KNDICLL   50 (230)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGG-TTTEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHhc-cCCeEEE
Confidence            4678899999999999999987 4444433

>2iwr_A Centaurin gamma 1; ANK repeat, zinc-finger, GTP-binding, polymorphism, nucleotide-binding, alternative splicing, protein transport; HET: CAF; 1.5A {Homo sapiens} PDB: 2bmj_A

Probab=91.94  E-value=0.064  Score=47.13  Aligned_cols=22  Identities=23%  Similarity=0.235  Sum_probs=20.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus         9 ki~~vG~~~vGKTsli~~l~~~   30 (178)
T 2iwr_A            9 RLGVLGDARSGKSSLIHRFLTG   30 (178)
T ss_dssp             EEEEECCGGGCHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999874

>2a5j_A RAS-related protein RAB-2B; GTPase, signal transduction, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 1.50A {Homo sapiens} SCOP: c.37.1.8 PDB: 1z0a_A*

Probab=91.93  E-value=0.087  Score=47.15  Aligned_cols=22  Identities=27%  Similarity=0.572  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+.++.+.
T Consensus        23 ki~v~G~~~~GKSsli~~l~~~   44 (191)
T 2a5j_A           23 KYIIIGDTGVGKSCLLLQFTDK   44 (191)
T ss_dssp             EEEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999863

>3reg_A RHO-like small GTPase; cytoskeleton, nucleotide-binding, GTP-binding, signaling Pro lipoprotein, prenylation; HET: GSP; 1.80A {Entamoeba histolytica} PDB: 3ref_B* 4dvg_A*

Probab=91.88  E-value=0.088  Score=47.16  Aligned_cols=22  Identities=18%  Similarity=0.300  Sum_probs=20.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        25 ki~~vG~~~~GKSsl~~~l~~~   46 (194)
T 3reg_A           25 KIVVVGDGAVGKTCLLLAFSKG   46 (194)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhcC
Confidence            5899999999999999999874

>2rcn_A Probable GTPase ENGC; YJEQ, circularly permuted, GTP-binding, hydrolase, nucleotide-binding; HET: GDP; 2.25A {Salmonella typhimurium} PDB: 2ykr_W 4a2i_V

Probab=91.83  E-value=0.073  Score=53.93  Aligned_cols=25  Identities=36%  Similarity=0.531  Sum_probs=22.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||||+|||||+++++....
T Consensus       216 ~~~~lvG~sG~GKSTLln~L~g~~~  240 (358)
T 2rcn_A          216 RISIFAGQSGVGKSSLLNALLGLQN  240 (358)
T ss_dssp             SEEEEECCTTSSHHHHHHHHHCCSS
T ss_pred             CEEEEECCCCccHHHHHHHHhcccc
Confidence            3588999999999999999998665

>3cph_A RAS-related protein SEC4; RAB GTPase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, GTP-binding; HET: GDP; 2.90A {Saccharomyces cerevisiae} SCOP: c.37.1.8

Probab=91.82  E-value=0.089  Score=47.64  Aligned_cols=23  Identities=35%  Similarity=0.429  Sum_probs=20.5

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-+++.|++|+|||+|+.++.+.
T Consensus        21 ~~i~v~G~~~~GKSsli~~l~~~   43 (213)
T 3cph_A           21 MKILLIGDSGVGKSCLLVRFVED   43 (213)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHhC
Confidence            46899999999999999999853

>3oes_A GTPase rhebl1; small GTPase, structural genomics, structural genomics conso SGC, hydrolase; HET: GNP; 2.30A {Homo sapiens}

Probab=91.80  E-value=0.089  Score=47.57  Aligned_cols=23  Identities=26%  Similarity=0.338  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        25 ~ki~vvG~~~~GKSsli~~l~~~   47 (201)
T 3oes_A           25 RKVVILGYRCVGKTSLAHQFVEG   47 (201)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEEECCCCcCHHHHHHHHHhC
Confidence            35899999999999999999874

>1u0l_A Probable GTPase ENGC; permutation, OB-fold, zinc-finger, structural genomics, BSGC structure funded by NIH, protein structure initiative, PSI; HET: GDP; 2.80A {Thermotoga maritima} SCOP: b.40.4.5 c.37.1.8

Probab=91.78  E-value=0.072  Score=52.35  Aligned_cols=26  Identities=31%  Similarity=0.370  Sum_probs=22.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-+.|.||+|+|||||+++++.....
T Consensus       170 eiv~l~G~sG~GKSTll~~l~g~~~~  195 (301)
T 1u0l_A          170 KISTMAGLSGVGKSSLLNAINPGLKL  195 (301)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCC
T ss_pred             CeEEEECCCCCcHHHHHHHhcccccc
Confidence            35789999999999999999986653

>2gks_A Bifunctional SAT/APS kinase; transferase, sulfurylase; HET: ADP; 2.31A {Aquifex aeolicus}

Probab=91.72  E-value=0.11  Score=55.49  Aligned_cols=32  Identities=28%  Similarity=0.320  Sum_probs=26.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~  256 (480)
                      .-++|.|+||+|||++++.++..++   .+++.++
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            4588999999999999999998764   4566665

>1ksh_A ARF-like protein 2; small GTPase, small GTP-binding protein, ARF family; HET: CME GDP; 1.80A {Mus musculus} SCOP: c.37.1.8 PDB: 1ksg_A* 1ksj_A* 3doe_A* 3dof_A*

Probab=91.69  E-value=0.083  Score=46.84  Aligned_cols=24  Identities=17%  Similarity=0.293  Sum_probs=21.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ...+++.|++|+|||+|+.++.+.
T Consensus        18 ~~~i~v~G~~~~GKssl~~~l~~~   41 (186)
T 1ksh_A           18 ELRLLMLGLDNAGKTTILKKFNGE   41 (186)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHTTC
T ss_pred             eeEEEEECCCCCCHHHHHHHHhcC
Confidence            446999999999999999999853

>1gwn_A RHO-related GTP-binding protein RHOE; GTPase, inactive GTPase, signal transduction; HET: GTP; 2.1A {Mus musculus} SCOP: c.37.1.8

Probab=91.63  E-value=0.094  Score=48.02  Aligned_cols=22  Identities=23%  Similarity=0.314  Sum_probs=20.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus        30 ki~vvG~~~vGKSsLi~~l~~~   51 (205)
T 1gwn_A           30 KIVVVGDSQCGKTALLHVFAKD   51 (205)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5999999999999999999874

>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=91.58  E-value=0.086  Score=49.41  Aligned_cols=23  Identities=26%  Similarity=0.392  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      .-++|.|++|+|||+|+.++.+.
T Consensus        30 ~~i~lvG~~g~GKStlin~l~g~   52 (239)
T 3lxx_A           30 LRIVLVGKTGAGKSATGNSILGR   52 (239)
T ss_dssp             EEEEEECCTTSSHHHHHHHHHTS
T ss_pred             eEEEEECCCCCCHHHHHHHHcCC
Confidence            46899999999999999999863

>2qag_B Septin-6, protein NEDD5; cell cycle, cell division, GTP-binding, nucleotide-binding, phosphorylation, acetylation, alternative splicing, coiled coil; HET: GDP GTP; 4.00A {Homo sapiens}

Probab=91.58  E-value=0.093  Score=54.40  Aligned_cols=21  Identities=29%  Similarity=0.444  Sum_probs=19.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      +.|.||+|+|||||+++|++.
T Consensus        45 vaLvG~nGaGKSTLln~L~G~   65 (427)
T 2qag_B           45 ILCVGETGLGKSTLMDTLFNT   65 (427)
T ss_dssp             EEEECSTTSSSHHHHHHHHTS
T ss_pred             EEEECCCCCCHHHHHHHHhCc
Confidence            789999999999999999975

>4f4c_A Multidrug resistance protein PGP-1; ABC transporter, ATPase, multi-drug transporter, exporter, A binding, hydrolase,protein transport; HET: NDG NAG BMA MAN 0SA; 3.40A {Caenorhabditis elegans}

Probab=91.54  E-value=0.2  Score=59.17  Aligned_cols=26  Identities=38%  Similarity=0.583  Sum_probs=22.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +..-+-++||+|+|||||++++.+..
T Consensus      1104 ~Ge~vaIVG~SGsGKSTL~~lL~rl~ 1129 (1321)
T 4f4c_A         1104 PGQTLALVGPSGCGKSTVVALLERFY 1129 (1321)
T ss_dssp             TTCEEEEECSTTSSTTSHHHHHTTSS
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcCc
Confidence            33457899999999999999999865

>1zj6_A ADP-ribosylation factor-like protein 5; ARL, GTP-binding, transport protein; HET: G3D; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.53  E-value=0.12  Score=45.93  Aligned_cols=23  Identities=13%  Similarity=0.329  Sum_probs=20.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ...+++.|++|+|||+|+.++.+
T Consensus        16 ~~~i~v~G~~~~GKssl~~~l~~   38 (187)
T 1zj6_A           16 EHKVIIVGLDNAGKTTILYQFSM   38 (187)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHT
T ss_pred             ccEEEEECCCCCCHHHHHHHHhc
Confidence            44699999999999999999984

>2hf9_A Probable hydrogenase nickel incorporation protein HYPB; alpha and beta protein; HET: GSP; 1.90A {Methanocaldococcus jannaschii} PDB: 2hf8_A*

Probab=91.42  E-value=0.1  Score=48.05  Aligned_cols=25  Identities=16%  Similarity=0.344  Sum_probs=21.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+++.|++|+|||+|+..++...
T Consensus        38 ~~~i~ivG~~gvGKTtl~~~l~~~~   62 (226)
T 2hf9_A           38 VVAFDFMGAIGSGKTLLIEKLIDNL   62 (226)
T ss_dssp             CEEEEEEESTTSSHHHHHHHHHHHH
T ss_pred             CeEEEEEcCCCCCHHHHHHHHHHHh
Confidence            3468888999999999999999864

>2h17_A ADP-ribosylation factor-like protein 5A; GDP, GTPase, membrane trafficking, structural genomics consortium, SGC, transport protein; HET: GDP; 1.70A {Homo sapiens} PDB: 2h16_A* 1z6y_A* 1yzg_A*

Probab=91.40  E-value=0.089  Score=46.63  Aligned_cols=22  Identities=14%  Similarity=0.270  Sum_probs=20.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        23 ~i~v~G~~~~GKSsli~~l~~~   44 (181)
T 2h17_A           23 KVIIVGLDNAGKTTILYQFSMN   44 (181)
T ss_dssp             EEEEEEETTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999863

>2ew1_A RAS-related protein RAB-30; G-protein, GTP analogue, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GNP; 2.00A {Homo sapiens} SCOP: c.37.1.8

Probab=91.38  E-value=0.1  Score=47.62  Aligned_cols=22  Identities=23%  Similarity=0.416  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        28 ki~lvG~~~vGKSsLi~~l~~~   49 (201)
T 2ew1_A           28 KIVLIGNAGVGKTCLVRRFTQG   49 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHHhC
Confidence            5899999999999999999863

>2fu5_C RAS-related protein RAB-8A; MSS4:RAB8 protein complex, GEF:GTPase nucleotide free complex; 2.00A {Mus musculus} SCOP: c.37.1.8 PDB: 3qbt_A* 3tnf_A*

Probab=91.35  E-value=0.063  Score=47.44  Aligned_cols=22  Identities=32%  Similarity=0.443  Sum_probs=9.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      ..+++.|++|+|||+|+.++.+
T Consensus         9 ~ki~v~G~~~~GKssl~~~l~~   30 (183)
T 2fu5_C            9 FKLLLIGDSGVGKTCVLFRFSE   30 (183)
T ss_dssp             EEEEEECCCCC-----------
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3689999999999999999875

>1f6b_A SAR1; gtpases, N-terminal helix, Mg-containing complex, protein transport; HET: GDP; 1.70A {Cricetulus griseus} SCOP: c.37.1.8 PDB: 2fmx_A* 2fa9_A* 2gao_A*

Probab=91.30  E-value=0.091  Score=47.67  Aligned_cols=22  Identities=14%  Similarity=0.360  Sum_probs=19.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      .-+++.|+||+|||+|+.++.+
T Consensus        26 ~ki~lvG~~~vGKSsLi~~l~~   47 (198)
T 1f6b_A           26 GKLVFLGLDNAGKTTLLHMLKD   47 (198)
T ss_dssp             EEEEEEEETTSSHHHHHHHHSC
T ss_pred             cEEEEECCCCCCHHHHHHHHhc
Confidence            3589999999999999999974

>2yv5_A YJEQ protein; hydrolase, GTPase, permutation, structural genomics, NPPSFA, national project on protein structural and functional analyses; HET: GDP; 1.90A {Aquifex aeolicus}

Probab=91.25  E-value=0.12  Score=50.95  Aligned_cols=24  Identities=38%  Similarity=0.459  Sum_probs=20.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+.|.||+|+|||||+++++ ...
T Consensus       166 ~i~~l~G~sG~GKSTLln~l~-~~~  189 (302)
T 2yv5_A          166 FICILAGPSGVGKSSILSRLT-GEE  189 (302)
T ss_dssp             CEEEEECSTTSSHHHHHHHHH-SCC
T ss_pred             cEEEEECCCCCCHHHHHHHHH-Hhh
Confidence            357899999999999999999 654

>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=91.24  E-value=0.13  Score=47.22  Aligned_cols=53  Identities=19%  Similarity=0.184  Sum_probs=31.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhC---CCCCceEEEEccCCCcHHHH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLG---RVWKRSYLLYGPSGTGKSSF  240 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g---~~~~rgiLL~GPpGTGKT~L  240 (480)
                      +..+|+++...+.+.+.+.+.-   ...+..+....   ....+.+++.+|+|+|||..
T Consensus        12 ~~~~f~~l~l~~~l~~~l~~~g---~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~   67 (224)
T 1qde_A           12 VVYKFDDMELDENLLRGVFGYG---FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGT   67 (224)
T ss_dssp             CCCCGGGGTCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHH
T ss_pred             ccCChhhcCCCHHHHHHHHHCC---CCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHH
Confidence            3467999988888777765421   11111111110   01125699999999999976

>2atx_A Small GTP binding protein TC10; GTPase, P-loop, alpha-beta, hydrolase; HET: GNP; 2.65A {Homo sapiens} SCOP: c.37.1.8

Probab=91.19  E-value=0.11  Score=46.34  Aligned_cols=22  Identities=18%  Similarity=0.306  Sum_probs=20.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        20 ki~v~G~~~~GKssli~~l~~~   41 (194)
T 2atx_A           20 KCVVVGDGAVGKTCLLMSYAND   41 (194)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999874

>2qtf_A Protein HFLX, GTP-binding protein; beta-alpha-barrels, nucleotide-binding, nucleotide binding protein; 2.00A {Sulfolobus solfataricus P2} PDB: 2qth_A* 3kxi_A* 3kxl_A 3kxk_A

Probab=91.18  E-value=0.18  Score=51.11  Aligned_cols=22  Identities=23%  Similarity=0.387  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+.|.|+||+|||||+.++++.
T Consensus       181 ~V~lvG~~naGKSTLln~L~~~  202 (364)
T 2qtf_A          181 SIGIVGYTNSGKTSLFNSLTGL  202 (364)
T ss_dssp             EEEEECBTTSSHHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999999864

>3qks_A DNA double-strand break repair RAD50 ATPase; RECA-like fold, coiled-coils, ATPase, exonuclease, endonucle binding, DNA binding; HET: DNA; 2.10A {Pyrococcus furiosus} PDB: 3qkr_A*

Probab=91.16  E-value=0.12  Score=47.75  Aligned_cols=25  Identities=32%  Similarity=0.474  Sum_probs=21.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -.+++||.|+|||++..||.-.++.
T Consensus        25 ~~~I~G~NgsGKStil~ai~~~l~g   49 (203)
T 3qks_A           25 INLIIGQNGSGKSSLLDAILVGLYW   49 (203)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHT
T ss_pred             eEEEEcCCCCCHHHHHHHHHHHhcC
Confidence            4689999999999999999876654

>3t34_A Dynamin-related protein 1A, linker, dynamin-relat 1A; dynamin-like protein 1A, GTPase, membrane fission, motor Pro; HET: GDP; 2.40A {Arabidopsis thaliana} PDB: 3t35_A*

Probab=91.13  E-value=0.82  Score=45.66  Aligned_cols=21  Identities=24%  Similarity=0.385  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -|.+.|++|+|||+|+.++.+
T Consensus        36 ~I~vvG~~~sGKSSLln~l~g   56 (360)
T 3t34_A           36 AIAVVGGQSSGKSSVLESIVG   56 (360)
T ss_dssp             EEEEECBTTSSHHHHHHHHHT
T ss_pred             EEEEECCCCCcHHHHHHHHhC
Confidence            689999999999999999997

>2o52_A RAS-related protein RAB-4B; G-protein, GDP, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.20A {Homo sapiens}

Probab=91.11  E-value=0.097  Score=47.43  Aligned_cols=22  Identities=32%  Similarity=0.564  Sum_probs=19.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      -.+++.|++|+|||+|+.++.+
T Consensus        26 ~ki~v~G~~~~GKSsLi~~l~~   47 (200)
T 2o52_A           26 FKFLVIGSAGTGKSCLLHQFIE   47 (200)
T ss_dssp             EEEEEEESTTSSHHHHHHHHHC
T ss_pred             eEEEEECcCCCCHHHHHHHHHh
Confidence            3689999999999999999974

>2fv8_A H6, RHO-related GTP-binding protein RHOB; GDP/GTP binding, GTP hydrolysis, structural genomics, structural genomics consortium, SGC; HET: GDP; 1.90A {Homo sapiens} SCOP: c.37.1.8

Probab=91.07  E-value=0.12  Score=47.08  Aligned_cols=23  Identities=13%  Similarity=0.312  Sum_probs=20.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      ..+++.|++|+|||+|+.++.+.
T Consensus        26 ~ki~vvG~~~~GKSsli~~l~~~   48 (207)
T 2fv8_A           26 KKLVVVGDGACGKTCLLIVFSKD   48 (207)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHS
T ss_pred             cEEEEECcCCCCHHHHHHHHhcC
Confidence            36999999999999999999873

>2q3h_A RAS homolog gene family, member U; GTPase, structural genomics, structural genomics consortium,; HET: GDP; 1.73A {Homo sapiens}

Probab=90.96  E-value=0.1  Score=46.88  Aligned_cols=22  Identities=23%  Similarity=0.422  Sum_probs=19.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      -.+++.|++|+|||+|+.++.+
T Consensus        21 ~ki~~~G~~~~GKssl~~~l~~   42 (201)
T 2q3h_A           21 VKCVLVGDGAVGKTSLVVSYTT   42 (201)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHC
T ss_pred             eEEEEECCCCCCHHHHHHHHHh
Confidence            3689999999999999999975

>4hlc_A DTMP kinase, thymidylate kinase; TMK, MRSA, pipiridine, transfera transferase inhibitor complex; HET: T05; 1.55A {Staphylococcus aureus subsp} PDB: 2cck_A 4gfd_A* 4gsy_A* 4hdc_A* 4hej_A* 2ccj_A* 4hld_A* 2ccg_A*

Probab=90.93  E-value=0.16  Score=47.06  Aligned_cols=29  Identities=28%  Similarity=0.496  Sum_probs=23.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC--CCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM--SYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l--~~~~~~i  255 (480)
                      |.+-|+.|+||||+++.++..+  |.+++..
T Consensus         5 I~~EG~dGsGKsTq~~~L~~~L~~~~~v~~~   35 (205)
T 4hlc_A            5 ITFEGPEGSGKTTVINEVYHRLVKDYDVIMT   35 (205)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHTTTSCEEEE
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHCCCCEEEe
Confidence            5688999999999999999977  4555544

>2gco_A H9, RHO-related GTP-binding protein RHOC; GTPase,signaling protein, signaling Pro; HET: GNP; 1.40A {Homo sapiens} PDB: 2gcn_A* 2gcp_A* 1z2c_A* 1x86_B 2rgn_C* 1lb1_B 1s1c_A* 3kz1_E* 3lxr_A* 3lwn_A* 3lw8_A* 1cxz_A* 1a2b_A* 1ow3_B* 1ftn_A* 1cc0_A* 3msx_A* 1xcg_B 3t06_B 1tx4_B* ...

Probab=90.85  E-value=0.13  Score=46.60  Aligned_cols=22  Identities=14%  Similarity=0.300  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+.++.+.
T Consensus        27 ki~vvG~~~~GKSsli~~l~~~   48 (201)
T 2gco_A           27 KLVIVGDGACGKTCLLIVFSKD   48 (201)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            5899999999999999999873

>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=90.84  E-value=0.2  Score=51.41  Aligned_cols=25  Identities=20%  Similarity=0.333  Sum_probs=21.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+++.||||||||+|++.||+..
T Consensus       174 GQr~~IvG~sG~GKTtLl~~Iar~i  198 (422)
T 3ice_A          174 GQRGLIVAPPKAGKTMLLQNIAQSI  198 (422)
T ss_dssp             TCEEEEECCSSSSHHHHHHHHHHHH
T ss_pred             CcEEEEecCCCCChhHHHHHHHHHH
Confidence            3468999999999999999998754

>2cjw_A GTP-binding protein GEM; nucleotide-binding, small GTPase, conformational change, cysteine-modified, G-protein hydrolase; HET: GDP; 2.10A {Homo sapiens} PDB: 2cjw_B* 2ht6_A*

Probab=90.82  E-value=0.13  Score=46.41  Aligned_cols=21  Identities=38%  Similarity=0.602  Sum_probs=19.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -++|.|+||+|||+|+..+.+
T Consensus         8 kv~lvG~~~vGKSsL~~~~~~   28 (192)
T 2cjw_A            8 RVVLIGEQGVGKSTLANIFAG   28 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999999985

>2hup_A RAS-related protein RAB-43; G-protein, GDP, structural genomics, structural genomics consortium, SGC, signaling protein; HET: GDP; 2.05A {Homo sapiens}

Probab=90.76  E-value=0.13  Score=46.65  Aligned_cols=22  Identities=18%  Similarity=0.312  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus        31 ki~vvG~~~vGKSsli~~l~~~   52 (201)
T 2hup_A           31 KLVLVGDASVGKTCVVQRFKTG   52 (201)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHS
T ss_pred             EEEEECcCCCCHHHHHHHHhhC
Confidence            5899999999999999999763

>1qhl_A Protein (cell division protein MUKB); SMC, chromosome partitioning; 2.20A {Escherichia coli} SCOP: c.37.1.12

Probab=90.68  E-value=0.041  Score=52.13  Aligned_cols=23  Identities=35%  Similarity=0.426  Sum_probs=19.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +.|.||+|+|||+|+++|+..+.
T Consensus        30 ~~i~GpnGsGKSTll~~i~g~~~   52 (227)
T 1qhl_A           30 TTLSGGNGAGKSTTMAAFVTALI   52 (227)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhcccc
Confidence            34679999999999999998764

>2j0v_A RAC-like GTP-binding protein ARAC7; nucleotide-binding protein, ROP9, atrac7, membrane, palmitate, RHO GTPase; HET: GDP; 1.78A {Arabidopsis thaliana}

Probab=90.67  E-value=0.13  Score=46.64  Aligned_cols=22  Identities=18%  Similarity=0.256  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .+++.|++|+|||+|+..+.+.
T Consensus        11 ki~i~G~~~~GKTsli~~l~~~   32 (212)
T 2j0v_A           11 KCVTVGDGAVGKTCMLICYTSN   32 (212)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5899999999999999999863

>2p67_A LAO/AO transport system kinase; ARGK, structural GEN PSI-2, protein structure initiative, NEW YORK SGX research for structural genomics; 1.80A {Escherichia coli} SCOP: c.37.1.10

Probab=90.61  E-value=0.17  Score=50.48  Aligned_cols=25  Identities=28%  Similarity=0.464  Sum_probs=21.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ..-+.+.|+||+||||++.+++..+
T Consensus        56 ~~~i~i~G~~g~GKSTl~~~l~~~~   80 (341)
T 2p67_A           56 TLRLGVTGTPGAGKSTFLEAFGMLL   80 (341)
T ss_dssp             SEEEEEEECTTSCHHHHHHHHHHHH
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHHH
Confidence            3457899999999999999998754

>2il1_A RAB12; G-protein, GDP, GTPase, predicted, structural genomics, structural genomics consortium, SGC, protein transport; HET: GDP; 2.10A {Homo sapiens}

Probab=90.61  E-value=0.13  Score=46.25  Aligned_cols=21  Identities=24%  Similarity=0.545  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .+++.|++|+|||+|+.++.+
T Consensus        28 ki~vvG~~~~GKSsLi~~l~~   48 (192)
T 2il1_A           28 QVIIIGSRGVGKTSLMERFTD   48 (192)
T ss_dssp             EEEEECSTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999974

>1dek_A Deoxynucleoside monophosphate kinase; transferase, phosphotransferase; HET: DGP; 2.00A {Enterobacteria phage T4} SCOP: c.37.1.1 PDB: 1del_A*

Probab=90.59  E-value=0.13  Score=49.25  Aligned_cols=27  Identities=26%  Similarity=0.153  Sum_probs=23.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      -+.|+|++|||||++++.++..+|+++
T Consensus         3 ~i~ltG~~~sGK~tv~~~l~~~~g~~~   29 (241)
T 1dek_A            3 LIFLSGVKRSGKDTTADFIMSNYSAVK   29 (241)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHSCEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHhcCCeE
Confidence            367999999999999999999888664

---

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	480
d1ixza_	247	c.37.1.20 (A:) AAA domain of cell division protein	4e-23
d1r7ra3	265	c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p	5e-22
d1lv7a_	256	c.37.1.20 (A:) AAA domain of cell division protein	9e-22
d1e32a2	258	c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p	2e-14
d1svma_	362	c.37.1.20 (A:) Papillomavirus large T antigen heli	6e-14
d1d2na_	246	c.37.1.20 (A:) Hexamerization domain of N-ethylmal	7e-08
d1w44a_	321	c.37.1.11 (A:) NTPase P4 {Bacteriophage phi-12 [Ta	4e-07
d1gvnb_	273	c.37.1.21 (B:) Plasmid maintenance system epsilon/	5e-07
d1sxja2	253	c.37.1.20 (A:295-547) Replication factor C1 {Baker	1e-05
d1in4a2	238	c.37.1.20 (A:17-254) Holliday junction helicase Ru	1e-05
d1ixsb2	239	c.37.1.20 (B:4-242) Holliday junction helicase Ruv	1e-04
d1sxje2	252	c.37.1.20 (E:4-255) Replication factor C5 {Baker's	7e-04
d1ofha_	309	c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId	0.001

>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 = 95.7 bits (238), Expect = 4e-23
 Identities = 51/237 (21%), Positives = 91/237 (38%), Gaps = 23/237 (9%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           TF  ++   + K  +K  +E FLK    +H +G    +  LL GP G GK+  A A+A  
Sbjct: 7   TFKDVAGAEEAKEELKEIVE-FLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGE 65

Query: 248 MSYDVYDVDLSRVADD------ADLKSL--LLQTTSKSVILIEDLDRFLVEKPAAVS--- 296
                     S   +       A ++ L    +  +  ++ I+++D    ++ + V    
Sbjct: 66  ARVPFITASGSDFVEMFVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGN 125

Query: 297 ------LSGVLNFMDGVLNSCCFEERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDF 349
                 L+ +L  MDG       +  ++V    N  D +D ALLRPGR D  I     D 
Sbjct: 126 DEREQTLNQLLVEMDGFEK----DTAIVVMAATNRPDILDPALLRPGRFDRQIAIDAPDV 181

Query: 350 SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT 406
              + +   +   K       +  + +       A++  L+       +R  +  IT
Sbjct: 182 KGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEAALLAAREGRRKIT 238

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 265

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 93.3 bits (231), Expect = 5e-22
 Identities = 44/221 (19%), Positives = 94/221 (42%), Gaps = 22/221 (9%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           T++ I    D+K  ++  ++  ++    + + G    +  L YGP G GK+  A A+A+ 
Sbjct: 5   TWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANE 64

Query: 248 MSYDVYDVDLSRVAD------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAAVS--- 296
              +   +    +        +A+++ +  +    +  V+  ++LD     +   +    
Sbjct: 65  CQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGG 124

Query: 297 ------LSGVLNFMDGVLNSCCFEERVMVF-TMNSKDHVDQALLRPGRIDVHIHFPLCDF 349
                 ++ +L  MDG+      ++ V +    N  D +D A+LRPGR+D  I+ PL D 
Sbjct: 125 GAADRVINQILTEMDGMST----KKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDE 180

Query: 350 SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELM 390
            S   +  + L          +E + +  +  S A++ E+ 
Sbjct: 181 KSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEIC 221

>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 = 92.2 bits (229), Expect = 9e-22
 Identities = 50/236 (21%), Positives = 96/236 (40%), Gaps = 21/236 (8%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
           TF  ++   + K  V   +E +L+    + +LG    +  L+ GP GTGK+  A A+A  
Sbjct: 10  TFADVAGCDEAKEEVAELVE-YLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGE 68

Query: 248 MSYDVYDVDLSRVAD------DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAAVS--- 296
                + +  S   +       + ++ +  Q    +  +I I+++D    ++ A +    
Sbjct: 69  AKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGH 128

Query: 297 ------LSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFS 350
                 L+ +L  MDG   +   E  +++   N  D +D ALLRPGR D  +   L D  
Sbjct: 129 DEREQTLNQMLVEMDGFEGN---EGIIVIAATNRPDVLDPALLRPGRFDRQVVVGLPDVR 185

Query: 351 SFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVIT 406
             + +   ++             I +     S A++  L+       +R  K V++
Sbjct: 186 GREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVS 241

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]} Length = 258

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 71.2 bits (173), Expect = 2e-14
 Identities = 37/237 (15%), Positives = 89/237 (37%), Gaps = 14/237 (5%)

Query: 188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF 247
            +D +        ++K  +E  L+    +  +G    R  LLYGP GTGK+  A A+A+ 
Sbjct: 2   GYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANE 61

Query: 248 MSYDVYDVDLSRV--------ADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVS--L 297
                + ++   +          +        +  + ++I I++LD    ++        
Sbjct: 62  TGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVE 121

Query: 298 SGVLNFMDGVLNSCCFEERV-MVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLA 356
             +++ +  +++       V ++   N  + +D AL R GR D  +   + D +    + 
Sbjct: 122 RRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEIL 181

Query: 357 SSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQTDGE 413
             +           +E++         A++  L      +  +A++  +  +  + E
Sbjct: 182 QIHTKNMKLADDVDLEQVANETHGHVGADLAALC---SEAALQAIRKKMDLIDLEDE 235

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]} Length = 362

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

 Score = 70.9 bits (173), Expect = 6e-14
 Identities = 34/209 (16%), Positives = 69/209 (33%), Gaps = 31/209 (14%)

Query: 197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD 256
            + + V   L+  +             KR +L  GP  +GK++ AAA+         +V+
Sbjct: 135 KMDSVVYDFLKCMVY--------NIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVN 186

Query: 257 LSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVS------LSGVLNFMDGVLNS 310
           L     + +L   +     + +++ ED+     E     S      L  + +++DG +  
Sbjct: 187 LPLDRLNFELGVAI----DQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKV 242

Query: 311 CCFEE---------RVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG 361
              ++            + TMN             R    I F   D+       S +L 
Sbjct: 243 NLEKKHLNKRTQIFPPGIVTMN---EYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFL- 298

Query: 362 LKDHKLFPQVEEIFQNGSSLSPAEIGELM 390
           L+   +   +  +         AE  + +
Sbjct: 299 LEKRIIQSGIALLLMLIWYRPVAEFAQSI 327

>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 = 51.1 bits (121), Expect = 7e-08
 Identities = 25/160 (15%), Positives = 54/160 (33%), Gaps = 20/160 (12%)

Query: 200 NRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR 259
            RV  D E  ++         R    S LL GP  +GK++ AA +A   ++    +    
Sbjct: 19  TRVLDDGELLVQ---QTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPD 75

Query: 260 ---------VADDADLKSLLLQTTSKSVILIEDLD-----RFLVEKPAAVSLSGVLNFMD 305
                                  +  S ++++D++       +  + + + L  +L  + 
Sbjct: 76  KMIGFSETAKCQAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLK 135

Query: 306 GVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFP 345
                      +++ T + KD + +  +        IH P
Sbjct: 136 KAPPQGRK--LLIIGTTSRKDVLQEMEML-NAFSTTIHVP 172

>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 = 49.6 bits (118), Expect = 4e-07
 Identities = 19/175 (10%), Positives = 42/175 (24%), Gaps = 26/175 (14%)

Query: 196 TDLKNRVKSDLESFLKAKH---YYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDV 252
                    DL   L             R      ++ G   +GK+    A+   +    
Sbjct: 92  KQGHRGWLVDLTGELVGCSPVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKD 151

Query: 253 --YDVDLSRVAD------DADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVS-------L 297
               V             +  +  +        VI+I+ L   +       +        
Sbjct: 152 KYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDSLKNVIGAAGGNTTSGGISRGA 211

Query: 298 SGVLNFMDGVLNSCCFEERVMVFTMN----SKDHVDQALLRPGRIDVHIHFPLCD 348
             +L+ +  +  S       +V        + D + + +    R +        D
Sbjct: 212 FDLLSDIGAMAAS----RGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTD 262

>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 = 48.8 bits (115), Expect = 5e-07
 Identities = 25/243 (10%), Positives = 62/243 (25%), Gaps = 40/243 (16%)

Query: 197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD 256
             +NR+  +LE  ++      +       ++LL G  G+GK+S  +A+      +V  +D
Sbjct: 10  QFENRLNDNLEELIQ-----GKKAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVID 64

Query: 257 LSR-----------VADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSG------ 299
                         V          +   S  +                +  +G      
Sbjct: 65  NDTFKQQHPNFDELVKLYEKDVVKHVTPYSNRMTEAIISRLSDQGYNLVIEGTGRTTDVP 124

Query: 300 -------VLNFMDGVLNSCCFEERVMV-FTMNSKDHVDQALLRPGRIDVHIHFPLCDF-- 349
                       +  +      +      T+   + +        R        +     
Sbjct: 125 IQTATMLQAKGYETKMYVMAVPKINSYLGTIERYETMYADDPMTARATPKQAHDIVVKNL 184

Query: 350 -SSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSP------SRALK 402
            ++ +TL  + L         +  +++ +          E +    N           L+
Sbjct: 185 PTNLETLHKTGLFSDIRLYNREGVKLY-SSLETPSISPKETLEKELNRKVSGKEIQPTLE 243

Query: 403 SVI 405
            + 
Sbjct: 244 RIE 246

>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 = 44.4 bits (103), Expect = 1e-05
 Identities = 31/229 (13%), Positives = 70/229 (30%), Gaps = 13/229 (5%)

Query: 186 PSTFDTISMETDLKNRVKSDLESFLKAKHY----YHRLGRVWKRSYLLYGPSGTGKSSFA 241
           P+    +        ++K+ L ++  +K        + G    R+ +LYGP G GK++ A
Sbjct: 10  PTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA 69

Query: 242 AAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVL 301
             +A  + YD+ + + S V     L + +      ++ ++         +        ++
Sbjct: 70  HLVAQELGYDILEQNASDVRSKTLLNAGVKNALD-NMSVVGYFKHNEEAQNLNGKHFVII 128

Query: 302 NFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG 361
                 ++         +     K      L+   R    +          +        
Sbjct: 129 MDEVDGMSGGDRGGVGQLAQFCRKTSTPLILICNERNLPKMRPFDRVCLDIQFRRPDANS 188

Query: 362 LKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITALQT 410
           +K       +    +    L P  I    +         ++ VI  L T
Sbjct: 189 IKSR----LMTIAIREKFKLDPNVIDR--LIQTTRGD--IRQVINLLST 229

>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 = 44.2 bits (103), Expect = 1e-05
 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 8/102 (7%)

Query: 186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA 245
           P + D    + ++K ++   LE+                   LL GP G GK++ A  +A
Sbjct: 5   PKSLDEFIGQENVKKKLSLALEAAKMRGEVLD--------HVLLAGPPGLGKTTLAHIIA 56

Query: 246 SFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRF 287
           S +  +++      +    D+ ++L       V+ I+++ R 
Sbjct: 57  SELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRL 98

>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 = 41.1 bits (95), Expect = 1e-04
 Identities = 38/234 (16%), Positives = 78/234 (33%), Gaps = 25/234 (10%)

Query: 186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA 245
           P T D    +  LK +++  LE+         +  +      LL+GP G GK++ A  +A
Sbjct: 5   PKTLDEYIGQERLKQKLRVYLEA--------AKARKEPLEHLLLFGPPGLGKTTLAHVIA 56

Query: 246 SFMSYDVYDVDLSRVADDADLKSLLLQTTSK-SVILIEDLDRFLVEKPAAV--------- 295
             +  ++       +    DL ++L  +  +  ++ I+++ R   +    +         
Sbjct: 57  HELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVM 116

Query: 296 --SLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFK 353
              +          L    F    ++        +   LL    I  H+ +   +  +  
Sbjct: 117 DIVIGQGPAARTIRLELPRF---TLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQG 173

Query: 354 TLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVITA 407
            +  + L L          EI +  S  +      L    R+    A + VIT 
Sbjct: 174 VMRDARL-LGVRITEEAALEIGRR-SRGTMRVAKRLFRRVRDFAQVAGEEVITR 225

>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 = 39.0 bits (89), Expect = 7e-04
 Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 12/69 (17%)

Query: 186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA 245
           P + + +S   +L N     L+S                   LLYGP+GTGK +   A+ 
Sbjct: 7   PKSLNALSHNEELTNF----LKSLSDQPRDLP--------HLLLYGPNGTGKKTRCMALL 54

Query: 246 SFMSYDVYD 254
             +      
Sbjct: 55  ESIFGPGVY 63

>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 = 38.3 bits (88), Expect = 0.001
 Identities = 35/228 (15%), Positives = 73/228 (32%), Gaps = 51/228 (22%)

Query: 224 KRSYLLYGPSGTGKSSFAAAMAS---------------FMSYDVYDVDLSRVADDADLKS 268
            ++ L+ GP+G GK+  A  +A                 + Y   +VD            
Sbjct: 49  PKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEVDSIIRDLTDSAGG 108

Query: 269 LLLQTTSKSVILIEDLDRFLVEK---PAAVSLSGVL------------NFMDGVLNSCCF 313
            +       ++ I+++D+   +     A VS  GV             +   G++ +   
Sbjct: 109 AIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKT--- 165

Query: 314 EERVMVFTMNSKDHVDQALLRP---GRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ 370
            + ++     +      + L P   GR+ + +       + F+      L      L  Q
Sbjct: 166 -DHILFIASGAFQVARPSDLIPELQGRLPIRVELTALSAADFE----RILTEPHASLTEQ 220

Query: 371 VEEIF-QNGSSLSPAEIGELMIAN---------RNSPSRALKSVITAL 408
            + +    G +++        IA           N  +R L +V+  L
Sbjct: 221 YKALMATEGVNIAFTTDAVKKIAEAAFRVNEKTENIGARRLHTVMERL 268

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	480
d1e32a2	258	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	100.0
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	100.0
d1r7ra3	265	Membrane fusion ATPase VCP/p97 {Mouse (Mus musculu	100.0
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	99.9
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	99.89
d1w44a_	321	NTPase P4 {Bacteriophage phi-12 [TaxId: 161736]}	99.89
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	99.86
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	99.85
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	99.82
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	99.77
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	99.76
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	99.74
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	99.74
d1svma_	362	Papillomavirus large T antigen helicase domain {Si	99.71
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	99.65
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	99.64
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	99.61
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	99.53
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	99.5
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	99.49
d1r6bx3	315	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.48
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	99.46
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	99.43
d1qvra3	315	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.38
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	99.32
d1g8pa_	333	ATPase subunit of magnesium chelatase, BchI {Rhodo	99.3
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	99.2
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	99.2
d1ny5a2	247	Transcriptional activator sigm54 (NtrC1), C-termin	99.15
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	99.04
d2fnaa2	283	Archaeal ATPase SSO1545 {Sulfolobus solfataricus [	99.01
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	98.9
d2a5yb3	277	CED-4, NB-ARC domain {Caenorhabditis elegans [TaxI	98.25
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	98.17
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	98.12
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	98.03
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	97.97
d1tuea_	205	Replication protein E1 helicase domain {Human papi	97.95
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	97.93
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	97.91
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	97.89
d1e6ca_	170	Shikimate kinase (AroK) {Erwinia chrysanthemi [Tax	97.87
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	97.75
d1knqa_	171	Gluconate kinase {Escherichia coli [TaxId: 562]}	97.75
d2iyva1	165	Shikimate kinase (AroK) {Mycobacterium tuberculosi	97.73
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	97.68
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	97.64
d1yj5a2	172	5' polynucleotide kinase-3' phosphatase, C-termina	97.6
d1m8pa3	183	ATP sulfurylase C-terminal domain {Fungus (Penicil	97.56
d1qf9a_	194	UMP/CMP kinase {Dictyostelium discoideum [TaxId: 4	97.54
d1zina1	182	Adenylate kinase {Bacillus stearothermophilus [Tax	97.49
d1zaka1	189	Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}	97.45
d2cdna1	181	Adenylate kinase {Mycobacterium tuberculosis [TaxI	97.42
d3adka_	194	Adenylate kinase {Pig (Sus scrofa) [TaxId: 9823]}	97.4
d1ak2a1	190	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.39
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	97.39
d1x6va3	195	Adenosine-5'phosphosulfate kinase (APS kinase) {Hu	97.37
d1ukza_	196	Uridylate kinase {Baker's yeast (Saccharomyces cer	97.36
d1s3ga1	182	Adenylate kinase {Bacillus globisporus [TaxId: 145	97.34
d2ak3a1	189	Adenylate kinase {Cow (Bos taurus), mitochondrial	97.34
d1ckea_	225	CMP kinase {Escherichia coli [TaxId: 562]}	97.32
d1u0ja_	267	Rep 40 protein helicase domain {Adeno-associated v	97.32
d1akya1	180	Adenylate kinase {Baker's yeast (Saccharomyces cer	97.3
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	97.3
d1teva_	194	UMP/CMP kinase {Human (Homo sapiens) [TaxId: 9606]	97.28
d1e4va1	179	Adenylate kinase {Escherichia coli [TaxId: 562]}	97.25
d1xp8a1	268	RecA protein, ATPase-domain {Deinococcus radiodura	97.25
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	97.2
d1u94a1	263	RecA protein, ATPase-domain {Escherichia coli [Tax	97.19
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	97.16
d1q3ta_	223	CMP kinase {Streptococcus pneumoniae [TaxId: 1313]	97.16
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	97.11
d2qy9a2	211	GTPase domain of the signal recognition particle r	97.07
d1okkd2	207	GTPase domain of the signal recognition particle r	97.06
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	97.04
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	97.01
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	97.01
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	96.99
d1khta_	190	Adenylate kinase {Archaeon Methanococcus voltae [T	96.96
d1szpa2	251	DNA repair protein Rad51, catalytic domain {Baker'	96.92
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.92
d1np6a_	170	Molybdopterin-guanine dinucleotide biosynthesis pr	96.92
d1bifa1	213	6-phosphofructo-2-kinase/fructose-2,6-bisphosphata	96.89
d1vmaa2	213	GTPase domain of the signal recognition particle r	96.86
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.81
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	96.77
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	96.74
d1pzna2	254	DNA repair protein Rad51, catalytic domain {Archae	96.74
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	96.73
d1htwa_	158	Hypothetical protein HI0065 {Haemophilus influenza	96.71
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	96.68
d1n0wa_	242	DNA repair protein Rad51, catalytic domain {Human	96.66
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	96.62
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	96.61
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	96.6
d1v5wa_	258	Meiotic recombination protein DMC1/LIM15 homolog {	96.58
d1nksa_	194	Adenylate kinase {Archaeon Sulfolobus acidocaldari	96.58
d1j8yf2	211	GTPase domain of the signal sequence recognition p	96.56
d1gkya_	186	Guanylate kinase {Baker's yeast (Saccharomyces cer	96.55
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	96.5
d1m7ga_	208	Adenosine-5'phosphosulfate kinase (APS kinase) {Fu	96.49
d1lvga_	190	Guanylate kinase {Mouse (Mus musculus) [TaxId: 100	96.45
d1r8sa_	160	ADP-ribosylation factor {Human (Homo sapiens), ARF	96.45
d2awna2	232	Maltose transport protein MalK, N-terminal domain	96.43
d1g2912	240	Maltose transport protein MalK, N-terminal domain	96.42
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	96.4
d3d31a2	229	Sulfate/molybdate ABC transporter, ATP-binding pro	96.37
d1rz3a_	198	Hypothetical protein rbstp0775 {Bacillus stearothe	96.34
d1oxxk2	242	Glucose transport protein GlcV, N-terminal domain	96.22
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.15
d2i1qa2	258	DNA repair protein Rad51, catalytic domain {Archae	95.94
d1xjca_	165	Molybdopterin-guanine dinucleotide biosynthesis pr	95.75
d1znwa1	182	Guanylate kinase {Mycobacterium tuberculosis [TaxI	95.71
d1x3sa1	177	Rab18 {Human (Homo sapiens) [TaxId: 9606]}	95.66
d1h65a_	257	Chloroplast protein translocon GTPase Toc34 {Garde	95.66
d1zj6a1	177	ADP-ribosylation factor {Human (Homo sapiens), ARL	95.65
d1kkma_	176	HPr kinase HprK C-terminal domain {Lactobacillus c	95.59
d1ksha_	165	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.57
d1uj2a_	213	Uridine-cytidine kinase 2 {Human (Homo sapiens) [T	95.49
d1sq5a_	308	Pantothenate kinase PanK {Escherichia coli [TaxId:	95.4
d1nrjb_	209	Signal recognition particle receptor beta-subunit	95.38
d1kgda_	178	Guanylate kinase-like domain of Cask {Human (Homo	95.3
d1odfa_	286	Hypothetical protein Ygr205W {Baker's yeast (Sacch	95.29
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	95.28
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	95.24
d1knxa2	177	HPr kinase HprK C-terminal domain {Mycoplasma pneu	95.21
d1nn5a_	209	Thymidylate kinase {Human (Homo sapiens) [TaxId: 9	95.21
d1ko7a2	169	HPr kinase HprK C-terminal domain {Staphylococcus	95.13
d1uf9a_	191	Dephospho-CoA kinase {Thermus thermophilus [TaxId:	95.12
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	95.12
d1fzqa_	176	ADP-ribosylation factor {Mouse (Mus musculus), ARL	95.03
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	95.0
d2qtvb1	166	SAR1 {Baker's yeast (Saccharomyces cerevisiae) [Ta	94.93
d1ctqa_	166	cH-p21 Ras protein {Human (Homo sapiens) [TaxId: 9	94.85
d1yrba1	244	ATP(GTP)-binding protein PAB0955 {Pyrococcus abyss	94.8
d2fh5b1	207	Signal recognition particle receptor beta-subunit	94.8
d2gjsa1	168	Rad {Human (Homo sapiens) [TaxId: 9606]}	94.75
d1upta_	169	ADP-ribosylation factor {Human (Homo sapiens), ARL	94.71
d1z0fa1	166	Rab14 {Human (Homo sapiens) [TaxId: 9606]}	94.64
d1s96a_	205	Guanylate kinase {Escherichia coli [TaxId: 562]}	94.6
d1u8za_	168	Ras-related protein RalA {Cotton-top tamarin (Sagu	94.59
d1jjva_	205	Dephospho-CoA kinase {Haemophilus influenzae [TaxI	94.5
d1r2qa_	170	Rab5a {Human (Homo sapiens) [TaxId: 9606]}	94.44
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	94.36
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	94.35
d1vhta_	208	Dephospho-CoA kinase {Escherichia coli [TaxId: 562	94.34
d1f6ba_	186	SAR1 {Chinese hamster (Cricetulus griseus) [TaxId:	94.33
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	94.33
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	94.26
d2a5ja1	173	Rab2b {Human (Homo sapiens) [TaxId: 9606]}	94.17
d2cxxa1	184	GTP-binding protein engB {Pyrococcus horikoshii [T	94.14
d2vp4a1	197	Deoxyribonucleoside kinase {Fruit fly (Drosophila	94.1
d1e0sa_	173	ADP-ribosylation factor {Human (Homo sapiens), ARF	94.1
d1mkya1	171	Probable GTPase Der, N-terminal and middle domains	93.84
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	93.82
d1zd9a1	164	ADP-ribosylation factor {Human (Homo sapiens), ARL	93.73
d1z2aa1	164	Rab23 {Mouse (Mus musculus) [TaxId: 10090]}	93.73
d2ew1a1	171	Rab30 {Human (Homo sapiens) [TaxId: 9606]}	93.67
d1gsia_	208	Thymidylate kinase {Mycobacterium tuberculosis [Ta	93.64
d1kaoa_	167	Rap2a {Human (Homo sapiens) [TaxId: 9606]}	93.58
d3raba_	169	Rab3a {Rat (Rattus norvegicus) [TaxId: 10116]}	93.55
d1svia_	195	Probable GTPase EngB {Bacillus subtilis [TaxId: 14	93.45
d1ek0a_	170	Ypt51 {Baker's yeast (Saccharomyces cerevisiae) [T	93.43
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	93.42
d1c1ya_	167	Rap1A {Human (Homo sapiens) [TaxId: 9606]}	93.42
d2gj8a1	161	Probable tRNA modification GTPase TrmE (MnmE), G d	93.41
d2f7sa1	186	Rab27b {Human (Homo sapiens) [TaxId: 9606]}	93.4
d2atva1	168	Ras-like estrogen-regulated growth inhibitor, RERG	93.33
d4tmka_	210	Thymidylate kinase {Escherichia coli [TaxId: 562]}	93.24
d2f9la1	175	Rab11b {Human (Homo sapiens) [TaxId: 9606]}	93.21
g1f2t.1	292	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	93.21
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	93.15
d2erya1	171	r-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	93.12
d1g16a_	166	Rab-related protein Sec4 {Baker's yeast (Saccharom	93.11
d2p67a1	327	LAO/AO transport system kinase ArgK {Escherichia c	93.05
d1ky3a_	175	Rab-related protein ypt7p {Baker's yeast (Saccharo	93.04
d1vg8a_	184	Rab7 {Rat (Rattus norvegicus) [TaxId: 10116]}	93.01
d1moza_	182	ADP-ribosylation factor {Baker's yeast (Saccharomy	92.96
d1z08a1	167	Rab21 {Human (Homo sapiens) [TaxId: 9606]}	92.89
d2erxa1	171	di-Ras2 {Human (Homo sapiens) [TaxId: 9606]}	92.87
d1z06a1	165	Rab-33b {Mouse (Mus musculus) [TaxId: 10090]}	92.81
d1xtqa1	167	GTP-binding protein RheB {Human (Homo sapiens) [Ta	92.7
d1deka_	241	Deoxynucleoside monophosphate kinase {Bacteriophag	92.69
d2ocpa1	241	Deoxyguanosine kinase {Human (Homo sapiens) [TaxId	92.68
d2fn4a1	173	r-Ras {Human (Homo sapiens) [TaxId: 9606]}	92.67
d2g6ba1	170	Rab26 {Human (Homo sapiens) [TaxId: 9606]}	92.62
d1tmka_	214	Thymidylate kinase {Baker's yeast (Saccharomyces c	92.61
d2bmea1	174	Rab4a {Human (Homo sapiens) [TaxId: 9606]}	92.58
d1wmsa_	174	Rab9a {Human (Homo sapiens) [TaxId: 9606]}	92.53
d2qm8a1	323	Metallochaperone MeaB {Methylobacterium extorquens	92.42
d1wf3a1	178	GTPase Era, N-terminal domain {Thermus thermophilu	92.37
d1yzqa1	164	Rab6 {Human (Homo sapiens) [TaxId: 9606]}	92.32
d1ihua1	296	Arsenite-translocating ATPase ArsA {Escherichia co	92.31
d1kmqa_	177	RhoA {Human (Homo sapiens) [TaxId: 9606]}	92.31
d1b0ua_	258	ATP-binding subunit of the histidine permease {Sal	92.31
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	91.93
d1z0ja1	167	Rab-22a {Mouse (Mus musculus) [TaxId: 10090]}	91.93
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	91.87
d1p5zb_	241	Deoxycytidine kinase {Human (Homo sapiens) [TaxId:	91.8
d1x1ra1	169	Ras-related protein M-Ras (XRas) {Mouse (Mus muscu	91.68
d2bcgy1	194	GTPase Ytp1 {Baker's yeast (Saccharomyces cerevisi	91.65
d2g3ya1	172	GTP-binding protein GEM {Human (Homo sapiens) [Tax	91.62
d1egaa1	179	GTPase Era, N-terminal domain {Escherichia coli [T	91.51
d2fu5c1	173	Rab8a {Mouse (Mus musculus) [TaxId: 10090]}	91.49
d1i2ma_	170	Ran {Human (Homo sapiens) [TaxId: 9606]}	91.45
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	91.44
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	91.32
d1u0la2	225	Probable GTPase EngC (YjeQ), C-terminal domain {Th	91.3
d1mkya2	186	Probable GTPase Der, N-terminal and middle domains	91.24
d1m7ba_	179	RhoE (RND3) {Mouse (Mus musculus) [TaxId: 10090]}	91.21
g1xew.1	329	Smc head domain {Pyrococcus furiosus [TaxId: 2261]	91.17
d1mh1a_	183	Rac {Human (Homo sapiens) [TaxId: 9606]}	91.08
d2atxa1	185	RhoQ {Human (Homo sapiens) [TaxId: 9606]}	91.02
d1xzpa2	160	TrmE GTPase domain {Thermotoga maritima [TaxId: 23	91.0
d1g6ha_	254	MJ1267 {Archaeon Methanococcus jannaschii [TaxId:	90.97
d2ngra_	191	CDC42 {Human (Homo sapiens) [TaxId: 9606]}	90.87
g1ii8.1	369	Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.85
d1puia_	188	Probable GTPase EngB {Escherichia coli [TaxId: 562	90.7
d1qhla_	222	Cell division protein MukB {Escherichia coli [TaxI	90.67
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	90.62
d1lnza2	185	Obg GTP-binding protein middle domain {Bacillus su	90.54
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	90.44
d1a7ja_	288	Phosphoribulokinase {Rhodobacter sphaeroides [TaxI	90.39
d1byia_	224	Dethiobiotin synthetase {Escherichia coli [TaxId:	90.3
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	90.03
d1udxa2	180	Obg GTP-binding protein middle domain {Thermus the	89.76
d1e69a_	308	Smc head domain {Thermotoga maritima [TaxId: 2336]	88.81
d1zcba2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	88.71
d2bmja1	175	Centaurin gamma 1, G domain {Human (Homo sapiens)	88.19
d1ihua2	279	Arsenite-translocating ATPase ArsA {Escherichia co	88.17
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	88.12
d1t9ha2	231	Probable GTPase EngC (YjeQ), C-terminal domain {Ba	88.11
d1w1wa_	427	Smc head domain {Baker's yeast (Saccharomyces cere	87.35
d1azta2	221	Transducin (alpha subunit) {Cow (Bos taurus) [TaxI	87.08
d1nija1	222	Hypothetical protein YjiA, N-terminal domain {Esch	86.89
d1xpua3	289	Transcription termination factor Rho, ATPase domai	86.31
d1p6xa_	333	Thymidine kinase {Equine herpesvirus type 4 [TaxId	86.2
d2bcjq2	200	Transducin (alpha subunit) {Mouse (Mus musculus) [	85.88
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	85.47
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	85.16
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	84.83
d1ry6a_	330	Kinesin {Malaria parasite (Plasmodium falciparum)	84.23
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	84.16
d1cp2a_	269	Nitrogenase iron protein {Clostridium pasteurianum	84.03
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	83.2
d1osna_	331	Thymidine kinase {Varicella-zoster virus [TaxId: 1	83.17
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	82.88
d1j3ba1	318	Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxalo	82.32
d1tq4a_	400	Interferon-inducible GTPase {Mouse (Mus musculus)	82.06
d1hyqa_	232	Cell division regulator MinD {Archaeon Archaeoglob	81.43
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	81.02
d1svsa1	195	Transducin (alpha subunit) {Rat (Rattus norvegicus	81.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	80.8
d2jdid3	276	Central domain of beta subunit of F1 ATP synthase	80.72
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	80.29
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	80.19

>d1e32a2 c.37.1.20 (A:201-458) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=2.6e-42  Score=337.11  Aligned_cols=205  Identities=20%  Similarity=0.272  Sum_probs=180.9

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC----
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD----  262 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~----  262 (480)
                      ++|+||+|.+++|++|.+.+..++++++.|.+.|.++++|+|||||||||||++++++|++++.+++.++++.+.+    
T Consensus         1 ~~~~dv~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~GppGtGKT~l~~ala~~~~~~~~~i~~~~l~~~~~g   80 (258)
T d1e32a2           1 VGYDDVGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAG   80 (258)
T ss_dssp             CCGGGCCSCSHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCTTSSHHHHHHHHHHHTTCEEEEECHHHHTTSCTT
T ss_pred             CChhhhccHHHHHHHHHHHHHHHhcCHHHHHhCCCCCCceeEEecCCCCCchHHHHHHHHHhCCeEEEEEchhhcccccc
Confidence            5799999999999999999999999999999999999999999999999999999999999999999999765432    


Q ss_pred             --hHHHHHHHHh--hcCCcEEEEecccccccCcccc------cchhhhhhhcccccccccCCceEEEEecCCCccCcccc
Q 011664          263 --DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQAL  332 (480)
Q Consensus       263 --~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aL  332 (480)
                        +..++.+|..  ..+||||||||+|.++..+...      ..++.+++.+++...   ..+++||+|||+|+.+|+|+
T Consensus        81 ~~~~~l~~~f~~A~~~~p~il~iDeid~l~~~r~~~~~~~~~~~~~~~~~~~~~~~~---~~~vlvi~tTn~~~~ld~al  157 (258)
T d1e32a2          81 ESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQ---RAHVIVMAATNRPNSIDPAL  157 (258)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCCC---SSCEEEEEEESCGGGSCGGG
T ss_pred             cHHHHHHHHHHHHHhcCCeEEEehhhhhhccCCCCCCCchHHHHHHHhccccccccc---cCCccEEEeCCCccccchhh
Confidence              3457777754  5799999999999998754332      346778888887765   67788999999999999999


Q ss_pred             cCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          333 LRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       333 lrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      +||||||++|+|++|+.++|.+|++.+++........+++.|+..|.|||++||.++|+.+.
T Consensus       158 ~r~gRfd~~i~~~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adl~~lv~~A~  219 (258)
T d1e32a2         158 RRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAA  219 (258)
T ss_dssp             TSTTSSCEEEECCCCCHHHHHHHHHHTTTTSCBCTTCCHHHHHHHCTTCCHHHHHHHHHHHH
T ss_pred             hhcccccceeECCCCCHHHHHHHhhhhccCcccccccchhhhhhcccCCCHHHHHHHHHHHH
Confidence            99999999999999999999999999998766555567899999999999999999998653

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=100.00  E-value=3.4e-41  Score=327.20  Aligned_cols=206  Identities=22%  Similarity=0.292  Sum_probs=179.2

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC--
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA--  261 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~--  261 (480)
                      .|+++|+||+|.+++|+.|.+. ..++.+++.|.++|..+++|+|||||||||||++|+++|++++.+++.++++++.  
T Consensus         3 ~p~~~~~di~G~~~~k~~l~~~-i~~l~~~~~~~~~g~~~~~giLl~GppGtGKT~la~aia~~~~~~~~~i~~~~l~~~   81 (247)
T d1ixza_           3 APKVTFKDVAGAEEAKEELKEI-VEFLKNPSRFHEMGARIPKGVLLVGPPGVGKTHLARAVAGEARVPFITASGSDFVEM   81 (247)
T ss_dssp             CCSCCGGGCCSCHHHHHHHHHH-HHHHHCHHHHHHTTCCCCSEEEEECCTTSSHHHHHHHHHHHTTCCEEEEEHHHHHHS
T ss_pred             CCCCcHHHHccHHHHHHHHHHH-HHHHHCHHHHHHcCCCCCceEEEecCCCCChhHHHHHHHHHcCCCEEEEEhHHhhhc
Confidence            4678999999999999999765 5678999999999999999999999999999999999999999999999987653  


Q ss_pred             --C--hHHHHHHHHh--hcCCcEEEEecccccccCcccc---------cchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          262 --D--DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA---------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       262 --~--~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~---------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                        +  +..++++|..  ..+||||||||+|.++..+...         ..+++|++.||++..   ..+++||+|||+|+
T Consensus        82 ~~g~~~~~l~~~f~~a~~~~p~Ii~iDeid~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~---~~~vivi~tTn~~~  158 (247)
T d1ixza_          82 FVGVGAARVRDLFETAKRHAPCIVFIDEIDAVGRKRGSGVGGGNDEREQTLNQLLVEMDGFEK---DTAIVVMAATNRPD  158 (247)
T ss_dssp             CTTHHHHHHHHHHHHHTTSSSEEEEEETHHHHHC---------CHHHHHHHHHHHHHHHTCCT---TCCEEEEEEESCGG
T ss_pred             cccHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCC---CCCEEEEEeCCCcc
Confidence              2  3457888855  4689999999999998754322         347889999999876   56788889999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .||++++||||||.+|+|++|+.++|.+|++.++.........+++.+++.+.|||++||.++|+.+
T Consensus       159 ~ld~al~R~~Rf~~~i~~~~P~~~eR~~il~~~l~~~~~~~~~~~~~la~~t~g~s~~di~~lv~~A  225 (247)
T d1ixza_         159 ILDPALLRPGRFDRQIAIDAPDVKGREQILRIHARGKPLAEDVDLALLAKRTPGFVGADLENLLNEA  225 (247)
T ss_dssp             GSCGGGGSTTSSCEEEECCSCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             ccCHhHcCCCCCcEEEEECCcCHHHHHHHHHHHhcccCCccccCHHHHHHHCCCCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999877666666789999999999999999999755

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=100.00  E-value=5e-41  Score=327.61  Aligned_cols=206  Identities=22%  Similarity=0.328  Sum_probs=177.9

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC-
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD-  262 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~-  262 (480)
                      ..++||+||+|.+++|++|.+.+ .++++++.|.++|..+++|+|||||||||||++|+++|++++.+++.++++++.+ 
T Consensus         6 ~~~~t~~Di~Gl~~~k~~l~e~v-~~~~~~~~~~~~g~~~~~~iLL~GppGtGKT~la~~iA~~~~~~~~~i~~~~l~~~   84 (256)
T d1lv7a_           6 QIKTTFADVAGCDEAKEEVAELV-EYLREPSRFQKLGGKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM   84 (256)
T ss_dssp             SSCCCGGGSCSCHHHHHHTHHHH-HHHHCGGGC-----CCCCEEEEECCTTSCHHHHHHHHHHHHTCCEEEECSCSSTTS
T ss_pred             CCCCCHHHHhchHHHHHHHHHHH-HHHHCHHHHHHcCCCCCCeEEeeCCCCCCccHHHHHHHHHcCCCEEEEEhHHhhhc
Confidence            35689999999999999998865 5788999999999999999999999999999999999999999999999988753 


Q ss_pred             -----hHHHHHHHHh--hcCCcEEEEecccccccCcccc---------cchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          263 -----DADLKSLLLQ--TTSKSVILIEDLDRFLVEKPAA---------VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       263 -----~~~l~~l~~~--~~~~sII~IDEiD~l~~~~~~~---------~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                           +..++++|..  ..+||||||||+|.+++.++..         ..+++|++.||++.+   .++++||+|||+|+
T Consensus        85 ~~g~~~~~l~~~f~~A~~~~P~il~iDeiD~l~~~r~~~~~~~~~~~~~~~~~ll~~~d~~~~---~~~v~vIatTn~~~  161 (256)
T d1lv7a_          85 FVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGGGHDEREQTLNQMLVEMDGFEG---NEGIIVIAATNRPD  161 (256)
T ss_dssp             CCCCCHHHHHHHHHHHHTTCSEEEEETTHHHHTCCCSTTSCCTTCHHHHHHHHHHHHHHTCCS---SSCEEEEEEESCTT
T ss_pred             chhHHHHHHHHHHHHHHHcCCEEEEEEChhhhCccCCCCCCCCcHHHHHHHHHHHHHhhCCCC---CCCEEEEEeCCCcc
Confidence                 5668888855  4689999999999998755322         246789999999866   56788999999999


Q ss_pred             cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          327 HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       327 ~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      .|||+++||||||.+|+|++|+.++|.+|++.++.........++..+++.+.|||++||..+|..+
T Consensus       162 ~ld~al~R~gRfd~~i~i~~P~~~~R~~il~~~l~~~~~~~~~~~~~la~~t~G~s~adi~~l~~~A  228 (256)
T d1lv7a_         162 VLDPALLRPGRFDRQVVVGLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEA  228 (256)
T ss_dssp             TSCGGGGSTTSSCEEEECCCCCHHHHHHHHHHHHTTSCBCTTCCHHHHHHTCTTCCHHHHHHHHHHH
T ss_pred             cCCHhHcCCCCCCEEEECCCcCHHHHHHHHHHhccCCCcCcccCHHHHHHhCCCCCHHHHHHHHHHH
Confidence            9999999999999999999999999999999999877766666889999999999999999999765

>d1r7ra3 c.37.1.20 (A:471-735) Membrane fusion ATPase VCP/p97 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Membrane fusion ATPase VCP/p97
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=4.8e-39  Score=315.12  Aligned_cols=208  Identities=21%  Similarity=0.310  Sum_probs=175.8

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC---
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA---  261 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~---  261 (480)
                      |..+|++|+|.+++|++|.+.+..|+.+++.|.+.|.++++|+|||||||||||++|+++|++++.+++.++++.+.   
T Consensus         2 p~~~f~di~G~~~~k~~l~~~i~~~l~~~~~~~~~g~~~~~giLL~Gp~GtGKT~l~~ala~~~~~~~~~~~~~~l~~~~   81 (265)
T d1r7ra3           2 PQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMW   81 (265)
T ss_dssp             CCCSCSSCSSSSCCCCHHHHHTHHHHHCHHHHHHCCCCCCCEEEEBCCTTSSHHHHHHHHHHHTTCEEEEECHHHHHTSC
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhCCCCCCCeEEEECCCCCcchhHHHHHHHHhCCcEEEEEHHHhhhcc
Confidence            46799999999999999999999999999999999999999999999999999999999999999999999976543   


Q ss_pred             -C--hHHHHHHHH--hhcCCcEEEEecccccccCccc---------ccchhhhhhhcccccccccCCceEEEEecCCCcc
Q 011664          262 -D--DADLKSLLL--QTTSKSVILIEDLDRFLVEKPA---------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDH  327 (480)
Q Consensus       262 -~--~~~l~~l~~--~~~~~sII~IDEiD~l~~~~~~---------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~  327 (480)
                       +  +..++.+|.  +..+||||+|||+|.++..++.         ...++.|++.||++..   ..+++||+|||+|+.
T Consensus        82 ~~~~~~~l~~~f~~A~~~~p~il~ideid~l~~~~~~~~~~~~~~~~~~~~~ll~~l~~~~~---~~~v~vi~ttn~~~~  158 (265)
T d1r7ra3          82 FGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMST---KKNVFIIGATNRPDI  158 (265)
T ss_dssp             TTTHHHHHHHHHHHHHHTCSEEEEESSGGGTCCHHHHCCCTTHHHHHHHHHHHHHTCC---------CCEEEECCBSCTT
T ss_pred             ccchHHHHHHHHHHHHhcCCcceeHHhhhhccccCCCcCCCCcHHHHHHHHHHHHHhhCcCC---CCCEEEEEeCCCchh
Confidence             2  355777774  4578999999999999875421         1246889999999876   467899999999999


Q ss_pred             CcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          328 VDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       328 LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                      |||+++|||||+.+|+|++|+.++|.+|++.+++........+++.++..+.|||++||..+|+.+..
T Consensus       159 ld~al~r~gRf~~~i~~~~p~~~~R~~il~~~l~~~~~~~~~~l~~la~~t~g~s~~di~~lv~~A~~  226 (265)
T d1r7ra3         159 IDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACK  226 (265)
T ss_dssp             TSCGGGSSTTSEEEEECCCCCCHHHHHHHHHHTTCC----CCCCHHHHHHHCSSCCHHHHHHHHHHHH
T ss_pred             CCHHHhCCCCccEEEEecchHHHHHHHHHHHHhccCCchhhhhHHHHHhcCCCCCHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999976544444577899999999999999999976543

>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=99.90  E-value=6.4e-24  Score=204.73  Aligned_cols=211  Identities=18%  Similarity=0.183  Sum_probs=141.3

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC-C------h
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA-D------D  263 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~-~------~  263 (480)
                      -++|..+..+.+.+.+..+......   ....+++|+|||||||||||++|+++|++++.+++.+++++.. +      .
T Consensus        10 ~~i~~~~~i~~i~~~~~~~~~~~~~---~~~~p~~~vLL~GppGtGKT~la~alA~~~~~~~~~i~~~~~~~g~~~~~~~   86 (246)
T d1d2na_          10 GIIKWGDPVTRVLDDGELLVQQTKN---SDRTPLVSVLLEGPPHSGKTALAAKIAEESNFPFIKICSPDKMIGFSETAKC   86 (246)
T ss_dssp             CCCCCSHHHHHHHHHHHHHHHHHHH---CSSCSEEEEEEECSTTSSHHHHHHHHHHHHTCSEEEEECGGGCTTCCHHHHH
T ss_pred             CCcCcCHHHHHHHHHHHHHHHHHhc---cCCCCCeEEEEECcCCCCHHHHHHHHhhcccccccccccccccccccccchh
Confidence            3566666777888888877765322   2234578999999999999999999999999999999977532 1      2


Q ss_pred             HHHHHHHHhh--cCCcEEEEecccccccCcc-----cccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCC
Q 011664          264 ADLKSLLLQT--TSKSVILIEDLDRFLVEKP-----AAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPG  336 (480)
Q Consensus       264 ~~l~~l~~~~--~~~sII~IDEiD~l~~~~~-----~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpG  336 (480)
                      ..++.+|..+  .+||||||||||.+++.+.     .+..+..|+..|++....  ...++||+|||+|+.+|++.++ +
T Consensus        87 ~~i~~if~~A~~~~p~il~iDEid~l~~~~~~~~~~~~~~~~~ll~~l~~~~~~--~~~v~vi~tTn~~~~ld~~~~~-~  163 (246)
T d1d2na_          87 QAMKKIFDDAYKSQLSCVVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQ--GRKLLIIGTTSRKDVLQEMEML-N  163 (246)
T ss_dssp             HHHHHHHHHHHTSSEEEEEECCHHHHTTCBTTTTBCCHHHHHHHHHHTTCCCST--TCEEEEEEEESCHHHHHHTTCT-T
T ss_pred             hhhhhhhhhhhhcccceeehhhhhhHhhhcccccchhHHHHHHHHHHhcCCCcc--ccceeeeeccCChhhccchhhc-C
Confidence            3477787544  5789999999999876432     234567889999988652  4456788899999999976443 5


Q ss_pred             ceeEEEEcCCCC-HHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHH-HHHHHHH----HhhhcHHHHHHHHHHHHHh
Q 011664          337 RIDVHIHFPLCD-FSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPA-EIGELMI----ANRNSPSRALKSVITALQT  410 (480)
Q Consensus       337 Rfd~~I~~~~p~-~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~a-dI~~ll~----~a~~~~~~al~~~i~~~~~  410 (480)
                      ||+.+|++|.+. .++...+++...    .....+...++..+.|.+.. .++.++.    .....+.....+.+..++.
T Consensus       164 rF~~~i~~P~~~~r~~il~~l~~~~----~~~~~~~~~i~~~~~g~~~~~~ik~ll~~ie~a~~~~~~~~~~~~l~~l~e  239 (246)
T d1d2na_         164 AFSTTIHVPNIATGEQLLEALELLG----NFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDPEYRVRKFLALLRE  239 (246)
T ss_dssp             TSSEEEECCCEEEHHHHHHHHHHHT----CSCHHHHHHHHHHHTTSEEEECHHHHHHHHHHHTTSCGGGHHHHHHHHHHH
T ss_pred             ccceEEecCCchhHHHHHHHHHhcc----CCChHHHHHHHHHcCCCccchhHHHHHHHHHHHHhcCcccHHHHHHHHHHh
Confidence            999999996554 333333443331    12234556666666554321 1233221    1223445556666666665


Q ss_pred             c
Q 011664          411 D  411 (480)
Q Consensus       411 ~  411 (480)
                      .
T Consensus       240 ~  240 (246)
T d1d2na_         240 E  240 (246)
T ss_dssp             T
T ss_pred             c
Confidence            5

>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=99.89  E-value=1.3e-22  Score=192.75  Aligned_cols=193  Identities=16%  Similarity=0.215  Sum_probs=148.1

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD  263 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~  263 (480)
                      -+|.+|++++|++++++.+...+......       + .+..++|||||||||||++|+++|++++.+++.++.+.....
T Consensus         3 ~RP~~~~divGqe~~~~~l~~~i~~~~~~-------~-~~~~~~L~~GPpGtGKT~lA~~la~~~~~~~~~~~~~~~~~~   74 (238)
T d1in4a2           3 LRPKSLDEFIGQENVKKKLSLALEAAKMR-------G-EVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQ   74 (238)
T ss_dssp             TSCSSGGGCCSCHHHHHHHHHHHHHHHHH-------T-CCCCCEEEESSTTSSHHHHHHHHHHHHTCCEEEEETTTCCSH
T ss_pred             CCCCcHHHcCChHHHHHHHHHHHHHHHhc-------C-CCCCeEEEECCCCCcHHHHHHHHHhccCCCcccccCcccccH
Confidence            36889999999999999999887655332       2 234589999999999999999999999999999999888888


Q ss_pred             HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccc-----------c--cccCCceEEEEecCCCccCcc
Q 011664          264 ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVL-----------N--SCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       264 ~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~-----------~--~~~~~~~ivI~tTN~~~~LD~  330 (480)
                      .++...+......++++|||+|.+.....     ..++..++...           .  .......++|++||++..+++
T Consensus        75 ~~~~~~~~~~~~~~~~~ide~~~~~~~~~-----~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~at~~~~~~~~  149 (238)
T d1in4a2          75 GDMAAILTSLERGDVLFIDEIHRLNKAVE-----ELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSS  149 (238)
T ss_dssp             HHHHHHHHHCCTTCEEEEETGGGCCHHHH-----HHHHHHHHTSCCCC---------------CCCEEEEEESCGGGSCH
T ss_pred             HHHHHHHHhhccCCchHHHHHHHhhhHHH-----hhcccceeeeeeeeeecCcccccccccCCCCeEEEEecCCCccccc
Confidence            88888888888899999999998843211     11222221100           0  001235688999999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhCCCCCHHHHHHHHHH
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNGSSLSPAEIGELMIA  392 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~~g~s~adI~~ll~~  392 (480)
                      ++++  ||...+.++.|+.+++..+++.+....+..+.++ ++.++..+ +.+..++.+++..
T Consensus       150 ~~~~--r~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~l~~i~~~s-~gd~R~ai~~l~~  209 (238)
T d1in4a2         150 PLRS--RFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRS-RGTPRIAIRLTKR  209 (238)
T ss_dssp             HHHT--TCSEEEECCCCCHHHHHHHHHHHHHHTTCCBCHHHHHHHHHTS-TTCHHHHHHHHHH
T ss_pred             ccee--eeeEEEEecCCCHHHHHHHHHHhhhhccchhhHHHHHHHHHhC-CCCHHHHHHHHHH
Confidence            9999  9999999999999999999999998888777766 45666554 4466666665543

>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=99.89  E-value=1.9e-26  Score=229.63  Aligned_cols=146  Identities=11%  Similarity=0.111  Sum_probs=118.8

Q ss_pred             hhHHhhhCCCCCceEEE-EccCCCcHHHHHHHHHHcCC--CcEEEEeCCCcCC------hHHHHHHHHhhcCCcEEEEec
Q 011664          213 KHYYHRLGRVWKRSYLL-YGPSGTGKSSFAAAMASFMS--YDVYDVDLSRVAD------DADLKSLLLQTTSKSVILIED  283 (480)
Q Consensus       213 ~~~~~~~g~~~~rgiLL-~GPpGTGKT~La~aiA~~l~--~~~~~i~~s~~~~------~~~l~~l~~~~~~~sII~IDE  283 (480)
                      |..+..+|...++|++| |||||||||++|+++|++++  .+|+.++.+++.+      +..++.+|.++..||||||||
T Consensus       111 ~~~~~~~~~~~~~g~~l~~G~pG~GKT~la~ala~~~~~~~~~~~~~~~~~~~~~~G~~e~~~~~~f~~a~~~~ilf~DE  190 (321)
T d1w44a_         111 PVVAEFGGHRYASGMVIVTGKGNSGKTPLVHALGEALGGKDKYATVRFGEPLSGYNTDFNVFVDDIARAMLQHRVIVIDS  190 (321)
T ss_dssp             CEEEEETTEEEESEEEEEECSSSSCHHHHHHHHHHHHHTTSCCEEEEBSCSSTTCBCCHHHHHHHHHHHHHHCSEEEEEC
T ss_pred             hHHHHHhhcccCCceEEEECCCCccHHHHHHHHHHHhcCCCCeEEEEhhHhhhcccchHHHHHHHHHHHHhhccEEEeeh
Confidence            44556667666777665 89999999999999999986  6799999887653      566999998888899999999


Q ss_pred             ccccccCccc-------ccchhhhhhhcccccccccCCceEEEEecCC---CccCcccccCCCceeEEEEcCCCCHHHHH
Q 011664          284 LDRFLVEKPA-------AVSLSGVLNFMDGVLNSCCFEERVMVFTMNS---KDHVDQALLRPGRIDVHIHFPLCDFSSFK  353 (480)
Q Consensus       284 iD~l~~~~~~-------~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~---~~~LD~aLlrpGRfd~~I~~~~p~~~~r~  353 (480)
                      ||.+.+.++.       .+++++||..|||+..   ..+++||+|||+   ++.||++++||||||++|++++|+.+.|.
T Consensus       191 id~~~~~r~~~~~~~~~~r~v~~lL~e~dg~~~---~~~v~viaatN~~~~~~~i~~~~~r~~Rf~~~v~v~~pd~~~r~  267 (321)
T d1w44a_         191 LKNVIGAAGGNTTSGGISRGAFDLLSDIGAMAA---SRGCVVIASLNPTSNDDKIVELVKEASRSNSTSLVISTDVDGEW  267 (321)
T ss_dssp             CTTTC-----------CCHHHHHHHHHHHHHHH---HHTCEEEEECCCCCCCHHHHHHHHHHHHHSCSEEEEECSSTTEE
T ss_pred             hhhhccccccCCCCCcchhhhhhhhhhcccccc---CCCeEEEEeCCCcccccchhhhhhccCcccceeecCCCChHHHH
Confidence            9999876532       2568999999999987   567899999994   24466777899999999999999999999


Q ss_pred             HHHHHHhc
Q 011664          354 TLASSYLG  361 (480)
Q Consensus       354 ~il~~~l~  361 (480)
                      +|+..+..
T Consensus       268 ~il~~~~~  275 (321)
T d1w44a_         268 QVLTRTGE  275 (321)
T ss_dssp             EEEEECBT
T ss_pred             HHHHHhcc
Confidence            99877654

>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=99.86  E-value=2.7e-22  Score=199.36  Aligned_cols=166  Identities=16%  Similarity=0.279  Sum_probs=126.7

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhhC-CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCC--------
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRLG-RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVAD--------  262 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~g-~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~--------  262 (480)
                      |+|++++|+.|.+.+...+++........ ..+++|+||+||||||||+||+++|++++.+++.++++.+..        
T Consensus        16 ViGQd~A~~~l~~av~~~~~r~~~~~~~~~~~~~~~iLl~GPpG~GKT~lAkalA~~~~~~~~~i~~s~~~~~~~~~~~~   95 (309)
T d1ofha_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGKEV   95 (309)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHTTSSCHHHHHHCCCCCEEEECCTTSSHHHHHHHHHHHHTCCEEEEEGGGGSSCCSGGGST
T ss_pred             ccChHHHHHHHHHHHHHHHHHhccCCCCccCCCCceEEEECCCCCCHHHHHHHHhhccccchhcccccccccceeEeeec
Confidence            79999999999988866655443322221 225689999999999999999999999999999999987752        


Q ss_pred             hHHHHHHHHhhc-------CCcEEEEecccccccCcccc-------cchhhhhhhcccccccc-----cCCceEEEEe--
Q 011664          263 DADLKSLLLQTT-------SKSVILIEDLDRFLVEKPAA-------VSLSGVLNFMDGVLNSC-----CFEERVMVFT--  321 (480)
Q Consensus       263 ~~~l~~l~~~~~-------~~sII~IDEiD~l~~~~~~~-------~~ls~lL~~ldg~~~~~-----~~~~~ivI~t--  321 (480)
                      ++.++.+|..+.       +||||||||||.+++.+...       ..+++||..|||.....     ...++++|++  
T Consensus        96 ~~~~~~~f~~a~~~~~~~~~~~IIf~DEIdki~~~~~~~~~~~~~~gv~~~LL~~~dg~~~~~~~~~i~~s~ilfi~~ga  175 (309)
T d1ofha_          96 DSIIRDLTDSAGGAIDAVEQNGIVFIDEIDKICKKGEYSGADVSREGVQRDLLPLVEGSTVSTKHGMVKTDHILFIASGA  175 (309)
T ss_dssp             THHHHHHHHTTTTCHHHHHHHCEEEEECGGGGSCCSSCCSSHHHHHHHHHHHHHHHHCCEEEETTEEEECTTCEEEEEEC
T ss_pred             cccccccchhhhcccccccCCceEEehhhhhhhhhccCcccchhhhHHHHHhhHHhcCCEEecCCeEEEccceeEEeccc
Confidence            345777776542       48999999999998755432       24677999999854310     0123445554  


Q ss_pred             --cCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHH
Q 011664          322 --MNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSY  359 (480)
Q Consensus       322 --TN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~  359 (480)
                        +|.++.++|+++.  ||+..+.++.|+..++.+|+..+
T Consensus       176 ~~~~~~~~~~p~l~~--R~~~~i~~~~~~~~~~~~Il~~~  213 (309)
T d1ofha_         176 FQVARPSDLIPELQG--RLPIRVELTALSAADFERILTEP  213 (309)
T ss_dssp             CSSSCGGGSCHHHHH--TCCEEEECCCCCHHHHHHHHHSS
T ss_pred             hhhcCcccchhhhhh--hhheeeeccCCCHHHHHHHHHHH
Confidence              5788888999886  99999999999999999998654

>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=99.85  E-value=1.7e-20  Score=178.29  Aligned_cols=181  Identities=16%  Similarity=0.239  Sum_probs=132.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA  264 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~  264 (480)
                      +|.+|++++|++++++.+...+..+..        +...+.++|||||||||||++|+++|+++++++..++.+......
T Consensus         4 RP~~~ddivGq~~~~~~L~~~i~~~~~--------~~~~~~~~Ll~GPpG~GKTtla~~la~~~~~~~~~~~~~~~~~~~   75 (239)
T d1ixsb2           4 RPKTLDEYIGQERLKQKLRVYLEAAKA--------RKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPG   75 (239)
T ss_dssp             CCCSGGGSCSCHHHHHHHHHHHHHHTT--------SSSCCCCEEEECCTTSCHHHHHHHHHHHHTCCEEEEETTTCCSHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHh--------cCCCCCeEEEECCCCCCHHHHHHHHHHHhCCCeEeccCCccccch
Confidence            688999999999999999877654322        223456899999999999999999999999999999988876655


Q ss_pred             HHHHHHHhh-cCCcEEEEecccccccCcccccchhhhhhhcccc-----cc--------cccCCceEEEEecCCCccCcc
Q 011664          265 DLKSLLLQT-TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV-----LN--------SCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       265 ~l~~l~~~~-~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~-----~~--------~~~~~~~ivI~tTN~~~~LD~  330 (480)
                      .....+... ...+|++|||+|.+.....     ..++..|+..     ..        .......++|++||++...++
T Consensus        76 ~~~~~~~~~~~~~~i~~iDe~~~~~~~~~-----~~l~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~  150 (239)
T d1ixsb2          76 DLAAILANSLEEGDILFIDEIHRLSRQAE-----EHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITA  150 (239)
T ss_dssp             HHHHHHHTTCCTTCEEEEETGGGCCHHHH-----HHHHHHHHHSEEEEECSCTTCCCEEEEECCCCEEEEEESCCSSCSC
T ss_pred             hhHHHHHhhccCCCeeeeecccccchhHH-----HhhhhhhhhhhhhhhhccchhhhhcccCCCCEEEEeeccCcccccc
Confidence            544444433 3568999999998853211     2222222110     00        011345678889999999888


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCC
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSS  380 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g  380 (480)
                      +.++  |+...+.+..|+.+.+..++...+...+.....+. +.++..+.|
T Consensus       151 ~~l~--~~~~~~~~~~~~~~~~~~i~~~~~~~~~i~~~~~~l~~ia~~s~g  199 (239)
T d1ixsb2         151 PLLS--RFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRG  199 (239)
T ss_dssp             GGGG--GCSEEEECCCCCHHHHHHHHHHHHGGGCCCBCHHHHHHHHHHTTS
T ss_pred             hhhc--ccceeeEeeccChhhhhHHHHHHHHHhCCccchHHHHHHHHHcCC
Confidence            8888  88889999999999999999998887776665443 556555544

>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=99.82  E-value=1.7e-19  Score=171.98  Aligned_cols=184  Identities=18%  Similarity=0.259  Sum_probs=127.1

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhH----HhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHY----YHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR  259 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~----~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~  259 (480)
                      -.|.+|++++|+++.+++|.+.+..+......    +...+..+.+++|||||||||||++|+++|++++.+++.++.+.
T Consensus         8 y~P~~~~dlig~~~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a~~la~~~~~~~~~~~~~~   87 (253)
T d1sxja2           8 YAPTNLQQVCGNKGSVMKLKNWLANWENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAAHLVAQELGYDILEQNASD   87 (253)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHHTHHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHHHHHHHHTTCEEEEECTTS
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHHhhhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHHHHHHHHHHhhhhcccccc
Confidence            46889999999999999999988876543321    23345566779999999999999999999999999999999998


Q ss_pred             cCChHHHHHHHHh--------------------hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEE
Q 011664          260 VADDADLKSLLLQ--------------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMV  319 (480)
Q Consensus       260 ~~~~~~l~~l~~~--------------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI  319 (480)
                      ..+...+...+..                    ...+.++++||+|.+....  ......++......     ....+++
T Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vi~ide~~~~~~~~--~~~~~~~~~~~~~~-----~~~ii~i  160 (253)
T d1sxja2          88 VRSKTLLNAGVKNALDNMSVVGYFKHNEEAQNLNGKHFVIIMDEVDGMSGGD--RGGVGQLAQFCRKT-----STPLILI  160 (253)
T ss_dssp             CCCHHHHHHTGGGGTTBCCSTTTTTC----CCSSTTSEEEEECSGGGCCTTS--TTHHHHHHHHHHHC-----SSCEEEE
T ss_pred             chhhHHHHHHHHHHhhcchhhhhhhhhhhcccccccceEEEeeeccccccch--hhhhHHHhhhhccc-----ccccccc
Confidence            8766555443211                    1235799999999885432  22223333333211     2233444


Q ss_pred             EecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHhC
Q 011664          320 FTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQNG  378 (480)
Q Consensus       320 ~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~~  378 (480)
                      ++++....+++ ++   |+...|+|++|+.+++..+++.++..++..+.++ ++.++..+
T Consensus       161 ~~~~~~~~~~~-l~---~~~~~i~f~~~~~~~i~~~l~~i~~~e~i~i~~~~l~~i~~~s  216 (253)
T d1sxja2         161 CNERNLPKMRP-FD---RVCLDIQFRRPDANSIKSRLMTIAIREKFKLDPNVIDRLIQTT  216 (253)
T ss_dssp             ESCTTSSTTGG-GT---TTSEEEECCCCCHHHHHHHHHHHHHHHTCCCCTTHHHHHHHHT
T ss_pred             ccccccccccc-cc---ceeeeeeccccchhHHHHHHHHHHHHhCCCCCHHHHHHHHHhC
Confidence            44455555554 44   4557999999999999999999887655554442 35555544

>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=99.77  E-value=1.5e-17  Score=158.40  Aligned_cols=179  Identities=20%  Similarity=0.289  Sum_probs=130.9

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC--------------
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY--------------  250 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~--------------  250 (480)
                      +|.+|++++|++++++.+...+..            ...+.++|||||||||||++|+++|++++.              
T Consensus         7 rP~~~~dlig~~~~~~~L~~~i~~------------~~~~~~~Ll~Gp~G~GKtt~a~~~~~~l~~~~~~~~~~~~~~~~   74 (239)
T d1njfa_           7 RPQTFADVVGQEHVLTALANGLSL------------GRIHHAYLFSGTRGVGKTSIARLLAKGLNCETGITATPCGVCDN   74 (239)
T ss_dssp             CCSSGGGSCSCHHHHHHHHHHHHT------------TCCCSEEEEECSTTSSHHHHHHHHHHHHHCTTCSCSSCCSCSHH
T ss_pred             CCCCHHHccChHHHHHHHHHHHHc------------CCCCeeEEEECCCCCcHHHHHHHHHHHhcCccccccCccccchH
Confidence            578999999999999888765431            124568999999999999999999987632              


Q ss_pred             ----------cEEEEeCCCcCChHHHHHHHHhhc------CCcEEEEecccccccCcccccchhhhhhhcccccccccCC
Q 011664          251 ----------DVYDVDLSRVADDADLKSLLLQTT------SKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFE  314 (480)
Q Consensus       251 ----------~~~~i~~s~~~~~~~l~~l~~~~~------~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~  314 (480)
                                +++.++.+...+-..++.++....      ...|++|||+|.+.     ....+.|+..|+..     ..
T Consensus        75 ~~~i~~~~~~~~~~~~~~~~~~i~~ir~~~~~~~~~~~~~~~kviiIde~d~l~-----~~~q~~Llk~lE~~-----~~  144 (239)
T d1njfa_          75 CREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRFKVYLIDEVHMLS-----RHSFNALLKTLEEP-----PE  144 (239)
T ss_dssp             HHHHHHTCCTTEEEEETTCSSSHHHHHHHHHSCCCSCSSSSSEEEEEETGGGSC-----HHHHHHHHHHHHSC-----CT
T ss_pred             HHHHHcCCCCeEEEecchhcCCHHHHHHHHHHHHhccccCCCEEEEEECcccCC-----HHHHHHHHHHHhcC-----CC
Confidence                      367777766556666777665432      34699999999883     23346688888643     34


Q ss_pred             ceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhh
Q 011664          315 ERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANR  394 (480)
Q Consensus       315 ~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~  394 (480)
                      ..++|++||.++.+.+++++  |+ ..+.++.|+.++.+.++...+...+.              .+++..+..++..+.
T Consensus       145 ~~~~il~tn~~~~i~~~i~S--Rc-~~i~~~~~~~~~i~~~l~~i~~~e~~--------------~~~~~~l~~i~~~s~  207 (239)
T d1njfa_         145 HVKFLLATTDPQKLPVTILS--RC-LQFHLKALDVEQIRHQLEHILNEEHI--------------AHEPRALQLLARAAE  207 (239)
T ss_dssp             TEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTC--------------CBCHHHHHHHHHHTT
T ss_pred             CeEEEEEcCCccccChhHhh--hh-cccccccCcHHHhhhHHHHHHhhhcc--------------CCCHHHHHHHHHHcC
Confidence            67889999999999999999  98 58999999999988888777654433              344444555555544


Q ss_pred             hcHHHHHH
Q 011664          395 NSPSRALK  402 (480)
Q Consensus       395 ~~~~~al~  402 (480)
                      .++.+++.
T Consensus       208 Gd~R~ain  215 (239)
T d1njfa_         208 GSLRDALS  215 (239)
T ss_dssp             TCHHHHHH
T ss_pred             CCHHHHHH
Confidence            44444443

>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=2.2e-18  Score=162.54  Aligned_cols=169  Identities=15%  Similarity=0.192  Sum_probs=123.9

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEeC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVDL  257 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~~  257 (480)
                      .-.|.+|++++|++++++.|...+..           +  ....+|||||||||||++|+++|++++     .+++.+++
T Consensus        17 ky~P~~~~diig~~~~~~~l~~~i~~-----------~--~~~~lll~Gp~G~GKTtla~~iak~l~~~~~~~~~~e~n~   83 (231)
T d1iqpa2          17 KYRPQRLDDIVGQEHIVKRLKHYVKT-----------G--SMPHLLFAGPPGVGKTTAALALARELFGENWRHNFLELNA   83 (231)
T ss_dssp             HTCCCSTTTCCSCHHHHHHHHHHHHH-----------T--CCCEEEEESCTTSSHHHHHHHHHHHHHGGGHHHHEEEEET
T ss_pred             HhCCCCHHHccCcHHHHHHHHHHHHc-----------C--CCCeEEEECCCCCcHHHHHHHHHHHHHhcccCCCeeEEec
Confidence            34688999999999999888776532           1  123699999999999999999999864     47888888


Q ss_pred             CCcCChHHHHHHHHh--------hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCc
Q 011664          258 SRVADDADLKSLLLQ--------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVD  329 (480)
Q Consensus       258 s~~~~~~~l~~l~~~--------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD  329 (480)
                      ++..+...++..+..        ...+.|++|||+|.+...     ....|+..++..     ....++|++||.+..++
T Consensus        84 s~~~~~~~~~~~~~~~~~~~~~~~~~~~iilide~d~~~~~-----~~~~ll~~l~~~-----~~~~~~i~~~n~~~~i~  153 (231)
T d1iqpa2          84 SDERGINVIREKVKEFARTKPIGGASFKIIFLDEADALTQD-----AQQALRRTMEMF-----SSNVRFILSCNYSSKII  153 (231)
T ss_dssp             TCHHHHHTTHHHHHHHHHSCCGGGCSCEEEEEETGGGSCHH-----HHHHHHHHHHHT-----TTTEEEEEEESCGGGSC
T ss_pred             CcccchhHHHHHHHHHHhhhhccCCCceEEeehhhhhcchh-----HHHHHhhhcccC-----CcceEEEeccCChhhch
Confidence            765443333333221        236789999999987532     234566666432     34567889999999999


Q ss_pred             ccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchh-HHHHHHh
Q 011664          330 QALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQ-VEEIFQN  377 (480)
Q Consensus       330 ~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~-i~~l~~~  377 (480)
                      +++++  |+. .+.++.|+..+...+++..+...+..+.++ ++.+++.
T Consensus       154 ~~l~s--R~~-~i~~~~~~~~~~~~~l~~~~~~e~i~i~~~~l~~I~~~  199 (231)
T d1iqpa2         154 EPIQS--RCA-IFRFRPLRDEDIAKRLRYIAENEGLELTEEGLQAILYI  199 (231)
T ss_dssp             HHHHH--TEE-EEECCCCCHHHHHHHHHHHHHTTTCEECHHHHHHHHHH
T ss_pred             HhHhC--ccc-cccccccchhhHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence            99999  985 799999999999999999987666554433 2444433

>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=99.74  E-value=1.9e-17  Score=155.56  Aligned_cols=159  Identities=18%  Similarity=0.260  Sum_probs=117.0

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-----cEEEEeCC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-----DVYDVDLS  258 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-----~~~~i~~s  258 (480)
                      ..|.+|++++|++++++.|...+.    .       +. . .++|||||||||||++|+++|++++.     .++..+.+
T Consensus         8 yrP~~~~divg~~~~~~~L~~~i~----~-------~~-~-~~lLl~Gp~G~GKttl~~~la~~l~~~~~~~~~~e~~~~   74 (227)
T d1sxjc2           8 YRPETLDEVYGQNEVITTVRKFVD----E-------GK-L-PHLLFYGPPGTGKTSTIVALAREIYGKNYSNMVLELNAS   74 (227)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHH----T-------TC-C-CCEEEECSSSSSHHHHHHHHHHHHHTTSHHHHEEEECTT
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHH----c-------CC-C-CeEEEECCCCCChhHHHHHHHHHhhcCCCcceeEEeccc
Confidence            468899999999999988876553    1       21 1 25999999999999999999998753     36677776


Q ss_pred             CcCChHHHHHHH---Hhh-----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcc
Q 011664          259 RVADDADLKSLL---LQT-----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQ  330 (480)
Q Consensus       259 ~~~~~~~l~~l~---~~~-----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~  330 (480)
                      +..+........   ...     ....+|+|||+|.+..     .....|+..|+..     ....+++++||.+..+++
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~~~kiiiiDe~d~~~~-----~~~~~Ll~~le~~-----~~~~~~~~~~~~~~~i~~  144 (227)
T d1sxjc2          75 DDRGIDVVRNQIKDFASTRQIFSKGFKLIILDEADAMTN-----AAQNALRRVIERY-----TKNTRFCVLANYAHKLTP  144 (227)
T ss_dssp             SCCSHHHHHTHHHHHHHBCCSSSCSCEEEEETTGGGSCH-----HHHHHHHHHHHHT-----TTTEEEEEEESCGGGSCH
T ss_pred             ccCCeeeeecchhhccccccccCCCeEEEEEeccccchh-----hHHHHHHHHhhhc-----ccceeeccccCcHHHhHH
Confidence            665543332222   111     2346999999998742     2346677777543     345778889999999999


Q ss_pred             cccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCc
Q 011664          331 ALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLF  368 (480)
Q Consensus       331 aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~  368 (480)
                      ++++  |+ ..+.|+.|+.++...++.+.+..++..++
T Consensus       145 ~i~s--r~-~~i~~~~~~~~~i~~~l~~I~~~e~i~i~  179 (227)
T d1sxjc2         145 ALLS--QC-TRFRFQPLPQEAIERRIANVLVHEKLKLS  179 (227)
T ss_dssp             HHHT--TS-EEEECCCCCHHHHHHHHHHHHHTTTCCBC
T ss_pred             HHHH--HH-hhhccccccccccccccccccccccccCC
Confidence            9999  88 58899999999999999888765554443

>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=99.74  E-value=4.2e-17  Score=153.23  Aligned_cols=183  Identities=11%  Similarity=0.175  Sum_probs=132.4

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC-----cEEEEeC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY-----DVYDVDL  257 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~-----~~~~i~~  257 (480)
                      .-.|.+|++++|++++++.|...+.    .       +.  ..++|||||||||||++|+++|++++.     +++.++.
T Consensus         8 KyrP~~~~d~ig~~~~~~~L~~~~~----~-------~~--~~~~ll~Gp~G~GKTt~a~~la~~l~~~~~~~~~~~~n~   74 (224)
T d1sxjb2           8 KYRPQVLSDIVGNKETIDRLQQIAK----D-------GN--MPHMIISGMPGIGKTTSVHCLAHELLGRSYADGVLELNA   74 (224)
T ss_dssp             HTCCSSGGGCCSCTHHHHHHHHHHH----S-------CC--CCCEEEECSTTSSHHHHHHHHHHHHHGGGHHHHEEEECT
T ss_pred             HhCCCCHHHhcCCHHHHHHHHHHHH----c-------CC--CCeEEEECCCCCCchhhHHHHHHHHhccccccccccccc
Confidence            3578999999999999888876543    1       11  125999999999999999999998863     5888888


Q ss_pred             CCcCChHHHHHHH---Hhh------cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC
Q 011664          258 SRVADDADLKSLL---LQT------TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV  328 (480)
Q Consensus       258 s~~~~~~~l~~l~---~~~------~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L  328 (480)
                      ++..+...+...+   ...      ....+++|||+|.+..     .....|+..++..     ....+++++||....+
T Consensus        75 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~kviiiDe~d~~~~-----~~~~~ll~~~e~~-----~~~~~~i~~~~~~~~i  144 (224)
T d1sxjb2          75 SDDRGIDVVRNQIKHFAQKKLHLPPGKHKIVILDEADSMTA-----GAQQALRRTMELY-----SNSTRFAFACNQSNKI  144 (224)
T ss_dssp             TSCCSHHHHHTHHHHHHHBCCCCCTTCCEEEEEESGGGSCH-----HHHHTTHHHHHHT-----TTTEEEEEEESCGGGS
T ss_pred             cccCCceehhhHHHHHHHhhccCCCcceEEEEEecccccch-----hHHHHHhhhcccc-----ccceeeeeccCchhhh
Confidence            8877765544333   222      2346999999998843     2234555555432     3467788899999999


Q ss_pred             cccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhhcHHHHHHHHH
Q 011664          329 DQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRNSPSRALKSVI  405 (480)
Q Consensus       329 D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~~~~~al~~~i  405 (480)
                      .+++++  |+. .|.|+.|+.++...++...+..++.              .+++..+..++..+..+...++..+-
T Consensus       145 ~~~l~s--r~~-~i~~~~~~~~~i~~~l~~i~~~e~~--------------~i~~~~l~~I~~~s~Gd~R~ai~~Lq  204 (224)
T d1sxjb2         145 IEPLQS--QCA-ILRYSKLSDEDVLKRLLQIIKLEDV--------------KYTNDGLEAIIFTAEGDMRQAINNLQ  204 (224)
T ss_dssp             CHHHHT--TSE-EEECCCCCHHHHHHHHHHHHHHHTC--------------CBCHHHHHHHHHHHTTCHHHHHHHHH
T ss_pred             hhHHHH--HHH-HhhhcccchhhhHHHHHHHHHhccc--------------CCCHHHHHHHHHHcCCcHHHHHHHHH
Confidence            999999  984 7999999999999999888754433              44555566666655555555554443

>d1svma_ c.37.1.20 (A:) Papillomavirus large T antigen helicase domain {Simian virus 40 [TaxId: 10633]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: Papillomavirus large T antigen helicase domain
species: Simian virus 40 [TaxId: 10633]

Probab=99.71  E-value=4e-18  Score=172.43  Aligned_cols=182  Identities=18%  Similarity=0.169  Sum_probs=119.8

Q ss_pred             cChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhh
Q 011664          194 METDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQT  273 (480)
Q Consensus       194 g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~  273 (480)
                      |.++++..+.+.+..++        .|.|.++++|||||||||||++|+++|++++.+++.+++++..+...    +...
T Consensus       132 ~~~~~~~~i~~~l~~~~--------~~~~~~~~~~~~g~~~~gk~~~~~~~~~~~~~~~i~in~s~~rs~~~----l~~~  199 (362)
T d1svma_         132 LLPKMDSVVYDFLKCMV--------YNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFE----LGVA  199 (362)
T ss_dssp             TSTTHHHHHHHHHHHHH--------HCCTTCCEEEEECSTTSSHHHHHHHHHHHHCCEEECCSSCTTTHHHH----HGGG
T ss_pred             cccchHHHHHHHHHHHH--------hCCCCcCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEECcchhhHHH----HHhH
Confidence            34455655555444332        36788899999999999999999999999999999999887654322    2334


Q ss_pred             cCCcEEEEecccccccCcccccc------hhhhhhhcccccccccCC----------ceEEEEecCCCccCcccccCCCc
Q 011664          274 TSKSVILIEDLDRFLVEKPAAVS------LSGVLNFMDGVLNSCCFE----------ERVMVFTMNSKDHVDQALLRPGR  337 (480)
Q Consensus       274 ~~~sII~IDEiD~l~~~~~~~~~------ls~lL~~ldg~~~~~~~~----------~~ivI~tTN~~~~LD~aLlrpGR  337 (480)
                      ..+.+.++||++.....+....+      +..+.+.+||... .+.+          ...+|+|||+   ++.+++||||
T Consensus       200 ~~~~~~l~d~~~~~~~~~~~~~~~~~~DeiD~l~~~~dg~~~-~~~~~~~~~~~~~~~~p~i~ttN~---~~~~~~r~~R  275 (362)
T d1svma_         200 IDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVK-VNLEKKHLNKRTQIFPPGIVTMNE---YSVPKTLQAR  275 (362)
T ss_dssp             TTCSCEEETTCCCSTTTTTTCCCCSHHHHHHTTHHHHHCSSC-EEECCSSSCCEEECCCCEEEEECS---CCCCHHHHTT
T ss_pred             HHHHHHHHHHHHHhhhhccCCCCeEEEehHhhcccccCCcch-hhhhhhhhchhhhccCCceeeccc---cccccccccc
Confidence            45666777777765543322211      2334444554322 1010          1237889994   5778889999


Q ss_pred             eeEEEEcCCCCHHHHH-HHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh
Q 011664          338 IDVHIHFPLCDFSSFK-TLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN  393 (480)
Q Consensus       338 fd~~I~~~~p~~~~r~-~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a  393 (480)
                      |++.|.+..|+...+. .++..++.....  ..+.+.|+..+.+++++|+.+.++.+
T Consensus       276 f~~~i~~~~~~~~~~~~~~l~~i~~~~~l--~~~~~~L~~li~~~s~~D~~~~i~~~  330 (362)
T d1svma_         276 FVKQIDFRPKDYLKHCLERSEFLLEKRII--QSGIALLLMLIWYRPVAEFAQSIQSR  330 (362)
T ss_dssp             EEEEEECCCCHHHHHHHHTCTHHHHTTCT--TCHHHHHHHHHHHSCGGGSCGGGHHH
T ss_pred             CceEEeecCCCcHHHHHHHHHHHhcccCC--CCCHHHHHHHccCCCHHHHHHHHHHH
Confidence            9999999999877764 333444443333  33455666666789999988877654

>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=99.65  E-value=5.8e-16  Score=145.52  Aligned_cols=168  Identities=17%  Similarity=0.206  Sum_probs=118.3

Q ss_pred             CCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC------CCcEEEEeC
Q 011664          184 THPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM------SYDVYDVDL  257 (480)
Q Consensus       184 ~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l------~~~~~~i~~  257 (480)
                      ..|.+|++++|++++++.|+..+.    .       +  ....+||+||||||||++++++|+++      ....+.++.
T Consensus         6 y~P~~~~diig~~~~~~~l~~~i~----~-------~--~~~~lll~Gp~G~GKTtl~~~i~~~l~~~~~~~~~~~~~~~   72 (237)
T d1sxjd2           6 YRPKNLDEVTAQDHAVTVLKKTLK----S-------A--NLPHMLFYGPPGTGKTSTILALTKELYGPDLMKSRILELNA   72 (237)
T ss_dssp             TCCSSTTTCCSCCTTHHHHHHHTT----C-------T--TCCCEEEECSTTSSHHHHHHHHHHHHHHHHHHTTSEEEECS
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHH----c-------C--CCCeEEEECCCCCChHHHHHHHHHHHcCCcccccchhheec
Confidence            478999999999999888775432    1       1  12259999999999999999999986      567788887


Q ss_pred             CCcCChHHHHHHHHh------------------hcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEE
Q 011664          258 SRVADDADLKSLLLQ------------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMV  319 (480)
Q Consensus       258 s~~~~~~~l~~l~~~------------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI  319 (480)
                      +...+.......+..                  .....||+|||+|.+...     ..+.++..++-.     ....++|
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~viiiDe~d~l~~~-----~~~~l~~~~~~~-----~~~~~~i  142 (237)
T d1sxjd2          73 SDERGISIVREKVKNFARLTVSKPSKHDLENYPCPPYKIIILDEADSMTAD-----AQSALRRTMETY-----SGVTRFC  142 (237)
T ss_dssp             SSCCCHHHHTTHHHHHHHSCCCCCCTTHHHHSCCCSCEEEEETTGGGSCHH-----HHHHHHHHHHHT-----TTTEEEE
T ss_pred             cccccchHHHHHHHHHhhhhhhhhhHHHHhhccccCceEEEEecccccCHH-----HHHHHhhccccc-----ccccccc
Confidence            766553322211110                  113359999999988432     223444444321     3456778


Q ss_pred             EecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHh
Q 011664          320 FTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQN  377 (480)
Q Consensus       320 ~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~  377 (480)
                      +++|..+.+.+++++  |+ ..|.|++|+.++...+++..+..++..++++. +.++..
T Consensus       143 ~~~~~~~~~~~~l~s--r~-~~i~f~~~~~~~~~~~L~~i~~~e~i~i~~~~l~~ia~~  198 (237)
T d1sxjd2         143 LICNYVTRIIDPLAS--QC-SKFRFKALDASNAIDRLRFISEQENVKCDDGVLERILDI  198 (237)
T ss_dssp             EEESCGGGSCHHHHH--HS-EEEECCCCCHHHHHHHHHHHHHTTTCCCCHHHHHHHHHH
T ss_pred             ccccccccccccccc--hh-hhhccccccccccchhhhhhhhhhcCcCCHHHHHHHHHH
Confidence            889999999999999  98 58999999999999999988876665555433 444443

>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=1.8e-16  Score=150.48  Aligned_cols=159  Identities=18%  Similarity=0.223  Sum_probs=104.6

Q ss_pred             CCCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCC---cE------
Q 011664          182 PFTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSY---DV------  252 (480)
Q Consensus       182 ~~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~---~~------  252 (480)
                      ..-.|.+|++++|++++++.|...+    ..       +.. ..++|||||||||||++|+++|+++..   ..      
T Consensus         3 eky~P~~~~diig~~~~~~~L~~~~----~~-------~~~-~~~lll~Gp~G~GKTt~~~~la~~l~~~~~~~~~~~~~   70 (252)
T d1sxje2           3 DKYRPKSLNALSHNEELTNFLKSLS----DQ-------PRD-LPHLLLYGPNGTGKKTRCMALLESIFGPGVYRLKIDVR   70 (252)
T ss_dssp             TTTCCCSGGGCCSCHHHHHHHHTTT----TC-------TTC-CCCEEEECSTTSSHHHHHHTHHHHHSCTTCCC------
T ss_pred             cccCCCCHHHccCcHHHHHHHHHHH----Hc-------CCC-CCeEEEECCCCCCHHHHHHHHHHhhcCccccccccccc
Confidence            3446889999999999888776432    11       111 236999999999999999999997511   11      


Q ss_pred             --------------------EEEeCCCcCCh--HHHHHHHH---h-------------hcCCcEEEEecccccccCcccc
Q 011664          253 --------------------YDVDLSRVADD--ADLKSLLL---Q-------------TTSKSVILIEDLDRFLVEKPAA  294 (480)
Q Consensus       253 --------------------~~i~~s~~~~~--~~l~~l~~---~-------------~~~~sII~IDEiD~l~~~~~~~  294 (480)
                                          ..+........  ........   .             .....+++|||+|.+..     
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~iiiide~d~l~~-----  145 (252)
T d1sxje2          71 QFVTASNRKLELNVVSSPYHLEITPSDMGNNDRIVIQELLKEVAQMEQVDFQDSKDGLAHRYKCVIINEANSLTK-----  145 (252)
T ss_dssp             ------------CCEECSSEEEECCC----CCHHHHHHHHHHHTTTTC------------CCEEEEEECTTSSCH-----
T ss_pred             cccccccchhhhhhccCCccceeeecccccCCcceeeehhhhhhhhhhhhhhhcccccCCCceEEEecccccccc-----
Confidence                                11111111110  00111110   0             12346999999998732     


Q ss_pred             cchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCC
Q 011664          295 VSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDH  365 (480)
Q Consensus       295 ~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~  365 (480)
                      .....++..++..     .....+|++||+++.+++++++  || ..|+|++|+.++..+++...+...+.
T Consensus       146 ~~~~~l~~~~e~~-----~~~~~~Il~tn~~~~i~~~l~s--R~-~~i~~~~~~~~~~~~~l~~i~~~e~~  208 (252)
T d1sxje2         146 DAQAALRRTMEKY-----SKNIRLIMVCDSMSPIIAPIKS--QC-LLIRCPAPSDSEISTILSDVVTNERI  208 (252)
T ss_dssp             HHHHHHHHHHHHS-----TTTEEEEEEESCSCSSCHHHHT--TS-EEEECCCCCHHHHHHHHHHHHHHHTC
T ss_pred             ccchhhhcccccc-----cccccceeeeccccchhhhhhc--ch-heeeecccchhhHHHHHHHHHHHcCC
Confidence            2334555555432     3456789999999999999998  99 58999999999999999887765443

>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=99.61  E-value=1.8e-15  Score=141.87  Aligned_cols=187  Identities=15%  Similarity=0.221  Sum_probs=121.5

Q ss_pred             CCCCCcccc-ccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          184 THPSTFDTI-SMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       184 ~~~~~~~~i-~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      ++..||++. +|..+..  ....+..+...+      |. ...+++||||||||||+|++|+|+++   +..++++++.+
T Consensus         4 n~~~tFdnF~vg~~N~~--a~~~~~~~~~~~------~~-~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~   74 (213)
T d1l8qa2           4 NPKYTLENFIVGEGNRL--AYEVVKEALENL------GS-LYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADD   74 (213)
T ss_dssp             CTTCCSSSCCCCTTTHH--HHHHHHHHHHTT------TT-SCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHH
T ss_pred             CCCCChhhccCCCcHHH--HHHHHHHHHhCc------CC-CCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHH
Confidence            456789995 4543321  112222222222      22 23469999999999999999999976   56788887655


Q ss_pred             cCCh-------HHHHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccC---c
Q 011664          260 VADD-------ADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHV---D  329 (480)
Q Consensus       260 ~~~~-------~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~L---D  329 (480)
                      +...       ......+.......+|+|||||.+.+....+..+..++|.+   ..   .+..+|+.+...|..+   .
T Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~---~~---~~~~iiits~~~p~~l~~~~  148 (213)
T d1l8qa2          75 FAQAMVEHLKKGTINEFRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTL---YL---LEKQIILASDRHPQKLDGVS  148 (213)
T ss_dssp             HHHHHHHHHHHTCHHHHHHHHHTCSEEEEECGGGGTTCHHHHHHHHHHHHHH---HH---TTCEEEEEESSCGGGCTTSC
T ss_pred             HHHHHHHHHHccchhhHHHHHhhccchhhhhhhhhcCchHHHHHHHHHHHHH---hh---ccceEEEecCCcchhccccc
Confidence            4321       11223334445789999999999976655555555555543   33   3456666666677665   4


Q ss_pred             ccccCCCcee--EEEEcCCCCHHHHHHHHHHHhccCCCCCchhH-HHHHHhCCCCCHHHHHHHH
Q 011664          330 QALLRPGRID--VHIHFPLCDFSSFKTLASSYLGLKDHKLFPQV-EEIFQNGSSLSPAEIGELM  390 (480)
Q Consensus       330 ~aLlrpGRfd--~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i-~~l~~~~~g~s~adI~~ll  390 (480)
                      +.|.+  |+.  ..+.++ |+.+.+.++++.++...+..+.+++ +-|++++.  +..|+..++
T Consensus       149 ~dL~S--RL~~g~~~~i~-p~d~~~~~iL~~~a~~rgl~l~~~v~~yl~~~~~--~~R~L~~~l  207 (213)
T d1l8qa2         149 DRLVS--RFEGGILVEIE-LDNKTRFKIIKEKLKEFNLELRKEVIDYLLENTK--NVREIEGKI  207 (213)
T ss_dssp             HHHHH--HHHTSEEEECC-CCHHHHHHHHHHHHHHTTCCCCHHHHHHHHHHCS--SHHHHHHHH
T ss_pred             hHHHH--HhhCceEEEEC-CCcHHHHHHHHHHHHHcCCCCCHHHHHHHHHhcC--cHHHHHHHH
Confidence            77888  876  778886 6778999999999988888887766 45555542  455655554

>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=99.53  E-value=2.4e-13  Score=128.61  Aligned_cols=165  Identities=10%  Similarity=0.039  Sum_probs=109.8

Q ss_pred             CCCCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeCC
Q 011664          183 FTHPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDLS  258 (480)
Q Consensus       183 ~~~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~s  258 (480)
                      +.+.-.+++++|.++..+.|.+.+...++++.       ..++++||+||||||||++++++|+.+    +..++.+++.
T Consensus         9 l~~~y~p~~l~~Re~ei~~l~~~l~~~l~~~~-------~~~~~lll~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~   81 (276)
T d1fnna2           9 FSPSYVPKRLPHREQQLQQLDILLGNWLRNPG-------HHYPRATLLGRPGTGKTVTLRKLWELYKDKTTARFVYINGF   81 (276)
T ss_dssp             GSTTCCCSCCTTCHHHHHHHHHHHHHHHHSTT-------SSCCEEEEECCTTSSHHHHHHHHHHHHTTSCCCEEEEEETT
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHhCCC-------CCCCceEEECCCCCCHHHHHHHHHHHHhcccCCcEEEecch
Confidence            33444557789999999999988877665542       256789999999999999999999876    4567777765


Q ss_pred             CcCChHH----------------------H----HHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccccccccc
Q 011664          259 RVADDAD----------------------L----KSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCC  312 (480)
Q Consensus       259 ~~~~~~~----------------------l----~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~  312 (480)
                      .......                      +    ...+.......++++|++|.+....  ......++..+...    .
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~--~~~~~~~~~~~~~~----~  155 (276)
T d1fnna2          82 IYRNFTAIIGEIARSLNIPFPRRGLSRDEFLALLVEHLRERDLYMFLVLDDAFNLAPDI--LSTFIRLGQEADKL----G  155 (276)
T ss_dssp             TCCSHHHHHHHHHHHTTCCCCSSCCCHHHHHHHHHHHHHHTTCCEEEEEETGGGSCHHH--HHHHHHHTTCHHHH----S
T ss_pred             hhhhhhhhhhhhHHhhhhhhhhhccchhHHHHHHHHHHhhcccccccchhHHHHhhhhh--hhhHHHHHhccccc----c
Confidence            4432111                      1    1112233456788899999764221  11122222222221    1


Q ss_pred             CCceEEEEecCCC---ccCcccccCCCcee-EEEEcCCCCHHHHHHHHHHHhcc
Q 011664          313 FEERVMVFTMNSK---DHVDQALLRPGRID-VHIHFPLCDFSSFKTLASSYLGL  362 (480)
Q Consensus       313 ~~~~ivI~tTN~~---~~LD~aLlrpGRfd-~~I~~~~p~~~~r~~il~~~l~~  362 (480)
                      ....++|+++|..   +.+++++.+  |+. ..|.|++|+.++...|++..+..
T Consensus       156 ~~~~~~i~~~~~~~~~~~~~~~~~~--r~~~~~i~~~~~~~~e~~~il~~r~~~  207 (276)
T d1fnna2         156 AFRIALVIVGHNDAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKA  207 (276)
T ss_dssp             SCCEEEEEEESSTHHHHTSCHHHHH--HHTTCEEECCCCBHHHHHHHHHHHHHH
T ss_pred             ccceEEeecCCchhhhhhcchhhhh--hhcchhccccchhHHHHHHHHHHHHHH
Confidence            3456677777753   567888877  654 57899999999999999887653

>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=99.50  E-value=2.7e-13  Score=129.03  Aligned_cols=166  Identities=11%  Similarity=0.052  Sum_probs=104.2

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC---------CcEEEEeC
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS---------YDVYDVDL  257 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~---------~~~~~i~~  257 (480)
                      -..+.+.|-++..+.|.+.+..++.+...    .......++||||||||||++++++++++.         ..+..+++
T Consensus        13 ~~P~~~~~Re~e~~~l~~~l~~~~~~~~~----~~~~~~~l~l~GppGtGKT~l~~~l~~~l~~~~~~~~~~~~~~~~~~   88 (287)
T d1w5sa2          13 YIPPELRVRRGEAEALARIYLNRLLSGAG----LSDVNMIYGSIGRVGIGKTTLAKFTVKRVSEAAAKEGLTVKQAYVNA   88 (287)
T ss_dssp             CCCSSCSSSCHHHHHHHHHHHHHHHTSSC----BCCEEEEEECTTCCSSSHHHHHHHHHHHHHHHHHHTTCCEEEEEEEG
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHcCCC----CCCcceEEEeECCCCCCHHHHHHHHHHHHHhhcccccCCceeeeecc
Confidence            34577888888889888877666543210    111122467899999999999999998762         34555555


Q ss_pred             CCcCCh----------------------HHHHHHH----HhhcCCcEEEEecccccccCcccc-cc---hhhhhhhcccc
Q 011664          258 SRVADD----------------------ADLKSLL----LQTTSKSVILIEDLDRFLVEKPAA-VS---LSGVLNFMDGV  307 (480)
Q Consensus       258 s~~~~~----------------------~~l~~l~----~~~~~~sII~IDEiD~l~~~~~~~-~~---ls~lL~~ldg~  307 (480)
                      ......                      ..+...+    .....+.++++||+|.+....... ..   +..+.+.+...
T Consensus        89 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iide~d~l~~~~~~~~~~~~~l~~l~~~l~~~  168 (287)
T d1w5sa2          89 FNAPNLYTILSLIVRQTGYPIQVRGAPALDILKALVDNLYVENHYLLVILDEFQSMLSSPRIAAEDLYTLLRVHEEIPSR  168 (287)
T ss_dssp             GGCCSHHHHHHHHHHHHTCCCCCTTCCHHHHHHHHHHHHHHHTCEEEEEEESTHHHHSCTTSCHHHHHHHHTHHHHSCCT
T ss_pred             ccccchhhHHHHHhhhcccccccccchHHHHHHHHHHHHHhccCccccceeEEEEeccccccchhHHHHHHHHHHhcchh
Confidence            443321                      1111122    233466789999999886544332 12   23333333333


Q ss_pred             cccccCCceEEEEecCCCc------cCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          308 LNSCCFEERVMVFTMNSKD------HVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       308 ~~~~~~~~~ivI~tTN~~~------~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      ..   .....+|+.+|.++      ..++++.+  |+..+++|+.|+.++..+|++..+.
T Consensus       169 ~~---~~~~~~i~i~~~~~~~~~~~~~~~~~~~--r~~~~i~f~~y~~~el~~Il~~r~~  223 (287)
T d1w5sa2         169 DG---VNRIGFLLVASDVRALSYMREKIPQVES--QIGFKLHLPAYKSRELYTILEQRAE  223 (287)
T ss_dssp             TS---CCBEEEEEEEEETHHHHHHHHHCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hc---ccceeEEeecccHHHHHHHHhhccchhc--ccceeeeccCCcHHHHHHHHhhhHH
Confidence            32   23445555555443      23467777  9999999999999999999988764

>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=99.49  E-value=1.8e-13  Score=137.97  Aligned_cols=212  Identities=17%  Similarity=0.254  Sum_probs=132.9

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhh-----------------CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRL-----------------GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~-----------------g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      -|+|++++|+.+..++....++...-.++                 ...++.++||.||+|||||.||+++|..++.+|+
T Consensus        18 ~ViGQd~Akkava~Avrn~~rR~~~~~~~r~~~~~~~~~~~~~~~~~~~p~~niLfiGPTGvGKTElAk~LA~~~~~~~i   97 (364)
T d1um8a_          18 YVIGQEQAKKVFSVAVYNHYKRLSFKEKLKKQDNQDSNVELEHLEEVELSKSNILLIGPTGSGKTLMAQTLAKHLDIPIA   97 (364)
T ss_dssp             TCCSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHHHHTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEE
T ss_pred             eecChHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccccCCCcceeeeCCCCccHHHHHHHHHhhccccee
Confidence            48999999999988775443322111110                 1235678999999999999999999999999999


Q ss_pred             EEeCCCcCC--------hHHHHHHHHh------hcCCcEEEEecccccccCc---------ccccchhhhhhhccccccc
Q 011664          254 DVDLSRVAD--------DADLKSLLLQ------TTSKSVILIEDLDRFLVEK---------PAAVSLSGVLNFMDGVLNS  310 (480)
Q Consensus       254 ~i~~s~~~~--------~~~l~~l~~~------~~~~sII~IDEiD~l~~~~---------~~~~~ls~lL~~ldg~~~~  310 (480)
                      .++++.+..        +..++.++..      ..+.+|+++||+|...+..         ........||+.+|+-...
T Consensus        98 r~D~s~~~e~gyvg~dv~~~i~~l~~~~~~~v~~~~~~iv~lDEieK~~~~s~~~~~~~d~a~~~V~~~lLqild~~~~~  177 (364)
T d1um8a_          98 ISDATSLTEAGYVGEDVENILTRLLQASDWNVQKAQKGIVFIDEIDKISRLSENRSITRDVSGEGVQQALLKIVEGSLVN  177 (364)
T ss_dssp             EEEGGGCC--------CTHHHHHHHHHTTTCHHHHTTSEEEEETGGGC--------------CHHHHHHHHHHHHCCEEC
T ss_pred             ehhhhhcccchhhHhhhccchhhhhhhchhHHHHhhcccchhhhhhhhccccccccccccccchHHHHhhhhhhcCceec
Confidence            999998875        4556666643      3467999999999976432         2223467788888852210


Q ss_pred             --------ccCCceEEEEecCCC-------------------------------------------------ccCccccc
Q 011664          311 --------CCFEERVMVFTMNSK-------------------------------------------------DHVDQALL  333 (480)
Q Consensus       311 --------~~~~~~ivI~tTN~~-------------------------------------------------~~LD~aLl  333 (480)
                              ....+.+++.|+|-.                                                 ..+-|.++
T Consensus       178 ~~~~~gr~~~~~~~i~i~t~~i~~~~~ga~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PEf~  257 (364)
T d1um8a_         178 IPPKGGRKHPEGNFIQIDTSDILFICAGAFDGLAEIIKKRTTQNVLGFTQEKMSKKEQEAILHLVQTHDLVTYGLIPELI  257 (364)
T ss_dssp             ---------------CEECTTCEEEEEECCTTHHHHTTTSCSSCCCSCCCSSCCTTTTTTSGGGCCHHHHHHTTCCHHHH
T ss_pred             cCCCCCCcCCcceeEEEeehhhhhhhcccchhhhhhhhhhcccccccccccccchhhhhhhhccccHHHHhhhhhHHHHH
Confidence                    112234556666541                                                 11344555


Q ss_pred             CCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCCchhHHHHHHhC---CCCCHHHHHHHHHHhh--hcHHHHHHHHHHHH
Q 011664          334 RPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKLFPQVEEIFQNG---SSLSPAEIGELMIANR--NSPSRALKSVITAL  408 (480)
Q Consensus       334 rpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l~~~i~~l~~~~---~g~s~adI~~ll~~a~--~~~~~al~~~i~~~  408 (480)
                        ||+|.++.|...+.+...+|+....    ..+..+...+.+.-   -.|++.-+..+...+.  ....|.|+++++.+
T Consensus       258 --gRi~~iv~f~~L~~~~l~~Il~~~~----~~l~kq~~~~l~~~gi~L~~td~a~~~la~~g~d~~~GAR~L~riie~~  331 (364)
T d1um8a_         258 --GRLPVLSTLDSISLEAMVDILQKPK----NALIKQYQQLFKMDEVDLIFEEEAIKEIAQLALERKTGARGLRAIIEDF  331 (364)
T ss_dssp             --TTCCEEEECCCCCHHHHHHHHHSST----TCHHHHHHHHHHTTTCEEEECHHHHHHHHHHHHHTTCTGGGHHHHHHHH
T ss_pred             --HHhcchhhHhhhhHHHHHHHHHHHH----HHHHHHHHHHHHhCCcEEEECHHHHHHHHHhccCCCCCchHHHHHHHHH
Confidence              4999999999999999999886432    12223344433321   1357777777766532  23345666666544

>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=99.48  E-value=1.2e-13  Score=136.76  Aligned_cols=157  Identities=17%  Similarity=0.278  Sum_probs=112.8

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhC--CCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChH----
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLG--RVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDA----  264 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g--~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~----  264 (480)
                      .|+|++++++.|.+.+.....      .+.  ..+...+||+||||||||.||+++|..++.+++.++++.+....    
T Consensus        23 ~viGQ~~a~~~v~~~v~~~~~------~l~~~~~p~~~~lf~Gp~GvGKT~lak~la~~l~~~~i~~d~s~~~~~~~~~~   96 (315)
T d1r6bx3          23 LVFGQDKAIEALTEAIKMARA------GLGHEHKPVGSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSEYMERHTVSR   96 (315)
T ss_dssp             TSCSCHHHHHHHHHHHHHHHT------TCSCTTSCSEEEEEECSTTSSHHHHHHHHHHHHTCEEEEEEGGGCSSSSCCSS
T ss_pred             eecChHHHHHHHHHHHHHHHc------cCCCCCCCceEEEEECCCcchhHHHHHHHHhhccCCeeEeccccccchhhhhh
Confidence            478999999999987764422      111  11333688999999999999999999999999999988765311    


Q ss_pred             --------------H-HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhccc------ccccccCCceEEEEecC
Q 011664          265 --------------D-LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG------VLNSCCFEERVMVFTMN  323 (480)
Q Consensus       265 --------------~-l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg------~~~~~~~~~~ivI~tTN  323 (480)
                                    . +.. .....+.+|+++||||...     ....+.||..+|.      ........+.++|+|||
T Consensus        97 l~g~~~gy~g~~~~~~l~~-~~~~~~~~vvl~DeieKa~-----~~V~~~lLqild~G~ltd~~Gr~vdf~n~iiI~Tsn  170 (315)
T d1r6bx3          97 LIGAPPGYVGFDQGGLLTD-AVIKHPHAVLLLDEIEKAH-----PDVFNILLQVMDNGTLTDNNGRKADFRNVVLVMTTN  170 (315)
T ss_dssp             SCCCCSCSHHHHHTTHHHH-HHHHCSSEEEEEETGGGSC-----HHHHHHHHHHHHHSEEEETTTEEEECTTEEEEEEEC
T ss_pred             hcccCCCccccccCChhhH-HHHhCccchhhhccccccc-----chHhhhhHHhhccceecCCCCCccCccceEEEeccc
Confidence                          1 222 2344567999999999863     2345666666642      11112245678999998


Q ss_pred             CC-------------------------ccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          324 SK-------------------------DHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       324 ~~-------------------------~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      --                         ..+.|.++.  |+|..|.|.+.+.++..+|+..++.
T Consensus       171 ig~~~i~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~ii~f~~l~~~~~~~I~~~~l~  231 (315)
T d1r6bx3         171 AGVRETERKSIGLIHQDNSTDAMEEIKKIFTPEFRN--RLDNIIWFDHLSTDVIHQVVDKFIV  231 (315)
T ss_dssp             SSCC-----------------CHHHHHHHSCHHHHT--TCSEEEECCCCCHHHHHHHHHHHHH
T ss_pred             hhhHHHHhhhccchhhhhhHhHHHHHHHhcCHHHHh--hhhhhhcccchhhhHHHHHHHHHHH
Confidence            32                         125667777  9999999999999999999887764

>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=99.46  E-value=1.3e-12  Score=121.29  Aligned_cols=123  Identities=11%  Similarity=0.107  Sum_probs=92.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC------------------------CcEEEEeCCCc---CChHHHHHHHHhh--
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS------------------------YDVYDVDLSRV---ADDADLKSLLLQT--  273 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~------------------------~~~~~i~~s~~---~~~~~l~~l~~~~--  273 (480)
                      .+.++||+||||+|||++|+++|+.+-                        .+++.+....-   ..-..++.+....  
T Consensus        23 l~h~lLl~Gp~G~GKtt~a~~~a~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~i~~~~ir~l~~~~~~  102 (207)
T d1a5ta2          23 GHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNE  102 (207)
T ss_dssp             CCSEEEEECCTTSCHHHHHHHHHHHHTCSSCBTTBCCSCSHHHHHHHHTCCTTEEEECCCTTCSSBCHHHHHHHHHHTTS
T ss_pred             cCeEEEEECCCCCcHHHHHHHHHHhcccccccccccccccchhhhhhhccccccchhhhhhcccccccchhhHHhhhhhh
Confidence            466899999999999999999998651                        24555543322   2334466555432  


Q ss_pred             ----cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          274 ----TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       274 ----~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                          ....|++|||+|.+.     ....+.|+..|+.-     ..+.++|++||++..|.|++++  |+ ..|.|+.|+.
T Consensus       103 ~~~~~~~kviIide~d~l~-----~~a~n~Llk~lEep-----~~~~~fIl~t~~~~~ll~tI~S--Rc-~~i~~~~~~~  169 (207)
T d1a5ta2         103 HARLGGAKVVWVTDAALLT-----DAAANALLKTLEEP-----PAETWFFLATREPERLLATLRS--RC-RLHYLAPPPE  169 (207)
T ss_dssp             CCTTSSCEEEEESCGGGBC-----HHHHHHHHHHHTSC-----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCCH
T ss_pred             ccccCccceEEechhhhhh-----hhhhHHHHHHHHhh-----cccceeeeeecChhhhhhhhcc--ee-EEEecCCCCH
Confidence                245699999999884     33457788888643     4567889999999999999999  98 6999999999


Q ss_pred             HHHHHHHHH
Q 011664          350 SSFKTLASS  358 (480)
Q Consensus       350 ~~r~~il~~  358 (480)
                      ++...+++.
T Consensus       170 ~~~~~~L~~  178 (207)
T d1a5ta2         170 QYAVTWLSR  178 (207)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            988777754

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.43  E-value=1.5e-12  Score=125.50  Aligned_cols=154  Identities=20%  Similarity=0.263  Sum_probs=106.4

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHc----------CCCcEEEEeC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASF----------MSYDVYDVDL  257 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~----------l~~~~~~i~~  257 (480)
                      .++.++|.++..+++.+.+             ....+.++||.||||+|||++++.+|..          .+..++.+++
T Consensus        16 ~ld~~igRd~Ei~~l~~iL-------------~r~~k~n~lLVG~~GvGKTalv~~la~ri~~~~vp~~l~~~~i~~l~~   82 (268)
T d1r6bx2          16 GIDPLIGREKELERAIQVL-------------CRRRKNNPLLVGESGVGKTAIAEGLAWRIVQGDVPEVMADCTIYSLDI   82 (268)
T ss_dssp             CSCCCCSCHHHHHHHHHHH-------------TSSSSCEEEEECCTTSSHHHHHHHHHHHHHHTCSCGGGTTCEEEECCC
T ss_pred             CCCcccChHHHHHHHHHHH-------------hcCccCCcEEECCCCCcHHHHHHHHHHHHHhCCcccccccceeEEeee
Confidence            4667888887666666443             2335678999999999999999999974          3678999998


Q ss_pred             CCcCC--------hHHHHHHHHhh--cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC----
Q 011664          258 SRVAD--------DADLKSLLLQT--TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN----  323 (480)
Q Consensus       258 s~~~~--------~~~l~~l~~~~--~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN----  323 (480)
                      +.+..        +..+..++...  ..+.|+||||++.++....+......+-+.|....+   .++.-+|++|.    
T Consensus        83 ~~liag~~~~g~~e~r~~~i~~~~~~~~~iIlfiDeih~l~~~g~~~g~~~d~a~~Lkp~L~---rg~i~vIgatT~eey  159 (268)
T d1r6bx2          83 GSLLAGTKYRGDFEKRFKALLKQLEQDTNSILFIDEIHTIIGAGAASGGQVDAANLIKPLLS---SGKIRVIGSTTYQEF  159 (268)
T ss_dssp             C---CCCCCSSCHHHHHHHHHHHHSSSSCEEEEETTTTTTTTSCCSSSCHHHHHHHHSSCSS---SCCCEEEEEECHHHH
T ss_pred             chHhccCccchhHHHHHHHHHHHhhccCCceEEecchHHHhcCCCCCCccccHHHHhhHHHh---CCCCeEEEeCCHHHH
Confidence            77653        33456666554  456899999999998644333222334444444444   34566666553    


Q ss_pred             -CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          324 -SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       324 -~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                       ....-|+||.|  ||. .|.+..|+.++-..|++.+.
T Consensus       160 ~~~~e~d~al~r--rF~-~I~V~Eps~e~t~~IL~~~~  194 (268)
T d1r6bx2         160 SNIFEKDRALAR--RFQ-KIDITEPSIEETVQIINGLK  194 (268)
T ss_dssp             HCCCCCTTSSGG--GEE-EEECCCCCHHHHHHHHHHHH
T ss_pred             HHHHhhcHHHHh--hhc-ccccCCCCHHHHHHHHHHhh
Confidence             22345999999  995 89999999999888887653

>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=6.3e-13  Score=131.43  Aligned_cols=157  Identities=19%  Similarity=0.319  Sum_probs=111.0

Q ss_pred             ccccChHHHHHHHHHHHHHHhhhhHHhhhC--CCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHH
Q 011664          191 TISMETDLKNRVKSDLESFLKAKHYYHRLG--RVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDAD  265 (480)
Q Consensus       191 ~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g--~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~  265 (480)
                      .|+|++++++.|.+.+......      +.  ..+...+||+||||||||.+|+++|..+   +.+++.++++++.+...
T Consensus        24 ~v~GQ~~ai~~v~~~i~~~~~~------l~~~~kp~~~~lf~Gp~G~GKt~lak~la~~l~~~~~~~~~~~~~~~~~~~~   97 (315)
T d1qvra3          24 RVVGQDEAIRAVADAIRRARAG------LKDPNRPIGSFLFLGPTGVGKTELAKTLAATLFDTEEAMIRIDMTEYMEKHA   97 (315)
T ss_dssp             HSCSCHHHHHHHHHHHHHHGGG------CSCSSSCSEEEEEBSCSSSSHHHHHHHHHHHHHSSGGGEEEECTTTCCSSGG
T ss_pred             eEeCHHHHHHHHHHHHHHHhcC------CCCCCCCceEEEEECCCcchHHHHHHHHHHHhcCCCcceEEEeccccccchh
Confidence            4689999999998877654221      11  1123357888999999999999999987   67899999987764211


Q ss_pred             -------------------HHHHHHhhcCCcEEEEecccccccCcccccchhhhhhhcccc-cc-----cccCCceEEEE
Q 011664          266 -------------------LKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGV-LN-----SCCFEERVMVF  320 (480)
Q Consensus       266 -------------------l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~-~~-----~~~~~~~ivI~  320 (480)
                                         +...+. ..+.|||+|||||...     .....-|+..+|.- ..     .....+.++|+
T Consensus        98 ~~~L~g~~~gyvG~~~~~~l~~~~~-~~p~~Vvl~DEieK~~-----~~v~~~ll~~l~~g~~~~~~gr~v~~~~~i~i~  171 (315)
T d1qvra3          98 VSRLIGAPPGYVGYEEGGQLTEAVR-RRPYSVILFDEIEKAH-----PDVFNILLQILDDGRLTDSHGRTVDFRNTVIIL  171 (315)
T ss_dssp             GGGC--------------CHHHHHH-HCSSEEEEESSGGGSC-----HHHHHHHHHHHTTTEECCSSSCCEECTTEEEEE
T ss_pred             hhhhcCCCCCCcCcccCChHHHHHH-hCCCcEEEEehHhhcC-----HHHHHHHHHHhccCceeCCCCcEecCcceEEEE
Confidence                               322222 3456999999999874     23345555555421 11     12235678999


Q ss_pred             ecCC--------------------------CccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhc
Q 011664          321 TMNS--------------------------KDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLG  361 (480)
Q Consensus       321 tTN~--------------------------~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~  361 (480)
                      |||-                          ...+.|.++.  |||..+.|.+.+.++..+|+...+.
T Consensus       172 tsnlG~~~i~~~~~~~~~~~~~~~~~~~~l~~~f~pEfln--Rid~Ii~F~~L~~~~~~~I~~~~l~  236 (315)
T d1qvra3         172 TSNLGSPLILEGLQKGWPYERIRDEVFKVLQQHFRPEFLN--RLDEIVVFRPLTKEQIRQIVEIQLS  236 (315)
T ss_dssp             ECCTTHHHHHHHHHTTCCHHHHHHHHHHHHHTTSCHHHHH--TCSBCCBCCCCCHHHHHHHHHHHHH
T ss_pred             ecccChHHHhhhcccccchhhhhHHHHHHHHhhcCHHHHh--cCCeeeeccchhhhhhHHHHHHHHH
Confidence            9994                          2447788888  9999999999999998888876653

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=99.32  E-value=1.2e-12  Score=120.24  Aligned_cols=149  Identities=19%  Similarity=0.225  Sum_probs=96.8

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDL  257 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~  257 (480)
                      .++.++|.++..+++.+.+             ....+.+++|.||||+|||++++.+|..+          +.+++.+|+
T Consensus        20 ~ld~~igRd~Ei~~l~~iL-------------~r~~k~n~lLvG~pGVGKTalv~~LA~ri~~~~vp~~L~~~~i~~ld~   86 (195)
T d1jbka_          20 KLDPVIGRDEEIRRTIQVL-------------QRRTKNNPVLIGEPGVGKTAIVEGLAQRIINGEVPEGLKGRRVLALDM   86 (195)
T ss_dssp             CSCCCCSCHHHHHHHHHHH-------------TSSSSCEEEEECCTTSCHHHHHHHHHHHHHHTCSCGGGTTCEEEEECH
T ss_pred             CCCCCcCcHHHHHHHHHHH-------------hccCCCCeEEEecCCcccHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            3566788877766665433             23346689999999999999999999733          678999998


Q ss_pred             CCcCC--------hHHHHHHHHhh---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC-CC
Q 011664          258 SRVAD--------DADLKSLLLQT---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN-SK  325 (480)
Q Consensus       258 s~~~~--------~~~l~~l~~~~---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN-~~  325 (480)
                      +.+..        +..+..++.+.   ..+.||||||++.+.+...+... ..+-+.+....+   .++..+|+||. ..
T Consensus        87 ~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILfIDeih~l~~~g~~~g~-~d~~~~Lkp~L~---rg~l~~IgatT~ee  162 (195)
T d1jbka_          87 GALVAGAKYRGEFEERLKGVLNDLAKQEGNVILFIDELHTMVGAGKADGA-MDAGNMLKPALA---RGELHCVGATTLDE  162 (195)
T ss_dssp             HHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEEEETGGGGTT------C-CCCHHHHHHHHH---TTSCCEEEEECHHH
T ss_pred             HHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEEcchHHHHhcCCCCCCc-ccHHHHHHHHHh---CCCceEEecCCHHH
Confidence            76542        23356666543   23579999999999764332211 122333333333   23444555443 11


Q ss_pred             ----ccCcccccCCCceeEEEEcCCCCHHHHHHHH
Q 011664          326 ----DHVDQALLRPGRIDVHIHFPLCDFSSFKTLA  356 (480)
Q Consensus       326 ----~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il  356 (480)
                          -.-|+||.|  ||. .|.+..|+.++-..|+
T Consensus       163 y~~~~e~d~aL~r--rF~-~I~V~Ep~~e~t~~IL  194 (195)
T d1jbka_         163 YRQYIEKDAALER--RFQ-KVFVAEPSVEDTIAIL  194 (195)
T ss_dssp             HHHHTTTCHHHHT--TEE-EEECCCCCHHHHHTTC
T ss_pred             HHHHHHcCHHHHh--cCC-EeecCCCCHHHHHHHh
Confidence                234999999  996 8999999998766553

>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=99.30  E-value=1.7e-12  Score=128.67  Aligned_cols=152  Identities=18%  Similarity=0.212  Sum_probs=95.5

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCC----------------
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMS----------------  249 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~----------------  249 (480)
                      .-.|.+|+|++.+|..+.-.+...          |   ..++||+||||||||++|+++|.-|-                
T Consensus         3 ~~~f~~I~Gq~~~kral~laa~~~----------~---~h~vLl~G~pG~GKT~lar~~~~iLp~~~~~~~~~~~~~~~~   69 (333)
T d1g8pa_           3 VFPFSAIVGQEDMKLALLLTAVDP----------G---IGGVLVFGDRGTGKSTAVRALAALLPEIEAVEGCPVSSPNVE   69 (333)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHHCG----------G---GCCEEEECCGGGCTTHHHHHHHHHSCCEEEETTCTTCCSSGG
T ss_pred             CCChhhccCcHHHHHHHHHHHhcc----------C---CCeEEEECCCCccHHHHHHHHHHhCCCchhhccCccccCccc
Confidence            347999999999998766333210          1   13799999999999999999998651                


Q ss_pred             -----------------CcEEEEeCCC----cCChHHHHHHHHh-----------hcCCcEEEEecccccccCcccccch
Q 011664          250 -----------------YDVYDVDLSR----VADDADLKSLLLQ-----------TTSKSVILIEDLDRFLVEKPAAVSL  297 (480)
Q Consensus       250 -----------------~~~~~i~~s~----~~~~~~l~~l~~~-----------~~~~sII~IDEiD~l~~~~~~~~~l  297 (480)
                                       .+++....+.    +.+..++...+..           .....|+||||++.+-     ..++
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~G~~d~~~~~~~g~~~~~~G~l~~A~~gvl~iDEi~~~~-----~~~~  144 (333)
T d1g8pa_          70 MIPDWATVLSTNVIRKPTPVVDLPLGVSEDRVVGALDIERAISKGEKAFEPGLLARANRGYLYIDECNLLE-----DHIV  144 (333)
T ss_dssp             GSCTTCCCSCCCEEEECCCEEEECTTCCHHHHHCEECHHHHHHHCGGGEECCHHHHHTTEEEEETTGGGSC-----HHHH
T ss_pred             cccchhhccccCcccccCceeeccCCCCcccccCcchhhhccccCcceeeccccccccccEeecccHHHHH-----HHHH
Confidence                             1112211110    0111111222211           1235799999999773     3567


Q ss_pred             hhhhhhccc---------ccccccCCceEEEEecCC-CccCcccccCCCceeEEEEcCCCC-HHHHHHHHHH
Q 011664          298 SGVLNFMDG---------VLNSCCFEERVMVFTMNS-KDHVDQALLRPGRIDVHIHFPLCD-FSSFKTLASS  358 (480)
Q Consensus       298 s~lL~~ldg---------~~~~~~~~~~ivI~tTN~-~~~LD~aLlrpGRfd~~I~~~~p~-~~~r~~il~~  358 (480)
                      +.|++.|+.         ... ..+...++|+|+|. +..+.++++.  ||+.++.+++|. ...+..+...
T Consensus       145 ~aLl~~me~~~v~i~r~g~~~-~~p~~f~liaa~Np~~~~l~~~llD--Rf~~~i~v~~~~~~~~~~~~~~~  213 (333)
T d1g8pa_         145 DLLLDVAQSGENVVERDGLSI-RHPARFVLVGSGNPEEGDLRPQLLD--RFGLSVEVLSPRDVETRVEVIRR  213 (333)
T ss_dssp             HHHHHHHHHSEEEECCTTCCE-EEECCEEEEEEECSCSCCCCHHHHT--TCSEEEECCCCCSHHHHHHHHHH
T ss_pred             HHHhhhhcCCeEEecccCcee-cCCCCEEEEEecCccccccccchhh--hhcceeeccCcchhhHHHHHHHh
Confidence            888888852         111 11223466777774 4679999999  999999999874 4555555443

>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=99.20  E-value=1.5e-10  Score=119.08  Aligned_cols=70  Identities=23%  Similarity=0.339  Sum_probs=55.2

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhh-CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRL-GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~-g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      |+|++++|+.+--.+....++...-... ....|.+|||.||||||||.||+++|..++.||+.++++.+.
T Consensus        16 VvGQ~~AKk~lsvav~nhyrR~~~~~~~~~ei~ksNILliGPTGvGKTlLAr~LAk~l~VPFv~~daT~fT   86 (443)
T d1g41a_          16 IIGQADAKRAVAIALRNRWRRMQLQEPLRHEVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFT   86 (443)
T ss_dssp             CCSCHHHHHHHHHHHHHHHHHHHSCTTTTTTCCCCCEEEECCTTSSHHHHHHHHHHHTTCCEEEEEGGGGC
T ss_pred             ccCcHHHHHHHHHHHHHHHHHhhcccccccccccccEEEECCCCCCHHHHHHHHHHHhCCCEEEeecceee
Confidence            7999999999988876654432211111 122466999999999999999999999999999999998775

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=99.20  E-value=1.8e-11  Score=123.96  Aligned_cols=153  Identities=18%  Similarity=0.220  Sum_probs=90.7

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----------CCcEEEEeC
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----------SYDVYDVDL  257 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----------~~~~~~i~~  257 (480)
                      .+|.++|-++-.+.+.+.+.             ...+.+++|.||||+|||.++..+|..+          +..++.+++
T Consensus        20 ~ld~~~gr~~ei~~~~~~L~-------------r~~k~n~llvG~~GvGKtaiv~~la~~i~~~~vp~~l~~~~i~~ld~   86 (387)
T d1qvra2          20 KLDPVIGRDEEIRRVIQILL-------------RRTKNNPVLIGEPGVGKTAIVEGLAQRIVKGDVPEGLKGKRIVSLQM   86 (387)
T ss_dssp             CSCCCCSCHHHHHHHHHHHH-------------CSSCCCCEEEECTTSCHHHHHHHHHHHHHHTCSCTTSTTCEEEEECC
T ss_pred             CCCCCcCcHHHHHHHHHHHh-------------cCCCCCCeEECCCCCCHHHHHHHHHHHHHhCCCCHHHcCceEEEeeH
Confidence            36678888877777765443             2245678999999999999999998643          567999999


Q ss_pred             CCcCC--------hHHHHHHHHhh---cCCcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecC---
Q 011664          258 SRVAD--------DADLKSLLLQT---TSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMN---  323 (480)
Q Consensus       258 s~~~~--------~~~l~~l~~~~---~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN---  323 (480)
                      +.+..        +..+..++...   ..+.||||||++.+.+...+... ..+-+.|....+.  ++-++|..||.   
T Consensus        87 ~~l~ag~~~~g~~e~r~~~i~~~~~~~~~~~ilfide~h~l~~~g~~~g~-~d~a~~Lkp~L~r--g~~~~I~~tT~~ey  163 (387)
T d1qvra2          87 GSLLAGAKYRGEFEERLKAVIQEVVQSQGEVILFIDELHTVVGAGKAEGA-VDAGNMLKPALAR--GELRLIGATTLDEY  163 (387)
T ss_dssp             -----------CHHHHHHHHHHHHHTTCSSEEEEECCC--------------------HHHHHT--TCCCEEEEECHHHH
T ss_pred             hhhhcccCcchhHHHHHHHHHHHhccCCCceEEEeccHHHHhcCCCCCCc-ccHHHHHHHHHhC--CCcceeeecCHHHH
Confidence            88763        23355555443   34678999999999864432221 2223333333331  33344444552   


Q ss_pred             -CCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHh
Q 011664          324 -SKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYL  360 (480)
Q Consensus       324 -~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l  360 (480)
                       ..+. |+||.|  ||. .|.+..|+.++-..|++...
T Consensus       164 ~~~e~-d~al~r--rF~-~v~v~ep~~~~~~~il~~~~  197 (387)
T d1qvra2         164 REIEK-DPALER--RFQ-PVYVDEPTVEETISILRGLK  197 (387)
T ss_dssp             HHHTT-CTTTCS--CCC-CEEECCCCHHHHHHHHHHHH
T ss_pred             HHhcc-cHHHHH--hcc-cccCCCCcHHHHHHHHHHHH
Confidence             2233 899999  996 89999999999888877543

>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=99.15  E-value=3.1e-10  Score=107.94  Aligned_cols=195  Identities=13%  Similarity=0.150  Sum_probs=121.1

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCChHHHHH
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADDADLKS  268 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~~~l~~  268 (480)
                      .+|....-+.+.+.+......           ...+||+||+|||||.+|++|+...   ..+++.+++..+........
T Consensus         2 ~v~~S~~~~~~~~~~~~~a~~-----------~~pvlI~Ge~GtGK~~~A~~ih~~s~~~~~~~~~~~~~~~~~~~~~~~   70 (247)
T d1ny5a2           2 YVFESPKMKEILEKIKKISCA-----------ECPVLITGESGVGKEVVARLIHKLSDRSKEPFVALNVASIPRDIFEAE   70 (247)
T ss_dssp             CCCCSHHHHHHHHHHHHHTTC-----------CSCEEEECSTTSSHHHHHHHHHHHSTTTTSCEEEEETTTSCHHHHHHH
T ss_pred             eEecCHHHHHHHHHHHHHhCC-----------CCCEEEECCCCcCHHHHHHHHHHhcCCcccccccchhhhhhhcccHHH
Confidence            456667777777666654222           3469999999999999999999765   45689999988765544455


Q ss_pred             HHHh-----------------hcCCcEEEEecccccccCcccccchhhhhhhccc-c----ccc-ccCCceEEEEecCCC
Q 011664          269 LLLQ-----------------TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDG-V----LNS-CCFEERVMVFTMNSK  325 (480)
Q Consensus       269 l~~~-----------------~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg-~----~~~-~~~~~~ivI~tTN~~  325 (480)
                      +|..                 ....+.|||||||.+..     .....|++.++. .    .+. ......-+|++|+.+
T Consensus        71 lfg~~~~~~~~~~~~~~g~l~~a~gGtL~l~~i~~L~~-----~~Q~~L~~~l~~~~~~~~~~~~~~~~~~RlI~~s~~~  145 (247)
T d1ny5a2          71 LFGYEKGAFTGAVSSKEGFFELADGGTLFLDEIGELSL-----EAQAKLLRVIESGKFYRLGGRKEIEVNVRILAATNRN  145 (247)
T ss_dssp             HHCBCTTSSTTCCSCBCCHHHHTTTSEEEEESGGGCCH-----HHHHHHHHHHHHSEECCBTCCSBEECCCEEEEEESSC
T ss_pred             hcCcccCCcCCcccccCCHHHccCCCEEEEeChHhCCH-----HHHHHHHHHHHhCCEEECCCCCceecCeEEEEecCCC
Confidence            5421                 22346899999998832     222344444431 0    000 001123466666543


Q ss_pred             -c------cCcccccCCCcee-EEEEcCCCC--HHHHHHHHHHHhccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHhhh
Q 011664          326 -D------HVDQALLRPGRID-VHIHFPLCD--FSSFKTLASSYLGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIANRN  395 (480)
Q Consensus       326 -~------~LD~aLlrpGRfd-~~I~~~~p~--~~~r~~il~~~l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a~~  395 (480)
                       +      .+++.|+.  |+. ..|.+|+..  .++...|++.++...       ..+......++|++-+..+....+.
T Consensus       146 l~~l~~~~~f~~~L~~--~l~~~~i~lPpLreR~~Di~~l~~~~l~~~-------~~~~~~~~~~ls~~al~~L~~~~WP  216 (247)
T d1ny5a2         146 IKELVKEGKFREDLYY--RLGVIEIEIPPLRERKEDIIPLANHFLKKF-------SRKYAKEVEGFTKSAQELLLSYPWY  216 (247)
T ss_dssp             HHHHHHTTSSCHHHHH--HHTTEEEECCCGGGCHHHHHHHHHHHHHHH-------HHHTTCCCCEECHHHHHHHHHSCCT
T ss_pred             HHHHHHcCCCcHHHHh--hcCeeeecCCChhhchhhHhhhhhhhhhhh-------hhhcCCCCCCCCHHHHHHHHhCCCC
Confidence             2      24444544  443 467777664  345566666665321       1111123357899999999988888


Q ss_pred             cHHHHHHHHHHHHHhc
Q 011664          396 SPSRALKSVITALQTD  411 (480)
Q Consensus       396 ~~~~al~~~i~~~~~~  411 (480)
                      ...+.|+.+++.+-..
T Consensus       217 GNl~EL~~~l~~a~~~  232 (247)
T d1ny5a2         217 GNVRELKNVIERAVLF  232 (247)
T ss_dssp             THHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHh
Confidence            9999999998877554

>d2gnoa2 c.37.1.20 (A:11-208) gamma subunit of DNA polymerase III, N-domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Extended AAA-ATPase domain
domain: gamma subunit of DNA polymerase III, N-domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.04  E-value=3.8e-10  Score=103.79  Aligned_cols=113  Identities=12%  Similarity=0.167  Sum_probs=87.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC------CcEEEEeCCC-cCChHHHHHHHHhh------cCCcEEEEecccccccC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS------YDVYDVDLSR-VADDADLKSLLLQT------TSKSVILIEDLDRFLVE  290 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~------~~~~~i~~s~-~~~~~~l~~l~~~~------~~~sII~IDEiD~l~~~  290 (480)
                      ...+|||||||||||++|..+|+...      .+++.+.... -.+-.++|.+....      ....|++|||+|.+.  
T Consensus        15 ~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~--   92 (198)
T d2gnoa2          15 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMT--   92 (198)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBC--
T ss_pred             CceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCccccc--
Confidence            45899999999999999999998662      4688887653 23556677765433      234699999999883  


Q ss_pred             cccccchhhhhhhcccccccccCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCH
Q 011664          291 KPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDF  349 (480)
Q Consensus       291 ~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~  349 (480)
                         ....+.||..|+.-     +.+.++|++||.++.|.|++++  |+ .++.++.|..
T Consensus        93 ---~~aqNaLLK~LEEP-----p~~t~fiLit~~~~~ll~TI~S--RC-~~i~~~~p~~  140 (198)
T d2gnoa2          93 ---QQAANAFLKALEEP-----PEYAVIVLNTRRWHYLLPTIKS--RV-FRVVVNVPKE  140 (198)
T ss_dssp             ---HHHHHHTHHHHHSC-----CTTEEEEEEESCGGGSCHHHHT--TS-EEEECCCCHH
T ss_pred             ---hhhhhHHHHHHhCC-----CCCceeeeccCChhhCHHHHhc--ce-EEEeCCCchH
Confidence               34557888888643     4567888999999999999999  98 5889988764

>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=99.01  E-value=1e-08  Score=95.97  Aligned_cols=196  Identities=11%  Similarity=0.119  Sum_probs=117.7

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCCh-
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADD-  263 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~-  263 (480)
                      |...-++++|-++..+.+.+                 ...+.++++||+|+|||+|++.++..++..+..+++...... 
T Consensus         7 p~~~~~~f~GR~~el~~l~~-----------------~~~~~i~i~G~~G~GKTsLl~~~~~~~~~~~~~i~~~~~~~~~   69 (283)
T d2fnaa2           7 PKDNRKDFFDREKEIEKLKG-----------------LRAPITLVLGLRRTGKSSIIKIGINELNLPYIYLDLRKFEERN   69 (283)
T ss_dssp             CCCSGGGSCCCHHHHHHHHH-----------------TCSSEEEEEESTTSSHHHHHHHHHHHHTCCEEEEEGGGGTTCS
T ss_pred             CCCChhhCCChHHHHHHHHh-----------------ccCCEEEEEcCCCCcHHHHHHHHHHHCCCCeEEEEeccccccc
Confidence            33457889999887766643                 134689999999999999999999999998888876433211 


Q ss_pred             ----HH-----------------------------------------------HHHHH----HhhcCCcEEEEecccccc
Q 011664          264 ----AD-----------------------------------------------LKSLL----LQTTSKSVILIEDLDRFL  288 (480)
Q Consensus       264 ----~~-----------------------------------------------l~~l~----~~~~~~sII~IDEiD~l~  288 (480)
                          ..                                               +..++    .....+.++++||++.+.
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~i~id~~~~~~  149 (283)
T d2fnaa2          70 YISYKDFLLELQKEINKLVKRLPSLLKALKNIQGIVIMGNEIKFNWNRKDRLSFANLLESFEQASKDNVIIVLDEAQELV  149 (283)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHCTTHHHHTTTSTTEEECSSSEEEC-----CCCHHHHHHHHHHTCSSCEEEEEETGGGGG
T ss_pred             cccHHHHHHHHHHHhhhhhhhhHHHHHHHHhhhcccccccccccccchhhhhHHHHHHHHHHhhcccccccccchhhhhc
Confidence                00                                               11111    112456789999999875


Q ss_pred             cCcccccchhhhhhhcccccccccCCceEEEE-ecCCC--ccC------cccccCCCceeEEEEcCCCCHHHHHHHHHHH
Q 011664          289 VEKPAAVSLSGVLNFMDGVLNSCCFEERVMVF-TMNSK--DHV------DQALLRPGRIDVHIHFPLCDFSSFKTLASSY  359 (480)
Q Consensus       289 ~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~-tTN~~--~~L------D~aLlrpGRfd~~I~~~~p~~~~r~~il~~~  359 (480)
                      ....     ..++..+......  ......++ ++...  ..+      ...+  .||....+++++.+.++..+++...
T Consensus       150 ~~~~-----~~~~~~l~~~~~~--~~~~~~i~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~i~L~~l~~~e~~~~l~~~  220 (283)
T d2fnaa2         150 KLRG-----VNLLPALAYAYDN--LKRIKFIMSGSEMGLLYDYLRVEDPESPL--FGRAFSTVELKPFSREEAIEFLRRG  220 (283)
T ss_dssp             GCTT-----CCCHHHHHHHHHH--CTTEEEEEEESSHHHHHHHTTTTCTTSTT--TTCCCEEEEECCCCHHHHHHHHHHH
T ss_pred             ccch-----HHHHHHHHHHHHh--hhhhhhhhccccchHHHHHHHhhhhcchh--cccceeEEeeCCCCHHHHHHHHHhh
Confidence            4221     2223232222110  12233333 32211  111      1122  2466688999999999999999887


Q ss_pred             hccCCCCCchhHHHHHHhCCCCCHHHHHHHHHHh--hhcHHHHHHHHHHHH
Q 011664          360 LGLKDHKLFPQVEEIFQNGSSLSPAEIGELMIAN--RNSPSRALKSVITAL  408 (480)
Q Consensus       360 l~~~~~~l~~~i~~l~~~~~g~s~adI~~ll~~a--~~~~~~al~~~i~~~  408 (480)
                      +...+... ++++.+.+.+.| .|.-|..++...  ......++..+++..
T Consensus       221 ~~~~~~~~-~~~~~i~~~~~G-~P~~L~~~~~~~~~~~~~~~~~~~~~~~~  269 (283)
T d2fnaa2         221 FQEADIDF-KDYEVVYEKIGG-IPGWLTYFGFIYLDNKNLDFAINQTLEYA  269 (283)
T ss_dssp             HHHHTCCC-CCHHHHHHHHCS-CHHHHHHHHHHHHHHCCHHHHHHHHHHHH
T ss_pred             hhhcCCCH-HHHHHHHHHhCC-CHHHHHHHHHHHHhcccHHHHHHHHHHHH
Confidence            76544433 356777777755 487787765432  234455555555543

>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=98.90  E-value=3.3e-10  Score=107.09  Aligned_cols=60  Identities=25%  Similarity=0.382  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcC
Q 011664          197 DLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVA  261 (480)
Q Consensus       197 ~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~  261 (480)
                      +.++.+.+.+..+....     .+...|++||||||||||||++|+++|++++.+++.++.+.+.
T Consensus        10 ~~~~~~~~~~~~~~~~~-----~~~~~P~~ilL~GpPGtGKT~la~~la~~~~~~~~~i~~d~~~   69 (273)
T d1gvnb_          10 QFENRLNDNLEELIQGK-----KAVESPTAFLLGGQPGSGKTSLRSAIFEETQGNVIVIDNDTFK   69 (273)
T ss_dssp             HHHHHHHHHHHHHHTTC-----CCCSSCEEEEEECCTTSCTHHHHHHHHHHTTTCCEEECTHHHH
T ss_pred             HHHHHHHHHHHHHHhcc-----cCCCCCEEEEEECCCCCCHHHHHHHHHHHhhcceEEEecHHHH
Confidence            34444555554444332     2556788999999999999999999999999999999976543

>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=98.25  E-value=3.4e-05  Score=73.29  Aligned_cols=187  Identities=13%  Similarity=0.129  Sum_probs=102.2

Q ss_pred             cccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC----CCc---EEEEeCCCcCChH
Q 011664          192 ISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM----SYD---VYDVDLSRVADDA  264 (480)
Q Consensus       192 i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l----~~~---~~~i~~s~~~~~~  264 (480)
                      +.|-+...++|.+.+...          +-...+-+.|||++|+|||+||+.+++..    +..   ++-++.+......
T Consensus        22 ~~gR~~~~~~i~~~L~~~----------~~~~~~~v~I~GmgGiGKTtLA~~v~~~~~~~~~~~f~~~~Wv~vs~~~~~~   91 (277)
T d2a5yb3          22 CYIREYHVDRVIKKLDEM----------CDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKS   91 (277)
T ss_dssp             SCCCHHHHHHHHHHHHHH----------TTSSSEEEEEECSTTSSHHHHHHHHHHHCSSTBTTTBSEEEEEECCCCSTTH
T ss_pred             eeCcHHHHHHHHHHHHhc----------cCCCceEEEEECCCCCCHHHHHHHHHHhhhhhhhhcCceEEEEEecCCCCHH
Confidence            568888888887766432          11123467899999999999999998763    222   3445544433222


Q ss_pred             HH------------------------------HHHHH-h--hcCCcEEEEecccccccCcccccchhhhhhhcccccccc
Q 011664          265 DL------------------------------KSLLL-Q--TTSKSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSC  311 (480)
Q Consensus       265 ~l------------------------------~~l~~-~--~~~~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~  311 (480)
                      .+                              +..+. .  ...+++|++||++...          + +..+..     
T Consensus        92 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~kr~LlVLDDv~~~~----------~-~~~~~~-----  155 (277)
T d2a5yb3          92 TFDLFTDILLMLKSEDDLLNFPSVEHVTSVVLKRMICNALIDRPNTLFVFDDVVQEE----------T-IRWAQE-----  155 (277)
T ss_dssp             HHHHHHHHHHHHTTTSCCTTCCCCTTCCHHHHHHHHHHHHTTSTTEEEEEEEECCHH----------H-HHHHHH-----
T ss_pred             HHHHHHHHHHHHhcchhhcCCccchhhhhHHHHHHHHHHHhccCCeeEecchhhHHh----------h-hhhhcc-----
Confidence            11                              11111 1  1357899999997421          1 111111     


Q ss_pred             cCCceEEEEecCCCccCcccccCCCceeEEEEcCCCCHHHHHHHHHHHhccCCCCC-chhH-HHHHHhCCCCCHHHHHHH
Q 011664          312 CFEERVMVFTMNSKDHVDQALLRPGRIDVHIHFPLCDFSSFKTLASSYLGLKDHKL-FPQV-EEIFQNGSSLSPAEIGEL  389 (480)
Q Consensus       312 ~~~~~ivI~tTN~~~~LD~aLlrpGRfd~~I~~~~p~~~~r~~il~~~l~~~~~~l-~~~i-~~l~~~~~g~s~adI~~l  389 (480)
                       ...+ ||+||....-.. .+..  +. ..+.+...+.++-.+++..+....+... .+++ .++++...| .|--|.-+
T Consensus       156 -~~sr-ilvTTR~~~v~~-~~~~--~~-~~~~l~~L~~~ea~~Lf~~~~~~~~~~~~~~~~~~~iv~~c~G-lPLAl~~i  228 (277)
T d2a5yb3         156 -LRLR-CLVTTRDVEISN-AASQ--TC-EFIEVTSLEIDECYDFLEAYGMPMPVGEKEEDVLNKTIELSSG-NPATLMMF  228 (277)
T ss_dssp             -TTCE-EEEEESBGGGGG-GCCS--CE-EEEECCCCCHHHHHHHHHHTSCCCC--CHHHHHHHHHHHHHTT-CHHHHHHH
T ss_pred             -cCce-EEEEeehHHHHH-hcCC--CC-ceEECCCCCHHHHHHHHHHHhCCccCchhhHHHHHHHHHHhCC-CHHHHHHH
Confidence             1223 556665443222 2222  22 4678999999999999987653322211 1222 466666644 47666554


Q ss_pred             HHHhhhcHHHHHHHHHHHHHhc
Q 011664          390 MIANRNSPSRALKSVITALQTD  411 (480)
Q Consensus       390 l~~a~~~~~~al~~~i~~~~~~  411 (480)
                      -..-+..+......+...++.+
T Consensus       229 g~~l~~k~~~~~~~~~~~L~~~  250 (277)
T d2a5yb3         229 FKSCEPKTFEKMAQLNNKLESR  250 (277)
T ss_dssp             HTTCCSSSHHHHHHHHHHHHHH
T ss_pred             HHHhccCCHHHHHHHHHHHhcC
Confidence            3332333444555666666543

>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=98.17  E-value=5.2e-07  Score=77.06  Aligned_cols=33  Identities=39%  Similarity=0.732  Sum_probs=29.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ++.|+|.|||||||||+|+++|..++++++..+
T Consensus         2 ~k~I~l~G~~GsGKSTvak~La~~L~~~~id~~   34 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSD   34 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHHHHHHHTTCEEEEHH
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            357999999999999999999999999988654

>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=98.12  E-value=2.3e-06  Score=74.81  Aligned_cols=25  Identities=16%  Similarity=0.409  Sum_probs=22.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      ++|.||||||||||++++++.+..+
T Consensus         3 i~I~G~~G~GKSTLl~~i~~~l~~~   27 (178)
T d1ye8a1           3 IIITGEPGVGKTTLVKKIVERLGKR   27 (178)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHGGG
T ss_pred             EEEECCCCcHHHHHHHHHHhcCCCC
Confidence            8999999999999999999977543

>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=98.03  E-value=1.3e-06  Score=76.11  Aligned_cols=34  Identities=15%  Similarity=0.211  Sum_probs=30.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ..+.|++.|||||||||||+++|..++.+++..+
T Consensus         6 ~~K~I~i~G~~GsGKTTla~~La~~~~~~~i~~~   39 (192)
T d1lw7a2           6 FAKTVAILGGESSGKSVLVNKLAAVFNTTSAWEY   39 (192)
T ss_dssp             TCEEEEEECCTTSHHHHHHHHHHHHTTCEEECCT
T ss_pred             cceEEEEECCCCCCHHHHHHHHHHHhCCCeEeee
Confidence            3568999999999999999999999999887654

>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=97.97  E-value=1.2e-06  Score=75.87  Aligned_cols=30  Identities=30%  Similarity=0.471  Sum_probs=27.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .|+|.|||||||||+|+++|..+|++++.+
T Consensus         6 ~I~i~G~pGsGKTTia~~La~~l~~~~i~~   35 (173)
T d1rkba_           6 NILLTGTPGVGKTTLGKELASKSGLKYINV   35 (173)
T ss_dssp             CEEEECSTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEec
Confidence            488999999999999999999999998764

>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=97.95  E-value=2.4e-06  Score=77.59  Aligned_cols=113  Identities=24%  Similarity=0.250  Sum_probs=66.1

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccccccCcccccchhh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDRFLVEKPAAVSLSG  299 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~l~~~~~~~~~ls~  299 (480)
                      |.|.++.++|||||+||||+++.++++.++..++.  ...-.    ....++......++++||+-..+.     .....
T Consensus        49 ~~PKkn~i~~~GP~~TGKS~f~~sl~~~l~G~vis--~~N~~----s~F~Lq~l~~~kv~l~dD~t~~~~-----~~~d~  117 (205)
T d1tuea_          49 GTPKKNCLVFCGPANTGKSYFGMSFIHFIQGAVIS--FVNST----SHFWLEPLTDTKVAMLDDATTTCW-----TYFDT  117 (205)
T ss_dssp             TCTTCSEEEEESCGGGCHHHHHHHHHHHHTCEECC--CCCSS----SCGGGGGGTTCSSEEEEEECHHHH-----HHHHH
T ss_pred             CCCCceEEEEECCCCccHHHHHHHHHHHhCCEEEe--ccCCC----CCcccccccCCeEEEEeccccchH-----HHHHH
Confidence            56777899999999999999999999998654432  22111    112344555678999999854321     11111


Q ss_pred             -hhhhccccccc--c-cCC-----ceEEEEecCCC---ccCcccccCCCceeEEEEcCC
Q 011664          300 -VLNFMDGVLNS--C-CFE-----ERVMVFTMNSK---DHVDQALLRPGRIDVHIHFPL  346 (480)
Q Consensus       300 -lL~~ldg~~~~--~-~~~-----~~ivI~tTN~~---~~LD~aLlrpGRfd~~I~~~~  346 (480)
                       +-+.+||-.-.  + ...     -.-+|+|||..   ++-.++|.+  |+ ..++|+.
T Consensus       118 ~lK~ll~G~~vsvd~KhK~~vqi~~pPliITsN~~~~~~d~~~~L~s--Ri-~~f~F~~  173 (205)
T d1tuea_         118 YMRNALDGNPISIDRKHKPLIQLKCPPILLTTNIHPAKDNRWPYLES--RI-TVFEFPN  173 (205)
T ss_dssp             HCHHHHHTCCEEEC----CCEEECCCCEEEEESSCTTSSSSCHHHHT--SC-EEEECCS
T ss_pred             HHHhccCCCeeeeecccCCcccccCCCEEEEcCCCCCccccchhhhh--eE-EEEECCC
Confidence             23344442100  0 000     11256788832   333467888  88 5778774

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=97.93  E-value=2.3e-06  Score=74.37  Aligned_cols=34  Identities=29%  Similarity=0.381  Sum_probs=30.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS  258 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s  258 (480)
                      +-|+|.|||||||||+|+++|..+|.+++.++..
T Consensus         5 ~iI~l~G~~GsGKSTia~~La~~lg~~~~~~~~d   38 (176)
T d1zp6a1           5 NILLLSGHPGSGKSTIAEALANLPGVPKVHFHSD   38 (176)
T ss_dssp             EEEEEEECTTSCHHHHHHHHHTCSSSCEEEECTT
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHhCCCEEEecHH
Confidence            4588999999999999999999999999998753

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=97.91  E-value=4e-06  Score=72.60  Aligned_cols=34  Identities=24%  Similarity=0.330  Sum_probs=30.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      ++-|+|+||||+||||+|+++|..++.+++.++.
T Consensus         3 ~kiI~l~G~~GsGKsTva~~L~~~l~~~~~~~~~   36 (178)
T d1qhxa_           3 TRMIILNGGSSAGKSGIVRCLQSVLPEPWLAFGV   36 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHSSSCEEEEEH
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHcCCCeEEeec
Confidence            4578999999999999999999999999888764

>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=97.89  E-value=2.1e-06  Score=75.10  Aligned_cols=31  Identities=32%  Similarity=0.455  Sum_probs=29.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +|+|.||||+|||++++++|..+|++|++.+
T Consensus         2 ~I~liG~~GsGKsTi~k~La~~l~~~~~d~d   32 (161)
T d1viaa_           2 NIVFIGFMGSGKSTLARALAKDLDLVFLDSD   32 (161)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHTCEEEEHH
T ss_pred             cEEEECCCCCCHHHHHHHHHHHhCCCEEecC
Confidence            5889999999999999999999999999865

>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=97.87  E-value=2.7e-06  Score=74.75  Aligned_cols=32  Identities=22%  Similarity=0.517  Sum_probs=29.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.|+|.|||||||||+++.+|..+|+++++.|
T Consensus         3 ~~Iil~G~~GsGKSTia~~LA~~Lg~~~id~D   34 (170)
T d1e6ca_           3 EPIFMVGARGCGMTTVGRELARALGYEFVDTD   34 (170)
T ss_dssp             CCEEEESCTTSSHHHHHHHHHHHHTCEEEEHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHhCCCEEehh
Confidence            46889999999999999999999999998754

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=97.75  E-value=7.2e-06  Score=70.50  Aligned_cols=29  Identities=31%  Similarity=0.676  Sum_probs=25.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      +-++|.|||||||||+|+++|..++..++
T Consensus         3 klI~i~G~~GsGKTTva~~L~~~~~~~~~   31 (176)
T d2bdta1           3 KLYIITGPAGVGKSTTCKRLAAQLDNSAY   31 (176)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSSEEE
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHcCCCEE
Confidence            46899999999999999999999987654

>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=97.75  E-value=5.8e-06  Score=71.57  Aligned_cols=33  Identities=36%  Similarity=0.527  Sum_probs=28.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ++-++|.|||||||||+++++|..++..++..+
T Consensus         6 ~~iivl~G~~GsGKsT~a~~La~~l~~~~~~~d   38 (171)
T d1knqa_           6 HHIYVLMGVSGSGKSAVASEVAHQLHAAFLDGD   38 (171)
T ss_dssp             SEEEEEECSTTSCHHHHHHHHHHHHTCEEEEGG
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHhCCCeechh
Confidence            345789999999999999999999998776654

>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=97.73  E-value=5.4e-06  Score=72.37  Aligned_cols=30  Identities=30%  Similarity=0.506  Sum_probs=27.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      +.|.|+|||||||+++.+|..+|.+|++.|
T Consensus         4 IvliG~~G~GKSTig~~La~~l~~~fiD~D   33 (165)
T d2iyva1           4 AVLVGLPGSGKSTIGRRLAKALGVGLLDTD   33 (165)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCCeEeec
Confidence            667799999999999999999999999765

>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=97.68  E-value=7.1e-06  Score=71.14  Aligned_cols=24  Identities=29%  Similarity=0.625  Sum_probs=22.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      |+++|+||||||||+|+++++..+
T Consensus         2 k~v~ItG~~GtGKTtl~~~i~~~l   25 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLIHKASEVL   25 (189)
T ss_dssp             CCEEEESCCSSCHHHHHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHHHHHHHHH
Confidence            579999999999999999999876

>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=97.64  E-value=1.9e-05  Score=68.29  Aligned_cols=28  Identities=32%  Similarity=0.388  Sum_probs=24.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .+..|+|.|||||||||+++.+|..++.
T Consensus         4 k~~~I~i~G~~GsGKTT~~~~La~~l~~   31 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMAEMIAAELDG   31 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHHHHHHHHSTT
T ss_pred             CCCEEEEEeCCCCCHHHHHHHHHHHhCC
Confidence            3445999999999999999999999864

>d1yj5a2 c.37.1.1 (A:351-522) 5' polynucleotide kinase-3' phosphatase, C-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: 5' polynucleotide kinase-3' phosphatase, C-terminal domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.60  E-value=2.6e-05  Score=68.86  Aligned_cols=33  Identities=21%  Similarity=0.195  Sum_probs=27.6

Q ss_pred             CCCceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          222 VWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       222 ~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      +.|.-++|+|+|||||||+|+.++...++.++.
T Consensus        12 ~~p~liil~G~pGsGKST~a~~l~~~~~~~~i~   44 (172)
T d1yj5a2          12 PNPEVVVAVGFPGAGKSTFIQEHLVSAGYVHVN   44 (172)
T ss_dssp             SSCCEEEEECCTTSSHHHHHHHHTGGGTCEEEE
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHhcCCEEEc
Confidence            456679999999999999999999888765543

>d1m8pa3 c.37.1.15 (A:391-573) ATP sulfurylase C-terminal domain {Fungus (Penicillium chrysogenum) [TaxId: 5076]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ATP sulfurylase C-terminal domain
domain: ATP sulfurylase C-terminal domain
species: Fungus (Penicillium chrysogenum) [TaxId: 5076]

Probab=97.56  E-value=7.5e-06  Score=70.85  Aligned_cols=25  Identities=24%  Similarity=0.360  Sum_probs=22.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .|+|.|+||+||||+|+++|..++.
T Consensus         8 ~I~l~G~~GsGKTTia~~La~~L~~   32 (183)
T d1m8pa3           8 TIFLTGYMNSGKDAIARALQVTLNQ   32 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhh
Confidence            3788999999999999999998753

>d1qf9a_ c.37.1.1 (A:) UMP/CMP kinase {Dictyostelium discoideum [TaxId: 44689]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: UMP/CMP kinase
species: Dictyostelium discoideum [TaxId: 44689]

Probab=97.54  E-value=2.5e-05  Score=69.51  Aligned_cols=32  Identities=16%  Similarity=0.238  Sum_probs=27.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      .|.-|++.||||+||||+|+.+|..+|...+.
T Consensus         5 kp~iI~i~G~pGSGKsT~a~~La~~~g~~~i~   36 (194)
T d1qf9a_           5 KPNVVFVLGGPGSGKGTQCANIVRDFGWVHLS   36 (194)
T ss_dssp             CCEEEEEEESTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHCCceEc
Confidence            35578999999999999999999999876554

>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=97.49  E-value=2.6e-05  Score=68.26  Aligned_cols=29  Identities=21%  Similarity=0.307  Sum_probs=26.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+|.|||||||||+|+.+|..+|...+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~~~~~i~~   31 (182)
T d1zina1           3 LVLMGLPGAGKGTQAEKIVAAYGIPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceech
Confidence            78999999999999999999998876654

>d1zaka1 c.37.1.1 (A:3-127,A:159-222) Adenylate kinase {Maize (Zea mays) [TaxId: 4577]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Maize (Zea mays) [TaxId: 4577]

Probab=97.45  E-value=2.1e-05  Score=69.79  Aligned_cols=30  Identities=10%  Similarity=0.205  Sum_probs=26.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .|+|.|||||||||+|+.+|..+|...+..
T Consensus         5 ~I~i~GppGsGKsT~a~~La~~~~~~~is~   34 (189)
T d1zaka1           5 KVMISGAPASGKGTQCELIKTKYQLAHISA   34 (189)
T ss_dssp             CEEEEESTTSSHHHHHHHHHHHHCCEECCH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCcEEeh
Confidence            589999999999999999999998876543

>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=97.42  E-value=2.6e-05  Score=68.62  Aligned_cols=30  Identities=30%  Similarity=0.467  Sum_probs=26.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .++|.|||||||||+|+.+|..+|...+.+
T Consensus         2 ~I~i~G~pGsGKsT~a~~La~~~g~~~i~~   31 (181)
T d2cdna1           2 RVLLLGPPGAGKGTQAVKLAEKLGIPQIST   31 (181)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCceEch
Confidence            378999999999999999999998877654

>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=97.40  E-value=5e-05  Score=67.63  Aligned_cols=31  Identities=16%  Similarity=0.342  Sum_probs=26.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      ++-|+|.|||||||||+|+.+|..+|...+.
T Consensus         8 ~~iI~l~G~pGSGKsT~a~~La~~~g~~~is   38 (194)
T d3adka_           8 SKIIFVVGGPGSGKGTQCEKIVQKYGYTHLS   38 (194)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHTCCEEEE
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHhCCeeEe
Confidence            3568999999999999999999998876554

>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=97.39  E-value=5e-05  Score=67.26  Aligned_cols=30  Identities=27%  Similarity=0.378  Sum_probs=25.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -++|.|||||||||+|+.+|..+|...+..
T Consensus         5 riil~G~pGSGKsT~a~~La~~~g~~~i~~   34 (190)
T d1ak2a1           5 RAVLLGPPGAGKGTQAPKLAKNFCVCHLAT   34 (190)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCeEEeH
Confidence            467889999999999999999998766553

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=97.39  E-value=0.00018  Score=65.64  Aligned_cols=38  Identities=18%  Similarity=0.163  Sum_probs=30.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      |++...-++++||||||||+++..+|...   +..+.++++
T Consensus        22 Gi~~gsl~li~G~pGsGKT~l~~qia~~~~~~~~~~~~is~   62 (242)
T d1tf7a2          22 GFFKDSIILATGATGTGKTLLVSRFVENACANKERAILFAY   62 (242)
T ss_dssp             SEESSCEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEES
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhccccceeec
Confidence            57777789999999999999999998765   556666654

>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=97.37  E-value=9.9e-06  Score=71.50  Aligned_cols=26  Identities=27%  Similarity=0.526  Sum_probs=22.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      .|+|+|+|||||||+|+++|..++..
T Consensus        21 vI~L~G~pGSGKTTiAk~La~~l~~~   46 (195)
T d1x6va3          21 TVWLTGLSGAGKTTVSMALEEYLVCH   46 (195)
T ss_dssp             EEEEESSCHHHHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHhc
Confidence            46789999999999999999988543

>d1ukza_ c.37.1.1 (A:) Uridylate kinase {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Uridylate kinase
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=97.36  E-value=6.2e-05  Score=66.99  Aligned_cols=31  Identities=16%  Similarity=0.270  Sum_probs=26.6

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      .-++|.|||||||||+|+.+|..+|...+..
T Consensus         9 ~iI~i~GppGSGKsT~a~~La~~~g~~~is~   39 (196)
T d1ukza_           9 SVIFVLGGPGAGKGTQCEKLVKDYSFVHLSA   39 (196)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHSSCEEEEH
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHhCCeEEeh
Confidence            3578899999999999999999998766553

>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=97.34  E-value=5.1e-05  Score=66.84  Aligned_cols=29  Identities=21%  Similarity=0.258  Sum_probs=26.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      |+|.|||||||||+|+.+|..+|...+..
T Consensus         3 I~i~G~pGSGKsT~a~~La~~~g~~~is~   31 (182)
T d1s3ga1           3 IVLMGLPGAGKGTQADRIVEKYGTPHIST   31 (182)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCceeeH
Confidence            78999999999999999999998876653

>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=97.34  E-value=5.7e-05  Score=67.47  Aligned_cols=30  Identities=13%  Similarity=0.342  Sum_probs=26.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -++|.||||+||||+++.+|..+|+..+++
T Consensus         8 rIiliG~PGSGKtT~a~~La~~~g~~~is~   37 (189)
T d2ak3a1           8 RAAIMGAPGSGKGTVSSRITKHFELKHLSS   37 (189)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHBCCEEEEH
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHCCeEEcH
Confidence            478889999999999999999998776544

>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=97.32  E-value=5.3e-05  Score=68.10  Aligned_cols=29  Identities=34%  Similarity=0.637  Sum_probs=26.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      -|.+.|||||||||+|+.||+.+|.++++
T Consensus         5 iI~I~GppGSGKgT~ak~La~~~gl~~iS   33 (225)
T d1ckea_           5 VITIDGPSGAGKGTLCKAMAEALQWHLLD   33 (225)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHTCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            57888999999999999999999887754

>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=97.32  E-value=0.00047  Score=65.01  Aligned_cols=60  Identities=23%  Similarity=0.276  Sum_probs=42.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCCcCChHHHHHHHHhhcCCcEEEEecccc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSRVADDADLKSLLLQTTSKSVILIEDLDR  286 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~~~~~~~l~~l~~~~~~~sII~IDEiD~  286 (480)
                      +.+.+..+.|+|||+||||+++.+|+..+|.-. .++-+  .+.    .-++......++++||.+.
T Consensus       100 ~~~k~n~~~l~G~~~tGKS~f~~~i~~~lg~~~-~~~~~--~~~----f~l~~l~~k~~~~~~e~~~  159 (267)
T d1u0ja_         100 KFGKRNTIWLFGPATTGKTNIAEAIAHTVPFYG-CVNWT--NEN----FPFNDCVDKMVIWWEEGKM  159 (267)
T ss_dssp             CSTTCCEEEEECSTTSSHHHHHHHHHHHSSCEE-ECCTT--CSS----CTTGGGSSCSEEEECSCCE
T ss_pred             CCCccEEEEEEcCCCCCHHHHHHHHHHHhcchh-hcccc--CCC----ccccccCCCEEEEEeCCCc
Confidence            346677899999999999999999999996532 22211  111    1245566788999999874

>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=97.30  E-value=6e-05  Score=66.37  Aligned_cols=29  Identities=24%  Similarity=0.397  Sum_probs=25.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ++|.|||||||||+++.+|..+|...+..
T Consensus         5 Ivl~G~pGSGKtT~a~~La~~~g~~~i~~   33 (180)
T d1akya1           5 MVLIGPPGAGKGTQAPNLQERFHAAHLAT   33 (180)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHHCCEEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceEec
Confidence            77889999999999999999998775554

>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=97.30  E-value=7.8e-05  Score=63.00  Aligned_cols=25  Identities=32%  Similarity=0.437  Sum_probs=21.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      ++-|+|+||||+||||+|+.++...
T Consensus         2 kklIii~G~pGsGKTTla~~L~~~~   26 (152)
T d1ly1a_           2 KKIILTIGCPGSGKSTWAREFIAKN   26 (152)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHS
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHhC
Confidence            3458899999999999999987654

>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=97.28  E-value=7.2e-05  Score=66.28  Aligned_cols=29  Identities=21%  Similarity=0.366  Sum_probs=25.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      -|+|.||||+||||.|+.+|..+|...+.
T Consensus         3 iI~i~GppGSGKsT~a~~La~~~g~~~i~   31 (194)
T d1teva_           3 VVFVLGGPGAGKGTQCARIVEKYGYTHLS   31 (194)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCceEc
Confidence            48899999999999999999999865543

>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=97.25  E-value=7.3e-05  Score=65.49  Aligned_cols=29  Identities=17%  Similarity=0.180  Sum_probs=25.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      ++|.||||+||||+++.+|..++...+..
T Consensus         3 I~i~G~pGSGKsT~~~~La~~~~~~~i~~   31 (179)
T d1e4va1           3 IILLGAPVAGKGTQAQFIMEKYGIPQIST   31 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHCCCEEEH
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCceech
Confidence            78899999999999999999998776653

>d1xp8a1 c.37.1.11 (A:15-282) RecA protein, ATPase-domain {Deinococcus radiodurans [TaxId: 1299]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Deinococcus radiodurans [TaxId: 1299]

Probab=97.25  E-value=0.00033  Score=66.11  Aligned_cols=70  Identities=19%  Similarity=0.303  Sum_probs=48.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCCh---------------------HHHHHH---HHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVADD---------------------ADLKSL---LLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~~---------------------~~l~~l---~~~  272 (480)
                      |++..+-+.++||||||||++|..++...   |..++++|...-.+.                     ++..++   +.+
T Consensus        53 Gip~g~itei~G~~~sGKT~l~l~~~~~aqk~g~~v~yiDtE~~~~~~~a~~~Gvd~d~i~~~~~~~~E~~~~~~~~l~~  132 (268)
T d1xp8a1          53 GIPRGRITEIYGPESGGKTTLALAIVAQAQKAGGTCAFIDAEHALDPVYARALGVNTDELLVSQPDNGEQALEIMELLVR  132 (268)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHT
T ss_pred             CccCceEEEEecCCccchHHHHHHHHHHHHhCCCEEEEEECCccCCHHHHHHhCCCchhEEEEcCCCHHHHHHHHHHHHh
Confidence            55666778899999999999998887643   677888886542211                     111112   233


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|++|=+.++.+
T Consensus       133 ~~~~~liIiDSi~al~~  149 (268)
T d1xp8a1         133 SGAIDVVVVDSVAALTP  149 (268)
T ss_dssp             TTCCSEEEEECTTTCCC
T ss_pred             cCCCcEEEEeccccccc
Confidence            45689999999999885

>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=97.20  E-value=0.00029  Score=63.18  Aligned_cols=38  Identities=32%  Similarity=0.295  Sum_probs=28.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc----CCCcEEEEeC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF----MSYDVYDVDL  257 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~----l~~~~~~i~~  257 (480)
                      |+++..-++++||||+|||+++..+|..    -+..+++++.
T Consensus        22 Gi~~G~~~~I~G~~G~GKT~la~~~~~~~~~~~~~~~~~~s~   63 (242)
T d1tf7a1          22 GLPIGRSTLVSGTSGTGKTLFSIQFLYNGIIEFDEPGVFVTF   63 (242)
T ss_dssp             SEETTSEEEEEESTTSSHHHHHHHHHHHHHHHHCCCEEEEES
T ss_pred             CCcCCeEEEEEeCCCCCHHHHHHHHHHHHHHhcCCCcccccc
Confidence            5677778999999999999999766532    2445665553

>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=97.19  E-value=0.00027  Score=66.55  Aligned_cols=70  Identities=17%  Similarity=0.278  Sum_probs=48.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcCC---------------------hHHH---HHHHHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVAD---------------------DADL---KSLLLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~~---------------------~~~l---~~l~~~  272 (480)
                      |++..+-+.|+||||||||+++-.+|...   |..++++|...-..                     .++.   ...+.+
T Consensus        50 Gi~~g~itei~G~~gsGKTtl~l~~~~~~q~~g~~~vyidtE~~~~~~~a~~~Gvd~d~v~~~~~~~~E~~~~~i~~l~~  129 (263)
T d1u94a1          50 GLPMGRIVEIYGPESSGKTTLTLQVIAAAQREGKTCAFIDAEHALDPIYARKLGVDIDNLLCSQPDTGEQALEICDALAR  129 (263)
T ss_dssp             SEETTSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESSCCCCHHHHHHTTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CccCceEEEEecCCCcHHHHHHHHHHHHHHcCCCEEEEEccccccCHHHHHHhCCCHHHEEEecCCCHHHHHHHHHHHHh
Confidence            56666778999999999999998877543   66777887543221                     1111   122334


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+++|+||-+.++.+
T Consensus       130 ~~~~~liViDSi~al~~  146 (263)
T d1u94a1         130 SGAVDVIVVDSVAALTP  146 (263)
T ss_dssp             HTCCSEEEEECGGGCCC
T ss_pred             cCCCCEEEEECcccccc
Confidence            46789999999988864

>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=97.16  E-value=0.00038  Score=65.73  Aligned_cols=70  Identities=17%  Similarity=0.296  Sum_probs=48.9

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHH---cCCCcEEEEeCCCcCCh---------------------HHHHH---HHHh
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMAS---FMSYDVYDVDLSRVADD---------------------ADLKS---LLLQ  272 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~---~l~~~~~~i~~s~~~~~---------------------~~l~~---l~~~  272 (480)
                      |++..+-..++||||||||++|..++.   ..|..++++|...-.+.                     +++.+   .+.+
T Consensus        56 G~~~g~i~e~~G~~~~GKT~l~l~~~~~~q~~g~~~vyIDtE~~~~~e~a~~~GvD~d~il~~~~~~~E~~~~~~~~l~~  135 (269)
T d1mo6a1          56 GLPRGRVIEIYGPESSGKTTVALHAVANAQAAGGVAAFIDAEHALDPDYAKKLGVDTDSLLVSQPDTGEQALEIADMLIR  135 (269)
T ss_dssp             SBCSSSEEEEECSSSSSHHHHHHHHHHHHHHTTCEEEEEESSCCCCHHHHHHHTCCGGGCEEECCSSHHHHHHHHHHHHH
T ss_pred             CcccceeEEEecCCCcHHHHHHHHHHHHHhcCCCEEEEEECCccCCHHHHHHhCCCHHHeEEecCCCHHHHHHHHHHHHh
Confidence            677777889999999999999876654   34777888886543221                     11111   1233


Q ss_pred             hcCCcEEEEeccccccc
Q 011664          273 TTSKSVILIEDLDRFLV  289 (480)
Q Consensus       273 ~~~~sII~IDEiD~l~~  289 (480)
                      ...+.+|+||-+.++.+
T Consensus       136 ~~~~~liIiDSi~al~~  152 (269)
T d1mo6a1         136 SGALDIVVIDSVAALVP  152 (269)
T ss_dssp             TTCEEEEEEECSTTCCC
T ss_pred             cCCCCEEEEeccccccc
Confidence            45678999999998885

>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=97.16  E-value=0.0001  Score=66.51  Aligned_cols=28  Identities=29%  Similarity=0.492  Sum_probs=24.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      |.+-|||||||||+|+.||..+|+++++
T Consensus         6 IaIdGp~GsGKgT~ak~La~~lg~~~is   33 (223)
T d1q3ta_           6 IAIDGPASSGKSTVAKIIAKDFGFTYLD   33 (223)
T ss_dssp             EEEECSSCSSHHHHHHHHHHHHCCEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCCcEEC
Confidence            4577999999999999999999988665

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=97.11  E-value=0.00049  Score=57.28  Aligned_cols=34  Identities=29%  Similarity=0.363  Sum_probs=27.9

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLS  258 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s  258 (480)
                      +..+|.+|+|+|||.++-.++...+..++.+-..
T Consensus         9 ~~~ll~apTGsGKT~~~~~~~~~~~~~vli~~P~   42 (136)
T d1a1va1           9 QVAHLHAPTGSGKSTKVPAAYAAQGYKVLVLNPS   42 (136)
T ss_dssp             EEEEEECCTTSCTTTHHHHHHHTTTCCEEEEESC
T ss_pred             CEEEEEeCCCCCHHHHHHHHHHHcCCcEEEEcCh
Confidence            4679999999999999887777888877777554

>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=97.07  E-value=0.00071  Score=61.49  Aligned_cols=38  Identities=18%  Similarity=0.148  Sum_probs=28.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV  260 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~  260 (480)
                      .|.-++|.||+|+||||.+.-+|..+   |..+.-+.+..+
T Consensus         8 ~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~Dt~   48 (211)
T d2qy9a2           8 APFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAGDTF   48 (211)
T ss_dssp             TTEEEEEECCTTSCHHHHHHHHHHHHHTTTCCEEEECCCTT
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            35568899999999999999888654   556666655443

>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=97.06  E-value=0.00037  Score=63.31  Aligned_cols=36  Identities=22%  Similarity=0.292  Sum_probs=27.3

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSR  259 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~  259 (480)
                      ++-++|.||+|+||||.+.-+|..+   |..+.-+.+..
T Consensus         6 ~~vi~lvGptGvGKTTTiaKLA~~~~~~g~kV~lit~Dt   44 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIAKLGRYYQNLGKKVMFCAGDT   44 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHHHHHHHHHTTTCCEEEECCCC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEEecc
Confidence            4578999999999999988888754   55666555544

>d1jj7a_ c.37.1.12 (A:) Peptide transporter Tap1, C-terminal ABC domain {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Peptide transporter Tap1, C-terminal ABC domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.04  E-value=0.00079  Score=62.80  Aligned_cols=27  Identities=33%  Similarity=0.482  Sum_probs=22.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+-+.||+|+|||||++.+++.+.
T Consensus        39 ~Ge~vaivG~sGsGKSTLl~li~gl~~   65 (251)
T d1jj7a_          39 PGEVTALVGPNGSGKSTVAALLQNLYQ   65 (251)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHhcccC
Confidence            344588999999999999999998663

>d2pmka1 c.37.1.12 (A:467-707) Haemolysin B ATP-binding protein {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Haemolysin B ATP-binding protein
species: Escherichia coli [TaxId: 562]

Probab=97.01  E-value=0.00086  Score=62.19  Aligned_cols=27  Identities=26%  Similarity=0.369  Sum_probs=23.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+-+.||+|+|||||++++++.+.
T Consensus        28 ~Ge~vaIvG~sGsGKSTLl~ll~gl~~   54 (241)
T d2pmka1          28 QGEVIGIVGRSGSGKSTLTKLIQRFYI   54 (241)
T ss_dssp             TTCEEEEECSTTSSHHHHHHHHTTSSC
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHhcCC
Confidence            344688999999999999999998764

>d3b60a1 c.37.1.12 (A:329-581) Multidrug resistance ABC transporter MsbA, C-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Multidrug resistance ABC transporter MsbA, C-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=97.01  E-value=0.00096  Score=62.29  Aligned_cols=27  Identities=33%  Similarity=0.533  Sum_probs=22.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+-|.||+|||||||++.+++...
T Consensus        40 ~Ge~iaivG~sGsGKSTLl~ll~gl~~   66 (253)
T d3b60a1          40 AGKTVALVGRSGSGKSTIASLITRFYD   66 (253)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHTTTTC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhcccC
Confidence            344688999999999999999998663

>d2hyda1 c.37.1.12 (A:324-578) Putative multidrug export ATP-binding/permease protein SAV1866 {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Putative multidrug export ATP-binding/permease protein SAV1866
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.99  E-value=0.00075  Score=63.15  Aligned_cols=27  Identities=26%  Similarity=0.383  Sum_probs=22.9

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+.+.||+|+|||||++.+++...
T Consensus        43 ~Ge~vaivG~sGsGKSTLl~ll~gl~~   69 (255)
T d2hyda1          43 KGETVAFVGMSGGGKSTLINLIPRFYD   69 (255)
T ss_dssp             TTCEEEEECSTTSSHHHHHTTTTTSSC
T ss_pred             CCCEEEEECCCCCcHHHHHHHHHhcCC
Confidence            444688999999999999999997664

>d1khta_ c.37.1.1 (A:) Adenylate kinase {Archaeon Methanococcus voltae [TaxId: 2188]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Methanococcus voltae [TaxId: 2188]

Probab=96.96  E-value=0.00014  Score=62.74  Aligned_cols=26  Identities=12%  Similarity=0.222  Sum_probs=22.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      +-|++.|||||||||+++.++..++.
T Consensus         2 kiI~i~G~~GsGKsT~~~~L~~~l~~   27 (190)
T d1khta_           2 KVVVVTGVPGVGSTTSSQLAMDNLRK   27 (190)
T ss_dssp             CEEEEECCTTSCHHHHHHHHHHHHHT
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH
Confidence            45889999999999999999987743

>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=96.92  E-value=0.00041  Score=62.57  Aligned_cols=42  Identities=21%  Similarity=0.147  Sum_probs=32.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCCcC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSRVA  261 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~~~  261 (480)
                      |++..+-++|+||||||||+++..+|...         +..+++++...-.
T Consensus        30 Gi~~G~~~li~G~pGsGKT~l~lq~~~~~~~~~~~~~~~~~~~~i~~~~~~   80 (251)
T d1szpa2          30 GVETGSITELFGEFRTGKSQLCHTLAVTCQIPLDIGGGEGKCLYIDTEGTF   80 (251)
T ss_dssp             SEESSSEEEEEESTTSSHHHHHHHHTTTTTSCTTTTCCSCEEEEEESSSCC
T ss_pred             CCcCCeEEEEEcCCCCCHHHHHHHHHHHhhhhhhhccCCceEEEEeecchH
Confidence            67777889999999999999999887542         4567777765433

>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=96.92  E-value=0.001  Score=60.23  Aligned_cols=36  Identities=25%  Similarity=0.335  Sum_probs=27.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRV  260 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~  260 (480)
                      +-++|.||+|+||||.+.-+|..+   |..+.-+++...
T Consensus        11 ~vi~lvGp~GvGKTTTiaKLA~~~~~~g~kV~lit~Dt~   49 (207)
T d1ls1a2          11 NLWFLVGLQGSGKTTTAAKLALYYKGKGRRPLLVAADTQ   49 (207)
T ss_dssp             EEEEEECCTTTTHHHHHHHHHHHHHHTTCCEEEEECCSS
T ss_pred             cEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEecccc
Confidence            447889999999999999888755   566666665443

>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=96.92  E-value=0.00028  Score=60.15  Aligned_cols=31  Identities=16%  Similarity=0.133  Sum_probs=25.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      -+.+.|+||||||||++.+++++   |..+..+.
T Consensus         4 vi~itG~~GSGKTTL~~~L~~~l~~~g~~v~v~~   37 (170)
T d1np6a_           4 LLAFAAWSGTGKTTLLKKLIPALCARGIRPGLIK   37 (170)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHHHHCCCeEEEec
Confidence            47899999999999999999875   55555544

>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=96.89  E-value=0.00016  Score=64.16  Aligned_cols=33  Identities=9%  Similarity=0.294  Sum_probs=25.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC---CcEEEEe
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS---YDVYDVD  256 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~---~~~~~i~  256 (480)
                      |.-|+++|+||+||||+|+++|..++   .+...++
T Consensus         2 p~li~l~GlpgsGKSTla~~L~~~l~~~~~~~~~~~   37 (213)
T d1bifa1           2 PTLIVMVGLPARGKTYISKKLTRYLNFIGVPTREFN   37 (213)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHhcCCCCeEEc
Confidence            33588999999999999999998764   4444443

>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=96.86  E-value=0.0011  Score=60.34  Aligned_cols=36  Identities=19%  Similarity=0.216  Sum_probs=26.4

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .|.-++|.||+|+||||.+.-+|..+   +..+.-+.+.
T Consensus        10 ~p~vi~lvGptGvGKTTTiAKLAa~~~~~~~kV~lit~D   48 (213)
T d1vmaa2          10 PPFVIMVVGVNGTGKTTSCGKLAKMFVDEGKSVVLAAAD   48 (213)
T ss_dssp             SCEEEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEEEC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEeec
Confidence            45568899999999999988888654   4555444443

>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=96.81  E-value=0.0014  Score=60.46  Aligned_cols=97  Identities=15%  Similarity=0.220  Sum_probs=55.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH-----cCCCc--------------EEEEeCCC--------cCCh-HHHHHHHHhhcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS-----FMSYD--------------VYDVDLSR--------VADD-ADLKSLLLQTTS  275 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~-----~l~~~--------------~~~i~~s~--------~~~~-~~l~~l~~~~~~  275 (480)
                      .+.++|.||..+|||+++|++|-     .+|..              +..+...+        +..+ .++..++..+..
T Consensus        41 ~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~  120 (234)
T d1wb9a2          41 RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATE  120 (234)
T ss_dssp             SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCT
T ss_pred             ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccCcccccchhHHHHHHHHHHHHHHhccc
Confidence            46789999999999999999984     23321              11121111        1111 235666777788


Q ss_pred             CcEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          276 KSVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       276 ~sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                      +++++|||+-+=....++......++..+   ..   .....+|+||...+
T Consensus       121 ~sLvliDE~~~gT~~~eg~~l~~a~l~~l---~~---~~~~~~i~tTH~~~  165 (234)
T d1wb9a2         121 YSLVLMDEIGRGTSTYDGLSLAWACAENL---AN---KIKALTLFATHYFE  165 (234)
T ss_dssp             TEEEEEESCCCCSSSSHHHHHHHHHHHHH---HH---TTCCEEEEECSCGG
T ss_pred             ccEEeecccccCCChhhhhHHHHHhhhhh---hc---cccceEEEecchHH
Confidence            99999999985322222222223344433   11   23345677776544

>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=96.77  E-value=0.0012  Score=62.44  Aligned_cols=27  Identities=19%  Similarity=0.297  Sum_probs=23.0

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ...-+-|.||+|+|||||+++|++.+.
T Consensus        61 ~Ge~vaivG~nGsGKSTLl~~i~Gl~~   87 (281)
T d1r0wa_          61 KGEMLAITGSTGSGKTSLLMLILGELE   87 (281)
T ss_dssp             TTCEEEEEESTTSSHHHHHHHHHTSSC
T ss_pred             CCCEEEEECCCCChHHHHHHHHhCCCc
Confidence            344578999999999999999998774

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=96.74  E-value=0.0017  Score=64.58  Aligned_cols=87  Identities=15%  Similarity=0.230  Sum_probs=57.3

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC-Cc-
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS-RV-  260 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s-~~-  260 (480)
                      ..++++++..++..+.+.+.+.              .+..-+|+.||+|+||||++.++-+++   +.+++.+.=. +. 
T Consensus       134 ~~~l~~LG~~~~~~~~l~~l~~--------------~~~GliLvtGpTGSGKSTTl~~~l~~~~~~~~~i~tiEdPiE~~  199 (401)
T d1p9ra_         134 RLDLHSLGMTAHNHDNFRRLIK--------------RPHGIILVTGPTGSGKSTTLYAGLQELNSSERNILTVEDPIEFD  199 (401)
T ss_dssp             CCCGGGSCCCHHHHHHHHHHHT--------------SSSEEEEEECSTTSCHHHHHHHHHHHHCCTTSCEEEEESSCCSC
T ss_pred             chhhhhhcccHHHHHHHHHHHh--------------hhhceEEEEcCCCCCccHHHHHHhhhhcCCCceEEEeccCcccc
Confidence            3579999999888777764332              133457888999999999999998876   3456666411 11 


Q ss_pred             ---------CC--hHHHHHHHHh--hcCCcEEEEecccc
Q 011664          261 ---------AD--DADLKSLLLQ--TTSKSVILIEDLDR  286 (480)
Q Consensus       261 ---------~~--~~~l~~l~~~--~~~~sII~IDEiD~  286 (480)
                               ..  .......+..  ...|.||+|.||-.
T Consensus       200 ~~~~~q~~v~~~~~~~~~~~l~~~lR~dPDvi~igEiRd  238 (401)
T d1p9ra_         200 IDGIGQTQVNPRVDMTFARGLRAILRQDPDVVMVGEIRD  238 (401)
T ss_dssp             CSSSEEEECBGGGTBCHHHHHHHHGGGCCSEEEESCCCS
T ss_pred             cCCCCeeeecCCcCCCHHHHHHHHHhhcCCEEEecCcCC
Confidence                     00  1123333322  35899999999974

>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=96.74  E-value=0.00092  Score=60.70  Aligned_cols=47  Identities=19%  Similarity=0.255  Sum_probs=33.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC---------CCcEEEEeCCCcCChHHH
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM---------SYDVYDVDLSRVADDADL  266 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l---------~~~~~~i~~s~~~~~~~l  266 (480)
                      |++..+-++++||||||||+++-.+|...         +...+.++...-.....+
T Consensus        32 Glp~G~~~li~G~pGsGKT~~~lq~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (254)
T d1pzna2          32 GIETQAITEVFGEFGSGKTQLAHTLAVMVQLPPEEGGLNGSVIWIDTENTFRPERI   87 (254)
T ss_dssp             SEESSEEEEEEESTTSSHHHHHHHHHHHTTSCGGGTSCSCEEEEEESSSCCCHHHH
T ss_pred             CccCCEEEEEEcCCCCCHHHHHHHHHHHhhchHHhcCCCceEEEEeccchhHHHHH
Confidence            57777789999999999999999887643         345666666544433333

>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=96.73  E-value=0.0023  Score=59.15  Aligned_cols=28  Identities=32%  Similarity=0.321  Sum_probs=22.0

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      |..+..-.+|+|+||+|||+++..+|..
T Consensus        25 G~~pg~~~~i~G~~G~GKS~l~l~la~~   52 (274)
T d1nlfa_          25 NMVAGTVGALVSPGGAGKSMLALQLAAQ   52 (274)
T ss_dssp             TEETTSEEEEEESTTSSHHHHHHHHHHH
T ss_pred             CccCCcEEEEEeCCCCCHHHHHHHHHHH
Confidence            3334456789999999999999888764

>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=96.71  E-value=0.0063  Score=52.45  Aligned_cols=62  Identities=27%  Similarity=0.387  Sum_probs=41.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC--------------------cEEEEeCCCcCChHHHHHH-HHh-hcCCcEEEEec
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY--------------------DVYDVDLSRVADDADLKSL-LLQ-TTSKSVILIED  283 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~--------------------~~~~i~~s~~~~~~~l~~l-~~~-~~~~sII~IDE  283 (480)
                      -++|.|+=|+|||++++++++.+|.                    .++.+|+=.+.+..++..+ +.. ....+|++|+=
T Consensus        35 ii~L~G~LGaGKTtfvr~~~~~lg~~~~V~SPTF~l~~~Y~~~~~~i~H~DlYRl~~~~El~~lg~~e~~~~~~i~~IEW  114 (158)
T d1htwa_          35 MVYLNGDLGAGKTTLTRGMLQGIGHQGNVKSPTYTLVEEYNIAGKMIYHFDLYRLADPEELEFMGIRDYFNTDSICLIEW  114 (158)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHTTCCSCCCCCTTTCEEEEEETTEEEEEEECTTCSCTTHHHHSTHHHHHSSSCEEEEES
T ss_pred             EEEEecCCCccHHHHHHHHHhhcccccccCCCceEEEEeeccCCceEEEEEEeccCChhhhhhCCchhHhccCCEEEEEC
Confidence            4789999999999999999998864                    2455565555555444332 222 23456777775


Q ss_pred             cccc
Q 011664          284 LDRF  287 (480)
Q Consensus       284 iD~l  287 (480)
                      -+.+
T Consensus       115 pe~~  118 (158)
T d1htwa_         115 SEKG  118 (158)
T ss_dssp             GGGG
T ss_pred             chhh
Confidence            5543

>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=96.68  E-value=0.00085  Score=62.47  Aligned_cols=39  Identities=28%  Similarity=0.206  Sum_probs=29.6

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHH----cCCCcEEEEeCC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMAS----FMSYDVYDVDLS  258 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~----~l~~~~~~i~~s  258 (480)
                      |..+..-+++.|+||+|||+++..+|.    ..|.++..+++.
T Consensus        31 G~~~G~l~vi~G~~G~GKT~~~~~la~~~a~~~g~~v~~~s~E   73 (277)
T d1cr2a_          31 GARGGEVIMVTSGSGMGKSTFVRQQALQWGTAMGKKVGLAMLE   73 (277)
T ss_dssp             SBCTTCEEEEECSTTSSHHHHHHHHHHHHHHTSCCCEEEEESS
T ss_pred             CCCCCeEEEEEeCCCCCHHHHHHHHHHhhhhhcccceeEeeec
Confidence            555555688999999999999888874    337777777653

>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=96.66  E-value=0.00041  Score=60.64  Aligned_cols=29  Identities=21%  Similarity=0.204  Sum_probs=25.2

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      |+++..-++++||||+|||+++..+|...
T Consensus        19 Gi~~G~v~~i~G~~GsGKT~l~l~la~~~   47 (242)
T d1n0wa_          19 GIETGSITEMFGEFRTGKTQICHTLAVTC   47 (242)
T ss_dssp             SEETTSEEEEECCTTSSHHHHHHHHHHHT
T ss_pred             CCcCCEEEEEEeCCCCCHHHHHHHHHHHH
Confidence            67777789999999999999999988644

>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=96.62  E-value=0.0022  Score=61.87  Aligned_cols=62  Identities=13%  Similarity=0.379  Sum_probs=40.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC--CcEEEEe-CCCcC-------------ChHHHHHHHHh--hcCCcEEEEeccc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS--YDVYDVD-LSRVA-------------DDADLKSLLLQ--TTSKSVILIEDLD  285 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~--~~~~~i~-~s~~~-------------~~~~l~~l~~~--~~~~sII~IDEiD  285 (480)
                      ++++|+.||+|+|||++++|++++..  ..++.+. ..++.             .+-.+..++..  ...|..|++.|+-
T Consensus       166 ~~nili~G~tgSGKTT~l~al~~~i~~~~rivtiEd~~El~l~~~~~~~~~~~~~~~~~~~ll~~~lR~~pd~iivgEiR  245 (323)
T d1g6oa_         166 GKNVIVCGGTGSGKTTYIKSIMEFIPKEERIISIEDTEEIVFKHHKNYTQLFFGGNITSADCLKSCLRMRPDRIILGELR  245 (323)
T ss_dssp             TCCEEEEESTTSSHHHHHHHHGGGSCTTCCEEEEESSCCCCCSSCSSEEEEECBTTBCHHHHHHHHTTSCCSEEEESCCC
T ss_pred             CCCEEEEeeccccchHHHHHHhhhcccccceeeccchhhhhcccccccceeccccchhHHHHHHHHhccCCCcccCCccC
Confidence            45799999999999999999999873  3455552 11111             11123334322  2478888888885

>d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: MJ0796
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.61  E-value=0.0021  Score=59.04  Aligned_cols=24  Identities=29%  Similarity=0.506  Sum_probs=21.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+-|.||+|||||||++.++...
T Consensus        32 e~~~iiG~sGsGKSTLl~~i~gl~   55 (230)
T d1l2ta_          32 EFVSIMGPSGSGKSTMLNIIGCLD   55 (230)
T ss_dssp             CEEEEECSTTSSHHHHHHHHTTSS
T ss_pred             CEEEEECCCCCCcchhhHhccCCC
Confidence            357799999999999999999855

>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=96.60  E-value=0.0013  Score=60.98  Aligned_cols=26  Identities=31%  Similarity=0.451  Sum_probs=22.2

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      +..-+-+.||+|+|||||++.+++.+
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            34457899999999999999999765

>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=96.58  E-value=0.0019  Score=58.35  Aligned_cols=28  Identities=18%  Similarity=0.165  Sum_probs=24.7

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHc
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      |++..+-++++||||||||+++..+|..
T Consensus        33 Gip~G~~~~i~G~~GsGKT~lalq~~~~   60 (258)
T d1v5wa_          33 GIESMAITEAFGEFRTGKTQLSHTLCVT   60 (258)
T ss_dssp             SBCSSEEEEEECCTTCTHHHHHHHHHHH
T ss_pred             CCcCCEEEEEECCCCCCHHHHHHHHHHH
Confidence            6777778999999999999999999863

>d1nksa_ c.37.1.1 (A:) Adenylate kinase {Archaeon Sulfolobus acidocaldarius [TaxId: 2285]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Archaeon Sulfolobus acidocaldarius [TaxId: 2285]

Probab=96.58  E-value=0.00028  Score=61.15  Aligned_cols=25  Identities=24%  Similarity=0.356  Sum_probs=22.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -+++.|+||+||||+++.+|..++.
T Consensus         3 iivi~G~~GsGKTT~~~~La~~L~~   27 (194)
T d1nksa_           3 IGIVTGIPGVGKSTVLAKVKEILDN   27 (194)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Confidence            4788999999999999999998744

>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=96.56  E-value=0.0016  Score=59.15  Aligned_cols=36  Identities=31%  Similarity=0.380  Sum_probs=22.6

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .|.-++|.||+|+||||.+.-+|..+   |..+--+.+.
T Consensus        11 ~p~vi~lvGptGvGKTTTiAKLA~~~~~~g~kV~lit~D   49 (211)
T d1j8yf2          11 IPYVIMLVGVQGTGKATTAGKLAYFYKKKGFKVGLVGAD   49 (211)
T ss_dssp             SSEEEEEECSCCC----HHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCceEEEEee
Confidence            35568899999999999988888654   4555555443

>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=96.55  E-value=0.00069  Score=59.76  Aligned_cols=28  Identities=32%  Similarity=0.498  Sum_probs=24.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      |.|+|.||+|+|||+|++.++++....+
T Consensus         2 rpIvl~GpsG~GK~tl~~~L~~~~~~~~   29 (186)
T d1gkya_           2 RPIVISGPSGTGKSTLLKKLFAEYPDSF   29 (186)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHCTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCcce
Confidence            4599999999999999999999875544

>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=96.50  E-value=0.0019  Score=59.71  Aligned_cols=25  Identities=32%  Similarity=0.527  Sum_probs=21.7

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .-+-|.||+|+|||||++.+++.+.
T Consensus        33 e~~~liGpsGaGKSTLl~~i~Gl~~   57 (239)
T d1v43a3          33 EFLVLLGPSGCGKTTTLRMIAGLEE   57 (239)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSSC
T ss_pred             CEEEEECCCCChHHHHHHHHHcCCC
Confidence            3467999999999999999998664

>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=96.49  E-value=0.00076  Score=60.97  Aligned_cols=33  Identities=27%  Similarity=0.386  Sum_probs=27.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC----CCcEEEEeC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM----SYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l----~~~~~~i~~  257 (480)
                      ..|+|+|.||+|||++|++++..+    +.+++.++.
T Consensus        25 ~vIwltGlsGsGKTTia~~L~~~l~~~~~~~~~~ldg   61 (208)
T d1m7ga_          25 LTIWLTGLSASGKSTLAVELEHQLVRDRRVHAYRLDG   61 (208)
T ss_dssp             EEEEEECSTTSSHHHHHHHHHHHHHHHHCCCEEEECH
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHHhcCceEEEEcc
Confidence            468899999999999999999755    567777764

>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=96.45  E-value=0.00075  Score=59.84  Aligned_cols=28  Identities=36%  Similarity=0.443  Sum_probs=24.0

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      |.|.|.||+|+|||++++.++...+..+
T Consensus         1 rpIvl~GPsGsGK~tl~~~L~~~~~~~~   28 (190)
T d1lvga_           1 RPVVLSGPSGAGKSTLLKKLFQEHSSIF   28 (190)
T ss_dssp             CCEEEECCTTSSHHHHHHHHHHHHTTTE
T ss_pred             CeEEEECCCCCCHHHHHHHHHHhCCCce
Confidence            3589999999999999999998876544

>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=96.45  E-value=0.0057  Score=50.89  Aligned_cols=20  Identities=20%  Similarity=0.355  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|+||+|||+|+..+..
T Consensus         3 ivlvG~~~vGKSsLi~~l~~   22 (160)
T d1r8sa_           3 ILMVGLDAAGKTTILYKLKL   22 (160)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhc
Confidence            78999999999999999975

>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=96.43  E-value=0.0015  Score=60.08  Aligned_cols=24  Identities=33%  Similarity=0.556  Sum_probs=21.1

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+-|.||+|||||||++.++...
T Consensus        27 ei~~liGpsGsGKSTLl~~i~Gl~   50 (232)
T d2awna2          27 EFVVFVGPSGCGKSTLLRMIAGLE   50 (232)
T ss_dssp             CEEEEECCTTSSHHHHHHHHHTSS
T ss_pred             CEEEEECCCCChHHHHHHHHhcCC
Confidence            357799999999999999999865

>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=96.42  E-value=0.0019  Score=59.76  Aligned_cols=24  Identities=33%  Similarity=0.555  Sum_probs=21.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -+-|.||+|+|||||+++|++...
T Consensus        31 ~~~liG~sGaGKSTll~~i~gl~~   54 (240)
T d1g2912          31 FMILLGPSGCGKTTTLRMIAGLEE   54 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTSSC
T ss_pred             EEEEECCCCChHHHHHHHHhcCCC
Confidence            467999999999999999998653

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=96.40  E-value=0.0015  Score=53.39  Aligned_cols=18  Identities=22%  Similarity=0.126  Sum_probs=15.2

Q ss_pred             CceEEEEccCCCcHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La  241 (480)
                      .+.++|++|||+|||..+
T Consensus         7 ~~~~il~~~tGsGKT~~~   24 (140)
T d1yksa1           7 GMTTVLDFHPGAGKTRRF   24 (140)
T ss_dssp             TCEEEECCCTTSSTTTTH
T ss_pred             CCcEEEEcCCCCChhHHH
Confidence            457899999999999655

>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=96.37  E-value=0.0019  Score=59.24  Aligned_cols=24  Identities=33%  Similarity=0.757  Sum_probs=21.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -+-|.||+|+|||||++++++...
T Consensus        28 ~~~liGpsGaGKSTll~~l~Gl~~   51 (229)
T d3d31a2          28 YFVILGPTGAGKTLFLELIAGFHV   51 (229)
T ss_dssp             EEEEECCCTHHHHHHHHHHHTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHhcCcC
Confidence            477999999999999999998664

>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=96.34  E-value=0.00097  Score=58.01  Aligned_cols=31  Identities=19%  Similarity=0.250  Sum_probs=24.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC---CcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS---YDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~---~~~~~i~  256 (480)
                      -|-+.||+|+||||+|+.++..++   .....++
T Consensus        24 iIgI~G~~GSGKSTla~~L~~~l~~~~~~~~~~~   57 (198)
T d1rz3a_          24 VLGIDGLSRSGKTTLANQLSQTLREQGISVCVFH   57 (198)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhccccccceecc
Confidence            356999999999999999998664   4444444

>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=96.22  E-value=0.002  Score=59.54  Aligned_cols=24  Identities=33%  Similarity=0.685  Sum_probs=21.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      .-+-|.||+|||||||++.+++..
T Consensus        32 e~~~iiG~sGsGKSTll~~i~gl~   55 (242)
T d1oxxk2          32 ERFGILGPSGAGKTTFMRIIAGLD   55 (242)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTSS
T ss_pred             CEEEEECCCCCcHHHHHHHHHcCc
Confidence            357799999999999999999855

>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=96.15  E-value=0.0019  Score=59.08  Aligned_cols=95  Identities=18%  Similarity=0.232  Sum_probs=53.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH-----cCCCc----E----------EEEeCCC-cCC--------hHHHHHHHHhhcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS-----FMSYD----V----------YDVDLSR-VAD--------DADLKSLLLQTTSK  276 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~-----~l~~~----~----------~~i~~s~-~~~--------~~~l~~l~~~~~~~  276 (480)
                      +.++|+||...|||++.+++|-     ..|..    -          ..+...+ +..        -.++..++......
T Consensus        36 ~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~~~  115 (224)
T d1ewqa2          36 ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATEN  115 (224)
T ss_dssp             CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCCTT
T ss_pred             cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECCCccccCCccHHHHhHHHHHHHhccCCCC
Confidence            3689999999999999999874     23321    1          1111111 111        13356667777889


Q ss_pred             cEEEEecccccccCcccccchhhhhhhcccccccccCCceEEEEecCCCc
Q 011664          277 SVILIEDLDRFLVEKPAAVSLSGVLNFMDGVLNSCCFEERVMVFTMNSKD  326 (480)
Q Consensus       277 sII~IDEiD~l~~~~~~~~~ls~lL~~ldg~~~~~~~~~~ivI~tTN~~~  326 (480)
                      ++++|||+-.=....++......+++.+.   .    .+..+++||.+.+
T Consensus       116 sLvliDE~~~gT~~~eg~ala~aile~L~---~----~~~~~i~tTH~~e  158 (224)
T d1ewqa2         116 SLVLLDEVGRGTSSLDGVAIATAVAEALH---E----RRAYTLFATHYFE  158 (224)
T ss_dssp             EEEEEESTTTTSCHHHHHHHHHHHHHHHH---H----HTCEEEEECCCHH
T ss_pred             cEEeecccccCcchhhhcchHHHHHHHHh---h----cCcceEEeeechh
Confidence            99999999743211111122333444442   2    1235677776653

>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=95.94  E-value=0.0057  Score=54.52  Aligned_cols=29  Identities=17%  Similarity=0.155  Sum_probs=24.8

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHHcC
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~~l  248 (480)
                      |++...-++|+||||+|||+++..+|..+
T Consensus        30 Gl~~G~l~~i~G~~G~GKT~~~l~~a~~~   58 (258)
T d2i1qa2          30 GLESQSVTEFAGVFGSGKTQIMHQSCVNL   58 (258)
T ss_dssp             SEETTEEEEEEESTTSSHHHHHHHHHHHT
T ss_pred             CccCCeEEEEEeCCCCCHHHHHHHHHHHH
Confidence            46666778999999999999999998654

>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=95.75  E-value=0.0036  Score=53.48  Aligned_cols=31  Identities=16%  Similarity=0.263  Sum_probs=25.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      -+-+.|++|||||||+..++.++   |..+..+.
T Consensus         3 ii~I~G~~gSGKTTli~~l~~~L~~~g~~v~vik   36 (165)
T d1xjca_           3 VWQVVGYKHSGKTTLMEKWVAAAVREGWRVGTVK   36 (165)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEEEeCCCCCHHHHHHHHHHHHHhCCCeEEEEE
Confidence            45689999999999999999876   56666654

>d1znwa1 c.37.1.1 (A:20-201) Guanylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=95.71  E-value=0.0025  Score=55.56  Aligned_cols=25  Identities=32%  Similarity=0.522  Sum_probs=21.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +-++|.||+|+|||++++.++.+..
T Consensus         3 ~iivl~GpsG~GK~tl~~~L~~~~~   27 (182)
T d1znwa1           3 RVVVLSGPSAVGKSTVVRCLRERIP   27 (182)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHHHST
T ss_pred             eEEEEECCCCCCHHHHHHHHHhhCC
Confidence            3478999999999999999998763

>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=95.66  E-value=0.0093  Score=51.32  Aligned_cols=20  Identities=40%  Similarity=0.604  Sum_probs=18.9

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.+|+|||+|+..+.+
T Consensus        10 i~vvG~~~vGKTsli~~l~~   29 (177)
T d1x3sa1          10 ILIIGESGVGKSSLLLRFTD   29 (177)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999986

>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=95.66  E-value=0.014  Score=53.97  Aligned_cols=24  Identities=29%  Similarity=0.396  Sum_probs=21.1

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~  247 (480)
                      +-.|+|.|.||+|||+++.+|.++
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            346999999999999999999863

>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=95.65  E-value=0.0058  Score=52.12  Aligned_cols=22  Identities=14%  Similarity=0.270  Sum_probs=20.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|.||+|||+|+.++.+.
T Consensus        17 kI~vvG~~~~GKSsLi~rl~~~   38 (177)
T d1zj6a1          17 KVIIVGLDNAGKTTILYQFSMN   38 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhcC
Confidence            5999999999999999999863

>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=95.59  E-value=0.0043  Score=54.50  Aligned_cols=30  Identities=27%  Similarity=0.284  Sum_probs=24.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      .+|+||.||+|+|||++|.++... |..++.
T Consensus        14 g~gvl~~G~sG~GKStlal~l~~~-g~~lv~   43 (176)
T d1kkma_          14 GLGVLITGDSGVGKSETALELVQR-GHRLIA   43 (176)
T ss_dssp             TEEEEEECCTTSCHHHHHHHHHHT-TCEEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEEe
Confidence            469999999999999999998875 665543

>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=95.57  E-value=0.0038  Score=53.02  Aligned_cols=22  Identities=18%  Similarity=0.335  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|+||+|||+|++.+.+.
T Consensus         4 ki~ivG~~~~GKTsLi~~l~~~   25 (165)
T d1ksha_           4 RLLMLGLDNAGKTTILKKFNGE   25 (165)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHcCC
Confidence            3899999999999999999763

>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=95.49  E-value=0.0036  Score=55.77  Aligned_cols=24  Identities=25%  Similarity=0.368  Sum_probs=21.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      |-+.||+|+||||+++.++..++.
T Consensus         5 IgI~G~~gSGKSTla~~L~~~l~~   28 (213)
T d1uj2a_           5 IGVSGGTASGKSSVCAKIVQLLGQ   28 (213)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTG
T ss_pred             EEEECCCCCCHHHHHHHHHHHhch
Confidence            558899999999999999998865

>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=95.40  E-value=0.01  Score=56.62  Aligned_cols=39  Identities=18%  Similarity=0.147  Sum_probs=30.3

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcCC-----CcEEEEeCCCcC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFMS-----YDVYDVDLSRVA  261 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l~-----~~~~~i~~s~~~  261 (480)
                      .|--|-+.||+|+||||+|+.++..+.     ..+..+++..+.
T Consensus        79 ~P~iIGIaG~sgSGKSTla~~L~~lL~~~~~~~~v~~Is~D~F~  122 (308)
T d1sq5a_          79 IPYIISIAGSVAVGKSTTARVLQALLSRWPEHRRVELITTDGFL  122 (308)
T ss_dssp             CCEEEEEEECTTSSHHHHHHHHHHHHTTSTTCCCEEEEEGGGGB
T ss_pred             CCEEEEEeCCCCCCCcHHHHHHHHHHhhhcCCCceEEEeeeeeE
Confidence            344566899999999999999998763     557777776654

>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=95.38  E-value=0.017  Score=50.36  Aligned_cols=22  Identities=27%  Similarity=0.535  Sum_probs=20.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .|+|.|+||+|||+|..++.+.
T Consensus         5 ~V~lvG~~n~GKTSLln~l~~~   26 (209)
T d1nrjb_           5 SIIIAGPQNSGKTSLLTLLTTD   26 (209)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            6999999999999999999865

>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=95.30  E-value=0.0054  Score=53.66  Aligned_cols=26  Identities=15%  Similarity=0.451  Sum_probs=22.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      ++.++|.||+|+|||+|++.+.....
T Consensus         3 ~k~ivl~Gpsg~GK~tl~~~L~~~~~   28 (178)
T d1kgda_           3 RKTLVLLGAHGVGRRHIKNTLITKHP   28 (178)
T ss_dssp             CCEEEEECCTTSSHHHHHHHHHHHCT
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHhCC
Confidence            46799999999999999999987653

>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=95.29  E-value=0.021  Score=53.80  Aligned_cols=38  Identities=16%  Similarity=0.227  Sum_probs=27.9

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC------CCcEEEEeCCCcC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM------SYDVYDVDLSRVA  261 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l------~~~~~~i~~s~~~  261 (480)
                      |--|-|.|++|||||||+..+...+      ...+..+++.++.
T Consensus        27 P~iIGi~G~qGSGKSTl~~~l~~~L~~~~~~~~~v~~iS~DdfY   70 (286)
T d1odfa_          27 PLFIFFSGPQGSGKSFTSIQIYNHLMEKYGGEKSIGYASIDDFY   70 (286)
T ss_dssp             CEEEEEECCTTSSHHHHHHHHHHHHHHHHGGGSCEEEEEGGGGB
T ss_pred             CEEEEeECCCCCCHHHHHHHHHHHHHHHhCCCcceEeeccCCCC
Confidence            3334578999999999999887654      3456677776654

>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=95.28  E-value=0.0059  Score=59.57  Aligned_cols=20  Identities=35%  Similarity=0.562  Sum_probs=16.4

Q ss_pred             ceEEEEccCCCcHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAM  244 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~ai  244 (480)
                      +-.++.||||||||+++..+
T Consensus       164 ~~~vI~G~pGTGKTt~i~~~  183 (359)
T d1w36d1         164 RISVISGGPGTGKTTTVAKL  183 (359)
T ss_dssp             SEEEEECCTTSTHHHHHHHH
T ss_pred             CeEEEEcCCCCCceehHHHH
Confidence            35889999999999887544

>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=95.24  E-value=0.0091  Score=54.08  Aligned_cols=32  Identities=34%  Similarity=0.544  Sum_probs=21.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEe
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVD  256 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~  256 (480)
                      +.+++.+|+|+|||..+-..+-.   -|..++.+-
T Consensus        59 ~~~~i~apTGsGKT~~~~~~~~~~~~~~~rvliv~   93 (237)
T d1gkub1          59 ESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIF   93 (237)
T ss_dssp             CCEECCCCBTSCSHHHHHHHHHHHHTTSCCEEEEE
T ss_pred             CCEEEEecCCChHHHHHHHHHHHHHHhcCeEEEEe
Confidence            47999999999999765544432   244455443

>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=95.21  E-value=0.0059  Score=53.62  Aligned_cols=30  Identities=30%  Similarity=0.245  Sum_probs=24.4

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVYD  254 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~  254 (480)
                      .+|+||.||+|+|||++|.++... |..++.
T Consensus        15 g~gvli~G~sG~GKS~lal~l~~~-G~~lva   44 (177)
T d1knxa2          15 GVGVLLTGRSGIGKSECALDLINK-NHLFVG   44 (177)
T ss_dssp             TEEEEEEESSSSSHHHHHHHHHTT-TCEEEE
T ss_pred             CEEEEEEcCCCCCHHHHHHHHHHc-CCceec
Confidence            469999999999999999988754 655543

>d1nn5a_ c.37.1.1 (A:) Thymidylate kinase {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.21  E-value=0.0058  Score=54.84  Aligned_cols=30  Identities=17%  Similarity=0.165  Sum_probs=24.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~  256 (480)
                      |.|.||.|+||||+++.+++.+   |.++..+.
T Consensus         6 I~ieG~dGsGKsT~~~~L~~~L~~~g~~v~~~~   38 (209)
T d1nn5a_           6 IVLEGVDRAGKSTQSRKLVEALCAAGHRAELLR   38 (209)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEe
Confidence            3455999999999999999866   66776654

>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=95.13  E-value=0.0074  Score=52.59  Aligned_cols=29  Identities=28%  Similarity=0.276  Sum_probs=23.6

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      .+|+|+.||+|+|||+++-++... |..++
T Consensus        15 g~gvli~G~sg~GKS~la~~l~~~-g~~li   43 (169)
T d1ko7a2          15 GVGVLITGDSGIGKSETALELIKR-GHRLV   43 (169)
T ss_dssp             TEEEEEEESTTSSHHHHHHHHHHT-TCEEE
T ss_pred             CEEEEEEeCCCCCHHHHHHHHHHc-CCeEE
Confidence            469999999999999999888775 54433

>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=95.12  E-value=0.0049  Score=53.84  Aligned_cols=29  Identities=34%  Similarity=0.449  Sum_probs=23.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i  255 (480)
                      -+-++|++|+|||++|+.+. +.|++++..
T Consensus         5 IIgitG~~gSGKstva~~l~-~~g~~~~~~   33 (191)
T d1uf9a_           5 IIGITGNIGSGKSTVAALLR-SWGYPVLDL   33 (191)
T ss_dssp             EEEEEECTTSCHHHHHHHHH-HTTCCEEEH
T ss_pred             EEEEECCCCCCHHHHHHHHH-HCCCeEEEc
Confidence            35588999999999999984 578877653

>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=95.12  E-value=0.035  Score=48.24  Aligned_cols=30  Identities=27%  Similarity=0.313  Sum_probs=20.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHH----cCCCcEEEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS----FMSYDVYDV  255 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~----~l~~~~~~i  255 (480)
                      ..|+++|+|+|||.++..++.    .-+..++.+
T Consensus        25 n~lv~~pTGsGKT~i~~~~~~~~~~~~~~~il~i   58 (200)
T d1wp9a1          25 NCLIVLPTGLGKTLIAMMIAEYRLTKYGGKVLML   58 (200)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHHHSCSCEEEE
T ss_pred             CeEEEeCCCCcHHHHHHHHHHHHHHhcCCcEEEE
Confidence            578999999999986665553    224445444

>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=95.03  E-value=0.023  Score=48.26  Aligned_cols=21  Identities=33%  Similarity=0.529  Sum_probs=19.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|+||+|||+|+..+.+
T Consensus        18 kI~vvG~~~vGKSsLi~~l~~   38 (176)
T d1fzqa_          18 RILLLGLDNAGKTTLLKQLAS   38 (176)
T ss_dssp             EEEEEESTTSSHHHHHHHHCC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            589999999999999999865

>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=95.00  E-value=0.024  Score=49.80  Aligned_cols=18  Identities=33%  Similarity=0.530  Sum_probs=15.5

Q ss_pred             CceEEEEccCCCcHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La  241 (480)
                      .+.+++.+|+|+|||..+
T Consensus        40 ~~~~il~apTGsGKT~~a   57 (202)
T d2p6ra3          40 GKNLLLAMPTAAGKTLLA   57 (202)
T ss_dssp             CSCEEEECSSHHHHHHHH
T ss_pred             CCCEEEEcCCCCchhHHH
Confidence            346899999999999876

>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=94.93  E-value=0.0064  Score=50.42  Aligned_cols=21  Identities=19%  Similarity=0.362  Sum_probs=19.4

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      ++|.|+||+|||+|+..+.+.
T Consensus         3 I~liG~~nvGKSSLln~l~~~   23 (166)
T d2qtvb1           3 LLFLGLDNAGKTTLLHMLKND   23 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            789999999999999999873

>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=94.85  E-value=0.02  Score=48.50  Aligned_cols=21  Identities=24%  Similarity=0.480  Sum_probs=19.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      +++.|+||+|||+|+..+.+.
T Consensus         6 i~viG~~~vGKTsli~~l~~~   26 (166)
T d1ctqa_           6 LVVVGAGGVGKSALTIQLIQN   26 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCCCHHHHHHHHHhC
Confidence            899999999999999999863

>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=94.80  E-value=0.01  Score=53.15  Aligned_cols=30  Identities=23%  Similarity=0.627  Sum_probs=23.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC--CCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM--SYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l--~~~~~~i~  256 (480)
                      +++.||+|+|||||+.++...+  +.....++
T Consensus         3 i~v~G~~GsGKTTLl~~ll~~~~~~~~~~ivn   34 (244)
T d1yrba1           3 VVFVGTAGSGKTTLTGEFGRYLEDNYKVAYVN   34 (244)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHTTTSCEEEEE
T ss_pred             EEEEcCCCCcHHHHHHHHHHHHhhCCeEEEEe
Confidence            6789999999999999998654  44555554

>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=94.80  E-value=0.0074  Score=53.24  Aligned_cols=22  Identities=23%  Similarity=0.412  Sum_probs=20.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      |.|+|.|+||+|||+|..++.+
T Consensus         1 k~V~ivG~~~~GKTsLl~~l~~   22 (207)
T d2fh5b1           1 RAVLFVGLCDSGKTLLFVRLLT   22 (207)
T ss_dssp             CEEEEECSTTSSHHHHHHHHHH
T ss_pred             CEEEEECCCCCCHHHHHHHHHc
Confidence            4799999999999999999986

>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=94.75  E-value=0.013  Score=49.87  Aligned_cols=20  Identities=40%  Similarity=0.657  Sum_probs=18.5

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|++|+|||+|++.+.+
T Consensus         4 i~lvG~~~vGKTsLi~~~~~   23 (168)
T d2gjsa1           4 VLLLGAPGVGKSALARIFGG   23 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCcCHHHHHHHHhC
Confidence            78999999999999999875

>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=94.71  E-value=0.0078  Score=50.31  Aligned_cols=22  Identities=23%  Similarity=0.366  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -++|.|+||+|||+|++++.+.
T Consensus         7 kI~ivG~~~vGKSSLi~~~~~~   28 (169)
T d1upta_           7 RILILGLDGAGKTTILYRLQVG   28 (169)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            3899999999999999999863

>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=94.64  E-value=0.028  Score=47.53  Aligned_cols=20  Identities=30%  Similarity=0.635  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.||+|||+|+..+.+
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (166)
T d1z0fa1           7 YIIIGDMGVGKSCLLHQFTE   26 (166)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999986

>d1s96a_ c.37.1.1 (A:) Guanylate kinase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Guanylate kinase
species: Escherichia coli [TaxId: 562]

Probab=94.60  E-value=0.011  Score=52.97  Aligned_cols=24  Identities=38%  Similarity=0.589  Sum_probs=21.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -++|.||+|+|||+|++.+.....
T Consensus         4 livi~GPSG~GK~tl~~~L~~~~p   27 (205)
T d1s96a_           4 LYIVSAPSGAGKSSLIQALLKTQP   27 (205)
T ss_dssp             EEEEECCTTSCHHHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHHhhCC
Confidence            378999999999999999988754

>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=94.59  E-value=0.022  Score=48.44  Aligned_cols=20  Identities=25%  Similarity=0.512  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.+|+|||+|+..+..
T Consensus         7 ivlvG~~~vGKTsli~~~~~   26 (168)
T d1u8za_           7 VIMVGSGGVGKSALTLQFMY   26 (168)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999999875

>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=94.50  E-value=0.0091  Score=53.02  Aligned_cols=29  Identities=28%  Similarity=0.368  Sum_probs=24.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      |-++|++||||||+++.+. ++|+++++.|
T Consensus         5 IgITG~igSGKStv~~~l~-~~G~~vidaD   33 (205)
T d1jjva_           5 VGLTGGIGSGKTTIANLFT-DLGVPLVDAD   33 (205)
T ss_dssp             EEEECSTTSCHHHHHHHHH-TTTCCEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HCCCeEEEch
Confidence            4489999999999999886 6898888755

>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=94.44  E-value=0.029  Score=47.65  Aligned_cols=20  Identities=35%  Similarity=0.516  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.+|+|||+|+..+.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (170)
T d1r2qa_           9 LVLLGESAVGKSSLVLRFVK   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999985

>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=94.36  E-value=0.028  Score=50.50  Aligned_cols=52  Identities=15%  Similarity=0.185  Sum_probs=32.4

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCC---CCceEEEEccCCCcHHHHH
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRV---WKRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~---~~rgiLL~GPpGTGKT~La  241 (480)
                      .+|+++...+.+.+.|.+.-   +..+.......++   ..+.+++..|+|||||...
T Consensus        12 ~sF~~l~L~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlay   66 (218)
T d2g9na1          12 DSFDDMNLSESLLRGIYAYG---FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATF   66 (218)
T ss_dssp             CCGGGSCCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHH
T ss_pred             CCHHHCCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhh
Confidence            48999998988888875421   1111111111111   2357999999999999644

>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=94.35  E-value=0.056  Score=48.64  Aligned_cols=52  Identities=25%  Similarity=0.329  Sum_probs=32.4

Q ss_pred             CCCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCC---CCCceEEEEccCCCcHHH
Q 011664          185 HPSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGR---VWKRSYLLYGPSGTGKSS  239 (480)
Q Consensus       185 ~~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~---~~~rgiLL~GPpGTGKT~  239 (480)
                      ...+|+++...+++.+.|.+.-  | ..|..-....+   -..+.++...|+|||||.
T Consensus        15 ~~~sF~~l~L~~~l~~~L~~~g--~-~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTl   69 (222)
T d2j0sa1          15 VTPTFDTMGLREDLLRGIYAYG--F-EKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTA   69 (222)
T ss_dssp             CCCSGGGGCCCHHHHHHHHHHT--C-CSCCHHHHHHHHHHHTTCCEEEECCTTSSHHH
T ss_pred             CCCCHHHCCCCHHHHHHHHHCC--C-CCCCHHHHHHHHHHHCCCCeEEEcCcchhhhh
Confidence            4458999999988888876531  1 11111111110   123579999999999995

>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=94.34  E-value=0.01  Score=52.93  Aligned_cols=29  Identities=41%  Similarity=0.525  Sum_probs=24.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      |-|+|++|||||++++.+. .+|+++++.|
T Consensus         6 IgitG~igSGKStv~~~l~-~~G~~vidaD   34 (208)
T d1vhta_           6 VALTGGIGSGKSTVANAFA-DLGINVIDAD   34 (208)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HTTCEEEEHH
T ss_pred             EEEECCCcCCHHHHHHHHH-HCCCcEEEch
Confidence            5589999999999999886 7788777653

>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=94.33  E-value=0.0087  Score=50.85  Aligned_cols=21  Identities=14%  Similarity=0.393  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -++|.|+||+|||+|+.++..
T Consensus        15 kI~lvG~~~vGKTsLl~~l~~   35 (186)
T d1f6ba_          15 KLVFLGLDNAGKTTLLHMLKD   35 (186)
T ss_dssp             EEEEEEETTSSHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            489999999999999999865

>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=94.33  E-value=0.0081  Score=53.65  Aligned_cols=26  Identities=19%  Similarity=0.512  Sum_probs=22.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      .-+.|.||.|+|||||.+.|++.+..
T Consensus        28 ei~~l~G~NGsGKSTLl~~i~gl~~p   53 (200)
T d1sgwa_          28 NVVNFHGPNGIGKTTLLKTISTYLKP   53 (200)
T ss_dssp             CCEEEECCTTSSHHHHHHHHTTSSCC
T ss_pred             CEEEEECCCCChHHHHHHHHhccccc
Confidence            34779999999999999999987744

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=94.26  E-value=0.009  Score=55.44  Aligned_cols=35  Identities=17%  Similarity=0.368  Sum_probs=22.9

Q ss_pred             ceEEEEccCCCcHHHHH-HHHHHcC---C---CcEEEEeCCC
Q 011664          225 RSYLLYGPSGTGKSSFA-AAMASFM---S---YDVYDVDLSR  259 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La-~aiA~~l---~---~~~~~i~~s~  259 (480)
                      ..+|+.||||||||+++ ..++..+   +   ..+..+..+.
T Consensus        15 ~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~~~~~ILvlt~tn   56 (306)
T d1uaaa1          15 GPCLVLAGAGSGKTRVITNKIAHLIRGCGYQARHIAAVTFTN   56 (306)
T ss_dssp             SEEEECCCTTSCHHHHHHHHHHHHHHHHCCCGGGEEEEESSH
T ss_pred             CCEEEEeeCCccHHHHHHHHHHHHHHhcCCChhHEEEEeCcH
Confidence            45899999999999754 4444322   2   2566666653

>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=94.17  E-value=0.012  Score=50.41  Aligned_cols=21  Identities=29%  Similarity=0.597  Sum_probs=19.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      +++.|+||+|||+|+..+.+.
T Consensus         6 ivvvG~~~vGKTsli~r~~~~   26 (173)
T d2a5ja1           6 YIIIGDTGVGKSCLLLQFTDK   26 (173)
T ss_dssp             EEEESSTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHhcC
Confidence            789999999999999998763

>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=94.14  E-value=0.011  Score=50.71  Aligned_cols=22  Identities=23%  Similarity=0.366  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      .|+|.|+||+|||||+.++.++
T Consensus         2 ~I~lvG~~nvGKSsLin~l~~~   23 (184)
T d2cxxa1           2 TIIFAGRSNVGKSTLIYRLTGK   23 (184)
T ss_dssp             EEEEEEBTTSSHHHHHHHHHSC
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4899999999999999999863

>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=94.10  E-value=0.0099  Score=51.80  Aligned_cols=28  Identities=18%  Similarity=0.380  Sum_probs=24.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      -|.+.|+.|+||||+++.++..++...+
T Consensus        11 ~I~ieG~~GsGKTTl~~~L~~~l~~~~~   38 (197)
T d2vp4a1          11 TVLIEGNIGSGKTTYLNHFEKYKNDICL   38 (197)
T ss_dssp             EEEEECSTTSCHHHHHHTTGGGTTTEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHhCCcEE
Confidence            4678899999999999999999976544

>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=94.10  E-value=0.017  Score=49.37  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=19.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|+||+|||+|+..+.+
T Consensus        14 kIvlvG~~~vGKTSli~rl~~   34 (173)
T d1e0sa_          14 RILMLGLDAAGKTTILYKLKL   34 (173)
T ss_dssp             EEEEEEETTSSHHHHHHHTTC
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            499999999999999999975

>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=93.84  E-value=0.013  Score=50.00  Aligned_cols=21  Identities=24%  Similarity=0.447  Sum_probs=19.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      .|.+.|+||+|||+|++++.+
T Consensus         2 ~V~liG~~n~GKSsLi~~L~~   22 (171)
T d1mkya1           2 TVLIVGRPNVGKSTLFNKLVK   22 (171)
T ss_dssp             EEEEECCTTSSHHHHHHHHHC
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999975

>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=93.82  E-value=0.015  Score=53.35  Aligned_cols=24  Identities=38%  Similarity=0.677  Sum_probs=20.8

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      +-|.||+|+|||||++.+++.+..
T Consensus        27 ~~liGpnGaGKSTll~~i~Gl~~p   50 (240)
T d2onka1          27 CVLLGPTGAGKSVFLELIAGIVKP   50 (240)
T ss_dssp             EEEECCTTSSHHHHHHHHHTSSCC
T ss_pred             EEEECCCCChHHHHHHHHHcCCCC
Confidence            447899999999999999997754

>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=93.73  E-value=0.016  Score=48.96  Aligned_cols=21  Identities=33%  Similarity=0.487  Sum_probs=19.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -++|.|++|+|||+|+..+..
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            378999999999999999976

>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=93.73  E-value=0.016  Score=48.95  Aligned_cols=20  Identities=25%  Similarity=0.393  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|+||+|||+|+..+.+
T Consensus         5 v~liG~~~vGKSsLi~rl~~   24 (164)
T d1z2aa1           5 MVVVGNGAVGKSSMIQRYCK   24 (164)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998886

>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=93.67  E-value=0.017  Score=49.28  Aligned_cols=20  Identities=25%  Similarity=0.542  Sum_probs=19.0

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|++|+|||+|++.+.+
T Consensus         8 i~lvG~~~vGKTsLi~~l~~   27 (171)
T d2ew1a1           8 IVLIGNAGVGKTCLVRRFTQ   27 (171)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999986

>d1gsia_ c.37.1.1 (A:) Thymidylate kinase {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidylate kinase
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.64  E-value=0.024  Score=49.61  Aligned_cols=31  Identities=16%  Similarity=0.334  Sum_probs=25.6

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      |.+.|+.|+||||+++.++..+   |.++..+..
T Consensus         3 I~ieG~dGsGKST~~~~L~~~l~~~g~~v~~~~~   36 (208)
T d1gsia_           3 IAIEGVDGAGKRTLVEKLSGAFRAAGRSVATLAF   36 (208)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEES
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEec
Confidence            5678999999999999999865   677776653

>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=93.58  E-value=0.018  Score=48.77  Aligned_cols=21  Identities=24%  Similarity=0.479  Sum_probs=19.3

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      ++|.|+||+|||+|+..+.+.
T Consensus         6 i~lvG~~~vGKTsLi~r~~~~   26 (167)
T d1kaoa_           6 VVVLGSGGVGKSALTVQFVTG   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHHS
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            899999999999999999863

>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=93.55  E-value=0.018  Score=48.96  Aligned_cols=20  Identities=40%  Similarity=0.547  Sum_probs=18.9

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|++|+|||+|+..+.+
T Consensus         8 i~vvG~~~vGKTsLi~~l~~   27 (169)
T d3raba_           8 ILIIGNSSVGKTSFLFRYAD   27 (169)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            89999999999999999986

>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=93.45  E-value=0.017  Score=50.30  Aligned_cols=21  Identities=38%  Similarity=0.517  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -|.|.|+||+|||||+.++.+
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            489999999999999999975

>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=93.43  E-value=0.045  Score=46.26  Aligned_cols=20  Identities=35%  Similarity=0.516  Sum_probs=18.4

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.+|+|||+|+..+.+
T Consensus         6 i~vvG~~~vGKTsLi~~~~~   25 (170)
T d1ek0a_           6 LVLLGEAAVGKSSIVLRFVS   25 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>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=93.42  E-value=0.016  Score=53.18  Aligned_cols=26  Identities=27%  Similarity=0.379  Sum_probs=22.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      -+-|.||+|||||||++.|+.....+
T Consensus        33 ~~~iiG~sGsGKSTLl~~i~Gl~~p~   58 (240)
T d3dhwc1          33 IYGVIGASGAGKSTLIRCVNLLERPT   58 (240)
T ss_dssp             EEEEEESTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHcCCcccc
Confidence            46799999999999999999877544

>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=93.42  E-value=0.052  Score=45.79  Aligned_cols=20  Identities=25%  Similarity=0.586  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.+|+|||+|++.+..
T Consensus         6 ivvvG~~~vGKTsli~r~~~   25 (167)
T d1c1ya_           6 LVVLGSGGVGKSALTVQFVQ   25 (167)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHc
Confidence            89999999999999999886

>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=93.41  E-value=0.018  Score=48.20  Aligned_cols=20  Identities=35%  Similarity=0.519  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|+||+|||+|+.++.+
T Consensus         4 I~lvG~~nvGKSsLin~l~~   23 (161)
T d2gj8a1           4 VVIAGRPNAGKSSLLNALAG   23 (161)
T ss_dssp             EEEEESTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999974

>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=93.40  E-value=0.016  Score=49.96  Aligned_cols=20  Identities=35%  Similarity=0.571  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|+||+|||+|++.+.+
T Consensus         8 i~ivG~~~vGKTsLi~~l~~   27 (186)
T d2f7sa1           8 LLALGDSGVGKTTFLYRYTD   27 (186)
T ss_dssp             EEEESCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHhc
Confidence            88999999999999999985

>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=93.33  E-value=0.021  Score=48.60  Aligned_cols=20  Identities=25%  Similarity=0.612  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|++|+|||+|+..+.+
T Consensus         5 i~lvG~~~vGKTsli~r~~~   24 (168)
T d2atva1           5 LAIFGRAGVGKSALVVRFLT   24 (168)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999999986

>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=93.24  E-value=0.018  Score=50.91  Aligned_cols=22  Identities=18%  Similarity=0.382  Sum_probs=19.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l  248 (480)
                      |.+.|++|+||||+++.++..+
T Consensus         5 IviEG~dGsGKsT~~~~L~~~L   26 (210)
T d4tmka_           5 IVIEGLEGAGKTTARNVVVETL   26 (210)
T ss_dssp             EEEEECTTSCHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
Confidence            6678999999999999999866

>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=93.21  E-value=0.022  Score=48.70  Aligned_cols=20  Identities=35%  Similarity=0.582  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|+||+|||+|+..+.+
T Consensus         7 i~vvG~~~vGKTsLi~~~~~   26 (175)
T d2f9la1           7 VVLIGDSGVGKSNLLSRFTR   26 (175)
T ss_dssp             EEEESSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999999876

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=93.15  E-value=0.02  Score=53.61  Aligned_cols=35  Identities=17%  Similarity=0.456  Sum_probs=23.0

Q ss_pred             ceEEEEccCCCcHHHHH-HHHHHcC---C---CcEEEEeCCC
Q 011664          225 RSYLLYGPSGTGKSSFA-AAMASFM---S---YDVYDVDLSR  259 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La-~aiA~~l---~---~~~~~i~~s~  259 (480)
                      ..+|+.||||||||+.+ +.+|..+   +   ..+..+..+.
T Consensus        25 g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~~p~~il~lt~t~   66 (318)
T d1pjra1          25 GPLLIMAGAGSGKTRVLTHRIAYLMAEKHVAPWNILAITFTN   66 (318)
T ss_dssp             SCEEEEECTTSCHHHHHHHHHHHHHHTTCCCGGGEEEEESSH
T ss_pred             CCEEEEecCCccHHHHHHHHHHHHHHcCCCCHHHeEeEeccH
Confidence            45899999999999654 4454432   2   2466666654

>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=93.12  E-value=0.023  Score=48.34  Aligned_cols=20  Identities=25%  Similarity=0.504  Sum_probs=18.9

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.||+|||+|+..+.+
T Consensus         8 i~lvG~~~vGKTsLi~r~~~   27 (171)
T d2erya1           8 LVVVGGGGVGKSALTIQFIQ   27 (171)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999999876

>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=93.11  E-value=0.023  Score=47.96  Aligned_cols=21  Identities=38%  Similarity=0.494  Sum_probs=19.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      +++.|+||+|||+|++++.+.
T Consensus         5 i~vvG~~~vGKTSli~~l~~~   25 (166)
T d1g16a_           5 ILLIGDSGVGKSCLLVRFVED   25 (166)
T ss_dssp             EEEEESTTSSHHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHhC
Confidence            789999999999999998863

>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=93.05  E-value=0.056  Score=51.70  Aligned_cols=34  Identities=32%  Similarity=0.452  Sum_probs=25.4

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---C--CcEEEEeCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---S--YDVYDVDLSR  259 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~--~~~~~i~~s~  259 (480)
                      -|=+.||||+|||||+.+++..+   |  .-++.+|.++
T Consensus        56 ~IgitG~pGaGKSTLi~~l~~~~~~~g~~vavlavDpss   94 (327)
T d2p67a1          56 RLGVTGTPGAGKSTFLEAFGMLLIREGLKVAVIAVDPSS   94 (327)
T ss_dssp             EEEEEECTTSCHHHHHHHHHHHHHHTTCCEEEEEECCC-
T ss_pred             EEEeeCCCCCCHHHHHHHHHHHHHhcCCceeeecCCCce
Confidence            46789999999999999998754   3  3456666554

>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=93.04  E-value=0.024  Score=48.14  Aligned_cols=20  Identities=30%  Similarity=0.557  Sum_probs=18.5

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|+||+|||+|+..+.+
T Consensus         5 i~~vG~~~vGKSsLi~~~~~   24 (175)
T d1ky3a_           5 VIILGDSGVGKTSLMHRYVN   24 (175)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHc
Confidence            78999999999999999875

>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=93.01  E-value=0.024  Score=48.76  Aligned_cols=20  Identities=30%  Similarity=0.572  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.||||||+|+..+.+
T Consensus         5 v~vvG~~~vGKSSLi~~l~~   24 (184)
T d1vg8a_           5 VIILGDSGVGKTSLMNQYVN   24 (184)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999886

>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=92.96  E-value=0.031  Score=47.90  Aligned_cols=27  Identities=22%  Similarity=0.350  Sum_probs=21.5

Q ss_pred             CCCCCceEEEEccCCCcHHHHHHHHHH
Q 011664          220 GRVWKRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       220 g~~~~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      +....--+++.|+||+|||+|+..+..
T Consensus        13 ~~~k~~KI~lvG~~~vGKTsLi~~l~~   39 (182)
T d1moza_          13 GSNKELRILILGLDGAGKTTILYRLQI   39 (182)
T ss_dssp             TCSSCEEEEEEEETTSSHHHHHHHTCC
T ss_pred             CCCceEEEEEECCCCCCHHHHHHHHhc
Confidence            333444699999999999999998853

>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=92.89  E-value=0.026  Score=47.72  Aligned_cols=20  Identities=25%  Similarity=0.393  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.+|+|||+|+..+.+
T Consensus         6 ivlvG~~~vGKTsLi~r~~~   25 (167)
T d1z08a1           6 VVLLGEGCVGKTSLVLRYCE   25 (167)
T ss_dssp             EEEECCTTSCHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999885

>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=92.87  E-value=0.024  Score=48.08  Aligned_cols=20  Identities=30%  Similarity=0.581  Sum_probs=18.5

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.||+|||+|+..+.+
T Consensus         5 i~viG~~~vGKTsLi~r~~~   24 (171)
T d2erxa1           5 VAVFGAGGVGKSSLVLRFVK   24 (171)
T ss_dssp             EEEECCTTSSHHHHHHHHHT
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            78999999999999999875

>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=92.81  E-value=0.028  Score=47.28  Aligned_cols=20  Identities=20%  Similarity=0.436  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|++|+|||+|+..+.+
T Consensus         5 v~liG~~~vGKTsLl~~~~~   24 (165)
T d1z06a1           5 IIVIGDSNVGKTCLTYRFCA   24 (165)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999999986

>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=92.70  E-value=0.029  Score=47.42  Aligned_cols=21  Identities=24%  Similarity=0.357  Sum_probs=19.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -++|.|++|+|||+|+..+.+
T Consensus         6 Kv~liG~~~vGKTsLl~~~~~   26 (167)
T d1xtqa1           6 KIAILGYRSVGKSSLTIQFVE   26 (167)
T ss_dssp             EEEEEESTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            488999999999999999876

>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=92.69  E-value=0.026  Score=50.82  Aligned_cols=26  Identities=27%  Similarity=0.185  Sum_probs=22.5

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcE
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDV  252 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~  252 (480)
                      |-|+|+.||||||+|+.++...|+.+
T Consensus         4 IgiTG~igSGKsTva~~l~e~~g~~~   29 (241)
T d1deka_           4 IFLSGVKRSGKDTTADFIMSNYSAVK   29 (241)
T ss_dssp             EEEECCTTSSHHHHHHHHHHHSCEEE
T ss_pred             EEEECCCCCCHHHHHHHHHHhCCCeE
Confidence            66899999999999999999877543

>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=92.68  E-value=0.042  Score=49.17  Aligned_cols=30  Identities=20%  Similarity=0.178  Sum_probs=25.2

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcCCCcEE
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFMSYDVY  253 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l~~~~~  253 (480)
                      |+=|.+-|+-||||||+++.++..++...+
T Consensus         2 pk~IviEG~~GsGKST~~~~L~~~l~~~~i   31 (241)
T d2ocpa1           2 PRRLSIEGNIAVGKSTFVKLLTKTYPEWHV   31 (241)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHHHCTTSEE
T ss_pred             CeEEEEECCCCCcHHHHHHHHHHHHhhcCC
Confidence            445789999999999999999999865443

>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=92.67  E-value=0.029  Score=47.88  Aligned_cols=21  Identities=24%  Similarity=0.482  Sum_probs=19.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|.+|+|||+|+..+.+
T Consensus         8 Kv~lvG~~~vGKTsLi~r~~~   28 (173)
T d2fn4a1           8 KLVVVGGGGVGKSALTIQFIQ   28 (173)
T ss_dssp             EEEEEECTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCcCHHHHHHHHHh
Confidence            389999999999999999876

>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=92.62  E-value=0.03  Score=47.48  Aligned_cols=20  Identities=30%  Similarity=0.546  Sum_probs=18.8

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|+||+|||+|++.+.+
T Consensus         9 i~vvG~~~vGKTsli~~~~~   28 (170)
T d2g6ba1           9 VMLVGDSGVGKTCLLVRFKD   28 (170)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999876

>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=92.61  E-value=0.046  Score=48.68  Aligned_cols=31  Identities=16%  Similarity=0.185  Sum_probs=26.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCCcEEEEeC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSYDVYDVDL  257 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~~~~~i~~  257 (480)
                      |.+.|+-||||||+++.++..+..+...+..
T Consensus         6 I~iEG~DGsGKST~~~~L~~~L~~~~~~~~~   36 (214)
T d1tmka_           6 ILIEGLDRTGKTTQCNILYKKLQPNCKLLKF   36 (214)
T ss_dssp             EEEEESTTSSHHHHHHHHHHHTTTSEEEEES
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHhCCEEEEE
Confidence            6688999999999999999999877766653

>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=92.58  E-value=0.03  Score=47.61  Aligned_cols=20  Identities=35%  Similarity=0.650  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.||+|||+|+..+..
T Consensus         8 I~lvG~~~vGKTsll~~~~~   27 (174)
T d2bmea1           8 FLVIGNAGTGKSCLLHQFIE   27 (174)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            89999999999999999875

>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=92.53  E-value=0.031  Score=47.56  Aligned_cols=20  Identities=35%  Similarity=0.577  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|+||+|||+|+..+.+
T Consensus         9 I~vvG~~~vGKSSli~~~~~   28 (174)
T d1wmsa_           9 VILLGDGGVGKSSLMNRYVT   28 (174)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHh
Confidence            89999999999999998876

>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=92.42  E-value=0.027  Score=53.95  Aligned_cols=33  Identities=33%  Similarity=0.394  Sum_probs=25.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHcC---CC--cEEEEeCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFM---SY--DVYDVDLSR  259 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l---~~--~~~~i~~s~  259 (480)
                      +=+.||||+|||||+.+++..+   |.  -++.+|.++
T Consensus        54 igitG~pGaGKSTli~~l~~~~~~~g~~vaViavDpss   91 (323)
T d2qm8a1          54 VGITGVPGVGKSTTIDALGSLLTAAGHKVAVLAVDPSS   91 (323)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHHHHTTCCEEEEEECGGG
T ss_pred             EeeeCCCCCCHHHHHHHHHHHHhhcCCceeeeeccccc
Confidence            6689999999999999999753   33  456666543

>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=92.37  E-value=0.03  Score=47.85  Aligned_cols=22  Identities=18%  Similarity=0.292  Sum_probs=19.9

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -|.|.|.||+|||+|+.++.+.
T Consensus         7 ~I~lvG~~~~GKSSLin~l~~~   28 (178)
T d1wf3a1           7 FVAIVGKPNVGKSTLLNNLLGV   28 (178)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHhCC
Confidence            4889999999999999999863

>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=92.32  E-value=0.035  Score=46.67  Aligned_cols=20  Identities=20%  Similarity=0.404  Sum_probs=18.6

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.+|+|||+|++.+.+
T Consensus         3 v~vvG~~~vGKTsLi~r~~~   22 (164)
T d1yzqa1           3 LVFLGEQSVGKTSLITRFMY   22 (164)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999985

>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=92.31  E-value=0.06  Score=49.39  Aligned_cols=36  Identities=25%  Similarity=0.265  Sum_probs=30.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .|+-+++.|.=|+||||++.++|..+   |..+.-+|+.
T Consensus         7 ~p~~i~~sGKGGVGKTTvaa~lA~~lA~~G~rVLlvD~D   45 (296)
T d1ihua1           7 IPPYLFFTGKGGVGKTSISCATAIRLAEQGKRVLLVSTD   45 (296)
T ss_dssp             CCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             CCeEEEEECCCcChHHHHHHHHHHHHHHCCCCEEEEeCC
Confidence            57788899999999999999999765   7888888865

>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=92.31  E-value=0.034  Score=47.46  Aligned_cols=22  Identities=14%  Similarity=0.243  Sum_probs=19.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus         4 KivvvG~~~vGKTsLi~~~~~~   25 (177)
T d1kmqa_           4 KLVIVGDGACGKTCLLIVNSKD   25 (177)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHS
T ss_pred             EEEEECCCCcCHHHHHHHHHhC
Confidence            4789999999999999998863

>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=92.31  E-value=0.029  Score=51.95  Aligned_cols=24  Identities=29%  Similarity=0.477  Sum_probs=21.1

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      -+-|.||+|+|||||+++|++...
T Consensus        30 i~~iiG~sGsGKSTLl~~i~Gl~~   53 (258)
T d1b0ua_          30 VISIIGSSGSGKSTFLRCINFLEK   53 (258)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSC
T ss_pred             EEEEECCCCCcHHHHHHHHHcCcc
Confidence            467999999999999999998654

>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=91.93  E-value=0.16  Score=44.66  Aligned_cols=31  Identities=26%  Similarity=0.203  Sum_probs=25.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCcEEEEe
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYDVYDVD  256 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~~~~i~  256 (480)
                      ..++.+|+|+|||.++-+++.+++.+++.+-
T Consensus        87 ~~ll~~~tG~GKT~~a~~~~~~~~~~~Liv~  117 (206)
T d2fz4a1          87 RGCIVLPTGSGKTHVAMAAINELSTPTLIVV  117 (206)
T ss_dssp             EEEEEESSSTTHHHHHHHHHHHSCSCEEEEE
T ss_pred             CcEEEeCCCCCceehHHhHHHHhcCceeEEE
Confidence            3467899999999999999988887766554

>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=91.93  E-value=0.041  Score=46.42  Aligned_cols=20  Identities=35%  Similarity=0.461  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.+|+|||+|++.+.+
T Consensus         7 i~lvG~~~vGKTsli~rl~~   26 (167)
T d1z0ja1           7 VCLLGDTGVGKSSIMWRFVE   26 (167)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999999886

>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=91.87  E-value=0.036  Score=50.76  Aligned_cols=26  Identities=27%  Similarity=0.442  Sum_probs=22.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      -+-|.||.|+|||||++++++.+..+
T Consensus        34 i~~liGpnGaGKSTl~~~i~Gl~~p~   59 (240)
T d1ji0a_          34 IVTLIGANGAGKTTTLSAIAGLVRAQ   59 (240)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCcHHHHHHHHhCCCCCC
Confidence            46799999999999999999987554

>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=91.80  E-value=0.031  Score=49.82  Aligned_cols=25  Identities=20%  Similarity=0.308  Sum_probs=22.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      =|.+-||-|+||||+++.++..+..
T Consensus         4 ~I~ieG~dGsGKST~~~~L~~~l~~   28 (241)
T d1p5zb_           4 KISIEGNIAAGKSTFVNILKQLCED   28 (241)
T ss_dssp             EEEEECSTTSSHHHHHTTTGGGCTT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHhc
Confidence            4789999999999999999998854

>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=91.68  E-value=0.046  Score=46.43  Aligned_cols=20  Identities=25%  Similarity=0.494  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.+|+|||+|+..+.+
T Consensus         7 i~lvG~~~vGKTsll~~~~~   26 (169)
T d1x1ra1           7 LVVVGDGGVGKSALTIQFFQ   26 (169)
T ss_dssp             EEEECCTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999999986

>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=91.65  E-value=0.044  Score=47.62  Aligned_cols=20  Identities=40%  Similarity=0.602  Sum_probs=18.6

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|++|+|||+|+..+.+
T Consensus         9 ivvvG~~~vGKTsli~~l~~   28 (194)
T d2bcgy1           9 LLLIGNSGVGKSCLLLRFSD   28 (194)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHhh
Confidence            88999999999999999876

>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=91.62  E-value=0.044  Score=46.66  Aligned_cols=20  Identities=40%  Similarity=0.635  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.+|+|||+|+..+..
T Consensus         6 v~lvG~~~vGKTsLi~~~~~   25 (172)
T d2g3ya1           6 VVLIGEQGVGKSTLANIFAG   25 (172)
T ss_dssp             EEEECCTTSSHHHHHHHHHC
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999999875

>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=91.51  E-value=0.043  Score=46.46  Aligned_cols=21  Identities=19%  Similarity=0.305  Sum_probs=19.3

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -|.|.|.||+|||||+.++.+
T Consensus         7 ~I~iiG~~nvGKSSLin~L~~   27 (179)
T d1egaa1           7 FIAIVGRPNVGKSTLLNKLLG   27 (179)
T ss_dssp             EEEEECSSSSSHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHhC
Confidence            478999999999999999975

>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=91.49  E-value=0.028  Score=47.93  Aligned_cols=20  Identities=35%  Similarity=0.539  Sum_probs=8.5

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.||||||+|++++.+
T Consensus         9 i~vvG~~~vGKTsLi~~l~~   28 (173)
T d2fu5c1           9 LLLIGDSGVGKTCVLFRFSE   28 (173)
T ss_dssp             EEEECCCCC-----------
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>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=91.45  E-value=0.025  Score=48.24  Aligned_cols=20  Identities=35%  Similarity=0.634  Sum_probs=17.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|++|+|||+|+..+.+
T Consensus         6 i~vvG~~~vGKTsli~~~~~   25 (170)
T d1i2ma_           6 LVLVGDGGTGKTTFVKRHLT   25 (170)
T ss_dssp             EEEEECTTSSHHHHHHTTC-
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            88999999999999998765

>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=91.44  E-value=0.047  Score=49.82  Aligned_cols=26  Identities=23%  Similarity=0.508  Sum_probs=22.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      -+-|.||.|+|||||.+++++.+..+
T Consensus        30 i~glvG~nGaGKSTLl~~l~G~~~p~   55 (238)
T d1vpla_          30 IFGLIGPNGAGKTTTLRIISTLIKPS   55 (238)
T ss_dssp             EEEEECCTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCCHHHHHHHHhcCCCCC
Confidence            45699999999999999999977543

>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=91.32  E-value=0.49  Score=43.45  Aligned_cols=33  Identities=21%  Similarity=0.175  Sum_probs=22.7

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH---cCCCcEEEE
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS---FMSYDVYDV  255 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~---~l~~~~~~i  255 (480)
                      .+..-||+|..|||||.++-..+.   ..|..+..+
T Consensus       103 ~~m~rLL~GdvGSGKT~Va~~a~~~~~~~g~q~~~m  138 (264)
T d1gm5a3         103 KPMNRLLQGDVGSGKTVVAQLAILDNYEAGFQTAFM  138 (264)
T ss_dssp             SCCCCEEECCSSSSHHHHHHHHHHHHHHHTSCEEEE
T ss_pred             CcceeeeeccccccccHHHHHHHHHHHhcccceeEE
Confidence            455689999999999988765543   225544443

>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=91.30  E-value=0.048  Score=49.41  Aligned_cols=27  Identities=30%  Similarity=0.353  Sum_probs=22.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      +...|.|++|+|||||+.++.......
T Consensus        96 kt~~~~G~SGVGKSTLiN~L~~~~~~~  122 (225)
T d1u0la2          96 KISTMAGLSGVGKSSLLNAINPGLKLR  122 (225)
T ss_dssp             SEEEEECSTTSSHHHHHHHHSTTCCCC
T ss_pred             CeEEEECCCCCCHHHHHHhhcchhhhh
Confidence            467899999999999999998655443

>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=91.24  E-value=0.048  Score=46.60  Aligned_cols=22  Identities=23%  Similarity=0.308  Sum_probs=19.5

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -|.+.|.||+|||+|+.++.+.
T Consensus        10 kV~iiG~~~~GKSTLin~l~~~   31 (186)
T d1mkya2          10 KVAIVGRPNVGKSTLFNAILNK   31 (186)
T ss_dssp             EEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
Confidence            4789999999999999999863

>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=91.21  E-value=0.053  Score=46.56  Aligned_cols=20  Identities=25%  Similarity=0.418  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|.+|+|||+|+..+.+
T Consensus         5 ivliG~~~vGKTsli~r~~~   24 (179)
T d1m7ba_           5 IVVVGDSQCGKTALLHVFAK   24 (179)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998886

>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=91.08  E-value=0.054  Score=46.47  Aligned_cols=21  Identities=14%  Similarity=0.371  Sum_probs=19.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+++.|.+|+|||+|+..+..
T Consensus         7 KivviG~~~vGKTsli~~~~~   27 (183)
T d1mh1a_           7 KCVVVGDGAVGKTCLLISYTT   27 (183)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHh
Confidence            489999999999999999876

>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=91.02  E-value=0.057  Score=46.53  Aligned_cols=20  Identities=20%  Similarity=0.409  Sum_probs=18.7

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      +++.|.+|+|||+|+..+.+
T Consensus        12 i~lvG~~~vGKTsLi~r~~~   31 (185)
T d2atxa1          12 CVVVGDGAVGKTCLLMSYAN   31 (185)
T ss_dssp             EEEEECTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            78999999999999999876

>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=91.00  E-value=0.018  Score=48.12  Aligned_cols=21  Identities=19%  Similarity=0.352  Sum_probs=19.2

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      +.|.|.||+|||+|+.++.++
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            789999999999999999864

>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=90.97  E-value=0.05  Score=50.14  Aligned_cols=26  Identities=35%  Similarity=0.728  Sum_probs=22.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCCc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSYD  251 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~~  251 (480)
                      -+-|.||.|+|||||++++++.+..+
T Consensus        32 i~~liG~nGaGKSTLl~~i~Gl~~p~   57 (254)
T d1g6ha_          32 VTLIIGPNGSGKSTLINVITGFLKAD   57 (254)
T ss_dssp             EEEEECSTTSSHHHHHHHHTTSSCCS
T ss_pred             EEEEECCCCCcHHHHHHHHHCCCcCC
Confidence            47799999999999999999977554

>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=90.87  E-value=0.059  Score=46.59  Aligned_cols=20  Identities=15%  Similarity=0.388  Sum_probs=18.4

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|++|+|||+|+..+..
T Consensus         6 vvllG~~~vGKTSli~r~~~   25 (191)
T d2ngra_           6 CVVVGDGAVGKTCLLISYTT   25 (191)
T ss_dssp             EEEEESTTSSHHHHHHHHHH
T ss_pred             EEEECCCCcCHHHHHHHHHh
Confidence            78999999999999998875

>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=90.70  E-value=0.046  Score=46.19  Aligned_cols=22  Identities=27%  Similarity=0.297  Sum_probs=19.4

Q ss_pred             ceEEEEccCCCcHHHHHHHHHH
Q 011664          225 RSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      .-|.|.|+|++|||+|+.++.+
T Consensus        17 ~~I~lvG~~NvGKSSL~n~L~~   38 (188)
T d1puia_          17 IEVAFAGRSNAGKSSALNTLTN   38 (188)
T ss_dssp             EEEEEEECTTSSHHHHHTTTCC
T ss_pred             CEEEEECCCCCCHHHHHHHHhC
Confidence            3599999999999999999854

>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=90.67  E-value=0.016  Score=49.43  Aligned_cols=23  Identities=35%  Similarity=0.426  Sum_probs=20.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      .+|+||.|+|||++..||.-.++
T Consensus        27 tvi~G~NGsGKStil~Ai~~~L~   49 (222)
T d1qhla_          27 TTLSGGNGAGKSTTMAAFVTALI   49 (222)
T ss_dssp             HHHHSCCSHHHHHHHHHHHHHHS
T ss_pred             EEEECCCCCCHHHHHHHHHHHhc
Confidence            56889999999999999987653

>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=90.62  E-value=0.08  Score=51.57  Aligned_cols=35  Identities=31%  Similarity=0.355  Sum_probs=27.0

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHc---CCCcEEEEeCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASF---MSYDVYDVDLS  258 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~---l~~~~~~i~~s  258 (480)
                      .+++++.|++|+|||.+++.+...   .|..++.+|..
T Consensus        50 ~~H~~I~G~tGsGKT~~l~~li~~~~~~g~~~iiiD~k   87 (433)
T d1e9ra_          50 PRHLLVNGATGTGKSVLLRELAYTGLLRGDRMVIVDPN   87 (433)
T ss_dssp             GGCEEEEECTTSSHHHHHHHHHHHHHHTTCEEEEEEET
T ss_pred             cceEEEEeCCCCcHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            357999999999999988766543   36677777753

>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=90.54  E-value=0.048  Score=46.71  Aligned_cols=20  Identities=30%  Similarity=0.358  Sum_probs=18.2

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      |-|.|+||+|||||+.++.+
T Consensus         4 VaiiG~~nvGKSSLin~L~~   23 (185)
T d1lnza2           4 VGLVGFPSVGKSTLLSVVSS   23 (185)
T ss_dssp             EEEESSTTSSHHHHHHHSEE
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            77999999999999999864

>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=90.44  E-value=0.42  Score=43.07  Aligned_cols=40  Identities=20%  Similarity=0.090  Sum_probs=28.8

Q ss_pred             CCceEEEEccCCCcHHHHHHHHHH---cCCCcEEEEeCCCcCC
Q 011664          223 WKRSYLLYGPSGTGKSSFAAAMAS---FMSYDVYDVDLSRVAD  262 (480)
Q Consensus       223 ~~rgiLL~GPpGTGKT~La~aiA~---~l~~~~~~i~~s~~~~  262 (480)
                      .+...||+|.+|+|||.++-..+.   ..|..+..+-.+....
T Consensus        75 ~~~~~LL~GdvGsGKT~V~~~a~~~~~~~g~qv~~l~Pt~~La  117 (233)
T d2eyqa3          75 LAMDRLVCGDVGFGKTEVAMRAAFLAVDNHKQVAVLVPTTLLA  117 (233)
T ss_dssp             SCCEEEEECCCCTTTHHHHHHHHHHHHTTTCEEEEECSSHHHH
T ss_pred             CccCeEEEcCCCCCcHHHHHHHHHHHHHcCCceEEEccHHHhH
Confidence            456789999999999988765544   3477777776654443

>d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Phosphoribulokinase/pantothenate kinase
domain: Phosphoribulokinase
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=90.39  E-value=0.045  Score=51.40  Aligned_cols=36  Identities=14%  Similarity=0.239  Sum_probs=25.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCCCcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLSRVA  261 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s~~~  261 (480)
                      -|-+.|++|+|||++++++++.+   +.+...+...++.
T Consensus         6 IIgIaG~SGSGKTTva~~l~~i~~~~~v~~~iI~~Dsfy   44 (288)
T d1a7ja_           6 IISVTGSSGAGTSTVKHTFDQIFRREGVKAVSIEGDAFH   44 (288)
T ss_dssp             EEEEESCC---CCTHHHHHHHHHHHHTCCEEEEEGGGGB
T ss_pred             EEEEECCCCCcHHHHHHHHHHHHhhcCCCeEEEeCCCCC
Confidence            46799999999999999998866   5566667766653

>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=90.30  E-value=0.1  Score=45.30  Aligned_cols=33  Identities=18%  Similarity=0.338  Sum_probs=26.9

Q ss_pred             ceEEEEcc-CCCcHHHHHHHHHHcC---CCcEEEEeC
Q 011664          225 RSYLLYGP-SGTGKSSFAAAMASFM---SYDVYDVDL  257 (480)
Q Consensus       225 rgiLL~GP-pGTGKT~La~aiA~~l---~~~~~~i~~  257 (480)
                      +-|++.|- +|+|||+++..+|..+   |..+..++.
T Consensus         2 ~~~~i~gt~~GVGKTtvs~~La~aLa~~G~rVl~id~   38 (224)
T d1byia_           2 KRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKP   38 (224)
T ss_dssp             EEEEEEESSTTSCHHHHHHHHHHHHHHTTCCEEEECS
T ss_pred             ceEEEEECCCCccHHHHHHHHHHHHHHCCCeEEEECc
Confidence            35899999 6999999999999755   777777763

>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=90.03  E-value=0.051  Score=49.31  Aligned_cols=23  Identities=43%  Similarity=0.663  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+-|.||.|+|||||.+++++..
T Consensus        27 i~~iiG~nGaGKSTLl~~l~Gl~   49 (231)
T d1l7vc_          27 ILHLVGPNGAGKSTLLARMAGMT   49 (231)
T ss_dssp             EEECBCCTTSSHHHHHHHHHTSC
T ss_pred             EEEEECCCCCcHHHHHHHHhCCC
Confidence            46788999999999999999843

>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=89.76  E-value=0.057  Score=46.06  Aligned_cols=20  Identities=45%  Similarity=0.448  Sum_probs=18.4

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      |.|.|.||+|||+|+.++.+
T Consensus         4 VaivG~~nvGKSTLin~L~~   23 (180)
T d1udxa2           4 VGLVGYPNAGKSSLLAAMTR   23 (180)
T ss_dssp             EEEECCGGGCHHHHHHHHCS
T ss_pred             EEEECCCCCCHHHHHHHHhC
Confidence            78999999999999999964

>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=88.81  E-value=0.078  Score=48.96  Aligned_cols=24  Identities=29%  Similarity=0.490  Sum_probs=21.0

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -+|+||.|+|||++..||+-.++.
T Consensus        27 nvlvG~NgsGKS~iL~Ai~~~lg~   50 (308)
T d1e69a_          27 TAIVGPNGSGKSNIIDAIKWVFGE   50 (308)
T ss_dssp             EEEECCTTTCSTHHHHHHHHTSCC
T ss_pred             EEEECCCCCcHHHHHHHHHHHhCC
Confidence            479999999999999999876653

>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=88.71  E-value=0.1  Score=44.77  Aligned_cols=19  Identities=42%  Similarity=0.662  Sum_probs=17.7

Q ss_pred             EEEEccCCCcHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA  245 (480)
                      ++|.|.+|+|||+|+..+.
T Consensus         5 ivllG~~~vGKTsll~r~~   23 (200)
T d1zcba2           5 ILLLGAGESGKSTFLKQMR   23 (200)
T ss_dssp             EEEECSTTSSHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHh
Confidence            7899999999999999983

>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=88.19  E-value=0.13  Score=43.96  Aligned_cols=22  Identities=23%  Similarity=0.235  Sum_probs=19.7

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|+|||+|+..+.+.
T Consensus         7 ki~vlG~~~vGKTsLi~~~~~~   28 (175)
T d2bmja1           7 RLGVLGDARSGKSSLIHRFLTG   28 (175)
T ss_dssp             EEEEECCTTTTHHHHHHHHHHS
T ss_pred             EEEEECCCCCCHHHHHHHHHhC
Confidence            4899999999999999988763

>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=88.17  E-value=0.21  Score=45.27  Aligned_cols=35  Identities=31%  Similarity=0.451  Sum_probs=28.7

Q ss_pred             CceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      .+-++++|.=|+||||++..+|..+   |..+..+|+.
T Consensus        20 ~~iii~sGKGGVGKTT~a~nLA~~lA~~G~rVllvD~D   57 (279)
T d1ihua2          20 HGLIMLMGKGGVGKTTMAAAIAVRLADMGFDVHLTTSD   57 (279)
T ss_dssp             CEEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEESC
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCcEEEEeCC
Confidence            4567888999999999988877644   8888888876

>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=88.12  E-value=0.37  Score=41.63  Aligned_cols=26  Identities=31%  Similarity=0.335  Sum_probs=18.8

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      +.+++.-|+|+|||..+....-....
T Consensus        41 ~~vlv~apTGsGKT~~~~~~~~~~~~   66 (206)
T d1oywa2          41 RDCLVVMPTGGGKSLCYQIPALLLNG   66 (206)
T ss_dssp             CCEEEECSCHHHHHHHHHHHHHHSSS
T ss_pred             CCEEEEcCCCCCCcchhhhhhhhccC
Confidence            46999999999999876544433333

>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=88.11  E-value=0.043  Score=49.89  Aligned_cols=25  Identities=32%  Similarity=0.527  Sum_probs=19.2

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFMS  249 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l~  249 (480)
                      +..+|.|++|+|||||+.++.....
T Consensus        98 ~~~vl~G~SGVGKSSLiN~L~~~~~  122 (231)
T d1t9ha2          98 KTTVFAGQSGVGKSSLLNAISPELG  122 (231)
T ss_dssp             SEEEEEESHHHHHHHHHHHHCC---
T ss_pred             ceEEEECCCCccHHHHHHhhccHhH
Confidence            3567889999999999999976443

>d1w1wa_ c.37.1.12 (A:) Smc head domain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Smc head domain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.35  E-value=0.14  Score=49.09  Aligned_cols=24  Identities=29%  Similarity=0.559  Sum_probs=20.9

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -+++||.|+|||++..||+-.+|.
T Consensus        28 ~~i~G~NGsGKS~ileAi~~~lg~   51 (427)
T d1w1wa_          28 TSIIGPNGSGKSNMMDAISFVLGV   51 (427)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHTTC
T ss_pred             EEEECCCCCCHHHHHHHHHHHhCC
Confidence            479999999999999999876654

>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=87.08  E-value=0.14  Score=45.40  Aligned_cols=21  Identities=33%  Similarity=0.504  Sum_probs=18.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~  246 (480)
                      -+||.|++|+|||+|++.+..
T Consensus         8 KilllG~~~vGKTsll~~~~~   28 (221)
T d1azta2           8 RLLLLGAGESGKSTIVKQMRI   28 (221)
T ss_dssp             EEEEECSTTSSHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            489999999999999998864

>d1nija1 c.37.1.10 (A:2-223) Hypothetical protein YjiA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: Hypothetical protein YjiA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=86.89  E-value=0.13  Score=45.89  Aligned_cols=23  Identities=26%  Similarity=0.300  Sum_probs=20.2

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -+++.|..|+|||||++.+.+..
T Consensus         5 v~iitGFLGaGKTTll~~lL~~~   27 (222)
T d1nija1           5 VTLLTGFLGAGKTTLLRHILNEQ   27 (222)
T ss_dssp             EEEEEESSSSSCHHHHHHHHHSC
T ss_pred             EEEEeeCCCCCHHHHHHHHHhcC
Confidence            47899999999999999988754

>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=86.31  E-value=0.17  Score=47.24  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=20.6

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFM  248 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l  248 (480)
                      -.++.||+|||||+|+..+++..
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            48999999999999999998754

>d1p6xa_ c.37.1.1 (A:) Thymidine kinase {Equine herpesvirus type 4 [TaxId: 10331]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Equine herpesvirus type 4 [TaxId: 10331]

Probab=86.20  E-value=0.16  Score=48.48  Aligned_cols=25  Identities=40%  Similarity=0.329  Sum_probs=22.0

Q ss_pred             eEEEEccCCCcHHHHHHHHHHcCCC
Q 011664          226 SYLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      -|.+-|+-|+||||+++.+++.++.
T Consensus         8 rI~iEG~iGsGKSTl~~~L~~~l~~   32 (333)
T d1p6xa_           8 RIYLDGVYGIGKSTTGRVMASAASG   32 (333)
T ss_dssp             EEEEECSTTSSHHHHHHHHHSGGGC
T ss_pred             EEEEECCccCCHHHHHHHHHHHhcc
Confidence            3678899999999999999998753

>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=85.88  E-value=0.2  Score=42.49  Aligned_cols=21  Identities=38%  Similarity=0.600  Sum_probs=19.1

Q ss_pred             EEEEccCCCcHHHHHHHHHHc
Q 011664          227 YLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~  247 (480)
                      ++|.|.+|+|||+|+..+...
T Consensus         5 iv~lG~~~vGKTsll~r~~~~   25 (200)
T d2bcjq2           5 LLLLGTGESGKSTFIKQMRII   25 (200)
T ss_dssp             EEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhCC
Confidence            899999999999999999753

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=85.47  E-value=0.82  Score=37.61  Aligned_cols=60  Identities=13%  Similarity=0.306  Sum_probs=37.5

Q ss_pred             EEEccCCCcHHH-HHHHHHH--cCCCcEEEEeCCC-------cC-------------ChHHHHHHHHhh---cCCcEEEE
Q 011664          228 LLYGPSGTGKSS-FAAAMAS--FMSYDVYDVDLSR-------VA-------------DDADLKSLLLQT---TSKSVILI  281 (480)
Q Consensus       228 LL~GPpGTGKT~-La~aiA~--~l~~~~~~i~~s~-------~~-------------~~~~l~~l~~~~---~~~sII~I  281 (480)
                      +++||-.+|||+ |++.+-+  ..|.+++.+..+.       +.             ...++...+...   ....+|+|
T Consensus         6 ~i~GpMfsGKTteLi~~~~~~~~~~~kv~~ikp~~D~R~~~~i~s~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~dvI~I   85 (139)
T d2b8ta1           6 FITGPMFAGKTAELIRRLHRLEYADVKYLVFKPKIDTRSIRNIQSRTGTSLPSVEVESAPEILNYIMSNSFNDETKVIGI   85 (139)
T ss_dssp             EEECSTTSCHHHHHHHHHHHHHHTTCCEEEEEECCCGGGCSSCCCCCCCSSCCEEESSTHHHHHHHHSTTSCTTCCEEEE
T ss_pred             EEEccccCHHHHHHHHHHHHHHHCCCcEEEEEEcccccccceEEcccCceeeeEEeccchhhHHHHHhhccccCcCEEEe
Confidence            688999999997 7777644  4577776665321       11             122233333222   35689999


Q ss_pred             eccccc
Q 011664          282 EDLDRF  287 (480)
Q Consensus       282 DEiD~l  287 (480)
                      ||+.-+
T Consensus        86 DE~QFf   91 (139)
T d2b8ta1          86 DEVQFF   91 (139)
T ss_dssp             CSGGGS
T ss_pred             chhhhc
Confidence            999865

>d1bg2a_ c.37.1.9 (A:) Kinesin {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.16  E-value=0.31  Score=45.86  Aligned_cols=50  Identities=18%  Similarity=0.359  Sum_probs=33.2

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHH
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La  241 (480)
                      -+||.+.+.+.-.+++-+.+..++-.. .+.  |  ....++-||+.|+|||+.+
T Consensus        44 f~FD~vf~~~~~q~~vf~~~~~~lv~~-~l~--G--~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          44 YAFDRVFQSSTSQEQVYNDCAKKIVKD-VLE--G--YNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             EECSEEECTTCCHHHHHHHHTHHHHHH-HHT--T--CCEEEEEECSTTSSHHHHH
T ss_pred             eECCEEECCCCCHHHHHHHHHHHHHHH-HHc--C--CCcceeeecccCCCCceec
Confidence            468888777666666655554443322 111  2  4558999999999999886

>d1t5la1 c.37.1.19 (A:2-414) Nucleotide excision repair enzyme UvrB {Bacillus caldotenax [TaxId: 1395]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Nucleotide excision repair enzyme UvrB
species: Bacillus caldotenax [TaxId: 1395]

Probab=84.83  E-value=1.3  Score=43.19  Aligned_cols=59  Identities=12%  Similarity=0.191  Sum_probs=42.8

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHHHcCCCcEEEEeCCC
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMASFMSYDVYDVDLSR  259 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA~~l~~~~~~i~~s~  259 (480)
                      ..|.--+-++++.++|.+.+..              -.+..+|.|-+|||||.++++++...+.+++.|.-+.
T Consensus         8 ~~~~p~gDQP~aI~~l~~~l~~--------------g~~~q~l~GltGS~ka~~iA~l~~~~~rp~LVVt~n~   66 (413)
T d1t5la1           8 APYEPQGDQPQAIAKLVDGLRR--------------GVKHQTLLGATGTGKTFTISNVIAQVNKPTLVIAHNK   66 (413)
T ss_dssp             CSSCCCTTHHHHHHHHHHHHHH--------------TCSEEEEEECTTSCHHHHHHHHHHHHTCCEEEECSSH
T ss_pred             cCCCCCCCCHHHHHHHHHHHhc--------------CCCcEEEeCCCCcHHHHHHHHHHHHhCCCEEEEeCCH
Confidence            3455555556666666654431              1346889999999999999999999999998886543

>d1ry6a_ c.37.1.9 (A:) Kinesin {Malaria parasite (Plasmodium falciparum) [TaxId: 5833]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Malaria parasite (Plasmodium falciparum) [TaxId: 5833]

Probab=84.23  E-value=0.3  Score=46.22  Aligned_cols=51  Identities=24%  Similarity=0.215  Sum_probs=32.3

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAA  242 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~  242 (480)
                      +||.+.+.+.-.+++-+.+..++-..-+..  |  ....++-||..|||||+.+.
T Consensus        53 ~fD~Vf~~~~~q~~vy~~~~~plv~~~~~~--G--~n~~i~aYGqTGSGKTyTm~  103 (330)
T d1ry6a_          53 IVDKVFDDTVDNFTVYENTIKPLIIDLYEN--G--CVCSCFAYGQTGSGKTYTML  103 (330)
T ss_dssp             ECSEEECTTCCHHHHHHHHTHHHHHHHHHH--C--CEEEEEEECCTTSSHHHHHH
T ss_pred             eCCeecCCCCCHHHHHHHHHHHHHHHHHhc--C--CCeEEEeeeccccccceeee
Confidence            467777766666666655544433221111  2  34569999999999998764

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.16  E-value=0.13  Score=45.38  Aligned_cols=51  Identities=16%  Similarity=0.147  Sum_probs=30.1

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCC---CCCceEEEEccCCCcHHHH
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGR---VWKRSYLLYGPSGTGKSSF  240 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~---~~~rgiLL~GPpGTGKT~L  240 (480)
                      ++|+++...+++.+.|.+.-   +..|.......+   --.+.+++..|+|||||..
T Consensus         1 s~F~dl~L~~~l~~~l~~~g---~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla   54 (207)
T d1t6na_           1 SGFRDFLLKPELLRAIVDCG---FEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAV   54 (207)
T ss_dssp             CCSTTSCCCHHHHHHHHHTT---CCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHH
T ss_pred             CCccccCcCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCeEEEeccccccccc
Confidence            36888888888777776421   111111111100   1235799999999999843

>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=84.03  E-value=0.38  Score=43.43  Aligned_cols=34  Identities=26%  Similarity=0.403  Sum_probs=27.3

Q ss_pred             ceEEEEccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          225 RSYLLYGPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       225 rgiLL~GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      |.|-++|.=|+||||++..+|..+   |.++.-+|+.
T Consensus         2 r~Iai~gKGGvGKTT~a~nLA~~LA~~G~rVllID~D   38 (269)
T d1cp2a_           2 RQVAIYGKGGIGKSTTTQNLTSGLHAMGKTIMVVGCD   38 (269)
T ss_dssp             EEEEEEECTTSSHHHHHHHHHHHHHTTTCCEEEEEEC
T ss_pred             CEEEEECCCcCCHHHHHHHHHHHHHhCCCcEEEEecC
Confidence            346679999999999998888654   7788888765

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=83.20  E-value=0.38  Score=45.88  Aligned_cols=50  Identities=20%  Similarity=0.212  Sum_probs=32.1

Q ss_pred             CCccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHH
Q 011664          187 STFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La  241 (480)
                      -+||.+.+.+.-.++|-+.+..++-.. .+.  |  +...++-||++|+|||+.+
T Consensus        48 f~FD~vf~~~~~q~~vy~~~~~plv~~-~l~--G--~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          48 FTFDRVFDMSCKQSDIFDFSIKPTVDD-ILN--G--YNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             EECSEEECTTCCHHHHHHHHTHHHHHH-HTT--T--CCEEEEEECSTTSSHHHHH
T ss_pred             EECCeEcCCCCCHHHHHHHHHHHHHHH-hhc--c--CceeEEecccCCCCcceee
Confidence            368888877665566655444443321 111  2  3457999999999999775

>d1osna_ c.37.1.1 (A:) Thymidine kinase {Varicella-zoster virus [TaxId: 10335]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Thymidine kinase
species: Varicella-zoster virus [TaxId: 10335]

Probab=83.17  E-value=0.25  Score=47.01  Aligned_cols=24  Identities=25%  Similarity=0.369  Sum_probs=21.7

Q ss_pred             EEEEccCCCcHHHHHHHHHHcCCC
Q 011664          227 YLLYGPSGTGKSSFAAAMASFMSY  250 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~~l~~  250 (480)
                      |.+-|+-|+||||+++.+++.++.
T Consensus         8 I~IEG~iGsGKSTl~~~L~~~l~~   31 (331)
T d1osna_           8 IYLDGAYGIGKTTAAEEFLHHFAI   31 (331)
T ss_dssp             EEEEESSSSCTTHHHHHHHHTTTT
T ss_pred             EEEECCCCCCHHHHHHHHHHHHhh
Confidence            678899999999999999998864

>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=82.88  E-value=0.23  Score=43.84  Aligned_cols=53  Identities=19%  Similarity=0.182  Sum_probs=31.6

Q ss_pred             CCCccccccChHHHHHHHHHHHHHHhhhhHHhhhCC---CCCceEEEEccCCCcHHHHH
Q 011664          186 PSTFDTISMETDLKNRVKSDLESFLKAKHYYHRLGR---VWKRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       186 ~~~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~---~~~rgiLL~GPpGTGKT~La  241 (480)
                      -.+|+++...+++.+.+.+.-   ...+.......+   -..+.+++.+|+|||||...
T Consensus         9 ~~sF~~l~l~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~   64 (212)
T d1qdea_           9 VYKFDDMELDENLLRGVFGYG---FEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTF   64 (212)
T ss_dssp             CCCGGGGTCCHHHHHHHHHHT---CCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHH
T ss_pred             ccChhhCCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEeecccccchhhhh
Confidence            357999988888777775421   111111111110   12357999999999999643

>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=82.32  E-value=0.22  Score=47.01  Aligned_cols=18  Identities=33%  Similarity=0.695  Sum_probs=15.7

Q ss_pred             eEEEEccCCCcHHHHHHH
Q 011664          226 SYLLYGPSGTGKSSFAAA  243 (480)
Q Consensus       226 giLL~GPpGTGKT~La~a  243 (480)
                      .-|++|.+|||||||...
T Consensus        16 valffGLSGTGKTTLs~~   33 (318)
T d1j3ba1          16 VAVFFGLSGTGKTTLSTD   33 (318)
T ss_dssp             EEEEEECTTSCHHHHTCB
T ss_pred             EEEEEccCCCCccccccC
Confidence            479999999999998754

>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=82.06  E-value=0.71  Score=44.74  Aligned_cols=23  Identities=30%  Similarity=0.488  Sum_probs=20.5

Q ss_pred             CceEEEEccCCCcHHHHHHHHHH
Q 011664          224 KRSYLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       224 ~rgiLL~GPpGTGKT~La~aiA~  246 (480)
                      +-.|.+.|.||+|||||+.++-+
T Consensus        56 ~l~Iai~G~~n~GKSSLiNaL~G   78 (400)
T d1tq4a_          56 VLNVAVTGETGSGKSSFINTLRG   78 (400)
T ss_dssp             CEEEEEEECTTSSHHHHHHHHHT
T ss_pred             CcEEEEECCCCCCHHHHHHHHhC
Confidence            44699999999999999999974

>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=81.43  E-value=0.63  Score=40.45  Aligned_cols=32  Identities=31%  Similarity=0.422  Sum_probs=25.2

Q ss_pred             EEEE-ccCCCcHHHHHHHHHHcC---CCcEEEEeCC
Q 011664          227 YLLY-GPSGTGKSSFAAAMASFM---SYDVYDVDLS  258 (480)
Q Consensus       227 iLL~-GPpGTGKT~La~aiA~~l---~~~~~~i~~s  258 (480)
                      |.++ |..|+|||+++..+|..+   |.++..+|+.
T Consensus         4 Iav~s~KGGvGKTtia~nlA~~la~~g~~VlliD~D   39 (232)
T d1hyqa_           4 ITVASGKGGTGKTTITANLGVALAQLGHDVTIVDAD   39 (232)
T ss_dssp             EEEEESSSCSCHHHHHHHHHHHHHHTTCCEEEEECC
T ss_pred             EEEECCCCCChHHHHHHHHHHHHHhCCCCEEEEeCC
Confidence            4444 889999999999988754   7788888764

>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=81.02  E-value=0.12  Score=45.11  Aligned_cols=49  Identities=16%  Similarity=0.124  Sum_probs=28.2

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCC---CCceEEEEccCCCcHHH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRV---WKRSYLLYGPSGTGKSS  239 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~---~~rgiLL~GPpGTGKT~  239 (480)
                      +|+++...+.+.+.|.+.-  | ..|...+..-++   -.+.+++..|+|||||.
T Consensus         2 ~F~~l~L~~~l~~~l~~~g--~-~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTl   53 (209)
T d1q0ua_           2 QFTRFPFQPFIIEAIKTLR--F-YKPTEIQERIIPGALRGESMVGQSQTGTGKTH   53 (209)
T ss_dssp             CGGGSCCCHHHHHHHHHTT--C-CSCCHHHHHHHHHHHHTCCEEEECCSSHHHHH
T ss_pred             ccccCCcCHHHHHHHHHCC--C-CCCCHHHHHHHHHHHCCCCeEeecccccccce
Confidence            5788887877777765311  1 111111110000   12479999999999996

>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=81.00  E-value=0.39  Score=40.41  Aligned_cols=20  Identities=35%  Similarity=0.536  Sum_probs=18.1

Q ss_pred             EEEEccCCCcHHHHHHHHHH
Q 011664          227 YLLYGPSGTGKSSFAAAMAS  246 (480)
Q Consensus       227 iLL~GPpGTGKT~La~aiA~  246 (480)
                      ++|.|..|+|||+|++.+-.
T Consensus         5 ivllG~~~vGKTsl~~r~~~   24 (195)
T d1svsa1           5 LLLLGAGESGKSTIVKQMKI   24 (195)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHhh
Confidence            79999999999999998754

>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=80.80  E-value=0.18  Score=44.23  Aligned_cols=50  Identities=18%  Similarity=0.208  Sum_probs=29.4

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCC---CCCceEEEEccCCCcHHHH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGR---VWKRSYLLYGPSGTGKSSF  240 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~---~~~rgiLL~GPpGTGKT~L  240 (480)
                      +|+++...+++.+.|.+.-   +..+.......+   --.+.+++.+|+|||||..
T Consensus         2 sF~~l~L~~~l~~~L~~~g---~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTla   54 (206)
T d1s2ma1           2 TFEDFYLKRELLMGIFEAG---FEKPSPIQEEAIPVAITGRDILARAKNGTGKTAA   54 (206)
T ss_dssp             CGGGGCCCHHHHHHHHHTT---CCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHH
T ss_pred             ChHHcCCCHHHHHHHHHCC---CCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhh
Confidence            6888888888888776530   011100000000   0124699999999999943

>d2jdid3 c.37.1.11 (D:82-357) Central domain of beta subunit of F1 ATP synthase {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Central domain of beta subunit of F1 ATP synthase
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=80.72  E-value=0.42  Score=44.23  Aligned_cols=22  Identities=23%  Similarity=0.416  Sum_probs=19.8

Q ss_pred             eEEEEccCCCcHHHHHHHHHHc
Q 011664          226 SYLLYGPSGTGKSSFAAAMASF  247 (480)
Q Consensus       226 giLL~GPpGTGKT~La~aiA~~  247 (480)
                      -+++.|++|||||+|+..+++.
T Consensus        70 r~~If~~~g~GKt~l~~~i~~~   91 (276)
T d2jdid3          70 KIGLFGGAGVGKTVLIMELINN   91 (276)
T ss_dssp             EEEEEECTTSSHHHHHHHHHHH
T ss_pred             EEEeeCCCCCCHHHHHHHHHHH
Confidence            3899999999999999999865

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=80.29  E-value=0.61  Score=44.15  Aligned_cols=49  Identities=22%  Similarity=0.313  Sum_probs=30.4

Q ss_pred             CccccccChHHHHHHHHHHHHHHhhhhHHhhhCCCCCceEEEEccCCCcHHHHH
Q 011664          188 TFDTISMETDLKNRVKSDLESFLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFA  241 (480)
Q Consensus       188 ~~~~i~g~~~~k~~l~e~l~~~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La  241 (480)
                      +||.+.+.+.--++|-+.+..++-.. .+.  |  ....++-||+.|||||+.+
T Consensus        50 ~FD~vf~~~~~q~~vy~~~~~~lv~~-~l~--G--~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          50 TFDMVFGASTKQIDVYRSVVCPILDE-VIM--G--YNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             ECSEEECTTCCHHHHHHHHHHHHHHH-HHT--T--CEEEEEEEECTTSSHHHHH
T ss_pred             ecCEEeCCCCCHHHHHHHHHHHhHHH-Hhc--c--CCceEEeeeeccccceEEe
Confidence            47777766555555554444443321 121  2  3457899999999999776

>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=80.19  E-value=0.31  Score=42.70  Aligned_cols=57  Identities=12%  Similarity=0.163  Sum_probs=32.1

Q ss_pred             CCccccccChHHHHHHHHHH-HH--HHhhhhHHhhhCCCCCceEEEEccCCCcHHHHHHHHH
Q 011664          187 STFDTISMETDLKNRVKSDL-ES--FLKAKHYYHRLGRVWKRSYLLYGPSGTGKSSFAAAMA  245 (480)
Q Consensus       187 ~~~~~i~g~~~~k~~l~e~l-~~--~l~~~~~~~~~g~~~~rgiLL~GPpGTGKT~La~aiA  245 (480)
                      .+|+++...+++.+.+.+.- ..  +++. ..+... ..-+..+++..|+|+|||...-..+
T Consensus         4 msf~~l~l~~~l~~~l~~~g~~~pt~iQ~-~~ip~~-l~g~~d~iv~a~TGsGKT~~~~l~~   63 (208)
T d1hv8a1           4 MNFNELNLSDNILNAIRNKGFEKPTDIQM-KVIPLF-LNDEYNIVAQARTGSGKTASFAIPL   63 (208)
T ss_dssp             CCGGGSSCCHHHHHHHHHHTCCSCCHHHH-HHHHHH-HHTCSEEEEECCSSSSHHHHHHHHH
T ss_pred             cCHHHcCCCHHHHHHHHHCCCCCCCHHHH-HHHHHH-HcCCCCeeeechhcccccceeeccc
Confidence            37888877777777665420 00  0111 111100 1113479999999999998665443